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Volumn 106, Issue 30, 2009, Pages 12347-12352

Protein elastic network models and the ranges of cooperativity

Author keywords

B factors; Conformational entropy

Indexed keywords

PROTEIN;

EID: 68149141470     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0902159106     Document Type: Article
Times cited : (222)

References (56)
  • 1
    • 0021918946 scopus 로고
    • Prediction of chain flexibility in proteins - A tool for the selection of peptide antigens
    • Karplus PA, Schulz GE (1985) Prediction of chain flexibility in proteins - A tool for the selection of peptide antigens. Naturwiss 72:212-213.
    • (1985) Naturwiss , vol.72 , pp. 212-213
    • Karplus, P.A.1    Schulz, G.E.2
  • 2
    • 0028361031 scopus 로고
    • Accuracy of protein flexibility predictions
    • Vihinen M, Torkkila E, Riikonen P (1994) Accuracy of protein flexibility predictions. Proteins 19:141-149.
    • (1994) Proteins , vol.19 , pp. 141-149
    • Vihinen, M.1    Torkkila, E.2    Riikonen, P.3
  • 4
    • 0347364621 scopus 로고    scopus 로고
    • Protein flexibility and intrinsic disorder
    • Radivojac P, et al. (2004) Protein flexibility and intrinsic disorder. Protein Sci 13:71-80.
    • (2004) Protein Sci , vol.13 , pp. 71-80
    • Radivojac, P.1
  • 5
    • 13944277320 scopus 로고    scopus 로고
    • Prediction of protein B-factor profiles
    • Yuan Z, Bailey TL, Teasdale RD (2005) Prediction of protein B-factor profiles. Proteins 58:905-912.
    • (2005) Proteins , vol.58 , pp. 905-912
    • Yuan, Z.1    Bailey, T.L.2    Teasdale, R.D.3
  • 6
    • 24344503079 scopus 로고    scopus 로고
    • Protein flexibility and rigidity predicted from sequence
    • Schlessinger A, Rost B (2005) Protein flexibility and rigidity predicted from sequence. Proteins 61:115-126.
    • (2005) Proteins , vol.61 , pp. 115-126
    • Schlessinger, A.1    Rost, B.2
  • 7
    • 33846965982 scopus 로고    scopus 로고
    • Prediction of protein B-factors using multiclass bounded SVM
    • Chen P, Wang B, Wong HS, Huang DS (2007) Prediction of protein B-factors using multiclass bounded SVM. Protein Pept Lett 14:185-190.
    • (2007) Protein Pept Lett , vol.14 , pp. 185-190
    • Chen, P.1    Wang, B.2    Wong, H.S.3    Huang, D.S.4
  • 8
    • 0030623823 scopus 로고    scopus 로고
    • Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
    • Bahar I, Atilgan AR, Erman B (1997) Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold Des 2:173-181.
    • (1997) Fold Des , vol.2 , pp. 173-181
    • Bahar, I.1    Atilgan, A.R.2    Erman, B.3
  • 9
    • 0032749098 scopus 로고    scopus 로고
    • Structure-based analysis of protein dynamics: Comparison of theoretical results for hen lysozyme with X-ray diffraction and NMR relaxation data
    • Haliloglu T, Bahar I (1999) Structure-based analysis of protein dynamics: Comparison of theoretical results for hen lysozyme with X-ray diffraction and NMR relaxation data. Proteins 37:654-667.
    • (1999) Proteins , vol.37 , pp. 654-667
    • Haliloglu, T.1    Bahar, I.2
  • 10
    • 0035996990 scopus 로고    scopus 로고
    • Dynamics of proteins in crystals: Comparison of experiment with simple models
    • Kundu S, Melton JS, Sorensen DC, Phillips GN, Jr (2002) Dynamics of proteins in crystals: Comparison of experiment with simple models. Biophys J 83:723-732.
    • (2002) Biophys J , vol.83 , pp. 723-732
    • Kundu, S.1    Melton, J.S.2    Sorensen, D.C.3    Phillips Jr, G.N.4
  • 11
    • 33747829284 scopus 로고    scopus 로고
    • oGNM: Online computation of structural dynamics using the Gaussian network model
    • Yang LW, et al. (2006) oGNM: Online computation of structural dynamics using the Gaussian network model. Nucl Acids Res 34:W24-W31.
    • (2006) Nucl Acids Res , vol.34
    • Yang, L.W.1
  • 12
    • 33748189629 scopus 로고    scopus 로고
    • The extent of cooperativity of protein motions observed with elastic network models is similar for atomic and coarser-grained models
    • Sen TZ, Feng Y, Garcia JV, Kloczkowski A, Jernigan RL (2006) The extent of cooperativity of protein motions observed with elastic network models is similar for atomic and coarser-grained models. J Chem Theo Comp 2:696-704.
    • (2006) J Chem Theo Comp , vol.2 , pp. 696-704
    • Sen, T.Z.1    Feng, Y.2    Garcia, J.V.3    Kloczkowski, A.4    Jernigan, R.L.5
  • 13
    • 34248182936 scopus 로고    scopus 로고
    • vGNM: A better model for understanding the dynamics of proteins in crystals
    • Song G, Jernigan RL (2007) vGNM: A better model for understanding the dynamics of proteins in crystals. J Mol Biol 369:880-893.
    • (2007) J Mol Biol , vol.369 , pp. 880-893
    • Song, G.1    Jernigan, R.L.2
  • 14
    • 0037173062 scopus 로고    scopus 로고
    • How to describe protein motion without amino acid sequence and atomic coordinates
    • Ming D, Kong Y, Lambert MA, Huang Z, Ma J (2002) How to describe protein motion without amino acid sequence and atomic coordinates. Proc Natl Acad Sci USA 99:8620-8625.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 8620-8625
    • Ming, D.1    Kong, Y.2    Lambert, M.A.3    Huang, Z.4    Ma, J.5
  • 15
    • 51149211502 scopus 로고
    • Improved simulation of liquid water by molecular dynamics
    • Stillinger FH, Rahman A (1974) Improved simulation of liquid water by molecular dynamics. J Chem Phys 60:1545-1557.
    • (1974) J Chem Phys , vol.60 , pp. 1545-1557
    • Stillinger, F.H.1    Rahman, A.2
  • 17
    • 27344436659 scopus 로고    scopus 로고
    • Scalable molecular dynamics with NAMD
    • Phillips JC, et al. (2005) Scalable molecular dynamics with NAMD. J Comp Chem 26:1781-1802.
    • (2005) J Comp Chem , vol.26 , pp. 1781-1802
    • Phillips, J.C.1
  • 18
    • 84986512474 scopus 로고
    • CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
    • Brooks BR, et al. (1983) CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J Comp Chem 4:187-217.
    • (1983) J Comp Chem , vol.4 , pp. 187-217
    • Brooks, B.R.1
  • 19
    • 0023613529 scopus 로고
    • Normal modes of vibration in bovine pancreatic trypsin inhibitor and its mechanical property
    • Nishikawa T, Go N (1987) Normal modes of vibration in bovine pancreatic trypsin inhibitor and its mechanical property. Proteins 2:308-329.
    • (1987) Proteins , vol.2 , pp. 308-329
    • Nishikawa, T.1    Go, N.2
  • 20
    • 0022111715 scopus 로고
    • Normal modes for specific motions of macromolecules: Application to the hinge-bending mode of lysozyme
    • Brooks B, Karplus M (1985) Normal modes for specific motions of macromolecules: Application to the hinge-bending mode of lysozyme. Proc Natl Acad Sci USA 82:4995-4999.
    • (1985) Proc Natl Acad Sci USA , vol.82 , pp. 4995-4999
    • Brooks, B.1    Karplus, M.2
  • 21
    • 0001031179 scopus 로고
    • Proteins: A theoretical perspective of dynamics, structure, and thermodynamics
    • Brooks CL, Karplus M, Pettitt BM (1988) Proteins: A theoretical perspective of dynamics, structure, and thermodynamics. Adv Chem Phys 71:1-249.
    • (1988) Adv Chem Phys , vol.71 , pp. 1-249
    • Brooks, C.L.1    Karplus, M.2    Pettitt, B.M.3
  • 22
    • 0028331255 scopus 로고
    • Normal mode analysis of protein dynamics
    • Case DA (1994) Normal mode analysis of protein dynamics. Curr Opin Struct Biol 4:285-290.
    • (1994) Curr Opin Struct Biol , vol.4 , pp. 285-290
    • Case, D.A.1
  • 23
    • 0345973041 scopus 로고    scopus 로고
    • Gaussian dynamics of folded proteins
    • Haliloglu T, Bahar I, Erman B (1997) Gaussian dynamics of folded proteins. Phys Rev Lett 79:3090-3093.
    • (1997) Phys Rev Lett , vol.79 , pp. 3090-3093
    • Haliloglu, T.1    Bahar, I.2    Erman, B.3
  • 24
    • 0032483483 scopus 로고    scopus 로고
    • Vibrational dynamics of transfer RNAs: Comparison of the free and synthetase-bound forms
    • Bahar I, Jernigan RL (1998) Vibrational dynamics of transfer RNAs: Comparison of the free and synthetase-bound forms. J Mol Biol 281:871-884.
    • (1998) J Mol Biol , vol.281 , pp. 871-884
    • Bahar, I.1    Jernigan, R.L.2
  • 25
    • 0035132230 scopus 로고    scopus 로고
    • Anisotropy of fluctuation dynamics of proteins with an elastic network model
    • Atilgan AR, et al. (2001) Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys J 80:505-515.
    • (2001) Biophys J , vol.80 , pp. 505-515
    • Atilgan, A.R.1
  • 26
    • 66249121357 scopus 로고    scopus 로고
    • Comparisons of experimental and computed protein anisotropic temperature factors
    • Yang, L, Song, G, Jernigan, RL (2009) Comparisons of experimental and computed protein anisotropic temperature factors. Proteins 76:164-175.
    • (2009) Proteins , vol.76 , pp. 164-175
    • Yang, L.1    Song, G.2    Jernigan, R.L.3
  • 27
    • 43649085777 scopus 로고    scopus 로고
    • Toward a molecular understanding of the anisotropic response of proteins to external forces: Insights from elastic network models
    • Eyal E, Bahar I (2008) Toward a molecular understanding of the anisotropic response of proteins to external forces: Insights from elastic network models. Biophys J 94:3424-3435.
    • (2008) Biophys J , vol.94 , pp. 3424-3435
    • Eyal, E.1    Bahar, I.2
  • 28
    • 34249950182 scopus 로고    scopus 로고
    • Anisotropic fluctuations of amino acids in protein structures: Insights from X-ray crystallography and elastic network models
    • Eyal E, Chennubhotla C, Yang LW, Bahar I (2007) Anisotropic fluctuations of amino acids in protein structures: Insights from X-ray crystallography and elastic network models. Bioinformatics 23:i175-184.
    • (2007) Bioinformatics , vol.23 , Issue.I175-184
    • Eyal, E.1    Chennubhotla, C.2    Yang, L.W.3    Bahar, I.4
  • 29
    • 58849116413 scopus 로고    scopus 로고
    • Application of elastic network models to proteins in the crystalline state
    • Riccardi D, Cui Q, Phillips GN, Jr (2009) Application of elastic network models to proteins in the crystalline state. Biophys J 96:464-475.
    • (2009) Biophys J , vol.96 , pp. 464-475
    • Riccardi, D.1    Cui, Q.2    Phillips Jr, G.N.3
  • 31
    • 33645019704 scopus 로고    scopus 로고
    • An enhanced elastic network model to represent the motions of domain-swapped proteins
    • Song G, Jernigan RL (2006) An enhanced elastic network model to represent the motions of domain-swapped proteins. Proteins 63:197-209.
    • (2006) Proteins , vol.63 , pp. 197-209
    • Song, G.1    Jernigan, R.L.2
  • 32
    • 34547666968 scopus 로고    scopus 로고
    • How well can we understand large-scale protein motions using normal modes from elastic network models?
    • Yang L, Song G, Jernigan RL (2007) How well can we understand large-scale protein motions using normal modes from elastic network models? Biophys J 93:920-929.
    • (2007) Biophys J , vol.93 , pp. 920-929
    • Yang, L.1    Song, G.2    Jernigan, R.L.3
  • 33
    • 33751225684 scopus 로고    scopus 로고
    • The Gaussian network model: Precise prediction of residue fluctuations and application to binding problems
    • Erman B (2006) The Gaussian network model: Precise prediction of residue fluctuations and application to binding problems. Biophys J 91:3589-3599.
    • (2006) Biophys J , vol.91 , pp. 3589-3599
    • Erman, B.1
  • 34
    • 0032533790 scopus 로고    scopus 로고
    • Analysis of domain motions by approximate normal mode calculations
    • Hinsen K, Kneller GR (1998) Analysis of domain motions by approximate normal mode calculations. Proteins 33:417-429.
    • (1998) Proteins , vol.33 , pp. 417-429
    • Hinsen, K.1    Kneller, G.R.2
  • 35
    • 0042503333 scopus 로고    scopus 로고
    • A simplified force field for describing vibrational protein dynamics over the whole frequency range
    • Hinsen K, Kneller GR (1999) A simplified force field for describing vibrational protein dynamics over the whole frequency range. J Chem Phys 111:10766-10769.
    • (1999) J Chem Phys , vol.111 , pp. 10766-10769
    • Hinsen, K.1    Kneller, G.R.2
  • 37
    • 39149108868 scopus 로고    scopus 로고
    • Structural flexibility in proteins:Impact of the crystal environment
    • Hinsen K (2008) Structural flexibility in proteins:Impact of the crystal environment. Bioinformatics 24:521-528.
    • (2008) Bioinformatics , vol.24 , pp. 521-528
    • Hinsen, K.1
  • 38
    • 47349097554 scopus 로고    scopus 로고
    • Deriving protein dynamical properties from weighted protein contact number
    • Lin CP, et al. (2008) Deriving protein dynamical properties from weighted protein contact number. Proteins 72:929-935.
    • (2008) Proteins , vol.72 , pp. 929-935
    • Lin, C.P.1
  • 39
    • 0037022347 scopus 로고    scopus 로고
    • Flexibility and packing in proteins
    • Halle B (2002) Flexibility and packing in proteins. Proc Natl Acad Sci USA 99:1274-1279.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 1274-1279
    • Halle, B.1
  • 40
    • 36849087583 scopus 로고    scopus 로고
    • On the interrelationship between atomic displacement parameters (ADPs) and coordinates in protein structures
    • Weiss MS (2007) On the interrelationship between atomic displacement parameters (ADPs) and coordinates in protein structures. Acta Crystallogr D 63:1235-1242.
    • (2007) Acta Crystallogr D , vol.63 , pp. 1235-1242
    • Weiss, M.S.1
  • 41
    • 0000197372 scopus 로고    scopus 로고
    • Large amplitude elastic motions from a single-parameter, atomic analysis
    • Tirion MM (1996) Large amplitude elastic motions from a single-parameter, atomic analysis. Phys Rev Lett 77:1905-1908.
    • (1996) Phys Rev Lett , vol.77 , pp. 1905-1908
    • Tirion, M.M.1
  • 42
    • 0017021957 scopus 로고
    • Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins
    • Tanaka S, Scheraga H (1976) Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins. Macromolecules 9:945-950.
    • (1976) Macromolecules , vol.9 , pp. 945-950
    • Tanaka, S.1    Scheraga, H.2
  • 43
    • 33845377127 scopus 로고
    • Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation
    • Miyazawa S, Jernigan RL (1985) Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation. Macromolecules 18:534-552.
    • (1985) Macromolecules , vol.18 , pp. 534-552
    • Miyazawa, S.1    Jernigan, R.L.2
  • 44
    • 0033386039 scopus 로고    scopus 로고
    • Comparing anisotropic displacement parameters in protein structures
    • Merritt EA (1999) Comparing anisotropic displacement parameters in protein structures. Acta Crystallogr D55:Pt 12:1997-2004.
    • (1999) Acta Crystallogr , vol.D55 , Issue.PART 12 , pp. 1997-2004
    • Merritt, E.A.1
  • 45
    • 0036708474 scopus 로고    scopus 로고
    • Efficient generation of feasible pathways for protein conformational transitions
    • Kim MK, Jernigan RL, Chirikjian GS (2002) Efficient generation of feasible pathways for protein conformational transitions. Biophys J 83:1620-1630.
    • (2002) Biophys J , vol.83 , pp. 1620-1630
    • Kim, M.K.1    Jernigan, R.L.2    Chirikjian, G.S.3
  • 46
    • 0041334008 scopus 로고    scopus 로고
    • An elastic network model of HK97 capsid maturation
    • Kim MK, Jernigan RL, Chirikjian GS (2003) An elastic network model of HK97 capsid maturation. J Struct Biol 143:107-117.
    • (2003) J Struct Biol , vol.143 , pp. 107-117
    • Kim, M.K.1    Jernigan, R.L.2    Chirikjian, G.S.3
  • 47
    • 23244465157 scopus 로고    scopus 로고
    • Rigid-cluster models of conformational transitions in macromolecular machines and assemblies
    • Kim MK, Jernigan RL, Chirikjian GS (2005) Rigid-cluster models of conformational transitions in macromolecular machines and assemblies, Biophys J 89:43-55.
    • (2005) Biophys J , vol.89 , pp. 43-55
    • Kim, M.K.1    Jernigan, R.L.2    Chirikjian, G.S.3
  • 48
    • 0035044995 scopus 로고    scopus 로고
    • Conformational change of proteins arising from normal mode calculations
    • Tama F, Sanejouand YH (2001) Conformational change of proteins arising from normal mode calculations. Protein Eng 14:1-6.
    • (2001) Protein Eng , vol.14 , pp. 1-6
    • Tama, F.1    Sanejouand, Y.H.2
  • 49
    • 0036721233 scopus 로고    scopus 로고
    • Normal mode analysis of macromolecular motions in a database framework: Developing mode concentration as a useful classifying statistic
    • Krebs WG, et al. (2002) Normal mode analysis of macromolecular motions in a database framework: Developing mode concentration as a useful classifying statistic. Proteins 48:682-695.
    • (2002) Proteins , vol.48 , pp. 682-695
    • Krebs, W.G.1
  • 50
    • 3342877839 scopus 로고    scopus 로고
    • Collective motions in HIV-1 Reverse Transcriptase: Examination of flexibility and enzyme function
    • Bahar I, Erman B, Jernigan RL, Covell DG (1999) Collective motions in HIV-1 Reverse Transcriptase: Examination of flexibility and enzyme function. J Mol Biol 285:1023-1037.
    • (1999) J Mol Biol , vol.285 , pp. 1023-1037
    • Bahar, I.1    Erman, B.2    Jernigan, R.L.3    Covell, D.G.4
  • 51
    • 0034029144 scopus 로고    scopus 로고
    • Proteins with similar architecture exhibit similar large-scale dynamic behavior
    • Keskin O, Jernigan RL, Bahar I (2000) Proteins with similar architecture exhibit similar large-scale dynamic behavior. Biophys J 78:2093-2106.
    • (2000) Biophys J , vol.78 , pp. 2093-2106
    • Keskin, O.1    Jernigan, R.L.2    Bahar, I.3
  • 52
    • 4344685227 scopus 로고    scopus 로고
    • Global ribosomemotions revealed with elastic network model
    • Wang Y, Rader AJ, Bahar I, Jernigan RL (2004) Global ribosomemotions revealed with elastic network model. J Struct Biol 147:302-314.
    • (2004) J Struct Biol , vol.147 , pp. 302-314
    • Wang, Y.1    Rader, A.J.2    Bahar, I.3    Jernigan, R.L.4
  • 53
    • 31544444687 scopus 로고    scopus 로고
    • Loop motions of triosephosphate isomerase observed with elastic networks
    • Kurkcuoglu O, Jernigan RL, Doruker P (2006) Loop motions of triosephosphate isomerase observed with elastic networks. Biochemistry 45:1173-1182.
    • (2006) Biochemistry , vol.45 , pp. 1173-1182
    • Kurkcuoglu, O.1    Jernigan, R.L.2    Doruker, P.3
  • 54
    • 78049283691 scopus 로고    scopus 로고
    • Sen TZ, Jernigan RL (2006) Optimizing the parameters of the Gaussian network model for ATP-binding proteins. In Normal Mode Analysis: Theory and Applications to Biological and Chemical Systems, eds Bahar I, Cui Q (Chapman and Hall/CRC, Boca Raton), pp 171-186.
    • Sen TZ, Jernigan RL (2006) Optimizing the parameters of the Gaussian network model for ATP-binding proteins. In Normal Mode Analysis: Theory and Applications to Biological and Chemical Systems, eds Bahar I, Cui Q (Chapman and Hall/CRC, Boca Raton), pp 171-186.
  • 55
    • 0037250308 scopus 로고    scopus 로고
    • PDB-REPRDB: A database of representative protein chains from the Protein Data Bank (PDB) in 2003
    • Noguchi T, Akiyama Y (2003) PDB-REPRDB: A database of representative protein chains from the Protein Data Bank (PDB) in 2003. Nucleic Acids Res 31:492-493.
    • (2003) Nucleic Acids Res , vol.31 , pp. 492-493
    • Noguchi, T.1    Akiyama, Y.2
  • 56
    • 0033954256 scopus 로고    scopus 로고
    • The protein data bank
    • Berman HM, et al. (2000) The protein data bank. Nucleic Acids Res 28:235-242.
    • (2000) Nucleic Acids Res , vol.28 , pp. 235-242
    • Berman, H.M.1


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