메뉴 건너뛰기




Volumn 33, Issue 4, 1998, Pages 496-517

Energy landscape of a native protein: Jumping-among-minima model

Author keywords

Energy landscape; Hierarchical conformational substates; Human lysozyme; Jumping among minima model; Molecular dynamics; Normal mode analysis; Principal component analysis

Indexed keywords

ARTICLE; ENERGY; MATHEMATICAL MODEL; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN STRUCTURE; SIMULATION;

EID: 0032374086     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19981201)33:4<496::AID-PROT4>3.0.CO;2-1     Document Type: Article
Times cited : (229)

References (73)
  • 1
    • 0026320866 scopus 로고
    • The energy landscapes and motions of proteins
    • Frauenfelder, H., Sligar, S.G., Wolynes, P.G. The energy landscapes and motions of proteins. Science 254:1598-1603, 1991.
    • (1991) Science , vol.254 , pp. 1598-1603
    • Frauenfelder, H.1    Sligar, S.G.2    Wolynes, P.G.3
  • 2
    • 0002237761 scopus 로고
    • Biomolecules: Where the Physics of complexity and simplicity meet
    • Frauenfelder, H., Wolynes, P.G. Biomolecules: Where the Physics of complexity and simplicity meet. Physics Today February 47:58-64, 1994.
    • (1994) Physics Today February , vol.47 , pp. 58-64
    • Frauenfelder, H.1    Wolynes, P.G.2
  • 3
    • 0029099219 scopus 로고
    • Looking into the energy landscape of myoglobin: Evidence for self-similarity
    • Leeson, D.T., Wiersma, D.A. Looking into the energy landscape of myoglobin: Evidence for self-similarity. Nat. Struct. Biol. 2:848-851, 1995.
    • (1995) Nat. Struct. Biol. , vol.2 , pp. 848-851
    • Leeson, D.T.1    Wiersma, D.A.2
  • 4
    • 0023140044 scopus 로고
    • Multiple conformational states of proteins: A molecular dynamics analysis of myoglobin
    • Elber, R., Karplus, M. Multiple conformational states of proteins: A molecular dynamics analysis of myoglobin. Science 235:318-321, 1987.
    • (1987) Science , vol.235 , pp. 318-321
    • Elber, R.1    Karplus, M.2
  • 5
    • 0024585391 scopus 로고
    • Structural basis of hierarchical multiple substates of a protein. I: Introduction
    • Noguti, T., Go, N. Structural basis of hierarchical multiple substates of a protein. I: Introduction. Proteins 5:97-103, 1989.
    • (1989) Proteins , vol.5 , pp. 97-103
    • Noguti, T.1    Go, N.2
  • 6
    • 0024567779 scopus 로고
    • Structural basis of hierarchical multiple substates of a protein. II: Monte Carlo simulation of native thermal fluctuations and energy minimization
    • Noguti, T., Go, N. Structural basis of hierarchical multiple substates of a protein. II: Monte Carlo simulation of native thermal fluctuations and energy minimization. Proteins 5:104-112, 1989.
    • (1989) Proteins , vol.5 , pp. 104-112
    • Noguti, T.1    Go, N.2
  • 7
    • 0024486487 scopus 로고
    • Structural basis of hierarchical multiple substates of a protein. III: Side chain and main chain local conformations
    • Noguti, T., Go, N. Structural basis of hierarchical multiple substates of a protein. III: Side chain and main chain local conformations. Proteins 5:113-124, 1989.
    • (1989) Proteins , vol.5 , pp. 113-124
    • Noguti, T.1    Go, N.2
  • 8
    • 0024486623 scopus 로고
    • Structural basis of hierarchical multiple substates of a protein. IV: Rearrangements in atom packing and local deformations
    • Noguti, T., Go, N. Structural basis of hierarchical multiple substates of a protein. IV: Rearrangements in atom packing and local deformations. Proteins 5:125-131, 1989.
    • (1989) Proteins , vol.5 , pp. 125-131
    • Noguti, T.1    Go, N.2
  • 9
    • 0024486201 scopus 로고
    • Structural basis of hierarchical multiple substates of a protein. V: Nonlocal deformations
    • Noguti, T., Go, N. Structural basis of hierarchical multiple substates of a protein. V: Nonlocal deformations. Proteins 5:132-138, 1989.
    • (1989) Proteins , vol.5 , pp. 132-138
    • Noguti, T.1    Go, N.2
  • 10
    • 0029152775 scopus 로고
    • Protein conformational landscapes: Energy minimization and clustering of a long molecular dynamics trajectory
    • Troyer, J.M., Cohen, F.E. Protein conformational landscapes: Energy minimization and clustering of a long molecular dynamics trajectory. Proteins 23:97-110, 1995.
    • (1995) Proteins , vol.23 , pp. 97-110
    • Troyer, J.M.1    Cohen, F.E.2
  • 11
    • 0021449809 scopus 로고
    • Quasi-harmonic method for studying very low frequency modes in proteins
    • Levy, R.M., Srinivasan, A.R., Olson, W.K., McCammon, JA. Quasi-harmonic method for studying very low frequency modes in proteins. Biopolymers 23:1099-1112, 1984.
    • (1984) Biopolymers , vol.23 , pp. 1099-1112
    • Levy, R.M.1    Srinivasan, A.R.2    Olson, W.K.3    McCammon, J.A.4
  • 12
    • 0000998079 scopus 로고
    • The effects of solvent on the conformation and the collective motions of protein: Normal mode analysis and molecular dynamics simulation of melittin in water and in vacuum
    • Kitao, A., Hirata, F., Go, N. The effects of solvent on the conformation and the collective motions of protein: Normal mode analysis and molecular dynamics simulation of melittin in water and in vacuum. Chem. Phys. 158:447-472, 1991.
    • (1991) Chem. Phys. , vol.158 , pp. 447-472
    • Kitao, A.1    Hirata, F.2    Go, N.3
  • 13
    • 0000577041 scopus 로고
    • Large-amplitude nonlinear motions in proteins
    • García, A.E. Large-amplitude nonlinear motions in proteins. Phys. Rev. Lett. 68:2696-2699, 1992.
    • (1992) Phys. Rev. Lett. , vol.68 , pp. 2696-2699
    • García, A.E.1
  • 14
    • 0027732618 scopus 로고
    • Effect of solvent on collective motions in globular proteins
    • Hayward, S., Kitao, A., Hirata, F., Go, N. Effect of solvent on collective motions in globular proteins. J. Mol. Biol. 234:1207-1217, 1993.
    • (1993) J. Mol. Biol. , vol.234 , pp. 1207-1217
    • Hayward, S.1    Kitao, A.2    Hirata, F.3    Go, N.4
  • 15
    • 0028292635 scopus 로고
    • Harmonic and anharmonic effects in the dynamics of BPTI: A normal mode analysis and principal component analysis
    • Hayward, S., Kitao, A., Go, N. Harmonic and anharmonic effects in the dynamics of BPTI: A normal mode analysis and principal component analysis. Protein Sci. 3:936-943, 1994.
    • (1994) Protein Sci. , vol.3 , pp. 936-943
    • Hayward, S.1    Kitao, A.2    Go, N.3
  • 16
    • 0028877423 scopus 로고
    • Harmonicity and anharmonicity in protein dynamics: A normal mode analysis and principal component analysis
    • Hayward, S., Kitao, A., Go, N. Harmonicity and anharmonicity in protein dynamics: a normal mode analysis and principal component analysis. Proteins 23:177-186, 1995
    • (1995) Proteins , vol.23 , pp. 177-186
    • Hayward, S.1    Kitao, A.2    Go, N.3
  • 18
    • 0026717834 scopus 로고
    • Normal mode refinement: Crystallographic refinement of protein dynamic structure. II. Application to human lysozyme
    • Kidera, A., Inaka, K., Matsushima, M., Go, N. Normal mode refinement: Crystallographic refinement of protein dynamic structure. II. Application to human lysozyme. J. Mol. Biol. 225:477-486, 1992.
    • (1992) J. Mol. Biol. , vol.225 , pp. 477-486
    • Kidera, A.1    Inaka, K.2    Matsushima, M.3    Go, N.4
  • 19
    • 0029150760 scopus 로고
    • Protein flexibility and adaptability seen in 25 crystal forms of T4 lysozyme
    • Zhang, X., Woxniak, J.A., Matthews, B.W. Protein flexibility and adaptability seen in 25 crystal forms of T4 lysozyme. J. Mol. Biol. 250:527-552, 1995.
    • (1995) J. Mol. Biol. , vol.250 , pp. 527-552
    • Zhang, X.1    Woxniak, J.A.2    Matthews, B.W.3
  • 21
    • 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 82:4995-4999, 1985.
    • (1985) Proc. Natl. Acad. Sci. USA , vol.82 , pp. 4995-4999
    • Brooks, B.1    Karplus, M.2
  • 23
    • 0023512803 scopus 로고
    • Anisotropy and anharmonicity of the atomic fluctuations in proteins: Analysis of a molecular dynamics simulation
    • Ichiye, T., Karplus, M. Anisotropy and anharmonicity of the atomic fluctuations in proteins: Analysis of a molecular dynamics simulation. Proteins 2:236-259, 1987.
    • (1987) Proteins , vol.2 , pp. 236-259
    • Ichiye, T.1    Karplus, M.2
  • 24
    • 0024354001 scopus 로고
    • Solvent effects on protein motion and protein effects on solvent motion
    • Brooks III, C.L., Karplus, M. Solvent effects on protein motion and protein effects on solvent motion. J. Mol. Biol. 208:159-181, 1989.
    • (1989) J. Mol. Biol. , vol.208 , pp. 159-181
    • Brooks III, C.L.1    Karplus, M.2
  • 25
    • 0029162947 scopus 로고
    • Comparison of MD simulations and NMR experiments for hen lysozyme. Analysis of local fluctuations, cooperative motions, and global changes
    • Smith, L.J., Mark, A.E., Dobson, C.M., van Gunsteren, W.F. Comparison of MD simulations and NMR experiments for hen lysozyme. Analysis of local fluctuations, cooperative motions, and global changes. Biochemistry 34:10918-10931, 1995.
    • (1995) Biochemistry , vol.34 , pp. 10918-10931
    • Smith, L.J.1    Mark, A.E.2    Dobson, C.M.3    Van Gunsteren, W.F.4
  • 26
    • 0025066772 scopus 로고
    • Normal mode analysis of human lysozyme: Study of the relative motion of the two domains and characterization of the harmonic motion
    • Gibrat, J., Go, N. Normal mode analysis of human lysozyme: Study of the relative motion of the two domains and characterization of the harmonic motion. Proteins 8:258-279, 1990.
    • (1990) Proteins , vol.8 , pp. 258-279
    • Gibrat, J.1    Go, N.2
  • 27
    • 0025753631 scopus 로고
    • Projection of Monte Carlo and molecular dynamics trajectories onto the normal mode axes: Human lysozyme
    • Horiuchi, T., Go, N. Projection of Monte Carlo and molecular dynamics trajectories onto the normal mode axes: Human lysozyme. Proteins 10:106-116, 1991.
    • (1991) Proteins , vol.10 , pp. 106-116
    • Horiuchi, T.1    Go, N.2
  • 28
    • 0026459304 scopus 로고
    • A molecular dynamics simulation of bacteriophage T4 lysozyme
    • Arnold, G.E., Ornstein, R.L. A molecular dynamics simulation of bacteriophage T4 lysozyme. Protein Eng. 5:703-714, 1992.
    • (1992) Protein Eng. , vol.5 , pp. 703-714
    • Arnold, G.E.1    Ornstein, R.L.2
  • 29
    • 0030888546 scopus 로고    scopus 로고
    • Model-free methods of analyzing domain motions in proteins from simulations: A comparison of normal mode analysis and molecular dynamics simulation of lysozyme
    • Hayward, S., Kitao, A., Berendsen, H.J.C. Model-free methods of analyzing domain motions in proteins from simulations: A comparison of normal mode analysis and molecular dynamics simulation of lysozyme. Proteins 27: 425-437, 1997.
    • (1997) Proteins , vol.27 , pp. 425-437
    • Hayward, S.1    Kitao, A.2    Berendsen, H.J.C.3
  • 30
    • 0032032108 scopus 로고    scopus 로고
    • Improved Protein Free Energy Calculation by More Accurate Treatment of Nonbonded Energy: Application to Chymotrypsin Inhibitor 2, V57A
    • Sugita, Y., Kitao, A. Improved Protein Free Energy Calculation by More Accurate Treatment of Nonbonded Energy: Application to Chymotrypsin Inhibitor 2, V57A. Proteins 30:388-400, 1998.
    • (1998) Proteins , vol.30 , pp. 388-400
    • Sugita, Y.1    Kitao, A.2
  • 31
    • 0001655657 scopus 로고
    • Finite representation of an infinite bulk system: Solvent boundary potential for computer simulations
    • Beglov, D., Roux, B. Finite representation of an infinite bulk system: Solvent boundary potential for computer simulations. J. Chem. Phys. 100:9050-9063, 1994.
    • (1994) J. Chem. Phys. , vol.100 , pp. 9050-9063
    • Beglov, D.1    Roux, B.2
  • 32
    • 5244247401 scopus 로고
    • Atomic level simulations on million particles: The cell multipole method for Coulomb and London nonbond interactions
    • Ding, H.-Q., Karasawa, N., Goddard III, W.A. Atomic level simulations on million particles: The cell multipole method for Coulomb and London nonbond interactions. J. Chem. Phys. 97:4309-4315, 1992.
    • (1992) J. Chem. Phys. , vol.97 , pp. 4309-4315
    • Ding, H.-Q.1    Karasawa, N.2    Goddard III, W.A.3
  • 33
    • 84943502952 scopus 로고
    • A molecular dynamics method for simulations in the canonical ensemble
    • Nosé, S. A molecular dynamics method for simulations in the canonical ensemble. Mol. Phys. 52:255-268, 1984.
    • (1984) Mol. Phys. , vol.52 , pp. 255-268
    • Nosé, S.1
  • 34
    • 0001538909 scopus 로고
    • Canonical dynamics: Equilibrium phase-space distributions
    • Hoover, W.G. Canonical dynamics: Equilibrium phase-space distributions. Phys. Rev. A31:1695-1697, 1985.
    • (1985) Phys. Rev. , vol.A31 , pp. 1695-1697
    • Hoover, W.G.1
  • 35
    • 84988053694 scopus 로고
    • An all atom force field for simulations of proteins and nucleic acids
    • Weiner, S.J., Kollman, P.A., Nguyen, D.T., Case, D.A. An all atom force field for simulations of proteins and nucleic acids J. Comp. Chem. 7:230-252, 1986.
    • (1986) J. Comp. Chem. , vol.7 , pp. 230-252
    • Weiner, S.J.1    Kollman, P.A.2    Nguyen, D.T.3    Case, D.A.4
  • 36
    • 0004016501 scopus 로고
    • Comparison of simple potential functions for simulating liquid water
    • Jorgensen, W.L., Chandrasekhar, J., Madura, J.D. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926-935, 1983.
    • (1983) J. Chem. Phys. , vol.79 , pp. 926-935
    • Jorgensen, W.L.1    Chandrasekhar, J.2    Madura, J.D.3
  • 38
    • 84986472098 scopus 로고
    • Conformational dynamics of polypeptides and proteins in the dihedral angle space and in the cartesian coordinate space: Normal mode analysis of decaalanine
    • Kitao, A., Go, N. Conformational dynamics of polypeptides and proteins in the dihedral angle space and in the cartesian coordinate space: Normal mode analysis of decaalanine. J. Comp. Chem. 12:359-368, 1991.
    • (1991) J. Comp. Chem. , vol.12 , pp. 359-368
    • Kitao, A.1    Go, N.2
  • 39
    • 36149010019 scopus 로고
    • Some Studies Concerning Rotating Axes and Polyatomic Molecules
    • Eckart, C. Some Studies Concerning Rotating Axes and Polyatomic Molecules. Phys. Rev. 47:552-558, 1935.
    • (1935) Phys. Rev. , vol.47 , pp. 552-558
    • Eckart, C.1
  • 40
    • 0027983643 scopus 로고
    • Comparison of normal mode analyses on a small globular protein in dihedral angle space and cartesian coordinate space
    • Kitao, A., Hayward, S., Go, N. Comparison of normal mode analyses on a small globular protein in dihedral angle space and cartesian coordinate space. Biophys. Chem. 52:107-114, 1994.
    • (1994) Biophys. Chem. , vol.52 , pp. 107-114
    • Kitao, A.1    Hayward, S.2    Go, N.3
  • 41
    • 3743054071 scopus 로고    scopus 로고
    • Normal mode analysis of a nucleic acid with flexible furanose rings in dihedral angle space
    • Tomimoto, M., Kitao, A., Go, N. Normal mode analysis of a nucleic acid with flexible furanose rings in dihedral angle space. Electro. J. Theor. Chem. 1:122-134, 1996.
    • (1996) Electro. J. Theor. Chem. , vol.1 , pp. 122-134
    • Tomimoto, M.1    Kitao, A.2    Go, N.3
  • 42
    • 0028786432 scopus 로고
    • Contribution of hydrophobic residues to the stability of human lysozyme: Calorimetric studies and X-ray structural analysis of the five isoleucine to valine mutants
    • Takano, K., Ogasahara, K., Kaneda, H. et al. Contribution of hydrophobic residues to the stability of human lysozyme: Calorimetric studies and X-ray structural analysis of the five isoleucine to valine mutants. J. Mol. Biol. 254:62-76, 1995.
    • (1995) J. Mol. Biol. , vol.254 , pp. 62-76
    • Takano, K.1    Ogasahara, K.2    Kaneda, H.3
  • 43
    • 0019816864 scopus 로고
    • Refinement of human lysozyme at 1.5Å resolution analysis of non-bonded and hydrogen-bonded interactions
    • Artymuik, P.J., Blake, C.C.F. Refinement of human lysozyme at 1.5Å resolution analysis of non-bonded and hydrogen-bonded interactions. J. Mol. Biol. 152:737-762, 1981.
    • (1981) J. Mol. Biol. , vol.152 , pp. 737-762
    • Artymuik, P.J.1    Blake, C.C.F.2
  • 44
    • 36149005118 scopus 로고
    • On the theory of the Brownian motion
    • Uhlenbeck, G.E., Ornstein, L.S. On the theory of the Brownian motion. Phys. Rev. 36:823-841, 1930.
    • (1930) Phys. Rev. , vol.36 , pp. 823-841
    • Uhlenbeck, G.E.1    Ornstein, L.S.2
  • 45
    • 0002121327 scopus 로고
    • Stochastic problems in physics and astronomy
    • Chandrasekhar, S. Stochastic problems in physics and astronomy. Reviews of Modern Physics 15:1-89, 1943.
    • (1943) Reviews of Modern Physics , vol.15 , pp. 1-89
    • Chandrasekhar, S.1
  • 46
    • 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 80:3696-3700, 1983.
    • (1983) Proc. Natl. Acad. Sci. USA , vol.80 , pp. 3696-3700
    • Go, N.1    Noguti, T.2    Nishikawa, T.3
  • 47
    • 0023613529 scopus 로고
    • Normal modes of vibration in bovine pancreatic inhibitor and its mechanical properties
    • Nishikawa, T., Go, N. Normal modes of vibration in bovine pancreatic inhibitor and its mechanical properties. Proteins 2:308-329, 1987.
    • (1987) Proteins , vol.2 , pp. 308-329
    • Nishikawa, T.1    Go, N.2
  • 48
    • 0026663419 scopus 로고
    • Normal mode refinement: Crystallographic refinement of protein dynamic structure. I. Theory and test by simulated diffraction data
    • Kidera, A., Go, N. Normal mode refinement: Crystallographic refinement of protein dynamic structure. I. Theory and test by simulated diffraction data. J. Mol. Biol. 225:457-475, 1992.
    • (1992) J. Mol. Biol. , vol.225 , pp. 457-475
    • Kidera, A.1    Go, N.2
  • 49
    • 0000081668 scopus 로고
    • Collective variable description of native protein dynamics
    • Hayward, S., Go, N. Collective variable description of native protein dynamics. Annu. Rev. Phys. Chem. 46:223-250, 1995.
    • (1995) Annu. Rev. Phys. Chem. , vol.46 , pp. 223-250
    • Hayward, S.1    Go, N.2
  • 50
    • 0025938315 scopus 로고
    • Protein dynamics: Comparison of simulations with inelastic neutron scattering experiments
    • Smith, J.C. Protein dynamics: comparison of simulations with inelastic neutron scattering experiments. Q. Rev. Biophys. 24:227-291, 1991.
    • (1991) Q. Rev. Biophys. , vol.24 , pp. 227-291
    • Smith, J.C.1
  • 51
    • 0000078368 scopus 로고
    • Effects of solvent on the conformation and the collective motions of a protein. 2. Structure of hydration in melittin
    • Kitao, A., Hirata, F., Go, N. Effects of solvent on the conformation and the collective motions of a protein. 2. Structure of hydration in melittin. J. Phys. Chem. 97: 10223-10230, 1993.
    • (1993) J. Phys. Chem. , vol.97 , pp. 10223-10230
    • Kitao, A.1    Hirata, F.2    Go, N.3
  • 52
    • 0000078369 scopus 로고
    • Effects of solvent on the conformation and the collective motions of a protein. 3. Free energy analysis by the extended RISM Theory
    • Kitao, A., Hirata, F., Go, N. Effects of solvent on the conformation and the collective motions of a protein. 3. Free energy analysis by the extended RISM Theory. J. Phys. Chem. 97:10231-10235, 1993.
    • (1993) J. Phys. Chem. , vol.97 , pp. 10231-10235
    • Kitao, A.1    Hirata, F.2    Go, N.3
  • 53
    • 0000902576 scopus 로고
    • Structural basis of hierarchical multiple substates of a protein
    • Go, N., Noguti, T. Structural basis of hierarchical multiple substates of a protein. Chemica Scripta 29A:151-164, 1989.
    • (1989) Chemica Scripta , vol.29 A , pp. 151-164
    • Go, N.1    Noguti, T.2
  • 54
    • 0000999856 scopus 로고    scopus 로고
    • Structural relaxations in H2-substituted myoglobin observed by temperature-cycling hole burning
    • Shibata, Y., Kurita, A., Kushida, T. Structural relaxations in H2-substituted myoglobin observed by temperature-cycling hole burning. J. Chem. Phys. 104:4396-4405, 1996.
    • (1996) J. Chem. Phys. , vol.104 , pp. 4396-4405
    • Shibata, Y.1    Kurita, A.2    Kushida, T.3
  • 55
    • 0026890721 scopus 로고
    • Structural dynamics of proteins investigated by hole-burning spectroscopy
    • Kurita, A., Ohmukai, R., Kushida, T. Structural dynamics of proteins investigated by hole-burning spectroscopy. Journal of Luminescence 53:255-258, 1992.
    • (1992) Journal of Luminescence , vol.53 , pp. 255-258
    • Kurita, A.1    Ohmukai, R.2    Kushida, T.3
  • 56
    • 0010425813 scopus 로고
    • Two-level systems in myoglobin probed by non-lorenzian hole broadening in temperature-cycling experiment
    • Kurita, A., Shibata, Y., Kushida, T. Two-level systems in myoglobin probed by non-lorenzian hole broadening in temperature-cycling experiment. Phys. Rev. Lett. 74:4349-4352, 1995.
    • (1995) Phys. Rev. Lett. , vol.74 , pp. 4349-4352
    • Kurita, A.1    Shibata, Y.2    Kushida, T.3
  • 58
    • 0008994613 scopus 로고
    • Extracting the energy barrier distribution of a disordered system from the instantaneous normal mode density of states: Applications to peptides and proteins
    • Straub, J.E., Choi, J.-K. Extracting the energy barrier distribution of a disordered system from the instantaneous normal mode density of states: Applications to peptides and proteins. J. Phys. Chem. 98:10978-10987, 1994.
    • (1994) J. Phys. Chem. , vol.98 , pp. 10978-10987
    • Straub, J.E.1    Choi, J.-K.2
  • 59
    • 0000885331 scopus 로고
    • Harmonic analysis of large systems. I. Methodology
    • Brooks, B.R., Janezic, D., Karplus, M. Harmonic analysis of large systems. I. Methodology. J. Comp. Chem. 16:1522-1542, 1995.
    • (1995) J. Comp. Chem. , vol.16 , pp. 1522-1542
    • Brooks, B.R.1    Janezic, D.2    Karplus, M.3
  • 60
    • 84986469420 scopus 로고
    • Harmonic analysis of large systems. II. Comparison of different protein models
    • Janezic, D., Brooks, B.R. Harmonic analysis of large systems. II. Comparison of different protein models. J. Comp. Chem. 16:1543-1553, 1995.
    • (1995) J. Comp. Chem. , vol.16 , pp. 1543-1553
    • Janezic, D.1    Brooks, B.R.2
  • 61
    • 84986473952 scopus 로고
    • Harmonic analysis of large systems. III. Comparison with molecular dynamics
    • Janezic, D., Veneble, R.M., Brooks, B.R. Harmonic analysis of large systems. III. Comparison with molecular dynamics. J. Comp. Chem. 16:1554-1566, 1995.
    • (1995) J. Comp. Chem. , vol.16 , pp. 1554-1566
    • Janezic, D.1    Veneble, R.M.2    Brooks, B.R.3
  • 62
    • 0029022540 scopus 로고
    • Anharmonic wave functions of proteins: Quantum self-consistent field calculations of BPTI
    • Roitberg, A., Gerber, R.B., Elber, R., Ratner, M.A. Anharmonic wave functions of proteins: Quantum self-consistent field calculations of BPTI. Science 268:1319-1322, 1995.
    • (1995) Science , vol.268 , pp. 1319-1322
    • Roitberg, A.1    Gerber, R.B.2    Elber, R.3    Ratner, M.A.4
  • 63
    • 0027975255 scopus 로고
    • 10-/α-helix transition: Implications for a natural reaction coordinate
    • 10-/α-helix transition: Implications for a natural reaction coordinate. J. Am. Chem. Soc. 116:6307-6315, 1994.
    • (1994) J. Am. Chem. Soc. , vol.116 , pp. 6307-6315
    • Basu, G.1    Kitao, A.2    Hirata, F.3    Go, N.4
  • 64
    • 0027254295 scopus 로고
    • Conformational classification of short backbone fragments in globular proteins and its use for coding backbone conformations
    • Takahashi, K., Go, N. Conformational classification of short backbone fragments in globular proteins and its use for coding backbone conformations. Biophys. Chem. 47:163-178, 1993.
    • (1993) Biophys. Chem. , vol.47 , pp. 163-178
    • Takahashi, K.1    Go, N.2
  • 65
    • 0000980795 scopus 로고
    • Quasi-harmonic method for calculating vibrational spectra from classica simulations on multidimensional anharmonic potential surfaces
    • Levy, R.M., Rojas, O.L., Friesner, R.A. Quasi-harmonic method for calculating vibrational spectra from classica simulations on multidimensional anharmonic potential surfaces. J. Phys. Chem. 88:4233-4238, 1984.
    • (1984) J. Phys. Chem. , vol.88 , pp. 4233-4238
    • Levy, R.M.1    Rojas, O.L.2    Friesner, R.A.3
  • 66
    • 0024094768 scopus 로고
    • Accurate simulation of protein dynamics in solution
    • Levitt, M., Sharon, R. Accurate simulation of protein dynamics in solution. Proc. Natl. Acad. Sci. USA 85:7557-7561, 1988.
    • (1988) Proc. Natl. Acad. Sci. USA , vol.85 , pp. 7557-7561
    • Levitt, M.1    Sharon, R.2
  • 67
    • 0024795316 scopus 로고
    • The effects of truncating long-range forces on protein dynamics
    • Loncharich, R.J., Brooks, B.R. The effects of truncating long-range forces on protein dynamics. Proteins 6:32-45, 1989.
    • (1989) Proteins , vol.6 , pp. 32-45
    • Loncharich, R.J.1    Brooks, B.R.2
  • 68
    • 36449006641 scopus 로고
    • Molecular dynamics simulations of proteins in solution: Artifacts caused by the cutoff approximation
    • Saito, M. Molecular dynamics simulations of proteins in solution: Artifacts caused by the cutoff approximation. J. Chem. Phys. 101:4055-4061, 1994.
    • (1994) J. Chem. Phys. , vol.101 , pp. 4055-4061
    • Saito, M.1
  • 70
    • 0008348735 scopus 로고
    • PRESTO (Protein Engineering SimulaTOr): A vectorized molecular mechamics program for biopolymers
    • Morikami, K., Nakai, T., Kidera, M., Saito, M., Nakamura, H. PRESTO (Protein Engineering SimulaTOr): A vectorized molecular mechamics program for biopolymers. Comput. Chem. 16:243-248, 1992.
    • (1992) Comput. Chem. , vol.16 , pp. 243-248
    • Morikami, K.1    Nakai, T.2    Kidera, M.3    Saito, M.4    Nakamura, H.5
  • 71
    • 0001295503 scopus 로고    scopus 로고
    • Principal component analysis and long time protein dynamics
    • Balsea, M.A., Wriggers, W. Oono, Y., Schulten, K. Principal component analysis and long time protein dynamics. J. Phys. Chem. 100:2567-2472, 1996.
    • (1996) J. Phys. Chem. , vol.100 , pp. 2567-12472
    • Balsea, M.A.1    Wriggers, W.2    Oono, Y.3    Schulten, K.4
  • 72
    • 0030068480 scopus 로고    scopus 로고
    • 2 in noncrystalline environments show a subunit transition from the open to the closed conformation
    • 2 in noncrystalline environments show a subunit transition from the open to the closed conformation, Protein Sci. 5:62-71, 1996.
    • (1996) Protein Sci. , vol.5 , pp. 62-71
    • García, A.E.1    Harman, J.G.2
  • 73
    • 0031231987 scopus 로고    scopus 로고
    • Multi-basin dynamics of a protein in a crystal environment
    • García, A.E., Blumenfeld, R., Hummer, G., Krumhansl, J.A. Multi-basin dynamics of a protein in a crystal environment. Physica D 107:225-239, 1997.
    • (1997) Physica D , vol.107 , pp. 225-239
    • García, A.E.1    Blumenfeld, R.2    Hummer, G.3    Krumhansl, J.A.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.