메뉴 건너뛰기




Volumn 6, Issue 9, 2010, Pages 2910-2923

Approaching elastic network models to molecular dynamics flexibility

Author keywords

[No Author keywords available]

Indexed keywords


EID: 77956593836     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct100208e     Document Type: Article
Times cited : (59)

References (58)
  • 1
    • 36849039429 scopus 로고    scopus 로고
    • A hierarchy of timescales in protein dynamics is linked to enzyme catalysis
    • Henzler-Wildman, K. A.; Lei, M.; Thai, V.; Kerns, S. J.; Karplus, M.; Kern, D. A hierarchy of timescales in protein dynamics is linked to enzyme catalysis Nature 2007, 450, 913-916
    • (2007) Nature , vol.450 , pp. 913-916
    • Henzler-Wildman, K.A.1    Lei, M.2    Thai, V.3    Kerns, S.J.4    Karplus, M.5    Kern, D.6
  • 8
    • 17044393884 scopus 로고    scopus 로고
    • Coarse-grained models for proteins
    • Tozzini, V. Coarse-grained models for proteins Curr. Opin. Struct. Biol. 2005, 15, 144-150
    • (2005) Curr. Opin. Struct. Biol. , vol.15 , pp. 144-150
    • Tozzini, V.1
  • 9
    • 25844431698 scopus 로고    scopus 로고
    • Coarse-grained normal mode analysis in structural biology
    • Bahar, I.; Rader, A. J. Coarse-grained normal mode analysis in structural biology Curr. Opin. Struct. Biol. 2005, 15, 586-592
    • (2005) Curr. Opin. Struct. Biol. , vol.15 , pp. 586-592
    • Bahar, I.1    Rader, A.J.2
  • 10
    • 51649113464 scopus 로고    scopus 로고
    • Exploring the suitability of coarse-grained techniques for the representation of protein dynamics
    • Emperador, A.; Carrillo, O.; Rueda, M.; Orozco, M. Exploring the suitability of coarse-grained techniques for the representation of protein dynamics Biophys. J. 2008, 95, 2127-2138
    • (2008) Biophys. J. , vol.95 , pp. 2127-2138
    • Emperador, A.1    Carrillo, O.2    Rueda, M.3    Orozco, M.4
  • 11
    • 0000197372 scopus 로고    scopus 로고
    • Large amplitude elastic motions in proteins from a single-parameter, atomic analysis
    • Tirion, M. M. Large amplitude elastic motions in proteins from a single-parameter, atomic analysis Phys. Rev. Lett. 1996, 77, 1905-1908
    • (1996) Phys. Rev. Lett. , vol.77 , pp. 1905-1908
    • Tirion, M.M.1
  • 12
    • 4043093460 scopus 로고    scopus 로고
    • Normal mode analysis of biomolecular dynamics
    • Eds.; Kluwer Academic Publishers: Dordrecht, The Netherlands
    • Case, D. A. Normal mode analysis of biomolecular dynamics. In Computer Simulation of Biomolecular Systems; Gunsteren, W. F.; Weiner, P. K.; Wilkinson, A. J., Eds.; Kluwer Academic Publishers: Dordrecht, The Netherlands, 1997; Vol. 3, pp 284 - 301.
    • (1997) Computer Simulation of Biomolecular Systems , vol.3 , pp. 284-301
    • Case, D.A.1    Gunsteren, W.F.2    Weiner, P.K.3    Wilkinson, A.J.4
  • 15
    • 33749521415 scopus 로고    scopus 로고
    • Optimization and evaluation of a coarse-grained model of protein motion using X-ray crystal data
    • Kondrashov, D. A.; Cui, Q.; Philips, G. N. Optimization and evaluation of a coarse-grained model of protein motion using X-ray crystal data Biophys. J. 2006, 91, 2760-2767
    • (2006) Biophys. J. , vol.91 , pp. 2760-2767
    • Kondrashov, D.A.1    Cui, Q.2    Philips, G.N.3
  • 16
    • 34547683322 scopus 로고    scopus 로고
    • Markov methods for hierarchical coarse-graining of large protein dynamics
    • Chennubhotla, C.; Bahar, I. Markov methods for hierarchical coarse-graining of large protein dynamics J. Comput. Biol. 2007, 14, 765-76
    • (2007) J. Comput. Biol. , vol.14 , pp. 765-76
    • Chennubhotla, C.1    Bahar, I.2
  • 20
    • 58849116413 scopus 로고    scopus 로고
    • Application of elastic network models to proteins in the crystalline state
    • Riccardi, D.; Cui, Q.; Phillips, G. N. Application of elastic network models to proteins in the crystalline state Biophys. J. 2009, 96, 464-475
    • (2009) Biophys. J. , vol.96 , pp. 464-475
    • Riccardi, D.1    Cui, Q.2    Phillips, G.N.3
  • 21
    • 36549005182 scopus 로고    scopus 로고
    • Coarse-grained biomolecular simulation with REACH, realistic extension algorithm via covariance Hessian
    • Moritsugu, K.; Smith, J. C. Coarse-grained biomolecular simulation with REACH, realistic extension algorithm via covariance Hessian Biophys. J. 2007, 93, 3460-3469
    • (2007) Biophys. J. , vol.93 , pp. 3460-3469
    • Moritsugu, K.1    Smith, J.C.2
  • 22
    • 28944434207 scopus 로고    scopus 로고
    • A connection rule for a-carbon coarse-grained elastic network models using chemical bond information
    • Jeong, J. I.; Jang, Y.; Kim, M. K. A connection rule for a-carbon coarse-grained elastic network models using chemical bond information J. Mol. Graphics Modell. 2006, 24, 296-306
    • (2006) J. Mol. Graphics Modell. , vol.24 , pp. 296-306
    • Jeong, J.I.1    Jang, Y.2    Kim, M.K.3
  • 23
    • 68149141470 scopus 로고    scopus 로고
    • Protein elastic network models and the ranges of cooperativity
    • Yang, L.; Song, G.; Jernigan, R. L. Protein elastic network models and the ranges of cooperativity Proc. Natl. Acad. Sci.U.S.A. 2009, 106, 12347-52
    • (2009) Proc. Natl. Acad. Sci.U.S.A. , vol.106 , pp. 12347-52
    • Yang, L.1    Song, G.2    Jernigan, R.L.3
  • 24
    • 0027482556 scopus 로고
    • NMR relaxation and protein mobility
    • Wagner, G. NMR relaxation and protein mobility Curr. Opin. Struct. Biol. 1993, 3, 748-754
    • (1993) Curr. Opin. Struct. Biol. , vol.3 , pp. 748-754
    • Wagner, G.1
  • 26
    • 33751225684 scopus 로고    scopus 로고
    • The Gaussian network model: Precise prediction of residue fluctuations and application to binding problems
    • Erman, B. The Gaussian network model: Precise prediction of residue fluctuations and application to binding problems Biophys. J. 2006, 91, 3589-3599
    • (2006) Biophys. J. , vol.91 , pp. 3589-3599
    • Erman, B.1
  • 27
    • 39149108868 scopus 로고    scopus 로고
    • Structural flexibility in proteins: Impact of the crystal environment
    • Hinsen, K. Structural flexibility in proteins: Impact of the crystal environment Bioinformatics 2008, 24, 521-528
    • (2008) Bioinformatics , vol.24 , pp. 521-528
    • Hinsen, K.1
  • 28
    • 0037022347 scopus 로고    scopus 로고
    • Flexibility and packing in proteins
    • Halle, B. Flexibility and packing in proteins Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 1274-1279
    • (2002) Proc. Natl. Acad. Sci. U.S.A. , vol.99 , pp. 1274-1279
    • Halle, B.1
  • 29
    • 48949119100 scopus 로고    scopus 로고
    • Critical evaluation of simple network models of protein dynamics and their comparison with crystallographic B-factors
    • 026008-026021
    • Soheilifard, R.; Makarov, D. E.; Rodin, G. J. Critical evaluation of simple network models of protein dynamics and their comparison with crystallographic B-factors Phys. Biol. 2008, 5 026008-026021
    • (2008) Phys. Biol. , vol.5
    • Soheilifard, R.1    Makarov, D.E.2    Rodin, G.J.3
  • 30
    • 0033082077 scopus 로고    scopus 로고
    • Reliability of atomic displacement parameters in protein crystal structures
    • Carugo, O.; Argos, P. Reliability of atomic displacement parameters in protein crystal structures Acta Crystallogr., D: Biol. Crystallogr. 1999, 55, 473-478
    • (1999) Acta Crystallogr., D: Biol. Crystallogr. , vol.55 , pp. 473-478
    • Carugo, O.1    Argos, P.2
  • 31
    • 0035044995 scopus 로고    scopus 로고
    • Conformational change of proteins arising from normal mode calculations
    • Tama, F.; Sanejouand, Y. H. Conformational change of proteins arising from normal mode calculations Protein Eng. 2001, 14, 1-6
    • (2001) Protein Eng. , vol.14 , pp. 1-6
    • Tama, F.1    Sanejouand, Y.H.2
  • 32
    • 38949218425 scopus 로고    scopus 로고
    • Close correspondence between the motions from principal component analysis of multiple HIV-1 protease structures and elastic network modes
    • Yang, L.; Song, G.; Carriquiry, A.; Jernigan, R. L. Close correspondence between the motions from principal component analysis of multiple HIV-1 protease structures and elastic network modes Structure 2008, 16, 321-330
    • (2008) Structure , vol.16 , pp. 321-330
    • Yang, L.1    Song, G.2    Carriquiry, A.3    Jernigan, R.L.4
  • 33
    • 61449106774 scopus 로고    scopus 로고
    • Principal component analysis of native ensembles of biomolecular structures (PCA-NEST): Insights into functional dynamics
    • Yang, L.; Eyal, E.; Bahar, I.; Kitao, A. Principal component analysis of native ensembles of biomolecular structures (PCA-NEST): Insights into functional dynamics Bioinformatics 2009, 25, 606-614
    • (2009) Bioinformatics , vol.25 , pp. 606-614
    • Yang, L.1    Eyal, E.2    Bahar, I.3    Kitao, A.4
  • 34
    • 34249945151 scopus 로고    scopus 로고
    • Insights into equilibrium dynamics of proteins from comparison of NMR and X-ray data with computational predictions
    • Yang, L.; Eyal, E.; Chennubhotla, C.; Jee, J. G.; Gronenborn, A.; Bahar, I. Insights into equilibrium dynamics of proteins from comparison of NMR and X-ray data with computational predictions Structure 2007, 15, 741-749
    • (2007) Structure , vol.15 , pp. 741-749
    • Yang, L.1    Eyal, E.2    Chennubhotla, C.3    Jee, J.G.4    Gronenborn, A.5    Bahar, I.6
  • 35
    • 0032101346 scopus 로고    scopus 로고
    • Essential spaces defined by NMR structure ensembles and molecular dynamics simulation show significant overlap
    • Abseher, R.; Horstink, L.; Hilbers, C. W.; Nilges, M. Essential spaces defined by NMR structure ensembles and molecular dynamics simulation show significant overlap Proteins: Struct., Funct., Genet. 1999, 31, 370-382
    • (1999) Proteins: Struct., Funct., Genet. , vol.31 , pp. 370-382
    • Abseher, R.1    Horstink, L.2    Hilbers, C.W.3    Nilges, M.4
  • 36
    • 0036283096 scopus 로고    scopus 로고
    • Molecular dynamics and NMR spin relaxation in proteins
    • Case, D. A. Molecular dynamics and NMR spin relaxation in proteins Acc. Chem. Res. 2002, 35, 325-331
    • (2002) Acc. Chem. Res. , vol.35 , pp. 325-331
    • Case, D.A.1
  • 38
    • 0030021471 scopus 로고    scopus 로고
    • Bio-molecular dynamics comes of age
    • Berendsen, H. J. C. Bio-molecular dynamics comes of age Science 1996, 271, 954-955
    • (1996) Science , vol.271 , pp. 954-955
    • Berendsen, H.J.C.1
  • 39
    • 0026076090 scopus 로고
    • Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations
    • Ichiye, T.; Karplus, M. Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations Proteins: Struct., Funct., Genet. 1991, 11, 205-217
    • (1991) Proteins: Struct., Funct., Genet. , vol.11 , pp. 205-217
    • Ichiye, T.1    Karplus, M.2
  • 40
    • 0033117937 scopus 로고    scopus 로고
    • Investigating protein dynamics in collective coordinate space
    • Kitao, A.; Go, N. Investigating protein dynamics in collective coordinate space Curr. Opin. Struct. Biol. 1999, 9, 164-9
    • (1999) Curr. Opin. Struct. Biol. , vol.9 , pp. 164-9
    • Kitao, A.1    Go, N.2
  • 41
    • 0028877423 scopus 로고
    • Harmonicity and anharmonicity in protein dynamics: A normal modes and principal component analysis
    • Hayward, S.; Kitao, A.; Go, N. Harmonicity and anharmonicity in protein dynamics: A normal modes and principal component analysis Proteins: Struct., Funct., Genet. 1995, 23, 177-186
    • (1995) Proteins: Struct., Funct., Genet. , vol.23 , pp. 177-186
    • Hayward, S.1    Kitao, A.2    Go, N.3
  • 42
    • 34248159870 scopus 로고    scopus 로고
    • Thorough validation of protein normal mode analysis: A comparative study with essential dynamics
    • Rueda, M.; Chacón, P.; Orozco, M. Thorough validation of protein normal mode analysis: A comparative study with essential dynamics Structure 2007, 15, 565-575
    • (2007) Structure , vol.15 , pp. 565-575
    • Rueda, M.1    Chacón, P.2    Orozco, M.3
  • 43
    • 3242875210 scopus 로고    scopus 로고
    • ElNemo: A normal mode Web server for protein movement analysis and the generation of templates for molecular replacement
    • Suhre, K.; Sanejouand, Y. H. ElNemo: A normal mode Web server for protein movement analysis and the generation of templates for molecular replacement Nucleic Acids Res. 2004, 32, W610-W614
    • (2004) Nucleic Acids Res. , vol.32
    • Suhre, K.1    Sanejouand, Y.H.2
  • 45
    • 6344260593 scopus 로고
    • An all-atom empirical energy function for the simulation of nucleic acids
    • MacKerell, A. D.; Wiorkiewicz-Kuczera, J.; Karplus, M. An all-atom empirical energy function for the simulation of nucleic acids J. Am. Chem. Soc. 1995, 117, 11946-11975
    • (1995) J. Am. Chem. Soc. , vol.117 , pp. 11946-11975
    • MacKerell, A.D.1    Wiorkiewicz-Kuczera, J.2    Karplus, M.3
  • 46
    • 0029912748 scopus 로고    scopus 로고
    • Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
    • Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids J. Am. Chem. Soc. 1996, 118, 11225-11236
    • (1996) J. Am. Chem. Soc. , vol.118 , pp. 11225-11236
    • Jorgensen, W.L.1    Maxwell, D.S.2    Tirado-Rives, J.3
  • 47
    • 0034500645 scopus 로고    scopus 로고
    • Similarities between principal components of protein dynamics and random diffusion
    • Hess, B. Similarities between principal components of protein dynamics and random diffusion Phys. Rev. E 2000, 62, 8438-8448
    • (2000) Phys. Rev. e , vol.62 , pp. 8438-8448
    • Hess, B.1
  • 49
    • 1242347628 scopus 로고    scopus 로고
    • Theoretical methods for the simulation of nucleic acids
    • Orozco, M.; Perez, A.; Noy, A.; Luque, F. J. Theoretical methods for the simulation of nucleic acids Chem. Soc. Rev. 2003, 32, 350-364
    • (2003) Chem. Soc. Rev. , vol.32 , pp. 350-364
    • Orozco, M.1    Perez, A.2    Noy, A.3    Luque, F.J.4
  • 51
    • 0032533790 scopus 로고    scopus 로고
    • Analysis of domain motions by approximate normal mode calculations
    • Hinsen, K. Analysis of domain motions by approximate normal mode calculations Proteins: Struct., Funct., Genet. 1998, 33, 417-429
    • (1998) Proteins: Struct., Funct., Genet. , vol.33 , pp. 417-429
    • Hinsen, K.1
  • 52
    • 0000216012 scopus 로고
    • Collective protein dynamics and nuclear spin relaxation
    • Brüschweiler, R. Collective protein dynamics and nuclear spin relaxation J. Chem. Phys. 1995, 102, 3396-3403
    • (1995) J. Chem. Phys. , vol.102 , pp. 3396-3403
    • Brüschweiler, R.1
  • 53
    • 0033613906 scopus 로고    scopus 로고
    • Native proteins are surface-molten solids: Application of the Lindemann criterion for the solid versus liquid state
    • Zhou, Y.; Vitkup, D.; Karplus, M. Native proteins are surface-molten solids: Application of the Lindemann criterion for the solid versus liquid state J. Mol. Biol. 1999, 285, 1371-1375
    • (1999) J. Mol. Biol. , vol.285 , pp. 1371-1375
    • Zhou, Y.1    Vitkup, D.2    Karplus, M.3
  • 54
    • 0036721233 scopus 로고    scopus 로고
    • Normal mode analysis of macromolecular motions in a database framework: Developing mode concentration as a useful classifying statistic
    • Krebs, W. G.; Alexandrov, V.; Wilson, C. A.; Echols, L.; Yu, H.; Gerstein, M. Normal mode analysis of macromolecular motions in a database framework: Developing mode concentration as a useful classifying statistic Proteins: Struct., Funct., Genet. 2002, 48, 682-695
    • (2002) Proteins: Struct., Funct., Genet. , vol.48 , pp. 682-695
    • Krebs, W.G.1    Alexandrov, V.2    Wilson, C.A.3    Echols, L.4    Yu, H.5    Gerstein, M.6
  • 55
    • 58149293838 scopus 로고    scopus 로고
    • United-atom discrete molecular dynamics of proteins using physics-based potentials
    • Emperador, A.; Meyer, T.; Orozco, M. United-atom discrete molecular dynamics of proteins using physics-based potentials J. Chem. Theory Comput. 2008, 4, 2001-2010
    • (2008) J. Chem. Theory Comput. , vol.4 , pp. 2001-2010
    • Emperador, A.1    Meyer, T.2    Orozco, M.3
  • 56
    • 33644517853 scopus 로고    scopus 로고
    • Functional modes of proteins are among the most robust ones
    • Nicolay, S.; Sanejouand, Y. H. Functional modes of proteins are among the most robust ones Phys. Rev. Lett. 2006, 96 078104
    • (2006) Phys. Rev. Lett. , vol.96 , pp. 078104
    • Nicolay, S.1    Sanejouand, Y.H.2
  • 57
    • 33646742004 scopus 로고    scopus 로고
    • Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations
    • Zheng, W.; Brooks, B. R.; Thirumalai, D. Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 7664-7669
    • (2006) Proc. Natl. Acad. Sci. U.S.A. , vol.103 , pp. 7664-7669
    • Zheng, W.1    Brooks, B.R.2    Thirumalai, D.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.