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Volumn 84, Issue 6, 2003, Pages 3583-3593

Molecular dynamics simulations of peptides and proteins with amplified collective motions

Author keywords

[No Author keywords available]

Indexed keywords

PEPTIDE; PROTEIN;

EID: 0037764042     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(03)75090-5     Document Type: Article
Times cited : (110)

References (54)
  • 1
    • 0033995345 scopus 로고    scopus 로고
    • Efficient sampling in collective coordinates space
    • Abseher, R., and M. Nilges. 2000. Efficient sampling in collective coordinates space. Proteins. 39:82-88.
    • (2000) Proteins , vol.39 , pp. 82-88
    • Abseher, R.1    Nilges, M.2
  • 4
    • 0019467025 scopus 로고
    • Crystallographic determination of the mode of binding of oligosaccharides to T4 bacteriophage lysozyme: Implications for the mechanism of catalysis
    • Anderson, W. F., M. G. Grutter, S. J. Remington, L. H. Weaver, and B. W. Matthews. 1981. Crystallographic determination of the mode of binding of oligosaccharides to T4 bacteriophage lysozyme: implications for the mechanism of catalysis. J. Mol. Biol. 147:523-543.
    • (1981) J. Mol. Biol. , vol.147 , pp. 523-543
    • Anderson, W.F.1    Grutter, M.G.2    Remington, S.J.3    Weaver, L.H.4    Matthews, B.W.5
  • 6
    • 0030623823 scopus 로고    scopus 로고
    • Direct evaluation of thermal fluctuations in proteins using a single parameter harmonic potential
    • Bahar, I., A. R. Atilgan, and B. Erman. 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
  • 7
    • 0031648813 scopus 로고    scopus 로고
    • Probability distributions for complex systems: Adaptive umbrella sampling of the potential energy
    • Bartels, C., and M. Karplus. 1998. Probability distributions for complex systems: adaptive umbrella sampling of the potential energy. J. Phys. Chem. B. 102:865-880.
    • (1998) J. Phys. Chem. B , vol.102 , pp. 865-880
    • Bartels, C.1    Karplus, M.2
  • 8
    • 0002775934 scopus 로고
    • Interaction models for water in relation to protein hydration
    • B. Pullman, editor. Reidel, Dordrecht, the Netherlands
    • Berendsen, H. J. C., J. P. M. Postma, W. F. van Gunsteren, and J. Hermans. 1981. Interaction models for water in relation to protein hydration. In Intermolecular Forces. B. Pullman, editor. Reidel, Dordrecht, the Netherlands. pp.331-342.
    • (1981) Intermolecular Forces , pp. 331-342
    • Berendsen, H.J.C.1    Postma, J.P.M.2    Van Gunsteren, W.F.3    Hermans, J.4
  • 10
    • 0034127361 scopus 로고    scopus 로고
    • Collective protein dynamics in relation to function
    • Berendsen, H. J. C., and S. Hayward. 2000. Collective protein dynamics in relation to function. Curr. Opin. Struct. Biol. 10:165-169.
    • (2000) Curr. Opin. Struct. Biol. , vol.10 , pp. 165-169
    • Berendsen, H.J.C.1    Hayward, S.2
  • 11
    • 0034033187 scopus 로고    scopus 로고
    • Long timescale simulations
    • Daggett, V. 2000. Long timescale simulations. Curr. Opin. Struct. Biol. 10:160-164.
    • (2000) Curr. Opin. Struct. Biol. , vol.10 , pp. 160-164
    • Daggett, V.1
  • 12
    • 0029967692 scopus 로고    scopus 로고
    • Towards an exhaustive sampling of the configurational spaces of the two forms of the peptide hormone guanylin
    • de Groot, B. L., A. Amadei, D. M. F. van Aalten, and H. J. C. Berendsen. 1996a. Towards an exhaustive sampling of the configurational spaces of the two forms of the peptide hormone guanylin. J. Biomol. Struct. Dyn. 13:741-751.
    • (1996) J. Biomol. Struct. Dyn. , vol.13 , pp. 741-751
    • De Groot, B.L.1    Amadei, A.2    Van Aalten, D.M.F.3    Berendsen, H.J.C.4
  • 13
    • 0029811307 scopus 로고    scopus 로고
    • An extended sampling of the configurational space of hpr form E. coli
    • de Groot, B. L., A. Amadei, N. A. J. van Nuland, and H. J. C. Berendsen. 1996b. An extended sampling of the configurational space of hpr form E. coli. Proteins. 26:314-333.
    • (1996) Proteins , vol.26 , pp. 314-333
    • De Groot, B.L.1    Amadei, A.2    Van Nuland, N.A.J.3    Berendsen, H.J.C.4
  • 15
    • 0032080528 scopus 로고    scopus 로고
    • Domain motions in bacteriophage T4 lysozyme: A comparison between molecular dynamics and crystallographic data
    • de Groot, B. L., S. Hayward, D. M. F. van Aalten, A. Amadei, and H. J. C. Berendsen. 1998. Domain motions in bacteriophage T4 lysozyme: a comparison between molecular dynamics and crystallographic data. Proteins. 31:116-127.
    • (1998) Proteins , vol.31 , pp. 116-127
    • De Groot, B.L.1    Hayward, S.2    Van Aalten, D.M.F.3    Amadei, A.4    Berendsen, H.J.C.5
  • 16
    • 0008813715 scopus 로고    scopus 로고
    • 2) algorithm for the symmetric tridiagonal eigenvalue/eigenvector problem
    • University of California at Berkeley, Berkeley, CA
    • 2) algorithm for the symmetric tridiagonal eigenvalue/eigenvector problem. In Computer Science Division Technical Report No. UCB//CSD-97-971, University of California at Berkeley, Berkeley, CA.
    • (1997) Computer Science Division Technical Report No. UCB//CSD-97-971
    • Dhillon, I.S.1
  • 17
    • 0028291376 scopus 로고
    • Molecular dynamics simulation of the docking of substrates to proteins
    • Di Nola, A., D. Roccatano, and H. J. C. Berendsen. 1994. Molecular dynamics simulation of the docking of substrates to proteins. Proteins. 19:174-182.
    • (1994) Proteins , vol.19 , pp. 174-182
    • Di Nola, A.1    Roccatano, D.2    Berendsen, H.J.C.3
  • 18
    • 0033117830 scopus 로고    scopus 로고
    • Protein dynamics simulations from nanoseconds to microseconds
    • Doniach, S., and P. Eastman. 1999. Protein dynamics simulations from nanoseconds to microseconds. Curr. Opin. Struct. Biol. 9:157-163.
    • (1999) Curr. Opin. Struct. Biol. , vol.9 , pp. 157-163
    • Doniach, S.1    Eastman, P.2
  • 19
    • 0000053123 scopus 로고    scopus 로고
    • Protein flexibility in solution and in crystals
    • Eastman, P., M. Pellegrini, and S. Doniach. 1999. Protein flexibility in solution and in crystals. J. Chem. Phys. 110:10141-10152.
    • (1999) J. Chem. Phys. , vol.110 , pp. 10141-10152
    • Eastman, P.1    Pellegrini, M.2    Doniach, S.3
  • 20
    • 0024620499 scopus 로고
    • Chain dimensions and fluctuations in random elastomeric networks. 2. Dependence of chain dimensions and fluctuations on macroscopic strain
    • Erman, B., A. Kloczkowski, and J. E. Mark. 1989. Chain dimensions and fluctuations in random elastomeric networks. 2. Dependence of chain dimensions and fluctuations on macroscopic strain. Macromolecules. 22:1432-1441.
    • (1989) Macromolecules , vol.22 , pp. 1432-1441
    • Erman, B.1    Kloczkowski, A.2    Mark, J.E.3
  • 21
    • 0025047629 scopus 로고
    • A mutant T4 lysozyme displays five different crystal conformations
    • Faber, H. R., and B. W. Matthews. 1990. A mutant T4 lysozyme displays five different crystal conformations. Nature. 348:263-266.
    • (1990) Nature , vol.348 , pp. 263-266
    • Faber, H.R.1    Matthews, B.W.2
  • 22
    • 0000689085 scopus 로고
    • Predicting slow structural transitions in macromolecular systems: Conformational flooding
    • Grubmuller, H. 1995. Predicting slow structural transitions in macromolecular systems: conformational flooding. Phys. Rev. E. 52:2893-2906.
    • (1995) Phys. Rev. E , vol.52 , pp. 2893-2906
    • Grubmuller, H.1
  • 23
    • 0345973041 scopus 로고    scopus 로고
    • Gaussian dynamics of folded proteins
    • Haliloglu, T., I. Bahar, and B. Erman. 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
    • 5244260010 scopus 로고
    • Prediction of peptide conformation by multicanonical algorithm: New approach to the multipleminima problem
    • Hansmann, U. H. E., and Y. Okamoto. 1993. Prediction of peptide conformation by multicanonical algorithm: new approach to the multipleminima problem. J. Comp. Chem. 14:1333-1338.
    • (1993) J. Comp. Chem. , vol.14 , pp. 1333-1338
    • Hansmann, U.H.E.1    Okamoto, Y.2
  • 25
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch, W., and C. Sander. 1983. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 22:2576-2637.
    • (1983) Biopolymers , vol.22 , pp. 2576-2637
    • Kabsch, W.1    Sander, C.2
  • 26
    • 84986472098 scopus 로고
    • Conformational dynamics of polypeptides and proteins in the dihedral angle space and in the Cartesian coordinate space: Normal mode analysis of deca-ananine
    • Kitao, A., and N. Go. 1991. Conformational dynamics of polypeptides and proteins in the dihedral angle space and in the Cartesian coordinate space: normal mode analysis of deca-ananine. J. Comp. Chem. 12:359-368.
    • (1991) J. Comp. Chem. , vol.12 , pp. 359-368
    • Kitao, A.1    Go, N.2
  • 27
    • 0027983643 scopus 로고
    • Comparison of normal mode analyses on a small globular protein in dihedral angle space and Cartesian coordinate space
    • Kitao, A., S. Hayward, and N. Go. 1994. Comparison of normal mode analyses on a small globular protein in dihedral angle space and Cartesian coordinate space. Biophys. Chem. 52:107-114.
    • (1994) Biophys. Chem. , vol.52 , pp. 107-114
    • Kitao, A.1    Hayward, S.2    Go, N.3
  • 28
    • 0032374086 scopus 로고    scopus 로고
    • Energy landscape of a native protein: Jumping-among-minimum model
    • Kitao, A., S. Hayward, and N. Go. 1998. Energy landscape of a native protein: Jumping-Among-Minimum model. Proteins. 33:496-517.
    • (1998) Proteins , vol.33 , pp. 496-517
    • Kitao, A.1    Hayward, S.2    Go, N.3
  • 29
    • 0033117937 scopus 로고    scopus 로고
    • Investigating protein dynamics in collective coordinate space
    • Kitao, A., and N. Go. 1999. Investigating protein dynamics in collective coordinate space. Curr. Opin. Struct. Biol. 9:164-169.
    • (1999) Curr. Opin. Struct. Biol. , vol.9 , pp. 164-169
    • Kitao, A.1    Go, N.2
  • 30
    • 0024621473 scopus 로고
    • Chain dimensions and fluctuations in random elastomeric networks. 1. Phantom Gaussian networks in the underformed state
    • Kloczkowski, A., J. E. Mark, and B. Erman. 1989. Chain dimensions and fluctuations in random elastomeric networks. 1. Phantom Gaussian networks in the underformed state. Macromolecules. 22:1423-1432.
    • (1989) Macromolecules , vol.22 , pp. 1423-1432
    • Kloczkowski, A.1    Mark, J.E.2    Erman, B.3
  • 31
    • 0026244229 scopus 로고
    • MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
    • Kraulis, P. J. 1991. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24:946-950.
    • (1991) J. Appl. Crystallog. , vol.24 , pp. 946-950
    • Kraulis, P.J.1
  • 32
    • 0033135477 scopus 로고    scopus 로고
    • Docking of flexible ligands to flexible receptors in solution by molecular dynamics simulation
    • Mangoni, M., D. Roccatano, and A. Di Nola. 1999. Docking of flexible ligands to flexible receptors in solution by molecular dynamics simulation. Proteins. 35:153-162.
    • (1999) Proteins , vol.35 , pp. 153-162
    • Mangoni, M.1    Roccatano, D.2    Di Nola, A.3
  • 33
    • 0037062479 scopus 로고    scopus 로고
    • Domain movements in human fatty acid synthase by quantized elastic deformational model
    • Ming, D., Y. Kong, S. J. Wakil, J. Brink, and J. Ma. 2002a. Domain movements in human fatty acid synthase by quantized elastic deformational model. Proc. Natl. Acad. Sci. USA. 99:7895-7899.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 7895-7899
    • Ming, D.1    Kong, Y.2    Wakil, S.J.3    Brink, J.4    Ma, J.5
  • 34
    • 0037173062 scopus 로고    scopus 로고
    • How to describe protein motion without amino acid sequence and atomic coordinates
    • Ming, D., Y. Kong, M. A. Lambert, Z. Huang, and J. Ma. 2002b. 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
  • 35
    • 33845377127 scopus 로고
    • Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation
    • Miyazawa, S., and R. L. Jernigan. 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
  • 36
    • 0037080723 scopus 로고    scopus 로고
    • Predicting unimolecular chemical reactions: Chemical flooding
    • Muller, E. M., A. de Meijere, and H. Grubmuller. 2002. Predicting unimolecular chemical reactions: chemical flooding. J. Chem. Phys. 116:897-905.
    • (2002) J. Chem. Phys. , vol.116 , pp. 897-905
    • Muller, E.M.1    De Meijere, A.2    Grubmuller, H.3
  • 37
    • 0030819348 scopus 로고    scopus 로고
    • Multicanonical ensemble generated by molecular dynamics simulations for enhanced conformational sampling of peptides
    • Nakajima, N., H. Nakamura, and A. Kidera. 1997. Multicanonical ensemble generated by molecular dynamics simulations for enhanced conformational sampling of peptides. J. Phys. Chem. B. 101:817-824.
    • (1997) J. Phys. Chem. B , vol.101 , pp. 817-824
    • Nakajima, N.1    Nakamura, H.2    Kidera, A.3
  • 38
    • 0022036264 scopus 로고
    • Efficient Monte Carlo method for simulation of fluctuating conformations of native proteins
    • Noguti, T., and N. Go. 1985. Efficient Monte Carlo method for simulation of fluctuating conformations of native proteins. Biopolymers. 24:527-546.
    • (1985) Biopolymers , vol.24 , pp. 527-546
    • Noguti, T.1    Go, N.2
  • 39
    • 33646940952 scopus 로고
    • Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkenes
    • Ryckaert, J. P., G. Ciccotti, and H. J. C. Berendsen. 1977. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkenes. J. Comp. Phys. 23:327-341.
    • (1977) J. Comp. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 40
    • 2242491482 scopus 로고
    • Consistent dielectric properties of the simple point charge and extended simple point charge water models at 277 and 300K
    • Smith, P. E., and W. F. van Gunsteren. 1994. Consistent dielectric properties of the simple point charge and extended simple point charge water models at 277 and 300K. J. Chem. Phys. 100:3169-3174.
    • (1994) J. Chem. Phys. , vol.100 , pp. 3169-3174
    • Smith, P.E.1    Van Gunsteren, W.F.2
  • 41
    • 0344778061 scopus 로고
    • Semianalytical treatment of solvation for molecular mechanics and dynamics
    • Still, W. C., A. Tempczyk, R. C. Hawley, and T. Hendrickson. 1990. Semianalytical treatment of solvation for molecular mechanics and dynamics. J. Am. Chem. Soc. 112:6127-6129.
    • (1990) J. Am. Chem. Soc. , vol.112 , pp. 6127-6129
    • Still, W.C.1    Tempczyk, A.2    Hawley, R.C.3    Hendrickson, T.4
  • 42
    • 0000118827 scopus 로고
    • Harmonic and quasiharmonic descriptions of crambin
    • Teeter, M. M., and D. A. Case. 1990. Harmonic and quasiharmonic descriptions of crambin. J. Phys. Chem. 94:8091-8097.
    • (1990) J. Phys. Chem. , vol.94 , pp. 8091-8097
    • Teeter, M.M.1    Case, D.A.2
  • 43
    • 0025858688 scopus 로고
    • Molecular dynamics simulations of an α-helical analogue of ribonuclease-A S-peptide in water
    • Tirado-Rives, J., and W. L. Jorgensen. 1991. Molecular dynamics simulations of an α-helical analogue of ribonuclease-A S-peptide in water. Biochemistry. 30:3864-3871.
    • (1991) Biochemistry , vol.30 , pp. 3864-3871
    • Tirado-Rives, J.1    Jorgensen, W.L.2
  • 44
    • 0000197372 scopus 로고    scopus 로고
    • Large amplitude elastic motions in proteins from a single-parameter, atomic analysis
    • Tirion, M. M. 1996. Large amplitude elastic motions in proteins 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
  • 45
    • 4544369164 scopus 로고
    • A generalized reaction field method for molecular dynamics simulations
    • Tironi, I. G., R. Sperb, P. E. Smith, and W. F. van Gunsteren. 1995. A generalized reaction field method for molecular dynamics simulations. J. Chem. Phys. 102:5451-5459.
    • (1995) J. Chem. Phys. , vol.102 , pp. 5451-5459
    • Tironi, I.G.1    Sperb, R.2    Smith, P.E.3    Van Gunsteren, W.F.4
  • 47
    • 9644301524 scopus 로고
    • Stochastic dynamics for molecules with constraints Brownian dynamics of n-alkanes
    • van Gunsteren, W. F., H. J. C. Berendsen, and J. A. C. Rullman. 1981. Stochastic dynamics for molecules with constraints Brownian dynamics of n-alkanes. Mol. Phys. 44:69-95.
    • (1981) Mol. Phys. , vol.44 , pp. 69-95
    • Van Gunsteren, W.F.1    Berendsen, H.J.C.2    Rullman, J.A.C.3
  • 50
    • 0025398721 scopus 로고
    • WHAT IF: A molecular modeling and drug design program
    • Vriend, G. 1990. WHAT IF: a molecular modeling and drug design program. J. Mol. Graph. 8:52-56.
    • (1990) J. Mol. Graph. , vol.8 , pp. 52-56
    • Vriend, G.1
  • 51
    • 0023104358 scopus 로고
    • Structure of bacteriophage T4 lysozyme refined at 1.7A resolution
    • Weaver, L. H., and B. W. Matthews. 1987. Structure of bacteriophage T4 lysozyme refined at 1.7A resolution. J. Mol. Biol. 193:189-199.
    • (1987) J. Mol. Biol. , vol.193 , pp. 189-199
    • Weaver, L.H.1    Matthews, B.W.2
  • 52
    • 0029150760 scopus 로고
    • Protein flexibility and adaptability seen in 25 crystal forms of T4 lysozyme
    • Zhang, X. J., J. A. Wozniak, and B. W. Matthews. 1995. Protein flexibility and adaptability seen in 25 crystal forms of T4 lysozyme. J. Mol. Biol. 250:527-552.
    • (1995) J. Mol. Biol. , vol.250 , pp. 527-552
    • Zhang, X.J.1    Wozniak, J.A.2    Matthews, B.W.3
  • 53
    • 0035865543 scopus 로고    scopus 로고
    • Molecular dynamics simulations of urea and thermal-induced denaturation of S-peptide analogue
    • Zhang, Z., Y. Zhu, and Y. Shi. 2001. Molecular dynamics simulations of urea and thermal-induced denaturation of S-peptide analogue. Biophys. Chem. 89:145-162.
    • (2001) Biophys. Chem. , vol.89 , pp. 145-162
    • Zhang, Z.1    Zhu, Y.2    Shi, Y.3
  • 54
    • 0037046727 scopus 로고    scopus 로고
    • Parametrization of a generalized Born/solvent-accessible surface area model and applications to the simulation of protein dynamics
    • Zhu, J., Y. Shi, and H. Liu. 2002. Parametrization of a generalized Born/solvent-accessible surface area model and applications to the simulation of protein dynamics. J. Phys. Chem. B. 106:4844-4853.
    • (2002) J. Phys. Chem. B , vol.106 , pp. 4844-4853
    • Zhu, J.1    Shi, Y.2    Liu, H.3


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