메뉴 건너뛰기




Volumn 94, Issue 9, 2008, Pages 3461-3474

Effects of surface water on protein dynamics studied by a novel coarse-grained normal mode approach

Author keywords

[No Author keywords available]

Indexed keywords

CYCLIC NUCLEOTIDE; HCN2 POTASSIUM CHANNEL; ION CHANNEL; PROTEIN; WATER;

EID: 43649087569     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1529/biophysj.107.115956     Document Type: Article
Times cited : (28)

References (93)
  • 1
    • 0034127361 scopus 로고    scopus 로고
    • Collective protein dynamics in relation to function
    • Berendsen, H. J., 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.1    Hayward, S.2
  • 2
    • 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
  • 3
    • 0036725277 scopus 로고    scopus 로고
    • Molecular dynamics simulations of biomolecules
    • Karplus, M., and J. A. McCammon. 2002. Molecular dynamics simulations of biomolecules. Nat. Struct. Biol. 9:646-652.
    • (2002) Nat. Struct. Biol , vol.9 , pp. 646-652
    • Karplus, M.1    McCammon, J.A.2
  • 4
    • 0017776823 scopus 로고
    • Dynamics of folded proteins
    • McCammon, J. A., B. R. Gelin, and M. Karplus. 1977. Dynamics of folded proteins. Nature. 267:585-590.
    • (1977) Nature , vol.267 , pp. 585-590
    • McCammon, J.A.1    Gelin, B.R.2    Karplus, M.3
  • 6
    • 0000577041 scopus 로고
    • Large-amplitude nonlinear motions in proteins
    • Garcia, A. E. 1992. Large-amplitude nonlinear motions in proteins. Phys. Rev. Lett. 68:2696-2699.
    • (1992) Phys. Rev. Lett , vol.68 , pp. 2696-2699
    • Garcia, A.E.1
  • 7
    • 0026076090 scopus 로고
    • Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations
    • Ichiye, T., and M. Karplus. 1991. Collective motions in proteins: a covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations. Proteins. 11:205-217.
    • (1991) Proteins , vol.11 , pp. 205-217
    • Ichiye, T.1    Karplus, M.2
  • 8
    • 84986473952 scopus 로고
    • Harmonic analysis of large systems. III. Comparison with molecular dynamics
    • Janezic, D., R. M. Venable, and B. R. Brooks. 1995. Harmonic analysis of large systems. III. Comparison with molecular dynamics. J. Comput. Chem. 16:1554-1566.
    • (1995) J. Comput. Chem , vol.16 , pp. 1554-1566
    • Janezic, D.1    Venable, R.M.2    Brooks, B.R.3
  • 9
    • 0034500645 scopus 로고    scopus 로고
    • Similarities between principal components of protein dynamics and random diffusion
    • Hess, B. 2000. Similarities between principal components of protein dynamics and random diffusion. Phys. Rev. E Stat. Phys. Plasmas Fluids Relat. Interdiscip. Topics. 62:8438-8448.
    • (2000) Phys. Rev. E Stat. Phys. Plasmas Fluids Relat. Interdiscip. Topics , vol.62 , pp. 8438-8448
    • Hess, B.1
  • 10
    • 0001295503 scopus 로고    scopus 로고
    • Principal component analysis and long time protein dynamics
    • Balsera, M. A., W. Wriggers, Y. Oono, and K. Schulten. 1996. Principal component analysis and long time protein dynamics. J. Phys. Chem. 100: 2567-2572.
    • (1996) J. Phys. Chem , vol.100 , pp. 2567-2572
    • Balsera, M.A.1    Wriggers, W.2    Oono, Y.3    Schulten, K.4
  • 11
    • 0000991642 scopus 로고
    • Harmonic dynamics of proteins: Normal modes and fluctuations in bovine pancreatic trypsin inhibitor
    • Brooks, B., and M. Karplus. 1983. Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor. Proc. Natl. Acad. Sci. USA. 80:6571-6575.
    • (1983) Proc. Natl. Acad. Sci. USA , vol.80 , pp. 6571-6575
    • Brooks, B.1    Karplus, M.2
  • 12
    • 0000885331 scopus 로고
    • Harmonic analysis of large systems. I. Methodology
    • Brooks, B. R., D. Janezic, and M. Karplus. 1995. Harmonic analysis of large systems. I. Methodology. J. Comput. Chem. 16:1522-1542.
    • (1995) J. Comput. Chem , vol.16 , pp. 1522-1542
    • Brooks, B.R.1    Janezic, D.2    Karplus, M.3
  • 13
    • 14844286108 scopus 로고    scopus 로고
    • Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes
    • Ma, J. 2005. Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes. Structure. 13:373-380.
    • (2005) Structure , vol.13 , pp. 373-380
    • Ma, J.1
  • 14
    • 0020771265 scopus 로고
    • Dynamics of a small globular protein in terms of low-frequency vibrational modes
    • Go, N., T. Noguti, and T. Nishikawa. 1983. Dynamics of a small globular protein in terms of low-frequency vibrational modes. Proc. Natl. Acad. Sci. USA. 80:3696-3700.
    • (1983) Proc. Natl. Acad. Sci. USA , vol.80 , pp. 3696-3700
    • Go, N.1    Noguti, T.2    Nishikawa, T.3
  • 15
    • 2942511344 scopus 로고    scopus 로고
    • A normal mode analysis of structural plasticity in the biomolecular motor F(1)-ATPase
    • Cui, Q., G. Li, J. Ma, and M. Karplus. 2004. A normal mode analysis of structural plasticity in the biomolecular motor F(1)-ATPase. J. Mol. Biol. 340:345-372.
    • (2004) J. Mol. Biol , vol.340 , pp. 345-372
    • Cui, Q.1    Li, G.2    Ma, J.3    Karplus, M.4
  • 16
    • 0030700726 scopus 로고    scopus 로고
    • Ligand-induced conformational changes in ras p21: A normal mode and energy minimization analysis
    • Ma, J., and M. Karplus. 1997. Ligand-induced conformational changes in ras p21: a normal mode and energy minimization analysis. J. Mol. Biol. 274:114-131.
    • (1997) J. Mol. Biol , vol.274 , pp. 114-131
    • Ma, J.1    Karplus, M.2
  • 17
    • 0345393320 scopus 로고    scopus 로고
    • Thermodynamics of protein hydration computed by molecular dynamics and normal modes
    • Yu, X., J. Park, and D. M. Leitner. 2003. Thermodynamics of protein hydration computed by molecular dynamics and normal modes. J. Phys. Chem. B. 107:12820-12828.
    • (2003) J. Phys. Chem. B , vol.107 , pp. 12820-12828
    • Yu, X.1    Park, J.2    Leitner, D.M.3
  • 18
    • 0028454915 scopus 로고
    • A new approach for determining low-frequency normal modes in macromolecules
    • Durand, P., G. Trinquier, and Y. H. Sanejouand. 1994. A new approach for determining low-frequency normal modes in macromolecules. Biopolymers. 34:759-771.
    • (1994) Biopolymers , vol.34 , pp. 759-771
    • Durand, P.1    Trinquier, G.2    Sanejouand, Y.H.3
  • 19
    • 0029374782 scopus 로고
    • Computation of low-frequency normal modes in macromolecules: Improvements to the method of diagonalization in a mixed basis and application to hemoglobin
    • Perahia, D., and L. Mouawad. 1995. Computation of low-frequency normal modes in macromolecules: improvements to the method of diagonalization in a mixed basis and application to hemoglobin. Comput. Chem. 19:241-246.
    • (1995) Comput. Chem , vol.19 , pp. 241-246
    • Perahia, D.1    Mouawad, L.2
  • 22
    • 0035789518 scopus 로고    scopus 로고
    • GROMACS 3.0: A package for molecular simulation and trajectory analysis
    • online computer file
    • Lindahl, E., B. Hess, and D. van der Spoel. 2001. GROMACS 3.0: a package for molecular simulation and trajectory analysis. J. Mol. Model. 7:306-317 (online computer file).
    • (2001) J. Mol. Model , vol.7 , pp. 306-317
    • Lindahl, E.1    Hess, B.2    van der Spoel, D.3
  • 24
    • 33751534910 scopus 로고    scopus 로고
    • Conformational hetero-geneity and low-frequency vibrational modes of proteins
    • Balog, E., J. C. Smith, and D. Perahia. 2006. Conformational hetero-geneity and low-frequency vibrational modes of proteins. Phys. Chem. Chem. Phys. 8:5543-5548.
    • (2006) Phys. Chem. Chem. Phys , vol.8 , pp. 5543-5548
    • Balog, E.1    Smith, J.C.2    Perahia, D.3
  • 25
    • 12944292929 scopus 로고    scopus 로고
    • Protein structural transitions and their functional role
    • discussion, 355-356
    • Karplus, M., Y. Q. Gao, J. Ma, A. van der Vaart, and W. Yang. 2005. Protein structural transitions and their functional role. Phil. Trans. R. Soc. Lond. 363:331-355; discussion, 355-356.
    • (2005) Phil. Trans. R. Soc. Lond , vol.363 , pp. 331-355
    • Karplus, M.1    Gao, Y.Q.2    Ma, J.3    van der Vaart, A.4    Yang, W.5
  • 27
    • 33846189408 scopus 로고    scopus 로고
    • Interpreting correlated motions using normal mode analysis
    • Van Wynsberghe, A. W., and Q. Cui. 2006. Interpreting correlated motions using normal mode analysis. Structure. 14:1647-1653.
    • (2006) Structure , vol.14 , pp. 1647-1653
    • Van Wynsberghe, A.W.1    Cui, Q.2
  • 28
    • 33646145523 scopus 로고    scopus 로고
    • Can conformational change be described by only a few normal modes?
    • Petrone, P., and V. S. Pande. 2006. Can conformational change be described by only a few normal modes? Biophys. J. 90:1583-1593.
    • (2006) Biophys. J , vol.90 , pp. 1583-1593
    • Petrone, P.1    Pande, V.S.2
  • 29
    • 0022111715 scopus 로고
    • Normal modes for specific motions of macromolecules: Application to the hinge-bending mode of lysozyme
    • Brooks, B., and M. Karplus. 1985. Normal modes for specific motions of macromolecules: application to the hinge-bending mode of lysozyme. Proc. Natl. Acad. Sci. USA. 82:4995-4999.
    • (1985) Proc. Natl. Acad. Sci. USA , vol.82 , pp. 4995-4999
    • Brooks, B.1    Karplus, M.2
  • 30
    • 0022419152 scopus 로고
    • Protein normal-mode dynamics: Trypsin inhibitor, crambin, ribonuclease and lysozyme
    • Levitt, M., C. Sander, and P. S. Stern. 1985. Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme. J. Mol. Biol. 181:423-447.
    • (1985) J. Mol. Biol , vol.181 , pp. 423-447
    • Levitt, M.1    Sander, C.2    Stern, P.S.3
  • 31
    • 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., V. Alexandrov, C. A. Wilson, N. Echols, H. Yu, and M. Gerstein. 2002. Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic. Proteins. 48:682-695.
    • (2002) Proteins , vol.48 , pp. 682-695
    • Krebs, W.G.1    Alexandrov, V.2    Wilson, C.A.3    Echols, N.4    Yu, H.5    Gerstein, M.6
  • 32
    • 0034308140 scopus 로고    scopus 로고
    • Building-block approach for determining low-frequency normal modes of macromolecules
    • Tama, F., F. X. Gadea, O. Marques, and Y. H. Sanejouand. 2000. Building-block approach for determining low-frequency normal modes of macromolecules. Proteins. 41:1-7.
    • (2000) Proteins , vol.41 , pp. 1-7
    • Tama, F.1    Gadea, F.X.2    Marques, O.3    Sanejouand, Y.H.4
  • 33
    • 0036840202 scopus 로고    scopus 로고
    • A coarse-grained normal mode approach for macromolecules: An efficient implementation and application to Ca+- ATPase
    • Li, G., and Q. Cui. 2002. A coarse-grained normal mode approach for macromolecules: an efficient implementation and application to Ca+- ATPase. Biophys. J. 83:2457-2474.
    • (2002) Biophys. J , vol.83 , pp. 2457-2474
    • Li, G.1    Cui, Q.2
  • 34
    • 0027576952 scopus 로고
    • Diagonalization in a mixed basis: A method to compute low-frequency normal modes for large macro- molecules
    • Mouawad, L., and D. Perahia. 1993. Diagonalization in a mixed basis: a method to compute low-frequency normal modes for large macro- molecules. Biopolymers. 33:599-611.
    • (1993) Biopolymers , vol.33 , pp. 599-611
    • Mouawad, L.1    Perahia, D.2
  • 35
    • 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
  • 36
    • 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
  • 37
    • 34249945151 scopus 로고    scopus 로고
    • Insights into equilibrium dynamics of proteins from comparison of NMR and x-ray data with computational predictions
    • Yang, L. W., E. Eyal, C. Chennubhotla, J. Jee, A. M. Gronenborn, and I. Bahar. 2007. Insights into equilibrium dynamics of proteins from comparison of NMR and x-ray data with computational predictions. Structure. 15:741-749.
    • (2007) Structure , vol.15 , pp. 741-749
    • Yang, L.W.1    Eyal, E.2    Chennubhotla, C.3    Jee, J.4    Gronenborn, A.M.5    Bahar, I.6
  • 38
    • 6344231648 scopus 로고    scopus 로고
    • Escherichia coli ade- nylate kinase dynamics: Comparison of elastic network model modes with mode-coupling (15)N-NMR relaxation data
    • Temiz, N. A., E. Meirovitch, and I. Bahar. 2004. Escherichia coli ade- nylate kinase dynamics: comparison of elastic network model modes with mode-coupling (15)N-NMR relaxation data. Proteins. 57:468-480.
    • (2004) Proteins , vol.57 , pp. 468-480
    • Temiz, N.A.1    Meirovitch, E.2    Bahar, I.3
  • 39
    • 33745024278 scopus 로고    scopus 로고
    • Symmetry, form, and shape: Guiding principles for robustness in macromolecular machines
    • Tama, F., and C. L. Brooks. 2006. Symmetry, form, and shape: guiding principles for robustness in macromolecular machines. Annu. Rev. Biophys. Biomol. Struct. 35:115-133.
    • (2006) Annu. Rev. Biophys. Biomol. Struct , vol.35 , pp. 115-133
    • Tama, F.1    Brooks, C.L.2
  • 42
    • 34248159870 scopus 로고    scopus 로고
    • Thorough validation of protein normal mode analysis: A comparative study with essential dynamics
    • Rueda, M., P. Chacon, and M. Orozco. 2007. Thorough validation of protein normal mode analysis: a comparative study with essential dynamics. Structure. 15:565-575.
    • (2007) Structure , vol.15 , pp. 565-575
    • Rueda, M.1    Chacon, P.2    Orozco, M.3
  • 43
    • 9644266693 scopus 로고    scopus 로고
    • Tama, F., and C. L. Brooks 3rd. 2005. Diversity and identity of mechanical properties of icosahedral viral capsids studied with elastic network normal mode analysis. J. Mol. Biol. 345:299-314.
    • Tama, F., and C. L. Brooks 3rd. 2005. Diversity and identity of mechanical properties of icosahedral viral capsids studied with elastic network normal mode analysis. J. Mol. Biol. 345:299-314.
  • 44
    • 0035044995 scopus 로고    scopus 로고
    • Conformational change of proteins arising from normal mode calculations
    • Tama, F., and Y. H. Sanejouand. 2001. Conformational change of proteins arising from normal mode calculations. Protein Eng. 14:1-6.
    • (2001) Protein Eng , vol.14 , pp. 1-6
    • Tama, F.1    Sanejouand, Y.H.2
  • 45
    • 25844441847 scopus 로고    scopus 로고
    • Comparison of mode analyses at different resolutions applied to nucleic acid systems
    • Van Wynsberghe, A. W., and Q. Cui. 2005. Comparison of mode analyses at different resolutions applied to nucleic acid systems. Biophys. J. 89:2939-2949.
    • (2005) Biophys. J , vol.89 , pp. 2939-2949
    • Van Wynsberghe, A.W.1    Cui, Q.2
  • 47
    • 0032577559 scopus 로고    scopus 로고
    • Identification of a gene encoding a hyperpolarization-activated pacemaker channel of brain
    • Santoro, B., D. T. Liu, H. Yao, D. Bartsch, E. R. Kandel, S. A. Siegelbaum, and G. R. Tibbs. 1998. Identification of a gene encoding a hyperpolarization-activated pacemaker channel of brain. Cell. 93:717-729.
    • (1998) Cell , vol.93 , pp. 717-729
    • Santoro, B.1    Liu, D.T.2    Yao, H.3    Bartsch, D.4    Kandel, E.R.5    Siegelbaum, S.A.6    Tibbs, G.R.7
  • 48
    • 0141831003 scopus 로고    scopus 로고
    • Structural basis for modulation and agonist speci-ficity of HCN pacemaker channels
    • Zagotta, W. N., N. B. Olivier, K. D. Black, E. C. Young, R. Olson, and E. Gouaux. 2003. Structural basis for modulation and agonist speci-ficity of HCN pacemaker channels. Nature. 425:200-205.
    • (2003) Nature , vol.425 , pp. 200-205
    • Zagotta, W.N.1    Olivier, N.B.2    Black, K.D.3    Young, E.C.4    Olson, R.5    Gouaux, E.6
  • 49
    • 34249869012 scopus 로고    scopus 로고
    • Gating of HCN channels by cyclic nucleotides: Residue contacts that underlie ligand binding, selectivity, and efficacy
    • Zhou, L., and S. A. Siegelbaum. 2007. Gating of HCN channels by cyclic nucleotides: residue contacts that underlie ligand binding, selectivity, and efficacy. Structure. 15:655-670.
    • (2007) Structure , vol.15 , pp. 655-670
    • Zhou, L.1    Siegelbaum, S.A.2
  • 52
    • 33846823909 scopus 로고
    • Particle mesh Ewald: An N.log(N) method for Ewald sums in large systems
    • Darden, T., D. York, and L. Pedersen. 1993. Particle mesh Ewald: an N.log(N) method for Ewald sums in large systems. J. Chem. Phys. 98: 10089-10092.
    • (1993) J. Chem. Phys , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 53
    • 33744824049 scopus 로고    scopus 로고
    • The origin of layer structure artifacts in simulations of liquid water
    • van der Spoel, D., and P. J. van Maaren. 2006. The origin of layer structure artifacts in simulations of liquid water. J. Chem. Theory Comput. 2:1-11.
    • (2006) J. Chem. Theory Comput , vol.2 , pp. 1-11
    • van der Spoel, D.1    van Maaren, P.J.2
  • 54
    • 0033562584 scopus 로고    scopus 로고
    • A kinetic model for the internal motions of proteins: Diffusion between multiple harmonic wells
    • Amadei, A., B. L. de Groot, M. A. Ceruso, M. Paci, A. Di Nola, and H. J. Berendsen. 1999. A kinetic model for the internal motions of proteins: diffusion between multiple harmonic wells. Proteins. 35:283-292.
    • (1999) Proteins , vol.35 , pp. 283-292
    • Amadei, A.1    de Groot, B.L.2    Ceruso, M.A.3    Paci, M.4    Di Nola, A.5    Berendsen, H.J.6
  • 56
    • 34248349449 scopus 로고    scopus 로고
    • Coarse-graining of protein structures for the normal mode studies
    • Eom, K., S. C. Baek, J. H. Ahn, and S. Na. 2007. Coarse-graining of protein structures for the normal mode studies. J. Comput. Chem. 28:1400-1410.
    • (2007) J. Comput. Chem , vol.28 , pp. 1400-1410
    • Eom, K.1    Baek, S.C.2    Ahn, J.H.3    Na, S.4
  • 57
    • 33846230007 scopus 로고    scopus 로고
    • On fast factorization pivoting methods for symmetric indefinite systems
    • Schenk, O., and K. Gartner. 2006. On fast factorization pivoting methods for symmetric indefinite systems. Electron. Trans. Numer. Anal. 23:158-179.
    • (2006) Electron. Trans. Numer. Anal , vol.23 , pp. 158-179
    • Schenk, O.1    Gartner, K.2
  • 58
    • 0023475026 scopus 로고
    • Configurational entropy of native proteins
    • Karplus, M., T. Ichiye, and B. M. Pettitt. 1987. Configurational entropy of native proteins. Biophys. J. 52:1083-1085.
    • (1987) Biophys. J , vol.52 , pp. 1083-1085
    • Karplus, M.1    Ichiye, T.2    Pettitt, B.M.3
  • 59
    • 0035828630 scopus 로고    scopus 로고
    • On the calculation of entropy from covariance matrices of the atomic fluctuations
    • Andricioaei, I., and M. Karplus. 2001. On the calculation of entropy from covariance matrices of the atomic fluctuations. J. Chem. Phys. 115:6289-6292.
    • (2001) J. Chem. Phys , vol.115 , pp. 6289-6292
    • Andricioaei, I.1    Karplus, M.2
  • 60
    • 0028877423 scopus 로고
    • Harmonicity and anharmo- nicity in protein dynamics: A normal mode analysis and principal component analysis
    • Hayward, S., A. Kitao, and N. Go. 1995. Harmonicity and anharmo- nicity in protein dynamics: a normal mode analysis and principal component analysis. Proteins. 23:177-186.
    • (1995) Proteins , vol.23 , pp. 177-186
    • Hayward, S.1    Kitao, A.2    Go, N.3
  • 62
    • 0041819710 scopus 로고    scopus 로고
    • Relative stability of protein structures determined by x-ray crystallography or NMR spectroscopy: A molecular dynamics simulation study
    • Fan, H., and A. E. Mark. 2003. Relative stability of protein structures determined by x-ray crystallography or NMR spectroscopy: a molecular dynamics simulation study. Proteins. 53:111-120.
    • (2003) Proteins , vol.53 , pp. 111-120
    • Fan, H.1    Mark, A.E.2
  • 63
    • 0030857672 scopus 로고    scopus 로고
    • Activation of f-channels by cAMP analogues in macropatches from rabbit sino-atrial node myocytes
    • Bois, P., B. Renaudon, M. Baruscotti, J. Lenfant, and D. DiFrancesco. 1997. Activation of f-channels by cAMP analogues in macropatches from rabbit sino-atrial node myocytes. J. Physiol. 501:565-571.
    • (1997) J. Physiol , vol.501 , pp. 565-571
    • Bois, P.1    Renaudon, B.2    Baruscotti, M.3    Lenfant, J.4    DiFrancesco, D.5
  • 65
    • 4344644050 scopus 로고    scopus 로고
    • Structure, dynamics and reactions of protein hydration water
    • discussion, 1189-1190
    • Smith, J. C., F. Merzel, A. N. Bondar, A. Tournier, and S. Fischer. 2004. Structure, dynamics and reactions of protein hydration water. Phil. Trans. R. Soc. Lond. 359:1181-1189; discussion, 1189-1190.
    • (2004) Phil. Trans. R. Soc. Lond , vol.359 , pp. 1181-1189
    • Smith, J.C.1    Merzel, F.2    Bondar, A.N.3    Tournier, A.4    Fischer, S.5
  • 67
    • 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
  • 68
    • 0027732618 scopus 로고
    • Effect of solvent on collective motions in globular protein
    • Hayward, S., A. Kitao, F. Hirata, and N. Go. 1993. Effect of solvent on collective motions in globular protein. J. Mol. Biol. 234:1207-1217.
    • (1993) J. Mol. Biol , vol.234 , pp. 1207-1217
    • Hayward, S.1    Kitao, A.2    Hirata, F.3    Go, N.4
  • 69
    • 22444438784 scopus 로고    scopus 로고
    • Langevin model of the temperature and hydration dependence of protein vibrational dynamics
    • Moritsugu, K., and J. C. Smith. 2005. Langevin model of the temperature and hydration dependence of protein vibrational dynamics. J. Phys. Chem. 109:12182-12194.
    • (2005) J. Phys. Chem , vol.109 , pp. 12182-12194
    • Moritsugu, K.1    Smith, J.C.2
  • 70
    • 33748548456 scopus 로고    scopus 로고
    • Insight into the role of hydration on protein dynamics
    • Hamelberg, D., T. Shen, and J. A. McCammon. 2006. Insight into the role of hydration on protein dynamics. J. Chem. Phys. 125:094905.
    • (2006) J. Chem. Phys , vol.125 , pp. 094905
    • Hamelberg, D.1    Shen, T.2    McCammon, J.A.3
  • 71
    • 33645675983 scopus 로고    scopus 로고
    • Temperature-dependent protein dynamics: A simulation-based probabilistic diffusion-vibration Lange- vin description
    • Moritsugu, K., and J. C. Smith. 2006. Temperature-dependent protein dynamics: a simulation-based probabilistic diffusion-vibration Lange- vin description. J. Phys. Chem. 110:5807-5816.
    • (2006) J. Phys. Chem , vol.110 , pp. 5807-5816
    • Moritsugu, K.1    Smith, J.C.2
  • 72
    • 34547649538 scopus 로고    scopus 로고
    • A rigid-body Newtonian propagation scheme based on instantaneous decomposition into rotation and translation blocks
    • Essiz, S., and R. D. Coalson. 2006. A rigid-body Newtonian propagation scheme based on instantaneous decomposition into rotation and translation blocks. J. Chem. Phys. 124:144116.
    • (2006) J. Chem. Phys , vol.124 , pp. 144116
    • Essiz, S.1    Coalson, R.D.2
  • 73
    • 0030037332 scopus 로고    scopus 로고
    • The application of different solvation and electrostatic models in molecular dynamics simulations of ubiquitin: How well is the x-ray structure "maintained"?
    • Fox, T., and P. A. Kollman. 1996. The application of different solvation and electrostatic models in molecular dynamics simulations of ubiquitin: How well is the x-ray structure "maintained"? Proteins Struct. Funct. Genet. 25:315-334.
    • (1996) Proteins Struct. Funct. Genet , vol.25 , pp. 315-334
    • Fox, T.1    Kollman, P.A.2
  • 74
    • 33645981305 scopus 로고    scopus 로고
    • Electrostatics calculations: Latest methodological advances
    • Koehl, P. 2006. Electrostatics calculations: latest methodological advances. Curr. Opin. Struct. Biol. 16:142-151.
    • (2006) Curr. Opin. Struct. Biol , vol.16 , pp. 142-151
    • Koehl, P.1
  • 75
    • 24144467366 scopus 로고    scopus 로고
    • Light-scattering studies of protein solutions: Role of hydration in weak protein-protein interactions
    • Paliwal, A., D. Asthagiri, D. Abras, A. M. Lenhoff, and M. E. Paulaitis. 2005. Light-scattering studies of protein solutions: role of hydration in weak protein-protein interactions. Biophys. J. 89:1564-1573.
    • (2005) Biophys. J , vol.89 , pp. 1564-1573
    • Paliwal, A.1    Asthagiri, D.2    Abras, D.3    Lenhoff, A.M.4    Paulaitis, M.E.5
  • 76
    • 4444323489 scopus 로고    scopus 로고
    • Solvation forces on biomo- lecular structures: A comparison of explicit solvent and Poisson- Boltzmann models
    • Wagoner, J., and A. Baker Nathan. 2004. Solvation forces on biomo- lecular structures: a comparison of explicit solvent and Poisson- Boltzmann models. J. Comput. Chem. 25:1623-1629.
    • (2004) J. Comput. Chem , vol.25 , pp. 1623-1629
    • Wagoner, J.1    Baker Nathan, A.2
  • 77
    • 0037117502 scopus 로고    scopus 로고
    • Is the first hydration shell of lysozyme of higher density than bulk water?
    • Merzel, F., and J. C. Smith. 2002. Is the first hydration shell of lysozyme of higher density than bulk water? Proc. Natl. Acad. Sci. USA. 99:5378-5383.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 5378-5383
    • Merzel, F.1    Smith, J.C.2
  • 79
    • 0034624691 scopus 로고    scopus 로고
    • Ligand binding and conformational motions in myoglobin
    • Ostermann, A., R. Waschipky, F. G. Parak, and G. U. Nienhaus. 2000. Ligand binding and conformational motions in myoglobin. Nature. 404:205-208.
    • (2000) Nature , vol.404 , pp. 205-208
    • Ostermann, A.1    Waschipky, R.2    Parak, F.G.3    Nienhaus, G.U.4
  • 81
    • 0027431378 scopus 로고
    • Protein hydration elucidated by molecular dynamics simulation
    • Steinbach, P. J., and B. R. Brooks. 1993. Protein hydration elucidated by molecular dynamics simulation. Proc. Natl. Acad. Sci. USA. 90:9135-9139.
    • (1993) Proc. Natl. Acad. Sci. USA , vol.90 , pp. 9135-9139
    • Steinbach, P.J.1    Brooks, B.R.2
  • 82
    • 33751244825 scopus 로고    scopus 로고
    • Structural and dynamical examination of the low-temperature glass transition in serum albumin
    • Goddard, Y. A., J. P. Korb, and R. G. Bryant. 2006. Structural and dynamical examination of the low-temperature glass transition in serum albumin. Biophys. J. 91:3841-3847.
    • (2006) Biophys. J , vol.91 , pp. 3841-3847
    • Goddard, Y.A.1    Korb, J.P.2    Bryant, R.G.3
  • 83
    • 33646528674 scopus 로고    scopus 로고
    • Hydration dependence of the mass fractal dimension and anomalous diffusion of vibrational energy in proteins
    • Enright, M. B., X. Yu, and D. M. Leitner. 2006. Hydration dependence of the mass fractal dimension and anomalous diffusion of vibrational energy in proteins. Phys. Rev. 73:051905.
    • (2006) Phys. Rev , vol.73 , pp. 051905
    • Enright, M.B.1    Yu, X.2    Leitner, D.M.3
  • 84
    • 0036193327 scopus 로고    scopus 로고
    • Temperature dependence of protein dynamics: Computer simulation analysis of neutron scattering properties
    • Hayward, J. A., and J. C. Smith. 2002. Temperature dependence of protein dynamics: computer simulation analysis of neutron scattering properties. Biophys. J. 82:1216-1225.
    • (2002) Biophys. J , vol.82 , pp. 1216-1225
    • Hayward, J.A.1    Smith, J.C.2
  • 85
    • 22144482668 scopus 로고    scopus 로고
    • Fluctuations and correlations in crystalline protein dynamics: A simulation analysis of staphylococcal nuclease
    • Meinhold, L., and J. C. Smith. 2005. Fluctuations and correlations in crystalline protein dynamics: a simulation analysis of staphylococcal nuclease. Biophys. J. 88:2554-2563.
    • (2005) Biophys. J , vol.88 , pp. 2554-2563
    • Meinhold, L.1    Smith, J.C.2
  • 86
    • 0032374086 scopus 로고    scopus 로고
    • Energy landscape of a native protein: Jumping-among-minima model
    • Kitao, A., S. Hayward, and N. Go. 1998. Energy landscape of a native protein: jumping-among-minima model. Proteins. 33:496-517.
    • (1998) Proteins , vol.33 , pp. 496-517
    • Kitao, A.1    Hayward, S.2    Go, N.3
  • 87
    • 33847060038 scopus 로고    scopus 로고
    • Protein dynamics from X-ray crystallography: Anisotropic, global motion in diffuse scattering patterns
    • Meinhold, L., and J. C. Smith. 2007. Protein dynamics from X-ray crystallography: anisotropic, global motion in diffuse scattering patterns. Proteins. 66:941-953.
    • (2007) Proteins , vol.66 , pp. 941-953
    • Meinhold, L.1    Smith, J.C.2
  • 88
    • 0041843665 scopus 로고    scopus 로고
    • Protein flexibility and conformational state: A comparison of collective vibrational modes of wild-type and D96N bacteriorhodopsin
    • Whitmire, S. E., D. Wolpert, A. G. Markelz, J. R. Hillebrecht, J. Galan, and R. R. Birge. 2003. Protein flexibility and conformational state: a comparison of collective vibrational modes of wild-type and D96N bacteriorhodopsin. Biophys. J. 85:1269-1277.
    • (2003) Biophys. J , vol.85 , pp. 1269-1277
    • Whitmire, S.E.1    Wolpert, D.2    Markelz, A.G.3    Hillebrecht, J.R.4    Galan, J.5    Birge, R.R.6
  • 89
    • 33846245528 scopus 로고    scopus 로고
    • Collective dynamics of lysozyme in water: Terahertz absorption spectroscopy and comparison with theory
    • Xu, J., K. W. Plaxco, and S. J. Allen. 2006. Collective dynamics of lysozyme in water: terahertz absorption spectroscopy and comparison with theory. J. Phys. Chem. 110:24255-24259.
    • (2006) J. Phys. Chem , vol.110 , pp. 24255-24259
    • Xu, J.1    Plaxco, K.W.2    Allen, S.J.3
  • 90
    • 33646155117 scopus 로고    scopus 로고
    • Probing the collective vibrational dynamics of a protein in liquid water by terahertz absorption spectroscopy
    • Xu, J., K. W. Plaxco, and S. J. Allen. 2006. Probing the collective vibrational dynamics of a protein in liquid water by terahertz absorption spectroscopy. Protein Sci. 15:1175-1181.
    • (2006) Protein Sci , vol.15 , pp. 1175-1181
    • Xu, J.1    Plaxco, K.W.2    Allen, S.J.3
  • 91
    • 0038061486 scopus 로고    scopus 로고
    • Ligand binding energy and catalytic efficiency from improved packing within receptors and enzymes
    • Williams, D. H., E. Stephens, and M. Zhou. 2003. Ligand binding energy and catalytic efficiency from improved packing within receptors and enzymes. J. Mol. Biol. 329:389-399.
    • (2003) J. Mol. Biol , vol.329 , pp. 389-399
    • Williams, D.H.1    Stephens, E.2    Zhou, M.3
  • 92
    • 24744470578 scopus 로고    scopus 로고
    • Probing the binding entropy of ligand-protein interactions by NMR
    • Homans, S. W. 2005. Probing the binding entropy of ligand-protein interactions by NMR. ChemBioChem. 6:1585-1591.
    • (2005) ChemBioChem , vol.6 , pp. 1585-1591
    • Homans, S.W.1
  • 93
    • 34347224684 scopus 로고    scopus 로고
    • Calculation of protein-ligand binding affinities
    • Gilson, M. K., and H. X. Zhou. 2007. Calculation of protein-ligand binding affinities. Annu Rev Biophys Biomol Struct. 36:21-42.
    • (2007) Annu Rev Biophys Biomol Struct , vol.36 , pp. 21-42
    • Gilson, M.K.1    Zhou, H.X.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.