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Volumn 9, Issue 11, 2013, Pages

Computational Protein Design Quantifies Structural Constraints on Amino Acid Covariation

Author keywords

[No Author keywords available]

Indexed keywords

PROTEINS; STRUCTURAL DESIGN;

EID: 84888273231     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1003313     Document Type: Article
Times cited : (31)

References (50)
  • 1
    • 0035823119 scopus 로고    scopus 로고
    • Understanding hierarchical protein evolution from first principles
    • Dokholyan NV, Shakhnovich EI, (2001) Understanding hierarchical protein evolution from first principles. J Mol Biol 312: 289-307.
    • (2001) J Mol Biol , vol.312 , pp. 289-307
    • Dokholyan, N.V.1    Shakhnovich, E.I.2
  • 2
    • 47549097539 scopus 로고    scopus 로고
    • Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution
    • Drummond DA, Wilke CO, (2008) Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell 134: 341-352.
    • (2008) Cell , vol.134 , pp. 341-352
    • Drummond, D.A.1    Wilke, C.O.2
  • 4
    • 0034641749 scopus 로고    scopus 로고
    • Native protein sequences are close to optimal for their structures
    • Kuhlman B, Baker D, (2000) Native protein sequences are close to optimal for their structures. Proc Natl Acad Sci USA 97: 10383-10388.
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 10383-10388
    • Kuhlman, B.1    Baker, D.2
  • 5
    • 84874028898 scopus 로고    scopus 로고
    • OSPREY: protein design with ensembles, flexibility, and provable algorithms
    • Gainza P, Roberts KE, Georgiev I, Lilien RH, Keedy DA, et al. (2013) OSPREY: protein design with ensembles, flexibility, and provable algorithms. Meth Enzymol 523: 87-107.
    • (2013) Meth Enzymol , vol.523 , pp. 87-107
    • Gainza, P.1    Roberts, K.E.2    Georgiev, I.3    Lilien, R.H.4    Keedy, D.A.5
  • 6
    • 7044239239 scopus 로고    scopus 로고
    • A simple physical model for the prediction and design of protein-DNA interactions
    • Havranek JJ, Duarte CM, Baker D, (2004) A simple physical model for the prediction and design of protein-DNA interactions. J Mol Biol 344: 59-70.
    • (2004) J Mol Biol , vol.344 , pp. 59-70
    • Havranek, J.J.1    Duarte, C.M.2    Baker, D.3
  • 7
    • 31944436020 scopus 로고    scopus 로고
    • Protein design simulations suggest that side-chain conformational entropy is not a strong determinant of amino acid environmental preferences
    • Hu X, Kuhlman B, (2006) Protein design simulations suggest that side-chain conformational entropy is not a strong determinant of amino acid environmental preferences. Proteins 62: 739-748.
    • (2006) Proteins , vol.62 , pp. 739-748
    • Hu, X.1    Kuhlman, B.2
  • 8
    • 34548383489 scopus 로고    scopus 로고
    • Design of multi-specificity in protein interfaces
    • Humphris EL, Kortemme T, (2007) Design of multi-specificity in protein interfaces. PLoS Comput Biol 3: e164.
    • (2007) PLoS Comput Biol , vol.3
    • Humphris, E.L.1    Kortemme, T.2
  • 9
    • 0036892389 scopus 로고    scopus 로고
    • Thoroughly sampling sequence space: large-scale protein design of structural ensembles
    • Larson SM, England JL, Desjarlais JR, Pande VS, (2002) Thoroughly sampling sequence space: large-scale protein design of structural ensembles. Protein Sci 11: 2804-2813.
    • (2002) Protein Sci , vol.11 , pp. 2804-2813
    • Larson, S.M.1    England, J.L.2    Desjarlais, J.R.3    Pande, V.S.4
  • 10
    • 0037022286 scopus 로고    scopus 로고
    • Protein topology and stability define the space of allowed sequences
    • Koehl P, Levitt M, (2002) Protein topology and stability define the space of allowed sequences. Proc Natl Acad Sci USA 99: 1280-1285.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 1280-1285
    • Koehl, P.1    Levitt, M.2
  • 11
    • 0023155210 scopus 로고
    • Tertiary Templates for Proteins - Use of Packing Criteria in the Enumeration of Allowed Sequences for Different Structural Classes
    • Ponder JW, Richards FM, (1987) Tertiary Templates for Proteins- Use of Packing Criteria in the Enumeration of Allowed Sequences for Different Structural Classes. J Mol Biol 193: 775-791.
    • (1987) J Mol Biol , vol.193 , pp. 775-791
    • Ponder, J.W.1    Richards, F.M.2
  • 12
    • 1842839788 scopus 로고    scopus 로고
    • Simulating protein evolution in sequence and structure space
    • Xia Y, Levitt M, (2004) Simulating protein evolution in sequence and structure space. Curr Opin Struct Biol 14: 202-207.
    • (2004) Curr Opin Struct Biol , vol.14 , pp. 202-207
    • Xia, Y.1    Levitt, M.2
  • 13
    • 12544260150 scopus 로고    scopus 로고
    • Recapitulation of Protein Family Divergence using Flexible Backbone Protein Design
    • Saunders CT, Baker D, (2005) Recapitulation of Protein Family Divergence using Flexible Backbone Protein Design. J Mol Biol 346: 631-644.
    • (2005) J Mol Biol , vol.346 , pp. 631-644
    • Saunders, C.T.1    Baker, D.2
  • 14
    • 34248674895 scopus 로고    scopus 로고
    • The Stability Effects of Protein Mutations Appear to be Universally Distributed
    • Tokuriki N, Stricher F, Schymkowitz J, Serrano L, Tawfik DS, (2007) The Stability Effects of Protein Mutations Appear to be Universally Distributed. J Mol Biol 369: 1318-1332.
    • (2007) J Mol Biol , vol.369 , pp. 1318-1332
    • Tokuriki, N.1    Stricher, F.2    Schymkowitz, J.3    Serrano, L.4    Tawfik, D.S.5
  • 15
    • 84866073112 scopus 로고    scopus 로고
    • Prediction of Mutational Tolerance in HIV-1 Protease and Reverse Transcriptase Using Flexible Backbone Protein Design
    • Humphris-Narayanan E, Akiva E, Varela R, Conchuir SO, Kortemme T, (2012) Prediction of Mutational Tolerance in HIV-1 Protease and Reverse Transcriptase Using Flexible Backbone Protein Design. PLoS Comput Biol 8: e1002639.
    • (2012) PLoS Comput Biol , vol.8
    • Humphris-Narayanan, E.1    Akiva, E.2    Varela, R.3    Conchuir, S.O.4    Kortemme, T.5
  • 16
    • 77956730468 scopus 로고    scopus 로고
    • Structure-Based Prediction of the Peptide Sequence Space Recognized by Natural and Synthetic PDZ Domains
    • Smith CA, Kortemme T, (2010) Structure-Based Prediction of the Peptide Sequence Space Recognized by Natural and Synthetic PDZ Domains. J Mol Biol 402: 460-474.
    • (2010) J Mol Biol , vol.402 , pp. 460-474
    • Smith, C.A.1    Kortemme, T.2
  • 17
    • 78349258533 scopus 로고    scopus 로고
    • Structure-based prediction of protein-peptide specificity in Rosetta
    • King CA, Bradley P, (2010) Structure-based prediction of protein-peptide specificity in Rosetta. Proteins 78: 3437-3449.
    • (2010) Proteins , vol.78 , pp. 3437-3449
    • King, C.A.1    Bradley, P.2
  • 18
    • 80055068044 scopus 로고    scopus 로고
    • Identification of a novel class of farnesylation targets by structure-based modeling of binding specificity
    • London N, Lamphear CL, Hougland JL, Fierke CA, Schueler-Furman O, (2011) Identification of a novel class of farnesylation targets by structure-based modeling of binding specificity. PLoS Comput Biol 7: e1002170.
    • (2011) PLoS Comput Biol , vol.7
    • London, N.1    Lamphear, C.L.2    Hougland, J.L.3    Fierke, C.A.4    Schueler-Furman, O.5
  • 19
    • 79960609097 scopus 로고    scopus 로고
    • Predicting the Tolerated Sequences for Proteins and Protein Interfaces Using RosettaBackrub Flexible Backbone Design
    • Smith CA, Kortemme T, (2011) Predicting the Tolerated Sequences for Proteins and Protein Interfaces Using RosettaBackrub Flexible Backbone Design. PLoS One 6: e20451.
    • (2011) PLoS One , vol.6
    • Smith, C.A.1    Kortemme, T.2
  • 20
    • 84864577143 scopus 로고    scopus 로고
    • Predictive Bcl-2 family binding models rooted in experiment or structure
    • DeBartolo J, Dutta S, Reich L, Keating AE, (2012) Predictive Bcl-2 family binding models rooted in experiment or structure. J Mol Biol 422: 124-144.
    • (2012) J Mol Biol , vol.422 , pp. 124-144
    • DeBartolo, J.1    Dutta, S.2    Reich, L.3    Keating, A.E.4
  • 21
    • 33846102955 scopus 로고    scopus 로고
    • Computationally designed libraries of fluorescent proteins evaluated by preservation and diversity of function
    • Treynor TP, Vizcarra CL, Nedelcu D, Mayo SL, (2007) Computationally designed libraries of fluorescent proteins evaluated by preservation and diversity of function. Proc Natl Acad Sci USA 104: 48-53.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 48-53
    • Treynor, T.P.1    Vizcarra, C.L.2    Nedelcu, D.3    Mayo, S.L.4
  • 22
    • 78650471329 scopus 로고    scopus 로고
    • Engineering Enzyme Specificity Using Computational Design of a Defined-Sequence Library
    • Lippow SM, Moon TS, Basu S, Yoon S-H, Li X, et al. (2010) Engineering Enzyme Specificity Using Computational Design of a Defined-Sequence Library. Chem Biol 17: 1306-1315.
    • (2010) Chem Biol , vol.17 , pp. 1306-1315
    • Lippow, S.M.1    Moon, T.S.2    Basu, S.3    Yoon, S.-H.4    Li, X.5
  • 23
    • 57049180165 scopus 로고    scopus 로고
    • Prediction of Protein-Protein Interface Sequence Diversity Using Flexible Backbone Computational Protein Design
    • Humphris EL, Kortemme T, (2008) Prediction of Protein-Protein Interface Sequence Diversity Using Flexible Backbone Computational Protein Design. Structure 16: 1777-1788.
    • (2008) Structure , vol.16 , pp. 1777-1788
    • Humphris, E.L.1    Kortemme, T.2
  • 24
    • 67049155677 scopus 로고    scopus 로고
    • A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family
    • Friedland GD, Lakomek N-A, Griesinger C, Meiler J, Kortemme T, (2009) A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family. PLoS Comput Biol 5: e1000393.
    • (2009) PLoS Comput Biol , vol.5
    • Friedland, G.D.1    Lakomek, N.-A.2    Griesinger, C.3    Meiler, J.4    Kortemme, T.5
  • 25
    • 79956222955 scopus 로고    scopus 로고
    • Assessment of flexible backbone protein design methods for sequence library prediction in the therapeutic antibody Herceptin-HER2 interface
    • Babor M, Mandell DJ, Kortemme T, (2011) Assessment of flexible backbone protein design methods for sequence library prediction in the therapeutic antibody Herceptin-HER2 interface. Protein Sci 20: 1082-1089.
    • (2011) Protein Sci , vol.20 , pp. 1082-1089
    • Babor, M.1    Mandell, D.J.2    Kortemme, T.3
  • 26
    • 18544362952 scopus 로고    scopus 로고
    • Mutual information in protein multiple sequence alignments reveals two classes of coevolving positions
    • Gloor GB, Martin LC, Wahl LM, Dunn SD, (2005) Mutual information in protein multiple sequence alignments reveals two classes of coevolving positions. Biochemistry 44: 7156-7165.
    • (2005) Biochemistry , vol.44 , pp. 7156-7165
    • Gloor, G.B.1    Martin, L.C.2    Wahl, L.M.3    Dunn, S.D.4
  • 27
    • 38849115223 scopus 로고    scopus 로고
    • Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction
    • Dunn SD, Wahl LM, Gloor GB, (2008) Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction. Bioinformatics 24: 333-340.
    • (2008) Bioinformatics , vol.24 , pp. 333-340
    • Dunn, S.D.1    Wahl, L.M.2    Gloor, G.B.3
  • 28
    • 77955330195 scopus 로고    scopus 로고
    • Identifying and Seeing beyond Multiple Sequence Alignment Errors Using Intra-Molecular Protein Covariation
    • Dickson RJ, Wahl LM, Fernandes AD, Gloor GB, (2010) Identifying and Seeing beyond Multiple Sequence Alignment Errors Using Intra-Molecular Protein Covariation. PLoS One 5: e11082.
    • (2010) PLoS One , vol.5
    • Dickson, R.J.1    Wahl, L.M.2    Fernandes, A.D.3    Gloor, G.B.4
  • 30
    • 0033536602 scopus 로고    scopus 로고
    • Evolutionarily conserved pathways of energetic connectivity in protein families
    • Lockless SW, Ranganathan R, (1999) Evolutionarily conserved pathways of energetic connectivity in protein families. Science 286: 295-299.
    • (1999) Science , vol.286 , pp. 295-299
    • Lockless, S.W.1    Ranganathan, R.2
  • 31
    • 0037219686 scopus 로고    scopus 로고
    • Evolutionarily conserved networks of residues mediate allosteric communication in proteins
    • Süel GM, Lockless SW, Wall MA, Ranganathan R, (2002) Evolutionarily conserved networks of residues mediate allosteric communication in proteins. Nat Struct Biol 10: 59-69.
    • (2002) Nat Struct Biol , vol.10 , pp. 59-69
    • Süel, G.M.1    Lockless, S.W.2    Wall, M.A.3    Ranganathan, R.4
  • 32
    • 0034721944 scopus 로고    scopus 로고
    • Analysis of covariation in an SH3 domain sequence alignment: applications in tertiary contact prediction and the design of compensating hydrophobic core substitutions
    • Larson SM, Di Nardo AA, Davidson AR, (2000) Analysis of covariation in an SH3 domain sequence alignment: applications in tertiary contact prediction and the design of compensating hydrophobic core substitutions. J Mol Biol 303: 433-446.
    • (2000) J Mol Biol , vol.303 , pp. 433-446
    • Larson, S.M.1    Di Nardo, A.A.2    Davidson, A.R.3
  • 33
    • 84874036318 scopus 로고    scopus 로고
    • Flexible backbone sampling methods to model and design protein alternative conformations
    • Ollikainen N, Smith CA, Fraser JS, Kortemme T, (2013) Flexible backbone sampling methods to model and design protein alternative conformations. Meth Enzymol 523: 61-85.
    • (2013) Meth Enzymol , vol.523 , pp. 61-85
    • Ollikainen, N.1    Smith, C.A.2    Fraser, J.S.3    Kortemme, T.4
  • 34
    • 0345306764 scopus 로고    scopus 로고
    • Design of a novel globular protein fold with atomic-level accuracy
    • Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, et al. (2003) Design of a novel globular protein fold with atomic-level accuracy. Science 302: 1364-1368.
    • (2003) Science , vol.302 , pp. 1364-1368
    • Kuhlman, B.1    Dantas, G.2    Ireton, G.C.3    Varani, G.4    Stoddard, B.L.5
  • 35
    • 32044456003 scopus 로고    scopus 로고
    • The Backrub Motion: How Protein Backbone Shrugs When a Sidechain Dances
    • Davis IW, Arendall WB, Richardson DC, Richardson JS, (2006) The Backrub Motion: How Protein Backbone Shrugs When a Sidechain Dances. Structure 14: 265-274.
    • (2006) Structure , vol.14 , pp. 265-274
    • Davis, I.W.1    Arendall, W.B.2    Richardson, D.C.3    Richardson, J.S.4
  • 36
    • 45649084560 scopus 로고    scopus 로고
    • Backrub-Like Backbone Simulation Recapitulates Natural Protein Conformational Variability and Improves Mutant Side-Chain Prediction
    • Smith CA, Kortemme T, (2008) Backrub-Like Backbone Simulation Recapitulates Natural Protein Conformational Variability and Improves Mutant Side-Chain Prediction. J Mol Biol 380: 742-756.
    • (2008) J Mol Biol , vol.380 , pp. 742-756
    • Smith, C.A.1    Kortemme, T.2
  • 37
    • 83755178457 scopus 로고    scopus 로고
    • Direct-coupling analysis of residue coevolution captures native contacts across many protein families
    • Morcos F, Pagnani A, Lunt B, Bertolino A, Marks DS, et al. (2011) Direct-coupling analysis of residue coevolution captures native contacts across many protein families. Proc Natl Acad Sci USA 108: E1293-E1301.
    • (2011) Proc Natl Acad Sci USA , vol.108
    • Morcos, F.1    Pagnani, A.2    Lunt, B.3    Bertolino, A.4    Marks, D.S.5
  • 38
    • 68349104348 scopus 로고    scopus 로고
    • Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling
    • Mandell DJ, Coutsias EA, Kortemme T, (2009) Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling. Nat Methods 6: 551-552.
    • (2009) Nat Methods , vol.6 , pp. 551-552
    • Mandell, D.J.1    Coutsias, E.A.2    Kortemme, T.3
  • 40
    • 78650918983 scopus 로고    scopus 로고
    • Alternate States of Proteins Revealed by Detailed Energy Landscape Mapping
    • Tyka MD, Keedy DA, Andre I, DiMaio F, Song Y, et al. (2011) Alternate States of Proteins Revealed by Detailed Energy Landscape Mapping. J Mol Biol 405: 607-618.
    • (2011) J Mol Biol , vol.405 , pp. 607-618
    • Tyka, M.D.1    Keedy, D.A.2    Andre, I.3    DiMaio, F.4    Song, Y.5
  • 42
    • 44649153450 scopus 로고    scopus 로고
    • Rewiring the specificity of two-component signal transduction systems
    • Skerker JM, Perchuk BS, Siryaporn A, Lubin EA, Ashenberg O, et al. (2008) Rewiring the specificity of two-component signal transduction systems. Cell 133: 1043-1054.
    • (2008) Cell , vol.133 , pp. 1043-1054
    • Skerker, J.M.1    Perchuk, B.S.2    Siryaporn, A.3    Lubin, E.A.4    Ashenberg, O.5
  • 43
    • 84859467082 scopus 로고    scopus 로고
    • Control of protein signaling using a computationally designed GTPase/GEF orthogonal pair
    • Kapp GT, Liu S, Stein A, Wong DT, Reményi A, et al. (2012) Control of protein signaling using a computationally designed GTPase/GEF orthogonal pair. Proc Natl Acad Sci USA 109: 5277-5282.
    • (2012) Proc Natl Acad Sci USA , vol.109 , pp. 5277-5282
    • Kapp, G.T.1    Liu, S.2    Stein, A.3    Wong, D.T.4    Reményi, A.5
  • 46
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: multiple sequence alignment with high accuracy and high throughput
    • Edgar RC, (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32: 1792-1797.
    • (2004) Nucleic Acids Research , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 47
    • 33745634395 scopus 로고    scopus 로고
    • Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
    • Li W, Godzik A, (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22: 1658-1659.
    • (2006) Bioinformatics , vol.22 , pp. 1658-1659
    • Li, W.1    Godzik, A.2
  • 48
    • 0036307493 scopus 로고    scopus 로고
    • Within the twilight zone: A sensitive profile-profile comparison tool based on information theory
    • Yona G, Levitt M, (2002) Within the twilight zone: A sensitive profile-profile comparison tool based on information theory. J Mol Biol 315: 1257-1275.
    • (2002) J Mol Biol , vol.315 , pp. 1257-1275
    • Yona, G.1    Levitt, M.2
  • 49
    • 84888252252 scopus 로고    scopus 로고
    • The PyMOL Molecular Graphics System, Version 1.2b0 Schrödinger, LLC
    • The PyMOL Molecular Graphics System, Version 1.2b0 Schrödinger, LLC.
  • 50
    • 79961135005 scopus 로고    scopus 로고
    • R Development Core Team, R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL
    • R Development Core Team (2011) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org/.
    • (2011) R: A language and environment for statistical computing


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