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Volumn 70, Issue 4, 2008, Pages 1595-1609

A finite element framework for computation of protein normal modes and mechanical response

Author keywords

Actin; Coarse grain; Modeling; Normal mode analysis; Simulation

Indexed keywords

BETA TUBULIN; CYTOCHROME C'; F ACTIN; G ACTIN; LYSOZYME; PROTEIN; SYNTENIN;

EID: 39749171104     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21708     Document Type: Article
Times cited : (54)

References (100)
  • 1
    • 0000991642 scopus 로고
    • Harmonic dynamics of proteins - normal modes and fluctuations in bovine pancreatic trypsin inhibitor
    • Brooks B, Karplus M. Harmonic dynamics of proteins - normal modes and fluctuations in bovine pancreatic trypsin inhibitor. Proc Natl Acad Sci USA 1983;80:6571-6575.
    • (1983) Proc Natl Acad Sci USA , vol.80 , pp. 6571-6575
    • Brooks, B.1    Karplus, M.2
  • 2
    • 0020771265 scopus 로고
    • Dynamics of a small globular protein in terms of low frequency vibrational modes
    • Go N, Noguti T, Nishikawa T. Dynamics of a small globular protein in terms of low frequency vibrational modes. Proc Natl Acad Sci USA 1983;80:3696-3700.
    • (1983) Proc Natl Acad Sci USA , vol.80 , pp. 3696-3700
    • Go, N.1    Noguti, T.2    Nishikawa, T.3
  • 3
    • 0022419152 scopus 로고
    • Protein normal-mode dynamics: Trypsin inhibitor, crambin, ribonuclease and lysozyme
    • Levitt M, Sander C, Stern PS. Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme. J Mol Biol 1985;181:423-447.
    • (1985) J Mol Biol , vol.181 , pp. 423-447
    • Levitt, M.1    Sander, C.2    Stern, P.S.3
  • 4
    • 0036725277 scopus 로고    scopus 로고
    • Molecular dynamics simulations of biomolecules
    • Karplus M, McCammon JA. Molecular dynamics simulations of biomolecules. Nat Struct Biol 2002;9:646-652.
    • (2002) Nat Struct Biol , vol.9 , pp. 646-652
    • Karplus, M.1    McCammon, J.A.2
  • 5
    • 0000197372 scopus 로고    scopus 로고
    • Large amplitude elastic motions in proteins from a single-parameter, atomic analysis
    • Tirion MM. 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
  • 6
    • 0030623823 scopus 로고    scopus 로고
    • Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
    • Bahar I, Atilgan AR, Erman B. Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Folding Des 1997;2:173-181.
    • (1997) Folding Des , vol.2 , pp. 173-181
    • Bahar, I.1    Atilgan, A.R.2    Erman, B.3
  • 7
    • 33745024278 scopus 로고    scopus 로고
    • Symmetry, form, and shape: Guiding principles for robustness in macromolecular machines
    • Tama F, Brooks CL. Symmetry, form, and shape: guiding principles for robustness in macromolecular machines. Annu Rev Biophys Biomol Struct 2006;35:115-133.
    • (2006) Annu Rev Biophys Biomol Struct , vol.35 , pp. 115-133
    • Tama, F.1    Brooks, C.L.2
  • 8
    • 25844431698 scopus 로고    scopus 로고
    • Coarse-grained normal mode analysis in structural biology
    • Bahar I, Rader AJ. 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
  • 9
    • 14844286108 scopus 로고    scopus 로고
    • Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes
    • Ma JP. Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes. Structure 2005;13: 373-380.
    • (2005) Structure , vol.13 , pp. 373-380
    • Ma, J.P.1
  • 10
    • 0016791469 scopus 로고
    • Breathing mode of conformational fluctuations in globular proteins
    • Suezaki Y, Gō N. Breathing mode of conformational fluctuations in globular proteins. Int J Peptide Protein Res 1975;7:333-334.
    • (1975) Int J Peptide Protein Res , vol.7 , pp. 333-334
    • Suezaki, Y.1    Gō, N.2
  • 11
    • 25844525600 scopus 로고    scopus 로고
    • The role of shape in determining molecular motions
    • Lu MY, Ma JP. The role of shape in determining molecular motions. Biophys J 2005;89:2395-2401.
    • (2005) Biophys J , vol.89 , pp. 2395-2401
    • Lu, M.Y.1    Ma, J.P.2
  • 12
    • 0141815545 scopus 로고    scopus 로고
    • Functional motions can be extracted from on-lattice construction of protein structures
    • Doruker P, Jernigan RL. Functional motions can be extracted from on-lattice construction of protein structures. Proteins: Struct Funct Genet 2003;53:174-181.
    • (2003) Proteins: Struct Funct Genet , vol.53 , pp. 174-181
    • Doruker, P.1    Jernigan, R.L.2
  • 15
    • 0024450809 scopus 로고
    • Structural studies of mutants of T4 lysozyme that alter hydrophobic stabilization
    • Matsumura M, Wozniak JA, Daopin S, Matthews BW. Structural studies of mutants of T4 lysozyme that alter hydrophobic stabilization. J Biol Chem 1989;264:16059-16066.
    • (1989) J Biol Chem , vol.264 , pp. 16059-16066
    • Matsumura, M.1    Wozniak, J.A.2    Daopin, S.3    Matthews, B.W.4
  • 16
    • 0035958757 scopus 로고    scopus 로고
    • The crystal structure of uncomplexed actin in the ADP state
    • Otterbein LR, Graceffa P, Dominguez R. The crystal structure of uncomplexed actin in the ADP state. Science 2001;293:708-711.
    • (2001) Science , vol.293 , pp. 708-711
    • Otterbein, L.R.1    Graceffa, P.2    Dominguez, R.3
  • 17
  • 18
    • 1842635588 scopus 로고    scopus 로고
    • The PDZ2 domain of syntenin at ultra-high resolution: Bridging the gap between macromolecular and small molecule crystallography
    • Kang BS, Devedjiev Y, Derewenda U, Derewenda ZS. The PDZ2 domain of syntenin at ultra-high resolution: bridging the gap between macromolecular and small molecule crystallography. J Mol Biol 2004;338:483-493.
    • (2004) J Mol Biol , vol.338 , pp. 483-493
    • Kang, B.S.1    Devedjiev, Y.2    Derewenda, U.3    Derewenda, Z.S.4
  • 19
    • 0022419653 scopus 로고
    • Structure of ferricytochrome-c′ from Rhodospirillum molischianum at 1.67-Å resolution
    • Finzel BC, Weber PC, Hardman KD, Salemme FR. Structure of ferricytochrome-c′ from Rhodospirillum molischianum at 1.67-Å resolution. J Mol Biol 1985;186:627-643.
    • (1985) J Mol Biol , vol.186 , pp. 627-643
    • Finzel, B.C.1    Weber, P.C.2    Hardman, K.D.3    Salemme, F.R.4
  • 20
    • 0032495513 scopus 로고    scopus 로고
    • Structure of the αβ tubulin dimer by electron crystallography
    • Nogales E, Wolf SG, Downing KH. Structure of the αβ tubulin dimer by electron crystallography. Nature 1998;391:199-203.
    • (1998) Nature , vol.391 , pp. 199-203
    • Nogales, E.1    Wolf, S.G.2    Downing, K.H.3
  • 21
    • 0037173062 scopus 로고    scopus 로고
    • How to describe protein motion without amino acid sequence and atomic coordinates
    • Ming D, Kong YF, Lambert MA, Huang Z, Ma JP. How to describe protein motion without amino acid sequence and atomic coordinates. Proc Natl Acad Sci USA 2002;99:8620-8625.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 8620-8625
    • Ming, D.1    Kong, Y.F.2    Lambert, M.A.3    Huang, Z.4    Ma, J.P.5
  • 22
    • 0036382958 scopus 로고    scopus 로고
    • Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory
    • Tama F, Wriggers W, Brooks CL. Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory. J Mol Biol 2002;321:297-305.
    • (2002) J Mol Biol , vol.321 , pp. 297-305
    • Tama, F.1    Wriggers, W.2    Brooks, C.L.3
  • 24
    • 0019438921 scopus 로고
    • The internal dynamics of globular proteins
    • Karplus M, McCammon JA. The internal dynamics of globular proteins. CRC Crit Rev Biochem 1981;9:293-349.
    • (1981) CRC Crit Rev Biochem , vol.9 , pp. 293-349
    • Karplus, M.1    McCammon, J.A.2
  • 25
    • 0023512803 scopus 로고
    • Anisotropy and anharmonicity of atomic fluctuations in proteins: Analysis of a molecular dynamics simulation
    • Ichiye T, Karplus M. Anisotropy and anharmonicity of atomic fluctuations in proteins: analysis of a molecular dynamics simulation. Proteins: Struct Funct Genet 1987;2:236-259.
    • (1987) Proteins: Struct Funct Genet , vol.2 , pp. 236-259
    • Ichiye, T.1    Karplus, M.2
  • 26
    • 0023053635 scopus 로고
    • Effect of anisotropy and anharmonicity on protein crystallographic refinement: An evaluation by molecular dynamics
    • Kuriyan J, Petsko GA, Levy RM, Karplus M. Effect of anisotropy and anharmonicity on protein crystallographic refinement: an evaluation by molecular dynamics. J Mol Biol 1986;190:227-254.
    • (1986) J Mol Biol , vol.190 , pp. 227-254
    • Kuriyan, J.1    Petsko, G.A.2    Levy, R.M.3    Karplus, M.4
  • 31
    • 33748264168 scopus 로고    scopus 로고
    • Actin-binding proteins sensitively mediate F-actin bundle stiffness
    • Claessens MMAE, Bathe M, Frey E, Bausch AR. Actin-binding proteins sensitively mediate F-actin bundle stiffness. Nat Mater 2006;5: 748-753.
    • (2006) Nat Mater , vol.5 , pp. 748-753
    • Claessens, M.M.A.E.1    Bathe, M.2    Frey, E.3    Bausch, A.R.4
  • 34
    • 33746828240 scopus 로고    scopus 로고
    • A finite element framework for studying the mechanical response of macromolecules: Application to the gating of the mechanosensitive channel MscL
    • Tang YY, Cao GX, Chen X, Yoo J, Yethiraj A, Cui Q. A finite element framework for studying the mechanical response of macromolecules: application to the gating of the mechanosensitive channel MscL. Biophys J 2006;91:1248-1263.
    • (2006) Biophys J , vol.91 , pp. 1248-1263
    • Tang, Y.Y.1    Cao, G.X.2    Chen, X.3    Yoo, J.4    Yethiraj, A.5    Cui, Q.6
  • 36
    • 3042579451 scopus 로고    scopus 로고
    • White JH, Bauer WR. Finite-element analysis of the displacement of closed DNA loops under torsional stress. Philos Trans R Soc Lond Ser A: Math Phys Eng Sci 2004;362:1335-1353.
    • White JH, Bauer WR. Finite-element analysis of the displacement of closed DNA loops under torsional stress. Philos Trans R Soc Lond Ser A: Math Phys Eng Sci 2004;362:1335-1353.
  • 37
    • 0028454915 scopus 로고
    • New approach for determining low frequency normal-modes in macromolecules
    • Durand P, Trinquier G, Sanejouand YH. New approach for determining low frequency normal-modes in macromolecules. Biopolymers 1994;34:759-771.
    • (1994) Biopolymers , vol.34 , pp. 759-771
    • Durand, P.1    Trinquier, G.2    Sanejouand, Y.H.3
  • 39
    • 0032534356 scopus 로고    scopus 로고
    • Spanning the continuum to quantum length scales in a dynamic simulation of brittle fracture
    • Abraham FF, Broughton JQ, Bernstein N, Kaxiras E. Spanning the continuum to quantum length scales in a dynamic simulation of brittle fracture. Europhys Lett 1998;44:783-787.
    • (1998) Europhys Lett , vol.44 , pp. 783-787
    • Abraham, F.F.1    Broughton, J.Q.2    Bernstein, N.3    Kaxiras, E.4
  • 40
    • 0028204490 scopus 로고
    • Do salt bridges stabilize proteins? A continuum electrostatic analysis
    • Hendsch ZS, Tidor B. Do salt bridges stabilize proteins? A continuum electrostatic analysis. Prot Sci 1994;3:211-226.
    • (1994) Prot Sci , vol.3 , pp. 211-226
    • Hendsch, Z.S.1    Tidor, B.2
  • 41
    • 4344595498 scopus 로고    scopus 로고
    • Escherichia coli glutaminyl-tRNA synthetase is electrostatically optimization for binding of its cognate substrates
    • Green DF, Tidor B. Escherichia coli glutaminyl-tRNA synthetase is electrostatically optimization for binding of its cognate substrates. J Mol Biol 2004;342:435-452.
    • (2004) J Mol Biol , vol.342 , pp. 435-452
    • Green, D.F.1    Tidor, B.2
  • 42
    • 0028331255 scopus 로고
    • Normal mode analysis of protein dynamics
    • Case DA. Normal mode analysis of protein dynamics. Curr Opin Struct Biol 1994;4:285-290.
    • (1994) Curr Opin Struct Biol , vol.4 , pp. 285-290
    • Case, D.A.1
  • 43
    • 0001439211 scopus 로고    scopus 로고
    • Numerical solution of the Poisson-Boltzmann equation using tetrahedral finite-element meshes
    • Cortis CM, Friesner RA. Numerical solution of the Poisson-Boltzmann equation using tetrahedral finite-element meshes. J Comput Chem 1997;18:1591-1608.
    • (1997) J Comput Chem , vol.18 , pp. 1591-1608
    • Cortis, C.M.1    Friesner, R.A.2
  • 44
    • 0000702975 scopus 로고    scopus 로고
    • On finite element analysis of fluid flows fully coupled with structural interactions. CMES
    • Rugonyi S, Bathe KJ. On finite element analysis of fluid flows fully coupled with structural interactions. CMES: Comput Model Eng Sci 2001;2:195-212.
    • (2001) Comput Model Eng Sci , vol.2 , pp. 195-212
    • Rugonyi, S.1    Bathe, K.J.2
  • 45
    • 0017429069 scopus 로고
    • Areas, volumes, packing, and protein-structure
    • Richards FM. Areas, volumes, packing, and protein-structure. Annu Rev Biophys Bioeng 1977;6:151-176.
    • (1977) Annu Rev Biophys Bioeng , vol.6 , pp. 151-176
    • Richards, F.M.1
  • 46
    • 2442595374 scopus 로고
    • Macromolecular shape and surface maps by solvent exclusion
    • Greer J, Bush BL. Macromolecular shape and surface maps by solvent exclusion. Proc Natl Acad Sci USA 1978;75:303-307.
    • (1978) Proc Natl Acad Sci USA , vol.75 , pp. 303-307
    • Greer, J.1    Bush, B.L.2
  • 47
    • 0000538815 scopus 로고
    • Analytical molecular surface calculation
    • Connolly ML. Analytical molecular surface calculation. J Appl Crystallogr 1983;16:548-558.
    • (1983) J Appl Crystallogr , vol.16 , pp. 548-558
    • Connolly, M.L.1
  • 48
    • 0030040323 scopus 로고    scopus 로고
    • Reduced surface: An efficient way to compute molecular surfaces
    • Sanner MF, Olson AJ, Spehner JC. Reduced surface: an efficient way to compute molecular surfaces. Biopolymers 1996;38:305-320.
    • (1996) Biopolymers , vol.38 , pp. 305-320
    • Sanner, M.F.1    Olson, A.J.2    Spehner, J.C.3
  • 50
    • 0002318603 scopus 로고    scopus 로고
    • Optimal triangulation and quadric-based surface simplification
    • Heckbert PS, Garland M. Optimal triangulation and quadric-based surface simplification. Comput Geom: Theory Appl 1999;14:49-65.
    • (1999) Comput Geom: Theory Appl , vol.14 , pp. 49-65
    • Heckbert, P.S.1    Garland, M.2
  • 51
    • 0033863336 scopus 로고    scopus 로고
    • Domain motions of EF-G bound to the 70S ribosome: Insights from a hand-shaking between multi-resolution structures
    • Wriggers W, Agrawal RK, Drew DL, McCammon A, Frank J. Domain motions of EF-G bound to the 70S ribosome: insights from a hand-shaking between multi-resolution structures. Biophys J 2000;79:1670-1678.
    • (2000) Biophys J , vol.79 , pp. 1670-1678
    • Wriggers, W.1    Agrawal, R.K.2    Drew, D.L.3    McCammon, A.4    Frank, J.5
  • 54
    • 0019621665 scopus 로고
    • On non-linear dynamic analysis using substructuring and mode superposition
    • Bathe KJ, Gracewski S. On non-linear dynamic analysis using substructuring and mode superposition. Comput Struct 1981;13:699-707.
    • (1981) Comput Struct , vol.13 , pp. 699-707
    • Bathe, K.J.1    Gracewski, S.2
  • 55
    • 0037422581 scopus 로고    scopus 로고
    • Substructure synthesis method for simulating large molecular complexes
    • Ming D, Kong YF, Wu YH, Ma JP. Substructure synthesis method for simulating large molecular complexes. Proc Natl Acad Sci USA 2003;100:104-109.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 104-109
    • Ming, D.1    Kong, Y.F.2    Wu, Y.H.3    Ma, J.P.4
  • 56
    • 84986486656 scopus 로고
    • A rapid finite difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation
    • Nicholls A, Honig B. A rapid finite difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation. J Comput Chem 1991;12:435-445.
    • (1991) J Comput Chem , vol.12 , pp. 435-445
    • Nicholls, A.1    Honig, B.2
  • 57
    • 0001620743 scopus 로고    scopus 로고
    • An automatic three-dimensional finite element mesh generation system for the Poisson-Boltzmann equation
    • Cortis CM, Friesner RA. An automatic three-dimensional finite element mesh generation system for the Poisson-Boltzmann equation. J Comput Chem 1997;18:1570-1590.
    • (1997) J Comput Chem , vol.18 , pp. 1570-1590
    • Cortis, C.M.1    Friesner, R.A.2
  • 58
    • 0000486194 scopus 로고    scopus 로고
    • Adaptive multilevel finite element solution of the Poisson-Boltzmann equation. II. Refinement at solvent-accessible surfaces in biomolecular systems
    • Baker N, Holst M, Wang F. Adaptive multilevel finite element solution of the Poisson-Boltzmann equation. II. Refinement at solvent-accessible surfaces in biomolecular systems. J Comput Chem 2000;21:1343-1352.
    • (2000) J Comput Chem , vol.21 , pp. 1343-1352
    • Baker, N.1    Holst, M.2    Wang, F.3
  • 59
    • 0028607563 scopus 로고
    • Direct measurement of stiffness of single actin-filaments with and without tropomyosin by in-vitro nanomanipulation
    • Kojima H, Ishijima A, Yanagida T. Direct measurement of stiffness of single actin-filaments with and without tropomyosin by in-vitro nanomanipulation. Proc Natl Acad Sci USA 1994;91:12962-12966.
    • (1994) Proc Natl Acad Sci USA , vol.91 , pp. 12962-12966
    • Kojima, H.1    Ishijima, A.2    Yanagida, T.3
  • 60
    • 0028905547 scopus 로고
    • Dynamic and elastic properties of F-actin: A normal modes analysis
    • ben-Avraham D, Tirion MM. Dynamic and elastic properties of F-actin: a normal modes analysis. Biophys J 1995;68:1231-1245.
    • (1995) Biophys J , vol.68 , pp. 1231-1245
    • ben-Avraham, D.1    Tirion, M.M.2
  • 61
    • 0033932840 scopus 로고    scopus 로고
    • Protein compressability, dynamics, and pressure
    • Kharakoz DP. Protein compressability, dynamics, and pressure. Biophys J 2000;79:511-525.
    • (2000) Biophys J , vol.79 , pp. 511-525
    • Kharakoz, D.P.1
  • 62
    • 84986512474 scopus 로고    scopus 로고
    • Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM - a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 1983; 4:187-217.
    • Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM - a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 1983; 4:187-217.
  • 63
    • 0033135638 scopus 로고    scopus 로고
    • Effective energy function for proteins in solution
    • Lazaridis T, Karplus M. Effective energy function for proteins in solution. Proteins: Struct Funct Genet 1999;35:133-152.
    • (1999) Proteins: Struct Funct Genet , vol.35 , pp. 133-152
    • Lazaridis, T.1    Karplus, M.2
  • 66
    • 0036840202 scopus 로고    scopus 로고
    • A coarse-grained normal mode approach for macromolecules: An efficient implementation and application to Ca2+-ATPase
    • Li GH, Cui Q. A coarse-grained normal mode approach for macromolecules: an efficient implementation and application to Ca2+-ATPase. Biophys J 2002;83:2457-2474.
    • (2002) Biophys J , vol.83 , pp. 2457-2474
    • Li, G.H.1    Cui, Q.2
  • 68
    • 0000885331 scopus 로고
    • Harmonic analysis of large systems. I. Methodology
    • Brooks BR, Janezic D, Karplus M. Harmonic analysis of large systems. I. Methodology. J Comput Chem 1995;16:1522-1542.
    • (1995) J Comput Chem , vol.16 , pp. 1522-1542
    • Brooks, B.R.1    Janezic, D.2    Karplus, M.3
  • 69
    • 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
  • 71
    • 25844441847 scopus 로고    scopus 로고
    • Comparison of mode analyses at different resolutions applied to nucleic acid systems
    • van Wynsberghe AW, Cui Q. Comparison of mode analyses at different resolutions applied to nucleic acid systems. Biophys J 2005; 89:2939-2949.
    • (2005) Biophys J , vol.89 , pp. 2939-2949
    • van Wynsberghe, A.W.1    Cui, Q.2
  • 72
    • 0032780181 scopus 로고    scopus 로고
    • Situs: A package for docking crystal structures into low-resolution maps from electron microscopy
    • Wriggers W, Milligan RA, McCammon JA. Situs: a package for docking crystal structures into low-resolution maps from electron microscopy. J Struct Biol 1999;125:185-195.
    • (1999) J Struct Biol , vol.125 , pp. 185-195
    • Wriggers, W.1    Milligan, R.A.2    McCammon, J.A.3
  • 73
    • 0041306048 scopus 로고    scopus 로고
    • Like-charge attraction between polyelectrolytes induced by counterion charge density waves
    • Angelini TE, Liang H, Wriggers W, Wong GCL. Like-charge attraction between polyelectrolytes induced by counterion charge density waves. Proc Natl Acad Sci USA 2003;100:8634-8637.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 8634-8637
    • Angelini, T.E.1    Liang, H.2    Wriggers, W.3    Wong, G.C.L.4
  • 75
    • 0027251071 scopus 로고
    • Structure of gelsolin segment-1-actin complex and the mechanism of filament severing
    • McLaughlin PJ, Gooch JT, Mannherz HG, Weeds AG. Structure of gelsolin segment-1-actin complex and the mechanism of filament severing. Nature 1993;364:685-692.
    • (1993) Nature , vol.364 , pp. 685-692
    • McLaughlin, P.J.1    Gooch, J.T.2    Mannherz, H.G.3    Weeds, A.G.4
  • 76
    • 0033136019 scopus 로고    scopus 로고
    • Investigating a back door mechanism of actin phosphate release by steered molecular dynamics
    • Wriggers W, Schulten K. Investigating a back door mechanism of actin phosphate release by steered molecular dynamics. Proteins: Struct Funct Genet 1999;35:262-273.
    • (1999) Proteins: Struct Funct Genet , vol.35 , pp. 262-273
    • Wriggers, W.1    Schulten, K.2
  • 77
    • 0141445972 scopus 로고    scopus 로고
    • Crystal structure of monomeric actin in the ATP state - structural basis of nucleotide-dependent actin dynamics
    • Graceffa P, Dominguez R. Crystal structure of monomeric actin in the ATP state - structural basis of nucleotide-dependent actin dynamics. J Biol Chem 2003;278:34172-34180.
    • (2003) J Biol Chem , vol.278 , pp. 34172-34180
    • Graceffa, P.1    Dominguez, R.2
  • 78
    • 0027533269 scopus 로고
    • Flexural rigidity of microtubules and actin filaments measured from thermal fluctuations in shape
    • Gittes F, Mickey B, Nettleton J, Howard J. Flexural rigidity of microtubules and actin filaments measured from thermal fluctuations in shape. J Cell Biol 1993;120:923-934.
    • (1993) J Cell Biol , vol.120 , pp. 923-934
    • Gittes, F.1    Mickey, B.2    Nettleton, J.3    Howard, J.4
  • 79
    • 0035996990 scopus 로고    scopus 로고
    • Dynamics of proteins in crystals: Comparison of experiment with simple models
    • Kundu S, Melton JS, Sorensen DC, Phillips GN. Dynamics of proteins in crystals: comparison of experiment with simple models. Biophys J 2002;83:723-732.
    • (2002) Biophys J , vol.83 , pp. 723-732
    • Kundu, S.1    Melton, J.S.2    Sorensen, D.C.3    Phillips, G.N.4
  • 80
    • 0030787462 scopus 로고    scopus 로고
    • Stability and dynamics of G-actin: Backdoor water diffusion and behavior of a subdomain 3/4 loop
    • Wriggers W, Schulten K. Stability and dynamics of G-actin: backdoor water diffusion and behavior of a subdomain 3/4 loop. Biophys J 1997;73:624-639.
    • (1997) Biophys J , vol.73 , pp. 624-639
    • Wriggers, W.1    Schulten, K.2
  • 81
    • 0027511431 scopus 로고
    • Normal mode analysis of G-actin
    • Tirion MM, Benavraham D. Normal mode analysis of G-actin. J Mol Biol 1993;230:186-195.
    • (1993) J Mol Biol , vol.230 , pp. 186-195
    • Tirion, M.M.1    Benavraham, D.2
  • 82
    • 28844448877 scopus 로고    scopus 로고
    • Channel opening motion of α7 nicotinic acetylcholine receptor as suggested by normal mode analysis
    • Cheng XL, Lu BZ, Grant B, Law RJ, McCammon JA. Channel opening motion of α7 nicotinic acetylcholine receptor as suggested by normal mode analysis. J Mol Biol 2006;355:310-324.
    • (2006) J Mol Biol , vol.355 , pp. 310-324
    • Cheng, X.L.1    Lu, B.Z.2    Grant, B.3    Law, R.J.4    McCammon, J.A.5
  • 84
    • 0022111715 scopus 로고
    • Normal-modes for specific motions of macromolecules - application to the hinge-bending mode of lysozyme
    • Brooks B, Karplus M. Normal-modes for specific motions of macromolecules - application to the hinge-bending mode of lysozyme. Proc Natl Acad Sci USA 1985;82:4995-4999.
    • (1985) Proc Natl Acad Sci USA , vol.82 , pp. 4995-4999
    • Brooks, B.1    Karplus, M.2
  • 85
    • 0025047629 scopus 로고
    • A mutant T4 lysozyme displays 5 different crystal conformations
    • Faber HR, Matthews BW. A mutant T4 lysozyme displays 5 different crystal conformations. Nature 1990;348:263-266.
    • (1990) Nature , vol.348 , pp. 263-266
    • Faber, H.R.1    Matthews, B.W.2
  • 86
    • 1842326248 scopus 로고    scopus 로고
    • Conformation of T4 lysozyme in solution. Hinge-bending motion and the substrate-induced conformational transition studied by site-directed spin labeling
    • McHaourab HS, Oh KJ, Fang CJ, Hubbell WL. Conformation of T4 lysozyme in solution. Hinge-bending motion and the substrate-induced conformational transition studied by site-directed spin labeling. Biochemistry 1997;36:307-316.
    • (1997) Biochemistry , vol.36 , pp. 307-316
    • McHaourab, H.S.1    Oh, K.J.2    Fang, C.J.3    Hubbell, W.L.4
  • 88
    • 0028787131 scopus 로고
    • Allostery, cooperativity, and different structural states in F-actin
    • Egelman EH, Orlova A. Allostery, cooperativity, and different structural states in F-actin. J Struct Biol 1995;115:159-162.
    • (1995) J Struct Biol , vol.115 , pp. 159-162
    • Egelman, E.H.1    Orlova, A.2
  • 90
    • 0032054640 scopus 로고    scopus 로고
    • F-actin-binding proteins
    • McGough A. F-actin-binding proteins. Curr Opin Struct Biol 1998;8:166-176.
    • (1998) Curr Opin Struct Biol , vol.8 , pp. 166-176
    • McGough, A.1
  • 91
    • 0029046139 scopus 로고
    • Flexibility of actin filaments derived from thermal fluctuations - effect of bound nucleotide, phalloidin, and muscle regulatory proteins
    • Isambert H, Venier P, Maggs AC, Fattoum A, Kassab R, Pantaloni D, Carlier MF. Flexibility of actin filaments derived from thermal fluctuations - effect of bound nucleotide, phalloidin, and muscle regulatory proteins. J Biol Chem 1995;270:11437-11444.
    • (1995) J Biol Chem , vol.270 , pp. 11437-11444
    • Isambert, H.1    Venier, P.2    Maggs, A.C.3    Fattoum, A.4    Kassab, R.5    Pantaloni, D.6    Carlier, M.F.7
  • 92
    • 0037636333 scopus 로고    scopus 로고
    • Simulation of F-actin filaments of several microns
    • Ming DM, Kong YF, Wu YH, Ma JP. Simulation of F-actin filaments of several microns. Biophys J 2003;85:27-35.
    • (2003) Biophys J , vol.85 , pp. 27-35
    • Ming, D.M.1    Kong, Y.F.2    Wu, Y.H.3    Ma, J.P.4
  • 93
    • 24944541377 scopus 로고    scopus 로고
    • Allostery of actin filaments: Molecular dynamics simulations and coarse-grained analysis
    • Chu JW, Voth GA. Allostery of actin filaments: molecular dynamics simulations and coarse-grained analysis. Proc Natl Acad Sci USA 2005;102:13111-13116.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 13111-13116
    • Chu, J.W.1    Voth, G.A.2
  • 94
    • 33646123091 scopus 로고    scopus 로고
    • Coarse-grained modeling of the actin filament derived from atomistic-scale simulations
    • Chu JW, Voth GA. Coarse-grained modeling of the actin filament derived from atomistic-scale simulations. Biophys J 2006;90:1572-1582.
    • (2006) Biophys J , vol.90 , pp. 1572-1582
    • Chu, J.W.1    Voth, G.A.2
  • 97
    • 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
  • 98
    • 33748046806 scopus 로고    scopus 로고
    • Anisotropic deformation response of single protein molecules
    • Dietz H, Berkemeier F, Bertz M, Rief M. Anisotropic deformation response of single protein molecules. Proc Natl Acad Sci USA 2006;103:12724-12728.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 12724-12728
    • Dietz, H.1    Berkemeier, F.2    Bertz, M.3    Rief, M.4
  • 99
    • 84986431462 scopus 로고
    • An analytical algorithm for the rapid determination of the solvent accessibility of points in a 3-dimensional lattice around a solute molecule
    • You T, Bashford D. An analytical algorithm for the rapid determination of the solvent accessibility of points in a 3-dimensional lattice around a solute molecule. J Comput Chem 1995;16:743-757.
    • (1995) J Comput Chem , vol.16 , pp. 743-757
    • You, T.1    Bashford, D.2
  • 100
    • 0015222647 scopus 로고
    • Interpretation of protein structures - estimation of static accessibility
    • Lee B, Richards FM. Interpretation of protein structures - estimation of static accessibility. J Mol Biol 1971;55:379-400.
    • (1971) J Mol Biol , vol.55 , pp. 379-400
    • Lee, B.1    Richards, F.M.2


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