51
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Scalvini B, Sheikhhassani V, Woodard J, Aupič J, Dame RT, Jerala R, Mashaghi A. Topology of Folded Molecular Chains: From Single Biomolecules to Engineered Origami. TRENDS IN CHEMISTRY 2020. [DOI: 10.1016/j.trechm.2020.04.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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52
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Lambert BP, Gillen AJ, Boghossian AA. Synthetic Biology: A Solution for Tackling Nanomaterial Challenges. J Phys Chem Lett 2020; 11:4791-4802. [PMID: 32441940 DOI: 10.1021/acs.jpclett.0c00929] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Bioengineers have mastered practical techniques for tuning a biomaterial's properties with only limited information on the relationship between the material's structure and function. These techniques have been quintessential to engineering proteins, which are most often riddled with ill-defined structure-function relationships. In this Perspective, we review bioengineering approaches aimed at overcoming the elusive protein structure-function relation. We extend these principles to engineering synthetic nanomaterials, specifically applying the underlying theory to optical sensors based on single-stranded DNA-wrapped single-walled carbon nanotubes (ssDNA-SWCNTs). Bioengineering techniques such as directed evolution, computational design, and noncanonical synthesis are reviewed in the broader context of nanomaterials engineering. We further provide an order-of-magnitude analysis of empirical approaches that rely on random or guided searches for designing new nanomaterials. The underlying concepts presented in these approaches can be further extended to a broad range of engineering fields confronted with empirical design strategies, including catalysis, metal-organic frameworks (MOFs), pharmaceutical dosing, and optimization algorithms.
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Affiliation(s)
- Benjamin P Lambert
- École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Alice J Gillen
- École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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53
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Lapenta F, Jerala R. Design of novel protein building modules and modular architectures. Curr Opin Struct Biol 2020; 63:90-96. [PMID: 32505942 DOI: 10.1016/j.sbi.2020.04.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 04/14/2020] [Accepted: 04/15/2020] [Indexed: 12/31/2022]
Abstract
Nature uses only a limited number of protein topologies and while several folds have evolved independently over time, there are clearly many possible topologies that have not been explored by evolution. With recent advances of protein design concepts, computational modeling tools, high resolution and high-throughput experimental methods it is now possible to design new protein architectures. The collection of building blocks and design principles widened both in size and complexity, offering an expanded toolset for building new modular folds and functional protein structures. Here we review and discuss recent achievements of protein design, focusing in particular on the use and prospects of modular approaches for assembling new protein folds.
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Affiliation(s)
- Fabio Lapenta
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia; EN-FIST Centre of Excellence, Ljubljana, Slovenia.
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54
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Kaushik R, Zhang KYJ. A protein sequence fitness function for identifying natural and nonnatural proteins. Proteins 2020; 88:1271-1284. [PMID: 32415863 DOI: 10.1002/prot.25900] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/26/2020] [Accepted: 05/07/2020] [Indexed: 12/17/2022]
Abstract
The infinitesimally small sequence space naturally scouted in the millions of years of evolution suggests that the natural proteins are constrained by some functional prerequisites and should differ from randomly generated sequences. We have developed a protein sequence fitness scoring function that implements sequence and corresponding secondary structural information at tripeptide levels to differentiate natural and nonnatural proteins. The proposed fitness function is extensively validated on a dataset of about 210 000 natural and nonnatural protein sequences and benchmarked with existing methods for differentiating natural and nonnatural proteins. The high sensitivity, specificity, and percentage accuracy (0.81%, 0.95%, and 91% respectively) of the fitness function demonstrates its potential application for sampling the protein sequences with higher probability of mimicking natural proteins. Moreover, the four major classes of proteins (α proteins, β proteins, α/β proteins, and α + β proteins) are separately analyzed and β proteins are found to score slightly lower as compared to other classes. Further, an analysis of about 250 designed proteins (adopted from previously reported cases) helped to define the boundaries for sampling the ideal protein sequences. The protein sequence characterization aided by the proposed fitness function could facilitate the exploration of new perspectives in the design of novel functional proteins.
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Affiliation(s)
- Rahul Kaushik
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, Yokohama, Kanagawa, Japan
| | - Kam Y J Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, Yokohama, Kanagawa, Japan
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55
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Quijano-Rubio A, Ulge UY, Walkey CD, Silva DA. The advent of de novo proteins for cancer immunotherapy. Curr Opin Chem Biol 2020; 56:119-128. [PMID: 32371023 DOI: 10.1016/j.cbpa.2020.02.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 02/06/2020] [Accepted: 02/07/2020] [Indexed: 12/22/2022]
Abstract
Engineered proteins are revolutionizing immunotherapy, but advances are still needed to harness their full potential. Traditional protein engineering methods use naturally existing proteins as a starting point, and therefore, are intrinsically limited to small alterations of a protein's natural structure and function. Conversely, computational de novo protein design is free of such limitation, and can produce a virtually infinite number of novel protein sequences, folds, and functions. Recently, we used de novo protein engineering to create Neoleukin-2/15 (Neo-2/15), a protein mimetic of the function of both interleukin-2 (IL-2) and interleukin-15 (IL-15). To our knowledge, Neo-2/15 is the first de novo protein with immunotherapeutic activity, and in murine cancer models, it has demonstrated enhanced therapeutic potency and reduced toxicity compared to IL-2. De novo protein design is already showcasing its tremendous potential for driving the next wave of protein-based therapeutics that are explicitly engineered to treat disease.
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Affiliation(s)
| | - Umut Y Ulge
- Neoleukin Therapeutics Inc., Seattle, WA, USA
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56
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Wei KY, Moschidi D, Bick MJ, Nerli S, McShan AC, Carter LP, Huang PS, Fletcher DA, Sgourakis NG, Boyken SE, Baker D. Computational design of closely related proteins that adopt two well-defined but structurally divergent folds. Proc Natl Acad Sci U S A 2020; 117:7208-7215. [PMID: 32188784 PMCID: PMC7132107 DOI: 10.1073/pnas.1914808117] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The plasticity of naturally occurring protein structures, which can change shape considerably in response to changes in environmental conditions, is critical to biological function. While computational methods have been used for de novo design of proteins that fold to a single state with a deep free-energy minimum [P.-S. Huang, S. E. Boyken, D. Baker, Nature 537, 320-327 (2016)], and to reengineer natural proteins to alter their dynamics [J. A. Davey, A. M. Damry, N. K. Goto, R. A. Chica, Nat. Chem. Biol. 13, 1280-1285 (2017)] or fold [P. A. Alexander, Y. He, Y. Chen, J. Orban, P. N. Bryan, Proc. Natl. Acad. Sci. U.S.A. 106, 21149-21154 (2009)], the de novo design of closely related sequences which adopt well-defined but structurally divergent structures remains an outstanding challenge. We designed closely related sequences (over 94% identity) that can adopt two very different homotrimeric helical bundle conformations-one short (∼66 Å height) and the other long (∼100 Å height)-reminiscent of the conformational transition of viral fusion proteins. Crystallographic and NMR spectroscopic characterization shows that both the short- and long-state sequences fold as designed. We sought to design bistable sequences for which both states are accessible, and obtained a single designed protein sequence that populates either the short state or the long state depending on the measurement conditions. The design of sequences which are poised to adopt two very different conformations sets the stage for creating large-scale conformational switches between structurally divergent forms.
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Affiliation(s)
- Kathy Y Wei
- Department of Biochemistry, University of Washington, Seattle, WA 98195
- Institute for Protein Design, University of Washington, Seattle, WA 98195
- Department of Bioengineering, University of California, Berkeley, CA 94720
| | - Danai Moschidi
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064
| | - Matthew J Bick
- Department of Biochemistry, University of Washington, Seattle, WA 98195
- Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - Santrupti Nerli
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064
- Department of Computer Science, University of California, Santa Cruz, CA 95064
| | - Andrew C McShan
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064
| | - Lauren P Carter
- Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - Po-Ssu Huang
- Department of Bioengineering, Stanford University, Stanford, CA 94305
| | - Daniel A Fletcher
- Department of Bioengineering, University of California, Berkeley, CA 94720
- Joint UC Berkeley-UC San Francisco Graduate Group in Bioengineering, Berkeley, CA 94720
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Chan Zuckerberg Biohub, San Francisco, CA 94158
| | - Nikolaos G Sgourakis
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064
| | - Scott E Boyken
- Department of Biochemistry, University of Washington, Seattle, WA 98195;
- Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195;
- Institute for Protein Design, University of Washington, Seattle, WA 98195
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195
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57
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Abstract
This commentary summarizes the recent biophysical research conducted at the National Institute for Basic Biology, the National Institute for Physiological Sciences, and the Institute for Molecular Science in Okazaki, Japan.
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58
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Abstract
Proteins are molecular machines whose function depends on their ability to achieve complex folds with precisely defined structural and dynamic properties. The rational design of proteins from first-principles, or de novo, was once considered to be impossible, but today proteins with a variety of folds and functions have been realized. We review the evolution of the field from its earliest days, placing particular emphasis on how this endeavor has illuminated our understanding of the principles underlying the folding and function of natural proteins, and is informing the design of macromolecules with unprecedented structures and properties. An initial set of milestones in de novo protein design focused on the construction of sequences that folded in water and membranes to adopt folded conformations. The first proteins were designed from first-principles using very simple physical models. As computers became more powerful, the use of the rotamer approximation allowed one to discover amino acid sequences that stabilize the desired fold. As the crystallographic database of protein structures expanded in subsequent years, it became possible to construct proteins by assembling short backbone fragments that frequently recur in Nature. The second set of milestones in de novo design involves the discovery of complex functions. Proteins have been designed to bind a variety of metals, porphyrins, and other cofactors. The design of proteins that catalyze hydrolysis and oxygen-dependent reactions has progressed significantly. However, de novo design of catalysts for energetically demanding reactions, or even proteins that bind with high affinity and specificity to highly functionalized complex polar molecules remains an importnant challenge that is now being achieved. Finally, the protein design contributed significantly to our understanding of membrane protein folding and transport of ions across membranes. The area of membrane protein design, or more generally of biomimetic polymers that function in mixed or non-aqueous environments, is now becoming increasingly possible.
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59
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Koga R, Koga N. Consistency principle for protein design. Biophys Physicobiol 2019; 16:304-309. [PMID: 31984185 PMCID: PMC6975900 DOI: 10.2142/biophysico.16.0_304] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 08/01/2019] [Indexed: 12/01/2022] Open
Abstract
Protein design holds promise for applications such as the control of cells, therapeutics, new enzymes and protein-based materials. Recently, there has been progress in rational design of protein molecules, and a lot of attempts have been made to create proteins with functions of our interests. The key to the progress is the development of methods for controlling desired protein tertiary structures with atomic-level accuracy. A theory for protein folding, the consistency principle, proposed by Nobuhiro Go in 1983, was a compass for the development. Anfinsen hypothesized that proteins fold into the free energy minimum structures, but Go further considered that local and non-local interactions in the free energy minimum structures are consistent with each other. Guided by the principle, we proposed a set of rules for designing ideal protein structures stabilized by consistent local and non-local interactions. The rules made possible designs of amino acid sequences with funnel-shaped energy landscapes toward our desired target structures. So far, various protein structures have been created using the rules, which demonstrates significance of our rules as intended. In this review, we briefly describe how the consistency principle impacts on our efforts for developing the design technology.
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Affiliation(s)
- Rie Koga
- Protein Design Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8585, Japan
| | - Nobuyasu Koga
- Protein Design Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8585, Japan
- Research Center of Integrative Molecular Systems, Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi 444-8585, Japan
- SOKENDAI, The Graduate University for Advanced Studies, Shonan Village, Hayama, Kanagawa 240-0193, Japan
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60
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Kuhlman B, Bradley P. Advances in protein structure prediction and design. Nat Rev Mol Cell Biol 2019; 20:681-697. [PMID: 31417196 PMCID: PMC7032036 DOI: 10.1038/s41580-019-0163-x] [Citation(s) in RCA: 387] [Impact Index Per Article: 77.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2019] [Indexed: 12/18/2022]
Abstract
The prediction of protein three-dimensional structure from amino acid sequence has been a grand challenge problem in computational biophysics for decades, owing to its intrinsic scientific interest and also to the many potential applications for robust protein structure prediction algorithms, from genome interpretation to protein function prediction. More recently, the inverse problem - designing an amino acid sequence that will fold into a specified three-dimensional structure - has attracted growing attention as a potential route to the rational engineering of proteins with functions useful in biotechnology and medicine. Methods for the prediction and design of protein structures have advanced dramatically in the past decade. Increases in computing power and the rapid growth in protein sequence and structure databases have fuelled the development of new data-intensive and computationally demanding approaches for structure prediction. New algorithms for designing protein folds and protein-protein interfaces have been used to engineer novel high-order assemblies and to design from scratch fluorescent proteins with novel or enhanced properties, as well as signalling proteins with therapeutic potential. In this Review, we describe current approaches for protein structure prediction and design and highlight a selection of the successful applications they have enabled.
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Affiliation(s)
- Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA.
| | - Philip Bradley
- Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
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61
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Abstract
In nature, DNA molecules carry the hereditary information. But DNA has physical and chemical properties that make it attractive for uses beyond heredity. In this Review, we discuss the potential of DNA for creating machines that are both encoded by and built from DNA molecules. We review the main methods of DNA nanostructure assembly, describe recent advances in building increasingly complex molecular structures and discuss strategies for creating machine-like nanostructures that can be actuated and move. We highlight opportunities for applications of custom DNA nanostructures as scientific tools to address challenges across biology, chemistry and engineering.
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62
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Barros EP, Schiffer JM, Vorobieva A, Dou J, Baker D, Amaro RE. Improving the Efficiency of Ligand-Binding Protein Design with Molecular Dynamics Simulations. J Chem Theory Comput 2019; 15:5703-5715. [PMID: 31442033 DOI: 10.1021/acs.jctc.9b00483] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Custom-designed ligand-binding proteins represent a promising class of macromolecules with exciting applications toward the design of new enzymes or the engineering of antibodies and small-molecule recruited proteins for therapeutic interventions. However, several challenges remain in designing a protein sequence such that the binding site organization results in high affinity interaction with a bound ligand. Here, we study the dynamics of explicitly solvated designed proteins through all-atom molecular dynamics (MD) simulations to gain insight into the causes that lead to the low affinity or instability of most of these designs, despite the prediction of their success by the computational design methodology. Simulations ranging from 500 to 1000 ns per replicate were conducted on 37 designed protein variants encompassing two distinct folds and a range of ligand affinities, resulting in more than 180 μs of combined sampling. The simulations provide retrospective insights into the properties affecting ligand affinity that can prove useful in guiding further steps of design optimization. Features indicate that entropic components are particularly important for affinity, which are not easily incorporated in the empirical models often used in design protocols. Additionally, we demonstrate that the application of machine learning approaches built upon the output from the simulations can help discriminate between successful and failed binders, such that MD could act as a screening step in protein design, resulting in a more efficient process.
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Affiliation(s)
| | - Jamie M Schiffer
- Janssen Pharmaceuticals, Inc. , San Diego , California 92121 , United States
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63
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Abstract
Online citizen science projects such as GalaxyZoo1, Eyewire2 and Phylo3 have been very successful for data collection, annotation, and processing, but for the most part have harnessed human pattern recognition skills rather than human creativity. An exception is the game EteRNA4, in which game players learn to build new RNA structures by exploring the discrete two-dimensional space of Watson-Crick base pairing possibilities. Building new proteins, however, is a more challenging task to present in a game, as both the representation and evaluation of a protein structure are intrinsically three-dimensional. We posed the challenge of de novo protein design in the online protein folding game Foldit5. Players were presented with a fully extended peptide chain and challenged to craft a folded protein structure with an amino acid sequence encoding that structure. After many iterations of player design, analysis of the top scoring solutions, and subsequent game improvement, Foldit players can now, starting from an extended polypeptide chain, generate a diversity of protein structures and sequences which encode them in silico. 146 Foldit player designs with sequences unrelated to naturally occurring proteins were encoded in synthetic genes; 56 were found to be expressed in E. coli with good solubility and to adopt stable monomeric folded structures in solution. The diversity of these structures is unprecedented in de novo protein design, representing 20 different folds—including a new fold not observed in natural proteins. High resolution structures were determined for four of the designs, and are nearly identical to the player models. This work makes explicit the considerable implicit knowledge contributing to success in de novo protein design, and shows that citizen scientists can discover creative new solutions to outstanding scientific challenges, such as the protein design problem.
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64
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Pei J, Zheng Z, Merz KM. Random Forest Refinement of the KECSA2 Knowledge-Based Scoring Function for Protein Decoy Detection. J Chem Inf Model 2019; 59:1919-1929. [DOI: 10.1021/acs.jcim.8b00734] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jun Pei
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| | - Zheng Zheng
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| | - Kenneth M. Merz
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States
- Institute for Cyber Enabled Research, Michigan State University, 567 Wilson Road, East Lansing, Michigan 48824, United States
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65
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Wang H, Chou C, Hsu K, Lee C, Wang AH. New paradigm of functional regulation by DNA mimic proteins: Recent updates. IUBMB Life 2018; 71:539-548. [DOI: 10.1002/iub.1992] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 11/21/2018] [Accepted: 11/24/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Hao‐Ching Wang
- Graduate Institute of Translational MedicineCollege of Medical Science and Technology, Taipei Medical University Taipei 110 Taiwan
| | - Chia‐Cheng Chou
- National Center for High‐performance ComputingNational Applied Research Laboratories Hsinchu 300 Taiwan
| | - Kai‐Cheng Hsu
- Graduate Institute of Cancer Molecular Biology and Drug DiscoveryCollege of Medical Science and Technology, Taipei Medical University Taipei 110 Taiwan
| | - Chi‐Hua Lee
- Institute of Biological Chemistry, Academia Sinica Taipei 115 Taiwan
| | - Andrew H.‐J. Wang
- Graduate Institute of Translational MedicineCollege of Medical Science and Technology, Taipei Medical University Taipei 110 Taiwan
- Institute of Biological Chemistry, Academia Sinica Taipei 115 Taiwan
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66
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Marcos E, Chidyausiku TM, McShan AC, Evangelidis T, Nerli S, Carter L, Nivón LG, Davis A, Oberdorfer G, Tripsianes K, Sgourakis NG, Baker D. De novo design of a non-local β-sheet protein with high stability and accuracy. Nat Struct Mol Biol 2018; 25:1028-1034. [PMID: 30374087 PMCID: PMC6219906 DOI: 10.1038/s41594-018-0141-6] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 09/11/2018] [Indexed: 11/08/2022]
Abstract
β-sheet proteins carry out critical functions in biology, and hence are attractive scaffolds for computational protein design. Despite this potential, de novo design of all-β-sheet proteins from first principles lags far behind the design of all-α or mixed-αβ domains owing to their non-local nature and the tendency of exposed β-strand edges to aggregate. Through study of loops connecting unpaired β-strands (β-arches), we have identified a series of structural relationships between loop geometry, side chain directionality and β-strand length that arise from hydrogen bonding and packing constraints on regular β-sheet structures. We use these rules to de novo design jellyroll structures with double-stranded β-helices formed by eight antiparallel β-strands. The nuclear magnetic resonance structure of a hyperthermostable design closely matched the computational model, demonstrating accurate control over the β-sheet structure and loop geometry. Our results open the door to the design of a broad range of non-local β-sheet protein structures.
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Affiliation(s)
- Enrique Marcos
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona, Spain.
| | - Tamuka M Chidyausiku
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Andrew C McShan
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Thomas Evangelidis
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Santrupti Nerli
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA, USA
- Department of Computer Science, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Lauren Carter
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Lucas G Nivón
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Cyrus Biotechnology, Seattle, WA, USA
| | - Audrey Davis
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Amazon, Seattle, WA, USA
| | - Gustav Oberdorfer
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Institute of Biochemistry, Graz University of Technology, Graz, Austria
| | | | - Nikolaos G Sgourakis
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
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67
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Dou J, Vorobieva AA, Sheffler W, Doyle LA, Park H, Bick MJ, Mao B, Foight GW, Lee MY, Gagnon LA, Carter L, Sankaran B, Ovchinnikov S, Marcos E, Huang PS, Vaughan JC, Stoddard BL, Baker D. De novo design of a fluorescence-activating β-barrel. Nature 2018; 561:485-491. [PMID: 30209393 PMCID: PMC6275156 DOI: 10.1038/s41586-018-0509-0] [Citation(s) in RCA: 228] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 08/10/2018] [Indexed: 01/07/2023]
Abstract
The regular arrangements of β-strands around a central axis in β-barrels and of α-helices in coiled coils contrast with the irregular tertiary structures of most globular proteins, and have fascinated structural biologists since they were first discovered. Simple parametric models have been used to design a wide range of α-helical coiled-coil structures, but to date there has been no success with β-barrels. Here we show that accurate de novo design of β-barrels requires considerable symmetry-breaking to achieve continuous hydrogen-bond connectivity and eliminate backbone strain. We then build ensembles of β-barrel backbone models with cavity shapes that match the fluorogenic compound DFHBI, and use a hierarchical grid-based search method to simultaneously optimize the rigid-body placement of DFHBI in these cavities and the identities of the surrounding amino acids to achieve high shape and chemical complementarity. The designs have high structural accuracy and bind and fluorescently activate DFHBI in vitro and in Escherichia coli, yeast and mammalian cells. This de novo design of small-molecule binding activity, using backbones custom-built to bind the ligand, should enable the design of increasingly sophisticated ligand-binding proteins, sensors and catalysts that are not limited by the backbone geometries available in known protein structures.
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Affiliation(s)
- Jiayi Dou
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Anastassia A. Vorobieva
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - William Sheffler
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Lindsey A. Doyle
- Division of Basic Science, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Hahnbeom Park
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Matthew J. Bick
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Binchen Mao
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Glenna W. Foight
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - Min Yen Lee
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - Lauren A. Gagnon
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - Lauren Carter
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Sergey Ovchinnikov
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Enrique Marcos
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Po-Ssu Huang
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Joshua C. Vaughan
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - Barry L. Stoddard
- Division of Basic Science, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA,Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA,# corresponding author
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68
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Marcos E, Silva D. Essentials of
de novo
protein design: Methods and applications. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1374] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Enrique Marcos
- Institute for Research in Biomedicine (IRB Barcelona)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Daniel‐Adriano Silva
- Department of BiochemistryUniversity of WashingtonSeattleWashington
- Institute for Protein DesignUniversity of WashingtonSeattleWashington
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69
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Setiawan D, Brender J, Zhang Y. Recent advances in automated protein design and its future challenges. Expert Opin Drug Discov 2018; 13:587-604. [PMID: 29695210 DOI: 10.1080/17460441.2018.1465922] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
INTRODUCTION Protein function is determined by protein structure which is in turn determined by the corresponding protein sequence. If the rules that cause a protein to adopt a particular structure are understood, it should be possible to refine or even redefine the function of a protein by working backwards from the desired structure to the sequence. Automated protein design attempts to calculate the effects of mutations computationally with the goal of more radical or complex transformations than are accessible by experimental techniques. Areas covered: The authors give a brief overview of the recent methodological advances in computer-aided protein design, showing how methodological choices affect final design and how automated protein design can be used to address problems considered beyond traditional protein engineering, including the creation of novel protein scaffolds for drug development. Also, the authors address specifically the future challenges in the development of automated protein design. Expert opinion: Automated protein design holds potential as a protein engineering technique, particularly in cases where screening by combinatorial mutagenesis is problematic. Considering solubility and immunogenicity issues, automated protein design is initially more likely to make an impact as a research tool for exploring basic biology in drug discovery than in the design of protein biologics.
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Affiliation(s)
- Dani Setiawan
- a Department of Computational Medicine and Bioinformatics , University of Michigan , Ann Arbor , MI , USA
| | - Jeffrey Brender
- b Radiation Biology Branch , Center for Cancer Research, National Cancer Institute - NIH , Bethesda , MD , USA
| | - Yang Zhang
- a Department of Computational Medicine and Bioinformatics , University of Michigan , Ann Arbor , MI , USA.,c Department of Biological Chemistry , University of Michigan , Ann Arbor , MI , USA
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70
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Chu H, Liu H. TetraBASE: A Side Chain-Independent Statistical Energy for Designing Realistically Packed Protein Backbones. J Chem Inf Model 2018; 58:430-442. [PMID: 29314837 DOI: 10.1021/acs.jcim.7b00677] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To construct backbone structures of high designability is a primary aspect of computational protein design. We report here a side chain-independent statistical energy that aims at realistic modeling of through-space packing of polypeptide backbones. To mitigate the lack of explicit amino acid side chains, the model treats the interbackbone site packing as being dependent on peptide local conformation. In addition, new variables suitable for statistical analysis, one for relative orientation and another for distance, have been introduced to represent the intersite geometry based on the asymmetrical tetrahedron organization of distinct chemical groups surrounding the Cα-carbon atoms. The resulting tetrahedron-based backbone statistical energy (tetraBASE) model has been used to optimize the tertiary organizations of secondary structure elements (SSEs) of designated types with Monte Caro simulated annealing, starting from artificial initial configurations. The tetraBASE minimum energy structures can reproduce SSE packing frequently observed in native proteins with atomic root-mean-square deviations of 1-2 Å. The model has also been tested by examining the stability of native SSE arrangements under tetraBASE. The results suggest that tetraBASE model can be used to effectively represent interbackbone packing when designing backbone structures without explicitly knowing side chain types.
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Affiliation(s)
- Huanyu Chu
- School of Life Sciences, University of Science and Technology of China , 230027 Hefei, Anhui China.,Hefei National Laboratory for Physical Sciences at the Microscales , 230027 Hefei, Anhui China
| | - Haiyan Liu
- School of Life Sciences, University of Science and Technology of China , 230027 Hefei, Anhui China.,Hefei National Laboratory for Physical Sciences at the Microscales , 230027 Hefei, Anhui China.,Collaborative Innovation Center of Chemistry for Life Sciences , 230027 Hefei, Anhui China
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71
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Hecht MH, Zarzhitsky S, Karas C, Chari S. Are natural proteins special? Can we do that? Curr Opin Struct Biol 2018; 48:124-132. [DOI: 10.1016/j.sbi.2017.11.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 11/29/2017] [Indexed: 12/23/2022]
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72
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Elfin: An algorithm for the computational design of custom three-dimensional structures from modular repeat protein building blocks. J Struct Biol 2018; 201:100-107. [DOI: 10.1016/j.jsb.2017.09.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Revised: 08/11/2017] [Accepted: 09/02/2017] [Indexed: 11/17/2022]
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73
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Rocklin GJ, Chidyausiku TM, Goreshnik I, Ford A, Houliston S, Lemak A, Carter L, Ravichandran R, Mulligan VK, Chevalier A, Arrowsmith CH, Baker D. Global analysis of protein folding using massively parallel design, synthesis, and testing. Science 2018; 357:168-175. [PMID: 28706065 PMCID: PMC5568797 DOI: 10.1126/science.aan0693] [Citation(s) in RCA: 294] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 06/09/2017] [Indexed: 12/18/2022]
Abstract
Proteins fold into unique native structures stabilized by thousands of weak interactions that collectively overcome the entropic cost of folding. Although these forces are "encoded" in the thousands of known protein structures, "decoding" them is challenging because of the complexity of natural proteins that have evolved for function, not stability. We combined computational protein design, next-generation gene synthesis, and a high-throughput protease susceptibility assay to measure folding and stability for more than 15,000 de novo designed miniproteins, 1000 natural proteins, 10,000 point mutants, and 30,000 negative control sequences. This analysis identified more than 2500 stable designed proteins in four basic folds-a number sufficient to enable us to systematically examine how sequence determines folding and stability in uncharted protein space. Iteration between design and experiment increased the design success rate from 6% to 47%, produced stable proteins unlike those found in nature for topologies where design was initially unsuccessful, and revealed subtle contributions to stability as designs became increasingly optimized. Our approach achieves the long-standing goal of a tight feedback cycle between computation and experiment and has the potential to transform computational protein design into a data-driven science.
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Affiliation(s)
- Gabriel J Rocklin
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Tamuka M Chidyausiku
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.,Graduate Program in Biological Physics, Structure, and Design, University of Washington, Seattle, WA 98195, USA
| | - Inna Goreshnik
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Alex Ford
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.,Graduate Program in Biological Physics, Structure, and Design, University of Washington, Seattle, WA 98195, USA
| | - Scott Houliston
- Princess Margaret Cancer Centre, Toronto, Ontario M5G 1L7, Canada.,Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Alexander Lemak
- Princess Margaret Cancer Centre, Toronto, Ontario M5G 1L7, Canada
| | - Lauren Carter
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Rashmi Ravichandran
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Vikram K Mulligan
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Aaron Chevalier
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Cheryl H Arrowsmith
- Princess Margaret Cancer Centre, Toronto, Ontario M5G 1L7, Canada.,Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - David Baker
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA. .,Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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74
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Arai R. Hierarchical design of artificial proteins and complexes toward synthetic structural biology. Biophys Rev 2017; 10:391-410. [PMID: 29243094 DOI: 10.1007/s12551-017-0376-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 11/23/2017] [Indexed: 12/14/2022] Open
Abstract
In multiscale structural biology, synthetic approaches are important to demonstrate biophysical principles and mechanisms underlying the structure, function, and action of bio-nanomachines. A central goal of "synthetic structural biology" is the design and construction of artificial proteins and protein complexes as desired. In this paper, I review recent remarkable progress of an array of approaches for hierarchical design of artificial proteins and complexes that signpost the path forward toward synthetic structural biology as an emerging interdisciplinary field. Topics covered include combinatorial and protein-engineering approaches for directed evolution of artificial binding proteins and membrane proteins, binary code strategy for structural and functional de novo proteins, protein nanobuilding block strategy for constructing nano-architectures, protein-metal-organic frameworks for 3D protein complex crystals, and rational and computational approaches for design/creation of artificial proteins and complexes, novel protein folds, ideal/optimized protein structures, novel binding proteins for targeted therapeutics, and self-assembling nanomaterials. Protein designers and engineers look toward a bright future in synthetic structural biology for the next generation of biophysics and biotechnology.
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Affiliation(s)
- Ryoichi Arai
- Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, Ueda, Nagano 386-8567, Japan. .,Department of Supramolecular Complexes, Research Center for Fungal and Microbial Dynamism, Shinshu University, Minamiminowa, Nagano 399-4598, Japan. .,Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Matsumoto, Nagano 390-8621, Japan. .,Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.
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75
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Lin Y, Koga N, Vorobiev SM, Baker D. Cyclic oligomer design with de novo αβ-proteins. Protein Sci 2017; 26:2187-2194. [PMID: 28801928 PMCID: PMC5654858 DOI: 10.1002/pro.3270] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 07/28/2017] [Accepted: 08/10/2017] [Indexed: 12/11/2022]
Abstract
We have previously shown that monomeric globular αβ-proteins can be designed de novo with considerable control over topology, size, and shape. In this paper, we investigate the design of cyclic homo-oligomers from these starting points. We experimented with both keeping the original monomer backbones fixed during the cyclic docking and design process, and allowing the backbone of the monomer to conform to that of adjacent subunits in the homo-oligomer. The latter flexible backbone protocol generated designs with shape complementarity approaching that of native homo-oligomers, but experimental characterization showed that the fixed backbone designs were more stable and less aggregation prone. Designed C2 oligomers with β-strand backbone interactions were structurally confirmed through x-ray crystallography and small-angle X-ray scattering (SAXS). In contrast, C3-C5 designed homo-oligomers with primarily nonpolar residues at interfaces all formed a range of oligomeric states. Taken together, our results suggest that for homo-oligomers formed from globular building blocks, improved structural specificity will be better achieved using monomers with increased shape complementarity and with more polar interfaces.
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Affiliation(s)
- Yu‐Ru Lin
- Department of BiochemistryUniversity of Washington, and Howard Hughes Medical InstituteSeattleWashington 98195
| | - Nobuyasu Koga
- Research Center of Integrative Molecular SystemsInstitute for Molecular Science, National Institute of Natural Sciences (NINS)Okazaki 444‐8585Japan
- JST, PRESTOKawaguchiSaitama 332‐0012Japan
| | - Sergey M. Vorobiev
- Department of Biological ScienceNortheast Structural Genomics Consortium, Columbia UniversityNew YorkNew York
| | - David Baker
- Department of BiochemistryUniversity of Washington, and Howard Hughes Medical InstituteSeattleWashington 98195
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76
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Agrawal DK, Jiang R, Reinhart S, Mohammed AM, Jorgenson TD, Schulman R. Terminating DNA Tile Assembly with Nanostructured Caps. ACS NANO 2017; 11:9770-9779. [PMID: 28901745 DOI: 10.1021/acsnano.7b02256] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Precise control over the nucleation, growth, and termination of self-assembly processes is a fundamental tool for controlling product yield and assembly dynamics. Mechanisms for altering these processes programmatically could allow the use of simple components to self-assemble complex final products or to design processes allowing for dynamic assembly or reconfiguration. Here we use DNA tile self-assembly to develop general design principles for building complexes that can bind to a growing biomolecular assembly and terminate its growth by systematically characterizing how different DNA origami nanostructures interact with the growing ends of DNA tile nanotubes. We find that nanostructures that present binding interfaces for all of the binding sites on a growing facet can bind selectively to growing ends and stop growth when these interfaces are presented on either a rigid or floppy scaffold. In contrast, nucleation of nanotubes requires the presentation of binding sites in an arrangement that matches the shape of the structure's facet. As a result, it is possible to build nanostructures that can terminate the growth of existing nanotubes but cannot nucleate a new structure. The resulting design principles for constructing structures that direct nucleation and termination of the growth of one-dimensional nanostructures can also serve as a starting point for programmatically directing two- and three-dimensional crystallization processes using nanostructure design.
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Affiliation(s)
- Deepak K Agrawal
- Chemical and Biomolecular Engineering, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Ruoyu Jiang
- Chemical and Biomolecular Engineering, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Seth Reinhart
- Chemical and Biomolecular Engineering, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Abdul M Mohammed
- Chemical and Biomolecular Engineering, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Tyler D Jorgenson
- Chemical and Biomolecular Engineering, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Rebecca Schulman
- Chemical and Biomolecular Engineering, Johns Hopkins University , Baltimore, Maryland 21218, United States
- Computer Science, Johns Hopkins University , Baltimore, Maryland 21218, United States
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77
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Chevalier A, Silva DA, Rocklin GJ, Hicks DR, Vergara R, Murapa P, Bernard SM, Zhang L, Lam KH, Yao G, Bahl CD, Miyashita SI, Goreshnik I, Fuller JT, Koday MT, Jenkins CM, Colvin T, Carter L, Bohn A, Bryan CM, Fernández-Velasco DA, Stewart L, Dong M, Huang X, Jin R, Wilson IA, Fuller DH, Baker D. Massively parallel de novo protein design for targeted therapeutics. Nature 2017; 550:74-79. [PMID: 28953867 PMCID: PMC5802399 DOI: 10.1038/nature23912] [Citation(s) in RCA: 278] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 08/17/2017] [Indexed: 12/24/2022]
Abstract
De novo protein design holds promise for creating small stable proteins with shapes customized to bind therapeutic targets. We describe a massively parallel approach for designing, manufacturing and screening mini-protein binders, integrating large-scale computational design, oligonucleotide synthesis, yeast display screening and next-generation sequencing. We designed and tested 22,660 mini-proteins of 37-43 residues that target influenza haemagglutinin and botulinum neurotoxin B, along with 6,286 control sequences to probe contributions to folding and binding, and identified 2,618 high-affinity binders. Comparison of the binding and non-binding design sets, which are two orders of magnitude larger than any previously investigated, enabled the evaluation and improvement of the computational model. Biophysical characterization of a subset of the binder designs showed that they are extremely stable and, unlike antibodies, do not lose activity after exposure to high temperatures. The designs elicit little or no immune response and provide potent prophylactic and therapeutic protection against influenza, even after extensive repeated dosing.
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Affiliation(s)
- Aaron Chevalier
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Daniel-Adriano Silva
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Gabriel J Rocklin
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Derrick R Hicks
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington 98195, USA
| | - Renan Vergara
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
- Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria, México City 04510, Mexico
| | - Patience Murapa
- Department of Microbiology, University of Washington, Seattle, Washington 98109, USA
| | - Steffen M Bernard
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Lu Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
- Department of Chemistry and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Kwok-Ho Lam
- Department of Physiology and Biophysics, University of California, Irvine, California 92697, USA
| | - Guorui Yao
- Department of Physiology and Biophysics, University of California, Irvine, California 92697, USA
| | - Christopher D Bahl
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Shin-Ichiro Miyashita
- Department of Urology, Boston Children's Hospital, Boston, Massachusetts 02115, USA
- Department of Microbiology and Immunobiology and Department of Surgery, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Inna Goreshnik
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - James T Fuller
- Department of Microbiology, University of Washington, Seattle, Washington 98109, USA
| | - Merika T Koday
- Department of Microbiology, University of Washington, Seattle, Washington 98109, USA
- Virvio Inc., Seattle, Washington 98195, USA
| | - Cody M Jenkins
- Department of Microbiology, University of Washington, Seattle, Washington 98109, USA
| | - Tom Colvin
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Lauren Carter
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Alan Bohn
- Department of Microbiology, University of Washington, Seattle, Washington 98109, USA
| | - Cassie M Bryan
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - D Alejandro Fernández-Velasco
- Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria, México City 04510, Mexico
| | - Lance Stewart
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Min Dong
- Department of Urology, Boston Children's Hospital, Boston, Massachusetts 02115, USA
- Department of Microbiology and Immunobiology and Department of Surgery, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Xuhui Huang
- Department of Chemistry and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Rongsheng Jin
- Department of Physiology and Biophysics, University of California, Irvine, California 92697, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Deborah H Fuller
- Department of Microbiology, University of Washington, Seattle, Washington 98109, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
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78
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Advances in design of protein folds and assemblies. Curr Opin Chem Biol 2017; 40:65-71. [DOI: 10.1016/j.cbpa.2017.06.020] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 05/29/2017] [Accepted: 06/27/2017] [Indexed: 11/20/2022]
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79
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Kobayashi N, Arai R. Design and construction of self-assembling supramolecular protein complexes using artificial and fusion proteins as nanoscale building blocks. Curr Opin Biotechnol 2017; 46:57-65. [DOI: 10.1016/j.copbio.2017.01.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Revised: 12/09/2016] [Accepted: 01/04/2017] [Indexed: 01/03/2023]
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80
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Computational design of trimeric influenza-neutralizing proteins targeting the hemagglutinin receptor binding site. Nat Biotechnol 2017; 35:667-671. [PMID: 28604661 PMCID: PMC5512607 DOI: 10.1038/nbt.3907] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 05/19/2017] [Indexed: 01/17/2023]
Abstract
Many viral surface glycoproteins and cell surface receptors are homo-oligomers, and thus can potentially be targeted by geometrically matched homo-oligomers that engage all subunits simultaneously to attain high avidity and/or lock subunits together. The adaptive immune system cannot generally employ this strategy since the individual antibody binding sites are not arranged with appropriate geometry to simultaneously engage multiple sites in a single target homo-oligomer. We describe a general strategy for the computational design of homo-oligomeric protein assemblies with binding functionality precisely matched to homo-oligomeric target sites. In the first step, a small protein is designed that binds a single site on the target. In the second step, the designed protein is assembled into a homo-oligomer such that the designed binding sites are aligned with the target sites. We use this approach to design high-avidity trimeric proteins that bind influenza A hemagglutinin (HA) at its conserved receptor binding site. The designed trimers can both capture and detect HA in a paper-based diagnostic format, neutralizes influenza in cell culture, and completely protects mice when given as a single dose 24 h before or after challenge with influenza.
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81
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Mackenzie CO, Grigoryan G. Protein structural motifs in prediction and design. Curr Opin Struct Biol 2017; 44:161-167. [PMID: 28460216 PMCID: PMC5513761 DOI: 10.1016/j.sbi.2017.03.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 03/18/2017] [Accepted: 03/28/2017] [Indexed: 01/11/2023]
Abstract
The Protein Data Bank (PDB) has been an integral resource for shaping our fundamental understanding of protein structure and for the advancement of such applications as protein design and structure prediction. Over the years, information from the PDB has been used to generate models ranging from specific structural mechanisms to general statistical potentials. With accumulating structural data, it has become possible to mine for more complete and complex structural observations, deducing more accurate generalizations. Motif libraries, which capture recurring structural features along with their sequence preferences, have exposed modularity in the structural universe and found successful application in various problems of structural biology. Here we summarize recent achievements in this arena, focusing on subdomain level structural patterns and their applications to protein design and structure prediction, and suggest promising future directions as the structural database continues to grow.
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Affiliation(s)
- Craig O Mackenzie
- Institute for Quantitative Biomedical Sciences, Dartmouth College, Hanover, NH 03755, United States
| | - Gevorg Grigoryan
- Institute for Quantitative Biomedical Sciences, Dartmouth College, Hanover, NH 03755, United States; Department of Computer Science, Dartmouth College, Hanover, NH 03755, United States.
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82
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Coluzza I. Computational protein design: a review. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:143001. [PMID: 28140371 DOI: 10.1088/1361-648x/aa5c76] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Proteins are one of the most versatile modular assembling systems in nature. Experimentally, more than 110 000 protein structures have been identified and more are deposited every day in the Protein Data Bank. Such an enormous structural variety is to a first approximation controlled by the sequence of amino acids along the peptide chain of each protein. Understanding how the structural and functional properties of the target can be encoded in this sequence is the main objective of protein design. Unfortunately, rational protein design remains one of the major challenges across the disciplines of biology, physics and chemistry. The implications of solving this problem are enormous and branch into materials science, drug design, evolution and even cryptography. For instance, in the field of drug design an effective computational method to design protein-based ligands for biological targets such as viruses, bacteria or tumour cells, could give a significant boost to the development of new therapies with reduced side effects. In materials science, self-assembly is a highly desired property and soon artificial proteins could represent a new class of designable self-assembling materials. The scope of this review is to describe the state of the art in computational protein design methods and give the reader an outline of what developments could be expected in the near future.
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Affiliation(s)
- Ivan Coluzza
- Computational Physics, Faculty of Physics, University of Vienna, Vienna, Austria
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83
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Johnston T, Zhang B, Liwo A, Crivelli S, Taufer M. In situ data analytics and indexing of protein trajectories. J Comput Chem 2017; 38:1419-1430. [PMID: 28093787 DOI: 10.1002/jcc.24729] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Revised: 10/22/2016] [Accepted: 10/27/2016] [Indexed: 11/06/2022]
Abstract
The transition toward exascale computing will be accompanied by a performance dichotomy. Computational peak performance will rapidly increase; I/O performance will either grow slowly or be completely stagnant. Essentially, the rate at which data are generated will grow much faster than the rate at which data can be read from and written to the disk. MD simulations will soon face the I/O problem of efficiently writing to and reading from disk on the next generation of supercomputers. This article targets MD simulations at the exascale and proposes a novel technique for in situ data analysis and indexing of MD trajectories. Our technique maps individual trajectories' substructures (i.e., α-helices, β-strands) to metadata frame by frame. The metadata captures the conformational properties of the substructures. The ensemble of metadata can be used for automatic, strategic analysis within a trajectory or across trajectories, without manually identify those portions of trajectories in which critical changes take place. We demonstrate our technique's effectiveness by applying it to 26.3k helices and 31.2k strands from 9917 PDB proteins and by providing three empirical case studies. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Travis Johnston
- Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA
| | - Boyu Zhang
- Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA
| | - Adam Liwo
- Department of Theort, Chemistry, University of Gdansk, 80-952, Gdańsk, Poland
| | - Silvia Crivelli
- Department of Computer Science, University of California, Davis, CA, 95616, USA
| | - Michela Taufer
- Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA
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84
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Marcos E, Basanta B, Chidyausiku TM, Tang Y, Oberdorfer G, Liu G, Swapna GVT, Guan R, Silva DA, Dou J, Pereira JH, Xiao R, Sankaran B, Zwart PH, Montelione GT, Baker D. Principles for designing proteins with cavities formed by curved β sheets. Science 2017; 355:201-206. [PMID: 28082595 PMCID: PMC5588894 DOI: 10.1126/science.aah7389] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 12/02/2016] [Indexed: 12/23/2022]
Abstract
Active sites and ligand-binding cavities in native proteins are often formed by curved β sheets, and the ability to control β-sheet curvature would allow design of binding proteins with cavities customized to specific ligands. Toward this end, we investigated the mechanisms controlling β-sheet curvature by studying the geometry of β sheets in naturally occurring protein structures and folding simulations. The principles emerging from this analysis were used to design, de novo, a series of proteins with curved β sheets topped with α helices. Nuclear magnetic resonance and crystal structures of the designs closely match the computational models, showing that β-sheet curvature can be controlled with atomic-level accuracy. Our approach enables the design of proteins with cavities and provides a route to custom design ligand-binding and catalytic sites.
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Affiliation(s)
- Enrique Marcos
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Benjamin Basanta
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Graduate Program in Biological Physics, Structure, and Design, University of Washington, Seattle, WA 98195, USA
| | - Tamuka M Chidyausiku
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Graduate Program in Biological Physics, Structure, and Design, University of Washington, Seattle, WA 98195, USA
| | - Yuefeng Tang
- Center for Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Northeast Structural Genomics Consortium, Piscataway, NJ 08854, USA
| | - Gustav Oberdorfer
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50/3, 8010-Graz, Austria
| | - Gaohua Liu
- Center for Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Northeast Structural Genomics Consortium, Piscataway, NJ 08854, USA
| | - G V T Swapna
- Center for Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Northeast Structural Genomics Consortium, Piscataway, NJ 08854, USA
| | - Rongjin Guan
- Center for Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Northeast Structural Genomics Consortium, Piscataway, NJ 08854, USA
| | - Daniel-Adriano Silva
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Jiayi Dou
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Graduate Program in Biological Physics, Structure, and Design, University of Washington, Seattle, WA 98195, USA
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Jose Henrique Pereira
- Berkeley Center for Structural Biology, Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley Laboratory, Berkeley, CA 94720, USA
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
| | - Rong Xiao
- Center for Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Northeast Structural Genomics Consortium, Piscataway, NJ 08854, USA
| | | | - Peter H Zwart
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
| | - Gaetano T Montelione
- Center for Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Northeast Structural Genomics Consortium, Piscataway, NJ 08854, USA
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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85
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Fallas JA, Ueda G, Sheffler W, Nguyen V, McNamara DE, Sankaran B, Pereira JH, Parmeggiani F, Brunette TJ, Cascio D, Yeates TR, Zwart P, Baker D. Computational design of self-assembling cyclic protein homo-oligomers. Nat Chem 2016; 9:353-360. [PMID: 28338692 PMCID: PMC5367466 DOI: 10.1038/nchem.2673] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 10/13/2016] [Indexed: 12/19/2022]
Abstract
Self-assembling cyclic protein homo-oligomers play important roles in biology and the ability to generate custom homo-oligomeric structures could enable new approaches to probe biological function. Here we report a general approach to design cyclic homo-oligomers that employs a new residue pair transform method for assessing the design ability of a protein-protein interface. This method is sufficiently rapid to enable systematic enumeration of cyclically docked arrangements of a monomer followed by sequence design of the newly formed interfaces. We use this method to design interfaces onto idealized repeat proteins that direct their assembly into complexes that possess cyclic symmetry. Of 96 designs that were experimentally characterized, 21 were found to form stable monodisperse homo-oligomers in solution, and 15 (4 homodimers, 6 homotrimers, 6 homotetramers and 1 homopentamer) had solution small angle X-ray scattering data consistent with the design models. X-ray crystal structures were obtained for five of the designs and each of these were shown to be very close to their design model.
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Affiliation(s)
- Jorge A Fallas
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - George Ueda
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - William Sheffler
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Vanessa Nguyen
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Dan E McNamara
- Department of Chemistry and Biochemistry, University of California Los Angles, Los Angeles, California 90095, USA
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley Laboratory, Berkeley, California 94720, USA
| | - Jose Henrique Pereira
- Berkeley Center for Structural Biology, Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley Laboratory, Berkeley, California 94720, USA.,Joint BioEnergy Institute, Emeryville, California 94608, USA
| | - Fabio Parmeggiani
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - T J Brunette
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Duilio Cascio
- Department of Chemistry and Biochemistry, University of California Los Angles, Los Angeles, California 90095, USA
| | - Todd R Yeates
- Department of Chemistry and Biochemistry, University of California Los Angles, Los Angeles, California 90095, USA
| | - Peter Zwart
- Berkeley Center for Structural Biology, Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley Laboratory, Berkeley, California 94720, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
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86
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Zhou X, Xiong P, Wang M, Ma R, Zhang J, Chen Q, Liu H. Proteins of well-defined structures can be designed without backbone readjustment by a statistical model. J Struct Biol 2016; 196:350-357. [DOI: 10.1016/j.jsb.2016.08.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 07/26/2016] [Accepted: 08/02/2016] [Indexed: 11/25/2022]
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87
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Bhardwaj G, Mulligan VK, Bahl CD, Gilmore JM, Harvey PJ, Cheneval O, Buchko GW, Pulavarti SV, Kaas Q, Eletsky A, Huang PS, Johnsen WA, Greisen P, Rocklin GJ, Song Y, Linsky TW, Watkins A, Rettie SA, Xu X, Carter LP, Bonneau R, Olson JM, Coutsias E, Correnti CE, Szyperski T, Craik DJ, Baker D. Accurate de novo design of hyperstable constrained peptides. Nature 2016; 538:329-335. [PMID: 27626386 PMCID: PMC5161715 DOI: 10.1038/nature19791] [Citation(s) in RCA: 282] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 08/18/2016] [Indexed: 02/06/2023]
Abstract
Naturally occurring, pharmacologically active peptides constrained with covalent crosslinks generally have shapes that have evolved to fit precisely into binding pockets on their targets. Such peptides can have excellent pharmaceutical properties, combining the stability and tissue penetration of small-molecule drugs with the specificity of much larger protein therapeutics. The ability to design constrained peptides with precisely specified tertiary structures would enable the design of shape-complementary inhibitors of arbitrary targets. Here we describe the development of computational methods for accurate de novo design of conformationally restricted peptides, and the use of these methods to design 18-47 residue, disulfide-crosslinked peptides, a subset of which are heterochiral and/or N-C backbone-cyclized. Both genetically encodable and non-canonical peptides are exceptionally stable to thermal and chemical denaturation, and 12 experimentally determined X-ray and NMR structures are nearly identical to the computational design models. The computational design methods and stable scaffolds presented here provide the basis for development of a new generation of peptide-based drugs.
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Affiliation(s)
- Gaurav Bhardwaj
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Vikram Khipple Mulligan
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Christopher D. Bahl
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Jason M. Gilmore
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Peta J. Harvey
- Institute for Molecular Bioscience, the University of Queensland, Brisbane, Queensland QLD 4072, Australia
| | - Olivier Cheneval
- Institute for Molecular Bioscience, the University of Queensland, Brisbane, Queensland QLD 4072, Australia
| | - Garry W. Buchko
- Seattle Structural Genomics Center for Infectious Diseases, Earth, and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | | | - Quentin Kaas
- Institute for Molecular Bioscience, the University of Queensland, Brisbane, Queensland QLD 4072, Australia
| | - Alexander Eletsky
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260, USA
| | - Po-Ssu Huang
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - William A. Johnsen
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Per Greisen
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
- Global Research, Novo Nordisk A/S, DK-2760 Måløv, Denmark
| | - Gabriel J. Rocklin
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Yifan Song
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
- Cyrus Biotechnology, Seattle, Washington 98109, USA
| | - Thomas W. Linsky
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Andrew Watkins
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Stephen A. Rettie
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Xianzhong Xu
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260, USA
| | - Lauren P. Carter
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Richard Bonneau
- Department of Biology, New York University, New York, NY 10003, USA
- Center for Computational Biology, Simons Foundation, NY, NY 10010
| | - James M. Olson
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Evangelos Coutsias
- Applied Mathematics and Statistics and Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, USA
| | - Colin E. Correnti
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Thomas Szyperski
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260, USA
| | - David J. Craik
- Institute for Molecular Bioscience, the University of Queensland, Brisbane, Queensland QLD 4072, Australia
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
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88
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Computational protein design with backbone plasticity. Biochem Soc Trans 2016; 44:1523-1529. [PMID: 27911735 PMCID: PMC5264498 DOI: 10.1042/bst20160155] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 08/01/2016] [Accepted: 08/03/2016] [Indexed: 11/17/2022]
Abstract
The computational algorithms used in the design of artificial proteins have become increasingly sophisticated in recent years, producing a series of remarkable successes. The most dramatic of these is the de novo design of artificial enzymes. The majority of these designs have reused naturally occurring protein structures as ‘scaffolds’ onto which novel functionality can be grafted without having to redesign the backbone structure. The incorporation of backbone flexibility into protein design is a much more computationally challenging problem due to the greatly increased search space, but promises to remove the limitations of reusing natural protein scaffolds. In this review, we outline the principles of computational protein design methods and discuss recent efforts to consider backbone plasticity in the design process.
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89
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The coming of age of de novo protein design. Nature 2016; 537:320-7. [DOI: 10.1038/nature19946] [Citation(s) in RCA: 803] [Impact Index Per Article: 100.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 07/20/2016] [Indexed: 12/24/2022]
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90
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Synthetic beta-solenoid proteins with the fragment-free computational design of a beta-hairpin extension. Proc Natl Acad Sci U S A 2016; 113:10346-51. [PMID: 27573845 DOI: 10.1073/pnas.1525308113] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The ability to design and construct structures with atomic level precision is one of the key goals of nanotechnology. Proteins offer an attractive target for atomic design because they can be synthesized chemically or biologically and can self-assemble. However, the generalized protein folding and design problem is unsolved. One approach to simplifying the problem is to use a repetitive protein as a scaffold. Repeat proteins are intrinsically modular, and their folding and structures are better understood than large globular domains. Here, we have developed a class of synthetic repeat proteins based on the pentapeptide repeat family of beta-solenoid proteins. We have constructed length variants of the basic scaffold and computationally designed de novo loops projecting from the scaffold core. The experimentally solved 3.56-Å resolution crystal structure of one designed loop matches closely the designed hairpin structure, showing the computational design of a backbone extension onto a synthetic protein core without the use of backbone fragments from known structures. Two other loop designs were not clearly resolved in the crystal structures, and one loop appeared to be in an incorrect conformation. We have also shown that the repeat unit can accommodate whole-domain insertions by inserting a domain into one of the designed loops.
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91
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Bekker GJ, Nakamura H, Kinjo AR. Molmil: a molecular viewer for the PDB and beyond. J Cheminform 2016; 8:42. [PMID: 27570544 PMCID: PMC5002144 DOI: 10.1186/s13321-016-0155-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 08/19/2016] [Indexed: 11/17/2022] Open
Abstract
We have developed a new platform-independent web-based molecular viewer using JavaScript and WebGL. The molecular viewer, Molmil, has been integrated into several services offered by Protein Data Bank Japan and can be easily extended with new functionality by third party developers. Furthermore, the viewer can be used to load files in various formats from the user’s local hard drive without uploading the data to a server. Molmil is available for all platforms supporting WebGL (e.g. Windows, Linux, iOS, Android) from http://gjbekker.github.io/molmil/. The source code is available at http://github.com/gjbekker/molmil under the LGPLv3 licence.
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Affiliation(s)
- Gert-Jan Bekker
- Laboratory of Protein Informatics, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 Japan ; Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871 Japan
| | - Haruki Nakamura
- Laboratory of Protein Informatics, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Akira R Kinjo
- Laboratory of Protein Informatics, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 Japan
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92
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Gainza P, Nisonoff HM, Donald BR. Algorithms for protein design. Curr Opin Struct Biol 2016; 39:16-26. [PMID: 27086078 PMCID: PMC5065368 DOI: 10.1016/j.sbi.2016.03.006] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 03/15/2016] [Accepted: 03/22/2016] [Indexed: 02/05/2023]
Abstract
Computational structure-based protein design programs are becoming an increasingly important tool in molecular biology. These programs compute protein sequences that are predicted to fold to a target structure and perform a desired function. The success of a program's predictions largely relies on two components: first, the input biophysical model, and second, the algorithm that computes the best sequence(s) and structure(s) according to the biophysical model. Improving both the model and the algorithm in tandem is essential to improving the success rate of current programs, and here we review recent developments in algorithms for protein design, emphasizing how novel algorithms enable the use of more accurate biophysical models. We conclude with a list of algorithmic challenges in computational protein design that we believe will be especially important for the design of therapeutic proteins and protein assemblies.
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Affiliation(s)
- Pablo Gainza
- Department of Computer Science, Duke University, Durham, NC, United States
| | - Hunter M Nisonoff
- Department of Computer Science, Duke University, Durham, NC, United States
| | - Bruce R Donald
- Department of Computer Science, Duke University, Durham, NC, United States; Department of Biochemistry, Duke University Medical Center, Durham, NC, United States; Department of Chemistry, Duke University, Durham, NC, United States.
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93
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Liu H, Chen Q. Computational protein design for given backbone: recent progresses in general method-related aspects. Curr Opin Struct Biol 2016; 39:89-95. [PMID: 27348345 DOI: 10.1016/j.sbi.2016.06.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Revised: 05/18/2016] [Accepted: 06/15/2016] [Indexed: 10/21/2022]
Abstract
To achieve high success rate in protein design requires a reliable sequence design method to find amino acid sequences that stably fold into a desired backbone structure. This problem is addressed by computational protein design through the approach of energy minimization. Here we review recent method progresses related to improving the accuracy of this approach. First, the quality of the energy model is a key factor. Second, with structure sensitive energy functions, whether and how backbone flexibility is considered can have large effects on design accuracy, although usually only small adjustments of the backbone structure itself are involved. Third, the effective accuracy of design results can be boosted by post-processing a small number of designed sequences with complementary models that may not be efficient enough for full sequence optimization. Finally, computational method development will benefit greatly from increasingly efficient experimental approaches that can be applied to obtain extensive feedbacks.
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Affiliation(s)
- Haiyan Liu
- School of Life Sciences, University of Science and Technology of China, China; Hefei National Laboratory for Physical Sciences at the Microscales, China; Collaborative Innovation Center of Chemistry for Life Sciences, Hefei, Anhui 230027, China; Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China.
| | - Quan Chen
- School of Life Sciences, University of Science and Technology of China, China
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94
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Laurino P, Tóth-Petróczy Á, Meana-Pañeda R, Lin W, Truhlar DG, Tawfik DS. An Ancient Fingerprint Indicates the Common Ancestry of Rossmann-Fold Enzymes Utilizing Different Ribose-Based Cofactors. PLoS Biol 2016; 14:e1002396. [PMID: 26938925 PMCID: PMC4777477 DOI: 10.1371/journal.pbio.1002396] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Accepted: 01/29/2016] [Indexed: 01/30/2023] Open
Abstract
Nucleoside-based cofactors are presumed to have preceded proteins. The Rossmann fold is one of the most ancient and functionally diverse protein folds, and most Rossmann enzymes utilize nucleoside-based cofactors. We analyzed an omnipresent Rossmann ribose-binding interaction: a carboxylate side chain at the tip of the second β-strand (β2-Asp/Glu). We identified a canonical motif, defined by the β2-topology and unique geometry. The latter relates to the interaction being bidentate (both ribose hydroxyls interacting with the carboxylate oxygens), to the angle between the carboxylate and the ribose, and to the ribose's ring configuration. We found that this canonical motif exhibits hallmarks of divergence rather than convergence. It is uniquely found in Rossmann enzymes that use different cofactors, primarily SAM (S-adenosyl methionine), NAD (nicotinamide adenine dinucleotide), and FAD (flavin adenine dinucleotide). Ribose-carboxylate bidentate interactions in other folds are not only rare but also have a different topology and geometry. We further show that the canonical geometry is not dictated by a physical constraint--geometries found in noncanonical interactions have similar calculated bond energies. Overall, these data indicate the divergence of several major Rossmann-fold enzyme classes, with different cofactors and catalytic chemistries, from a common pre-LUCA (last universal common ancestor) ancestor that possessed the β2-Asp/Glu motif.
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Affiliation(s)
- Paola Laurino
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Ágnes Tóth-Petróczy
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Rubén Meana-Pañeda
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Wei Lin
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Donald G. Truhlar
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Dan S. Tawfik
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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