The Baker Laboratory - Collaborative Publication http://www.bakerlab.org/taxonomy/term/2/0 This publication represents a collaboration with the Baker lab en Progressive engineering of a homing endonuclease genome editing reagent for the murine X-linked immunodeficiency locus. http://www.bakerlab.org/progressive-engineering-of-a-homing-endonuclease-genome-editing-reagent-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=Progressive+engineering+of+a+homing+endonuclease+genome+editing+reagent+for+the+murine+X-linked+immunodeficiency+locus.&amp;rft.title=Nucleic+acids+research&amp;rft.issn=1362-4962&amp;rft.date=2014&amp;rft.aulast=Wang&amp;rft.aufirst=Yupeng"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">Progressive engineering of a homing endonuclease genome editing reagent for the murine X-linked immunodeficiency locus.</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/1033">Wang, Y.</a>, <a href="/biblio/author/1034">Khan I. F.</a>, <a href="/biblio/author/987">Boissel S.</a>, <a href="/biblio/author/214">Jarjour J.</a>, <a href="/biblio/author/1035">Pangallo J.</a>, <a href="/biblio/author/1025">Thyme S.</a>, <a href="/biblio/author/8">Baker D.</a>, <a href="/biblio/author/216">Scharenberg A. M.</a>, & <a href="/biblio/author/1036">Rawlings D. J.</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">03/25/2014</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/327">Collaborative 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>LAGLIDADG homing endonucleases (LHEs) are compact endonucleases with 20-22 bp recognition sites, and thus are ideal scaffolds for engineering site-specific DNA cleavage enzymes for genome editing applications. Here, we describe a general approach to LHE engineering that combines rational design with directed evolution, using a yeast surface display high-throughput cleavage selection. This approach was employed to alter the binding and cleavage specificity of the I-Anil LHE to recognize a mutation in the mouse Bruton tyrosine kinase (Btk) gene causative for mouse X-linked immunodeficiency (XID)-a model of human X-linked agammaglobulinemia (XLA). The required re-targeting of I-AniI involved progressive resculpting of the DNA contact interface to accommodate nine base differences from the native cleavage sequence. The enzyme emerging from the progressive engineering process was specific for the XID mutant allele versus the wild-type (WT) allele, and exhibited activity equivalent to WT I-AniI in vitro and in cellulo reporter assays. Fusion of the enzyme to a site-specific DNA binding domain of transcription activator-like effector (TALE) resulted in a further enhancement of gene editing efficiency. These results illustrate the potential of LHE enzymes as specific and efficient tools for therapeutic genome engineering.</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/24682825?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/24682825?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/24682825?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><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/Boissel_NucleicAcids_2014.pdf">Boissel_NucleicAcids_2014.pdf</a></td><td>5.92 MB</td> </tr> </tbody> </table> http://www.bakerlab.org/progressive-engineering-of-a-homing-endonuclease-genome-editing-reagent-pub#comments Collaborative Publication Tue, 01 Apr 2014 22:17:51 +0000 bakerpg 527 at http://www.bakerlab.org Small molecule probes to quantify the functional fraction of a specific protein in a cell with minimal folding equilibrium shifts. http://www.bakerlab.org/small-molecule-probes-to-quantify-the-functional-fraction-of-a-specific-protein-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=Small+molecule+probes+to+quantify+the+functional+fraction+of+a+specific+protein+in+a+cell+with+minimal+folding+equilibrium+shifts.&amp;rft.title=Proceedings+of+the+National+Academy+of+Sciences+of+the+United+States+of+America&amp;rft.issn=1091-6490&amp;rft.date=2014&amp;rft.aulast=Liu&amp;rft.aufirst=Yu"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">Small molecule probes to quantify the functional fraction of a specific protein in a cell with minimal folding equilibrium shifts.</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/1026">Liu, Y.</a>, <a href="/biblio/author/1027">Tan Y. L.</a>, <a href="/biblio/author/1028">Zhang X.</a>, <a href="/biblio/author/1029">Bhabha G.</a>, <a href="/biblio/author/631">Ekiert D. C.</a>, <a href="/biblio/author/1030">Genereux J. C.</a>, <a href="/biblio/author/1031">Cho Y.</a>, <a href="/biblio/author/731">Kipnis Y.</a>, <a href="/biblio/author/858">Bjelic S.</a>, <a href="/biblio/author/8">Baker D.</a>, & <a href="/biblio/author/1032">Kelly J. W.</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">03/2014</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/327">Collaborative 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>Although much is known about protein folding in buffers, it remains unclear how the cellular protein homeostasis network functions as a system to partition client proteins between folded and functional, soluble and misfolded, and aggregated conformations. Herein, we develop small molecule folding probes that specifically react with the folded and functional fraction of the protein of interest, enabling fluorescence-based quantification of this fraction in cell lysate at a time point of interest. Importantly, these probes minimally perturb a protein's folding equilibria within cells during and after cell lysis, because sufficient cellular chaperone/chaperonin holdase activity is created by rapid ATP depletion during cell lysis. The folding probe strategy and the faithful quantification of a particular protein's functional fraction are exemplified with retroaldolase, a de novo designed enzyme, and transthyretin, a nonenzyme protein. Our findings challenge the often invoked assumption that the soluble fraction of a client protein is fully folded in the cell. Moreover, our results reveal that the partitioning of destabilized retroaldolase and transthyretin mutants between the aforementioned conformational states is strongly influenced by cytosolic proteostasis network perturbations. Overall, our results suggest that applying a chemical folding probe strategy to other client proteins offers opportunities to reveal how the proteostasis network functions as a system to regulate the folding and function of individual client proteins in vivo.</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/24591605?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/24591605?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/24591605?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/Liu_PNAS_2014.pdf">Liu_PNAS_2014.pdf</a></td><td>1.2 MB</td> </tr> </tbody> </table> http://www.bakerlab.org/small-molecule-probes-to-quantify-the-functional-fraction-of-a-specific-protein-pub#comments Collaborative Publication Wed, 19 Mar 2014 21:54:07 +0000 bakerpg 526 at http://www.bakerlab.org Proof of principle for epitope-focused vaccine design http://www.bakerlab.org/Proof-of-principle-for-epitope-focused-vaccine-design-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=Proof+of+principle+for+epitope-focused+vaccine+design&amp;rft.title=Nature&amp;rft.issn=1476-4687&amp;rft.date=2014&amp;rft.aulast=Correia&amp;rft.aufirst=Bruno&amp;rft_id=info%3Adoi%2F10.1038%2Fnature12966"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">Proof of principle for epitope-focused vaccine 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">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/350">Correia, B. E.</a>, <a href="/biblio/author/1010">Bates J. T.</a>, <a href="/biblio/author/1011">Loomis R. J.</a>, <a href="/biblio/author/1012">Baneyx G.</a>, <a href="/biblio/author/356">Carrico C.</a>, <a href="/biblio/author/1013">Jardine J. G.</a>, <a href="/biblio/author/1014">Rupert P.</a>, <a href="/biblio/author/1015">Correnti C.</a>, <a href="/biblio/author/363">Kalyuzhniy O.</a>, <a href="/biblio/author/1016">Vittal V.</a>, <a href="/biblio/author/1017">Connell M. J.</a>, <a href="/biblio/author/1018">Stevens E.</a>, <a href="/biblio/author/709">Schroeter A.</a>, <a href="/biblio/author/1019">Chen M.</a>, <a href="/biblio/author/836">MacPherson S.</a>, <a href="/biblio/author/1020">Serra A. M.</a>, <a href="/biblio/author/721">Adachi Y.</a>, <a href="/biblio/author/352">Holmes M. A.</a>, <a href="/biblio/author/1021">Li Y.</a>, <a href="/biblio/author/83">Klevit R. E.</a>, <a href="/biblio/author/1022">Graham B. S.</a>, <a href="/biblio/author/657">Wyatt R. T.</a>, <a href="/biblio/author/8">Baker D.</a>, <a href="/biblio/author/103">Strong R. K.</a>, <a href="/biblio/author/1023">Crowe J. E.</a>, <a href="/biblio/author/1024">Johnson P. R.</a>, & <a href="/biblio/author/127">Schief W. R.</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-date">Date Published</td><td class="biblio-field-contents-date">02/2014</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">1476-4687</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/327">Collaborative Publication</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>Vaccines prevent infectious disease largely by inducing protective neutralizing antibodies against vulnerable epitopes. Several major pathogens have resisted traditional vaccine development, although vulnerable epitopes targeted by neutralizing antibodies have been identified for several such cases. Hence, new vaccine design methods to induce epitope-specific neutralizing antibodies are needed. Here we show, with a neutralization epitope from respiratory syncytial virus, that computational protein design can generate small, thermally and conformationally stable protein scaffolds that accurately mimic the viral epitope structure and induce potent neutralizing antibodies. These scaffolds represent promising leads for the research and development of a human respiratory syncytial virus vaccine needed to protect infants, young children and the elderly. More generally, the results provide proof of principle for epitope-focused and scaffold-based vaccine design, and encourage the evaluation and further development of these strategies for a variety of other vaccine targets, including antigenically highly variable pathogens such as human immunodeficiency virus and influenza.</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/10.1038/nature12966">10.1038/nature12966</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/24499818?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/24499818?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/24499818?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">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/Correia14.pdf">Correia14.pdf</a></td><td>8.67 MB</td> </tr> </tbody> </table> http://www.bakerlab.org/Proof-of-principle-for-epitope-focused-vaccine-design-pub#comments Collaborative Publication Tue, 18 Feb 2014 21:52:18 +0000 bakerpg 522 at http://www.bakerlab.org Computationally designed libraries for rapid enzyme stabilization. http://www.bakerlab.org/Computationally-designed-libraries-for-rapid-enzyme-stabilization-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=Computationally+designed+libraries+for+rapid+enzyme+stabilization.&amp;rft.title=Protein+engineering%2C+design+%26amp%3B+selection+%3A+PEDS&amp;rft.issn=1741-0134&amp;rft.date=2014&amp;rft.volume=27&amp;rft.issue=2&amp;rft.spage=49&amp;rft.epage=58&amp;rft.aulast=Wijma&amp;rft.aufirst=Hein&amp;rft_id=info%3Adoi%2F10.1093%2Fprotein%2Fgzt061"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">Computationally designed libraries for rapid enzyme stabilization.</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/1005">Wijma, H. J.</a>, <a href="/biblio/author/1006">Floor R. J.</a>, <a href="/biblio/author/1007">Jekel P. A.</a>, <a href="/biblio/author/8">Baker D.</a>, <a href="/biblio/author/1008">Marrink S. J.</a>, & <a href="/biblio/author/1009">Janssen D. 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">Protein engineering, design &amp; selection : PEDS</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-volume">Volume</td><td class="biblio-field-contents-volume">27</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">49-58</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-date">Date Published</td><td class="biblio-field-contents-date">02/2014</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">1741-0134</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/327">Collaborative 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 engineer enzymes and other proteins to any desired stability would have wide-ranging applications. Here, we demonstrate that computational design of a library with chemically diverse stabilizing mutations allows the engineering of drastically stabilized and fully functional variants of the mesostable enzyme limonene epoxide hydrolase. First, point mutations were selected if they significantly improved the predicted free energy of protein folding. Disulfide bonds were designed using sampling of backbone conformational space, which tripled the number of experimentally stabilizing disulfide bridges. Next, orthogonal in silico screening steps were used to remove chemically unreasonable mutations and mutations that are predicted to increase protein flexibility. The resulting library of 64 variants was experimentally screened, which revealed 21 (pairs of) stabilizing mutations located both in relatively rigid and in flexible areas of the enzyme. Finally, combining 10-12 of these confirmed mutations resulted in multi-site mutants with an increase in apparent melting temperature from 50 to 85°C, enhanced catalytic activity, preserved regioselectivity and a >250-fold longer half-life. The developed Framework for Rapid Enzyme Stabilization by Computational libraries (FRESCO) requires far less screening than conventional directed 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/10.1093/protein/gzt061">10.1093/protein/gzt061</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/24402331?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/24402331?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/24402331?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 Eng. Des. Sel.</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/Wijma_PEDS_2014.pdf">Wijma_PEDS_2014.pdf</a></td><td>953.89 KB</td> </tr> </tbody> </table> http://www.bakerlab.org/Computationally-designed-libraries-for-rapid-enzyme-stabilization-pub#comments Collaborative Publication Tue, 21 Jan 2014 23:59:35 +0000 bakerpg 520 at http://www.bakerlab.org Protein NMR Structures Refined with Rosetta Have Higher Accuracy Relative to Corresponding X-ray Crystal Structures. http://www.bakerlab.org/Protein-NMR-Structures-Refined-with-Rosetta-Have-Higher-Accuracy-Relative-to-Corresponding-X-ray-Crystal-Structures-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=Protein+NMR+Structures+Refined+with+Rosetta+Have+Higher+Accuracy+Relative+to+Corresponding+X-ray+Crystal+Structures.&amp;rft.title=Journal+of+the+American+Chemical+Society&amp;rft.issn=1520-5126&amp;rft.date=2014&amp;rft.aulast=Mao&amp;rft.aufirst=Binchen"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">Protein NMR Structures Refined with Rosetta Have Higher Accuracy Relative to Corresponding X-ray Crystal 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">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/391">Mao, B.</a>, <a href="/biblio/author/1004">Tejero R.</a>, <a href="/biblio/author/8">Baker D.</a>, & <a href="/biblio/author/864">Montelione G. T.</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-date">Date Published</td><td class="biblio-field-contents-date">01/06/2014</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">1520-5126</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/327">Collaborative Publication</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>We have found that refinement of protein NMR structures using Rosetta with experimental NMR restraints yields more accurate protein NMR structures than those that have been deposited in the PDB using standard refinement protocols. Using 40 pairs of NMR and X-ray crystal structures determined by the Northeast Structural Genomics Consortium, for proteins ranging in size from 5 - 22 kDa, restrained-Rosetta refined structures fit better to the raw experimental data, are in better agreement with their X-ray counterparts, and have better phasing power compared to conventionally determined NMR structures. For 38 proteins for which NMR ensembles were available and which had similar structures in solution and in the crystal, all of the restrained-Rosetta refined NMR structures were sufficiently accurate to be used for solving the corresponding X-ray crystal structures by molecular replacement. The protocol for restrained refinement of protein NMR structures was also compared with restrained CS-Rosetta calculations. For proteins smaller than 10 kDa, restrained CS-Rosetta, starting from extended conformations, provides slightly more accurate structures, while for proteins in the size range of 10 - 25 kDa the less cpu intensive restrained-Rosetta refinement protocols provided more accurate structures. The restrained-Rosetta protocols described here can improve the accuracy of protein NMR structures, and should find broad and general for studies of protein structure and function.</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/24392845?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/24392845?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/24392845?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/Mao_JACS_2014.pdf">Mao_JACS_2014.pdf</a></td><td>2.16 MB</td> </tr> </tbody> </table> Collaborative Publication Tue, 21 Jan 2014 23:58:52 +0000 bakerpg 519 at http://www.bakerlab.org Forced protein unfolding leads to highly elastic and tough protein hydrogels. http://www.bakerlab.org/node/517 <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=Forced+protein+unfolding+leads+to+highly+elastic+and+tough+protein+hydrogels.&amp;rft.title=Nature+communications&amp;rft.issn=2041-1723&amp;rft.date=2013&amp;rft.volume=4&amp;rft.spage=2974&amp;rft.aulast=Fang&amp;rft.aufirst=Jie&amp;rft_id=info%3Adoi%2F10.1038%2Fncomms3974"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">Forced protein unfolding leads to highly elastic and tough protein hydrogels.</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/994">Fang, J.</a>, <a href="/biblio/author/995">Mehlich A.</a>, <a href="/biblio/author/639">Koga N.</a>, <a href="/biblio/author/996">Huang J.</a>, <a href="/biblio/author/997">Koga R.</a>, <a href="/biblio/author/998">Gao X.</a>, <a href="/biblio/author/999">Hu C.</a>, <a href="/biblio/author/1000">Jin C.</a>, <a href="/biblio/author/1001">Rief M.</a>, <a href="/biblio/author/1002">Kast J.</a>, <a href="/biblio/author/8">Baker D.</a>, & <a href="/biblio/author/1003">Li H.</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 communications</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-volume">Volume</td><td class="biblio-field-contents-volume">4</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-pages">Pagination</td><td class="biblio-field-contents-pages">2974</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 19</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">2041-1723</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/327">Collaborative 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>Protein-based hydrogels usually do not exhibit high stretchability or toughness, significantly limiting the scope of their potential biomedical applications. Here we report the engineering of a chemically cross-linked, highly elastic and tough protein hydrogel using a mechanically extremely labile, de novo-designed protein that assumes the classical ferredoxin-like fold structure. Due to the low mechanical stability of the ferredoxin-like fold structure, swelling of hydrogels causes a significant fraction of the folded domains to unfold. Subsequent collapse and aggregation of unfolded ferredoxin-like domains leads to intertwining of physically and chemically cross-linked networks, entailing hydrogels with unusual physical and mechanical properties: a negative swelling ratio, high stretchability and toughness. These hydrogels can withstand an average strain of 450% before breaking and show massive energy dissipation. Upon relaxation, refolding of the ferredoxin-like domains enables the hydrogel to recover its massive hysteresis. This novel biomaterial may expand the scope of hydrogel applications in tissue engineering.</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/10.1038/ncomms3974">10.1038/ncomms3974</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/24352111?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/24352111?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/24352111?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">Nat Commun</td> </tr> </tbody> </table> </div> http://www.bakerlab.org/node/517#comments Collaborative Publication Tue, 21 Jan 2014 23:38:47 +0000 bakerpg 517 at http://www.bakerlab.org Amyloid β peptide cleavage by kallikrein 7 attenuates fibril growth and rescues neurons from Aβ-mediated toxicity in vitro. http://www.bakerlab.org/node/510 <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=Amyloid+%CE%B2+peptide+cleavage+by+kallikrein+7+attenuates+fibril+growth+and+rescues+neurons+from+A%CE%B2-mediated+toxicity+in+vitro.&amp;rft.title=Biological+chemistry&amp;rft.issn=1437-4315&amp;rft.date=2014&amp;rft.volume=395&amp;rft.issue=1&amp;rft.aulast=Shropshire&amp;rft.aufirst=Tyler&amp;rft_id=info%3Adoi%2F10.1515%2Fhsz-2013-0230"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">Amyloid β peptide cleavage by kallikrein 7 attenuates fibril growth and rescues neurons from Aβ-mediated toxicity in vitro.</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/970">Shropshire, T. D.</a>, <a href="/biblio/author/971">Reifert J.</a>, <a href="/biblio/author/972">Rajagopalan S.</a>, <a href="/biblio/author/8">Baker D.</a>, <a href="/biblio/author/973">Feinstein S. C.</a>, & <a href="/biblio/author/974">Daugherty P. 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">Biological chemistry</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-volume">Volume</td><td class="biblio-field-contents-volume">395</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-issue">Issue</td><td class="biblio-field-contents-issue">1</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-pages">Pagination</td><td class="biblio-field-contents-pages">109-18</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-date">Date Published</td><td class="biblio-field-contents-date">01/2014</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">1437-4315</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/327">Collaborative 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>Abstract The gradual accumulation and assembly of β-amyloid (Aβ) peptide into neuritic plaques is a major pathological hallmark of Alzheimer disease (AD). Proteolytic degradation of Aβ is an important clearance mechanism under normal circumstances, and it has been found to be compromised in those with AD. Here, the extended substrate specificity and Aβ-degrading capacity of kallikrein 7 (KLK7), a serine protease with a unique chymotrypsin-like specificity, was characterized. Preferred peptide substrates of KLK7 identified using a bacterial display substrate library were found to exhibit a consensus motif of RXΦ(Y/F)↓(Y/F)↓(S/A/G/T) or RXΦ(Y/F)↓(S/T/A) (Φ=hydrophobic), which is remarkably similar to the hydrophobic core motif of Aβ (K16L17V18F19F20 A21) that is largely responsible for aggregation propensity. KLK7 was found to cleave after both Phe residues within the core of Aβ42 in vitro, thereby inhibiting Aβ fibril formation and promoting the degradation of preformed fibrils. Finally, the treatment of Aβ oligomer preparations with KLK7, but not inactive pro-KLK7, significantly reduced Aβ42-mediated toxicity to rat hippocampal neurons to the same extent as the known Aβ-degrading protease insulin-degrading enzyme (IDE). Taken together, these results indicate that KLK7 possesses an Aβ-degrading capacity that can ameliorate the toxic effects of the aggregated peptide in vitro.</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/10.1515/hsz-2013-0230">10.1515/hsz-2013-0230</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/23989112?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/23989112?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/23989112?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">Biol. Chem.</td> </tr> </tbody> </table> </div> http://www.bakerlab.org/node/510#comments Collaborative Publication Tue, 21 Jan 2014 23:34:00 +0000 bakerpg 510 at http://www.bakerlab.org Improved chemical shift based fragment selection for CS-Rosetta using Rosetta3 fragment picker. http://www.bakerlab.org/node/508 <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+chemical+shift+based+fragment+selection+for+CS-Rosetta+using+Rosetta3+fragment+picker.&amp;rft.title=Journal+of+biomolecular+NMR&amp;rft.issn=1573-5001&amp;rft.date=2013&amp;rft.volume=57&amp;rft.issue=2&amp;rft.aulast=Vernon&amp;rft.aufirst=Robert&amp;rft_id=info%3Adoi%2F10.1007%2Fs10858-013-9772-4"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">Improved chemical shift based fragment selection for CS-Rosetta using Rosetta3 fragment picker.</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/169">Vernon, R.</a>, <a href="/biblio/author/183">Shen Y.</a>, <a href="/biblio/author/8">Baker D.</a>, & <a href="/biblio/author/50" class="biblio-local-author">Lange O. F.</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 biomolecular NMR</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-volume">Volume</td><td class="biblio-field-contents-volume">57</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">117-27</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</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">1573-5001</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/327">Collaborative 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 new fragment picker has been developed for CS-Rosetta that combines beneficial features of the original fragment picker, MFR, used with CS-Rosetta, and the fragment picker, NNMake, that was used for purely sequence based fragment selection in the context of ROSETTA de-novo structure prediction. Additionally, the new fragment picker has reduced sensitivity to outliers and other difficult to match data points rendering the protocol more robust and less likely to introduce bias towards wrong conformations in cases where data is bad, missing or inconclusive. The fragment picker protocol gives significant improvements on 6 of 23 CS-Rosetta targets. An independent benchmark on 39 protein targets, whose NMR data sets were published only after protocol optimization had been finished, also show significantly improved performance for the new fragment picker (van der Schot et al. in J Biomol NMR, 2013).</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/s10858-013-9772-4">10.1007/s10858-013-9772-4</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/23975356?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/23975356?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/23975356?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. Biomol. NMR</td> </tr> </tbody> </table> </div> http://www.bakerlab.org/node/508#comments Collaborative Publication Tue, 21 Jan 2014 23:32:13 +0000 bakerpg 508 at http://www.bakerlab.org Improving 3D structure prediction from chemical shift data. http://www.bakerlab.org/node/507 <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=Improving+3D+structure+prediction+from+chemical+shift+data.&amp;rft.title=Journal+of+biomolecular+NMR&amp;rft.issn=1573-5001&amp;rft.date=2013&amp;rft.volume=57&amp;rft.issue=1&amp;rft.spage=27&amp;rft.epage=35&amp;rft.aulast=Schot&amp;rft.aufirst=Gijs&amp;rft_id=info%3Adoi%2F10.1007%2Fs10858-013-9762-6"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">Improving 3D structure prediction from chemical shift data.</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/501">van der Schot, G.</a>, <a href="/biblio/author/968">Zhang Z.</a>, <a href="/biblio/author/169">Vernon R.</a>, <a href="/biblio/author/183">Shen Y.</a>, <a href="/biblio/author/502">Vranken W. F.</a>, <a href="/biblio/author/8">Baker D.</a>, <a href="/biblio/author/504">Bonvin A. M. J. J.</a>, & <a href="/biblio/author/50" class="biblio-local-author">Lange O. F.</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 biomolecular NMR</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-volume">Volume</td><td class="biblio-field-contents-volume">57</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-issue">Issue</td><td class="biblio-field-contents-issue">1</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-pages">Pagination</td><td class="biblio-field-contents-pages">27-35</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</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">1573-5001</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/327">Collaborative 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 report advances in the calculation of protein structures from chemical shift nuclear magnetic resonance data alone. Our previously developed method, CS-Rosetta, assembles structures from a library of short protein fragments picked from a large library of protein structures using chemical shifts and sequence information. Here we demonstrate that combination of a new and improved fragment picker and the iterative sampling algorithm RASREC yield significant improvements in convergence and accuracy. Moreover, we introduce improved criteria for assessing the accuracy of the models produced by the method. The method was tested on 39 proteins in the 50-100 residue size range and yields reliable structures in 70 % of the cases. All structures that passed the reliability filter were accurate (&lt;2 Å RMSD from the reference).</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/s10858-013-9762-6">10.1007/s10858-013-9762-6</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/23912841?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/23912841?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/23912841?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. Biomol. NMR</td> </tr> </tbody> </table> </div> http://www.bakerlab.org/node/507#comments Collaborative Publication Tue, 21 Jan 2014 23:31:30 +0000 bakerpg 507 at http://www.bakerlab.org Evolution of a designed retro-aldolase leads to complete active site remodeling. http://www.bakerlab.org/node/504 <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=Evolution+of+a+designed+retro-aldolase+leads+to+complete+active+site+remodeling.&amp;rft.title=Nature+chemical+biology&amp;rft.issn=1552-4469&amp;rft.date=2013&amp;rft.volume=9&amp;rft.issue=8&amp;rft.aulast=Giger&amp;rft.aufirst=Lars&amp;rft_id=info%3Adoi%2F10.1038%2Fnchembio.1276"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">Evolution of a designed retro-aldolase leads to complete active site remodeling.</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/756">Giger, L.</a>, <a href="/biblio/author/899">Caner S.</a>, <a href="/biblio/author/900">Obexer R.</a>, <a href="/biblio/author/824">Kast P.</a>, <a href="/biblio/author/8">Baker D.</a>, <a href="/biblio/author/901">Ban N.</a>, & <a href="/biblio/author/136">Hilvert 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">9</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-issue">Issue</td><td class="biblio-field-contents-issue">8</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-pages">Pagination</td><td class="biblio-field-contents-pages">494-8</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-date">Date Published</td><td class="biblio-field-contents-date">2013 Aug</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/234">Aldehyde-Lyases</a>, <a href="/biblio/keyword/225">Biocatalysis</a>, <a href="/biblio/keyword/174">Catalytic Domain</a>, <a href="/biblio/keyword/327">Collaborative Publication</a>, <a href="/biblio/keyword/2">Computational Biology</a>, <a href="/biblio/keyword/60">Computer Simulation</a>, <a href="/biblio/keyword/315">Directed Molecular Evolution</a>, <a href="/biblio/keyword/10">Models, Molecular</a>, <a href="/biblio/keyword/123">Molecular Structure</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>Evolutionary advances are often fueled by unanticipated innovation. Directed evolution of a computationally designed enzyme suggests that pronounced molecular changes can also drive the optimization of primitive protein active sites. The specific activity of an artificial retro-aldolase was boosted >4,400-fold by random mutagenesis and screening, affording catalytic efficiencies approaching those of natural enzymes. However, structural and mechanistic studies reveal that the engineered catalytic apparatus, consisting of a reactive lysine and an ordered water molecule, was unexpectedly abandoned in favor of a new lysine residue in a substrate-binding pocket created during the optimization process. Structures of the initial in silico design, a mechanistically promiscuous intermediate and one of the most evolved variants highlight the importance of loop mobility and supporting functional groups in the emergence of the new catalytic center. Such internal competition between alternative reactive sites may have characterized the early evolution of many natural enzymes.</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.1276">10.1038/nchembio.1276</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/23748672?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/23748672?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/23748672?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> http://www.bakerlab.org/node/504#comments Collaborative Publication Tue, 21 Jan 2014 23:12:23 +0000 bakerpg 504 at http://www.bakerlab.org Expanding the product profile of a microbial alkane biosynthetic pathway. http://www.bakerlab.org/node/503 <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=Expanding+the+product+profile+of+a+microbial+alkane+biosynthetic+pathway.&amp;rft.title=ACS+synthetic+biology&amp;rft.issn=2161-5063&amp;rft.date=2013&amp;rft.volume=2&amp;rft.issue=1&amp;rft.spage=59&amp;rft.epage=62&amp;rft.aulast=Harger&amp;rft.aufirst=Matthew&amp;rft_id=info%3Adoi%2F10.1021%2Fsb300061x"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">Expanding the product profile of a microbial alkane biosynthetic pathway.</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/888">Harger, M.</a>, <a href="/biblio/author/889">Zheng L.</a>, <a href="/biblio/author/890">Moon A.</a>, <a href="/biblio/author/891">Ager C.</a>, <a href="/biblio/author/892">An J. H.</a>, <a href="/biblio/author/893">Choe C.</a>, <a href="/biblio/author/894">Lai Y. - L.</a>, <a href="/biblio/author/895">Mo B.</a>, <a href="/biblio/author/896">Zong D.</a>, <a href="/biblio/author/897">Smith M. D.</a>, <a href="/biblio/author/898">Egbert R. G.</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">ACS synthetic biology</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-volume">Volume</td><td class="biblio-field-contents-volume">2</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-issue">Issue</td><td class="biblio-field-contents-issue">1</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-pages">Pagination</td><td class="biblio-field-contents-pages">59-62</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-date">Date Published</td><td class="biblio-field-contents-date">2013 Jan 18</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">2161-5063</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/327">Collaborative 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>Microbially produced alkanes are a new class of biofuels that closely match the chemical composition of petroleum-based fuels. Alkanes can be generated from the fatty acid biosynthetic pathway by the reduction of acyl-ACPs followed by decarbonylation of the resulting aldehydes. A current limitation of this pathway is the restricted product profile, which consists of n-alkanes of 13, 15, and 17 carbons in length. To expand the product profile, we incorporated a new part, FabH2 from Bacillus subtilis , an enzyme known to have a broader specificity profile for fatty acid initiation than the native FabH of Escherichia coli . When provided with the appropriate substrate, the addition of FabH2 resulted in an altered alkane product profile in which significant levels of n-alkanes of 14 and 16 carbons in length are produced. The production of even chain length alkanes represents initial steps toward the expansion of this recently discovered microbial alkane production pathway to synthesize complex fuels. This work was conceived and performed as part of the 2011 University of Washington international Genetically Engineered Machines (iGEM) project.</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/sb300061x">10.1021/sb300061x</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/23656326?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/23656326?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/23656326?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">ACS Synth Biol</td> </tr> </tbody> </table> </div> http://www.bakerlab.org/node/503#comments Collaborative Publication Tue, 21 Jan 2014 23:11:10 +0000 bakerpg 503 at http://www.bakerlab.org Engineering V-type nerve agents detoxifying enzymes using computationally focused libraries http://www.bakerlab.org/Engineering-V-type-nerve-agents-detoxifying-enzymes-using-computationally-focused-libraries-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=Engineering+V-type+nerve+agents+detoxifying+enzymes+using+computationally+focused+libraries&amp;rft.title=ACS+chemical+biology&amp;rft.issn=1554-8937&amp;rft.date=2013&amp;rft.volume=8&amp;rft.issue=11&amp;rft.aulast=Cherny&amp;rft.aufirst=Izhack&amp;rft_id=info%3Adoi%2F10.1021%2Fcb4004892"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">Engineering V-type nerve agents detoxifying enzymes using computationally focused libraries</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/885">Cherny, I.</a>, <a href="/biblio/author/886">Greisen P.</a>, <a href="/biblio/author/733">Ashani Y.</a>, <a href="/biblio/author/638" class="biblio-local-author">Khare S. D.</a>, <a href="/biblio/author/671">Oberdorfer G.</a>, <a href="/biblio/author/736">Leader H.</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">ACS chemical biology</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-volume">Volume</td><td class="biblio-field-contents-volume">8</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">2394-403</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 15</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">1554-8937</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/327">Collaborative 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>VX and its Russian (RVX) and Chinese (CVX) analogues rapidly inactivate acetylcholinesterase and are the most toxic stockpile nerve agents. These organophosphates have a thiol leaving group with a choline-like moiety and are hydrolyzed very slowly by natural enzymes. We used an integrated computational and experimental approach to increase Brevundimonas diminuta phosphotriesterase's (PTE) detoxification rate of V-agents by 5000-fold. Computational models were built of the complex between PTE and V-agents. On the basis of these models, the active site was redesigned to be complementary in shape to VX and RVX and to include favorable electrostatic interactions with their choline-like leaving group. Small libraries based on designed sequences were constructed. The libraries were screened by a direct assay for V-agent detoxification, as our initial studies showed that colorimetric surrogates fail to report the detoxification rates of the actual agents. The experimental results were fed back to improve the computational models. Overall, five rounds of iterating between experiment and model refinement led to variants that hydrolyze the toxic SP isomers of all three V-agents with kcat/KM values of up to 5 × 10(6) M(-1) min(-1) and also efficiently detoxify G-agents. These new catalysts provide the basis for broad spectrum nerve agent detoxification.</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/cb4004892">10.1021/cb4004892</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/24041203?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/24041203?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/24041203?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">ACS 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/Cherny_cb4004892_13W.pdf">Cherny_cb4004892_13W.pdf</a></td><td>4.21 MB</td> </tr> </tbody> </table> Collaborative Publication Mon, 06 Jan 2014 16:58:37 +0000 bakerpg 497 at http://www.bakerlab.org Evaluation and optimization of discrete state models of protein folding. http://www.bakerlab.org/node/477 <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=Evaluation+and+optimization+of+discrete+state+models+of+protein+folding.&amp;rft.title=The+journal+of+physical+chemistry.+B&amp;rft.issn=1520-5207&amp;rft.date=2012&amp;rft.volume=116&amp;rft.issue=37&amp;rft.aulast=Kellogg&amp;rft.aufirst=Elizabeth"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">Evaluation and optimization of discrete state models of protein folding.</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/392">Kellogg, E. H.</a>, <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">The journal of physical chemistry. B</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-volume">Volume</td><td class="biblio-field-contents-volume">116</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-issue">Issue</td><td class="biblio-field-contents-issue">37</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-pages">Pagination</td><td class="biblio-field-contents-pages">11405-13</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 20</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">1520-5207</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/327">Collaborative Publication</a>, <a href="/biblio/keyword/52">Kinetics</a>, <a href="/biblio/keyword/513">Likelihood Functions</a>, <a href="/biblio/keyword/29">Protein Conformation</a>, <a href="/biblio/keyword/23">Protein Folding</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 space accessed by a folding macromolecule is vast, and how to best project computer simulations of protein folding trajectories into an interpretable sequence of discrete states is an open research problem. There are numerous alternative ways of associating individual configurations into collective states, and in deciding on the number of such clustered states there is a trade-off between human interpretability (smaller number of states) and accuracy of representation (larger number of states). Here we introduce a trajectory likelihood measure for assessing alternative discrete state models of protein folding. We find that widely used rmsd-based clustering methods require large numbers of initial states and a second agglomeration step based on kinetic connectivity to produce models with high predictive power; this is the approach taken in elegant recent work with Markov State Models of protein folding. In contrast, we find that grouping of states based on secondary structure pairings or contact maps, when refined with K-means clustering, yields higher likelihood models with many fewer states. Using the most predictive contact map representation to study the folding transitions of the WW domain in very long molecular dynamics simulations, we identify new states and transitions. The methods should be generally useful for investigating the structural transitions in protein folding simulations for larger proteins.</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/22958200?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/22958200?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/22958200?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 Phys Chem B</td> </tr> </tbody> </table> </div> http://www.bakerlab.org/node/477#comments Collaborative Publication Fri, 07 Jun 2013 21:27:57 +0000 bakerpg 477 at http://www.bakerlab.org Cryo-EM model validation using independent map reconstructions http://www.bakerlab.org/Cryo-EM-model-validation-using-independent-map-reconstructions <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=Cryo-EM+model+validation+using+independent+map+reconstructions&amp;rft.title=Protein+science+%3A+a+publication+of+the+Protein+Society&amp;rft.issn=1469-896X&amp;rft.date=2013&amp;rft.volume=22&amp;rft.issue=6&amp;rft.aulast=DiMaio&amp;rft.aufirst=Frank&amp;rft_id=info%3Adoi%2F10.1002%2Fpro.2267"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">Cryo-EM model validation using independent map reconstructions</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/867">Zhang J.</a>, <a href="/biblio/author/193">Chiu W.</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">22</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-issue">Issue</td><td class="biblio-field-contents-issue">6</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-pages">Pagination</td><td class="biblio-field-contents-pages">865-8</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-date">Date Published</td><td class="biblio-field-contents-date">2013 Jun</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/327">Collaborative 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>An increasing number of cryo-electron microscopy (cryo-EM) density maps are being generated with suitable resolution to trace the protein backbone and guide sidechain placement. Generating and evaluating atomic models based on such maps would be greatly facilitated by independent validation metrics for assessing the fit of the models to the data. We describe such a metric based on the fit of atomic models with independent test maps from single particle reconstructions not used in model refinement. The metric provides a means to determine the proper balance between the fit to the density and model energy and stereochemistry during refinement, and is likely to be useful in determining values of model building and refinement metaparameters quite generally.</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.2267">10.1002/pro.2267</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/23592445?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/23592445?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/23592445?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><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/DiMaio_pro2267_13Q.pdf">DiMaio_pro2267_13Q.pdf</a></td><td>225.1 KB</td> </tr> </tbody> </table> Collaborative Publication Fri, 07 Jun 2013 19:08:03 +0000 bakerpg 476 at http://www.bakerlab.org Computational design of enone-binding proteins with catalytic activity for the Morita-Baylis-Hillman reaction http://www.bakerlab.org/Computational-design-of-enone-binding-proteins-with-catalytic-activity-for-the-Morita-Baylis-Hillman-reaction <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+enone-binding+proteins+with+catalytic+activity+for+the+Morita-Baylis-Hillman+reaction&amp;rft.title=ACS+chemical+biology&amp;rft.issn=1554-8937&amp;rft.date=2013&amp;rft.volume=8&amp;rft.issue=4&amp;rft.aulast=Bjelic&amp;rft.aufirst=Sinisa&amp;rft_id=info%3Adoi%2F10.1021%2Fcb3006227"></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 enone-binding proteins with catalytic activity for the Morita-Baylis-Hillman reaction</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/859">Nivón L. G.</a>, <a href="/biblio/author/860">Çelebi-Ölçüm N.</a>, <a href="/biblio/author/132">Kiss G.</a>, <a href="/biblio/author/861">Rosewall C. F.</a>, <a href="/biblio/author/131">Lovick H. M.</a>, <a href="/biblio/author/862">Ingalls E. L.</a>, <a href="/biblio/author/863">Gallaher J. L.</a>, <a href="/biblio/author/803">Seetharaman J.</a>, <a href="/biblio/author/806">Lew S.</a>, <a href="/biblio/author/864">Montelione G. T.</a>, <a href="/biblio/author/865">Hunt J. F.</a>, <a href="/biblio/author/866">Michael F. E.</a>, <a href="/biblio/author/442">Houk K. N.</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">ACS chemical biology</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-volume">Volume</td><td class="biblio-field-contents-volume">8</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-issue">Issue</td><td class="biblio-field-contents-issue">4</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-pages">Pagination</td><td class="biblio-field-contents-pages">749-57</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-date">Date Published</td><td class="biblio-field-contents-date">2013 Apr 19</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">1554-8937</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/327">Collaborative 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 Morita-Baylis-Hillman reaction forms a carbon-carbon bond between the α-carbon of a conjugated carbonyl compound and a carbon electrophile. The reaction mechanism involves Michael addition of a nucleophile catalyst at the carbonyl β-carbon, followed by bond formation with the electrophile and catalyst disassociation to release the product. We used Rosetta to design 48 proteins containing active sites predicted to carry out this mechanism, of which two show catalytic activity by mass spectrometry (MS). Substrate labeling measured by MS and site-directed mutagenesis experiments show that the designed active-site residues are responsible for activity, although rate acceleration over background is modest. To characterize the designed proteins, we developed a fluorescence-based screen for intermediate formation in cell lysates, carried out microsecond molecular dynamics simulations, and solved X-ray crystal structures. These data indicate a partially formed active site and suggest several clear avenues for designing more active catalysts.</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/cb3006227">10.1021/cb3006227</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/23330600?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/23330600?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/23330600?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">ACS 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/Bjelic_cb3006227_13R.pdf">Bjelic_cb3006227_13R.pdf</a></td><td>442.21 KB</td> </tr> </tbody> </table> Collaborative Publication Fri, 07 Jun 2013 19:04:46 +0000 bakerpg 475 at http://www.bakerlab.org Computational design of novel protein binders and experimental affinity maturation http://www.bakerlab.org/Computational-design-of-novel-protein-binders-and-experimental-affinity-maturation <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+novel+protein+binders+and+experimental+affinity+maturation&amp;rft.title=Methods+in+enzymology&amp;rft.issn=1557-7988&amp;rft.date=2013&amp;rft.volume=523&amp;rft.spage=1&amp;rft.epage=19&amp;rft.aulast=Whitehead&amp;rft.aufirst=Timothy&amp;rft_id=info%3Adoi%2F10.1016%2FB978-0-12-394292-0.00001-1"></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 novel protein binders and experimental affinity maturation</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/630">Whitehead, T. A.</a>, <a href="/biblio/author/8">Baker D.</a>, & <a href="/biblio/author/159">Fleishman S. J.</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 enzymology</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-volume">Volume</td><td class="biblio-field-contents-volume">523</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-pages">Pagination</td><td class="biblio-field-contents-pages">1-19</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-date">Date Published</td><td class="biblio-field-contents-date">2013</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">1557-7988</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/327">Collaborative 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 of novel protein binders has recently emerged as a useful technique to study biomolecular recognition and generate molecules for use in biotechnology, research, and biomedicine. Current limitations in computational design methodology have led to the adoption of high-throughput screening and affinity maturation techniques to diagnose modeling inaccuracies and generate high activity binders. Here, we scrutinize this combination of computational and experimental aspects and propose areas for future methodological improvements.</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/B978-0-12-394292-0.00001-1">10.1016/B978-0-12-394292-0.00001-1</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/23422423?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/23422423?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/23422423?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">Meth. Enzymol.</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/Whitehead_MethEnzymology_13V.pdf">Whitehead_MethEnzymology_13V.pdf</a></td><td>1.18 MB</td> </tr> </tbody> </table> Collaborative Publication Fri, 07 Jun 2013 19:02:22 +0000 bakerpg 474 at http://www.bakerlab.org Scientific benchmarks for guiding macromolecular energy function improvement. http://www.bakerlab.org/node/473 <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=Scientific+benchmarks+for+guiding+macromolecular+energy+function+improvement.&amp;rft.title=Methods+in+enzymology&amp;rft.issn=1557-7988&amp;rft.date=2013&amp;rft.volume=523&amp;rft.aulast=Leaver-Fay&amp;rft.aufirst=Andrew&amp;rft_id=info%3Adoi%2F10.1016%2FB978-0-12-394292-0.00006-0"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">Scientific benchmarks for guiding macromolecular energy function improvement.</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/7">Leaver-Fay, A.</a>, <a href="/biblio/author/855">O&#039;Meara M. J.</a>, <a href="/biblio/author/521">Tyka M.</a>, <a href="/biblio/author/380">Jacak R.</a>, <a href="/biblio/author/394">Song Y.</a>, <a href="/biblio/author/392">Kellogg E. H.</a>, <a href="/biblio/author/170">Thompson J.</a>, <a href="/biblio/author/188">Davis I. W.</a>, <a href="/biblio/author/856">Pache R. A.</a>, <a href="/biblio/author/387">Lyskov S.</a>, <a href="/biblio/author/113">Gray J. J.</a>, <a href="/biblio/author/101">Kortemme T.</a>, <a href="/biblio/author/396">Richardson J. S.</a>, <a href="/biblio/author/143">Havranek J. J.</a>, <a href="/biblio/author/857">Snoeyink J.</a>, <a href="/biblio/author/8">Baker D.</a>, & <a href="/biblio/author/88">Kuhlman 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">Methods in enzymology</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-volume">Volume</td><td class="biblio-field-contents-volume">523</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-pages">Pagination</td><td class="biblio-field-contents-pages">109-43</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-date">Date Published</td><td class="biblio-field-contents-date">2013</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">1557-7988</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/327">Collaborative 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>Accurate energy functions are critical to macromolecular modeling and design. We describe new tools for identifying inaccuracies in energy functions and guiding their improvement, and illustrate the application of these tools to the improvement of the Rosetta energy function. The feature analysis tool identifies discrepancies between structures deposited in the PDB and low-energy structures generated by Rosetta; these likely arise from inaccuracies in the energy function. The optE tool optimizes the weights on the different components of the energy function by maximizing the recapitulation of a wide range of experimental observations. We use the tools to examine three proposed modifications to the Rosetta energy function: improving the unfolded state energy model (reference energies), using bicubic spline interpolation to generate knowledge-based torisonal potentials, and incorporating the recently developed Dunbrack 2010 rotamer library (Shapovalov &amp; Dunbrack, 2011).</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/B978-0-12-394292-0.00006-0">10.1016/B978-0-12-394292-0.00006-0</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/23422428?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/23422428?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/23422428?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">Meth. Enzymol.</td> </tr> </tbody> </table> </div> http://www.bakerlab.org/node/473#comments Collaborative Publication Fri, 07 Jun 2013 19:01:40 +0000 bakerpg 473 at http://www.bakerlab.org Computational enzyme design http://www.bakerlab.org/Computational-enzyme-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=Computational+enzyme+design&amp;rft.title=Angewandte+Chemie+%28International+ed.+in+English%29&amp;rft.issn=1521-3773&amp;rft.date=2013&amp;rft.volume=52&amp;rft.issue=22&amp;rft.aulast=Kiss&amp;rft.aufirst=Gert&amp;rft_id=info%3Adoi%2F10.1002%2Fanie.201204077"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">Computational enzyme 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/132">Kiss, G.</a>, <a href="/biblio/author/854">Celebi-Ölçüm N.</a>, <a href="/biblio/author/851">Moretti R.</a>, <a href="/biblio/author/8">Baker D.</a>, & <a href="/biblio/author/442">Houk K. 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">Angewandte Chemie (International ed. in English)</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-volume">Volume</td><td class="biblio-field-contents-volume">52</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-issue">Issue</td><td class="biblio-field-contents-issue">22</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-pages">Pagination</td><td class="biblio-field-contents-pages">5700-25</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-date">Date Published</td><td class="biblio-field-contents-date">2013 May 27</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">1521-3773</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/327">Collaborative 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>Recent developments in computational chemistry and biology have come together in the "inside-out" approach to enzyme engineering. Proteins have been designed to catalyze reactions not previously accelerated in nature. Some of these proteins fold and act as catalysts, but the success rate is still low. The achievements and limitations of the current technology are highlighted and contrasted to other protein engineering techniques. On its own, computational "inside-out" design can lead to the production of catalytically active and selective proteins, but their kinetic performances fall short of natural enzymes. When combined with directed evolution, molecular dynamics simulations, and crowd-sourced structure-prediction approaches, however, computational designs can be significantly improved in terms of binding, turnover, and thermal stability.</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/anie.201204077">10.1002/anie.201204077</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/23526810?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/23526810?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/23526810?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">Angew. Chem. Int. Ed. Engl.</td> </tr> </tbody> </table> </div> Collaborative Publication Fri, 07 Jun 2013 19:00:43 +0000 bakerpg 472 at http://www.bakerlab.org The common structural architecture of Shigella flexneri and Salmonella typhimurium type three secretion needles http://www.bakerlab.org/The-common-structural-architecture-of-Shigella-flexneri-and-Salmonella-typhimurium-type-three-secretion-needles <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=The+common+structural+architecture+of+Shigella+flexneri+and+Salmonella+typhimurium+type+three+secretion+needles&amp;rft.title=PLoS+pathogens&amp;rft.issn=1553-7374&amp;rft.date=2013&amp;rft.volume=9&amp;rft.issue=3&amp;rft.spage=e1003245&amp;rft.aulast=Demers&amp;rft.aufirst=Jean-Philippe&amp;rft_id=info%3Adoi%2F10.1371%2Fjournal.ppat.1003245"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">The common structural architecture of Shigella flexneri and Salmonella typhimurium type three secretion needles</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/852">Demers, J. - P.</a>, <a href="/biblio/author/635">Sgourakis N. G.</a>, <a href="/biblio/author/780">Gupta R.</a>, <a href="/biblio/author/779">Loquet A.</a>, <a href="/biblio/author/781">Giller K.</a>, <a href="/biblio/author/782">Riedel D.</a>, <a href="/biblio/author/853">Laube B.</a>, <a href="/biblio/author/785">Kolbe M.</a>, <a href="/biblio/author/8">Baker D.</a>, <a href="/biblio/author/786">Becker S.</a>, & <a href="/biblio/author/787">Lange A.</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">PLoS pathogens</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-volume">Volume</td><td class="biblio-field-contents-volume">9</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">e1003245</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-date">Date Published</td><td class="biblio-field-contents-date">2013 Mar</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">1553-7374</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/327">Collaborative 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 Type Three Secretion System (T3SS), or injectisome, is a macromolecular infection machinery present in many pathogenic Gram-negative bacteria. It consists of a basal body, anchored in both bacterial membranes, and a hollow needle through which effector proteins are delivered into the target host cell. Two different architectures of the T3SS needle have been previously proposed. First, an atomic model of the Salmonella typhimurium needle was generated from solid-state NMR data. The needle subunit protein, PrgI, comprises a rigid-extended N-terminal segment and a helix-loop-helix motif with the N-terminus located on the outside face of the needle. Second, a model of the Shigella flexneri needle was generated from a high-resolution 7.7-Å cryo-electron microscopy density map. The subunit protein, MxiH, contains an N-terminal α-helix, a loop, another α-helix, a 14-residue-long β-hairpin (Q51-Q64) and a C-terminal α-helix, with the N-terminus facing inward to the lumen of the needle. In the current study, we carried out solid-state NMR measurements of wild-type Shigella flexneri needles polymerized in vitro and identified the following secondary structure elements for MxiH: a rigid-extended N-terminal segment (S2-T11), an α-helix (L12-A38), a loop (E39-P44) and a C-terminal α-helix (Q45-R83). Using immunogold labeling in vitro and in vivo on functional needles, we located the N-terminus of MxiH subunits on the exterior of the assembly, consistent with evolutionary sequence conservation patterns and mutagenesis data. We generated a homology model of Shigella flexneri needles compatible with both experimental data: the MxiH solid-state NMR chemical shifts and the state-of-the-art cryoEM density map. These results corroborate the solid-state NMR structure previously solved for Salmonella typhimurium PrgI needles and establish that Shigella flexneri and Salmonella typhimurium subunit proteins adopt a conserved structure and orientation in their assembled state. Our study reveals a common structural architecture of T3SS needles, essential to understand T3SS-mediated infection and develop treatments.</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/10.1371/journal.ppat.1003245">10.1371/journal.ppat.1003245</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/23555258?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/23555258?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/23555258?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">PLoS Pathog.</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/Demers_PLosPathogen_13P.pdf">Demers_PLosPathogen_13P.pdf</a></td><td>5.7 MB</td> </tr> </tbody> </table> Collaborative Publication Fri, 07 Jun 2013 18:59:38 +0000 bakerpg 471 at http://www.bakerlab.org A Pareto-optimal refinement method for protein design scaffolds http://www.bakerlab.org/A-Pareto-optimal-refinement-method-for-protein-design-scaffolds <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=A+Pareto-optimal+refinement+method+for+protein+design+scaffolds&amp;rft.title=PloS+one&amp;rft.issn=1932-6203&amp;rft.date=2013&amp;rft.volume=8&amp;rft.issue=4&amp;rft.spage=e59004&amp;rft.aulast=Niv%C3%B3n&amp;rft.aufirst=Lucas+Gregorio&amp;rft_id=info%3Adoi%2F10.1371%2Fjournal.pone.0059004"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">A Pareto-optimal refinement method for protein design scaffolds</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/850">Nivón, L. G.</a>, <a href="/biblio/author/851">Moretti R.</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">PloS one</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-volume">Volume</td><td class="biblio-field-contents-volume">8</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-issue">Issue</td><td class="biblio-field-contents-issue">4</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-pages">Pagination</td><td class="biblio-field-contents-pages">e59004</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-date">Date Published</td><td class="biblio-field-contents-date">2013</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">1932-6203</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/327">Collaborative 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 of protein function involves a search for amino acids with the lowest energy subject to a set of constraints specifying function. In many cases a set of natural protein backbone structures, or "scaffolds", are searched to find regions where functional sites (an enzyme active site, ligand binding pocket, protein-protein interaction region, etc.) can be placed, and the identities of the surrounding amino acids are optimized to satisfy functional constraints. Input native protein structures almost invariably have regions that score very poorly with the design force field, and any design based on these unmodified structures may result in mutations away from the native sequence solely as a result of the energetic strain. Because the input structure is already a stable protein, it is desirable to keep the total number of mutations to a minimum and to avoid mutations resulting from poorly-scoring input structures. Here we describe a protocol using cycles of minimization with combined backbone/sidechain restraints that is Pareto-optimal with respect to RMSD to the native structure and energetic strain reduction. The protocol should be broadly useful in the preparation of scaffold libraries for functional site design.</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/10.1371/journal.pone.0059004">10.1371/journal.pone.0059004</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/23565140?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/23565140?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/23565140?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">PLoS ONE</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/Nivon_pone0059004_13U.pdf">Nivon_pone0059004_13U.pdf</a></td><td>180.73 KB</td> </tr> </tbody> </table> Collaborative Publication Fri, 07 Jun 2013 18:58:00 +0000 bakerpg 470 at http://www.bakerlab.org Structural and energetic basis of folded-protein transport by the FimD usher http://www.bakerlab.org/Structural-and-energetic-basis-of-folded-protein-transport-by-the-FimD-usher <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=Structural+and+energetic+basis+of+folded-protein+transport+by+the+FimD+usher&amp;rft.title=Nature&amp;rft.issn=1476-4687&amp;rft.date=2013&amp;rft.volume=496&amp;rft.issue=7444&amp;rft.aulast=Geibel&amp;rft.aufirst=Sebastian&amp;rft_id=info%3Adoi%2F10.1038%2Fnature12007"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">Structural and energetic basis of folded-protein transport by the FimD usher</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/846">Geibel, S.</a>, <a href="/biblio/author/847">Procko E.</a>, <a href="/biblio/author/848">Hultgren S. J.</a>, <a href="/biblio/author/8">Baker D.</a>, & <a href="/biblio/author/849">Waksman G.</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">496</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-issue">Issue</td><td class="biblio-field-contents-issue">7444</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-pages">Pagination</td><td class="biblio-field-contents-pages">243-6</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-date">Date Published</td><td class="biblio-field-contents-date">2013 Apr 11</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/327">Collaborative Publication</a>, <a href="/biblio/keyword/3">Crystallography, X-Ray</a>, <a href="/biblio/keyword/200">Escherichia coli</a>, <a href="/biblio/keyword/186">Escherichia coli Proteins</a>, <a href="/biblio/keyword/510">Fimbriae Proteins</a>, <a href="/biblio/keyword/511">Fimbriae, Bacterial</a>, <a href="/biblio/keyword/10">Models, Molecular</a>, <a href="/biblio/keyword/29">Protein Conformation</a>, <a href="/biblio/keyword/23">Protein Folding</a>, <a href="/biblio/keyword/512">Protein Stability</a>, <a href="/biblio/keyword/337">Protein Transport</a>, <a href="/biblio/keyword/55">Thermodynamics</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>Type 1 pili, produced by uropathogenic Escherichia coli, are multisubunit fibres crucial in recognition of and adhesion to host tissues. During pilus biogenesis, subunits are recruited to an outer membrane assembly platform, the FimD usher, which catalyses their polymerization and mediates pilus secretion. The recent determination of the crystal structure of an initiation complex provided insight into the initiation step of pilus biogenesis resulting in pore activation, but very little is known about the elongation steps that follow. Here, to address this question, we determine the structure of an elongation complex in which the tip complex assembly composed of FimC, FimF, FimG and FimH passes through FimD. This structure demonstrates the conformational changes required to prevent backsliding of the nascent pilus through the FimD pore and also reveals unexpected properties of the usher pore. We show that the circular binding interface between the pore lumen and the folded substrate participates in transport by defining a low-energy pathway along which the nascent pilus polymer is guided during secretion.</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/nature12007">10.1038/nature12007</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/23579681?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/23579681?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/23579681?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/Geibel_nature12007_13S.pdf">Geibel_nature12007_13S.pdf</a></td><td>1.18 MB</td> </tr> </tbody> </table> Collaborative Publication Fri, 07 Jun 2013 18:55:29 +0000 bakerpg 469 at http://www.bakerlab.org A Refined Model of the Prototypical Salmonella SPI-1 T3SS Basal Body Reveals the Molecular Basis for Its Assembly http://www.bakerlab.org/A-Refined-Model-of-the-Prototypical-Salmonella-SPI-1-T3SS-Basal-Body-Reveals-the-Molecular-Basis-for-Its-Assembly <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=A+Refined+Model+of+the+Prototypical+Salmonella+SPI-1+T3SS+Basal+Body+Reveals+the+Molecular+Basis+for+Its+Assembly&amp;rft.title=PLoS+pathogens&amp;rft.issn=1553-7374&amp;rft.date=2013&amp;rft.volume=9&amp;rft.issue=4&amp;rft.spage=e1003307&amp;rft.aulast=Bergeron&amp;rft.aufirst=Julien&amp;rft_id=info%3Adoi%2F10.1371%2Fjournal.ppat.1003307"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">A Refined Model of the Prototypical Salmonella SPI-1 T3SS Basal Body Reveals the Molecular Basis for Its Assembly</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/843">Bergeron, J. R. C.</a>, <a href="/biblio/author/844">Worrall L. J.</a>, <a href="/biblio/author/635">Sgourakis N. G.</a>, <a href="/biblio/author/191">DiMaio F.</a>, <a href="/biblio/author/399">Pfuetzner R. A.</a>, <a href="/biblio/author/845">Felise H. B.</a>, <a href="/biblio/author/469">Vuckovic M.</a>, <a href="/biblio/author/471">Yu A. C.</a>, <a href="/biblio/author/405">Miller S. I.</a>, <a href="/biblio/author/8">Baker D.</a>, & <a href="/biblio/author/402">Strynadka N. C. J.</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">PLoS pathogens</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-volume">Volume</td><td class="biblio-field-contents-volume">9</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-issue">Issue</td><td class="biblio-field-contents-issue">4</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-pages">Pagination</td><td class="biblio-field-contents-pages">e1003307</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-date">Date Published</td><td class="biblio-field-contents-date">2013 Apr</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">1553-7374</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/327">Collaborative 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 T3SS injectisome is a syringe-shaped macromolecular assembly found in pathogenic Gram-negative bacteria that allows for the direct delivery of virulence effectors into host cells. It is composed of a "basal body", a lock-nut structure spanning both bacterial membranes, and a "needle" that protrudes away from the bacterial surface. A hollow channel spans throughout the apparatus, permitting the translocation of effector proteins from the bacterial cytosol to the host plasma membrane. The basal body is composed largely of three membrane-embedded proteins that form oligomerized concentric rings. Here, we report the crystal structures of three domains of the prototypical Salmonella SPI-1 basal body, and use a new approach incorporating symmetric flexible backbone docking and EM data to produce a model for their oligomeric assembly. The obtained models, validated by biochemical and in vivo assays, reveal the molecular details of the interactions driving basal body assembly, and notably demonstrate a conserved oligomerization mechanism.</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/10.1371/journal.ppat.1003307">10.1371/journal.ppat.1003307</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/23633951?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/23633951?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/23633951?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">PLoS Pathog.</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/Bergeron_ppat1003307_13T.pdf">Bergeron_ppat1003307_13T.pdf</a></td><td>1.18 MB</td> </tr> </tbody> </table> Collaborative Publication Fri, 07 Jun 2013 18:53:06 +0000 bakerpg 468 at http://www.bakerlab.org Rational HIV immunogen design to target specific germline B cell receptors http://www.bakerlab.org/Rational-HIV-immunogen-design-to-target-specific-germline-B-cell-receptors <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=Rational+HIV+immunogen+design+to+target+specific+germline+B+cell+receptors&amp;rft.title=Science+%28New+York%2C+N.Y.%29&amp;rft.issn=1095-9203&amp;rft.date=2013&amp;rft.volume=340&amp;rft.issue=6133&amp;rft.aulast=Jardine&amp;rft.aufirst=Joseph&amp;rft_id=info%3Adoi%2F10.1126%2Fscience.1234150"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">Rational HIV immunogen design to target specific germline B cell receptors</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/831">Jardine, J.</a>, <a href="/biblio/author/718">Julien J. - P.</a>, <a href="/biblio/author/832">Menis S.</a>, <a href="/biblio/author/833">Ota T.</a>, <a href="/biblio/author/363">Kalyuzhniy O.</a>, <a href="/biblio/author/834">McGuire A.</a>, <a href="/biblio/author/835">Sok D.</a>, <a href="/biblio/author/710">Huang P. - S.</a>, <a href="/biblio/author/836">MacPherson S.</a>, <a href="/biblio/author/837">Jones M.</a>, <a href="/biblio/author/838">Nieusma T.</a>, <a href="/biblio/author/839">Mathison J.</a>, <a href="/biblio/author/8">Baker D.</a>, <a href="/biblio/author/840">Ward A. B.</a>, <a href="/biblio/author/841">Burton D. R.</a>, <a href="/biblio/author/364">Stamatatos L.</a>, <a href="/biblio/author/842">Nemazee D.</a>, <a href="/biblio/author/634">Wilson I. A.</a>, & <a href="/biblio/author/127">Schief W. R.</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">Science (New York, N.Y.)</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-volume">Volume</td><td class="biblio-field-contents-volume">340</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-issue">Issue</td><td class="biblio-field-contents-issue">6133</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-pages">Pagination</td><td class="biblio-field-contents-pages">711-6</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-date">Date Published</td><td class="biblio-field-contents-date">2013 May 10</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">1095-9203</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/501">AIDS Vaccines</a>, <a href="/biblio/keyword/12">Amino Acid Sequence</a>, <a href="/biblio/keyword/64">Animals</a>, <a href="/biblio/keyword/468">Antibodies, Neutralizing</a>, <a href="/biblio/keyword/471">Antigens, CD4</a>, <a href="/biblio/keyword/502">B-Lymphocytes</a>, <a href="/biblio/keyword/327">Collaborative Publication</a>, <a href="/biblio/keyword/3">Crystallography, X-Ray</a>, <a href="/biblio/keyword/121">DNA Mutational Analysis</a>, <a href="/biblio/keyword/503">Germ Cells</a>, <a href="/biblio/keyword/472">HIV Envelope Protein gp120</a>, <a href="/biblio/keyword/504">HIV Infections</a>, <a href="/biblio/keyword/505">HIV-1</a>, <a href="/biblio/keyword/128">Humans</a>, <a href="/biblio/keyword/506">Macaca</a>, <a href="/biblio/keyword/143">Mice</a>, <a href="/biblio/keyword/507">Models, Animal</a>, <a href="/biblio/keyword/19">Molecular Sequence Data</a>, <a href="/biblio/keyword/508">Nanoparticles</a>, <a href="/biblio/keyword/109">Protein Engineering</a>, <a href="/biblio/keyword/42">Protein Structure, Tertiary</a>, <a href="/biblio/keyword/509">Receptors, Antigen, B-Cell</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>Vaccine development to induce broadly neutralizing antibodies (bNAbs) against HIV-1 is a global health priority. Potent VRC01-class bNAbs against the CD4 binding site of HIV gp120 have been isolated from HIV-1-infected individuals; however, such bNAbs have not been induced by vaccination. Wild-type gp120 proteins lack detectable affinity for predicted germline precursors of VRC01-class bNAbs, making them poor immunogens to prime a VRC01-class response. We employed computation-guided, in vitro screening to engineer a germline-targeting gp120 outer domain immunogen that binds to multiple VRC01-class bNAbs and germline precursors, and elucidated germline binding crystallographically. When multimerized on nanoparticles, this immunogen (eOD-GT6) activates germline and mature VRC01-class B cells. Thus, eOD-GT6 nanoparticles have promise as a vaccine prime. In principle, germline-targeting strategies could be applied to other epitopes and pathogens.</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/10.1126/science.1234150">10.1126/science.1234150</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/23539181?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/23539181?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/23539181?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">Science</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/Jardine_Science_13O.pdf">Jardine_Science_13O.pdf</a></td><td>3.51 MB</td> </tr> </tbody> </table> Collaborative Publication Thu, 06 Jun 2013 22:12:45 +0000 bakerpg 467 at http://www.bakerlab.org Atomic model of the type III secretion system needle http://www.bakerlab.org/node/443 <div id="biblio-node"><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Adc&amp;rft.title=Atomic+model+of+the+type+III+secretion+system+needle&amp;rft.date=2012&amp;rft.aulast=Loquet&amp;rft.aufirst=Antoine&amp;rft_id=info%3Adoi%2F10.1038%2Fnature11079"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">Atomic model of the type III secretion system needle</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-type">Publication Type</td><td class="biblio-field-contents-type">Manuscript</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/779">Loquet, A.</a>, <a href="/biblio/author/635">Sgourakis N. G.</a>, <a href="/biblio/author/780">Gupta R.</a>, <a href="/biblio/author/781">Giller K.</a>, <a href="/biblio/author/782">Riedel D.</a>, <a href="/biblio/author/783">Goosmann C.</a>, <a href="/biblio/author/784">Griesinger C.</a>, <a href="/biblio/author/785">Kolbe M.</a>, <a href="/biblio/author/8">Baker D.</a>, <a href="/biblio/author/786">Becker S.</a>, & <a href="/biblio/author/787">Lange A.</a></td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-secondary-title">Collection Title</td><td class="biblio-field-contents-secondary-title">Nature</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/327">Collaborative Publication</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>Pathogenic bacteria using a type III secretion system (T3SS) to manipulate host cells cause many different infections including Shigella dysentery, typhoid fever, enterohaemorrhagic colitis and bubonic plague. An essential part of the T3SS is a hollow needlelike protein filament through which effector proteins are injected into eukaryotic host cells3–6. Currently, the three-dimensional structure of the needle is unknown because it is not amenable to X-ray crystallography and solution NMR, as a result of its inherent non-crystallinity and insolubility. Cryo-electron microscopy combined with crystal or solution NMRsubunit structures has recently provided a powerful hybrid approach for studying supramolecular assemblies7–12, esulting in low-resolution and medium-resolution models13–17. However, such approaches cannot deliver atomic details, especially of the crucial subunit–subunit interfaces, because of the limited cryo-electron microscopic resolution obtained in these studies. Here we report an alternative approach combining recombinant wild-type needle production, solid-state NMR, electron microscopy and Rosetta modelling to reveal the supramolecular interfaces and ultimately the complete atomic structure of the Salmonella typhimurium T3SS needle. We show that the 80-residue subunits form a right-handed helical assembly with roughly 11 subunits per two turns, similar to that of the flagellar filament of S. typhimurium. In contrast to established models of the needle in which the amino terminus of the protein subunit was assumed to be a-helical and positioned inside the needle, our model reveals an extended amino-terminal domain that is positioned on the surface of the needle, while the highly conserved carboxy terminus points towards the lumen. </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/10.1038/nature11079">10.1038/nature11079</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/sgourakis12A.pdf">sgourakis12A.pdf</a></td><td>1015.62 KB</td> </tr> </tbody> </table> Collaborative Publication Wed, 23 May 2012 19:13:29 +0000 bakerpg 443 at http://www.bakerlab.org Structural basis for gating charge movement in the voltage sensor of a sodium channel http://www.bakerlab.org/node/433 <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=Structural+basis+for+gating+charge+movement+in+the+voltage+sensor+of+a+sodium+channel&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=2&amp;rft.aulast=Yarov-Yarovoy&amp;rft.aufirst=Vladimir"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">Structural basis for gating charge movement in the voltage sensor of a sodium channel</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/263">Yarov-Yarovoy, V.</a>, <a href="/biblio/author/771">DeCaen P. G.</a>, <a href="/biblio/author/772">Westenbroek R. E.</a>, <a href="/biblio/author/773">Pan C. - Y.</a>, <a href="/biblio/author/774">Scheuer T.</a>, <a href="/biblio/author/8">Baker D.</a>, & <a href="/biblio/author/264">Catterall W. A.</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">2</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-pages">Pagination</td><td class="biblio-field-contents-pages">E93-102</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-date">Date Published</td><td class="biblio-field-contents-date">2012 Jan 10</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/327">Collaborative 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>Voltage-dependent gating of ion channels is essential for electrical signaling in excitable cells, but the structural basis for voltage sensor function is unknown. We constructed high-resolution structural models of resting, intermediate, and activated states of the voltage-sensing domain of the bacterial sodium channel NaChBac using the Rosetta modeling method, crystal structures of related channels, and experimental data showing state-dependent interactions between the gating charge-carrying arginines in the S4 segment and negatively charged residues in neighboring transmembrane segments. The resulting structural models illustrate a network of ionic and hydrogen-bonding interactions that are made sequentially by the gating charges as they move out under the influence of the electric field. The S4 segment slides 6-8 Å outward through a narrow groove formed by the S1, S2, and S3 segments, rotates ∼30°, and tilts sideways at a pivot point formed by a highly conserved hydrophobic region near the middle of the voltage sensor. The S4 segment has a 3(10)-helical conformation in the narrow inner gating pore, which allows linear movement of the gating charges across the inner one-half of the membrane. Conformational changes of the intracellular one-half of S4 during activation are rigidly coupled to lateral movement of the S4-S5 linker, which could induce movement of the S5 and S6 segments and open the intracellular gate of the pore. We confirmed the validity of these structural models by comparing with a high-resolution structure of a NaChBac homolog and showing predicted molecular interactions of hydrophobic residues in the S4 segment in disulfide-locking studies.</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/yarov-yarovoy12A.pdf">yarov-yarovoy12A.pdf</a></td><td>2.46 MB</td> </tr> </tbody> </table> Collaborative Publication Wed, 15 Feb 2012 20:02:56 +0000 bakerpg 433 at http://www.bakerlab.org Structure of the Ultra-High-Affinity Colicin E2 DNase-Im2 Complex http://www.bakerlab.org/node/432 <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=Structure+of+the+Ultra-High-Affinity+Colicin+E2+DNase-Im2+Complex&amp;rft.title=Journal+of+molecular+biology&amp;rft.issn=1089-8638&amp;rft.date=2012&amp;rft.aulast=Wojdyla&amp;rft.aufirst=Justyna+Aleksandra"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">Structure of the Ultra-High-Affinity Colicin E2 DNase-Im2 Complex</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/770">Wojdyla, J. A.</a>, <a href="/biblio/author/159">Fleishman S. J.</a>, <a href="/biblio/author/8">Baker D.</a>, & <a href="/biblio/author/314">Kleanthous C.</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-date">Date Published</td><td class="biblio-field-contents-date">2012 Jan 27</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/327">Collaborative 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>How proteins achieve high-affinity binding to a specific protein partner while simultaneously excluding all others is a major biological problem that has important implications for protein design. We report the crystal structure of the ultra-high-affinity protein-protein complex between the endonuclease domain of colicin E2 and its cognate immunity (Im) protein, Im2 (K(d)∼10(-)(15) M), which, by comparison to previous structural and biophysical data, provides unprecedented insight into how high affinity and selectivity are achieved in this model family of protein complexes. Our study pinpoints the role of structured water molecules in conjoining hotspot residues that govern stability with residues that control selectivity. A key finding is that a single residue, which in a noncognate context massively destabilizes the complex through frustration, does not participate in specificity directly but rather acts as an organizing center for a multitude of specificity interactions across the interface, many of which are water mediated.</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/wojdyla12A.pdf">wojdyla12A.pdf</a></td><td>2.09 MB</td> </tr> </tbody> </table> Collaborative Publication Wed, 15 Feb 2012 20:01:04 +0000 bakerpg 432 at http://www.bakerlab.org An engineered microbial platform for direct biofuel production from brown macroalgae http://www.bakerlab.org/node/431 <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=An+engineered+microbial+platform+for+direct+biofuel+production+from+brown+macroalgae&amp;rft.title=Science&amp;rft.issn=1095-9203&amp;rft.date=2012&amp;rft.volume=335&amp;rft.issue=6066&amp;rft.aulast=Wargacki&amp;rft.aufirst=Adam"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">An engineered microbial platform for direct biofuel production from brown macroalgae</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/758">Wargacki, A. J.</a>, <a href="/biblio/author/759">Leonard E.</a>, <a href="/biblio/author/760">Win M. N.</a>, <a href="/biblio/author/761">Regitsky D. D.</a>, <a href="/biblio/author/762">Santos C. N. S.</a>, <a href="/biblio/author/763">Kim P. B.</a>, <a href="/biblio/author/764">Cooper S. R.</a>, <a href="/biblio/author/765">Raisner R. M.</a>, <a href="/biblio/author/766">Herman A.</a>, <a href="/biblio/author/767">Sivitz A. B.</a>, <a href="/biblio/author/768">Lakshmanaswamy A.</a>, <a href="/biblio/author/769">Kashiyama Y.</a>, <a href="/biblio/author/8">Baker D.</a>, & <a href="/biblio/author/474">Yoshikuni Y.</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">Science</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-volume">Volume</td><td class="biblio-field-contents-volume">335</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-issue">Issue</td><td class="biblio-field-contents-issue">6066</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-pages">Pagination</td><td class="biblio-field-contents-pages">308-13</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-date">Date Published</td><td class="biblio-field-contents-date">2012 Jan 20</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">1095-9203</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/476">Alginates</a>, <a href="/biblio/keyword/13">Bacterial Proteins</a>, <a href="/biblio/keyword/477">Biofuels</a>, <a href="/biblio/keyword/435">Biological Transport</a>, <a href="/biblio/keyword/478">Biomass</a>, <a href="/biblio/keyword/132">Carrier Proteins</a>, <a href="/biblio/keyword/327">Collaborative Publication</a>, <a href="/biblio/keyword/200">Escherichia coli</a>, <a href="/biblio/keyword/479">Ethanol</a>, <a href="/biblio/keyword/480">Fermentation</a>, <a href="/biblio/keyword/481">Genes, Bacterial</a>, <a href="/biblio/keyword/482">Glucose</a>, <a href="/biblio/keyword/483">Glucuronic Acid</a>, <a href="/biblio/keyword/484">Hexuronic Acids</a>, <a href="/biblio/keyword/485">Lactic Acid</a>, <a href="/biblio/keyword/486">Mannitol</a>, <a href="/biblio/keyword/487">Metabolic Engineering</a>, <a href="/biblio/keyword/488">Metabolic Networks and Pathways</a>, <a href="/biblio/keyword/403">Open Reading Frames</a>, <a href="/biblio/keyword/489">Phaeophyta</a>, <a href="/biblio/keyword/490">Polysaccharide-Lyases</a>, <a href="/biblio/keyword/491">Seaweed</a>, <a href="/biblio/keyword/492">Vibrio</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>Prospecting macroalgae (seaweeds) as feedstocks for bioconversion into biofuels and commodity chemical compounds is limited primarily by the availability of tractable microorganisms that can metabolize alginate polysaccharides. Here, we present the discovery of a 36-kilo-base pair DNA fragment from Vibrio splendidus encoding enzymes for alginate transport and metabolism. The genomic integration of this ensemble, together with an engineered system for extracellular alginate depolymerization, generated a microbial platform that can simultaneously degrade, uptake, and metabolize alginate. When further engineered for ethanol synthesis, this platform enables bioethanol production directly from macroalgae via a consolidated process, achieving a titer of 4.7% volume/volume and a yield of 0.281 weight ethanol/weight dry macroalgae (equivalent to ~80% of the maximum theoretical yield from the sugar composition in macroalgae).</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">Science</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/wargacki12A.pdf">wargacki12A.pdf</a></td><td>1.41 MB</td> </tr> </tbody> </table> Collaborative Publication Wed, 15 Feb 2012 19:57:00 +0000 bakerpg 431 at http://www.bakerlab.org Protein Structure Determination from Pseudocontact Shifts Using ROSETTA http://www.bakerlab.org/node/429 <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=Protein+Structure+Determination+from+Pseudocontact+Shifts+Using+ROSETTA&amp;rft.title=Journal+of+molecular+biology&amp;rft.issn=1089-8638&amp;rft.date=2012&amp;rft.aulast=Schmitz&amp;rft.aufirst=Christophe"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">Protein Structure Determination from Pseudocontact Shifts Using 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/749">Schmitz, C.</a>, <a href="/biblio/author/169">Vernon R.</a>, <a href="/biblio/author/750">Otting G.</a>, <a href="/biblio/author/8">Baker D.</a>, & <a href="/biblio/author/751">Huber T.</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-date">Date Published</td><td class="biblio-field-contents-date">2012 Jan 18</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/327">Collaborative 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>Paramagnetic metal ions generate pseudocontact shifts (PCSs) in nuclear magnetic resonance spectra that are manifested as easily measurable changes in chemical shifts. Metals can be incorporated into proteins through metal binding tags, and PCS data constitute powerful long-range restraints on the positions of nuclear spins relative to the coordinate system of the magnetic susceptibility anisotropy tensor (Δχ-tensor) of the metal ion. We show that three-dimensional structures of proteins can reliably be determined using PCS data from a single metal binding site combined with backbone chemical shifts. The program PCS-ROSETTA automatically determines the Δχ-tensor and metal position from the PCS data during the structure calculations, without any prior knowledge of the protein structure. The program can determine structures accurately for proteins of up to 150 residues, offering a powerful new approach to protein structure determination that relies exclusively on readily measurable backbone chemical shifts and easily discriminates between correctly and incorrectly folded conformations.</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/schmitz12A.pdf">schmitz12A.pdf</a></td><td>1.03 MB</td> </tr> </tbody> </table> Collaborative Publication Wed, 15 Feb 2012 19:53:41 +0000 bakerpg 429 at http://www.bakerlab.org Blind testing of routine, fully automated determination of protein structures from NMR data http://www.bakerlab.org/node/428 <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=Blind+testing+of+routine%2C+fully+automated+determination+of+protein+structures+from+NMR+data&amp;rft.title=Structure&amp;rft.issn=1878-4186&amp;rft.date=2012&amp;rft.volume=20&amp;rft.issue=2&amp;rft.aulast=Rosato&amp;rft.aufirst=Antonio"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">Blind testing of routine, fully automated determination of protein structures from NMR data</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/489">Rosato, A.</a>, <a href="/biblio/author/374">Aramini J. M.</a>, <a href="/biblio/author/738">Arrowsmith C.</a>, <a href="/biblio/author/490">Bagaria A.</a>, <a href="/biblio/author/8">Baker D.</a>, <a href="/biblio/author/492">Cavalli A.</a>, <a href="/biblio/author/493">Doreleijers J. F.</a>, <a href="/biblio/author/57">Eletsky A.</a>, <a href="/biblio/author/494">Giachetti A.</a>, <a href="/biblio/author/495">Guerry P.</a>, <a href="/biblio/author/739">Gutmanas A.</a>, <a href="/biblio/author/496">Güntert P.</a>, <a href="/biblio/author/740">He Y.</a>, <a href="/biblio/author/497">Herrmann T.</a>, <a href="/biblio/author/390">Huang Y. J.</a>, <a href="/biblio/author/741">Jaravine V.</a>, <a href="/biblio/author/498">Jonker H. R. A.</a>, <a href="/biblio/author/59">Kennedy M. A.</a>, <a href="/biblio/author/50" class="biblio-local-author">Lange O. F.</a>, <a href="/biblio/author/55">Liu G.</a>, <a href="/biblio/author/499">Malliavin T. E.</a>, <a href="/biblio/author/742">Mani R.</a>, <a href="/biblio/author/391">Mao B.</a>, <a href="/biblio/author/61">Montelione G. T.</a>, <a href="/biblio/author/500">Nilges M.</a>, <a href="/biblio/author/51">Rossi P.</a>, <a href="/biblio/author/501">van der Schot G.</a>, <a href="/biblio/author/743">Schwalbe H.</a>, <a href="/biblio/author/744">Szyperski T. A.</a>, <a href="/biblio/author/745">Vendruscolo M.</a>, <a href="/biblio/author/169">Vernon R.</a>, <a href="/biblio/author/502">Vranken W. F.</a>, <a href="/biblio/author/746">de Vries S.</a>, <a href="/biblio/author/503">Vuister G. W.</a>, <a href="/biblio/author/747">Wu B.</a>, <a href="/biblio/author/748">Yang Y.</a>, & <a href="/biblio/author/504">Bonvin A. M. J. J.</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</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-volume">Volume</td><td class="biblio-field-contents-volume">20</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">227-36</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-date">Date Published</td><td class="biblio-field-contents-date">2012 Feb 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/327">Collaborative 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 protocols currently used for protein structure determination by nuclear magnetic resonance (NMR) depend on the determination of a large number of upper distance limits for proton-proton pairs. Typically, this task is performed manually by an experienced researcher rather than automatically by using a specific computer program. To assess whether it is indeed possible to generate in a fully automated manner NMR structures adequate for deposition in the Protein Data Bank, we gathered 10 experimental data sets with unassigned nuclear Overhauser effect spectroscopy (NOESY) peak lists for various proteins of unknown structure, computed structures for each of them using different, fully automatic programs, and compared the results to each other and to the manually solved reference structures that were not available at the time the data were provided. This constitutes a stringent "blind" assessment similar to the CASP and CAPRI initiatives. This study demonstrates the feasibility of routine, fully automated protein structure determination by NMR.</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> Collaborative Publication Wed, 15 Feb 2012 19:51:44 +0000 bakerpg 428 at http://www.bakerlab.org The acidic transcription activator Gcn4 binds the mediator subunit Gal11/Med15 using a simple protein interface forming a fuzzy complex http://www.bakerlab.org/node/426 <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=The+acidic+transcription+activator+Gcn4+binds+the+mediator+subunit+Gal11%2FMed15+using+a+simple+protein+interface+forming+a+fuzzy+complex&amp;rft.title=Molecular+cell&amp;rft.issn=1097-4164&amp;rft.date=2011&amp;rft.volume=44&amp;rft.issue=6&amp;rft.aulast=Brzovic&amp;rft.aufirst=Peter"></span><table> <tbody> <tr class="odd"><td class="biblio-row-title biblio-field-title-title">Title</td><td class="biblio-field-contents-title">The acidic transcription activator Gcn4 binds the mediator subunit Gal11/Med15 using a simple protein interface forming a fuzzy complex</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">2011</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/723">Brzovic, P. S.</a>, <a href="/biblio/author/724">Heikaus C. C.</a>, <a href="/biblio/author/725">Kisselev L.</a>, <a href="/biblio/author/169">Vernon R.</a>, <a href="/biblio/author/726">Herbig E.</a>, <a href="/biblio/author/727">Pacheco D.</a>, <a href="/biblio/author/728">Warfield L.</a>, <a href="/biblio/author/729">Littlefield P.</a>, <a href="/biblio/author/8">Baker D.</a>, <a href="/biblio/author/83">Klevit R. E.</a>, & <a href="/biblio/author/730">Hahn 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">Molecular cell</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-volume">Volume</td><td class="biblio-field-contents-volume">44</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-issue">Issue</td><td class="biblio-field-contents-issue">6</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-pages">Pagination</td><td class="biblio-field-contents-pages">942-53</td> </tr> <tr class="odd"><td class="biblio-row-title biblio-field-title-date">Date Published</td><td class="biblio-field-contents-date">2011 Dec 23</td> </tr> <tr class="even"><td class="biblio-row-title biblio-field-title-issn">ISSN</td><td class="biblio-field-contents-issn">1097-4164</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/327">Collaborative 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 structural basis for binding of the acidic transcription activator Gcn4 and one activator-binding domain of the Mediator subunit Gal11/Med15 was examined by NMR. Gal11 activator-binding domain 1 has a four-helix fold with a small shallow hydrophobic cleft at its center. In the bound complex, eight residues of Gcn4 adopt a helical conformation, allowing three Gcn4 aromatic/aliphatic residues to insert into the Gal11 cleft. The protein-protein interface is dynamic and surprisingly simple, involving only hydrophobic interactions. This allows Gcn4 to bind Gal11 in multiple conformations and orientations, an example of a "fuzzy" complex, where the Gcn4-Gal11 interface cannot be described by a single conformation. Gcn4 uses a similar mechanism to bind two other unrelated activator-binding domains. Functional studies in yeast show the importance of residues at the protein interface, define the minimal requirements for a functional activator, and suggest a mechanism by which activators bind to multiple unrelated targets.</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/22195967?dopt=Abstract" title="http://www.ncbi.nlm.nih.gov/pubmed/22195967?dopt=Abstract">http://www.ncbi.nlm.nih.gov/pubmed/22195967?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">Mol. Cell</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/brzovic11A.pdf">brzovic11A.pdf</a></td><td>1.14 MB</td> </tr> </tbody> </table> Collaborative Publication Wed, 15 Feb 2012 19:48:40 +0000 bakerpg 426 at http://www.bakerlab.org