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Volumn 78, Issue 1-2, 1999, Pages 195-205

ES/IS: Estimation of conformational free energy by combining dynamics simulations with explicit solvent with an implicit solvent continuum model

Author keywords

Conformational free energy; Continuum dielectric; Implicit solvation; Misfolded proteins; Molecular dynamics

Indexed keywords

CALCULATION; COMPUTER SIMULATION; CONFERENCE PAPER; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN STRUCTURE; QUANTUM MECHANICS; SOLVATION; TECHNIQUE; THEORY;

EID: 0033003955     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0301-4622(98)00230-0     Document Type: Conference Paper
Times cited : (76)

References (52)
  • 1
    • 7044239742 scopus 로고
    • Free energy calculations: Applications to chemical and biochemical phenomena
    • Kollman P. Free energy calculations: applications to chemical and biochemical phenomena. Chem. Rev. 93:1993;2395-2417.
    • (1993) Chem. Rev. , vol.93 , pp. 2395-2417
    • Kollman, P.1
  • 2
    • 0000003059 scopus 로고    scopus 로고
    • Free energy calculation methods: A theoretical and empirical comparison of numerical errors and a new method for qualitative estimates of free energy changes
    • Radmer R.J., Kollman P.A. Free energy calculation methods: a theoretical and empirical comparison of numerical errors and a new method for qualitative estimates of free energy changes. J. Comp. Chem. 18:1997;902-919.
    • (1997) J. Comp. Chem. , vol.18 , pp. 902-919
    • Radmer, R.J.1    Kollman, P.A.2
  • 3
    • 0031872292 scopus 로고    scopus 로고
    • Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamic simulations with explicit solvent, and an implicit solvent continuum model
    • Vorobjev Y.N., Almagro J.C., Hermans J. Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamic simulations with explicit solvent, and an implicit solvent continuum model. Proteins: Struct. Funct. Genet. 32:1998;399-413.
    • (1998) Proteins: Struct. Funct. Genet. , vol.32 , pp. 399-413
    • Vorobjev, Y.N.1    Almagro, J.C.2    Hermans, J.3
  • 4
    • 24344503448 scopus 로고    scopus 로고
    • A resource, exchange and discussion forum for development and application of potentials for protein structure evaluation and prediction. Website
    • J.A. Moult, Pro-Star: the protein potential site. A resource, exchange and discussion forum for development and application of potentials for protein structure evaluation and prediction. Website http://prostar.carb.nist.gov/, 1997.
    • (1997) Pro-Star: The Protein Potential Site
    • Moult, J.A.1
  • 5
    • 0001927132 scopus 로고
    • Molecular dynamic simulations of statistical mechanical systems
    • Varenna, North-Holland, Amsterdam
    • D. Frenkel, Molecular dynamic simulations of statistical mechanical systems. Proceedings of the Enrico Fermi Summer School, Varenna, 1985. North-Holland, Amsterdam, 1986, pp. 151-164.
    • (1985) Proceedings of the Enrico Fermi Summer School , pp. 151-164
    • Frenkel, D.1
  • 6
    • 0003241140 scopus 로고    scopus 로고
    • Free energies of hydration from thermodynamic integration: Comparison of molecular mechanics force fields and evaluation of calculation accuracy
    • Helms V., Wade R.C. Free energies of hydration from thermodynamic integration: comparison of molecular mechanics force fields and evaluation of calculation accuracy. J. Comp. Chem. 18:1997;449-462.
    • (1997) J. Comp. Chem. , vol.18 , pp. 449-462
    • Helms, V.1    Wade, R.C.2
  • 8
    • 33751232728 scopus 로고
    • Statistical mechanics of chemical equilibria and intramolecular structures of non-rigid molecules in condensed phases
    • Chandler D., Pratt L.R. Statistical mechanics of chemical equilibria and intramolecular structures of non-rigid molecules in condensed phases. J. Chem. Phys. 65:1976;2925-2940.
    • (1976) J. Chem. Phys. , vol.65 , pp. 2925-2940
    • Chandler, D.1    Pratt, L.R.2
  • 9
    • 0025261918 scopus 로고
    • Solvent effects on protein association and protein folding
    • Ben-Naim A. Solvent effects on protein association and protein folding. Biopolymers. 29:1990;567-596.
    • (1990) Biopolymers , vol.29 , pp. 567-596
    • Ben-Naim, A.1
  • 10
    • 33751385054 scopus 로고
    • Macroscopic models of aqueous solutions: Biological and chemical applications
    • Honig B., Sharp K., Yang A.S. Macroscopic models of aqueous solutions: biological and chemical applications. J. Phys. Chem. 97:1993;1101-1109.
    • (1993) J. Phys. Chem. , vol.97 , pp. 1101-1109
    • Honig, B.1    Sharp, K.2    Yang, A.S.3
  • 11
    • 32844457567 scopus 로고
    • Accurate calculation of hydration free energies using macroscopic solvent models
    • Sitkoff D., Sharp K.A., Honig B. Accurate calculation of hydration free energies using macroscopic solvent models. J. Phys. Chem. 98:1994;1978-1988.
    • (1994) J. Phys. Chem. , vol.98 , pp. 1978-1988
    • Sitkoff, D.1    Sharp, K.A.2    Honig, B.3
  • 12
    • 0000831520 scopus 로고
    • Solvation free energies estimated from macroscopic continuum theory: An accuracy assessment
    • Simonson T., Brünger A. Solvation free energies estimated from macroscopic continuum theory: an accuracy assessment. J. Phys. Chem. 98:1994;4683-4694.
    • (1994) J. Phys. Chem. , vol.98 , pp. 4683-4694
    • Simonson, T.1    Brünger, A.2
  • 13
    • 0000501772 scopus 로고
    • Improvements of the continuum model. 1. Application to the calculation of the vaporization thermodynamic quantities of non-associated liquids
    • Langlet J., Claverie P., Caillet J., Pullman A. Improvements of the continuum model. 1. Application to the calculation of the vaporization thermodynamic quantities of non-associated liquids. J. Phys. Chem. 92:1988;617-1631.
    • (1988) J. Phys. Chem. , vol.92 , pp. 617-1631
    • Langlet, J.1    Claverie, P.2    Caillet, J.3    Pullman, A.4
  • 14
    • 11744256643 scopus 로고
    • Molecular interactions in solution: An overview of methods based on continuum distribution of the solvent
    • Tomasi J., Persico M. Molecular interactions in solution: an overview of methods based on continuum distribution of the solvent. Chem. Rev. 94:1994;2027-2094.
    • (1994) Chem. Rev. , vol.94 , pp. 2027-2094
    • Tomasi, J.1    Persico, M.2
  • 17
    • 0000577041 scopus 로고
    • Large-amplitude nonlinear motions in proteins
    • Garcia A.E. Large-amplitude nonlinear motions in proteins. Phys. Rev. Lett. 68:1992;2696-2699.
    • (1992) Phys. Rev. Lett. , vol.68 , pp. 2696-2699
    • Garcia, A.E.1
  • 18
    • 0000885331 scopus 로고
    • Harmonic analysis of large systems. I. Methodology
    • Brooks B.R., Janezic D., Karplus M. Harmonic analysis of large systems. I. Methodology. J. Comp. Chem. 16:1995;1522-1542.
    • (1995) J. Comp. Chem. , vol.16 , pp. 1522-1542
    • Brooks, B.R.1    Janezic, D.2    Karplus, M.3
  • 19
    • 84986469420 scopus 로고
    • Harmonic analysis of large systems. II. Comparison of different protein models
    • Janezic D., Brooks B.R. Harmonic analysis of large systems. II. Comparison of different protein models. J. Comp. Chem. 16:1995;1543-1553.
    • (1995) J. Comp. Chem. , vol.16 , pp. 1543-1553
    • Janezic, D.1    Brooks, B.R.2
  • 20
    • 84986473952 scopus 로고
    • Harmonic analysis of large systems. III. Comparison with molecular dynamics
    • Janezic D., Venable R.M., Brooks B.R. Harmonic analysis of large systems. III. Comparison with molecular dynamics. J. Comp. Chem. 16:1995;1554-1566.
    • (1995) J. Comp. Chem. , vol.16 , pp. 1554-1566
    • Janezic, D.1    Venable, R.M.2    Brooks, B.R.3
  • 21
    • 0030793507 scopus 로고    scopus 로고
    • SIMS, Computation of a smooth invariant molecular surface
    • Vorobjev Y.N., Hermans J. SIMS, Computation of a smooth invariant molecular surface. Biophys. J. 73:1997;722-732.
    • (1997) Biophys. J. , vol.73 , pp. 722-732
    • Vorobjev, Y.N.1    Hermans, J.2
  • 22
    • 0001445346 scopus 로고    scopus 로고
    • A fast adaptive multigrid boundary element method for macromolecular electrostatics in a solvent
    • Vorobjev Y.N., Scheraga H.A. A fast adaptive multigrid boundary element method for macromolecular electrostatics in a solvent. J. Comp. Chem. 18:1997;569-583.
    • (1997) J. Comp. Chem. , vol.18 , pp. 569-583
    • Vorobjev, Y.N.1    Scheraga, H.A.2
  • 23
    • 0028818340 scopus 로고
    • Protein structure prediction by threading methods: Evaluation of current techniques
    • Lemer C.M.R., Rooman M.J., Wodak S.J. Protein structure prediction by threading methods: evaluation of current techniques. Proteins: Struct. Funct. Genet. 23:1995;337-355.
    • (1995) Proteins: Struct. Funct. Genet. , vol.23 , pp. 337-355
    • Lemer, C.M.R.1    Rooman, M.J.2    Wodak, S.J.3
  • 24
    • 0028318094 scopus 로고
    • Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches
    • Kocher J.P., Rooman M.J., Wodak S.J. Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches. J. Mol. Biol. 235:1994;1598-1613.
    • (1994) J. Mol. Biol. , vol.235 , pp. 1598-1613
    • Kocher, J.P.1    Rooman, M.J.2    Wodak, S.J.3
  • 25
    • 0029976427 scopus 로고    scopus 로고
    • Statistical potentials extracted from protein structures: What is wrong with them?
    • Thomas P.D., Dill K. Statistical potentials extracted from protein structures: what is wrong with them? J. Mol. Biol. 257:1996;457-469.
    • (1996) J. Mol. Biol. , vol.257 , pp. 457-469
    • Thomas, P.D.1    Dill, K.2
  • 26
    • 0029942661 scopus 로고    scopus 로고
    • Structure derived potentials and protein simulations
    • Jernigan R.L., Bahar I. Structure derived potentials and protein simulations. Curr. Opin. Struct. Biol. 6:1996;195-209.
    • (1996) Curr. Opin. Struct. Biol. , vol.6 , pp. 195-209
    • Jernigan, R.L.1    Bahar, I.2
  • 27
    • 33645903407 scopus 로고
    • Solvation thermodynamics of nonionic solutes
    • Ben-Naim A., Marcus Y. Solvation thermodynamics of nonionic solutes. J. Chem. Phys. 81:1984;2016-2027.
    • (1984) J. Chem. Phys. , vol.81 , pp. 2016-2027
    • Ben-Naim, A.1    Marcus, Y.2
  • 28
    • 0016352763 scopus 로고
    • Hydrophobic bonding and accessible area in proteins
    • Chothia C.H. Hydrophobic bonding and accessible area in proteins. Nature. 248:1974;338-339.
    • (1974) Nature , vol.248 , pp. 338-339
    • Chothia, C.H.1
  • 29
    • 0011930746 scopus 로고
    • Theory of hydrophobic bonding. II. The correlation of hydrocarbon solubility in water with solvent cavity surface area
    • Hermann R.B. Theory of hydrophobic bonding. II. The correlation of hydrocarbon solubility in water with solvent cavity surface area. J. Phys. Chem. 76:1972;2754-2759.
    • (1972) J. Phys. Chem. , vol.76 , pp. 2754-2759
    • Hermann, R.B.1
  • 32
    • 33751155475 scopus 로고
    • Computer simulation of hydrophobic hydration forces on stacked plates at short range
    • Wallqvist W., Berne B.J. Computer simulation of hydrophobic hydration forces on stacked plates at short range. J. Phys. Chem. 99:1995;2893-2899.
    • (1995) J. Phys. Chem. , vol.99 , pp. 2893-2899
    • Wallqvist, W.1    Berne, B.J.2
  • 33
    • 0001229923 scopus 로고
    • Molecular dynamics study of the dependence of water solvation free energy on solute curvature and surface area
    • Wallqvist W., Berne B.J. Molecular dynamics study of the dependence of water solvation free energy on solute curvature and surface area. J. Phys. Chem. 99:1995;2885-2892.
    • (1995) J. Phys. Chem. , vol.99 , pp. 2885-2892
    • Wallqvist, W.1    Berne, B.J.2
  • 35
    • 33747754400 scopus 로고
    • A Scaled particle theory of aqueous and non-aqueous solutions
    • Pierotti R.A. A Scaled particle theory of aqueous and non-aqueous solutions. Chem. Rev. 76:1976;717-726.
    • (1976) Chem. Rev. , vol.76 , pp. 717-726
    • Pierotti, R.A.1
  • 36
    • 0028180523 scopus 로고
    • Application of scaled particle theory to model the hydrophobic effect: Implications for molecular association and protein stability
    • Jackson R.M., Sternberg J.E. Application of scaled particle theory to model the hydrophobic effect: implications for molecular association and protein stability. Protein Eng. 7:1994;371-383.
    • (1994) Protein Eng. , vol.7 , pp. 371-383
    • Jackson, R.M.1    Sternberg, J.E.2
  • 38
    • 0029019869 scopus 로고
    • A continuum model for protein-protein interactions: Applications to the docking problem
    • Jackson R.M., Sternberg J.E. A continuum model for protein-protein interactions: applications to the docking problem. J. Mol. Biol. 250:1995;258-275.
    • (1995) J. Mol. Biol. , vol.250 , pp. 258-275
    • Jackson, R.M.1    Sternberg, J.E.2
  • 39
    • 0031547977 scopus 로고    scopus 로고
    • Empirical free energy calculations: A blind test and further improvements of the method
    • Novotny J., Brucooleri R.E., Davis M., Sharp K.A. Empirical free energy calculations: a blind test and further improvements of the method. J. Mol. Biol. 268:1997;401-411.
    • (1997) J. Mol. Biol. , vol.268 , pp. 401-411
    • Novotny, J.1    Brucooleri, R.E.2    Davis, M.3    Sharp, K.A.4
  • 40
    • 36749108636 scopus 로고
    • A Monte Carlo simulation of the hydrophobic interaction
    • Pangali C., Rao M., Berne B.J. A Monte Carlo simulation of the hydrophobic interaction. J. Chem. Phys. 71:1979;2975-2981.
    • (1979) J. Chem. Phys. , vol.71 , pp. 2975-2981
    • Pangali, C.1    Rao, M.2    Berne, B.J.3
  • 41
    • 36448999843 scopus 로고
    • Free energy, entropy and internal energy of hydrophobic interactions: Computer simulations
    • Smith D.E., Haymet A.D.J. Free energy, entropy and internal energy of hydrophobic interactions: computer simulations. J. Chem. Phys. 98:1993;6445-6454.
    • (1993) J. Chem. Phys. , vol.98 , pp. 6445-6454
    • Smith, D.E.1    Haymet, A.D.J.2
  • 42
    • 0030852818 scopus 로고    scopus 로고
    • Thermodynamics of reverse turn motif. Solvent effects and side-chain packing
    • Demchuk E., Bashford D., Gippert G.P. Thermodynamics of reverse turn motif. Solvent effects and side-chain packing. J. Mol. Biol. 270:1997;305-317.
    • (1997) J. Mol. Biol. , vol.270 , pp. 305-317
    • Demchuk, E.1    Bashford, D.2    Gippert, G.P.3
  • 43
    • 0031167555 scopus 로고    scopus 로고
    • Atomic radii for continuum electrostatic calculations based on molecular dynamics free energy simulations
    • Nina M., Beglov D., Roux B. Atomic radii for continuum electrostatic calculations based on molecular dynamics free energy simulations. J. Phys. Chem. 101:1997;5239-5248.
    • (1997) J. Phys. Chem. , vol.101 , pp. 5239-5248
    • Nina, M.1    Beglov, D.2    Roux, B.3
  • 44
    • 0000763912 scopus 로고
    • Molecular basis for the Born model of ion solvation
    • Roux B., Yu H.A., Karplus M. Molecular basis for the Born model of ion solvation. J. Phys. Chem. 94:1990;4683-4688.
    • (1990) J. Phys. Chem. , vol.94 , pp. 4683-4688
    • Roux, B.1    Yu, H.A.2    Karplus, M.3
  • 45
    • 5544264558 scopus 로고
    • Gaussian fluctuation formula for electrostatic free energy changes in solution
    • Levy R.M., Belhadj M., Kitchen D.B. Gaussian fluctuation formula for electrostatic free energy changes in solution. J. Chem. Phys. 95:1991;3627-3633.
    • (1991) J. Chem. Phys. , vol.95 , pp. 3627-3633
    • Levy, R.M.1    Belhadj, M.2    Kitchen, D.B.3
  • 46
    • 33749637456 scopus 로고
    • Free energy calculations of ion hydration: An analysis of the Born model in terms of microscopic simulations
    • Jayaram B., Fine R., Sharp K., Honig B. Free energy calculations of ion hydration: an analysis of the Born model in terms of microscopic simulations. J. Phys. Chem. 93:1989;4320-4327.
    • (1989) J. Phys. Chem. , vol.93 , pp. 4320-4327
    • Jayaram, B.1    Fine, R.2    Sharp, K.3    Honig, B.4
  • 47
    • 0001458825 scopus 로고
    • The aqueous solvation of water: A comparison of continuum methods with molecular dynamics
    • Rick S.W., Berne B.J. The aqueous solvation of water: a comparison of continuum methods with molecular dynamics. J. Am. Chem. Soc. 116:1994;3949-3954.
    • (1994) J. Am. Chem. Soc. , vol.116 , pp. 3949-3954
    • Rick, S.W.1    Berne, B.J.2
  • 48
    • 0030134110 scopus 로고    scopus 로고
    • On the validity of electrostatic linear response in polar solvent
    • Aqvist J., Hansson T. On the validity of electrostatic linear response in polar solvent. J. Phys. Chem. 100:1996;9512-9521.
    • (1996) J. Phys. Chem. , vol.100 , pp. 9512-9521
    • Aqvist, J.1    Hansson, T.2
  • 49
    • 0028155689 scopus 로고
    • A new method for predicting binding affinity in computer-aided drug design
    • Aqvist J., Medina C., Samuelsson J.E. A new method for predicting binding affinity in computer-aided drug design. Protein Eng. 7:1994;385-391.
    • (1994) Protein Eng. , vol.7 , pp. 385-391
    • Aqvist, J.1    Medina, C.2    Samuelsson, J.E.3
  • 50
    • 0001389474 scopus 로고
    • An extended linear response method for determining free energies of hydration
    • Carlson H.A., Jorgensen W.L. An extended linear response method for determining free energies of hydration. J. Phys. Chem. 99:1995;10667-10673.
    • (1995) J. Phys. Chem. , vol.99 , pp. 10667-10673
    • Carlson, H.A.1    Jorgensen, W.L.2
  • 51
    • 0345227094 scopus 로고    scopus 로고
    • Dielectric behavior in the interior of proteins: Result from a large-scale molecular dynamic simulation of solvated lysozyme
    • Figueirido F., Del Buono G.S., Levy R.M. Dielectric behavior in the interior of proteins: result from a large-scale molecular dynamic simulation of solvated lysozyme. Biophys. J. 72:1997;A216-A216.
    • (1997) Biophys. J. , vol.72
    • Figueirido, F.1    Del Buono, G.S.2    Levy, R.M.3


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