메뉴 건너뛰기




Volumn 53, Issue 2, 2003, Pages 148-161

Free energy landscape of protein folding in water: Explicit vs. implicit solvent

Author keywords

Explicit vs. implicit solvent; Free energy landscape; GB models; Protein folding; Salt bridge effect

Indexed keywords

PROTEIN G; WATER;

EID: 0141704162     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10483     Document Type: Article
Times cited : (284)

References (53)
  • 2
    • 1842298212 scopus 로고    scopus 로고
    • From Levinthal to pathways to funnels
    • Dill KA, Chan HS. From Levinthal to pathways to funnels. Nat Struc Biol 1997;4:10.
    • (1997) Nat Struc Biol , vol.4 , pp. 10
    • Dill, K.A.1    Chan, H.S.2
  • 4
    • 0033598375 scopus 로고    scopus 로고
    • Interpreting the folding kinetics of helical proteins
    • Zhou Y, Karplus M. Interpreting the folding kinetics of helical proteins. Nature 1999;401:400.
    • (1999) Nature , vol.401 , pp. 400
    • Zhou, Y.1    Karplus, M.2
  • 6
    • 0033610078 scopus 로고    scopus 로고
    • Global optimization of clusters, crystals and biomolecules
    • Wales DJ, Scheraga HA. Global optimization of clusters, crystals and biomolecules, Science 1999;285:1368.
    • (1999) Science , vol.285 , pp. 1368
    • Wales, D.J.1    Scheraga, H.A.2
  • 7
    • 0037038372 scopus 로고    scopus 로고
    • Absolute comparison of simulated and experimental protein-folding dynamics
    • Snow CD, Nguyen H, Pande VS, Gruebele M. Absolute comparison of simulated and experimental protein-folding dynamics. Nature 2002;420:102.
    • (2002) Nature , vol.420 , pp. 102
    • Snow, C.D.1    Nguyen, H.2    Pande, V.S.3    Gruebele, M.4
  • 8
    • 0028500779 scopus 로고
    • A short linear peptide that folds in a native stable β-hairpin in aqueous solution
    • Blanco FJ, Rivas G, Serrano L. A short linear peptide that folds in a native stable β-hairpin in aqueous solution. Nat Struct Biol 1994;1:584.
    • (1994) Nat Struct Biol , vol.1 , pp. 584
    • Blanco, F.J.1    Rivas, G.2    Serrano, L.3
  • 9
    • 0029070488 scopus 로고
    • Folding of protein g b1 domain studied by the conformational characterization of fragments comprising its secondary structure elements
    • Blanco FJ, Serrano L. Folding of protein g b1 domain studied by the conformational characterization of fragments comprising its secondary structure elements. Eur J Biochem. 1995;230:634.
    • (1995) Eur J Biochem , vol.230 , pp. 634
    • Blanco, F.J.1    Serrano, L.2
  • 10
    • 0038502170 scopus 로고    scopus 로고
    • Folding dynamics and mechanism of β-hairpin formation
    • Munoz V, Thompson PA, Hofrichter J, Eaton WA. Folding dynamics and mechanism of β-hairpin formation. Nature 1997;390:196.
    • (1997) Nature , vol.390 , pp. 196
    • Munoz, V.1    Thompson, P.A.2    Hofrichter, J.3    Eaton, W.A.4
  • 12
    • 0029016182 scopus 로고
    • Classical electrostatics in biology and chemistry
    • Honig B, Nicholls A. Classical electrostatics in biology and chemistry. Science 1995;268:1144.
    • (1995) Science , vol.268 , pp. 1144
    • Honig, B.1    Nicholls, A.2
  • 13
    • 0344778061 scopus 로고
    • Semi-analytical treatment of solvation for molecular mechanics and dynamics
    • Still W, Clark Tempczyk Anna, Hawley Ronald C, Hendrickson Thomas. Semi-analytical treatment of solvation for molecular mechanics and dynamics. J. Am Chem Soc 1990;112:6127.
    • (1990) J. Am Chem Soc , vol.112 , pp. 6127
    • Still, W.1    Clark, T.A.2    Hawley, R.C.3    Thomas, H.4
  • 14
    • 0001246294 scopus 로고    scopus 로고
    • Generalized born model based on a surface integral formulation
    • Ghosh A, Rapp CS, Friesner RA. Generalized born model based on a surface integral formulation. J Phys Chem 1998;102:10983.
    • (1998) J Phys Chem , vol.102 , pp. 10983
    • Ghosh, A.1    Rapp, C.S.2    Friesner, R.A.3
  • 15
    • 0033135638 scopus 로고    scopus 로고
    • Effective energy function for proteins in solution
    • Lazaridis T, Karplus M. Effective energy function for proteins in solution. Proteins 1999;35:133.
    • (1999) Proteins , vol.35 , pp. 133
    • Lazaridis, T.1    Karplus, M.2
  • 16
    • 0036789950 scopus 로고    scopus 로고
    • Can a continuum solvent model reproduce the free energy landscape of a β-hairpin folding in water?
    • Zhou R, Berne BJ. Can a continuum solvent model reproduce the free energy landscape of a β-hairpin folding in water? Proc Natl Acad Sci 2002;99:12777.
    • (2002) Proc Natl Acad Sci , vol.99 , pp. 12777
    • Zhou, R.1    Berne, B.J.2
  • 18
    • 0002098417 scopus 로고    scopus 로고
    • The development/application of a 'mini-malist' organic/biochemical molecular mechanic force field using a combination of ab initio calculations are experimental data in computer simulation of biomolecular systems
    • Eds. A. Wilkinson, P. Weiner and W.F. van Gunsteren
    • Kollman PA, Dixon R, Cornell W, Fox T, Chipot C, Pohorille A. The development/application of a 'mini-malist' organic/biochemical molecular mechanic force field using a combination of ab initio calculations are experimental data in computer simulation of biomolecular systems. Computer simulation of Biomolecular Systems, Eds. A. Wilkinson, P. Weiner and W.F. van Gunsteren 1997;3:83.
    • (1997) Computer Simulation of Biomolecular Systems , vol.3 , pp. 83
    • Kollman, P.A.1    Dixon, R.2    Cornell, W.3    Fox, T.4    Chipot, C.5    Pohorille, A.6
  • 19
    • 0001398008 scopus 로고    scopus 로고
    • How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?
    • Wang J, Cieplak P, Kollman PA. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J Comput Chem 2000;21:1049.
    • (2000) J Comput Chem , vol.21 , pp. 1049
    • Wang, J.1    Cieplak, P.2    Kollman, P.A.3
  • 20
    • 0033529908 scopus 로고    scopus 로고
    • Molecular dynamics simulations of unfolding and refolding of a β-hairpin fragment of protein g
    • Pande VS, Rokhsar DS. Molecular dynamics simulations of unfolding and refolding of a β-hairpin fragment of protein g. Proc Natl Acad Sci USA 1999;96:9062.
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 9062
    • Pande, V.S.1    Rokhsar, D.S.2
  • 21
    • 0035850758 scopus 로고    scopus 로고
    • β-hairpin folding simulation in atomistic detail
    • Zagrovic B, Sorin EJ, Pande VS. β-hairpin folding simulation in atomistic detail. J Mol Biol 2001;313:151.
    • (2001) J Mol Biol , vol.313 , pp. 151
    • Zagrovic, B.1    Sorin, E.J.2    Pande, V.S.3
  • 23
    • 0035865992 scopus 로고    scopus 로고
    • Exploring the energy landscape of a β hairpin in explicit solvent
    • Garcia AE, Sanbonmatsu KY. Exploring the energy landscape of a β hairpin in explicit solvent. Proteins 2001;42:345.
    • (2001) Proteins , vol.42 , pp. 345
    • Garcia, A.E.1    Sanbonmatsu, K.Y.2
  • 24
    • 0032881707 scopus 로고    scopus 로고
    • A molecular dynamics study of the 41-56 β-hairpin from b1 domain of protein g
    • Roccatano D, Amadei A, Nola A Di, Berendsen HJ. A molecular dynamics study of the 41-56 β-hairpin from b1 domain of protein g. Protein Sci 1999;10:2130.
    • (1999) Protein Sci , vol.10 , pp. 2130
    • Roccatano, D.1    Amadei, A.2    Nola, A.D.3    Berendsen, H.J.4
  • 25
    • 0032764074 scopus 로고    scopus 로고
    • Dynamics and thermodynamics of β-hairpin assembly: Insights from various simulation techniques
    • Kolinski A, Ilkowski B, Skolnick J. Dynamics and thermodynamics of β-hairpin assembly: insights from various simulation techniques. Biophys J 1999;77:2942.
    • (1999) Biophys J , vol.77 , pp. 2942
    • Kolinski, A.1    Ilkowski, B.2    Skolnick, J.3
  • 26
    • 0034646218 scopus 로고    scopus 로고
    • Mechanism and kinetics of β-hairpin formation
    • Klimov DK, Thirumalai D. Mechanism and kinetics of β-hairpin formation. Proc Natl Acad Sci USA 2000;97:2544.
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 2544
    • Klimov, D.K.1    Thirumalai, D.2
  • 27
    • 0035909921 scopus 로고    scopus 로고
    • The free energy landscape for β-hairpin folding in explicit water
    • Zhou R, Berne BJ, Germain R. The free energy landscape for β-hairpin folding in explicit water. Proc Natl Acad Sci USA 2001;98:14931.
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 14931
    • Zhou, R.1    Berne, B.J.2    Germain, R.3
  • 28
    • 0035424713 scopus 로고    scopus 로고
    • Efficient multiple time step method for use with ewald and particle mesh ewald for large biomolecular systems
    • Zhou R, Harder E, Xu H, Berne BJ. Efficient multiple time step method for use with ewald and particle mesh ewald for large biomolecular systems. J Chem Phys 2001;115:2348.
    • (2001) J Chem Phys , vol.115 , pp. 2348
    • Zhou, R.1    Harder, E.2    Xu, H.3    Berne, B.J.4
  • 29
    • 20644449471 scopus 로고    scopus 로고
    • A modification of the generalized born model suitable for macromolecules
    • Onufriev A, Bashford D, Case DA. A modification of the generalized born model suitable for macromolecules. J Phys Chem B 2000;104:3712.
    • (2000) J Phys Chem B , vol.104 , pp. 3712
    • Onufriev, A.1    Bashford, D.2    Case, D.A.3
  • 30
    • 0037089017 scopus 로고    scopus 로고
    • The sgb/np hydration free energy model based on the surface generalized born solvent reaction field and novel non-polar hydration free energy estimators
    • Gallicchio E, Zhang LY, Levy RM. The sgb/np hydration free energy model based on the surface generalized born solvent reaction field and novel non-polar hydration free energy estimators. J Comp Chem 2002;23:517.
    • (2002) J Comp Chem , vol.23 , pp. 517
    • Gallicchio, E.1    Zhang, L.Y.2    Levy, R.M.3
  • 31
    • 0035950792 scopus 로고    scopus 로고
    • New linear interaction method for binding affinity calculations using a continuum solvent model
    • Zhou R, Friesner RA, Ghosh Avijit, Rizzo RC, Jorgensen WL, Levy RM. New linear interaction method for binding affinity calculations using a continuum solvent model. J Phys Chem B 2001;105: 10388.
    • (2001) J Phys Chem B , vol.105 , pp. 10388
    • Zhou, R.1    Friesner, R.A.2    Ghosh, A.3    Rizzo, R.C.4    Jorgensen, W.L.5    Levy, R.M.6
  • 32
    • 0000666868 scopus 로고    scopus 로고
    • Smart walking: A new method for boltzmann sampling of protein conformations
    • Zhou R, Berne BJ. Smart walking: A new method for boltzmann sampling of protein conformations. J Chem Phys 1997;107:9185.
    • (1997) J Chem Phys , vol.107 , pp. 9185
    • Zhou, R.1    Berne, B.J.2
  • 34
    • 0001616080 scopus 로고    scopus 로고
    • Replica-exchange molecular dynamics method for protein folding
    • Sugita Y, Okamoto Y. Replica-exchange molecular dynamics method for protein folding. Chem Phys Lett 1999;314:141.
    • (1999) Chem Phys Lett , vol.314 , pp. 141
    • Sugita, Y.1    Okamoto, Y.2
  • 35
    • 0000408363 scopus 로고    scopus 로고
    • Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO)
    • Weiser J, Shenkin PS, Still WC. Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO). J Comp Chem 1999;20:217.
    • (1999) J Comp Chem , vol.20 , pp. 217
    • Weiser, J.1    Shenkin, P.S.2    Still, W.C.3
  • 36
    • 0033654297 scopus 로고    scopus 로고
    • Generalized born models of macromolecular solvation effects
    • Bashford D, Case DA. Generalized born models of macromolecular solvation effects. Annu Rev Phys Chem 2000;51:129.
    • (2000) Annu Rev Phys Chem , vol.51 , pp. 129
    • Bashford, D.1    Case, D.A.2
  • 37
    • 0035451052 scopus 로고    scopus 로고
    • What are the dielectric 'constants' of proteins and how to validate electrostatic models
    • Schutz CN, Warshel A. What are the dielectric 'constants' of proteins and how to validate electrostatic models. Proteins 2001; 44:400.
    • (2001) Proteins , vol.44 , pp. 400
    • Schutz, C.N.1    Warshel, A.2
  • 39
    • 0000577041 scopus 로고
    • Large-amplitude nolinear motions in proteins
    • Garcia AE. Large-amplitude nolinear motions in proteins. Phys Rev Lett 1992;68:2696.
    • (1992) Phys Rev Lett , vol.68 , pp. 2696
    • Garcia, A.E.1
  • 40
    • 0029619259 scopus 로고
    • Knowledge-based secondary structure assignment
    • Frishman D, Argos P. Knowledge-based secondary structure assignment. Proteins 1995;23:566.
    • (1995) Proteins , vol.23 , pp. 566
    • Frishman, D.1    Argos, P.2
  • 41
    • 0030745939 scopus 로고    scopus 로고
    • Accurate ab initio quantum chemical determination of the relative energetics of peptide conformations and assessment of empirical force fields
    • Beachy M, Chasman D, Murphy R, Halgren T, Friesner R. Accurate ab initio quantum chemical determination of the relative energetics of peptide conformations and assessment of empirical force fields. J Am Chem Soc 1997;119:5908.
    • (1997) J Am Chem Soc , vol.119 , pp. 5908
    • Beachy, M.1    Chasman, D.2    Murphy, R.3    Halgren, T.4    Friesner, R.5
  • 42
    • 0000538815 scopus 로고
    • Analytical molecular surface calculation
    • Connolly ML. Analytical molecular surface calculation. J Appl Cryst 1983;16:548.
    • (1983) J Appl Cryst , vol.16 , pp. 548
    • Connolly, M.L.1
  • 43
    • 0141753446 scopus 로고    scopus 로고
    • Getting to the folded state: Parallel-replica simulations of TRP-cage
    • Submitted for publication
    • Pitera J, Swope W. Getting to the folded state: parallel-replica simulations of TRP-cage. Nat Struc Biol 2003, Submitted for publication.
    • (2003) Nat Struc Biol
    • Pitera, J.1    Swope, W.2
  • 45
    • 0037174385 scopus 로고    scopus 로고
    • All-atom structure prediction and folding simulations of a stable protein
    • Simmerling C, Strockbine B, Roitberg AE. All-atom structure prediction and folding simulations of a stable protein. J. Am Chem Soc 2002;124:11258.
    • (2002) J. Am Chem Soc , vol.124 , pp. 11258
    • Simmerling, C.1    Strockbine, B.2    Roitberg, A.E.3
  • 46
    • 0037065310 scopus 로고    scopus 로고
    • The TRP cage: Folding kinetics and unfolded state topology via molecular dynamics simulations
    • Snow CD, Zargovic B, Pande VS. The TRP cage: Folding kinetics and unfolded state topology via molecular dynamics simulations. J Am Chem Soc 2002;124:14548.
    • (2002) J Am Chem Soc , vol.124 , pp. 14548
    • Snow, C.D.1    Zargovic, B.2    Pande, V.S.3
  • 47
    • 0037022662 scopus 로고    scopus 로고
    • Alpha-helical stabilization by side chain shielding of backbone hydrogen bonds
    • Garcia AE, Sanbonmatsu KY. Alpha-helical stabilization by side chain shielding of backbone hydrogen bonds. Proc Natl Acad Sci USA 2002;99:2782.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 2782
    • Garcia, A.E.1    Sanbonmatsu, K.Y.2
  • 48
    • 0037195097 scopus 로고    scopus 로고
    • On the simulation of protein folding by short time scale molecular dynamics and distributed computing
    • Fersht AR. On the simulation of protein folding by short time scale molecular dynamics and distributed computing. Proc Natl Acad Sci USA 2002;99:14122.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 14122
    • Fersht, A.R.1
  • 49
    • 0031249752 scopus 로고    scopus 로고
    • Monovalent and divalent salt effects on electrostatic free energies defined by the nonlinear poisson-boltzmann equation: Application to DNA reactions
    • Chen SW, Honig B. Monovalent and divalent salt effects on electrostatic free energies defined by the nonlinear poisson-boltzmann equation: Application to DNA reactions. J Phys Chem B 1997;101:9113.
    • (1997) J Phys Chem B , vol.101 , pp. 9113
    • Chen, S.W.1    Honig, B.2
  • 50
    • 0037093650 scopus 로고    scopus 로고
    • Simulations of ion current in realistic models of ion channels: The kcsa potassium channel
    • Burykin A, Schutz CN, Villa J, Warshel A. Simulations of ion current in realistic models of ion channels: the kcsa potassium channel. Proteins 2002;47:265.
    • (2002) Proteins , vol.47 , pp. 265
    • Burykin, A.1    Schutz, C.N.2    Villa, J.3    Warshel, A.4
  • 51
    • 0037442915 scopus 로고    scopus 로고
    • Potentials of mean force between ionizable amino acid side chains in water
    • Masunov A, Lazaridis T. Potentials of mean force between ionizable amino acid side chains in water. J Am Chem Soc 2003;125: 1722.
    • (2003) J Am Chem Soc , vol.125 , pp. 1722
    • Masunov, A.1    Lazaridis, T.2
  • 52
    • 0037154268 scopus 로고    scopus 로고
    • Onuchic, protein folding mediated by solvation: Water expulsion and formation of the hydrophobic core occur after the structural collapse
    • Cheung MS, Garcia AE. Onuchic, Protein folding mediated by solvation: water expulsion and formation of the hydrophobic core occur after the structural collapse. Proc Natl Acad Sci USA 2002;99:685.
    • (2002) Proc Natl AAcad Sci USA , vol.99 , pp. 685
    • Cheung, M.S.1    Garcia, A.E.2
  • 53
    • 0037459035 scopus 로고    scopus 로고
    • Solvation effects and driving forces for protein thermodynamics and kinetic cooperativity: How adequate is native-centric topological modeling?
    • Kaya H, Chan HS. Solvation effects and driving forces for protein thermodynamics and kinetic cooperativity: how adequate is native-centric topological modeling? J Mol Biol 2003;326:911.
    • (2003) J Mol Biol , vol.326 , pp. 911
    • Kaya, H.1    Chan, H.S.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.