@article{Pyles2019,

title = {Controlling protein assembly on inorganic crystals through designed protein interfaces},

author = {Harley Pyles and Shuai Zhang and James J. De Yoreo and David Baker },

url = {https://www.nature.com/articles/s41586-019-1361-6

https://www.bakerlab.org/wp-content/uploads/2019/07/2019_Pyles_MicaBinder.pdf},

doi = {10.1038/s41586-019-1361-6},

year  = {2019},

date = {2019-07-10},

journal = {Nature},

abstract = {The ability of proteins and other macromolecules to interact with inorganic surfaces is essential to biological function. The proteins involved in these interactions are highly charged and often rich in carboxylic acid side chains, but the structures of most protein–inorganic interfaces are unknown. We explored the possibility of systematically designing structured protein–mineral interfaces, guided by the example of ice-binding proteins, which present arrays of threonine residues (matched to the ice lattice) that order clathrate waters into an ice-like structure6. Here we design proteins displaying arrays of up to 54 carboxylate residues geometrically matched to the potassium ion (K+) sublattice on muscovite mica (001). At low K+ concentration, individual molecules bind independently to mica in the designed orientations, whereas at high K+ concentration, the designs form two-dimensional liquid-crystal phases, which accentuate the inherent structural bias in the muscovite lattice to produce protein arrays ordered over tens of millimetres. Incorporation of designed protein–protein interactions preserving the match between the proteins and the K+ lattice led to extended self-assembled structures on mica: designed end-to-end interactions produced micrometre-long single-protein-diameter wires and a designed trimeric interface yielded extensive honeycomb arrays. The nearest-neighbour distances in these hexagonal arrays could be set digitally between 7.5 and 15.9 nanometres with 2.1-nanometre selectivity by changing the number of repeat units in the monomer. These results demonstrate that protein–inorganic lattice interactions can be systematically programmed and set the stage for designing protein–inorganic hybrid materials.



},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Shen2018,

title = {De novo design of self-assembling helical protein filaments},

author = {Shen, Hao and Fallas, Jorge A. and Lynch, Eric and Sheffler, William and Parry, Bradley and Jannetty, Nicholas and Decarreau, Justin and Wagenbach, Michael and Vicente, Juan Jesus and Chen, Jiajun and Wang, Lei and Dowling, Quinton and Oberdorfer, Gustav and Stewart, Lance and Wordeman, Linda and De Yoreo, James and Jacobs-Wagner, Christine and Kollman, Justin and Baker, David},

url = {http://science.sciencemag.org/content/362/6415/705

https://www.bakerlab.org/wp-content/uploads/2018/12/Shen2018_filaments.pdf},

doi = {10.1126/science.aau3775},

issn = {0036-8075},

year  = {2018},

date = {2018-11-09},

journal = {Science},

volume = {362},

number = {6415},

pages = {705–709},

abstract = {There has been some success in designing stable peptide filaments; however, mimicking the reversible assembly of many natural protein filaments is challenging. Dynamic filaments usually comprise independently folded and asymmetric proteins and using such building blocks requires the design of multiple intermonomer interfaces. Shen et al. report the design of self-assembling helical filaments based on previously designed stable repeat proteins. The filaments are micron scale, and their diameter can be tuned by varying the number of repeats in the monomer. Anchor and capping units, built from monomers that lack an interaction interface, can be used to control assembly and disassembly.Science, this issue p. 705We describe a general computational approach to designing self-assembling helical filaments from monomeric proteins and use this approach to design proteins that assemble into micrometer-scale filaments with a wide range of geometries in vivo and in vitro. Cryo{textendash}electron microscopy structures of six designs are close to the computational design models. The filament building blocks are idealized repeat proteins, and thus the diameter of the filaments can be systematically tuned by varying the number of repeat units. The assembly and disassembly of the filaments can be controlled by engineered anchor and capping units built from monomers lacking one of the interaction surfaces. The ability to generate dynamic, highly ordered structures that span micrometers from protein monomers opens up possibilities for the fabrication of new multiscale metamaterials.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Butterfield2017,

title = {Evolution of a designed protein assembly encapsulating its own RNA genome},

author = {Butterfield, Gabriel L.*

and Lajoie, Marc J.*

and Gustafson, Heather H.

and Sellers, Drew L.

and Nattermann, Una

and Ellis, Daniel

and Bale, Jacob B.

and Ke, Sharon

and Lenz, Garreck H.

and Yehdego, Angelica

and Ravichandran, Rashmi

and Pun, Suzie H.

and King, Neil P.

and Baker, David},

url = {http://dx.doi.org/10.1038/nature25157

https://www.bakerlab.org/wp-content/uploads/2017/12/Nature_Butterfield_et_al_2017.pdf},

doi = {10.1038/nature25157},

issn = {1476-4687},

year  = {2017},

date = {2017-12-13},

journal = {Nature},

abstract = {The challenges of evolution in a complex biochemical environment, coupling genotype to phenotype and protecting the genetic material, are solved elegantly in biological systems by the encapsulation of nucleic acids. In the simplest examples, viruses use capsids to surround their genomes. Although these naturally occurring systems have been modified to change their tropism and to display proteins or peptides, billions of years of evolution have favoured efficiency at the expense of modularity, making viral capsids difficult to engineer. Synthetic systems composed of non-viral proteins could provide a ‘blank slate’ to evolve desired properties for drug delivery and other biomedical applications, while avoiding the safety risks and engineering challenges associated with viruses. Here we create synthetic nucleocapsids, which are computationally designed icosahedral protein assemblies with positively charged inner surfaces that can package their own full-length mRNA genomes. We explore the ability of these nucleocapsids to evolve virus-like properties by generating diversified populations using Escherichia coli as an expression host. Several generations of evolution resulted in markedly improved genome packaging (more than 133-fold), stability in blood (from less than 3.7% to 71% of packaged RNA protected after 6hours of treatment), and in vivo circulation time (from less than 5minutes to approximately 4.5hours). The resulting synthetic nucleocapsids package one full length RNA genome for every 11 icosahedral assemblies, similar to the best recombinant adeno-associated virus vectors. Our results show that there are simple evolutionary paths through which protein assemblies can acquire virus-like genome packaging and protection. Considerable effort has been directed at ‘top-down’ modification of viruses to be safe and effective for drug delivery and vaccine applications; the ability to design synthetic nanomaterials computationally and to optimize them through evolution now enables a complementary ‘bottom-up’ approach with considerable advantages in programmability and control.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Bale2016,

title = {Accurate design of megadalton-scale two-component icosahedral protein complexes},

author = {Jacob B. Bale and Shane Gonen and Yuxi Liu and William Sheffler and Daniel Ellis and Chantz Thomas and Duilio Cascio and Todd O. Yeates and Tamir Gonen and Neil P. King and David Baker},

url = {https://www.bakerlab.org/wp-content/uploads/2016/07/Bale_Science_2016.pdf},

doi = {10.1126/science.aaf8818},

year  = {2016},

date = {2016-07-22},

journal = {Science},

volume = {353},

number = {6297},

pages = {389-394},

abstract = {Nature provides many examples of self- and co-assembling protein-based molecular machines, including icosahedral protein cages that serve as scaffolds, enzymes, and compartments for essential biochemical reactions and icosahedral virus capsids, which encapsidate and protect viral genomes and mediate entry into host cells. Inspired by these natural materials, we report the computational design and experimental characterization of co-assembling, two-component, 120-subunit icosahedral protein nanostructures with molecular weights (1.8 to 2.8 megadaltons) and dimensions (24 to 40 nanometers in diameter) comparable to those of small viral capsids. Electron microscopy, small-angle x-ray scattering, and x-ray crystallography show that 10 designs spanning three distinct icosahedral architectures form materials closely matching the design models. In vitro assembly of icosahedral complexes from independently purified components occurs rapidly, at rates comparable to those of viral capsids, and enables controlled packaging of molecular cargo through charge complementarity. The ability to design megadalton-scale materials with atomic-level accuracy and controllable assembly opens the door to a new generation of genetically programmable protein-based molecular machines.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Boyken680,

title = {De novo design of protein homo-oligomers with modular hydrogen-bond network–mediated specificity},

author = { Scott E. Boyken and Zibo Chen and Benjamin Groves and Robert A. Langan and Gustav Oberdorfer and Alex Ford and Jason M. Gilmore and Chunfu Xu and Frank DiMaio and Jose Henrique Pereira and Banumathi Sankaran and Georg Seelig and Peter H. Zwart and David Baker},

url = {http://science.sciencemag.org/content/352/6286/680

https://www.bakerlab.org/wp-content/uploads/2016/05/680.full_.pdf},

doi = {10.1126/science.aad8865},

issn = {0036-8075},

year  = {2016},

date = {2016-01-01},

journal = {Science},

volume = {352},

number = {6286},

pages = {680--687},

publisher = {American Association for the Advancement of Science},

abstract = {General design principles for protein interaction specificity are challenging to extract. DNA nanotechnology, on the other hand, has harnessed the limited set of hydrogen-bonding interactions from Watson-Crick base-pairing to design and build a wide range of shapes. Protein-based materials have the potential for even greater geometric and chemical diversity, including additional functionality. Boyken et al. designed a class of protein oligomers that have interaction specificity determined by modular arrays of extensive hydrogen bond networks (see the Perspective by Netzer and Fleishman). They use the approach, which could one day become programmable, to build novel topologies with two concentric rings of helices.Science, this issue p. 680; see also p. 657In nature, structural specificity in DNA and proteins is encoded differently: In DNA, specificity arises from modular hydrogen bonds in the core of the double helix, whereas in proteins, specificity arises largely from buried hydrophobic packing complemented by irregular peripheral polar interactions. Here, we describe a general approach for designing a wide range of protein homo-oligomers with specificity determined by modular arrays of central hydrogen-bond networks. We use the approach to design dimers, trimers, and tetramers consisting of two concentric rings of helices, including previously not seen triangular, square, and supercoiled topologies. X-ray crystallography confirms that the structures overall, and the hydrogen-bond networks in particular, are nearly identical to the design models, and the networks confer interaction specificity in vivo. The ability to design extensive hydrogen-bond networks with atomic accuracy enables the programming of protein interaction specificity for a broad range of synthetic biology applications; more generally, our results demonstrate that, even with the tremendous diversity observed in nature, there are fundamentally new modes of interaction to be discovered in proteins.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{L2015,

title = {Rational design of α-helical tandem repeat proteins with closed architectures},

author = {L Doyle and J Hallinan and J Bolduc and F Parmeggiani and D Baker and BL Stoddard and P Bradley},

url = {https://www.bakerlab.org/wp-content/uploads/2015/12/Doyle_Nature_2015.pdf},

doi = {10.1038/nature16191},

year  = {2015},

date = {2015-12-24},

journal = {Nature},

volume = {528(7583)},

pages = {585-8},

abstract = {Tandem repeat proteins, which are formed by repetition of modular units of protein sequence and structure, play important biological roles as macromolecular binding and scaffolding domains, enzymes, and building blocks for the assembly of fibrous materials. The modular nature of repeat proteins enables the rapid construction and diversification of extended binding surfaces by duplication and recombination of simple building blocks. The overall architecture of tandem repeat protein structures--which is dictated by the internal geometry and local packing of the repeat building blocks--is highly diverse, ranging from extended, super-helical folds that bind peptide, DNA, and RNA partners, to closed and compact conformations with internal cavities suitable for small molecule binding and catalysis. Here we report the development and validation of computational methods for de novo design of tandem repeat protein architectures driven purely by geometric criteria defining the inter-repeat geometry, without reference to the sequences and structures of existing repeat protein families. We have applied these methods to design a series of closed α-solenoid repeat structures (α-toroids) in which the inter-repeat packing geometry is constrained so as to juxtapose the amino (N) and carboxy (C) termini; several of these designed structures have been validated by X-ray crystallography. Unlike previous approaches to tandem repeat protein engineering, our design procedure does not rely on template sequence or structural information taken from natural repeat proteins and hence can produce structures unlike those seen in nature. As an example, we have successfully designed and validated closed α-solenoid repeats with a left-handed helical architecture that--to our knowledge--is not yet present in the protein structure database.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{616,

title = {Structure of a designed tetrahedral protein assembly variant engineered to have improved soluble expression},

author = { Jacob B Bale and Rachel U Park and Yuxi Liu and Shane Gonen and Tamir Gonen and Duilio Cascio and Neil P. King and Todd O. Yeates and David Baker},

url = {http://www.bakerlab.org/wp-content/uploads/2015/12/Bale_designed_tetrahedral_ProteinSci2015.pdf},

doi = {10.1002/pro.2748},

issn = {1469-896X},

year  = {2015},

date = {2015-07-01},

journal = {Protein science : a publication of the Protein Society},

abstract = {We recently reported the development of a computational method for the design of coassembling multicomponent protein nanomaterials. While four such materials were validated at high-resolution by X-ray crystallography, low yield of soluble protein prevented X-ray structure determination of a fifth designed material, T33-09. Here we report the design and crystal structure of T33-31, a variant of T33-09 with improved soluble yield resulting from redesign efforts focused on mutating solvent-exposed side chains to charged amino acids. The structure is found to match the computational design model with atomic-level accuracy, providing further validation of the design approach and demonstrating a simple and potentially general means of improving the yield of designed protein nanomaterials.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{555,

title = {A General Computational Approach for Repeat Protein Design.},

author = { Fabio Parmeggiani and Po-Ssu Huang and Sergey Vorobiev and Rong Xiao and Keunwan Park and Silvia Caprari and Min Su and Jayaraman Seetharaman and Lei Mao and Haleema Janjua and Gaetano T Montelione and John Hunt and David Baker},

url = {http://www.bakerlab.org/wp-content/uploads/2015/12/Parmeggiani-2014.pdf},

doi = {10.1016/j.jmb.2014.11.005},

issn = {1089-8638},

year  = {2014},

date = {2014-11-01},

journal = {Journal of molecular biology},

abstract = {Repeat proteins have considerable potential for use as modular binding reagents or biomaterials in biomedical and nanotechnology applications. Here we describe a general computational method for building idealized repeats that integrates available family sequences and structural information with Rosetta de novo protein design calculations. Idealized designs from six different repeat families were generated and experimentally characterized; 80% of the proteins were expressed and soluble and more than 40% were folded and monomeric with high thermal stability. Crystal structures determined for members of three families are within 1r A root-mean-square deviation to the design models. The method provides a general approach for fast and reliable generation of stable modular repeat protein scaffolds.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{534,

title = {Accurate design of co-assembling multi-component protein nanomaterials.},

author = { Neil P. King and Jacob B Bale and William Sheffler and Dan E McNamara and Shane Gonen and Tamir Gonen and Todd O. Yeates and David Baker},

url = {http://www.bakerlab.org/wp-content/uploads/2015/12/King_Nature2014A.pdf},

doi = {10.1038/nature13404},

issn = {1476-4687},

year  = {2014},

date = {2014-05-01},

journal = {Nature},

abstract = {The self-assembly of proteins into highly ordered nanoscale architectures is a hallmark of biological systems. The sophisticated functions of these molecular machines have inspired the development of methods to engineer self-assembling protein nanostructures; however, the design of multi-component protein nanomaterials with high accuracy remains an outstanding challenge. Here we report a computational method for designing protein nanomaterials in which multiple copies of two distinct subunits co-assemble into a specific architecture. We use the method to design five 24-subunit cage-like protein nanomaterials in two distinct symmetric architectures and experimentally demonstrate that their structures are in close agreement with the computational design models. The accuracy of the method and the number and variety of two-component materials that it makes accessible suggest a route to the construction of functional protein nanomaterials tailored to specific applications.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{445,

title = {Computational design of self-assembling protein nanomaterials with atomic level accuracy},

author = { Neil P. King and Will Sheffler and Michael R Sawaya and Breanna S. Vollmar and John P. Sumida and Ingemar Andr'e and Tamir Gonen and Todd O. Yeates and David Baker},

doi = {10.1126/science.1219364},

year  = {2012},

date = {2012-06-01},

journal = {Science},

abstract = {We describe a general computational method for designing proteins that self-assemble to a desired symmetric architecture. Protein building blocks are docked together symmetrically to identify complementary packing arrangements, and low-energy protein-protein interfaces are then designed between the building blocks in order to drive self-assembly. We used trimeric protein building blocks to design a 24-subunit, 13-nm diameter complex with octahedral symmetry and a 12-subunit, 11-nm diameter complex with tetrahedral symmetry. The designed proteins assembled to the desired oligomeric states in solution, and the crystal structures of the complexes revealed that the resulting materials closely match the design models. The method can be used to design a wide variety of self-assembling protein nanomaterials.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}