The Baker Laboratory - Primary Publication http://www.bakerlab.org/taxonomy/term/1/0 This publication represents a primary interest of the Baker lab en Design of activated serine-containing catalytic triads with atomic-level accuracy http://www.bakerlab.org/Design-of-activated-serine-containing-catalytic-triads-with-atomic-level-accuracy-pub <div id="biblio-node"><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.atitle=Design+of+activated+serine-containing+catalytic+triads+with+atomic-level+accuracy&amp;rft.title=Nature+chemical+biology&amp;rft.issn=1552-4469&amp;rft.date=2014&amp;rft.volume=10&amp;rft.issue=5&amp;rft.spage=386&amp;rft.epage=391&amp;rft.aulast=Rajagopalan&amp;rft.aufirst=Sridharan&amp;rft_id=info%3Adoi%2F10.1038%2Fnchembio.1498"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">Design of activated serine-containing catalytic triads with atomic-level accuracy</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-type">Publication Type</td><td class="biblio-field-contents-type">Journal Article</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-year">Year of Publication</td><td class="biblio-field-contents-year">2014</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-authors">Authors</td><td class="biblio-field-contents-authors"><a href="/biblio/author/972">Rajagopalan, S.</a>, <a href="/biblio/author/115">Wang C.</a>, <a href="/biblio/author/1037">Yu K.</a>, <a href="/biblio/author/203">Kuzin A. P.</a>, <a href="/biblio/author/385">Richter F.</a>, <a href="/biblio/author/806">Lew S.</a>, <a href="/biblio/author/1038">Miklos A. E.</a>, <a href="/biblio/author/1039">Matthews M. L.</a>, <a href="/biblio/author/803">Seetharaman J.</a>, <a href="/biblio/author/804">Su M.</a>, <a href="/biblio/author/207">Hunt J. F.</a>, <a href="/biblio/author/448">Cravatt B. F.</a>, & <a href="/biblio/author/8">Baker D.</a></td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-secondary-title">Journal</td><td class="biblio-field-contents-secondary-title">Nature chemical biology</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-volume">Volume</td><td class="biblio-field-contents-volume">10</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-issue">Issue</td><td class="biblio-field-contents-issue">5</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-pages">Pagination</td><td class="biblio-field-contents-pages">386-391</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-date">Date Published</td><td class="biblio-field-contents-date">04/06/2014</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">1552-4469</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-keywords">Keywords</td><td class="biblio-field-contents-keywords"><a href="/biblio/keyword/325">Primary Publication</a></td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-abst-e">Abstract</td><td class="biblio-field-contents-abst-e"><p>A challenge in the computational design of enzymes is that multiple properties, including substrate binding, transition state stabilization and product release, must be simultaneously optimized, and this has limited the absolute activity of successful designs. Here, we focus on a single critical property of many enzymes: the nucleophilicity of an active site residue that initiates catalysis. We design proteins with idealized serine-containing catalytic triads and assess their nucleophilicity directly in native biological systems using activity-based organophosphate probes. Crystal structures of the most successful designs show unprecedented agreement with computational models, including extensive hydrogen bonding networks between the catalytic triad (or quartet) residues, and mutagenesis experiments demonstrate that these networks are critical for serine activation and organophosphate reactivity. Following optimization by yeast display, the designs react with organophosphate probes at rates comparable to natural serine hydrolases. Co-crystal structures with diisopropyl fluorophosphate bound to the serine nucleophile suggest that the designs could provide the basis for a new class of organophosphate capture agents.</p> </td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-doi">DOI</td><td class="biblio-field-contents-doi"><a href="http://dx.doi.org/10.1038/nchembio.1498">10.1038/nchembio.1498</a></td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-custom1">Custom1</td><td class="biblio-field-contents-custom1"><p><a href="http://www.ncbi.nlm.nih.gov/pubmed/24705591?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/24705591?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/24705591?dopt=Abstract</a></p> </td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-alternate-title">Alternate Journal</td><td class="biblio-field-contents-alternate-title">Nat. Chem. Biol.</td> </tr> </tbody> </table> </div><table id="attachments" class="sticky-enabled"> <thead><tr><th>Attachment</th><th>Size</th> </tr></thead> <tbody> <tr class="odd"><td><a href="http://www.bakerlab.org/system/files/Rajagopalan_nchembio_2014A.pdf">Rajagopalan_nchembio_2014A.pdf</a></td><td>1.1 MB</td> </tr> </tbody> </table> Primary Publication Tue, 15 Apr 2014 15:51:00 +0000 bakerpg 528 at http://www.bakerlab.org Redesigning the Specificity of Protein-DNA Interactions with Rosetta. http://www.bakerlab.org/redesigning-the-specificity-of-protein-dna-interactions-with-rosetta-pub <div id="biblio-node"><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.atitle=Redesigning+the+Specificity+of+Protein-DNA+Interactions+with+Rosetta.&amp;rft.title=Methods+in+molecular+biology+%28Clifton%2C+N.J.%29&amp;rft.issn=1940-6029&amp;rft.date=2014&amp;rft.volume=1123&amp;rft.aulast=Thyme&amp;rft.aufirst=Summer&amp;rft_id=info%3Adoi%2F10.1007%2F978-1-62703-968-0_17"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">Redesigning the Specificity of Protein-DNA Interactions with Rosetta.</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-type">Publication Type</td><td class="biblio-field-contents-type">Journal Article</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-year">Year of Publication</td><td class="biblio-field-contents-year">2014</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-authors">Authors</td><td class="biblio-field-contents-authors"><a href="/biblio/author/1025">Thyme, S.</a>, & <a href="/biblio/author/8">Baker D.</a></td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-secondary-title">Journal</td><td class="biblio-field-contents-secondary-title">Methods in molecular biology (Clifton, N.J.)</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-volume">Volume</td><td class="biblio-field-contents-volume">1123</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-pages">Pagination</td><td class="biblio-field-contents-pages">265-82</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-date">Date Published</td><td class="biblio-field-contents-date">2014</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">1940-6029</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-keywords">Keywords</td><td class="biblio-field-contents-keywords"><a href="/biblio/keyword/325">Primary Publication</a></td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-abst-e">Abstract</td><td class="biblio-field-contents-abst-e"><p>Building protein tools that can selectively bind or cleave specific DNA sequences requires efficient technologies for modifying protein-DNA interactions. Computational design is one method for accomplishing this goal. In this chapter, we present the current state of protein-DNA interface design with the Rosetta macromolecular modeling program. The LAGLIDADG endonuclease family of DNA-cleaving enzymes, under study as potential gene therapy reagents, has been the main testing ground for these in silico protocols. At this time, the computational methods are most useful for designing endonuclease variants that can accommodate small numbers of target site substitutions. Attempts to engineer for more extensive interface changes will likely benefit from an approach that uses the computational design results in conjunction with a high-throughput directed evolution or screening procedure. The family of enzymes presents an engineering challenge because their interfaces are highly integrated and there is significant coordination between the binding and catalysis events. Future developments in the computational algorithms depend on experimental feedback to improve understanding and modeling of these complex enzymatic features. This chapter presents both the basic method of design that has been successfully used to modulate specificity and more advanced procedures that incorporate DNA flexibility and other properties that are likely necessary for reliable modeling of more extensive target site changes.</p> </td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-doi">DOI</td><td class="biblio-field-contents-doi"><a href="http://dx.doi.org/10.1007/978-1-62703-968-0_17">10.1007/978-1-62703-968-0_17</a></td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-custom1">Custom1</td><td class="biblio-field-contents-custom1"><p><a href="http://www.ncbi.nlm.nih.gov/pubmed/24510272?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/24510272?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/24510272?dopt=Abstract</a></p> </td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-alternate-title">Alternate Journal</td><td class="biblio-field-contents-alternate-title">Methods Mol. Biol.</td> </tr> </tbody> </table> </div><table id="attachments" class="sticky-enabled"> <thead><tr><th>Attachment</th><th>Size</th> </tr></thead> <tbody> <tr class="odd"><td><a href="http://www.bakerlab.org/system/files/Thyme_2014.pdf">Thyme_2014.pdf</a></td><td>413.9 KB</td> </tr> </tbody> </table> http://www.bakerlab.org/redesigning-the-specificity-of-protein-dna-interactions-with-rosetta-pub#comments Primary Publication Fri, 07 Mar 2014 20:45:59 +0000 bakerpg 525 at http://www.bakerlab.org megaTALs: a rare-cleaving nuclease architecture for therapeutic genome engineering. http://www.bakerlab.org/node/516 <div id="biblio-node"><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.atitle=megaTALs%3A+a+rare-cleaving+nuclease+architecture+for+therapeutic+genome+engineering.&amp;rft.title=Nucleic+acids+research&amp;rft.issn=1362-4962&amp;rft.date=2013&amp;rft.aulast=Boissel&amp;rft.aufirst=Sandrine"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">megaTALs: a rare-cleaving nuclease architecture for therapeutic genome engineering.</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-type">Publication Type</td><td class="biblio-field-contents-type">Journal Article</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-year">Year of Publication</td><td class="biblio-field-contents-year">2013</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-authors">Authors</td><td class="biblio-field-contents-authors"><a href="/biblio/author/987">Boissel, S.</a>, <a href="/biblio/author/214">Jarjour J.</a>, <a href="/biblio/author/988">Astrakhan A.</a>, <a href="/biblio/author/989">Adey A.</a>, <a href="/biblio/author/990">Gouble A.</a>, <a href="/biblio/author/991">Duchateau P.</a>, <a href="/biblio/author/992">Shendure J.</a>, <a href="/biblio/author/107">Stoddard B. L.</a>, <a href="/biblio/author/993">Certo M. T.</a>, <a href="/biblio/author/8">Baker D.</a>, & <a href="/biblio/author/216">Scharenberg A. M.</a></td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-secondary-title">Journal</td><td class="biblio-field-contents-secondary-title">Nucleic acids research</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-date">Date Published</td><td class="biblio-field-contents-date">2013 Nov 26</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">1362-4962</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-keywords">Keywords</td><td class="biblio-field-contents-keywords"><a href="/biblio/keyword/325">Primary Publication</a></td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-abst-e">Abstract</td><td class="biblio-field-contents-abst-e"><p>Rare-cleaving endonucleases have emerged as important tools for making targeted genome modifications. While multiple platforms are now available to generate reagents for research applications, each existing platform has significant limitations in one or more of three key properties necessary for therapeutic application: efficiency of cleavage at the desired target site, specificity of cleavage (i.e. rate of cleavage at 'off-target' sites), and efficient/facile means for delivery to desired target cells. Here, we describe the development of a single-chain rare-cleaving nuclease architecture, which we designate 'megaTAL', in which the DNA binding region of a transcription activator-like (TAL) effector is used to 'address' a site-specific meganuclease adjacent to a single desired genomic target site. This architecture allows the generation of extremely active and hyper-specific compact nucleases that are compatible with all current viral and nonviral cell delivery methods.</p> </td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-custom1">Custom1</td><td class="biblio-field-contents-custom1"><p><a href="http://www.ncbi.nlm.nih.gov/pubmed/24285304?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/24285304?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/24285304?dopt=Abstract</a></p> </td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-alternate-title">Alternate Journal</td><td class="biblio-field-contents-alternate-title">Nucleic Acids Res.</td> </tr> </tbody> </table> </div> http://www.bakerlab.org/node/516#comments Primary Publication Tue, 21 Jan 2014 23:37:59 +0000 bakerpg 516 at http://www.bakerlab.org Reprogramming homing endonuclease specificity through computational design and directed evolution. http://www.bakerlab.org/node/515 <div id="biblio-node"><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.atitle=Reprogramming+homing+endonuclease+specificity+through+computational+design+and+directed+evolution.&amp;rft.title=Nucleic+acids+research&amp;rft.issn=1362-4962&amp;rft.date=2013&amp;rft.aulast=Thyme&amp;rft.aufirst=Summer"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">Reprogramming homing endonuclease specificity through computational design and directed evolution.</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-type">Publication Type</td><td class="biblio-field-contents-type">Journal Article</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-year">Year of Publication</td><td class="biblio-field-contents-year">2013</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-authors">Authors</td><td class="biblio-field-contents-authors"><a href="/biblio/author/213">Thyme, S. B.</a>, <a href="/biblio/author/778">Boissel S. J. S.</a>, <a href="/biblio/author/982">Arshiya Quadri S.</a>, <a href="/biblio/author/983">Nolan T.</a>, <a href="/biblio/author/984">Baker D. A.</a>, <a href="/biblio/author/985">Park R. U.</a>, <a href="/biblio/author/986">Kusak L.</a>, <a href="/biblio/author/11">Ashworth J.</a>, & <a href="/biblio/author/8">Baker D.</a></td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-secondary-title">Journal</td><td class="biblio-field-contents-secondary-title">Nucleic acids research</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-date">Date Published</td><td class="biblio-field-contents-date">2013 Nov 21</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">1362-4962</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-keywords">Keywords</td><td class="biblio-field-contents-keywords"><a href="/biblio/keyword/325">Primary Publication</a></td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-abst-e">Abstract</td><td class="biblio-field-contents-abst-e"><p>Homing endonucleases (HEs) can be used to induce targeted genome modification to reduce the fitness of pathogen vectors such as the malaria-transmitting Anopheles gambiae and to correct deleterious mutations in genetic diseases. We describe the creation of an extensive set of HE variants with novel DNA cleavage specificities using an integrated experimental and computational approach. Using computational modeling and an improved selection strategy, which optimizes specificity in addition to activity, we engineered an endonuclease to cleave in a gene associated with Anopheles sterility and another to cleave near a mutation that causes pyruvate kinase deficiency. In the course of this work we observed unanticipated context-dependence between bases which will need to be mechanistically understood for reprogramming of specificity to succeed more generally.</p> </td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-custom1">Custom1</td><td class="biblio-field-contents-custom1"><p><a href="http://www.ncbi.nlm.nih.gov/pubmed/24270794?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/24270794?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/24270794?dopt=Abstract</a></p> </td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-alternate-title">Alternate Journal</td><td class="biblio-field-contents-alternate-title">Nucleic Acids Res.</td> </tr> </tbody> </table> </div> http://www.bakerlab.org/node/515#comments Primary Publication Tue, 21 Jan 2014 23:37:24 +0000 bakerpg 515 at http://www.bakerlab.org Relaxation of backbone bond geometry improves protein energy landscape modeling. http://www.bakerlab.org/node/514 <div id="biblio-node"><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.atitle=Relaxation+of+backbone+bond+geometry+improves+protein+energy+landscape+modeling.&amp;rft.title=Protein+science+%3A+a+publication+of+the+Protein+Society&amp;rft.issn=1469-896X&amp;rft.date=2013&amp;rft.aulast=Conway&amp;rft.aufirst=Patrick&amp;rft_id=info%3Adoi%2F10.1002%2Fpro.2389"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">Relaxation of backbone bond geometry improves protein energy landscape modeling.</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-type">Publication Type</td><td class="biblio-field-contents-type">Journal Article</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-year">Year of Publication</td><td class="biblio-field-contents-year">2013</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-authors">Authors</td><td class="biblio-field-contents-authors"><a href="/biblio/author/980">Conway, P.</a>, <a href="/biblio/author/172">Tyka M. D.</a>, <a href="/biblio/author/191">DiMaio F.</a>, <a href="/biblio/author/981">Konerding D. E.</a>, & <a href="/biblio/author/8">Baker D.</a></td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-secondary-title">Journal</td><td class="biblio-field-contents-secondary-title">Protein science : a publication of the Protein Society</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-date">Date Published</td><td class="biblio-field-contents-date">2013 Oct 29</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">1469-896X</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-keywords">Keywords</td><td class="biblio-field-contents-keywords"><a href="/biblio/keyword/325">Primary Publication</a></td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-abst-e">Abstract</td><td class="biblio-field-contents-abst-e"><p>A key issue in macromolecular structure modeling is the granularity of the molecular representation. A fine-grained representation can approximate the actual structure more accurately, but may require many more degrees of freedom than a coarse-grained representation and hence make conformational search more challenging. We investigate this tradeoff between the accuracy and the size of protein conformational search space for two frequently used representations: one with fixed bond angles and lengths and one that has full flexibility. We performed large-scale explorations of the energy landscapes of 82 protein domains under each model, and find that the introduction of bond angle flexibility significantly increases the average energy gap between native and non-native structures. We also find that incorporating bonded geometry flexibility improves low resolution X-ray crystallographic refinement. These results suggest that backbone bond angle relaxation makes an important contribution to native structure energetics, that current energy functions are sufficiently accurate to capture the energetic gain associated with subtle deformations from chain ideality, and more speculatively, that backbone geometry distortions occur late in protein folding to optimize packing in the native state.</p> </td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-doi">DOI</td><td class="biblio-field-contents-doi"><a href="http://dx.doi.org/10.1002/pro.2389">10.1002/pro.2389</a></td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-custom1">Custom1</td><td class="biblio-field-contents-custom1"><p><a href="http://www.ncbi.nlm.nih.gov/pubmed/24265211?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/24265211?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/24265211?dopt=Abstract</a></p> </td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-alternate-title">Alternate Journal</td><td class="biblio-field-contents-alternate-title">Protein Sci.</td> </tr> </tbody> </table> </div> http://www.bakerlab.org/node/514#comments Primary Publication Tue, 21 Jan 2014 23:36:43 +0000 bakerpg 514 at http://www.bakerlab.org Improved low-resolution crystallographic refinement with Phenix and Rosetta. http://www.bakerlab.org/node/513 <div id="biblio-node"><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.atitle=Improved+low-resolution+crystallographic+refinement+with+Phenix+and+Rosetta.&amp;rft.title=Nature+methods&amp;rft.issn=1548-7105&amp;rft.date=2013&amp;rft.volume=10&amp;rft.issue=11&amp;rft.aulast=DiMaio&amp;rft.aufirst=Frank&amp;rft_id=info%3Adoi%2F10.1038%2Fnmeth.2648"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">Improved low-resolution crystallographic refinement with Phenix and Rosetta.</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-type">Publication Type</td><td class="biblio-field-contents-type">Journal Article</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-year">Year of Publication</td><td class="biblio-field-contents-year">2013</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-authors">Authors</td><td class="biblio-field-contents-authors"><a href="/biblio/author/191">DiMaio, F.</a>, <a href="/biblio/author/829">Echols N.</a>, <a href="/biblio/author/979">Headd J. J.</a>, <a href="/biblio/author/670">Terwilliger T. C.</a>, <a href="/biblio/author/826">Adams P. D.</a>, & <a href="/biblio/author/8">Baker D.</a></td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-secondary-title">Journal</td><td class="biblio-field-contents-secondary-title">Nature methods</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-volume">Volume</td><td class="biblio-field-contents-volume">10</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-issue">Issue</td><td class="biblio-field-contents-issue">11</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-pages">Pagination</td><td class="biblio-field-contents-pages">1102-4</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-date">Date Published</td><td class="biblio-field-contents-date">2013 Nov</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">1548-7105</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-keywords">Keywords</td><td class="biblio-field-contents-keywords"><a href="/biblio/keyword/3">Crystallography, X-Ray</a>, <a href="/biblio/keyword/10">Models, Molecular</a>, <a href="/biblio/keyword/325">Primary Publication</a></td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-abst-e">Abstract</td><td class="biblio-field-contents-abst-e"><p>Refinement of macromolecular structures against low-resolution crystallographic data is limited by the ability of current methods to converge on a structure with realistic geometry. We developed a low-resolution crystallographic refinement method that combines the Rosetta sampling methodology and energy function with reciprocal-space X-ray refinement in Phenix. On a set of difficult low-resolution cases, the method yielded improved model geometry and lower free R factors than alternate refinement methods.</p> </td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-doi">DOI</td><td class="biblio-field-contents-doi"><a href="http://dx.doi.org/10.1038/nmeth.2648">10.1038/nmeth.2648</a></td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-custom1">Custom1</td><td class="biblio-field-contents-custom1"><p><a href="http://www.ncbi.nlm.nih.gov/pubmed/24076763?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/24076763?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/24076763?dopt=Abstract</a></p> </td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-alternate-title">Alternate Journal</td><td class="biblio-field-contents-alternate-title">Nat. Methods</td> </tr> </tbody> </table> </div> http://www.bakerlab.org/node/513#comments Primary Publication Tue, 21 Jan 2014 23:36:10 +0000 bakerpg 513 at http://www.bakerlab.org High-resolution comparative modeling with RosettaCM. http://www.bakerlab.org/node/512 <div id="biblio-node"><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.atitle=High-resolution+comparative+modeling+with+RosettaCM.&amp;rft.title=Structure+%28London%2C+England+%3A+1993%29&amp;rft.issn=1878-4186&amp;rft.date=2013&amp;rft.volume=21&amp;rft.issue=10&amp;rft.aulast=Song&amp;rft.aufirst=Yifan&amp;rft_id=info%3Adoi%2F10.1016%2Fj.str.2013.08.005"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">High-resolution comparative modeling with RosettaCM.</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-type">Publication Type</td><td class="biblio-field-contents-type">Journal Article</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-year">Year of Publication</td><td class="biblio-field-contents-year">2013</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-authors">Authors</td><td class="biblio-field-contents-authors"><a href="/biblio/author/394">Song, Y.</a>, <a href="/biblio/author/191">DiMaio F.</a>, <a href="/biblio/author/967">Yu-Ruei Wang R.</a>, <a href="/biblio/author/463">Kim D.</a>, <a href="/biblio/author/977">Miles C.</a>, <a href="/biblio/author/978">Brunette T.</a>, <a href="/biblio/author/170">Thompson J.</a>, & <a href="/biblio/author/8">Baker D.</a></td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-secondary-title">Journal</td><td class="biblio-field-contents-secondary-title">Structure (London, England : 1993)</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-volume">Volume</td><td class="biblio-field-contents-volume">21</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-issue">Issue</td><td class="biblio-field-contents-issue">10</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-pages">Pagination</td><td class="biblio-field-contents-pages">1735-42</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-date">Date Published</td><td class="biblio-field-contents-date">2013 Oct 8</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">1878-4186</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-keywords">Keywords</td><td class="biblio-field-contents-keywords"><a href="/biblio/keyword/325">Primary Publication</a></td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-abst-e">Abstract</td><td class="biblio-field-contents-abst-e"><p>We describe an improved method for comparative modeling, RosettaCM, which optimizes a physically realistic all-atom energy function over the conformational space defined by homologous structures. Given a set of sequence alignments, RosettaCM assembles topologies by recombining aligned segments in Cartesian space and building unaligned regions de novo in torsion space. The junctions between segments are regularized using a loop closure method combining fragment superposition with gradient-based minimization. The energies of the resulting models are optimized by all-atom refinement, and the most representative low-energy model is selected. The CASP10 experiment suggests that RosettaCM yields models with more accurate side-chain and backbone conformations than other methods when the sequence identity to the templates is greater than ∼15%.</p> </td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-doi">DOI</td><td class="biblio-field-contents-doi"><a href="http://dx.doi.org/10.1016/j.str.2013.08.005">10.1016/j.str.2013.08.005</a></td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-custom1">Custom1</td><td class="biblio-field-contents-custom1"><p><a href="http://www.ncbi.nlm.nih.gov/pubmed/24035711?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/24035711?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/24035711?dopt=Abstract</a></p> </td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-alternate-title">Alternate Journal</td><td class="biblio-field-contents-alternate-title">Structure</td> </tr> </tbody> </table> </div> http://www.bakerlab.org/node/512#comments Primary Publication Tue, 21 Jan 2014 23:35:31 +0000 bakerpg 512 at http://www.bakerlab.org Computational design of a protein-based enzyme inhibitor. http://www.bakerlab.org/Computational-design-of-a-protein-based-enzyme-inhibitor-pub <div id="biblio-node"><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.atitle=Computational+design+of+a+protein-based+enzyme+inhibitor.&amp;rft.title=Journal+of+molecular+biology&amp;rft.issn=1089-8638&amp;rft.date=2013&amp;rft.volume=425&amp;rft.issue=18&amp;rft.aulast=Procko&amp;rft.aufirst=Erik&amp;rft_id=info%3Adoi%2F10.1016%2Fj.jmb.2013.06.035"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">Computational design of a protein-based enzyme inhibitor.</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-type">Publication Type</td><td class="biblio-field-contents-type">Journal Article</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-year">Year of Publication</td><td class="biblio-field-contents-year">2013</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-authors">Authors</td><td class="biblio-field-contents-authors"><a href="/biblio/author/847">Procko, E.</a>, <a href="/biblio/author/975">Hedman R.</a>, <a href="/biblio/author/976">Hamilton K.</a>, <a href="/biblio/author/803">Seetharaman J.</a>, <a href="/biblio/author/159">Fleishman S. J.</a>, <a href="/biblio/author/804">Su M.</a>, <a href="/biblio/author/54">Aramini J.</a>, <a href="/biblio/author/883">Kornhaber G.</a>, <a href="/biblio/author/207">Hunt J. F.</a>, <a href="/biblio/author/809">Tong L.</a>, <a href="/biblio/author/61">Montelione G. T.</a>, & <a href="/biblio/author/8">Baker D.</a></td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-secondary-title">Journal</td><td class="biblio-field-contents-secondary-title">Journal of molecular biology</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-volume">Volume</td><td class="biblio-field-contents-volume">425</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-issue">Issue</td><td class="biblio-field-contents-issue">18</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-pages">Pagination</td><td class="biblio-field-contents-pages">3563-75</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-date">Date Published</td><td class="biblio-field-contents-date">2013 Sep 23</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">1089-8638</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-keywords">Keywords</td><td class="biblio-field-contents-keywords"><a href="/biblio/keyword/12">Amino Acid Sequence</a>, <a href="/biblio/keyword/64">Animals</a>, <a href="/biblio/keyword/174">Catalytic Domain</a>, <a href="/biblio/keyword/2">Computational Biology</a>, <a href="/biblio/keyword/153">Enzyme Inhibitors</a>, <a href="/biblio/keyword/10">Models, Molecular</a>, <a href="/biblio/keyword/521">Molecular Docking Simulation</a>, <a href="/biblio/keyword/251">Muramidase</a>, <a href="/biblio/keyword/82">Mutagenesis, Site-Directed</a>, <a href="/biblio/keyword/325">Primary Publication</a>, <a href="/biblio/keyword/122">Protein Binding</a>, <a href="/biblio/keyword/29">Protein Conformation</a>, <a href="/biblio/keyword/109">Protein Engineering</a>, <a href="/biblio/keyword/474">Protein Interaction Domains and Motifs</a>, <a href="/biblio/keyword/500">Protein Interaction Maps</a></td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-abst-e">Abstract</td><td class="biblio-field-contents-abst-e"><p>While there has been considerable progress in designing protein-protein interactions, the design of proteins that bind polar surfaces is an unmet challenge. We describe the computational design of a protein that binds the acidic active site of hen egg lysozyme and inhibits the enzyme. The design process starts with two polar amino acids that fit deep into the enzyme active site, identifies a protein scaffold that supports these residues and is complementary in shape to the lysozyme active-site region, and finally optimizes the surrounding contact surface for high-affinity binding. Following affinity maturation, a protein designed using this method bound lysozyme with low nanomolar affinity, and a combination of NMR studies, crystallography, and knockout mutagenesis confirmed the designed binding surface and orientation. Saturation mutagenesis with selection and deep sequencing demonstrated that specific designed interactions extending well beyond the centrally grafted polar residues are critical for high-affinity binding.</p> </td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-doi">DOI</td><td class="biblio-field-contents-doi"><a href="http://dx.doi.org/10.1016/j.jmb.2013.06.035">10.1016/j.jmb.2013.06.035</a></td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-custom1">Custom1</td><td class="biblio-field-contents-custom1"><p><a href="http://www.ncbi.nlm.nih.gov/pubmed/23827138?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/23827138?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/23827138?dopt=Abstract</a></p> </td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-alternate-title">Alternate Journal</td><td class="biblio-field-contents-alternate-title">J. Mol. Biol.</td> </tr> </tbody> </table> </div><table id="attachments" class="sticky-enabled"> <thead><tr><th>Attachment</th><th>Size</th> </tr></thead> <tbody> <tr class="odd"><td><a href="http://www.bakerlab.org/system/files/Procko13.pdf">Procko13.pdf</a></td><td>2.98 MB</td> </tr> </tbody> </table> http://www.bakerlab.org/Computational-design-of-a-protein-based-enzyme-inhibitor-pub#comments Primary Publication Tue, 21 Jan 2014 23:34:47 +0000 bakerpg 511 at http://www.bakerlab.org Computational design of an unnatural amino acid dependent metalloprotein with atomic level accuracy. http://www.bakerlab.org/Computational-design-of-an-unnatural-amino-acid-dependent-metalloprotein-with-atomic-level-accuracy-pub <div id="biblio-node"><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.atitle=Computational+design+of+an+unnatural+amino+acid+dependent+metalloprotein+with+atomic+level+accuracy.&amp;rft.title=Journal+of+the+American+Chemical+Society&amp;rft.issn=1520-5126&amp;rft.date=2013&amp;rft.volume=135&amp;rft.issue=36&amp;rft.aulast=Mills&amp;rft.aufirst=Jeremy&amp;rft_id=info%3Adoi%2F10.1021%2Fja403503m"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">Computational design of an unnatural amino acid dependent metalloprotein with atomic level accuracy.</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-type">Publication Type</td><td class="biblio-field-contents-type">Journal Article</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-year">Year of Publication</td><td class="biblio-field-contents-year">2013</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-authors">Authors</td><td class="biblio-field-contents-authors"><a href="/biblio/author/874">Mills, J. H.</a>, <a href="/biblio/author/638" class="biblio-local-author">Khare S. D.</a>, <a href="/biblio/author/202">Bolduc J. M.</a>, <a href="/biblio/author/807">Forouhar F.</a>, <a href="/biblio/author/969">Mulligan V. K.</a>, <a href="/biblio/author/806">Lew S.</a>, <a href="/biblio/author/803">Seetharaman J.</a>, <a href="/biblio/author/809">Tong L.</a>, <a href="/biblio/author/107">Stoddard B. L.</a>, & <a href="/biblio/author/8">Baker D.</a></td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-secondary-title">Journal</td><td class="biblio-field-contents-secondary-title">Journal of the American Chemical Society</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-volume">Volume</td><td class="biblio-field-contents-volume">135</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-issue">Issue</td><td class="biblio-field-contents-issue">36</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-pages">Pagination</td><td class="biblio-field-contents-pages">13393-9</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-date">Date Published</td><td class="biblio-field-contents-date">2013 Sep 11</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">1520-5126</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-keywords">Keywords</td><td class="biblio-field-contents-keywords"><a href="/biblio/keyword/325">Primary Publication</a></td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-abst-e">Abstract</td><td class="biblio-field-contents-abst-e"><p>Genetically encoded unnatural amino acids could facilitate the design of proteins and enzymes of novel function, but correctly specifying sites of incorporation and the identities and orientations of surrounding residues represents a formidable challenge. Computational design methods have been used to identify optimal locations for functional sites in proteins and design the surrounding residues but have not incorporated unnatural amino acids in this process. We extended the Rosetta design methodology to design metalloproteins in which the amino acid (2,2'-bipyridin-5yl)alanine (Bpy-Ala) is a primary ligand of a bound metal ion. Following initial results that indicated the importance of buttressing the Bpy-Ala amino acid, we designed a buried metal binding site with octahedral coordination geometry consisting of Bpy-Ala, two protein-based metal ligands, and two metal-bound water molecules. Experimental characterization revealed a Bpy-Ala-mediated metalloprotein with the ability to bind divalent cations including Co(2+), Zn(2+), Fe(2+), and Ni(2+), with a Kd for Zn(2+) of ∼40 pM. X-ray crystal structures of the designed protein bound to Co(2+) and Ni(2+) have RMSDs to the design model of 0.9 and 1.0 Å respectively over all atoms in the binding site.</p> </td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-doi">DOI</td><td class="biblio-field-contents-doi"><a href="http://dx.doi.org/10.1021/ja403503m">10.1021/ja403503m</a></td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-custom1">Custom1</td><td class="biblio-field-contents-custom1"><p><a href="http://www.ncbi.nlm.nih.gov/pubmed/23924187?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/23924187?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/23924187?dopt=Abstract</a></p> </td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-alternate-title">Alternate Journal</td><td class="biblio-field-contents-alternate-title">J. Am. Chem. Soc.</td> </tr> </tbody> </table> </div><table id="attachments" class="sticky-enabled"> <thead><tr><th>Attachment</th><th>Size</th> </tr></thead> <tbody> <tr class="odd"><td><a href="http://www.bakerlab.org/system/files/Mills13.pdf">Mills13.pdf</a></td><td>987.3 KB</td> </tr> </tbody> </table> http://www.bakerlab.org/Computational-design-of-an-unnatural-amino-acid-dependent-metalloprotein-with-atomic-level-accuracy-pub#comments Primary Publication Tue, 21 Jan 2014 23:33:19 +0000 bakerpg 509 at http://www.bakerlab.org One contact for every twelve residues allows robust and accurate topology-level protein structure modeling. http://www.bakerlab.org/node/506 <div id="biblio-node"><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.atitle=One+contact+for+every+twelve+residues+allows+robust+and+accurate+topology-level+protein+structure+modeling.&amp;rft.title=Proteins&amp;rft.issn=1097-0134&amp;rft.date=2013&amp;rft.aulast=Kim&amp;rft.aufirst=David&amp;rft_id=info%3Adoi%2F10.1002%2Fprot.24374"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">One contact for every twelve residues allows robust and accurate topology-level protein structure modeling.</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-type">Publication Type</td><td class="biblio-field-contents-type">Journal Article</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-year">Year of Publication</td><td class="biblio-field-contents-year">2013</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-authors">Authors</td><td class="biblio-field-contents-authors"><a href="/biblio/author/121" class="biblio-local-author">Kim, D. E.</a>, <a href="/biblio/author/191">DiMaio F.</a>, <a href="/biblio/author/967">Yu-Ruei Wang R.</a>, <a href="/biblio/author/394">Song Y.</a>, & <a href="/biblio/author/8">Baker D.</a></td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-secondary-title">Journal</td><td class="biblio-field-contents-secondary-title">Proteins</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-date">Date Published</td><td class="biblio-field-contents-date">2013 Jul 31</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">1097-0134</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-keywords">Keywords</td><td class="biblio-field-contents-keywords"><a href="/biblio/keyword/325">Primary Publication</a></td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-abst-e">Abstract</td><td class="biblio-field-contents-abst-e"><p>A number of methods have been described for identifying pairs of contacting residues in protein three-dimensional structures, but it is unclear how many contacts are required for accurate structure modeling. The CASP10 assisted contact experiment provided a blind test of contact guided protein structure modeling. We describe the models generated for these contact guided prediction challenges using the Rosetta structure modeling methodology. For nearly all cases, the submitted models had the correct overall topology, and in some cases, they had near atomic-level accuracy; for example the model of the 384 residue homo-oligomeric tetramer (Tc680o) had only 2.9 Å root-mean-square deviation (RMSD) from the crystal structure. Our results suggest that experimental and bioinformatic methods for obtaining contact information may need to generate only one correct contact for every 12 residues in the protein to allow accurate topology level modeling. Proteins 2013;. © 2013 Wiley Periodicals, Inc.</p> </td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-doi">DOI</td><td class="biblio-field-contents-doi"><a href="http://dx.doi.org/10.1002/prot.24374">10.1002/prot.24374</a></td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-custom1">Custom1</td><td class="biblio-field-contents-custom1"><p><a href="http://www.ncbi.nlm.nih.gov/pubmed/23900763?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/23900763?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/23900763?dopt=Abstract</a></p> </td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-alternate-title">Alternate Journal</td><td class="biblio-field-contents-alternate-title">Proteins</td> </tr> </tbody> </table> </div> http://www.bakerlab.org/node/506#comments Primary Publication Tue, 21 Jan 2014 23:30:46 +0000 bakerpg 506 at http://www.bakerlab.org Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions. http://www.bakerlab.org/node/505 <div id="biblio-node"><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.atitle=Community-wide+evaluation+of+methods+for+predicting+the+effect+of+mutations+on+protein-protein+interactions.&amp;rft.title=Proteins&amp;rft.issn=1097-0134&amp;rft.date=2013&amp;rft.volume=81&amp;rft.issue=11&amp;rft.aulast=Moretti&amp;rft.aufirst=Rocco&amp;rft_id=info%3Adoi%2F10.1002%2Fprot.24356"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions.</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-type">Publication Type</td><td class="biblio-field-contents-type">Journal Article</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-year">Year of Publication</td><td class="biblio-field-contents-year">2013</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-authors">Authors</td><td class="biblio-field-contents-authors"><a href="/biblio/author/851">Moretti, R.</a>, <a href="/biblio/author/159">Fleishman S. J.</a>, <a href="/biblio/author/902">Agius R.</a>, <a href="/biblio/author/903">Torchala M.</a>, <a href="/biblio/author/904">Bates P. A.</a>, <a href="/biblio/author/905">Kastritis P. L.</a>, <a href="/biblio/author/906">Rodrigues J. P. G. L. M.</a>, <a href="/biblio/author/907">Trellet M.</a>, <a href="/biblio/author/504">Bonvin A. M. J. J.</a>, <a href="/biblio/author/908">Cui M.</a>, <a href="/biblio/author/909">Rooman M.</a>, <a href="/biblio/author/910">Gillis D.</a>, <a href="/biblio/author/911">Dehouck Y.</a>, <a href="/biblio/author/912">Moal I.</a>, <a href="/biblio/author/913">Romero-Durana M.</a>, <a href="/biblio/author/914">Perez-Cano L.</a>, <a href="/biblio/author/915">Pallara C.</a>, <a href="/biblio/author/916">Jimenez B.</a>, <a href="/biblio/author/917">Fernandez-Recio J.</a>, <a href="/biblio/author/918">Flores S.</a>, <a href="/biblio/author/919">Pacella M.</a>, <a href="/biblio/author/920">Praneeth Kilambi K.</a>, <a href="/biblio/author/113">Gray J. J.</a>, <a href="/biblio/author/921">Popov P.</a>, <a href="/biblio/author/922">Grudinin S.</a>, <a href="/biblio/author/923">Esquivel-Rodríguez J.</a>, <a href="/biblio/author/924">Kihara D.</a>, <a href="/biblio/author/925">Zhao N.</a>, <a href="/biblio/author/926">Korkin D.</a>, <a href="/biblio/author/927">Zhu X.</a>, <a href="/biblio/author/928">Demerdash O. N. A.</a>, <a href="/biblio/author/929">Mitchell J. C.</a>, <a href="/biblio/author/930">Kanamori E.</a>, <a href="/biblio/author/931">Tsuchiya Y.</a>, <a href="/biblio/author/932">Nakamura H.</a>, <a href="/biblio/author/933">Lee H.</a>, <a href="/biblio/author/934">Park H.</a>, <a href="/biblio/author/935">Seok C.</a>, <a href="/biblio/author/936">Sarmiento J.</a>, <a href="/biblio/author/937">Liang S.</a>, <a href="/biblio/author/938">Teraguchi S.</a>, <a href="/biblio/author/939">Standley D. M.</a>, <a href="/biblio/author/940">Shimoyama H.</a>, <a href="/biblio/author/941">Terashi G.</a>, <a href="/biblio/author/942">Takeda-Shitaka M.</a>, <a href="/biblio/author/943">Iwadate M.</a>, <a href="/biblio/author/944">Umeyama H.</a>, <a href="/biblio/author/945">Beglov D.</a>, <a href="/biblio/author/946">Hall D. R.</a>, <a href="/biblio/author/947">Kozakov D.</a>, <a href="/biblio/author/948">Vajda S.</a>, <a href="/biblio/author/949">Pierce B. G.</a>, <a href="/biblio/author/950">Hwang H.</a>, <a href="/biblio/author/951">Vreven T.</a>, <a href="/biblio/author/952">Weng Z.</a>, <a href="/biblio/author/953">Huang Y.</a>, <a href="/biblio/author/954">Li H.</a>, <a href="/biblio/author/955">Yang X.</a>, <a href="/biblio/author/956">Ji X.</a>, <a href="/biblio/author/957">Liu S.</a>, <a href="/biblio/author/958">Xiao Y.</a>, <a href="/biblio/author/959">Zacharias M.</a>, <a href="/biblio/author/960">Qin S.</a>, <a href="/biblio/author/961">Zhou H. - X.</a>, <a href="/biblio/author/962">Huang S. - Y.</a>, <a href="/biblio/author/963">Zou X.</a>, <a href="/biblio/author/964">Velankar S.</a>, <a href="/biblio/author/965">Janin J.</a>, <a href="/biblio/author/966">Wodak S. J.</a>, & <a href="/biblio/author/8">Baker D.</a></td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-secondary-title">Journal</td><td class="biblio-field-contents-secondary-title">Proteins</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-volume">Volume</td><td class="biblio-field-contents-volume">81</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-issue">Issue</td><td class="biblio-field-contents-issue">11</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-pages">Pagination</td><td class="biblio-field-contents-pages">1980-7</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-date">Date Published</td><td class="biblio-field-contents-date">2013 Nov</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">1097-0134</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-keywords">Keywords</td><td class="biblio-field-contents-keywords"><a href="/biblio/keyword/325">Primary Publication</a></td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-abst-e">Abstract</td><td class="biblio-field-contents-abst-e"><p>Community-wide blind prediction experiments such as CAPRI and CASP provide an objective measure of the current state of predictive methodology. Here we describe a community-wide assessment of methods to predict the effects of mutations on protein-protein interactions. Twenty-two groups predicted the effects of comprehensive saturation mutagenesis for two designed influenza hemagglutinin binders and the results were compared with experimental yeast display enrichment data obtained using deep sequencing. The most successful methods explicitly considered the effects of mutation on monomer stability in addition to binding affinity, carried out explicit side-chain sampling and backbone relaxation, evaluated packing, electrostatic, and solvation effects, and correctly identified around a third of the beneficial mutations. Much room for improvement remains for even the best techniques, and large-scale fitness landscapes should continue to provide an excellent test bed for continued evaluation of both existing and new prediction methodologies.</p> </td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-doi">DOI</td><td class="biblio-field-contents-doi"><a href="http://dx.doi.org/10.1002/prot.24356">10.1002/prot.24356</a></td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-custom1">Custom1</td><td class="biblio-field-contents-custom1"><p><a href="http://www.ncbi.nlm.nih.gov/pubmed/23843247?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/23843247?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/23843247?dopt=Abstract</a></p> </td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-alternate-title">Alternate Journal</td><td class="biblio-field-contents-alternate-title">Proteins</td> </tr> </tbody> </table> </div> http://www.bakerlab.org/node/505#comments Primary Publication Tue, 21 Jan 2014 23:29:51 +0000 bakerpg 505 at http://www.bakerlab.org Computational design of an α-gliadin peptidase. http://www.bakerlab.org/node/501 <div id="biblio-node"><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.atitle=Computational+design+of+an+%CE%B1-gliadin+peptidase.&amp;rft.title=Journal+of+the+American+Chemical+Society&amp;rft.issn=1520-5126&amp;rft.date=2012&amp;rft.volume=134&amp;rft.issue=50&amp;rft.aulast=Gordon&amp;rft.aufirst=Sydney&amp;rft_id=info%3Adoi%2F10.1021%2Fja3094795"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">Computational design of an α-gliadin peptidase.</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-type">Publication Type</td><td class="biblio-field-contents-type">Journal Article</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-year">Year of Publication</td><td class="biblio-field-contents-year">2012</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-authors">Authors</td><td class="biblio-field-contents-authors"><a href="/biblio/author/868">Gordon, S. R.</a>, <a href="/biblio/author/869">Stanley E. J.</a>, <a href="/biblio/author/870">Wolf S.</a>, <a href="/biblio/author/871">Toland A.</a>, <a href="/biblio/author/872">Wu S. J.</a>, <a href="/biblio/author/873">Hadidi D.</a>, <a href="/biblio/author/874">Mills J. H.</a>, <a href="/biblio/author/8">Baker D.</a>, <a href="/biblio/author/875">Pultz I. S.</a>, & <a href="/biblio/author/129">Siegel J. B.</a></td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-secondary-title">Journal</td><td class="biblio-field-contents-secondary-title">Journal of the American Chemical Society</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-volume">Volume</td><td class="biblio-field-contents-volume">134</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-issue">Issue</td><td class="biblio-field-contents-issue">50</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-pages">Pagination</td><td class="biblio-field-contents-pages">20513-20</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-date">Date Published</td><td class="biblio-field-contents-date">2012 Dec 19</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">1520-5126</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-keywords">Keywords</td><td class="biblio-field-contents-keywords"><a href="/biblio/keyword/12">Amino Acid Sequence</a>, <a href="/biblio/keyword/514">Gliadin</a>, <a href="/biblio/keyword/10">Models, Molecular</a>, <a href="/biblio/keyword/19">Molecular Sequence Data</a>, <a href="/biblio/keyword/463">Peptide Hydrolases</a>, <a href="/biblio/keyword/325">Primary Publication</a></td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-abst-e">Abstract</td><td class="biblio-field-contents-abst-e"><p>The ability to rationally modify enzymes to perform novel chemical transformations is essential for the rapid production of next-generation protein therapeutics. Here we describe the use of chemical principles to identify a naturally occurring acid-active peptidase, and the subsequent use of computational protein design tools to reengineer its specificity toward immunogenic elements found in gluten that are the proposed cause of celiac disease. The engineered enzyme exhibits a k(cat)/K(M) of 568 M(-1) s(-1), representing a 116-fold greater proteolytic activity for a model gluten tetrapeptide than the native template enzyme, as well as an over 800-fold switch in substrate specificity toward immunogenic portions of gluten peptides. The computationally engineered enzyme is resistant to proteolysis by digestive proteases and degrades over 95% of an immunogenic peptide implicated in celiac disease in under an hour. Thus, through identification of a natural enzyme with the pre-existing qualities relevant to an ultimate goal and redefinition of its substrate specificity using computational modeling, we were able to generate an enzyme with potential as a therapeutic for celiac disease.</p> </td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-doi">DOI</td><td class="biblio-field-contents-doi"><a href="http://dx.doi.org/10.1021/ja3094795">10.1021/ja3094795</a></td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-custom1">Custom1</td><td class="biblio-field-contents-custom1"><p><a href="http://www.ncbi.nlm.nih.gov/pubmed/23153249?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/23153249?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/23153249?dopt=Abstract</a></p> </td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-alternate-title">Alternate Journal</td><td class="biblio-field-contents-alternate-title">J. Am. Chem. Soc.</td> </tr> </tbody> </table> </div> http://www.bakerlab.org/node/501#comments Primary Publication Tue, 21 Jan 2014 23:07:25 +0000 bakerpg 501 at http://www.bakerlab.org Computational design of a pH-sensitive IgG binding protein http://www.bakerlab.org/Computational-design-of-a-pH-sensitive-IgG-binding-protein <div id="biblio-node"><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.atitle=Computational+design+of+a+pH-sensitive+IgG+binding+protein&amp;rft.title=Proceedings+of+the+National+Academy+of+Sciences+of+the+United+States+of+America&amp;rft.issn=1091-6490&amp;rft.date=2013&amp;rft.aulast=Strauch&amp;rft.aufirst=Eva-Maria"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">Computational design of a pH-sensitive IgG binding protein</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-type">Publication Type</td><td class="biblio-field-contents-type">Journal Article</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-year">Year of Publication</td><td class="biblio-field-contents-year">2013</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-authors">Authors</td><td class="biblio-field-contents-authors"><a href="/biblio/author/633">Strauch, E. - M.</a>, <a href="/biblio/author/159">Fleishman S. J.</a>, & <a href="/biblio/author/8">Baker D.</a></td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-secondary-title">Journal</td><td class="biblio-field-contents-secondary-title">Proceedings of the National Academy of Sciences of the United States of America</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-date">Date Published</td><td class="biblio-field-contents-date">2013 Dec 31</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">1091-6490</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-keywords">Keywords</td><td class="biblio-field-contents-keywords"><a href="/biblio/keyword/325">Primary Publication</a></td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-abst-e">Abstract</td><td class="biblio-field-contents-abst-e"><p>Computational design provides the opportunity to program protein-protein interactions for desired applications. We used de novo protein interface design to generate a pH-dependent Fc domain binding protein that buries immunoglobulin G (IgG) His-433. Using next-generation sequencing of naïve and selected pools of a library of design variants, we generated a molecular footprint of the designed binding surface, confirming the binding mode and guiding further optimization of the balance between affinity and pH sensitivity. In biolayer interferometry experiments, the optimized design binds IgG with a Kd of ∼4 nM at pH 8.2, and approximately 500-fold more weakly at pH 5.5. The protein is extremely stable, heat-resistant and highly expressed in bacteria, and allows pH-based control of binding for IgG affinity purification and diagnostic devices.</p> </td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-custom1">Custom1</td><td class="biblio-field-contents-custom1"><p><a href="http://www.ncbi.nlm.nih.gov/pubmed/24381156?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/24381156?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/24381156?dopt=Abstract</a></p> </td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-alternate-title">Alternate Journal</td><td class="biblio-field-contents-alternate-title">Proc. Natl. Acad. Sci. U.S.A.</td> </tr> </tbody> </table> </div><table id="attachments" class="sticky-enabled"> <thead><tr><th>Attachment</th><th>Size</th> </tr></thead> <tbody> <tr class="odd"><td><a href="http://www.bakerlab.org/system/files/Strauch-1313605111_PNAS_13W.pdf">Strauch-1313605111_PNAS_13W.pdf</a></td><td>1.32 MB</td> </tr> </tbody> </table> Primary Publication Sun, 12 Jan 2014 22:22:23 +0000 bakerpg 499 at http://www.bakerlab.org Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era. http://www.bakerlab.org/node/498 <div id="biblio-node"><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.atitle=Assessing+the+utility+of+coevolution-based+residue-residue+contact+predictions+in+a+sequence-+and+structure-rich+era.&amp;rft.title=Proceedings+of+the+National+Academy+of+Sciences+of+the+United+States+of+America&amp;rft.issn=1091-6490&amp;rft.date=2013&amp;rft.volume=110&amp;rft.issue=39&amp;rft.aulast=Kamisetty&amp;rft.aufirst=Hetunandan&amp;rft_id=info%3Adoi%2F10.1073%2Fpnas.1314045110"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era.</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-type">Publication Type</td><td class="biblio-field-contents-type">Journal Article</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-year">Year of Publication</td><td class="biblio-field-contents-year">2013</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-authors">Authors</td><td class="biblio-field-contents-authors"><a href="/biblio/author/791">Kamisetty, H.</a>, <a href="/biblio/author/887">Ovchinnikov S.</a>, & <a href="/biblio/author/8">Baker D.</a></td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-secondary-title">Journal</td><td class="biblio-field-contents-secondary-title">Proceedings of the National Academy of Sciences of the United States of America</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-volume">Volume</td><td class="biblio-field-contents-volume">110</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-issue">Issue</td><td class="biblio-field-contents-issue">39</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-pages">Pagination</td><td class="biblio-field-contents-pages">15674-9</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-date">Date Published</td><td class="biblio-field-contents-date">2013 Sep 24</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">1091-6490</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-keywords">Keywords</td><td class="biblio-field-contents-keywords"><a href="/biblio/keyword/75">Algorithms</a>, <a href="/biblio/keyword/12">Amino Acid Sequence</a>, <a href="/biblio/keyword/1">Amino Acids</a>, <a href="/biblio/keyword/2">Computational Biology</a>, <a href="/biblio/keyword/148">Databases, Protein</a>, <a href="/biblio/keyword/111">Evolution, Molecular</a>, <a href="/biblio/keyword/10">Models, Molecular</a>, <a href="/biblio/keyword/325">Primary Publication</a>, <a href="/biblio/keyword/30">Proteins</a></td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-abst-e">Abstract</td><td class="biblio-field-contents-abst-e"><p>Recently developed methods have shown considerable promise in predicting residue-residue contacts in protein 3D structures using evolutionary covariance information. However, these methods require large numbers of evolutionarily related sequences to robustly assess the extent of residue covariation, and the larger the protein family, the more likely that contact information is unnecessary because a reasonable model can be built based on the structure of a homolog. Here we describe a method that integrates sequence coevolution and structural context information using a pseudolikelihood approach, allowing more accurate contact predictions from fewer homologous sequences. We rigorously assess the utility of predicted contacts for protein structure prediction using large and representative sequence and structure databases from recent structure prediction experiments. We find that contact predictions are likely to be accurate when the number of aligned sequences (with sequence redundancy reduced to 90%) is greater than five times the length of the protein, and that accurate predictions are likely to be useful for structure modeling if the aligned sequences are more similar to the protein of interest than to the closest homolog of known structure. These conditions are currently met by 422 of the protein families collected in the Pfam database.</p> </td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-doi">DOI</td><td class="biblio-field-contents-doi"><a href="http://dx.doi.org/10.1073/pnas.1314045110">10.1073/pnas.1314045110</a></td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-custom1">Custom1</td><td class="biblio-field-contents-custom1"><p><a href="http://www.ncbi.nlm.nih.gov/pubmed/24009338?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/24009338?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/24009338?dopt=Abstract</a></p> </td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-alternate-title">Alternate Journal</td><td class="biblio-field-contents-alternate-title">Proc. Natl. Acad. Sci. U.S.A.</td> </tr> </tbody> </table> </div> http://www.bakerlab.org/node/498#comments Primary Publication Thu, 09 Jan 2014 20:18:49 +0000 bakerpg 498 at http://www.bakerlab.org Automating human intuition for protein design http://www.bakerlab.org/Automating-human-intuition-for-protein-design <div id="biblio-node"><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.atitle=Automating+human+intuition+for+protein+design&amp;rft.title=Proteins&amp;rft.issn=1097-0134&amp;rft.date=2013&amp;rft.aulast=Niv%C3%B3n&amp;rft.aufirst=Lucas&amp;rft_id=info%3Adoi%2F10.1002%2Fprot.24463"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">Automating human intuition for protein design</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-type">Publication Type</td><td class="biblio-field-contents-type">Journal Article</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-year">Year of Publication</td><td class="biblio-field-contents-year">2013</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-authors">Authors</td><td class="biblio-field-contents-authors"><a href="/biblio/author/859">Nivón, L. G.</a>, <a href="/biblio/author/858">Bjelic S.</a>, <a href="/biblio/author/884">King C.</a>, & <a href="/biblio/author/8">Baker D.</a></td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-secondary-title">Journal</td><td class="biblio-field-contents-secondary-title">Proteins</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-date">Date Published</td><td class="biblio-field-contents-date">2013 Oct 30</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">1097-0134</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-keywords">Keywords</td><td class="biblio-field-contents-keywords"><a href="/biblio/keyword/515">algorithm</a>, <a href="/biblio/keyword/516">benchmark</a>, <a href="/biblio/keyword/517">enzyme</a>, <a href="/biblio/keyword/325">Primary Publication</a>, <a href="/biblio/keyword/518">protein design</a>, <a href="/biblio/keyword/109">Protein Engineering</a>, <a href="/biblio/keyword/519">small-molecule binding</a></td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-abst-e">Abstract</td><td class="biblio-field-contents-abst-e"><p>In the design of new enzymes and binding proteins, human intuition is often used to modify computationally designed amino acid sequences prior to experimental characterization. The manual sequence changes involve both reversions of amino acid mutations back to the identity present in the parent scaffold and the introduction of residues making additional interactions with the binding partner or backing up first shell interactions. Automation of this manual sequence refinement process would allow more systematic evaluation and considerably reduce the amount of human designer effort involved. Here we introduce a benchmark for evaluating the ability of automated methods to recapitulate the sequence changes made to computer-generated models by human designers, and use it to assess alternative computational methods. We find the best performance for a greedy one-position-at-a-time optimization protocol that utilizes metrics (such as shape complementarity) and local refinement methods too computationally expensive for global Monte Carlo (MC) sequence optimization. This protocol should be broadly useful for improving the stability and function of designed binding proteins. Proteins 2013. © 2013 Wiley Periodicals, Inc.</p> </td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-doi">DOI</td><td class="biblio-field-contents-doi"><a href="http://dx.doi.org/10.1002/prot.24463">10.1002/prot.24463</a></td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-custom1">Custom1</td><td class="biblio-field-contents-custom1"><p><a href="http://www.ncbi.nlm.nih.gov/pubmed/24265170?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/24265170?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/24265170?dopt=Abstract</a></p> </td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-alternate-title">Alternate Journal</td><td class="biblio-field-contents-alternate-title">Proteins</td> </tr> </tbody> </table> </div><table id="attachments" class="sticky-enabled"> <thead><tr><th>Attachment</th><th>Size</th> </tr></thead> <tbody> <tr class="odd"><td><a href="http://www.bakerlab.org/system/files/Niv%C3%B3n_prot24463_13M.pdf">Nivón_prot24463_13M.pdf</a></td><td>332.97 KB</td> </tr> </tbody> </table> Primary Publication Tue, 10 Dec 2013 22:56:41 +0000 bakerpg 495 at http://www.bakerlab.org Exploration of Alternate Catalytic Mechanisms and Optimization Strategies for Retroaldolase Design http://www.bakerlab.org/Exploration-of-Alternate-Catalytic-Mechanisms-and-Optimization-Strategies-for-Retroaldolase-Design <div id="biblio-node"><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.atitle=Exploration+of+Alternate+Catalytic+Mechanisms+and+Optimization+Strategies+for+Retroaldolase+Design&amp;rft.title=Journal+of+molecular+biology&amp;rft.issn=1089-8638&amp;rft.date=2013&amp;rft.volume=426&amp;rft.issue=1&amp;rft.spage=256&amp;rft.epage=271&amp;rft.aulast=Bjelic&amp;rft.aufirst=Sinisa&amp;rft_id=info%3Adoi%2F10.1016%2Fj.jmb.2013.10.012"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">Exploration of Alternate Catalytic Mechanisms and Optimization Strategies for Retroaldolase Design</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-type">Publication Type</td><td class="biblio-field-contents-type">Journal Article</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-year">Year of Publication</td><td class="biblio-field-contents-year">2013</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-authors">Authors</td><td class="biblio-field-contents-authors"><a href="/biblio/author/858">Bjelic, S.</a>, <a href="/biblio/author/731">Kipnis Y.</a>, <a href="/biblio/author/752">Wang L.</a>, <a href="/biblio/author/800">Pianowski Z.</a>, <a href="/biblio/author/805">Vorobiev S.</a>, <a href="/biblio/author/804">Su M.</a>, <a href="/biblio/author/803">Seetharaman J.</a>, <a href="/biblio/author/204">Xiao R.</a>, <a href="/biblio/author/883">Kornhaber G.</a>, <a href="/biblio/author/207">Hunt J. F.</a>, <a href="/biblio/author/809">Tong L.</a>, <a href="/biblio/author/136">Hilvert D.</a>, & <a href="/biblio/author/8">Baker D.</a></td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-secondary-title">Journal</td><td class="biblio-field-contents-secondary-title">Journal of molecular biology</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-volume">Volume</td><td class="biblio-field-contents-volume">426</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-section">Start Page</td><td class="biblio-field-contents-section">256</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-issue">Issue</td><td class="biblio-field-contents-issue">1</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-pages">Pagination</td><td class="biblio-field-contents-pages">256-271</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-date">Date Published</td><td class="biblio-field-contents-date">2013 Oct 23</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">1089-8638</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-keywords">Keywords</td><td class="biblio-field-contents-keywords"><a href="/biblio/keyword/520">etroaldolase; enzyme design; protein engineering; enzyme optimization</a>, <a href="/biblio/keyword/325">Primary Publication</a></td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-abst-e">Abstract</td><td class="biblio-field-contents-abst-e"><p>Designed retroaldolases have utilized a nucleophilic lysine to promote carbon-carbon bond cleavage of β-hydroxy-ketones via a covalent Schiff base intermediate. Previous computational designs have incorporated a water molecule to facilitate formation and breakdown of the carbinolamine intermediate to give the Schiff base and to function as a general acid/base. Here we investigate an alternative active-site design in which the catalytic water molecule was replaced by the side chain of a glutamic acid. Five out of seven designs expressed solubly and exhibited catalytic efficiencies similar to previously designed retroaldolases for the conversion of 4-hydroxy-4-(6-methoxy-2-naphthyl)-2-butanone to 6-methoxy-2-naphthaldehyde and acetone. After one round of site-directed saturation mutagenesis, improved variants of the two best designs, RA114 and RA117, exhibited among the highest kcat (>10(-3)s(-1)) and kcat/KM (11-25M(-1)s(-1)) values observed for retroaldolase designs prior to comprehensive directed evolution. In both cases, the >10(5)-fold rate accelerations that were achieved are within 1-3 orders of magnitude of the rate enhancements reported for the best catalysts for related reactions, including catalytic antibodies (kcat/kuncat=10(6) to 10(8)) and an extensively evolved computational design (kcat/kuncat>10(7)). The catalytic sites, revealed by X-ray structures of optimized versions of the two active designs, are in close agreement with the design models except for the catalytic lysine in RA114. We further improved the variants by computational remodeling of the loops and yeast display selection for reactivity of the catalytic lysine with a diketone probe, obtaining an additional order of magnitude enhancement in activity with both approaches.</p> </td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-doi">DOI</td><td class="biblio-field-contents-doi"><a href="http://dx.doi.org/10.1016/j.jmb.2013.10.012">10.1016/j.jmb.2013.10.012</a></td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-custom1">Custom1</td><td class="biblio-field-contents-custom1"><p><a href="http://www.ncbi.nlm.nih.gov/pubmed/24161950?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/24161950?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/24161950?dopt=Abstract</a></p> </td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-alternate-title">Alternate Journal</td><td class="biblio-field-contents-alternate-title">J. Mol. Biol.</td> </tr> </tbody> </table> </div><table id="attachments" class="sticky-enabled"> <thead><tr><th>Attachment</th><th>Size</th> </tr></thead> <tbody> <tr class="odd"><td><a href="http://www.bakerlab.org/system/files/Bjelic_JMB_13N.pdf">Bjelic_JMB_13N.pdf</a></td><td>1.7 MB</td> </tr> </tbody> </table> http://www.bakerlab.org/Exploration-of-Alternate-Catalytic-Mechanisms-and-Optimization-Strategies-for-Retroaldolase-Design#comments Primary Publication Tue, 10 Dec 2013 22:55:09 +0000 bakerpg 494 at http://www.bakerlab.org Increasing public involvement in structural biology http://www.bakerlab.org/Increasing-public-involvement-in-structural-biology <div id="biblio-node"><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.atitle=Increasing+public+involvement+in+structural+biology&amp;rft.title=Structure+%28London%2C+England+%3A+1993%29&amp;rft.issn=1878-4186&amp;rft.date=2013&amp;rft.volume=21&amp;rft.issue=9&amp;rft.aulast=Cooper&amp;rft.aufirst=Seth&amp;rft_id=info%3Adoi%2F10.1016%2Fj.str.2013.08.009"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">Increasing public involvement in structural biology</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-type">Publication Type</td><td class="biblio-field-contents-type">Journal Article</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-year">Year of Publication</td><td class="biblio-field-contents-year">2013</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-authors">Authors</td><td class="biblio-field-contents-authors"><a href="/biblio/author/1">Cooper, S.</a>, <a href="/biblio/author/2">Khatib F.</a>, & <a href="/biblio/author/8">Baker D.</a></td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-secondary-title">Journal</td><td class="biblio-field-contents-secondary-title">Structure (London, England : 1993)</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-volume">Volume</td><td class="biblio-field-contents-volume">21</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-issue">Issue</td><td class="biblio-field-contents-issue">9</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-pages">Pagination</td><td class="biblio-field-contents-pages">1482-4</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-date">Date Published</td><td class="biblio-field-contents-date">2013 Sep 3</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">1878-4186</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-keywords">Keywords</td><td class="biblio-field-contents-keywords"><a href="/biblio/keyword/325">Primary Publication</a></td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-abst-e">Abstract</td><td class="biblio-field-contents-abst-e"><p>Public participation in scientific research can be a powerful supplement to more-traditional approaches. We discuss aspects of the public participation project Foldit that may help others interested in starting their own projects.</p> </td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-doi">DOI</td><td class="biblio-field-contents-doi"><a href="http://dx.doi.org/10.1016/j.str.2013.08.009">10.1016/j.str.2013.08.009</a></td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-custom1">Custom1</td><td class="biblio-field-contents-custom1"><p><a href="http://www.ncbi.nlm.nih.gov/pubmed/24010706?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/24010706?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/24010706?dopt=Abstract</a></p> </td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-alternate-title">Alternate Journal</td><td class="biblio-field-contents-alternate-title">Structure</td> </tr> </tbody> </table> </div><table id="attachments" class="sticky-enabled"> <thead><tr><th>Attachment</th><th>Size</th> </tr></thead> <tbody> <tr class="odd"><td><a href="http://www.bakerlab.org/system/files/Cooper13L.pdf">Cooper13L.pdf</a></td><td>512 KB</td> </tr> </tbody> </table> Primary Publication Fri, 20 Sep 2013 20:45:19 +0000 bakerpg 486 at http://www.bakerlab.org Computational design of ligand-binding proteins with high affinity and selectivity http://www.bakerlab.org/Computational-design-of-ligand-binding-proteins-with-high-affinity-and-selectivity-pub <div id="biblio-node"><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.atitle=Computational+design+of+ligand-binding+proteins+with+high+affinity+and+selectivity&amp;rft.title=Nature&amp;rft.issn=1476-4687&amp;rft.date=2013&amp;rft.volume=501&amp;rft.issue=7466&amp;rft.aulast=Tinberg&amp;rft.aufirst=Christine&amp;rft_id=info%3Adoi%2F10.1038%2Fnature12443"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">Computational design of ligand-binding proteins with high affinity and selectivity</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-type">Publication Type</td><td class="biblio-field-contents-type">Journal Article</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-year">Year of Publication</td><td class="biblio-field-contents-year">2013</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-authors">Authors</td><td class="biblio-field-contents-authors"><a href="/biblio/author/876">Tinberg, C. E.</a>, <a href="/biblio/author/638" class="biblio-local-author">Khare S. D.</a>, <a href="/biblio/author/877">Dou J.</a>, <a href="/biblio/author/246">Doyle L.</a>, <a href="/biblio/author/878">Nelson J. W.</a>, <a href="/biblio/author/879">Schena A.</a>, <a href="/biblio/author/880">Jankowski W.</a>, <a href="/biblio/author/881">Kalodimos C. G.</a>, <a href="/biblio/author/882">Johnsson K.</a>, <a href="/biblio/author/107">Stoddard B. L.</a>, & <a href="/biblio/author/8">Baker D.</a></td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-secondary-title">Journal</td><td class="biblio-field-contents-secondary-title">Nature</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-volume">Volume</td><td class="biblio-field-contents-volume">501</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-issue">Issue</td><td class="biblio-field-contents-issue">7466</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-pages">Pagination</td><td class="biblio-field-contents-pages">212-6</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-date">Date Published</td><td class="biblio-field-contents-date">2013 Sep 12</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">1476-4687</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-keywords">Keywords</td><td class="biblio-field-contents-keywords"><a href="/biblio/keyword/325">Primary Publication</a></td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-abst-e">Abstract</td><td class="biblio-field-contents-abst-e"><p>The ability to design proteins with high affinity and selectivity for any given small molecule is a rigorous test of our understanding of the physiochemical principles that govern molecular recognition. Attempts to rationally design ligand-binding proteins have met with little success, however, and the computational design of protein-small-molecule interfaces remains an unsolved problem. Current approaches for designing ligand-binding proteins for medical and biotechnological uses rely on raising antibodies against a target antigen in immunized animals and/or performing laboratory-directed evolution of proteins with an existing low affinity for the desired ligand, neither of which allows complete control over the interactions involved in binding. Here we describe a general computational method for designing pre-organized and shape complementary small-molecule-binding sites, and use it to generate protein binders to the steroid digoxigenin (DIG). Of seventeen experimentally characterized designs, two bind DIG; the model of the higher affinity binder has the most energetically favourable and pre-organized interface in the design set. A comprehensive binding-fitness landscape of this design, generated by library selections and deep sequencing, was used to optimize its binding affinity to a picomolar level, and X-ray co-crystal structures of two variants show atomic-level agreement with the corresponding computational models. The optimized binder is selective for DIG over the related steroids digitoxigenin, progesterone and β-oestradiol, and this steroid binding preference can be reprogrammed by manipulation of explicitly designed hydrogen-bonding interactions. The computational design method presented here should enable the development of a new generation of biosensors, therapeutics and diagnostics.</p> </td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-doi">DOI</td><td class="biblio-field-contents-doi"><a href="http://dx.doi.org/10.1038/nature12443">10.1038/nature12443</a></td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-custom1">Custom1</td><td class="biblio-field-contents-custom1"><p><a href="http://www.ncbi.nlm.nih.gov/pubmed/24005320?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/24005320?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/24005320?dopt=Abstract</a></p> </td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-alternate-title">Alternate Journal</td><td class="biblio-field-contents-alternate-title">Nature</td> </tr> </tbody> </table> </div><table id="attachments" class="sticky-enabled"> <thead><tr><th>Attachment</th><th>Size</th> </tr></thead> <tbody> <tr class="odd"><td><a href="http://www.bakerlab.org/system/files/Tinberg13K.pdf">Tinberg13K.pdf</a></td><td>2.96 MB</td> </tr> </tbody> </table> Primary Publication Wed, 18 Sep 2013 20:49:04 +0000 bakerpg 480 at http://www.bakerlab.org Computational Design of an α-gliadin Peptidase http://www.bakerlab.org/Computational-design-of-an-%CE%B1-gliadin-peptidase-pub <div id="biblio-node"><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.atitle=Computational+Design+of+an+%CE%B1-gliadin+Peptidase&amp;rft.title=Journal+of+the+American+Chemical+Society&amp;rft.issn=1520-5126&amp;rft.date=2012&amp;rft.volume=134&amp;rft.issue=50&amp;rft.aulast=Gordon&amp;rft.aufirst=Sydney&amp;rft_id=info%3Adoi%2F10.1021%2Fja3094795"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">Computational Design of an α-gliadin Peptidase</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-type">Publication Type</td><td class="biblio-field-contents-type">Journal Article</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-year">Year of Publication</td><td class="biblio-field-contents-year">2012</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-authors">Authors</td><td class="biblio-field-contents-authors"><a href="/biblio/author/868">Gordon, S. R.</a>, <a href="/biblio/author/869">Stanley E. J.</a>, <a href="/biblio/author/870">Wolf S.</a>, <a href="/biblio/author/871">Toland A.</a>, <a href="/biblio/author/872">Wu S. J.</a>, <a href="/biblio/author/873">Hadidi D.</a>, <a href="/biblio/author/874">Mills J. H.</a>, <a href="/biblio/author/8">Baker D.</a>, <a href="/biblio/author/875">Pultz I. S.</a>, & <a href="/biblio/author/129">Siegel J. B.</a></td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-secondary-title">Journal</td><td class="biblio-field-contents-secondary-title">Journal of the American Chemical Society</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-volume">Volume</td><td class="biblio-field-contents-volume">134</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-issue">Issue</td><td class="biblio-field-contents-issue">50</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-pages">Pagination</td><td class="biblio-field-contents-pages">20513-20</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-date">Date Published</td><td class="biblio-field-contents-date">2012 Dec 19</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">1520-5126</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-keywords">Keywords</td><td class="biblio-field-contents-keywords"><a href="/biblio/keyword/12">Amino Acid Sequence</a>, <a href="/biblio/keyword/514">Gliadin</a>, <a href="/biblio/keyword/10">Models, Molecular</a>, <a href="/biblio/keyword/19">Molecular Sequence Data</a>, <a href="/biblio/keyword/463">Peptide Hydrolases</a>, <a href="/biblio/keyword/325">Primary Publication</a></td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-abst-e">Abstract</td><td class="biblio-field-contents-abst-e"><p>The ability to rationally modify enzymes to perform novel chemical transformations is essential for the rapid production of next-generation protein therapeutics. Here we describe the use of chemical principles to identify a naturally occurring acid-active peptidase, and the subsequent use of computational protein design tools to reengineer its specificity toward immunogenic elements found in gluten that are the proposed cause of celiac disease. The engineered enzyme exhibits a k(cat)/K(M) of 568 M(-1) s(-1), representing a 116-fold greater proteolytic activity for a model gluten tetrapeptide than the native template enzyme, as well as an over 800-fold switch in substrate specificity toward immunogenic portions of gluten peptides. The computationally engineered enzyme is resistant to proteolysis by digestive proteases and degrades over 95% of an immunogenic peptide implicated in celiac disease in under an hour. Thus, through identification of a natural enzyme with the pre-existing qualities relevant to an ultimate goal and redefinition of its substrate specificity using computational modeling, we were able to generate an enzyme with potential as a therapeutic for celiac disease.</p> </td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-url">URL</td><td class="biblio-field-contents-url"><a href="http://www.ncbi.nlm.nih.gov/pubmed/23153249">http://www.ncbi.nlm.nih.gov/pubmed/23153249</a></td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-doi">DOI</td><td class="biblio-field-contents-doi"><a href="http://dx.doi.org/10.1021/ja3094795">10.1021/ja3094795</a></td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-custom1">Custom1</td><td class="biblio-field-contents-custom1"><p><a href="http://www.ncbi.nlm.nih.gov/pubmed/23153249?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/23153249?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/23153249?dopt=Abstract</a></p> </td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-alternate-title">Alternate Journal</td><td class="biblio-field-contents-alternate-title">J. Am. Chem. Soc.</td> </tr> <tr class="odd"><td valign="top">Full Text</td><td><p><span style="font-family: arial, helvetica, clean, sans-serif; font-size: 13px; line-height: 17px; text-align: left;">The ability to rationally modify enzymes to perform novel chemical transformations is essential for the rapid production of next-generation protein therapeutics. Here we describe the use of chemical principles to identify a naturally occurring acid-active peptidase, and the subsequent use of computational protein design tools to reengineer its specificity toward immunogenic elements found in gluten that are the proposed cause of celiac disease. The engineered enzyme exhibits a k(cat)/K(M) of 568 M(-1) s(-1), representing a 116-fold greater proteolytic activity for a model gluten tetrapeptide than the native template enzyme, as well as an over 800-fold switch in substrate specificity toward immunogenic portions of gluten peptides. The computationally engineered enzyme is resistant to proteolysis by digestive proteases and degrades over 95% of an immunogenic peptide implicated in celiac disease in under an hour. Thus, through identification of a natural enzyme with the pre-existing qualities relevant to an ultimate goal and redefinition of its substrate specificity using computational modeling, we were able to generate an enzyme with potential as a therapeutic for celiac disease.</span></p> </td> </tr> </tbody> </table> </div><table id="attachments" class="sticky-enabled"> <thead><tr><th>Attachment</th><th>Size</th> </tr></thead> <tbody> <tr class="odd"><td><a href="http://www.bakerlab.org/system/files/Gordon12E.pdf">Gordon12E.pdf</a></td><td>2.05 MB</td> </tr> </tbody> </table> Primary Publication Wed, 18 Sep 2013 20:18:31 +0000 bakerpg 479 at http://www.bakerlab.org Principles for designing ideal protein structures. http://www.bakerlab.org/node/465 <div id="biblio-node"><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.atitle=Principles+for+designing+ideal+protein+structures.&amp;rft.title=Nature&amp;rft.issn=1476-4687&amp;rft.date=2012&amp;rft.volume=491&amp;rft.issue=7423&amp;rft.aulast=Koga&amp;rft.aufirst=Nobuyasu&amp;rft_id=info%3Adoi%2F10.1038%2Fnature11600"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">Principles for designing ideal protein structures.</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-type">Publication Type</td><td class="biblio-field-contents-type">Journal Article</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-year">Year of Publication</td><td class="biblio-field-contents-year">2012</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-authors">Authors</td><td class="biblio-field-contents-authors"><a href="/biblio/author/639">Koga, N.</a>, <a href="/biblio/author/830">Tatsumi-Koga R.</a>, <a href="/biblio/author/55">Liu G.</a>, <a href="/biblio/author/204">Xiao R.</a>, <a href="/biblio/author/206">Acton T. B.</a>, <a href="/biblio/author/61">Montelione G. T.</a>, & <a href="/biblio/author/8">Baker D.</a></td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-secondary-title">Journal</td><td class="biblio-field-contents-secondary-title">Nature</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-volume">Volume</td><td class="biblio-field-contents-volume">491</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-issue">Issue</td><td class="biblio-field-contents-issue">7423</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-pages">Pagination</td><td class="biblio-field-contents-pages">222-7</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-date">Date Published</td><td class="biblio-field-contents-date">2012 Nov 8</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">1476-4687</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-keywords">Keywords</td><td class="biblio-field-contents-keywords"><a href="/biblio/keyword/325">Primary Publication</a></td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-abst-e">Abstract</td><td class="biblio-field-contents-abst-e"><p>Unlike random heteropolymers, natural proteins fold into unique ordered structures. Understanding how these are encoded in amino-acid sequences is complicated by energetically unfavourable non-ideal features--for example kinked α-helices, bulged β-strands, strained loops and buried polar groups--that arise in proteins from evolutionary selection for biological function or from neutral drift. Here we describe an approach to designing ideal protein structures stabilized by completely consistent local and non-local interactions. The approach is based on a set of rules relating secondary structure patterns to protein tertiary motifs, which make possible the design of funnel-shaped protein folding energy landscapes leading into the target folded state. Guided by these rules, we designed sequences predicted to fold into ideal protein structures consisting of α-helices, β-strands and minimal loops. Designs for five different topologies were found to be monomeric and very stable and to adopt structures in solution nearly identical to the computational models. These results illuminate how the folding funnels of natural proteins arise and provide the foundation for engineering a new generation of functional proteins free from natural evolution.</p> </td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-doi">DOI</td><td class="biblio-field-contents-doi"><a href="http://dx.doi.org/10.1038/nature11600">10.1038/nature11600</a></td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-custom1">Custom1</td><td class="biblio-field-contents-custom1"><p><a href="http://www.ncbi.nlm.nih.gov/pubmed/23135467?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/23135467?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/23135467?dopt=Abstract</a></p> </td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-alternate-title">Alternate Journal</td><td class="biblio-field-contents-alternate-title">Nature</td> </tr> </tbody> </table> </div><table id="attachments" class="sticky-enabled"> <thead><tr><th>Attachment</th><th>Size</th> </tr></thead> <tbody> <tr class="odd"><td><a href="http://www.bakerlab.org/system/files/nature11600.pdf">nature11600.pdf</a></td><td>2.17 MB</td> </tr> </tbody> </table> http://www.bakerlab.org/node/465#comments Primary Publication Fri, 09 Nov 2012 18:12:29 +0000 bakerpg 465 at http://www.bakerlab.org phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta. http://www.bakerlab.org/node/462 <div id="biblio-node"><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.atitle=phenix.mr_rosetta%3A+molecular+replacement+and+model+rebuilding+with+Phenix+and+Rosetta.&amp;rft.title=Journal+of+structural+and+functional+genomics&amp;rft.issn=1570-0267&amp;rft.date=2012&amp;rft.volume=13&amp;rft.issue=2&amp;rft.spage=81&amp;rft.epage=90&amp;rft.aulast=Terwilliger&amp;rft.aufirst=Thomas&amp;rft_id=info%3Adoi%2F10.1007%2Fs10969-012-9129-3"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta.</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-type">Publication Type</td><td class="biblio-field-contents-type">Journal Article</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-year">Year of Publication</td><td class="biblio-field-contents-year">2012</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-authors">Authors</td><td class="biblio-field-contents-authors"><a href="/biblio/author/670">Terwilliger, T. C.</a>, <a href="/biblio/author/191">DiMaio F.</a>, <a href="/biblio/author/165">Read R. J.</a>, <a href="/biblio/author/8">Baker D.</a>, <a href="/biblio/author/825">Bunkóczi G.</a>, <a href="/biblio/author/826">Adams P. D.</a>, <a href="/biblio/author/827">Grosse-Kunstleve R. W.</a>, <a href="/biblio/author/828">Afonine P. V.</a>, & <a href="/biblio/author/829">Echols N.</a></td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-secondary-title">Journal</td><td class="biblio-field-contents-secondary-title">Journal of structural and functional genomics</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-volume">Volume</td><td class="biblio-field-contents-volume">13</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-issue">Issue</td><td class="biblio-field-contents-issue">2</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-pages">Pagination</td><td class="biblio-field-contents-pages">81-90</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-date">Date Published</td><td class="biblio-field-contents-date">2012 Jun</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">1570-0267</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-keywords">Keywords</td><td class="biblio-field-contents-keywords"><a href="/biblio/keyword/75">Algorithms</a>, <a href="/biblio/keyword/2">Computational Biology</a>, <a href="/biblio/keyword/3">Crystallography, X-Ray</a>, <a href="/biblio/keyword/148">Databases, Protein</a>, <a href="/biblio/keyword/129">Internet</a>, <a href="/biblio/keyword/160">Macromolecular Substances</a>, <a href="/biblio/keyword/38">Magnetic Resonance Spectroscopy</a>, <a href="/biblio/keyword/10">Models, Molecular</a>, <a href="/biblio/keyword/325">Primary Publication</a>, <a href="/biblio/keyword/29">Protein Conformation</a>, <a href="/biblio/keyword/30">Proteins</a>, <a href="/biblio/keyword/151">Proteomics</a>, <a href="/biblio/keyword/86">Software</a></td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-abst-e">Abstract</td><td class="biblio-field-contents-abst-e"><p>The combination of algorithms from the structure-modeling field with those of crystallographic structure determination can broaden the range of templates that are useful for structure determination by the method of molecular replacement. Automated tools in phenix.mr_rosetta simplify the application of these combined approaches by integrating Phenix crystallographic algorithms and Rosetta structure-modeling algorithms and by systematically generating and evaluating models with a combination of these methods. The phenix.mr_rosetta algorithms can be used to automatically determine challenging structures. The approaches used in phenix.mr_rosetta are described along with examples that show roles that structure-modeling can play in molecular replacement.</p> </td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-doi">DOI</td><td class="biblio-field-contents-doi"><a href="http://dx.doi.org/10.1007/s10969-012-9129-3">10.1007/s10969-012-9129-3</a></td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-custom1">Custom1</td><td class="biblio-field-contents-custom1"><p><a href="http://www.ncbi.nlm.nih.gov/pubmed/22418934?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/22418934?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/22418934?dopt=Abstract</a></p> </td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-alternate-title">Alternate Journal</td><td class="biblio-field-contents-alternate-title">J. Struct. Funct. Genomics</td> </tr> </tbody> </table> </div> http://www.bakerlab.org/node/462#comments Primary Publication Sun, 21 Oct 2012 05:58:59 +0000 bakerpg 462 at http://www.bakerlab.org Robust design and optimization of retroaldol enzymes. http://www.bakerlab.org/node/461 <div id="biblio-node"><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.atitle=Robust+design+and+optimization+of+retroaldol+enzymes.&amp;rft.title=Protein+science+%3A+a+publication+of+the+Protein+Society&amp;rft.issn=1469-896X&amp;rft.date=2012&amp;rft.volume=21&amp;rft.issue=5&amp;rft.aulast=Althoff&amp;rft.aufirst=Eric&amp;rft_id=info%3Adoi%2F10.1002%2Fpro.2059"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">Robust design and optimization of retroaldol enzymes.</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-type">Publication Type</td><td class="biblio-field-contents-type">Journal Article</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-year">Year of Publication</td><td class="biblio-field-contents-year">2012</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-authors">Authors</td><td class="biblio-field-contents-authors"><a href="/biblio/author/244">Althoff, E. A.</a>, <a href="/biblio/author/752">Wang L.</a>, <a href="/biblio/author/145">Jiang L.</a>, <a href="/biblio/author/756">Giger L.</a>, <a href="/biblio/author/755">Lassila J. K.</a>, <a href="/biblio/author/821">Wang Z.</a>, <a href="/biblio/author/822">Smith M.</a>, <a href="/biblio/author/823">Hari S.</a>, <a href="/biblio/author/824">Kast P.</a>, <a href="/biblio/author/233">Herschlag D.</a>, <a href="/biblio/author/136">Hilvert D.</a>, & <a href="/biblio/author/8">Baker D.</a></td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-secondary-title">Journal</td><td class="biblio-field-contents-secondary-title">Protein science : a publication of the Protein Society</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-volume">Volume</td><td class="biblio-field-contents-volume">21</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-issue">Issue</td><td class="biblio-field-contents-issue">5</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-pages">Pagination</td><td class="biblio-field-contents-pages">717-26</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-date">Date Published</td><td class="biblio-field-contents-date">2012 May</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">1469-896X</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-keywords">Keywords</td><td class="biblio-field-contents-keywords"><a href="/biblio/keyword/234">Aldehyde-Lyases</a>, <a href="/biblio/keyword/174">Catalytic Domain</a>, <a href="/biblio/keyword/315">Directed Molecular Evolution</a>, <a href="/biblio/keyword/10">Models, Molecular</a>, <a href="/biblio/keyword/82">Mutagenesis, Site-Directed</a>, <a href="/biblio/keyword/325">Primary Publication</a>, <a href="/biblio/keyword/109">Protein Engineering</a>, <a href="/biblio/keyword/24">Recombinant Proteins</a></td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-abst-e">Abstract</td><td class="biblio-field-contents-abst-e"><p>Enzyme catalysts of a retroaldol reaction have been generated by computational design using a motif that combines a lysine in a nonpolar environment with water-mediated stabilization of the carbinolamine hydroxyl and β-hydroxyl groups. Here, we show that the design process is robust and repeatable, with 33 new active designs constructed on 13 different protein scaffold backbones. The initial activities are not high but are increased through site-directed mutagenesis and laboratory evolution. Mutational data highlight areas for improvement in design. Different designed catalysts give different borohydride-reduced reaction intermediates, suggesting a distribution of properties of the designed enzymes that may be further explored and exploited.</p> </td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-doi">DOI</td><td class="biblio-field-contents-doi"><a href="http://dx.doi.org/10.1002/pro.2059">10.1002/pro.2059</a></td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-custom1">Custom1</td><td class="biblio-field-contents-custom1"><p><a href="http://www.ncbi.nlm.nih.gov/pubmed/22407837?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/22407837?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/22407837?dopt=Abstract</a></p> </td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-alternate-title">Alternate Journal</td><td class="biblio-field-contents-alternate-title">Protein Sci.</td> </tr> </tbody> </table> </div> http://www.bakerlab.org/node/461#comments Primary Publication Sun, 21 Oct 2012 05:58:03 +0000 bakerpg 461 at http://www.bakerlab.org Resolution-adapted recombination of structural features significantly improves sampling in restraint-guided structure calculation. http://www.bakerlab.org/node/460 <div id="biblio-node"><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.atitle=Resolution-adapted+recombination+of+structural+features+significantly+improves+sampling+in+restraint-guided+structure+calculation.&amp;rft.title=Proteins&amp;rft.issn=1097-0134&amp;rft.date=2012&amp;rft.volume=80&amp;rft.issue=3&amp;rft.aulast=Lange&amp;rft.aufirst=Oliver"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">Resolution-adapted recombination of structural features significantly improves sampling in restraint-guided structure calculation.</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-type">Publication Type</td><td class="biblio-field-contents-type">Journal Article</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-year">Year of Publication</td><td class="biblio-field-contents-year">2012</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-authors">Authors</td><td class="biblio-field-contents-authors"><a href="/biblio/author/50" class="biblio-local-author">Lange, O. F.</a>, & <a href="/biblio/author/8">Baker D.</a></td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-secondary-title">Journal</td><td class="biblio-field-contents-secondary-title">Proteins</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-volume">Volume</td><td class="biblio-field-contents-volume">80</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-issue">Issue</td><td class="biblio-field-contents-issue">3</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-pages">Pagination</td><td class="biblio-field-contents-pages">884-95</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-date">Date Published</td><td class="biblio-field-contents-date">2012 Mar</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">1097-0134</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-keywords">Keywords</td><td class="biblio-field-contents-keywords"><a href="/biblio/keyword/10">Models, Molecular</a>, <a href="/biblio/keyword/73">Monte Carlo Method</a>, <a href="/biblio/keyword/97">Nuclear Magnetic Resonance, Biomolecular</a>, <a href="/biblio/keyword/325">Primary Publication</a>, <a href="/biblio/keyword/29">Protein Conformation</a>, <a href="/biblio/keyword/23">Protein Folding</a>, <a href="/biblio/keyword/30">Proteins</a>, <a href="/biblio/keyword/86">Software</a></td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-abst-e">Abstract</td><td class="biblio-field-contents-abst-e"><p>Recent work has shown that NMR structures can be determined by integrating sparse NMR data with structure prediction methods such as Rosetta. The experimental data serve to guide the search for the lowest energy state towards the deep minimum at the native state which is frequently missed in Rosetta de novo structure calculations. However, as the protein size increases, sampling again becomes limiting; for example, the standard Rosetta protocol involving Monte Carlo fragment insertion starting from an extended chain fails to converge for proteins over 150 amino acids even with guidance from chemical shifts (CS-Rosetta) and other NMR data. The primary limitation of this protocol--that every folding trajectory is completely independent of every other--was recently overcome with the development of a new approach involving resolution-adapted structural recombination (RASREC). Here we describe the RASREC approach in detail and compare it to standard CS-Rosetta. We show that the improved sampling of RASREC is essential in obtaining accurate structures over a benchmark set of 11 proteins in the 15-25 kDa size range using chemical shifts, backbone RDCs and HN-HN NOE data; in a number of cases the improved sampling methodology makes a larger contribution than incorporation of additional experimental data. Experimental data are invaluable for guiding sampling to the vicinity of the global energy minimum, but for larger proteins, the standard Rosetta fold-from-extended-chain protocol does not converge on the native minimum even with experimental data and the more powerful RASREC approach is necessary to converge to accurate solutions.</p> </td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-custom1">Custom1</td><td class="biblio-field-contents-custom1"><p><a href="http://www.ncbi.nlm.nih.gov/pubmed/22423358?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/22423358?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/22423358?dopt=Abstract</a></p> </td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-alternate-title">Alternate Journal</td><td class="biblio-field-contents-alternate-title">Proteins</td> </tr> </tbody> </table> </div> http://www.bakerlab.org/node/460#comments Primary Publication Sun, 21 Oct 2012 05:57:04 +0000 bakerpg 460 at http://www.bakerlab.org Improved modeling of side-chain--base interactions and plasticity in protein--DNA interface design. http://www.bakerlab.org/node/459 <div id="biblio-node"><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.atitle=Improved+modeling+of+side-chain--base+interactions+and+plasticity+in+protein--DNA+interface+design.&amp;rft.title=Journal+of+molecular+biology&amp;rft.issn=1089-8638&amp;rft.date=2012&amp;rft.volume=419&amp;rft.issue=3-4&amp;rft.aulast=Thyme&amp;rft.aufirst=Summer"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">Improved modeling of side-chain--base interactions and plasticity in protein--DNA interface design.</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-type">Publication Type</td><td class="biblio-field-contents-type">Journal Article</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-year">Year of Publication</td><td class="biblio-field-contents-year">2012</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-authors">Authors</td><td class="biblio-field-contents-authors"><a href="/biblio/author/213">Thyme, S. B.</a>, <a href="/biblio/author/8">Baker D.</a>, & <a href="/biblio/author/123">Bradley P.</a></td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-secondary-title">Journal</td><td class="biblio-field-contents-secondary-title">Journal of molecular biology</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-volume">Volume</td><td class="biblio-field-contents-volume">419</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-issue">Issue</td><td class="biblio-field-contents-issue">3-4</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-pages">Pagination</td><td class="biblio-field-contents-pages">255-74</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-date">Date Published</td><td class="biblio-field-contents-date">2012 Jun 8</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">1089-8638</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-keywords">Keywords</td><td class="biblio-field-contents-keywords"><a href="/biblio/keyword/75">Algorithms</a>, <a href="/biblio/keyword/1">Amino Acids</a>, <a href="/biblio/keyword/60">Computer Simulation</a>, <a href="/biblio/keyword/4">DNA</a>, <a href="/biblio/keyword/6">DNA-Binding Proteins</a>, <a href="/biblio/keyword/10">Models, Molecular</a>, <a href="/biblio/keyword/183">Nucleic Acid Conformation</a>, <a href="/biblio/keyword/325">Primary Publication</a>, <a href="/biblio/keyword/122">Protein Binding</a>, <a href="/biblio/keyword/29">Protein Conformation</a>, <a href="/biblio/keyword/42">Protein Structure, Tertiary</a>, <a href="/biblio/keyword/30">Proteins</a></td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-abst-e">Abstract</td><td class="biblio-field-contents-abst-e"><p>Combinatorial sequence optimization for protein design requires libraries of discrete side-chain conformations. The discreteness of these libraries is problematic, particularly for long, polar side chains, since favorable interactions can be missed. Previously, an approach to loop remodeling where protein backbone movement is directed by side-chain rotamers predicted to form interactions previously observed in native complexes (termed "motifs") was described. Here, we show how such motif libraries can be incorporated into combinatorial sequence optimization protocols and improve native complex recapitulation. Guided by the motif rotamer searches, we made improvements to the underlying energy function, increasing recapitulation of native interactions. To further test the methods, we carried out a comprehensive experimental scan of amino acid preferences in the I-AniI protein-DNA interface and found that many positions tolerated multiple amino acids. This sequence plasticity is not observed in the computational results because of the fixed-backbone approximation of the model. We improved modeling of this diversity by introducing DNA flexibility and reducing the convergence of the simulated annealing algorithm that drives the design process. In addition to serving as a benchmark, this extensive experimental data set provides insight into the types of interactions essential to maintain the function of this potential gene therapy reagent.</p> </td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-custom1">Custom1</td><td class="biblio-field-contents-custom1"><p><a href="http://www.ncbi.nlm.nih.gov/pubmed/22426128?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/22426128?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/22426128?dopt=Abstract</a></p> </td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-alternate-title">Alternate Journal</td><td class="biblio-field-contents-alternate-title">J. Mol. Biol.</td> </tr> </tbody> </table> </div> http://www.bakerlab.org/node/459#comments Primary Publication Sun, 21 Oct 2012 05:54:38 +0000 bakerpg 459 at http://www.bakerlab.org Role of the biomolecular energy gap in protein design, structure, and evolution. http://www.bakerlab.org/node/458 <div id="biblio-node"><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.atitle=Role+of+the+biomolecular+energy+gap+in+protein+design%2C+structure%2C+and+evolution.&amp;rft.title=Cell&amp;rft.issn=1097-4172&amp;rft.date=2012&amp;rft.volume=149&amp;rft.issue=2&amp;rft.aulast=Fleishman&amp;rft.aufirst=Sarel"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">Role of the biomolecular energy gap in protein design, structure, and evolution.</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-type">Publication Type</td><td class="biblio-field-contents-type">Journal Article</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-year">Year of Publication</td><td class="biblio-field-contents-year">2012</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-authors">Authors</td><td class="biblio-field-contents-authors"><a href="/biblio/author/159">Fleishman, S. J.</a>, & <a href="/biblio/author/8">Baker D.</a></td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-secondary-title">Journal</td><td class="biblio-field-contents-secondary-title">Cell</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-volume">Volume</td><td class="biblio-field-contents-volume">149</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-issue">Issue</td><td class="biblio-field-contents-issue">2</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-pages">Pagination</td><td class="biblio-field-contents-pages">262-73</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-date">Date Published</td><td class="biblio-field-contents-date">2012 Apr 13</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">1097-4172</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-keywords">Keywords</td><td class="biblio-field-contents-keywords"><a href="/biblio/keyword/64">Animals</a>, <a href="/biblio/keyword/498">Energy Metabolism</a>, <a href="/biblio/keyword/111">Evolution, Molecular</a>, <a href="/biblio/keyword/128">Humans</a>, <a href="/biblio/keyword/10">Models, Molecular</a>, <a href="/biblio/keyword/499">Nucleic Acids</a>, <a href="/biblio/keyword/325">Primary Publication</a>, <a href="/biblio/keyword/500">Protein Interaction Maps</a>, <a href="/biblio/keyword/30">Proteins</a></td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-abst-e">Abstract</td><td class="biblio-field-contents-abst-e"><p>The folding of natural biopolymers into unique three-dimensional structures that determine their function is remarkable considering the vast number of alternative states and requires a large gap in the energy of the functional state compared to the many alternatives. This Perspective explores the implications of this energy gap for computing the structures of naturally occurring biopolymers, designing proteins with new structures and functions, and optimally integrating experiment and computation in these endeavors. Possible parallels between the generation of functional molecules in computational design and natural evolution are highlighted.</p> </td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-custom1">Custom1</td><td class="biblio-field-contents-custom1"><p><a href="http://www.ncbi.nlm.nih.gov/pubmed/22500796?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/22500796?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/22500796?dopt=Abstract</a></p> </td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-alternate-title">Alternate Journal</td><td class="biblio-field-contents-alternate-title">Cell</td> </tr> </tbody> </table> </div> http://www.bakerlab.org/node/458#comments Primary Publication Sun, 21 Oct 2012 05:53:49 +0000 bakerpg 458 at http://www.bakerlab.org Accurate protein structure modeling using sparse NMR data and homologous structure information. http://www.bakerlab.org/node/457 <div id="biblio-node"><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.atitle=Accurate+protein+structure+modeling+using+sparse+NMR+data+and+homologous+structure+information.&amp;rft.title=Proceedings+of+the+National+Academy+of+Sciences+of+the+United+States+of+America&amp;rft.issn=1091-6490&amp;rft.date=2012&amp;rft.volume=109&amp;rft.issue=25&amp;rft.aulast=Thompson&amp;rft.aufirst=James"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">Accurate protein structure modeling using sparse NMR data and homologous structure information.</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-type">Publication Type</td><td class="biblio-field-contents-type">Journal Article</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-year">Year of Publication</td><td class="biblio-field-contents-year">2012</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-authors">Authors</td><td class="biblio-field-contents-authors"><a href="/biblio/author/819">Thompson, J. M.</a>, <a href="/biblio/author/635">Sgourakis N. G.</a>, <a href="/biblio/author/55">Liu G.</a>, <a href="/biblio/author/51">Rossi P.</a>, <a href="/biblio/author/438">Tang Y.</a>, <a href="/biblio/author/820">Mills J. L.</a>, <a href="/biblio/author/58">Szyperski T.</a>, <a href="/biblio/author/61">Montelione G. T.</a>, & <a href="/biblio/author/8">Baker D.</a></td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-secondary-title">Journal</td><td class="biblio-field-contents-secondary-title">Proceedings of the National Academy of Sciences of the United States of America</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-volume">Volume</td><td class="biblio-field-contents-volume">109</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-issue">Issue</td><td class="biblio-field-contents-issue">25</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-pages">Pagination</td><td class="biblio-field-contents-pages">9875-80</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-date">Date Published</td><td class="biblio-field-contents-date">2012 Jun 19</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">1091-6490</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-keywords">Keywords</td><td class="biblio-field-contents-keywords"><a href="/biblio/keyword/3">Crystallography, X-Ray</a>, <a href="/biblio/keyword/10">Models, Molecular</a>, <a href="/biblio/keyword/97">Nuclear Magnetic Resonance, Biomolecular</a>, <a href="/biblio/keyword/325">Primary Publication</a>, <a href="/biblio/keyword/29">Protein Conformation</a>, <a href="/biblio/keyword/30">Proteins</a></td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-abst-e">Abstract</td><td class="biblio-field-contents-abst-e"><p>While information from homologous structures plays a central role in X-ray structure determination by molecular replacement, such information is rarely used in NMR structure determination because it can be incorrect, both locally and globally, when evolutionary relationships are inferred incorrectly or there has been considerable evolutionary structural divergence. Here we describe a method that allows robust modeling of protein structures of up to 225 residues by combining (1)H(N), (13)C, and (15)N backbone and (13)Cβ chemical shift data, distance restraints derived from homologous structures, and a physically realistic all-atom energy function. Accurate models are distinguished from inaccurate models generated using incorrect sequence alignments by requiring that (i) the all-atom energies of models generated using the restraints are lower than models generated in unrestrained calculations and (ii) the low-energy structures converge to within 2.0 Å backbone rmsd over 75% of the protein. Benchmark calculations on known structures and blind targets show that the method can accurately model protein structures, even with very remote homology information, to a backbone rmsd of 1.2-1.9 Å relative to the conventional determined NMR ensembles and of 0.9-1.6 Å relative to X-ray structures for well-defined regions of the protein structures. This approach facilitates the accurate modeling of protein structures using backbone chemical shift data without need for side-chain resonance assignments and extensive analysis of NOESY cross-peak assignments.</p> </td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-custom1">Custom1</td><td class="biblio-field-contents-custom1"><p><a href="http://www.ncbi.nlm.nih.gov/pubmed/22665781?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/22665781?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/22665781?dopt=Abstract</a></p> </td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-alternate-title">Alternate Journal</td><td class="biblio-field-contents-alternate-title">Proc. Natl. Acad. Sci. U.S.A.</td> </tr> </tbody> </table> </div> http://www.bakerlab.org/node/457#comments Primary Publication Sun, 21 Oct 2012 05:53:08 +0000 bakerpg 457 at http://www.bakerlab.org Bridging the gaps in design methodologies by evolutionary optimization of the stability and proficiency of designed Kemp eliminase KE59. http://www.bakerlab.org/node/456 <div id="biblio-node"><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.atitle=Bridging+the+gaps+in+design+methodologies+by+evolutionary+optimization+of+the+stability+and+proficiency+of+designed+Kemp+eliminase+KE59.&amp;rft.title=Proceedings+of+the+National+Academy+of+Sciences+of+the+United+States+of+America&amp;rft.issn=1091-6490&amp;rft.date=2012&amp;rft.volume=109&amp;rft.issue=26&amp;rft.aulast=Khersonsky&amp;rft.aufirst=Olga"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">Bridging the gaps in design methodologies by evolutionary optimization of the stability and proficiency of designed Kemp eliminase KE59.</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-type">Publication Type</td><td class="biblio-field-contents-type">Journal Article</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-year">Year of Publication</td><td class="biblio-field-contents-year">2012</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-authors">Authors</td><td class="biblio-field-contents-authors"><a href="/biblio/author/365">Khersonsky, O.</a>, <a href="/biblio/author/132">Kiss G.</a>, <a href="/biblio/author/221">Röthlisberger D.</a>, <a href="/biblio/author/368">Dym O.</a>, <a href="/biblio/author/369">Albeck S.</a>, <a href="/biblio/author/138">Houk K. N.</a>, <a href="/biblio/author/8">Baker D.</a>, & <a href="/biblio/author/370">Tawfik D. S.</a></td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-secondary-title">Journal</td><td class="biblio-field-contents-secondary-title">Proceedings of the National Academy of Sciences of the United States of America</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-volume">Volume</td><td class="biblio-field-contents-volume">109</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-issue">Issue</td><td class="biblio-field-contents-issue">26</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-pages">Pagination</td><td class="biblio-field-contents-pages">10358-63</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-date">Date Published</td><td class="biblio-field-contents-date">2012 Jun 26</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">1091-6490</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-keywords">Keywords</td><td class="biblio-field-contents-keywords"><a href="/biblio/keyword/174">Catalytic Domain</a>, <a href="/biblio/keyword/315">Directed Molecular Evolution</a>, <a href="/biblio/keyword/77">Enzyme Stability</a>, <a href="/biblio/keyword/154">Enzymes</a>, <a href="/biblio/keyword/325">Primary Publication</a></td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-abst-e">Abstract</td><td class="biblio-field-contents-abst-e"><p>Computational design is a test of our understanding of enzyme catalysis and a means of engineering novel, tailor-made enzymes. While the de novo computational design of catalytically efficient enzymes remains a challenge, designed enzymes may comprise unique starting points for further optimization by directed evolution. Directed evolution of two computationally designed Kemp eliminases, KE07 and KE70, led to low to moderately efficient enzymes (k(cat)/K(m) values of ≤ 5 10(4) M(-1)s(-1)). Here we describe the optimization of a third design, KE59. Although KE59 was the most catalytically efficient Kemp eliminase from this design series (by k(cat)/K(m), and by catalyzing the elimination of nonactivated benzisoxazoles), its impaired stability prevented its evolutionary optimization. To boost KE59's evolvability, stabilizing consensus mutations were included in the libraries throughout the directed evolution process. The libraries were also screened with less activated substrates. Sixteen rounds of mutation and selection led to > 2,000-fold increase in catalytic efficiency, mainly via higher k(cat) values. The best KE59 variants exhibited k(cat)/K(m) values up to 0.6 10(6) M(-1)s(-1), and k(cat)/k(uncat) values of ≤ 10(7) almost regardless of substrate reactivity. Biochemical, structural, and molecular dynamics (MD) simulation studies provided insights regarding the optimization of KE59. Overall, the directed evolution of three different designed Kemp eliminases, KE07, KE70, and KE59, demonstrates that computational designs are highly evolvable and can be optimized to high catalytic efficiencies.</p> </td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-custom1">Custom1</td><td class="biblio-field-contents-custom1"><p><a href="http://www.ncbi.nlm.nih.gov/pubmed/22685214?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/22685214?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/22685214?dopt=Abstract</a></p> </td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-alternate-title">Alternate Journal</td><td class="biblio-field-contents-alternate-title">Proc. Natl. Acad. Sci. U.S.A.</td> </tr> </tbody> </table> </div> http://www.bakerlab.org/node/456#comments Primary Publication Sun, 21 Oct 2012 05:51:58 +0000 bakerpg 456 at http://www.bakerlab.org Engineering domain fusion chimeras from I-OnuI family LAGLIDADG homing endonucleases. http://www.bakerlab.org/node/455 <div id="biblio-node"><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.atitle=Engineering+domain+fusion+chimeras+from+I-OnuI+family+LAGLIDADG+homing+endonucleases.&amp;rft.title=Nucleic+acids+research&amp;rft.issn=1362-4962&amp;rft.date=2012&amp;rft.volume=40&amp;rft.issue=16&amp;rft.spage=7985&amp;rft.epage=8000&amp;rft.aulast=Baxter&amp;rft.aufirst=Sarah"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">Engineering domain fusion chimeras from I-OnuI family LAGLIDADG homing endonucleases.</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-type">Publication Type</td><td class="biblio-field-contents-type">Journal Article</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-year">Year of Publication</td><td class="biblio-field-contents-year">2012</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-authors">Authors</td><td class="biblio-field-contents-authors"><a href="/biblio/author/813">Baxter, S.</a>, <a href="/biblio/author/133">Lambert A. R.</a>, <a href="/biblio/author/814">Kuhar R.</a>, <a href="/biblio/author/214">Jarjour J.</a>, <a href="/biblio/author/815">Kulshina N.</a>, <a href="/biblio/author/816">Parmeggiani F.</a>, <a href="/biblio/author/817">Danaher P.</a>, <a href="/biblio/author/818">Gano J.</a>, <a href="/biblio/author/8">Baker D.</a>, <a href="/biblio/author/107">Stoddard B. L.</a>, & <a href="/biblio/author/216">Scharenberg A. M.</a></td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-secondary-title">Journal</td><td class="biblio-field-contents-secondary-title">Nucleic acids research</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-volume">Volume</td><td class="biblio-field-contents-volume">40</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-issue">Issue</td><td class="biblio-field-contents-issue">16</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-pages">Pagination</td><td class="biblio-field-contents-pages">7985-8000</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-date">Date Published</td><td class="biblio-field-contents-date">2012 Sep 1</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">1362-4962</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-keywords">Keywords</td><td class="biblio-field-contents-keywords"><a href="/biblio/keyword/325">Primary Publication</a></td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-abst-e">Abstract</td><td class="biblio-field-contents-abst-e"><p>Although engineered LAGLIDADG homing endonucleases (LHEs) are finding increasing applications in biotechnology, their generation remains a challenging, industrial-scale process. As new single-chain LAGLIDADG nuclease scaffolds are identified, however, an alternative paradigm is emerging: identification of an LHE scaffold whose native cleavage site is a close match to a desired target sequence, followed by small-scale engineering to modestly refine recognition specificity. The application of this paradigm could be accelerated if methods were available for fusing N- and C-terminal domains from newly identified LHEs into chimeric enzymes with hybrid cleavage sites. Here we have analyzed the structural requirements for fusion of domains extracted from six single-chain I-OnuI family LHEs, spanning 40-70% amino acid identity. Our analyses demonstrate that both the LAGLIDADG helical interface residues and the linker peptide composition have important effects on the stability and activity of chimeric enzymes. Using a simple domain fusion method in which linker peptide residues predicted to contact their respective domains are retained, and in which limited variation is introduced into the LAGLIDADG helix and nearby interface residues, catalytically active enzymes were recoverable for ∼70% of domain chimeras. This method will be useful for creating large numbers of chimeric LHEs for genome engineering applications.</p> </td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-custom1">Custom1</td><td class="biblio-field-contents-custom1"><p><a href="http://www.ncbi.nlm.nih.gov/pubmed/22684507?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/22684507?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/22684507?dopt=Abstract</a></p> </td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-alternate-title">Alternate Journal</td><td class="biblio-field-contents-alternate-title">Nucleic Acids Res.</td> </tr> </tbody> </table> </div> http://www.bakerlab.org/node/455#comments Primary Publication Sun, 21 Oct 2012 05:51:13 +0000 bakerpg 455 at http://www.bakerlab.org Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples. http://www.bakerlab.org/node/454 <div id="biblio-node"><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.atitle=Determination+of+solution+structures+of+proteins+up+to+40+kDa+using+CS-Rosetta+with+sparse+NMR+data+from+deuterated+samples.&amp;rft.title=Proceedings+of+the+National+Academy+of+Sciences+of+the+United+States+of+America&amp;rft.issn=1091-6490&amp;rft.date=2012&amp;rft.volume=109&amp;rft.issue=27&amp;rft.aulast=Lange&amp;rft.aufirst=Oliver"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples.</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-type">Publication Type</td><td class="biblio-field-contents-type">Journal Article</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-year">Year of Publication</td><td class="biblio-field-contents-year">2012</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-authors">Authors</td><td class="biblio-field-contents-authors"><a href="/biblio/author/50" class="biblio-local-author">Lange, O. F.</a>, <a href="/biblio/author/51">Rossi P.</a>, <a href="/biblio/author/635">Sgourakis N. G.</a>, <a href="/biblio/author/394">Song Y.</a>, <a href="/biblio/author/811">Lee H. - W.</a>, <a href="/biblio/author/374">Aramini J. M.</a>, <a href="/biblio/author/812">Ertekin A.</a>, <a href="/biblio/author/204">Xiao R.</a>, <a href="/biblio/author/206">Acton T. B.</a>, <a href="/biblio/author/61">Montelione G. T.</a>, & <a href="/biblio/author/8">Baker D.</a></td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-secondary-title">Journal</td><td class="biblio-field-contents-secondary-title">Proceedings of the National Academy of Sciences of the United States of America</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-volume">Volume</td><td class="biblio-field-contents-volume">109</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-issue">Issue</td><td class="biblio-field-contents-issue">27</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-pages">Pagination</td><td class="biblio-field-contents-pages">10873-8</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-date">Date Published</td><td class="biblio-field-contents-date">2012 Jul 3</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">1091-6490</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-keywords">Keywords</td><td class="biblio-field-contents-keywords"><a href="/biblio/keyword/75">Algorithms</a>, <a href="/biblio/keyword/64">Animals</a>, <a href="/biblio/keyword/3">Crystallography, X-Ray</a>, <a href="/biblio/keyword/495">Deuterium Exchange Measurement</a>, <a href="/biblio/keyword/100">Genomics</a>, <a href="/biblio/keyword/128">Humans</a>, <a href="/biblio/keyword/496">Maltose-Binding Proteins</a>, <a href="/biblio/keyword/238">Molecular Weight</a>, <a href="/biblio/keyword/97">Nuclear Magnetic Resonance, Biomolecular</a>, <a href="/biblio/keyword/325">Primary Publication</a>, <a href="/biblio/keyword/42">Protein Structure, Tertiary</a>, <a href="/biblio/keyword/169">Reproducibility of Results</a>, <a href="/biblio/keyword/497">Sensory Rhodopsins</a>, <a href="/biblio/keyword/256">Solutions</a></td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-abst-e">Abstract</td><td class="biblio-field-contents-abst-e"><p>We have developed an approach for determining NMR structures of proteins over 20 kDa that utilizes sparse distance restraints obtained using transverse relaxation optimized spectroscopy experiments on perdeuterated samples to guide RASREC Rosetta NMR structure calculations. The method was tested on 11 proteins ranging from 15 to 40 kDa, seven of which were previously unsolved. The RASREC Rosetta models were in good agreement with models obtained using traditional NMR methods with larger restraint sets. In five cases X-ray structures were determined or were available, allowing comparison of the accuracy of the Rosetta models and conventional NMR models. In all five cases, the Rosetta models were more similar to the X-ray structures over both the backbone and side-chain conformations than the "best effort" structures determined by conventional methods. The incorporation of sparse distance restraints into RASREC Rosetta allows routine determination of high-quality solution NMR structures for proteins up to 40 kDa, and should be broadly useful in structural biology.</p> </td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-custom1">Custom1</td><td class="biblio-field-contents-custom1"><p><a href="http://www.ncbi.nlm.nih.gov/pubmed/22733734?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/22733734?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/22733734?dopt=Abstract</a></p> </td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-alternate-title">Alternate Journal</td><td class="biblio-field-contents-alternate-title">Proc. Natl. Acad. Sci. U.S.A.</td> </tr> </tbody> </table> </div> http://www.bakerlab.org/node/454#comments Primary Publication Sun, 21 Oct 2012 05:50:19 +0000 bakerpg 454 at http://www.bakerlab.org Efficient sampling of protein conformational space using fast loop building and batch minimization on highly parallel computers. http://www.bakerlab.org/node/453 <div id="biblio-node"><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.atitle=Efficient+sampling+of+protein+conformational+space+using+fast+loop+building+and+batch+minimization+on+highly+parallel+computers.&amp;rft.title=Journal+of+computational+chemistry&amp;rft.issn=1096-987X&amp;rft.date=2012&amp;rft.volume=33&amp;rft.issue=31&amp;rft.aulast=Tyka&amp;rft.aufirst=Michael&amp;rft_id=info%3Adoi%2F10.1002%2Fjcc.23069"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">Efficient sampling of protein conformational space using fast loop building and batch minimization on highly parallel computers.</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-type">Publication Type</td><td class="biblio-field-contents-type">Journal Article</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-year">Year of Publication</td><td class="biblio-field-contents-year">2012</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-authors">Authors</td><td class="biblio-field-contents-authors"><a href="/biblio/author/172">Tyka, M. D.</a>, <a href="/biblio/author/810">Jung K.</a>, & <a href="/biblio/author/8">Baker D.</a></td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-secondary-title">Journal</td><td class="biblio-field-contents-secondary-title">Journal of computational chemistry</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-volume">Volume</td><td class="biblio-field-contents-volume">33</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-issue">Issue</td><td class="biblio-field-contents-issue">31</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-pages">Pagination</td><td class="biblio-field-contents-pages">2483-91</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-date">Date Published</td><td class="biblio-field-contents-date">2012 Dec 5</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">1096-987X</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-keywords">Keywords</td><td class="biblio-field-contents-keywords"><a href="/biblio/keyword/325">Primary Publication</a></td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-abst-e">Abstract</td><td class="biblio-field-contents-abst-e"><p>All-atom sampling is a critical and compute-intensive end stage to protein structural modeling. Because of the vast size and extreme ruggedness of conformational space, even close to the native structure, the high-resolution sampling problem is almost as difficult as predicting the rough fold of a protein. Here, we present a combination of new algorithms that considerably speed up the exploration of very rugged conformational landscapes and are capable of finding heretofore hidden low-energy states. The algorithm is based on a hierarchical workflow and can be parallelized on supercomputers with up to 128,000 compute cores with near perfect efficiency. Such scaling behavior is notable, as with Moore's law continuing only in the number of cores per chip, parallelizability is a critical property of new algorithms. Using the enhanced sampling power, we have uncovered previously invisible deficiencies in the Rosetta force field and created an extensive decoy training set for optimizing and testing force fields. © 2012 Wiley Periodicals, Inc.</p> </td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-doi">DOI</td><td class="biblio-field-contents-doi"><a href="http://dx.doi.org/10.1002/jcc.23069">10.1002/jcc.23069</a></td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-custom1">Custom1</td><td class="biblio-field-contents-custom1"><p><a href="http://www.ncbi.nlm.nih.gov/pubmed/22847521?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/22847521?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/22847521?dopt=Abstract</a></p> </td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-alternate-title">Alternate Journal</td><td class="biblio-field-contents-alternate-title">J Comput Chem</td> </tr> </tbody> </table> </div> http://www.bakerlab.org/node/453#comments Primary Publication Sun, 21 Oct 2012 05:49:28 +0000 bakerpg 453 at http://www.bakerlab.org