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Volumn 30, Issue 3, 2014, Pages 326-334

Coarse-grained versus atomistic simulations: Realistic interaction free energies for real proteins

Author keywords

[No Author keywords available]

Indexed keywords

MULTIPROTEIN COMPLEX;

EID: 84893257466     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt675     Document Type: Article
Times cited : (41)

References (50)
  • 1
    • 33750587438 scopus 로고
    • Molecular dynamics with coupling to an external bath
    • Berendsen, H.J.C., et al. (1984) Molecular dynamics with coupling to an external bath. J. Chem. Phys., 81, 3684.
    • (1984) J. Chem. Phys , vol.81 , pp. 3684
    • Berendsen, H.J.C.1
  • 2
    • 44949167588 scopus 로고    scopus 로고
    • Entropic contributions and the influence of the hydrophobic environment in promiscuous protein-protein association
    • Chang, C.E., et al. (2008) Entropic contributions and the influence of the hydrophobic environment in promiscuous protein-protein association. Proc. Natl Acad. Sci. USA, 105, 7456-7461.
    • (2008) Proc. Natl Acad. Sci. USA , vol.105 , pp. 7456-7461
    • Chang, C.E.1
  • 3
    • 0001207648 scopus 로고    scopus 로고
    • Application of the nosehoover chain algorithm to the study of protein dynamics
    • Cheng, A. and Merz, K.M. (1996) Application of the nosehoover chain algorithm to the study of protein dynamics. J. Phys. Chem., 100, 1927-1937.
    • (1996) J. Phys. Chem , vol.100 , pp. 1927-1937
    • Cheng, A.1    Merz, K.M.2
  • 4
    • 56049117665 scopus 로고    scopus 로고
    • Protein-protein interaction investigated by steered molecular dynamics: The TCR- pMHC complex
    • Cuendet, M.A. and Michielin, O. (2008) Protein-protein interaction investigated by steered molecular dynamics: the TCR- pMHC complex. Biophys. J., 95, 3575-3590.
    • (2008) Biophys. J , vol.95 , pp. 3575-3590
    • Cuendet, M.A.1    Michielin, O.2
  • 5
    • 44149094011 scopus 로고    scopus 로고
    • Molecular dynamics-solvated interaction energy studies of protein- protein interactions: The MP1-p14 scaffolding complex
    • Cui, Q., et al. (2008) Molecular dynamics-solvated interaction energy studies of protein- protein interactions: the MP1-p14 scaffolding complex. J. Mol. Biol., 379, 787-802.
    • (2008) J. Mol. Biol , vol.379 , pp. 787-802
    • Cui, Q.1
  • 6
    • 33847021917 scopus 로고    scopus 로고
    • T cell receptor binding transition states and recognition of peptide/MHC
    • Davis-Harrison, R., et al. (2007) T cell receptor binding transition states and recognition of peptide/MHC. Biochemistry, 46, 1840-1850.
    • (2007) Biochemistry , vol.46 , pp. 1840-1850
    • Davis-Harrison, R.1
  • 7
    • 0033165928 scopus 로고    scopus 로고
    • Four A6-TCR/peptide/HLA-A2 structures that generate very different T cell signals are nearly identical
    • Ding, Y., et al. (1999) Four A6-TCR/peptide/HLA-A2 structures that generate very different T cell signals are nearly identical. Immunity, 11, 45-56.
    • (1999) Immunity , vol.11 , pp. 45-56
    • Ding, Y.1
  • 8
    • 84861367246 scopus 로고    scopus 로고
    • Biomolecular simulation: A computational microscope for molecular biology
    • Dror, R.O., et al. (2012) Biomolecular simulation: a computational microscope for molecular biology. Annu. Rev. Biophys., 41, 429-452.
    • (2012) Annu. Rev. Biophys , vol.41 , pp. 429-452
    • Dror, R.O.1
  • 9
    • 65549107009 scopus 로고    scopus 로고
    • Progress and challenges in predicting protein-protein interaction sites
    • Ezkurdia, I., et al. (2009) Progress and challenges in predicting protein-protein interaction sites. Brief Bioinformatics, 10, 233-246.
    • (2009) Brief Bioinformatics , vol.10 , pp. 233-246
    • Ezkurdia, I.1
  • 10
    • 0001585978 scopus 로고    scopus 로고
    • Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems
    • Feenstra, K.A., et al. (1999) Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems. J. Comput. Chem., 20, 786-798.
    • (1999) J. Comput. Chem , vol.20 , pp. 786-798
    • Feenstra, K.A.1
  • 11
    • 81155131795 scopus 로고    scopus 로고
    • Physical modeling of aqueous solvation
    • Fennell, C.J. and Dill, K.A. (2011) Physical modeling of aqueous solvation. J. Stat. Phys., 145, 209-226.
    • (2011) J. Stat. Phys , vol.145 , pp. 209-226
    • Fennell, C.J.1    Dill, K.A.2
  • 13
    • 0029855347 scopus 로고    scopus 로고
    • Structure of the complex between human t-cell receptor, viral peptide and HLA-A2
    • Garboczi, D.N., et al. (1996) Structure of the complex between human t-cell receptor, viral peptide and HLA-A2. Nature, 384, 134-141.
    • (1996) Nature , vol.384 , pp. 134-141
    • Garboczi, D.N.1
  • 14
    • 0031058541 scopus 로고    scopus 로고
    • The statistical-thermodynamic basis for computation of binding affinities: A critical review
    • Gilson, M.K., et al. (1997) The statistical-thermodynamic basis for computation of binding affinities: a critical review. Biophys. J., 72, 1047-1069.
    • (1997) Biophys. J , vol.72 , pp. 1047-1069
    • Gilson, M.K.1
  • 15
    • 33645994825 scopus 로고    scopus 로고
    • Flexibility and conformational entropy in protein-protein binding
    • Grunberg, R., et al. (2006) Flexibility and conformational entropy in protein-protein binding. Structure, 14, 683-693.
    • (2006) Structure , vol.14 , pp. 683-693
    • Grunberg, R.1
  • 16
    • 27344440132 scopus 로고    scopus 로고
    • Conservation and relative importance of residues across protein-protein interfaces
    • Guharoy, M. and Chakrabarti, P. (2005) Conservation and relative importance of residues across protein-protein interfaces. Proc. Natl Acad. Sci. USA, 102, 15447-15452.
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 15447-15452
    • Guharoy, M.1    Chakrabarti, P.2
  • 17
    • 84863689619 scopus 로고    scopus 로고
    • Coarse-grained molecular models of water: A review
    • Hadley, K.R. and McCabe, C. (2012) Coarse-grained molecular models of water: a review. Mol. Simul., 38, 671-681.
    • (2012) Mol. Simul , vol.38 , pp. 671-681
    • Hadley, K.R.1    McCabe, C.2
  • 18
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • Henikoff, S. and Henikoff, J.G. (1992) Amino acid substitution matrices from protein blocks. Proc. Natl Acad. Sci. USA, 89, 10915-10919.
    • (1992) Proc. Natl Acad. Sci. USA , vol.89 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2
  • 19
    • 46249092554 scopus 로고    scopus 로고
    • Gromacs 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
    • Hess, B., et al. (2008) Gromacs 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J. Chem. Theory Comput., 4, 435-447.
    • (2008) J. Chem. Theory Comput , vol.4 , pp. 435-447
    • Hess, B.1
  • 20
    • 84857282935 scopus 로고    scopus 로고
    • Free energy calculations by the molecular mechanics Poisson-Boltzmann surface area method
    • Homeyer, N. and Gohlke, H. (2012) Free energy calculations by the molecular mechanics Poisson-Boltzmann surface area method. Mol. Inform., 31, 114-122.
    • (2012) Mol. Inform , vol.31 , pp. 114-122
    • Homeyer, N.1    Gohlke, H.2
  • 21
    • 0029878720 scopus 로고    scopus 로고
    • VMD - Visual molecular dynamics
    • Humphrey, W., et al. (1996) VMD - visual molecular dynamics. J. Mol. Graph., 14, 33-38.
    • (1996) J. Mol. Graph , vol.14 , pp. 33-38
    • Humphrey, W.1
  • 22
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch, W. and Sander, C. (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 23
    • 77952068704 scopus 로고    scopus 로고
    • Are scoring functions in protein-protein docking ready to predict interactomes? Clues from a novel binding affinity benchmark
    • Kastritis, P. and Bonvin, A. (2010) Are scoring functions in protein-protein docking ready to predict interactomes? Clues from a novel binding affinity benchmark. J. Proteome Res., 9, 2216-2225.
    • (2010) J. Proteome Res , vol.9 , pp. 2216-2225
    • Kastritis, P.1    Bonvin, A.2
  • 24
    • 3342936383 scopus 로고    scopus 로고
    • Crystal structure of the p14/mp1 scaffolding complex: How a twin couple attaches mitogen-activated protein kinase signaling to late endosomes
    • Kurzbauer, R., et al. (2004) Crystal structure of the p14/mp1 scaffolding complex: How a twin couple attaches mitogen-activated protein kinase signaling to late endosomes. Proc. Natl Acad. Sci. USA, 101, 10984-10989.
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 10984-10989
    • Kurzbauer, R.1
  • 25
    • 77957948556 scopus 로고    scopus 로고
    • Blind predictions of protein interfaces by docking calculations in capri
    • Lensink, M. and Wodak, S. (2010) Blind predictions of protein interfaces by docking calculations in capri. Proteins, 78, 3085-3095.
    • (2010) Proteins , vol.78 , pp. 3085-3095
    • Lensink, M.1    Wodak, S.2
  • 26
    • 33745440760 scopus 로고    scopus 로고
    • Dynamic distance disorder in proteins is caused by trapping
    • Luo, G., et al. (2006) Dynamic distance disorder in proteins is caused by trapping. J. Phys. Chem. B, 110, 9363-9367.
    • (2006) J. Phys. Chem. B , vol.110 , pp. 9363-9367
    • Luo, G.1
  • 27
    • 34547474332 scopus 로고    scopus 로고
    • The martini force field: Coarse grained model for biomolecular simulations
    • Marrink, S.J., et al. (2007) The martini force field: coarse grained model for biomolecular simulations. J. Phys. Chem. B, 111, 7812-7824.
    • (2007) J. Phys. Chem. B , vol.111 , pp. 7812-7824
    • Marrink, S.J.1
  • 28
    • 0031714858 scopus 로고    scopus 로고
    • Joy: Protein sequence-structure representation and analysis
    • Mizuguchi, K., et al. (1998) Joy: protein sequence-structure representation and analysis. Bioinformatics, 14, 617-623.
    • (1998) Bioinformatics , vol.14 , pp. 617-623
    • Mizuguchi, K.1
  • 29
    • 49449113010 scopus 로고    scopus 로고
    • The martini coarse-grained force field: Extension to proteins
    • Monticelli, L., et al. (2008) The martini coarse-grained force field: extension to proteins. J. Chem. Theory Comput., 4, 819-834.
    • (2008) J. Chem. Theory Comput , vol.4 , pp. 819-834
    • Monticelli, L.1
  • 30
    • 34547573955 scopus 로고    scopus 로고
    • Protein-protein interaction hotspots carved into sequences
    • Ofran, Y. and Rost, B. (2007) Protein-protein interaction hotspots carved into sequences. PLoS Comput. Biol., 3, e119.
    • (2007) PLoS Comput. Biol , vol.3
    • Ofran, Y.1    Rost, B.2
  • 31
    • 80053238893 scopus 로고    scopus 로고
    • Crucial importance of the water-entropy effect in predicting hot spots in protein-protein complexes
    • Oshima, H., et al. (2011) Crucial importance of the water-entropy effect in predicting hot spots in protein-protein complexes. Phys. Chem. Chem. Phys., 13, 16236-16246.
    • (2011) Phys. Chem. Chem. Phys , vol.13 , pp. 16236-16246
    • Oshima, H.1
  • 32
    • 0019707626 scopus 로고
    • Polymorphic transitions in single crystals: A new molecular dynamics method
    • Parrinello, M. and Rahman, A. (1981) Polymorphic transitions in single crystals: a new molecular dynamics method. J. Appl. Phys., 52, 7182-7190.
    • (1981) J. Appl. Phys , vol.52 , pp. 7182-7190
    • Parrinello, M.1    Rahman, A.2
  • 33
    • 84863535732 scopus 로고    scopus 로고
    • Structural determinants of the supramolecular organization of g protein-coupled receptors in bilayers
    • Periole, X., et al. (2012) Structural determinants of the supramolecular organization of g protein-coupled receptors in bilayers. J. Am. Chem. Soc., 134, 10959-10965.
    • (2012) J. Am. Chem. Soc , vol.134 , pp. 10959-10965
    • Periole, X.1
  • 34
    • 77949382951 scopus 로고    scopus 로고
    • Present and future challenges and limitations in protein-protein docking
    • Pons, C., et al. (2010) Present and future challenges and limitations in protein-protein docking. Proteins, 78, 95-108.
    • (2010) Proteins , vol.78 , pp. 95-108
    • Pons, C.1
  • 35
    • 78149265537 scopus 로고    scopus 로고
    • The influence of micelle formation on the stability of colloid surfactant mixtures
    • Pool, R. and Bolhuis, P.G. (2010) The influence of micelle formation on the stability of colloid surfactant mixtures. Phys. Chem. Chem. Phys., 12, 14789-14797.
    • (2010) Phys. Chem. Chem. Phys , vol.12 , pp. 14789-14797
    • Pool, R.1    Bolhuis, P.G.2
  • 36
    • 84862779788 scopus 로고    scopus 로고
    • Enabling grand-canonical monte carlo: Extending the flexibility of gromacs through the grompy python interface module
    • Pool, R., et al. (2012) Enabling grand-canonical monte carlo: extending the flexibility of gromacs through the grompy python interface module. J. Comput. Chem., 33, 1207-1214.
    • (2012) J. Comput. Chem , vol.33 , pp. 1207-1214
    • Pool, R.1
  • 37
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • Sali, A. and Blundell, T.L. (1993) Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol., 234, 779-815.
    • (1993) J. Mol. Biol , vol.234 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 38
    • 27344449197 scopus 로고    scopus 로고
    • Progress in modeling of protein structures and interactions
    • Schueler-Furman, O., et al. (2005) Progress in modeling of protein structures and interactions. Science, 310, 638-642.
    • (2005) Science , vol.310 , pp. 638-642
    • Schueler-Furman, O.1
  • 39
    • 0037432528 scopus 로고    scopus 로고
    • How reliable are experimental protein-protein interaction data?
    • Sprinzak, E., et al. (2003) How reliable are experimental protein-protein interaction data? J. Mol. Biol., 327, 919-923.
    • (2003) J. Mol. Biol , vol.327 , pp. 919-923
    • Sprinzak, E.1
  • 40
    • 0031567782 scopus 로고    scopus 로고
    • The entropy cost of protein association
    • Tamura, A. and Privalov, P.L. (1997) The entropy cost of protein association. J. Mol. Biol., 273, 1048-1060.
    • (1997) J. Mol. Biol , vol.273 , pp. 1048-1060
    • Tamura, A.1    Privalov, P.L.2
  • 41
    • 78149446109 scopus 로고    scopus 로고
    • Designing coarse grained-and atom based-potentials for proteinprotein docking
    • Tobi, D. (2010) Designing coarse grained-and atom based-potentials for proteinprotein docking. BMC Struct. Biol., 10, 40.
    • (2010) BMC Struct. Biol , vol.10 , pp. 40
    • Tobi, D.1
  • 42
    • 33846406882 scopus 로고    scopus 로고
    • A comparison of methods to compute the potential of mean force
    • Trzesniak, D., et al. (2007) A comparison of methods to compute the potential of mean force. ChemPhysChem., 8, 162-169.
    • (2007) Chem Phys Chem , vol.8 , pp. 162-169
    • Trzesniak, D.1
  • 43
    • 84855460321 scopus 로고    scopus 로고
    • Flexibility and binding affinity in protein- ligand, protein-protein and multi-component protein interactions: Limitations of current computational approaches
    • Tuffery, P. and Derreumaux, P. (2012) Flexibility and binding affinity in protein- ligand, protein-protein and multi-component protein interactions: limitations of current computational approaches. J. R. Soc. Interface, 9, 20-33.
    • (2012) J. R. Soc. Interface , vol.9 , pp. 20-33
    • Tuffery, P.1    Derreumaux, P.2
  • 44
    • 65549157572 scopus 로고    scopus 로고
    • A survey of available tools and web servers for analysis of protein-protein interactions and interfaces
    • Tuncbag, N., et al. (2009) A survey of available tools and web servers for analysis of protein-protein interactions and interfaces. Brief Bioinformatics, 10, 217-232.
    • (2009) Brief Bioinformatics , vol.10 , pp. 217-232
    • Tuncbag, N.1
  • 46
    • 84857537331 scopus 로고    scopus 로고
    • Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition
    • Wereszczynski, J. and McCammon, J.A. (2012) Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition. Q. Rev. Biophys., 45, 1-25.
    • (2012) Q. Rev. Biophys , vol.45 , pp. 1-25
    • Wereszczynski, J.1    McCammon, J.A.2
  • 47
    • 33846471085 scopus 로고    scopus 로고
    • Prediction of structures of multidomain proteins from structures of the individual domains
    • Wollacott, A., et al. (2007) Prediction of structures of multidomain proteins from structures of the individual domains. Protein Sci., 16, 165-175.
    • (2007) Protein Sci , vol.16 , pp. 165-175
    • Wollacott, A.1
  • 48
    • 0036682133 scopus 로고    scopus 로고
    • Two-step binding mechanism for T-cell receptor recognition of peptide MHC
    • Wu, L.C., et al. (2002) Two-step binding mechanism for T-cell receptor recognition of peptide MHC. Nature, 418, 552-556.
    • (2002) Nature , vol.418 , pp. 552-556
    • Wu, L.C.1
  • 49
    • 0034870959 scopus 로고    scopus 로고
    • Contribution of translational and rotational motions to molecular association in aqueous solution
    • Yu, Y.B., et al. (2001) Contribution of translational and rotational motions to molecular association in aqueous solution. Biophys. J., 81, 1632-1642.
    • (2001) Biophys. J , vol.81 , pp. 1632-1642
    • Yu, Y.B.1
  • 50
    • 84885396746 scopus 로고    scopus 로고
    • Quantification of solvent contribution to the stability of noncovalent complexes
    • Zhang, H., et al. (2013) Quantification of solvent contribution to the stability of noncovalent complexes. J. Chem. Theory Comput., 9, 4542-4551.
    • (2013) J. Chem. Theory Comput , vol.9 , pp. 4542-4551
    • Zhang, H.1


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