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Volumn 4, Issue , 2015, Pages 126-133

Low-mass molecular dynamics simulation for configurational sampling enhancement: More evidence and theoretical explanation

Author keywords

Chignolin; CLN025; Folding rate; Folding time; Molecular dynamics simulation; Protein folding

Indexed keywords


EID: 84942054674     PISSN: None     EISSN: 24055808     Source Type: Journal    
DOI: 10.1016/j.bbrep.2015.08.023     Document Type: Article
Times cited : (18)

References (56)
  • 1
    • 84907487161 scopus 로고    scopus 로고
    • Low-mass molecular dynamics simulation: a simple and generic technique to enhance configurational sampling
    • Pang Y.-P. Low-mass molecular dynamics simulation: a simple and generic technique to enhance configurational sampling. Biochem. Biophys. Res. Commun. 2014, 452:588-592.
    • (2014) Biochem. Biophys. Res. Commun. , vol.452 , pp. 588-592
    • Pang, Y.-P.1
  • 3
    • 5844335392 scopus 로고
    • The possibility of using a larger timestep in molecular dynamics studies of water
    • CECAM, Orsay, France, C. Moser (Ed.)
    • Jacucci G., Rahman A. The possibility of using a larger timestep in molecular dynamics studies of water. Report on Workshop Methods in Molecular Dynamics-Long Timescale Events 1974, 32-40. CECAM, Orsay, France. C. Moser (Ed.).
    • (1974) Report on Workshop Methods in Molecular Dynamics-Long Timescale Events , pp. 32-40
    • Jacucci, G.1    Rahman, A.2
  • 4
    • 84942023953 scopus 로고
    • C. Moser (Ed.), Report on Workshop Methods in Molecular Dynamics - Long Timescale Events, CECAM, Orsay, French
    • C.H. Bennett, Mass tensor molecular dynamics, in: C. Moser (Ed.), Report on Workshop Methods in Molecular Dynamics - Long Timescale Events, CECAM, Orsay, French, 1974, pp. 41-63.
    • (1974) Mass tensor molecular dynamics , pp. 41-63
    • Bennett, C.H.1
  • 5
    • 26044480933 scopus 로고
    • Mass tensor molecular dynamics
    • Bennett C.H. Mass tensor molecular dynamics. J. Comput. Phys. 1975, 19:267-279.
    • (1975) J. Comput. Phys. , vol.19 , pp. 267-279
    • Bennett, C.H.1
  • 6
    • 0000334103 scopus 로고
    • Computer simulation of water and aqueous solutions
    • Plenum Press, New York, F. Franks (Ed.)
    • Wood D.W. Computer simulation of water and aqueous solutions. Water: A Comprehensive Treatise 1979, 279-436. Plenum Press, New York. F. Franks (Ed.).
    • (1979) Water: A Comprehensive Treatise , pp. 279-436
    • Wood, D.W.1
  • 7
    • 0001652151 scopus 로고
    • Mass and step length optimization for the calculation of equilibrium properties by molecular dynamics simulation
    • Pomes R., McCammon J.A. Mass and step length optimization for the calculation of equilibrium properties by molecular dynamics simulation. Chem. Phys. Lett. 1990, 166:425-428.
    • (1990) Chem. Phys. Lett. , vol.166 , pp. 425-428
    • Pomes, R.1    McCammon, J.A.2
  • 8
    • 0025034114 scopus 로고
    • Molecular dynamics simulation by atomic mass weighting
    • Mao B., Friedman A.R. Molecular dynamics simulation by atomic mass weighting. Biophys. J. 1990, 58:803-805.
    • (1990) Biophys. J. , vol.58 , pp. 803-805
    • Mao, B.1    Friedman, A.R.2
  • 9
    • 0026048380 scopus 로고
    • Mass-weighted molecular dynamics simulation and conformational analysis of polypeptide
    • Mao B. Mass-weighted molecular dynamics simulation and conformational analysis of polypeptide. Biophys. J. 1991, 60:611-622.
    • (1991) Biophys. J. , vol.60 , pp. 611-622
    • Mao, B.1
  • 10
    • 0025934168 scopus 로고
    • Mass-weighted molecular dynamics simulation of the protein-ligand complex of rhizopuspepsin and inhibitor
    • Mao B. Mass-weighted molecular dynamics simulation of the protein-ligand complex of rhizopuspepsin and inhibitor. Biophys. J. 1991, 60:966-973.
    • (1991) Biophys. J. , vol.60 , pp. 966-973
    • Mao, B.1
  • 11
    • 0026206789 scopus 로고
    • Mass-weighted molecular dynamics simulation of cyclic polypeptides
    • Mao B., Maggiora G.M., Chou K.C. Mass-weighted molecular dynamics simulation of cyclic polypeptides. Biopolymers 1991, 31:1077-1086.
    • (1991) Biopolymers , vol.31 , pp. 1077-1086
    • Mao, B.1    Maggiora, G.M.2    Chou, K.C.3
  • 12
    • 0028258175 scopus 로고
    • Molecular dynamics simulation of a phospholipid membrane
    • Egberts E., Marrink S.-J., Berendsen H.J.C. Molecular dynamics simulation of a phospholipid membrane. Eur. Biophys. J. 1994, 22:423-436.
    • (1994) Eur. Biophys. J. , vol.22 , pp. 423-436
    • Egberts, E.1    Marrink, S.-J.2    Berendsen, H.J.C.3
  • 13
    • 0029886930 scopus 로고    scopus 로고
    • Study of global motions in proteins by weighted masses molecular dynamics: adenylate kinase as a test case
    • Elamrani S., Berry M.B., Phillips G.N., McCammon J.A. Study of global motions in proteins by weighted masses molecular dynamics: adenylate kinase as a test case. Proteins 1996, 25:79-88.
    • (1996) Proteins , vol.25 , pp. 79-88
    • Elamrani, S.1    Berry, M.B.2    Phillips, G.N.3    McCammon, J.A.4
  • 14
    • 0031576336 scopus 로고    scopus 로고
    • Torsion angle dynamics for NMR structure calculation with the new program DYANA
    • Guntert P., Mumenthaler C., Wuthrich K. Torsion angle dynamics for NMR structure calculation with the new program DYANA. J. Mol. Biol. 1997, 273:283-298.
    • (1997) J. Mol. Biol. , vol.273 , pp. 283-298
    • Guntert, P.1    Mumenthaler, C.2    Wuthrich, K.3
  • 15
    • 0001585978 scopus 로고    scopus 로고
    • Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems
    • Feenstra K.A., Hess B., Berendsen H.J.C. Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems. J. Comput. Chem. 1999, 20:786-798.
    • (1999) J. Comput. Chem. , vol.20 , pp. 786-798
    • Feenstra, K.A.1    Hess, B.2    Berendsen, H.J.C.3
  • 16
    • 8144230291 scopus 로고    scopus 로고
    • Increasing the time step and efficiency of molecular dynamics simulations: Optimal solutions for equilibrium simulations or structure refinement of large biomolecules
    • Stocker U., Juchli D., van Gunsteren W.F. Increasing the time step and efficiency of molecular dynamics simulations: Optimal solutions for equilibrium simulations or structure refinement of large biomolecules. Mol. Simul. 2003, 29:123-138.
    • (2003) Mol. Simul. , vol.29 , pp. 123-138
    • Stocker, U.1    Juchli, D.2    van Gunsteren, W.F.3
  • 17
    • 26044457002 scopus 로고    scopus 로고
    • Adaptive time stepping in biomolecular dynamics
    • Franklin J., Doniach S. Adaptive time stepping in biomolecular dynamics. J. Chem. Phys. 2005, 123:124909.
    • (2005) J. Chem. Phys. , vol.123 , pp. 124909
    • Franklin, J.1    Doniach, S.2
  • 18
    • 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
  • 19
    • 67650099787 scopus 로고    scopus 로고
    • ACEMD: accelerating biomolecular dynamics in the microsecond time scale
    • Harvey M.J., Giupponi G., De Fabritiis G. ACEMD: accelerating biomolecular dynamics in the microsecond time scale. J. Chem. Theory Comput. 2009, 5:1632-1639.
    • (2009) J. Chem. Theory Comput. , vol.5 , pp. 1632-1639
    • Harvey, M.J.1    Giupponi, G.2    De Fabritiis, G.3
  • 20
    • 70349895348 scopus 로고    scopus 로고
    • Increasing the time step with mass scaling in Born-Oppenheimer ab initio QM/MM molecular dynamics simulations
    • Zheng H., Wang S.L., Zhang Y.K. Increasing the time step with mass scaling in Born-Oppenheimer ab initio QM/MM molecular dynamics simulations. J. Comput. Chem. 2009, 30:2706-2711.
    • (2009) J. Comput. Chem. , vol.30 , pp. 2706-2711
    • Zheng, H.1    Wang, S.L.2    Zhang, Y.K.3
  • 21
    • 78149429881 scopus 로고    scopus 로고
    • PACE force field for protein simulations. 1. Full parameterization of version 1 and verification
    • Han W., Wan C.K., Jiang F., Wu Y.D. PACE force field for protein simulations. 1. Full parameterization of version 1 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
  • 22
    • 79551585811 scopus 로고    scopus 로고
    • Ab initio mass tensor molecular dynamics
    • Tsuchida E. Ab initio mass tensor molecular dynamics. J. Chem. Phys. 2011, 134:044112.
    • (2011) J. Chem. Phys. , vol.134 , pp. 044112
    • Tsuchida, E.1
  • 23
    • 84856209529 scopus 로고    scopus 로고
    • Thermodynamics and kinetics of large-time-step molecular dynamics
    • Rao F., Spichty M. Thermodynamics and kinetics of large-time-step molecular dynamics. J. Comput. Chem. 2012, 33:475-483.
    • (2012) J. Comput. Chem. , vol.33 , pp. 475-483
    • Rao, F.1    Spichty, M.2
  • 25
    • 84907495526 scopus 로고    scopus 로고
    • Mass-scaling replica-exchange molecular dynamics optimizes computational resources with simpler algorithm
    • Nagai T., Takahashi T. Mass-scaling replica-exchange molecular dynamics optimizes computational resources with simpler algorithm. J. Chem. Phys. 2014, 141:114111.
    • (2014) J. Chem. Phys. , vol.141 , pp. 114111
    • Nagai, T.1    Takahashi, T.2
  • 27
    • 29344442281 scopus 로고    scopus 로고
    • Numerical simulation of the effect of solvent viscosity on the motions of a beta-peptide heptamer
    • Gee P.J., van Gunsteren W.F. Numerical simulation of the effect of solvent viscosity on the motions of a beta-peptide heptamer. Chem. Eur. J. 2006, 12:72-75.
    • (2006) Chem. Eur. J. , vol.12 , pp. 72-75
    • Gee, P.J.1    van Gunsteren, W.F.2
  • 28
    • 77951109278 scopus 로고    scopus 로고
    • Replica exchange simulation method using temperature and solvent viscosity
    • Nguyen P.H. Replica exchange simulation method using temperature and solvent viscosity. J. Chem. Phys. 2010, 132:144109.
    • (2010) J. Chem. Phys. , vol.132 , pp. 144109
    • Nguyen, P.H.1
  • 29
    • 78650081823 scopus 로고    scopus 로고
    • Enhanced conformational sampling of peptides via reduced side-chain and solvent masses
    • Lin I.C., Tuckerman M.E. Enhanced conformational sampling of peptides via reduced side-chain and solvent masses. J. Phys. Chem. B 2010, 114:15935-15940.
    • (2010) J. Phys. Chem. B , vol.114 , pp. 15935-15940
    • Lin, I.C.1    Tuckerman, M.E.2
  • 30
    • 0001329269 scopus 로고    scopus 로고
    • Further investigation on the validity of Stokes-Einstein behaviour at the molecular level
    • Walser R., Hess B., Mark A.E., van Gunsteren W.F. Further investigation on the validity of Stokes-Einstein behaviour at the molecular level. Chem. Phys. Lett. 2001, 334:337-342.
    • (2001) Chem. Phys. Lett. , vol.334 , pp. 337-342
    • Walser, R.1    Hess, B.2    Mark, A.E.3    van Gunsteren, W.F.4
  • 31
    • 4143145167 scopus 로고    scopus 로고
    • 10 residue folded peptide designed by segment statistics
    • Honda S., Yamasaki K., Sawada Y., Morii H. 10 residue folded peptide designed by segment statistics. Structure 2004, 12:1507-1518.
    • (2004) Structure , vol.12 , pp. 1507-1518
    • Honda, S.1    Yamasaki, K.2    Sawada, Y.3    Morii, H.4
  • 33
    • 84923295175 scopus 로고    scopus 로고
    • At least 10% shorter C-H bonds in cryogenic protein crystal structures than in current AMBER forcefields
    • Pang Y.-P. At least 10% shorter C-H bonds in cryogenic protein crystal structures than in current AMBER forcefields. Biochem. Biophys. Res. Commun. 2015, 458:352-355.
    • (2015) Biochem. Biophys. Res. Commun. , vol.458 , pp. 352-355
    • Pang, Y.-P.1
  • 35
    • 84921818173 scopus 로고    scopus 로고
    • Use of 1-4 interaction scaling factors to control the conformational equilibrium between α-helix and β-strand
    • Pang Y.-P. Use of 1-4 interaction scaling factors to control the conformational equilibrium between α-helix and β-strand. Biochem. Biophys. Res. Commun. 2015, 457:183-186.
    • (2015) Biochem. Biophys. Res. Commun. , vol.457 , pp. 183-186
    • Pang, Y.-P.1
  • 37
    • 33846823909 scopus 로고
    • Particle mesh Ewald: an N log(N) method for Ewald sums in large systems
    • Darden T.A., York D.M., Pedersen L.G. Particle mesh Ewald: an N log(N) method for Ewald sums in large systems. J. Chem. Phys. 1993, 98:10089-10092.
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.A.1    York, D.M.2    Pedersen, L.G.3
  • 38
    • 49449085241 scopus 로고    scopus 로고
    • Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations
    • Joung I.S., Cheatham T.E. Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations. J. Phys. Chem. B 2008, 112:9020-9041.
    • (2008) J. Phys. Chem. B , vol.112 , pp. 9020-9041
    • Joung, I.S.1    Cheatham, T.E.2
  • 40
    • 33845382806 scopus 로고
    • Nonparametric estimation from incomplete observations
    • Kaplan E.L., Meier P. Nonparametric estimation from incomplete observations. J. Am. Stat. Assoc. 1958, 53:457-481.
    • (1958) J. Am. Stat. Assoc. , vol.53 , pp. 457-481
    • Kaplan, E.L.1    Meier, P.2
  • 42
    • 0031815749 scopus 로고    scopus 로고
    • How do small single-domain proteins fold?
    • Jackson S.E. How do small single-domain proteins fold?. Fold. Des. 1998, 3:R81-R91.
    • (1998) Fold. Des. , vol.3 , pp. R81-R91
    • Jackson, S.E.1
  • 43
    • 0003516749 scopus 로고
    • W. H. Freeman and Company, New York
    • Atkins P. Physical Chemistry 1994, W. H. Freeman and Company, New York.
    • (1994) Physical Chemistry
    • Atkins, P.1
  • 44
    • 0000510540 scopus 로고    scopus 로고
    • Novel zinc protein molecular dynamics simulations: steps toward antiangiogenesis for cancer treatment
    • Pang Y.-P. Novel zinc protein molecular dynamics simulations: steps toward antiangiogenesis for cancer treatment. J. Mol. Model. 1999, 5:196-202.
    • (1999) J. Mol. Model. , vol.5 , pp. 196-202
    • Pang, Y.-P.1
  • 45
    • 0033769641 scopus 로고    scopus 로고
    • Successful molecular dynamics simulation of the zinc-bound farnesyltransferase using the cationic dummy atom approach
    • Pang Y.-P., Xu K., El Yazal J., Prendergast F.G. Successful molecular dynamics simulation of the zinc-bound farnesyltransferase using the cationic dummy atom approach. Protein Sci. 2000, 9:1857-1865.
    • (2000) Protein Sci. , vol.9 , pp. 1857-1865
    • Pang, Y.-P.1    Xu, K.2    El Yazal, J.3    Prendergast, F.G.4
  • 46
    • 0035889687 scopus 로고    scopus 로고
    • Successful molecular dynamics simulation of two zinc complexes bridged by a hydroxide in phosphotriesterase using the cationic dummy atom method
    • Pang Y.-P. Successful molecular dynamics simulation of two zinc complexes bridged by a hydroxide in phosphotriesterase using the cationic dummy atom method. Proteins 2001, 45:183-189.
    • (2001) Proteins , vol.45 , pp. 183-189
    • Pang, Y.-P.1
  • 47
    • 0035937713 scopus 로고    scopus 로고
    • Predicted Michaelis-Menten complexes of cocaine-butyrylcholinesterase-engineering effective butyrylcholinesterase mutants for cocaine detoxication
    • Sun H., El Yazal J., Lockridge O., Schopfer L.M., Brimijoin S., Pang Y.-P. Predicted Michaelis-Menten complexes of cocaine-butyrylcholinesterase-engineering effective butyrylcholinesterase mutants for cocaine detoxication. J. Biol. Chem. 2001, 276:9330-9336.
    • (2001) J. Biol. Chem. , vol.276 , pp. 9330-9336
    • Sun, H.1    El Yazal, J.2    Lockridge, O.3    Schopfer, L.M.4    Brimijoin, S.5    Pang, Y.-P.6
  • 48
    • 10344222619 scopus 로고    scopus 로고
    • Three-dimensional model of a substrate-bound SARS chymotrypsin-like cysteine proteinase predicted by multiple molecular dynamics simulations: catalytic efficiency regulated by substrate binding
    • Pang Y.-P. Three-dimensional model of a substrate-bound SARS chymotrypsin-like cysteine proteinase predicted by multiple molecular dynamics simulations: catalytic efficiency regulated by substrate binding. Proteins 2004, 57:747-757.
    • (2004) Proteins , vol.57 , pp. 747-757
    • Pang, Y.-P.1
  • 50
    • 50649113765 scopus 로고    scopus 로고
    • Novel acetylcholinesterase target site for malaria mosquito control
    • Pang Y.-P. Novel acetylcholinesterase target site for malaria mosquito control. PLoS One 2006, 1:e58.
    • (2006) PLoS One , vol.1 , pp. e58
    • Pang, Y.-P.1
  • 51
    • 33845671661 scopus 로고    scopus 로고
    • Species marker for developing novel and safe pesticides
    • Pang Y.-P. Species marker for developing novel and safe pesticides. Bioorg. Med. Chem. Lett. 2007, 17:197-199.
    • (2007) Bioorg. Med. Chem. Lett. , vol.17 , pp. 197-199
    • Pang, Y.-P.1
  • 52
    • 65549109031 scopus 로고    scopus 로고
    • Configurational entropy in protein-peptide binding: computational study of TSG101 ubiquitin E2 variant domain with an HIV-derived PTAP nonapeptide
    • Killian B.J., Kravitz J.Y., Somani S., Dasgupta P., Pang Y.-P., Gilson M.K. Configurational entropy in protein-peptide binding: computational study of TSG101 ubiquitin E2 variant domain with an HIV-derived PTAP nonapeptide. J. Mol. Biol. 2009, 389:315-335.
    • (2009) J. Mol. Biol. , vol.389 , pp. 315-335
    • Killian, B.J.1    Kravitz, J.Y.2    Somani, S.3    Dasgupta, P.4    Pang, Y.-P.5    Gilson, M.K.6
  • 53
    • 67650099505 scopus 로고    scopus 로고
    • Structure of HI-6sarin-acetylcholinesterase determined by X-ray crystallography and molecular dynamics simulation: reactivator mechanism and design
    • Ekström F., Hörnberg A., Artursson E., Hammarström L.-G., Schneider G., Pang Y.-P. Structure of HI-6sarin-acetylcholinesterase determined by X-ray crystallography and molecular dynamics simulation: reactivator mechanism and design. PLoS ONE 2009, 4:e5957.
    • (2009) PLoS ONE , vol.4 , pp. e5957
    • Ekström, F.1    Hörnberg, A.2    Artursson, E.3    Hammarström, L.-G.4    Schneider, G.5    Pang, Y.-P.6
  • 54
    • 84859753178 scopus 로고    scopus 로고
    • Bak conformational changes induced by ligand binding: insight into BH3 domain binding and Bak homo-oligomerization
    • Pang Y.-P., Dai H., Smith A., Meng X.W., Schneider P.A., Kaufmann S.H. Bak conformational changes induced by ligand binding: insight into BH3 domain binding and Bak homo-oligomerization. Sci. Rep. 2012, 2:257.
    • (2012) Sci. Rep. , vol.2 , pp. 257
    • Pang, Y.-P.1    Dai, H.2    Smith, A.3    Meng, X.W.4    Schneider, P.A.5    Kaufmann, S.H.6


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