메뉴 건너뛰기




Volumn 82, Issue 5, 2014, Pages 771-784

Improving the accuracy of protein stability predictions with multistate design using a variety of backbone ensembles

Author keywords

Backrub; Computational protein design; Molecular dynamics; Off target ensemble; On target ensemble; Perturbation and energy minimization; Protein G domain 1; Receiver operating characteristic

Indexed keywords

PROTEIN G; BACTERIAL PROTEIN; IGG FC-BINDING PROTEIN, STREPTOCOCCUS;

EID: 84898046743     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24457     Document Type: Article
Times cited : (40)

References (43)
  • 1
    • 23444450226 scopus 로고    scopus 로고
    • Semi-rational approaches to engineering enzyme activity: combining the benefits of directed evolution and rational design
    • Chica RA, Doucet, N, Pelletier, JN. Semi-rational approaches to engineering enzyme activity: combining the benefits of directed evolution and rational design. Curr Opin Biotechnol 2005;16:378-384.
    • (2005) Curr Opin Biotechnol , vol.16 , pp. 378-384
    • Chica, R.A.1    Doucet, N.2    Pelletier, J.N.3
  • 2
    • 34147169516 scopus 로고    scopus 로고
    • Potential energy functions for protein design
    • Boas FE, Harbury PB. Potential energy functions for protein design. Curr Opin Struct Biol 2007;17:199-204.
    • (2007) Curr Opin Struct Biol , vol.17 , pp. 199-204
    • Boas, F.E.1    Harbury, P.B.2
  • 3
    • 0035807809 scopus 로고    scopus 로고
    • Enzyme-like proteins by computational design
    • Bolon DN, Mayo SL. Enzyme-like proteins by computational design. Proc Natl Acad Sci USA 2001;98:14274-14279.
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 14274-14279
    • Bolon, D.N.1    Mayo, S.L.2
  • 5
    • 0344392711 scopus 로고    scopus 로고
    • Exploring the origins of binding specificity through the computational redesign of calmodulin
    • Shifman JM, Mayo SL. Exploring the origins of binding specificity through the computational redesign of calmodulin. Proc Natl Acad Sci USA 2003;100:13274-13279.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 13274-13279
    • Shifman, J.M.1    Mayo, S.L.2
  • 6
    • 2542523113 scopus 로고    scopus 로고
    • Computational design of receptors for an organophosphate surrogate of the nerve agent soman
    • Allert M, Rizk SS, Looger LL, Hellinga HW. Computational design of receptors for an organophosphate surrogate of the nerve agent soman. Proc Natl Acad Sci USA 2004;101:7907-7912.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 7907-7912
    • Allert, M.1    Rizk, S.S.2    Looger, L.L.3    Hellinga, H.W.4
  • 8
    • 34547691430 scopus 로고    scopus 로고
    • Full-sequence computational design and solution structure of a thermostable protein variant
    • Shah PS, Hom GK, Ross SA, Lassila JK, Crowhurst KA, Mayo SL. Full-sequence computational design and solution structure of a thermostable protein variant. J Mol Biol 2007;372:1-6.
    • (2007) J Mol Biol , vol.372 , pp. 1-6
    • Shah, P.S.1    Hom, G.K.2    Ross, S.A.3    Lassila, J.K.4    Crowhurst, K.A.5    Mayo, S.L.6
  • 10
    • 84898025369 scopus 로고    scopus 로고
    • Chapter Eighteen - Future challenges of computational protein design
    • Park SJ, Cochran JR, editors. Boca Raton: Talor and Francis Group
    • Choi EJ, Guntas G, Kuhlman B. Chapter Eighteen - Future challenges of computational protein design. In: Park SJ, Cochran JR, editors. Protein engineering and design. Boca Raton: Talor and Francis Group; 2010. pp 367-370.
    • (2010) Protein engineering and design , pp. 367-370
    • Choi, E.J.1    Guntas, G.2    Kuhlman, B.3
  • 12
    • 79960609097 scopus 로고    scopus 로고
    • Predicting the tolerated sequences for proteins and protein interfaces using rosettabackrub flexible backbone design
    • Smith CA, Kortemme, T. Predicting the tolerated sequences for proteins and protein interfaces using rosettabackrub flexible backbone design. Plos One 2011;6:e20451.
    • (2011) Plos One , vol.6
    • Smith, C.A.1    Kortemme, T.2
  • 13
    • 84861966405 scopus 로고    scopus 로고
    • Increasing sequence diversity with flexible backbone protein design: the complete redesign of a protein hydrophobic core
    • Murphy GS, Mills, JL, Miley, MJ, Machius, M, Szyperski, T, Kuhlman, B. Increasing sequence diversity with flexible backbone protein design: the complete redesign of a protein hydrophobic core. Structure 2012;20:1086-1096.
    • (2012) Structure , vol.20 , pp. 1086-1096
    • Murphy, G.S.1    Mills, J.L.2    Miley, M.J.3    Machius, M.4    Szyperski, T.5    Kuhlman, B.6
  • 14
    • 84874036318 scopus 로고    scopus 로고
    • Flexible backbone sampling methods to model and design protein alternative conformations
    • Ollikainen N, Smith CA, Fraser JS, Kortemme T. Flexible backbone sampling methods to model and design protein alternative conformations. Methods Protein Design 2013;523:61-85.
    • (2013) Methods Protein Design , vol.523 , pp. 61-85
    • Ollikainen, N.1    Smith, C.A.2    Fraser, J.S.3    Kortemme, T.4
  • 15
    • 84865407431 scopus 로고    scopus 로고
    • Multistate approaches in computational protein design
    • Davey JA, Chica RA. Multistate approaches in computational protein design. Protein Sci 2012;21:1241-1252.
    • (2012) Protein Sci , vol.21 , pp. 1241-1252
    • Davey, J.A.1    Chica, R.A.2
  • 16
    • 78650566901 scopus 로고    scopus 로고
    • Experimental library screening demonstrates the successful application of computational protein design to large structural ensembles
    • Allen BD, Nisthal A, Mayo, SL. Experimental library screening demonstrates the successful application of computational protein design to large structural ensembles. Proc Natl Acad Sci USA 2010;107:19838-19843.
    • (2010) Proc Natl Acad Sci USA , vol.107 , pp. 19838-19843
    • Allen, B.D.1    Nisthal, A.2    Mayo, S.L.3
  • 17
    • 32044456003 scopus 로고    scopus 로고
    • The backrub motion: how protein backbone shrugs when a sidechain dances
    • Davis IW, Arendall WB, Richardson DC, Richardson JS. The backrub motion: how protein backbone shrugs when a sidechain dances. Structure 2006;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
  • 19
    • 0028354429 scopus 로고
    • 2 Crystal-structures of the B1 immunoglobulin-binding domain of streptococcal protein-G and comparison with Nmr
    • Gallagher T, Alexander P, Bryan P, Gilliland GL. 2 Crystal-structures of the B1 immunoglobulin-binding domain of streptococcal protein-G and comparison with Nmr. Biochemistry 1994;33:4721-4729.
    • (1994) Biochemistry , vol.33 , pp. 4721-4729
    • Gallagher, T.1    Alexander, P.2    Bryan, P.3    Gilliland, G.L.4
  • 20
    • 65249157397 scopus 로고    scopus 로고
    • Protonate3D: assignment of ionization states and hydrogen coordinates to macromolecular structures
    • Labute P. Protonate3D: assignment of ionization states and hydrogen coordinates to macromolecular structures. Proteins 2009;75:187-205.
    • (2009) Proteins , vol.75 , pp. 187-205
    • Labute, P.1
  • 21
    • 84855757480 scopus 로고    scopus 로고
    • Version 2011.13. Chemical Computing Group, Inc. Montreal, Quebec, Canada
    • Molecular Operating Environment (MOE), Version 2011.13. Chemical Computing Group, Inc. Montreal, Quebec, Canada, 2011.
    • (2011) Molecular Operating Environment (MOE)
  • 22
    • 0001398008 scopus 로고    scopus 로고
    • How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?
    • Wang JM, Cieplak P, Kollman PA. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J Comput Chem 2000;21:1049-1074.
    • (2000) J Comput Chem , vol.21 , pp. 1049-1074
    • Wang, J.M.1    Cieplak, P.2    Kollman, P.A.3
  • 23
    • 0001471515 scopus 로고    scopus 로고
    • The Nose-Poincare method for constant temperature molecular dynamics
    • Bond SD, Leimkuhler BJ, Laird BB. The Nose-Poincare method for constant temperature molecular dynamics. J Comput Phys 1999;151:114-134.
    • (1999) J Comput Phys , vol.151 , pp. 114-134
    • Bond, S.D.1    Leimkuhler, B.J.2    Laird, B.B.3
  • 24
    • 0001749606 scopus 로고    scopus 로고
    • Symplectic algorithm for constant-pressure molecular dynamics using a Nose-Poincare thermostat
    • Sturgeon JB, Laird BB. Symplectic algorithm for constant-pressure molecular dynamics using a Nose-Poincare thermostat. J Chem Phys 2000;112:3474-3482.
    • (2000) J Chem Phys , vol.112 , pp. 3474-3482
    • Sturgeon, J.B.1    Laird, B.B.2
  • 25
    • 0034538773 scopus 로고    scopus 로고
    • A survey of truncated-Newton methods
    • Nash SG. A survey of truncated-Newton methods. J Comput Appl Math 2000;124:45-59.
    • (2000) J Comput Appl Math , vol.124 , pp. 45-59
    • Nash, S.G.1
  • 27
    • 33745614865 scopus 로고    scopus 로고
    • Dramatic performance enhancements for the FASTER optimization algorithm
    • Allen BD, Mayo SL. Dramatic performance enhancements for the FASTER optimization algorithm. J Comput Chem 2006;27:1071-1075.
    • (2006) J Comput Chem , vol.27 , pp. 1071-1075
    • Allen, B.D.1    Mayo, S.L.2
  • 28
    • 77952849163 scopus 로고    scopus 로고
    • An efficient algorithm for multistate protein design based on FASTER
    • Allen BD, Mayo SL. An efficient algorithm for multistate protein design based on FASTER. J Comput Chem 2010;31:904-916.
    • (2010) J Comput Chem , vol.31 , pp. 904-916
    • Allen, B.D.1    Mayo, S.L.2
  • 29
    • 1842326139 scopus 로고    scopus 로고
    • Bayesian statistical analysis of protein side-chain rotamer preferences
    • Dunbrack RL, Cohen FE. Bayesian statistical analysis of protein side-chain rotamer preferences. Protein Sci 1997;6:1661-1681.
    • (1997) Protein Sci , vol.6 , pp. 1661-1681
    • Dunbrack, R.L.1    Cohen, F.E.2
  • 30
    • 9144240095 scopus 로고
    • Dreiding-a generic force-field for molecular simulations
    • Mayo SL, Olafson BD, Goddard WA. Dreiding-a generic force-field for molecular simulations. J Phys Chem 1990;94:8897-8909.
    • (1990) J Phys Chem , vol.94 , pp. 8897-8909
    • Mayo, S.L.1    Olafson, B.D.2    Goddard, W.A.3
  • 31
    • 0030987610 scopus 로고    scopus 로고
    • Probing the role of packing specificity in protein design
    • Dahiyat BI, Mayo SL. Probing the role of packing specificity in protein design. Proc Natl Acad Sci USA 1997;94:10172-10177.
    • (1997) Proc Natl Acad Sci USA , vol.94 , pp. 10172-10177
    • Dahiyat, B.I.1    Mayo, S.L.2
  • 32
    • 0033135638 scopus 로고    scopus 로고
    • Effective energy function for proteins in solution
    • Lazaridis T, Karplus M. Effective energy function for proteins in solution. Proteins 1999;35:133-152.
    • (1999) Proteins , vol.35 , pp. 133-152
    • Lazaridis, T.1    Karplus, M.2
  • 33
    • 0031844416 scopus 로고    scopus 로고
    • Pairwise calculation of protein solvent-accessible surface areas
    • Street AG, Mayo SL. Pairwise calculation of protein solvent-accessible surface areas. Folding Design 1998;3:253-258.
    • (1998) Folding Design , vol.3 , pp. 253-258
    • Street, A.G.1    Mayo, S.L.2
  • 34
    • 78650543850 scopus 로고    scopus 로고
    • Generation of longer emission wavelength red fluorescent proteins using computationally designed libraries
    • Chica RA, Moore MM, Allen BD, Mayo SL. Generation of longer emission wavelength red fluorescent proteins using computationally designed libraries. Proc Natl Acad Sci USA 2010;107:20257-20262.
    • (2010) Proc Natl Acad Sci USA , vol.107 , pp. 20257-20262
    • Chica, R.A.1    Moore, M.M.2    Allen, B.D.3    Mayo, S.L.4
  • 37
    • 38649131767 scopus 로고    scopus 로고
    • The effect of numerical error on the reproducibility of molecular geometry optimizations
    • Williams CI, Feher M. The effect of numerical error on the reproducibility of molecular geometry optimizations. J Comput Aided Mol Des 2008;22:39-51.
    • (2008) J Comput Aided Mol Des , vol.22 , pp. 39-51
    • Williams, C.I.1    Feher, M.2
  • 38
    • 77955579347 scopus 로고    scopus 로고
    • Designing ensembles in conformational and sequence space to characterize and engineer proteins
    • Friedland GD, Kortemme T. Designing ensembles in conformational and sequence space to characterize and engineer proteins. Cur Opin Struct Biol 2010;20:377-384.
    • (2010) Cur Opin Struct Biol , vol.20 , pp. 377-384
    • Friedland, G.D.1    Kortemme, T.2
  • 39
    • 79551470095 scopus 로고    scopus 로고
    • Role of conformational sampling in computing mutation-induced changes in protein structure and stability
    • Kellogg EH, Leaver-Fay A, Baker D. Role of conformational sampling in computing mutation-induced changes in protein structure and stability. Proteins 2011;79:830-838.
    • (2011) Proteins , vol.79 , pp. 830-838
    • Kellogg, E.H.1    Leaver-Fay, A.2    Baker, D.3
  • 40
    • 34249777526 scopus 로고    scopus 로고
    • Eris: an automated estimator of protein stability
    • Yin SY, Ding F, Dokholyan NV. Eris: an automated estimator of protein stability. Nat Methods 2007;4:466-467.
    • (2007) Nat Methods , vol.4 , pp. 466-467
    • Yin, S.Y.1    Ding, F.2    Dokholyan, N.V.3
  • 41
    • 36749018607 scopus 로고    scopus 로고
    • Modeling backbone flexibility improves protein stability estimation
    • Yin S, Ding F, Dokholyan NV. Modeling backbone flexibility improves protein stability estimation. Structure 2007;15:1567-1576.
    • (2007) Structure , vol.15 , pp. 1567-1576
    • Yin, S.1    Ding, F.2    Dokholyan, N.V.3
  • 42
    • 70349334428 scopus 로고    scopus 로고
    • X-ray vs. NMR structures as templates for computational protein design
    • Schneider M, Fu XR, Keating AE. X-ray vs. NMR structures as templates for computational protein design. Proteins 2009;77:97-110.
    • (2009) Proteins , vol.77 , pp. 97-110
    • Schneider, M.1    Fu, X.R.2    Keating, A.E.3
  • 43
    • 0036892389 scopus 로고    scopus 로고
    • Thoroughly sampling sequence space: large-scale protein design of structural ensembles
    • Larson SM, England JL, Desjarlais JR, Pande VS. Thoroughly sampling sequence space: large-scale protein design of structural ensembles. Protein Sci 2002;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


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.