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Volumn 13, Issue 11, 2012, Pages 14451-14469

A generic force field for protein coarse-grained molecular dynamics simulation

Author keywords

Coarse grained; Force field; Molecular dynamics; Protein

Indexed keywords

AMINO ACID ANALYSIS; ARTICLE; COARSE GRAINED FORCE FIELD; ENERGY TRANSFER; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; MOLECULAR DYNAMICS; PROCESS DEVELOPMENT; PROTEIN CONFORMATION; PROTEIN DETERMINATION; PROTEIN INTERACTION; STATISTICAL CONCEPTS; CHEMISTRY;

EID: 84870683475     PISSN: 16616596     EISSN: 14220067     Source Type: Journal    
DOI: 10.3390/ijms131114451     Document Type: Article
Times cited : (20)

References (44)
  • 1
    • 39449116285 scopus 로고    scopus 로고
    • Biomolecular simulation: Historical picture and future perspectives
    • Gunsteren, W.F.; Dolenc, J. Biomolecular simulation: Historical picture and future perspectives. Biochem. Soc. Trans. 2008, 36, 11-15.
    • (2008) Biochem. Soc. Trans. , vol.36 , pp. 11-15
    • Gunsteren, W.F.1    Dolenc, J.2
  • 2
    • 33646943202 scopus 로고    scopus 로고
    • Molecular dynamics: Survey of methods simulating the activity of proteins
    • Adcock, S.A.; McCammon, J.A. Molecular dynamics: Survey of methods simulating the activity of proteins. Chem. Rev. 2006, 106, 1589-1615.
    • (2006) Chem. Rev. , vol.106 , pp. 1589-1615
    • Adcock, S.A.1    McCammon, J.A.2
  • 3
    • 0017776823 scopus 로고
    • Dynamics of folded proteins
    • McCammon, J.A.; Gelin, B.R.; Kaplus, M. Dynamics of folded proteins. Nature 1977, 267, 585-590.
    • (1977) Nature , vol.267 , pp. 585-590
    • McCammon, J.A.1    Gelin, B.R.2    Kaplus, M.3
  • 4
    • 64649101249 scopus 로고    scopus 로고
    • Long-timescale molecular dynamics simulations of protein structure and function
    • Klepeis, J.L.; Lindorff-Larsen, K.; Dror, R.O.; Shaw, D.E. Long-timescale molecular dynamics simulations of protein structure and function. Curr. Opin. Struct. Biol. 2009, 19, 120-127.
    • (2009) Curr. Opin. Struct. Biol. , vol.19 , pp. 120-127
    • Klepeis, J.L.1    Lindorff-Larsen, K.2    Dror, R.O.3    Shaw, D.E.4
  • 5
    • 33847175935 scopus 로고    scopus 로고
    • High performance computing in biology: Multimillion atom simulations of nanoscale systems
    • Sanbonmatsun, K.Y.; Tung, C.-S. High performance computing in biology: Multimillion atom simulations of nanoscale systems. J. Struct. Biol. 2007, 157, 470-480.
    • (2007) J. Struct. Biol. , vol.157 , pp. 470-480
    • Sanbonmatsun, K.Y.1    Tung, C.-S.2
  • 6
    • 0037120092 scopus 로고    scopus 로고
    • Coarse-graining in polymer simulation: From the atomistic to the mesoscopic scale and back
    • Muller-Plathe, F. Coarse-graining in polymer simulation: From the atomistic to the mesoscopic scale and back. ChemPhysChem 2002, 3, 754-769.
    • (2002) ChemPhysChem , vol.3 , pp. 754-769
    • Muller-Plathe, F.1
  • 7
    • 0347753603 scopus 로고    scopus 로고
    • Reduced models of proteins and their applications
    • Kolinski, A.; Skolnick, J. Reduced models of proteins and their applications. Polymer 2004, 45, 511-524.
    • (2004) Polymer , vol.45 , pp. 511-524
    • Kolinski, A.1    Skolnick, J.2
  • 8
    • 17044393884 scopus 로고    scopus 로고
    • Coarse-grained models for proteins
    • Tozzini, V. Coarse-grained models for proteins. Curr. Opin. Struct. Biol. 2005, 15, 144-150.
    • (2005) Curr. Opin. Struct. Biol. , vol.15 , pp. 144-150
    • Tozzini, V.1
  • 9
    • 39149100599 scopus 로고    scopus 로고
    • Coarse-grained models of protein folding: Toy models or predictive tools
    • Clementi, C. Coarse-grained models of protein folding: Toy models or predictive tools. Curr. Opin. Struct. Biol. 2008, 18, 10-15.
    • (2008) Curr. Opin. Struct. Biol. , vol.18 , pp. 10-15
    • Clementi, C.1
  • 10
    • 49549083949 scopus 로고    scopus 로고
    • Membrane proteins: Molecular dynamics simulation
    • Lindahl, E.; Sansom, M.S. Membrane proteins: Molecular dynamics simulation. Curr. Opin. Struct. Biol. 2008, 18, 425-431.
    • (2008) Curr. Opin. Struct. Biol. , vol.18 , pp. 425-431
    • Lindahl, E.1    Sansom, M.S.2
  • 13
    • 77950114950 scopus 로고    scopus 로고
    • Protein backbone dynamics simulations using coarse-grained bonded potentials and simplified hydrogen bonds
    • Ha-Duong, T. Protein backbone dynamics simulations using coarse-grained bonded potentials and simplified hydrogen bonds. J. Chem. Theory Comput. 2010, 6, 761-773.
    • (2010) J. Chem. Theory Comput. , vol.6 , pp. 761-773
    • Ha-Duong, T.1
  • 14
    • 78149429881 scopus 로고    scopus 로고
    • PACE force field for protein simulations. 1. Full parameterization of version1 and verification
    • Han, W.; Wan, C.K.; Jiang, F.; Wu, Y.D. PACE force field for protein simulations. 1. Full parameterization of version1 and verification. J. Chem. Theory Comput. 2010, 6, 3373-3389.
    • (2010) J. Chem. Theory Comput. , vol.6 , pp. 3373-3389
    • Han, W.1    Wan, C.K.2    Jiang, F.3    Wu, Y.D.4
  • 15
    • 78149451041 scopus 로고    scopus 로고
    • PACE force field for protein simulations. 2. Folding simulations of peptides
    • Han, W.; Wan, C.K.; Jiang, F.; Wu, Y.D. PACE force field for protein simulations. 2. Folding simulations of peptides. J. Chem. Theory Comput. 2010, 6, 3390-3402.
    • (2010) J. Chem. Theory Comput. , vol.6 , pp. 3390-3402
    • Han, W.1    Wan, C.K.2    Jiang, F.3    Wu, Y.D.4
  • 16
    • 34548020295 scopus 로고    scopus 로고
    • A coarse-grained protein-protein potential derived from an all-atom force field
    • Basdevant, N.; Borgis, D.; Ha-Duong, T. A coarse-grained protein-protein potential derived from an all-atom force field. J. Phys. Chem. B 2007, 111, 9390-9399.
    • (2007) J. Phys. Chem. B , vol.111 , pp. 9390-9399
    • Basdevant, N.1    Borgis, D.2    Ha-Duong, T.3
  • 17
    • 36649024127 scopus 로고    scopus 로고
    • Coarse-grained protein model coupled with a coarse-grained water model: Molecular dynamics study of polyalanine-based peptides
    • Han, W.; Wu, Y.D. Coarse-grained protein model coupled with a coarse-grained water model: Molecular dynamics study of polyalanine-based peptides. J. Chem. Theory Comput. 2007, 3, 2146-2161.
    • (2007) J. Chem. Theory Comput. , vol.3 , pp. 2146-2161
    • Han, W.1    Wu, Y.D.2
  • 18
    • 67649101377 scopus 로고    scopus 로고
    • Generic coarse-grained model for protein folding and aggregation
    • Bereau, T.; Deserno, M. Generic coarse-grained model for protein folding and aggregation. J. Chem. Phys. 2009, 130, 235106.
    • (2009) J. Chem. Phys. , vol.130 , pp. 235106
    • Bereau, T.1    Deserno, M.2
  • 19
    • 58149250463 scopus 로고    scopus 로고
    • Toward a coarse-grained protein model coupled with a coarse-grained solvent model: Solvation free energies of amino acid side chains
    • Han, W.; Wan, C.K.; Wu, Y.D. Toward a coarse-grained protein model coupled with a coarse-grained solvent model: Solvation free energies of amino acid side chains. J. Chem. Theory Comput. 2008, 4, 1891-1901.
    • (2008) J. Chem. Theory Comput. , vol.4 , pp. 1891-1901
    • Han, W.1    Wan, C.K.2    Wu, Y.D.3
  • 20
    • 73549096657 scopus 로고    scopus 로고
    • Transferable coarse grain nonbonded interaction model for amino acids
    • DeVane, R.; Shinoda, W.; Moore, P.B.; Klein, M.L. Transferable coarse grain nonbonded interaction model for amino acids. J. Chem. Theory Comput. 2009, 5, 2115-2124.
    • (2009) J. Chem. Theory Comput. , vol.5 , pp. 2115-2124
    • DeVane, R.1    Shinoda, W.2    Moore, P.B.3    Klein, M.L.4
  • 21
    • 33644893631 scopus 로고    scopus 로고
    • A coarse grained protein-lipid model with application to lipprotein particles
    • Shih, A.Y.; Arkhipov, A.; Freddolino, P.L.; Schulten, K. A coarse grained protein-lipid model with application to lipprotein particles. J. Phys. Chem. B 2006, 110, 3674-3684.
    • (2006) J. Phys. Chem. B , vol.110 , pp. 3674-3684
    • Shih, A.Y.1    Arkhipov, A.2    Freddolino, P.L.3    Schulten, K.4
  • 22
    • 34247852583 scopus 로고    scopus 로고
    • Coarse-grained peptide modeling using a systematic multiscale approach
    • Zhou, J.; Thorpe, L.F.; Izvekov, S.; Voth, G.A. Coarse-grained peptide modeling using a systematic multiscale approach. Biophys. J. 2007, 92, 4289-4303.
    • (2007) Biophys. J. , vol.92 , pp. 4289-4303
    • Zhou, J.1    Thorpe, L.F.2    Izvekov, S.3    Voth, G.A.4
  • 23
    • 70349458094 scopus 로고    scopus 로고
    • A force field for virtual atom molecular mechanics of proteins
    • Korkut, A.; Hendrickson, W.A. A force field for virtual atom molecular mechanics of proteins. Proc. Natl. Acad. Sci. USA 2009, 106, 15667-15672.
    • (2009) Proc. Natl. Acad. Sci. USA , vol.106 , pp. 15667-15672
    • Korkut, A.1    Hendrickson, W.A.2
  • 24
    • 33846213672 scopus 로고    scopus 로고
    • Mapping all-atom models onto one-bead coarse grained models: General properties and applications to a minimal polypeptide model
    • Tozzini, V.; Rocchia, W.; McCammon, J.A. Mapping all-atom models onto one-bead coarse grained models: General properties and applications to a minimal polypeptide model. J. Chem. Theory Comput. 2006, 2, 667-673.
    • (2006) J. Chem. Theory Comput. , vol.2 , pp. 667-673
    • Tozzini, V.1    Rocchia, W.2    McCammon, J.A.3
  • 25
    • 33847126878 scopus 로고    scopus 로고
    • Binding pathways of ligands to HIV-1 protease: Coarse-grained and atomistic simulations
    • Chang, C.A.; Trylska, J.; Tozzini, V.; McCammon, J.A. Binding pathways of ligands to HIV-1 protease: Coarse-grained and atomistic simulations. Chem. Biol. Drug Des. 2007, 69, 5-13.
    • (2007) Chem. Biol. Drug Des. , vol.69 , pp. 5-13
    • Chang, C.A.1    Trylska, J.2    Tozzini, V.3    McCammon, J.A.4
  • 26
    • 70349462451 scopus 로고    scopus 로고
    • Computation of conformational transitions in proteins by virtual atom molecular mechanics as validated in application to adenylate kinase
    • Korkut, A.; Hendrickson, W.A. Computation of conformational transitions in proteins by virtual atom molecular mechanics as validated in application to adenylate kinase. Proc. Natl. Acad. Sci. USA 2009, 106, 15673-15678.
    • (2009) Proc. Natl. Acad. Sci. USA , vol.106 , pp. 15673-15678
    • Korkut, A.1    Hendrickson, W.A.2
  • 27
    • 77950142931 scopus 로고    scopus 로고
    • A nonradial coarse-grained potential for proteins produces naturally stable secondary structure elements
    • Alemani, D.; Collu, F.; Cascella, M.; Peraro, M.D. A nonradial coarse-grained potential for proteins produces naturally stable secondary structure elements. J. Chem. Theory Comput. 2010, 6, 315-324.
    • (2010) J. Chem. Theory Comput. , vol.6 , pp. 315-324
    • Alemani, D.1    Collu, F.2    Cascella, M.3    Peraro, M.D.4
  • 28
    • 33845204189 scopus 로고    scopus 로고
    • Stability and dynamics of virus capsids described by coarse-grained modeling
    • Arkhipov, A.; Freddolino, P.L.; Schulten, K. Stability and dynamics of virus capsids described by coarse-grained modeling. Structure 2006, 14, 1767-1777.
    • (2006) Structure , vol.14 , pp. 1767-1777
    • Arkhipov, A.1    Freddolino, P.L.2    Schulten, K.3
  • 29
    • 53249125167 scopus 로고    scopus 로고
    • Four-scale description of membrane sculpting by BAR domains
    • Arkhipov, A.; Yin, Y.; Schulten, K. Four-scale description of membrane sculpting by BAR domains. Biophys. J. 2008, 95, 2806-2861.
    • (2008) Biophys. J. , vol.95 , pp. 2806-2861
    • Arkhipov, A.1    Yin, Y.2    Schulten, K.3
  • 30
    • 33845381177 scopus 로고    scopus 로고
    • Coarse-grained molecular dynamics simulations of a rotating bacterial Flagellum
    • Arkhipov, A.; Freddolino, P.L.; Imada, K.; Namba, K.; Schulten, K. Coarse-grained molecular dynamics simulations of a rotating bacterial Flagellum. Biophys. J. 2006, 91, 4589-4597.
    • (2006) Biophys. J. , vol.91 , pp. 4589-4597
    • Arkhipov, A.1    Freddolino, P.L.2    Imada, K.3    Namba, K.4    Schulten, K.5
  • 31
    • 58849140540 scopus 로고    scopus 로고
    • Membrane-protein interactions in a generic coarse-grained model for lipid bilayers
    • West, B.; Brown, F.L.H.; Schmid, B. Membrane-protein interactions in a generic coarse-grained model for lipid bilayers. Biophys. J. 2009, 96, 101-115.
    • (2009) Biophys. J. , vol.96 , pp. 101-115
    • West, B.1    Brown, F.L.H.2    Schmid, B.3
  • 33
    • 45949109759 scopus 로고    scopus 로고
    • Gating motions in voltage-gated potassium channels revealed by coarse-grained molecular dynamics simulations
    • Treptow, W.; Marrink, S.; Tarek, M. Gating motions in voltage-gated potassium channels revealed by coarse-grained molecular dynamics simulations. J. Phys. Chem. B 2008, 112, 3277-3282.
    • (2008) J. Phys. Chem. B , vol.112 , pp. 3277-3282
    • Treptow, W.1    Marrink, S.2    Tarek, M.3
  • 34
    • 78650024592 scopus 로고    scopus 로고
    • Coarse grained modeling and approaches to protein folding
    • Guardiani, C.; Livi, R.; Cecconi, F. Coarse grained modeling and approaches to protein folding. Curr. Bioinforma. 2010, 5, 217-240.
    • (2010) Curr. Bioinforma. , vol.5 , pp. 217-240
    • Guardiani, C.1    Livi, R.2    Cecconi, F.3
  • 35
    • 14044266389 scopus 로고    scopus 로고
    • Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains
    • Liwo, A.; Khalili, M.; Scheraga, H.A. Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains. Proc. Natl. Acad. Sci. USA 2005, 102, 2362-2367.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 2362-2367
    • Liwo, A.1    Khalili, M.2    Scheraga, H.A.3
  • 36
    • 72749104760 scopus 로고    scopus 로고
    • Coarse-grained MD simulations and protein-protein interactions: The cohesion-dockerin system
    • Hall, B.; Sansom, M.S.P. Coarse-grained MD simulations and protein-protein interactions: The cohesion-dockerin system. J. Chem. Theory Comput. 2009, 5, 2465-2471.
    • (2009) J. Chem. Theory Comput. , vol.5 , pp. 2465-2471
    • Hall, B.1    Sansom, M.S.P.2
  • 37
    • 57949107089 scopus 로고    scopus 로고
    • Is alanine dipeptide a good model for representing the torsional preferences of protein backbone?
    • Feig, M. Is alanine dipeptide a good model for representing the torsional preferences of protein backbone? J. Chem. Theory Comput. 2008, 4, 1555-1564.
    • (2008) J. Chem. Theory Comput. , vol.4 , pp. 1555-1564
    • Feig, M.1
  • 38
    • 46249092554 scopus 로고    scopus 로고
    • GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
    • Hess, B.; Kutzner, C.; Spoel, D.; Lindahl, E. GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. J. Chem. Theory Comput. 2008, 4, 435-447.
    • (2008) J. Chem. Theory Comput. , vol.4 , pp. 435-447
    • Hess, B.1    Kutzner, C.2    Spoel, D.3    Lindahl, E.4
  • 39
    • 1842450481 scopus 로고    scopus 로고
    • Computational analysis of sequence selection mechanisms
    • Meyerguz, L.; Grasso, C.; Kleinberg, J.; Elber, R. Computational analysis of sequence selection mechanisms. Structure 2004, 12, 547-557.
    • (2004) Structure , vol.12 , pp. 547-557
    • Meyerguz, L.1    Grasso, C.2    Kleinberg, J.3    Elber, R.4
  • 41
    • 84928210708 scopus 로고    scopus 로고
    • Deriving effective mesoscale potentials from atomistic simulations
    • Reith, D.; Putz, M.; Muller-plathe, F. Deriving effective mesoscale potentials from atomistic simulations. J. Comput. Chem. 1997, 29, 292-308.
    • (1997) J. Comput. Chem. , vol.29 , pp. 292-308
    • Reith, D.1    Putz, M.2    Muller-plathe, F.3
  • 42
    • 24344438610 scopus 로고    scopus 로고
    • A coarse grained model for the dynamics of flap opening in HIV-1 protease
    • Tozzini, V.; McCammon, J.A. A coarse grained model for the dynamics of flap opening in HIV-1 protease. Chem. Phys. Lett. 2005, 413, 123-128.
    • (2005) Chem. Phys. Lett. , vol.413 , pp. 123-128
    • Tozzini, V.1    McCammon, J.A.2
  • 43
    • 0342929614 scopus 로고
    • Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling
    • Torrie, G.M.; Valleau, J.P. Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling. J. Comput. Phys. 1977, 23, 187-199.
    • (1977) J. Comput. Phys. , vol.23 , pp. 187-199
    • Torrie, G.M.1    Valleau, J.P.2
  • 44
    • 84986519238 scopus 로고
    • The weighted histogram analysis method for free-energy calculations on biomolecular. I. The method
    • Kumar, S.; Bouzida, D.; Swendsen, R.H.; Kollman, P.A.; Rosenberg, J.M. The weighted histogram analysis method for free-energy calculations on biomolecular. I. The method. J. Comput. Chem. 1992, 13, 1011-1021.
    • (1992) J. Comput. Chem. , vol.13 , pp. 1011-1021
    • Kumar, S.1    Bouzida, D.2    Swendsen, R.H.3    Kollman, P.A.4    Rosenberg, J.M.5


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