메뉴 건너뛰기




Volumn 104, Issue 2, 2013, Pages 453-462

Absolute hydration free energies of blocked amino acids: Implications for protein solvation and stability

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; PROTEIN; SOLVENT; WATER;

EID: 84872783761     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2012.12.008     Document Type: Article
Times cited : (53)

References (83)
  • 2
    • 0014722597 scopus 로고
    • Enthalpy-entropy compensation phenomena in water solutions of proteins and small molecules: A ubiquitous property of water
    • R. Lumry, and S. Rajender Enthalpy-entropy compensation phenomena in water solutions of proteins and small molecules: a ubiquitous property of water Biopolymers 9 1970 1125 1227
    • (1970) Biopolymers , vol.9 , pp. 1125-1227
    • Lumry, R.1    Rajender, S.2
  • 3
    • 77952387014 scopus 로고    scopus 로고
    • Limits of free energy computation for protein-ligand interactions
    • K.M. Merz Jr. Limits of free energy computation for protein-ligand interactions J. Chem. Theory Comput. 6 2010 1018 1027
    • (2010) J. Chem. Theory Comput. , vol.6 , pp. 1018-1027
    • Merz, Jr.K.M.1
  • 4
    • 0038519321 scopus 로고
    • Contribution of hydrophobic interactions to stability of globular conformation of proteins
    • C. Tanford Contribution of hydrophobic interactions to stability of globular conformation of proteins J. Am. Chem. Soc. 84 1962 4240 4247
    • (1962) J. Am. Chem. Soc. , vol.84 , pp. 4240-4247
    • Tanford, C.1
  • 5
    • 0008863560 scopus 로고
    • Some factors in the interpretation of protein denaturation
    • W. Kauzmann Some factors in the interpretation of protein denaturation Adv. Protein Chem. 14 1959 1 63
    • (1959) Adv. Protein Chem. , vol.14 , pp. 1-63
    • Kauzmann, W.1
  • 6
    • 33748349224 scopus 로고    scopus 로고
    • The role of hydrophobic interactions in initiation and propagation of protein folding
    • H.J. Dyson, P.E. Wright, and H.A. Scheraga The role of hydrophobic interactions in initiation and propagation of protein folding Proc. Natl. Acad. Sci. USA 103 2006 13057 13061
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 13057-13061
    • Dyson, H.J.1    Wright, P.E.2    Scheraga, H.A.3
  • 7
    • 0034612327 scopus 로고    scopus 로고
    • Analysis of a water-mediated protein-protein interaction within RNase T1
    • U. Langhorst, and J. Backmann J. Steyaert Analysis of a water-mediated protein-protein interaction within RNase T1 Biochemistry 39 2000 6586 6593
    • (2000) Biochemistry , vol.39 , pp. 6586-6593
    • Langhorst, U.1    Backmann, J.2    Steyaert, J.3
  • 8
    • 0032757044 scopus 로고    scopus 로고
    • Environmental dependence of the dynamics of protein hydration water
    • M. Tarek, and D. Tobias Environmental dependence of the dynamics of protein hydration water J. Am. Chem. Soc. 121 1999 9740
    • (1999) J. Am. Chem. Soc. , vol.121 , pp. 9740
    • Tarek, M.1    Tobias, D.2
  • 9
    • 0033572790 scopus 로고    scopus 로고
    • Wet and dry interfaces: The role of solvent in protein-protein and protein-DNA recognition
    • J. Janin Wet and dry interfaces: the role of solvent in protein-protein and protein-DNA recognition Structure 7 1999 R277 R279
    • (1999) Structure , vol.7
    • Janin, J.1
  • 10
    • 0342803187 scopus 로고    scopus 로고
    • Modeling cyclooxygenase inhibition. Implication of active site hydration on the selectivity of ketoprofen analogues
    • A. Palomer, and J.J. Pérez D. Mauleón Modeling cyclooxygenase inhibition. Implication of active site hydration on the selectivity of ketoprofen analogues J. Med. Chem. 43 2000 2280 2284
    • (2000) J. Med. Chem. , vol.43 , pp. 2280-2284
    • Palomer, A.1    Pérez, J.J.2    Mauleón, D.3
  • 11
    • 65249155929 scopus 로고    scopus 로고
    • A blind challenge for computational solvation free energies: Introduction and overview
    • J.P. Guthrie A blind challenge for computational solvation free energies: introduction and overview J. Phys. Chem. B 113 2009 4501 4507
    • (2009) J. Phys. Chem. B , vol.113 , pp. 4501-4507
    • Guthrie, J.P.1
  • 12
    • 39749178969 scopus 로고    scopus 로고
    • Predicting small-molecule solvation free energies: An informal blind test for computational chemistry
    • A. Nicholls, and D.L. Mobley V.S. Pande Predicting small-molecule solvation free energies: an informal blind test for computational chemistry J. Med. Chem. 51 2008 769 779
    • (2008) J. Med. Chem. , vol.51 , pp. 769-779
    • Nicholls, A.1    Mobley, D.L.2    Pande, V.S.3
  • 13
    • 0017855698 scopus 로고
    • Interaction of the peptide bond with solvent water: A vapor phase analysis
    • R. Wolfenden Interaction of the peptide bond with solvent water: a vapor phase analysis Biochemistry 17 1978 201 204
    • (1978) Biochemistry , vol.17 , pp. 201-204
    • Wolfenden, R.1
  • 14
    • 0019883174 scopus 로고
    • Affinities of amino acid side chains for solvent water
    • R. Wolfenden, and L. Andersson C.C. Southgate Affinities of amino acid side chains for solvent water Biochemistry 20 1981 849 855
    • (1981) Biochemistry , vol.20 , pp. 849-855
    • Wolfenden, R.1    Andersson, L.2    Southgate, C.C.3
  • 15
    • 0038777517 scopus 로고    scopus 로고
    • Evaluation of methods for measuring amino acid hydrophobicities and interactions
    • K.M. Biswas, D.R. DeVido, and J.G. Dorsey Evaluation of methods for measuring amino acid hydrophobicities and interactions J. Chromatogr. A 1000 2003 637 655
    • (2003) J. Chromatogr. A , vol.1000 , pp. 637-655
    • Biswas, K.M.1    Devido, D.R.2    Dorsey, J.G.3
  • 16
    • 0020475449 scopus 로고
    • A simple method for displaying the hydropathic character of a protein
    • J. Kyte, and R. Doolittle A simple method for displaying the hydropathic character of a protein J. Mol. Biol. 157 1982 105 132
    • (1982) J. Mol. Biol. , vol.157 , pp. 105-132
    • Kyte, J.1    Doolittle, R.2
  • 17
    • 0015755443 scopus 로고
    • Statistical analysis of a series of partition-coefficients with special reference to predictability of folding of drug molecules - Introduction of hydrophobic fragmental constants (F-values)
    • G.G. Nys, and R.F. Rekker Statistical analysis of a series of partition-coefficients with special reference to predictability of folding of drug molecules - introduction of hydrophobic fragmental constants (F-values) Chim. Ther. 8 1973 521 535
    • (1973) Chim. Ther. , vol.8 , pp. 521-535
    • Nys, G.G.1    Rekker, R.F.2
  • 18
    • 0016350063 scopus 로고
    • Concept of hydrophobic fragmental constants (F-values). 2. Extension of its applicability to calculation of lipophilicities of aromatic and heteroaromatic structures
    • G.G. Nys, and R.F. Rekker Concept of hydrophobic fragmental constants (F-values). 2. Extension of its applicability to calculation of lipophilicities of aromatic and heteroaromatic structures Chim. Ther. 9 1974 361 375
    • (1974) Chim. Ther. , vol.9 , pp. 361-375
    • Nys, G.G.1    Rekker, R.F.2
  • 20
    • 0034103896 scopus 로고    scopus 로고
    • The hydrophobic fragmental constant approach for calculating log P in octanol/water and aliphatic hydrocarbon/water systems
    • R. Mannhold, and R.F. Rekker The hydrophobic fragmental constant approach for calculating log P in octanol/water and aliphatic hydrocarbon/water systems Perspect. Drug Discov. Des. 18 2000 1 18
    • (2000) Perspect. Drug Discov. Des. , vol.18 , pp. 1-18
    • Mannhold, R.1    Rekker, R.F.2
  • 21
    • 9944232242 scopus 로고
    • Group contributions to the thermodynamic properties of non-ionic organic solutes in dilute aqueous solution
    • S. Cabani, and P. Gianni L. Lepori Group contributions to the thermodynamic properties of non-ionic organic solutes in dilute aqueous solution J. Solution Chem. 10 1981 563 595
    • (1981) J. Solution Chem. , vol.10 , pp. 563-595
    • Cabani, S.1    Gianni, P.2    Lepori, L.3
  • 22
    • 0031008576 scopus 로고    scopus 로고
    • Hydrophobicity regained
    • P.A. Karplus Hydrophobicity regained Protein Sci. 6 1997 1302 1307
    • (1997) Protein Sci. , vol.6 , pp. 1302-1307
    • Karplus, P.A.1
  • 23
    • 0029094346 scopus 로고
    • Enthalpic contribution to protein stability: Insights from atom-based calculations and statistical mechanics
    • T. Lazaridis, G. Archontis, and M. Karplus Enthalpic contribution to protein stability: insights from atom-based calculations and statistical mechanics Adv. Protein Chem. 47 1995 231 306
    • (1995) Adv. Protein Chem. , vol.47 , pp. 231-306
    • Lazaridis, T.1    Archontis, G.2    Karplus, M.3
  • 24
    • 33645286184 scopus 로고    scopus 로고
    • Limited validity of group additivity for the folding energetics of the peptide group
    • F. Avbelj, and R.L. Baldwin Limited validity of group additivity for the folding energetics of the peptide group Proteins 63 2006 283 289
    • (2006) Proteins , vol.63 , pp. 283-289
    • Avbelj, F.1    Baldwin, R.L.2
  • 25
    • 33745936149 scopus 로고    scopus 로고
    • Thermodynamics of solvation of some small peptides in water at T = 298.15 K
    • G. Della Gatta, and T. Usacheva D. Ichim Thermodynamics of solvation of some small peptides in water at T = 298.15 K J. Chem. Thermodyn. 38 2006 1054 1061
    • (2006) J. Chem. Thermodyn. , vol.38 , pp. 1054-1061
    • Della Gatta, G.1    Usacheva, T.2    Ichim, D.3
  • 26
    • 34447297323 scopus 로고    scopus 로고
    • Energetics of protein folding
    • R.L. Baldwin Energetics of protein folding J. Mol. Biol. 371 2007 283 301
    • (2007) J. Mol. Biol. , vol.371 , pp. 283-301
    • Baldwin, R.L.1
  • 27
    • 0000159569 scopus 로고    scopus 로고
    • Protein structure and the energetics of protein stability
    • A.D. Robertson, and K.P. Murphy Protein structure and the energetics of protein stability Chem. Rev. 97 1997 1251 1268
    • (1997) Chem. Rev. , vol.97 , pp. 1251-1268
    • Robertson, A.D.1    Murphy, K.P.2
  • 28
    • 33645903407 scopus 로고
    • Solvation thermodynamics of nonionic solutes
    • A. Ben-Naim, and Y.J. Marcus 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.J.2
  • 30
    • 0031335428 scopus 로고    scopus 로고
    • Size dependence of solvation Gibbs energies: A critique and a rebuttal of some recent publications
    • A. Ben-Naim, and R. Mazo Size dependence of solvation Gibbs energies: a critique and a rebuttal of some recent publications J. Phys. Chem. B 101 1997 11221 11225
    • (1997) J. Phys. Chem. B , vol.101 , pp. 11221-11225
    • Ben-Naim, A.1    Mazo, R.2
  • 31
    • 0031022887 scopus 로고    scopus 로고
    • Additivity principles in biochemistry
    • K.A. Dill Additivity principles in biochemistry J. Biol. Chem. 272 1997 701 704
    • (1997) J. Biol. Chem. , vol.272 , pp. 701-704
    • Dill, K.A.1
  • 32
    • 67649458222 scopus 로고    scopus 로고
    • Hydration free energies of amino acids: Why side chain analog data are not enough
    • G. König, and S. Boresch Hydration free energies of amino acids: why side chain analog data are not enough J. Phys. Chem. B 113 2009 8967 8974
    • (2009) J. Phys. Chem. B , vol.113 , pp. 8967-8974
    • König, G.1    Boresch, S.2
  • 33
    • 0015222647 scopus 로고
    • The interpretation of protein structures: Estimation of static accessibility
    • B. Lee, and F.M. Richards The interpretation of protein structures: estimation of static accessibility J. Mol. Biol. 55 1971 379 400
    • (1971) J. Mol. Biol. , vol.55 , pp. 379-400
    • Lee, B.1    Richards, F.M.2
  • 34
    • 0011930746 scopus 로고
    • Theory of hydrophobic bonding. II. The correlation of hydrocarbon solubility in water with cavity surface area
    • R.B. Hermann Theory of hydrophobic bonding. II. The correlation of hydrocarbon solubility in water with cavity surface area J. Phys. Chem. 76 1972 2754 2759
    • (1972) J. Phys. Chem. , vol.76 , pp. 2754-2759
    • Hermann, R.B.1
  • 35
    • 0016352763 scopus 로고
    • Hydrophobic bonding and accessible surface area in proteins
    • C. Chothia Hydrophobic bonding and accessible surface area in proteins Nature 248 1974 338 339
    • (1974) Nature , vol.248 , pp. 338-339
    • Chothia, C.1
  • 36
    • 0000398347 scopus 로고
    • Empirical correlation between hydrophobic free energy and aqueous cavity surface area
    • J.A. Reynolds, D.B. Gilbert, and C. Tanford Empirical correlation between hydrophobic free energy and aqueous cavity surface area Proc. Natl. Acad. Sci. USA 71 1974 2925 2927
    • (1974) Proc. Natl. Acad. Sci. USA , vol.71 , pp. 2925-2927
    • Reynolds, J.A.1    Gilbert, D.B.2    Tanford, C.3
  • 37
    • 0023338543 scopus 로고
    • Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides
    • T. Ooi, and M. Oobatake H.A. Scheraga Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides Proc. Natl. Acad. Sci. USA 84 1987 3086 3090
    • (1987) Proc. Natl. Acad. Sci. USA , vol.84 , pp. 3086-3090
    • Ooi, T.1    Oobatake, M.2    Scheraga, H.A.3
  • 38
    • 0027080909 scopus 로고
    • Atomic solvation parameters applied to molecular dynamics of proteins in solution
    • L. Wesson, and D. Eisenberg Atomic solvation parameters applied to molecular dynamics of proteins in solution Protein Sci. 1 1992 227 235
    • (1992) Protein Sci. , vol.1 , pp. 227-235
    • Wesson, L.1    Eisenberg, D.2
  • 40
    • 0022596727 scopus 로고
    • Solvation energy in protein folding and binding
    • D. Eisenberg, and A.D. McLachlan Solvation energy in protein folding and binding Nature 319 1986 199 203
    • (1986) Nature , vol.319 , pp. 199-203
    • Eisenberg, D.1    McLachlan, A.D.2
  • 41
    • 0033135638 scopus 로고    scopus 로고
    • Effective energy function for proteins in solution
    • T. Lazaridis, and M. Karplus Effective energy function for proteins in solution Proteins 35 1999 133 152
    • (1999) Proteins , vol.35 , pp. 133-152
    • Lazaridis, T.1    Karplus, M.2
  • 42
    • 0036138028 scopus 로고    scopus 로고
    • Evaluation of a fast implicit solvent model for molecular dynamics simulations
    • P. Ferrara, J. Apostolakis, and A. Caflisch Evaluation of a fast implicit solvent model for molecular dynamics simulations Proteins 46 2002 24 33
    • (2002) Proteins , vol.46 , pp. 24-33
    • Ferrara, P.1    Apostolakis, J.2    Caflisch, A.3
  • 43
    • 0019780781 scopus 로고
    • Measurement of correlation of partition coefficients of polar amino acids
    • L.M. Yunger, and R.D. Cramer 3rd Measurement of correlation of partition coefficients of polar amino acids Mol. Pharmacol. 20 1981 602 608
    • (1981) Mol. Pharmacol. , vol.20 , pp. 602-608
    • Yunger, L.M.1    Cramer III, R.D.2
  • 44
    • 0024278357 scopus 로고
    • Hydrophilicity of polar amino acid side-chains is markedly reduced by flanking peptide bonds
    • M.A. Roseman Hydrophilicity of polar amino acid side-chains is markedly reduced by flanking peptide bonds J. Mol. Biol. 200 1988 513 522
    • (1988) J. Mol. Biol. , vol.200 , pp. 513-522
    • Roseman, M.A.1
  • 45
    • 33947405744 scopus 로고    scopus 로고
    • Solvation free energy of amino acids and side-chain analogues
    • J. Chang, A.M. Lenhoff, and S.I. Sandler Solvation free energy of amino acids and side-chain analogues J. Phys. Chem. B 111 2007 2098 2106
    • (2007) J. Phys. Chem. B , vol.111 , pp. 2098-2106
    • Chang, J.1    Lenhoff, A.M.2    Sandler, S.I.3
  • 46
    • 0141990949 scopus 로고    scopus 로고
    • Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins
    • M.R. Shirts, and J.W. Pitera V.S. Pande Extremely precise free energy calculations of amino acid side chain analogs: comparison of common molecular mechanics force fields for proteins J. Chem. Phys. 119 2003 5740 5761
    • (2003) J. Chem. Phys. , vol.119 , pp. 5740-5761
    • Shirts, M.R.1    Pitera, J.W.2    Pande, V.S.3
  • 47
    • 84867344848 scopus 로고    scopus 로고
    • New interaction parameters for charged amino acid side chains in the GROMOS force field
    • 10.1021/ct300156h
    • M. Reif, P. Hünenberger, and C. Oostenbrink New interaction parameters for charged amino acid side chains in the GROMOS force field J. Chem. Theory Comput. 2012 10.1021/ct300156h
    • (2012) J. Chem. Theory Comput.
    • Reif, M.1    Hünenberger, P.2    Oostenbrink, C.3
  • 48
    • 0021582448 scopus 로고
    • Ligand-receptor interactions
    • B.L. Tembe, and J.A. McCammon Ligand-receptor interactions Comput. Chem. 8 1984 281 283
    • (1984) Comput. Chem. , vol.8 , pp. 281-283
    • Tembe, B.L.1    McCammon, J.A.2
  • 50
    • 84986512474 scopus 로고
    • CHARMM: A program for macromolecular energy, minimization and dynamics calculations
    • B.R. Brooks, and R.E. Bruccoleri M. Karplus CHARMM: a program for macromolecular energy, minimization and dynamics calculations J. Comput. Chem. 4 1983 187 217
    • (1983) J. Comput. Chem. , vol.4 , pp. 187-217
    • Brooks, B.R.1    Bruccoleri, R.E.2    Karplus, M.3
  • 51
    • 0041784950 scopus 로고    scopus 로고
    • All-atom empirical potential for molecular modeling and dynamics studies of protein
    • A.D. MacKerell Jr., and D. Bashford M. Karplus All-atom empirical potential for molecular modeling and dynamics studies of protein J. Phys. Chem. B 102 1998 3586 3616
    • (1998) J. Phys. Chem. B , vol.102 , pp. 3586-3616
    • MacKerell Jr., A.D.1    Bashford, D.2    Karplus, M.3
  • 52
    • 3142714765 scopus 로고    scopus 로고
    • Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
    • A.D. MacKerell Jr., M. Feig, and C.L. Brooks 3rd Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations J. Comput. Chem. 25 2004 1400 1415
    • (2004) J. Comput. Chem. , vol.25 , pp. 1400-1415
    • MacKerell Jr., A.D.1    Feig, M.2    Brooks III, C.L.3
  • 53
    • 5244304444 scopus 로고
    • Efficient estimation of free energy differences from Monte Carlo data
    • C.H. Bennett Efficient estimation of free energy differences from Monte Carlo data J. Comput. Phys. 22 1976 245 268
    • (1976) J. Comput. Phys. , vol.22 , pp. 245-268
    • Bennett, C.H.1
  • 54
    • 33646471468 scopus 로고
    • Statistical mechanics of fluid mixtures
    • J.G. Kirkwood Statistical mechanics of fluid mixtures J. Chem. Phys. 3 1935 300 313
    • (1935) J. Chem. Phys. , vol.3 , pp. 300-313
    • Kirkwood, J.G.1
  • 55
    • 0004016501 scopus 로고
    • Comparison of simple potential functions for simulating liquid water
    • W.L. Jorgensen, and H. Chandrasekhar M.L. Klein Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 79 1983 926
    • (1983) J. Chem. Phys. , vol.79 , pp. 926
    • Jorgensen, W.L.1    Chandrasekhar, H.2    Klein, M.L.3
  • 56
    • 0000036869 scopus 로고    scopus 로고
    • Simulation of activation free energies in molecular systems
    • E. Neria, S. Fischer, and M. Karplus Simulation of activation free energies in molecular systems J. Chem. Phys. 105 1996 1902
    • (1996) J. Chem. Phys. , vol.105 , pp. 1902
    • Neria, E.1    Fischer, S.2    Karplus, M.3
  • 57
    • 0041878923 scopus 로고    scopus 로고
    • Modeling induced polarization with classical Drude oscillators: Theory and molecular dynamics simulation algorithm
    • G. Lamoureux, and B. Roux Modeling induced polarization with classical Drude oscillators: theory and molecular dynamics simulation algorithm J. Chem. Phys. 119 2003 3025 3039
    • (2003) J. Chem. Phys. , vol.119 , pp. 3025-3039
    • Lamoureux, G.1    Roux, B.2
  • 58
    • 0001538909 scopus 로고
    • Canonical dynamics: Equilibrium phase-space distributions
    • W.G. Hoover Canonical dynamics: equilibrium phase-space distributions Phys. Rev. A 31 1985 1695 1697
    • (1985) Phys. Rev. A , vol.31 , pp. 1695-1697
    • Hoover, W.G.1
  • 59
    • 84946450438 scopus 로고
    • Algorithms for macromolecular dynamics and constraint dynamics
    • W.F. van Gunsteren, and H.J.C. Berendsen Algorithms for macromolecular dynamics and constraint dynamics Mol. Phys. 34 1977 1311 1327
    • (1977) Mol. Phys. , vol.34 , pp. 1311-1327
    • Van Gunsteren, W.F.1    Berendsen, H.J.C.2
  • 61
    • 79952501515 scopus 로고    scopus 로고
    • Non-Boltzmann Sampling and Bennett's acceptance ratio method: How free energy simulations can profit from bending the rules
    • 10.1002/jcc.21687 Early View
    • G. König, and S. Boresch Non-Boltzmann Sampling and Bennett's acceptance ratio method: how free energy simulations can profit from bending the rules J. Comput. Chem. 2010 10.1002/jcc.21687 Early View
    • (2010) J. Comput. Chem.
    • König, G.1    Boresch, S.2
  • 62
    • 47149096704 scopus 로고    scopus 로고
    • CHARMM-GUI: A web-based graphical user interface for CHARMM
    • S. Jo, and T. Kim W. Im CHARMM-GUI: a web-based graphical user interface for CHARMM J. Comput. Chem. 29 2008 1859 1865
    • (2008) J. Comput. Chem. , vol.29 , pp. 1859-1865
    • Jo, S.1    Kim, T.2    Im, W.3
  • 63
    • 0037089015 scopus 로고    scopus 로고
    • Calculation of the free energy of solvation for neutral analogs of amino acid side chains
    • A. Villa, and A.E. Mark Calculation of the free energy of solvation for neutral analogs of amino acid side chains J. Comput. Chem. 23 2002 548 553
    • (2002) J. Comput. Chem. , vol.23 , pp. 548-553
    • Villa, A.1    Mark, A.E.2
  • 64
    • 7544232432 scopus 로고    scopus 로고
    • Hydration of amino acid side chains: Nonpolar and electrostatic contributions calculated from staged molecular dynamics free energy simulations with explicit water molecules
    • Y.Q. Deng, and B. Roux Hydration of amino acid side chains: nonpolar and electrostatic contributions calculated from staged molecular dynamics free energy simulations with explicit water molecules J. Phys. Chem. B 108 2004 16567 16576
    • (2004) J. Phys. Chem. B , vol.108 , pp. 16567-16576
    • Deng, Y.Q.1    Roux, B.2
  • 65
    • 33947397110 scopus 로고    scopus 로고
    • Comparison of charge models for fixed-charge force fields: Small-molecule hydration free energies in explicit solvent
    • D.L. Mobley, and E. Dumont K.A. Dill Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent J. Phys. Chem. B 111 2007 2242 2254
    • (2007) J. Phys. Chem. B , vol.111 , pp. 2242-2254
    • Mobley, D.L.1    Dumont, E.2    Dill, K.A.3
  • 66
    • 84872806468 scopus 로고    scopus 로고
    • Reference deleted in proof
    • Reference deleted in proof.
  • 67
    • 65249187748 scopus 로고    scopus 로고
    • Small molecule hydration free energies in explicit solvent: An extensive test of fixed-charge atomistic simulations
    • D.L. Mobley, and C.I. Bayly K.A. Dill Small molecule hydration free energies in explicit solvent: an extensive test of fixed-charge atomistic simulations J. Chem. Theory Comput. 5 2009 350 358
    • (2009) J. Chem. Theory Comput. , vol.5 , pp. 350-358
    • Mobley, D.L.1    Bayly, C.I.2    Dill, K.A.3
  • 68
    • 27144466024 scopus 로고    scopus 로고
    • Are solvation free energies of homogeneous helical peptides additive?
    • R. Staritzbichler, W. Gu, and V. Helms Are solvation free energies of homogeneous helical peptides additive? J. Phys. Chem. B 109 2005 19000 19007
    • (2005) J. Phys. Chem. B , vol.109 , pp. 19000-19007
    • Staritzbichler, R.1    Gu, W.2    Helms, V.3
  • 69
    • 77952786853 scopus 로고    scopus 로고
    • Protein thermostability calculations using alchemical free energy simulations
    • D. Seeliger, and B.L. de Groot Protein thermostability calculations using alchemical free energy simulations Biophys. J. 98 2010 2309 2316
    • (2010) Biophys. J. , vol.98 , pp. 2309-2316
    • Seeliger, D.1    De Groot, B.L.2
  • 70
    • 0030777402 scopus 로고    scopus 로고
    • Modeling protein stability: A theoretical analysis of the stability of T4 lysozyme mutants
    • D.L. Veenstra, and P.A. Kollman Modeling protein stability: a theoretical analysis of the stability of T4 lysozyme mutants Protein Eng. 10 1997 789 807
    • (1997) Protein Eng. , vol.10 , pp. 789-807
    • Veenstra, D.L.1    Kollman, P.A.2
  • 71
    • 1542297762 scopus 로고    scopus 로고
    • Solvation in protein folding analysis: Combination of theoretical and experimental approaches
    • A.M. Fernández-Escamilla, and M.S. Cheung L. Serrano Solvation in protein folding analysis: combination of theoretical and experimental approaches Proc. Natl. Acad. Sci. USA 101 2004 2834 2839
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 2834-2839
    • Fernández-Escamilla, A.M.1    Cheung, M.S.2    Serrano, L.3
  • 72
    • 0027485997 scopus 로고
    • Energetic cost and structural consequences of burying a hydroxyl group within the core of a protein determined from Ala→Ser and Val→Thr substitutions in T4 lysozyme
    • M. Blaber, and J.D. Lindstrom B.W. Matthews Energetic cost and structural consequences of burying a hydroxyl group within the core of a protein determined from Ala→Ser and Val→Thr substitutions in T4 lysozyme Biochemistry 32 1993 11363 11373
    • (1993) Biochemistry , vol.32 , pp. 11363-11373
    • Blaber, M.1    Lindstrom, J.D.2    Matthews, B.W.3
  • 73
    • 0027371147 scopus 로고
    • Intestinal fatty acid binding protein: Characterization of mutant proteins containing inserted cysteine residues
    • N. Jiang, and C. Frieden Intestinal fatty acid binding protein: characterization of mutant proteins containing inserted cysteine residues Biochemistry 32 1993 11015 11021
    • (1993) Biochemistry , vol.32 , pp. 11015-11021
    • Jiang, N.1    Frieden, C.2
  • 74
    • 0026613604 scopus 로고
    • Phospholipase A2 engineering. The structural and functional roles of aromaticity and hydrophobicity in the conserved phenylalanine-22 and phenylalanine-106 aromatic sandwich
    • C.M. Dupureur, and B.Z. Yu M.D. Tsai Phospholipase A2 engineering. The structural and functional roles of aromaticity and hydrophobicity in the conserved phenylalanine-22 and phenylalanine-106 aromatic sandwich Biochemistry 31 1992 10576 10583
    • (1992) Biochemistry , vol.31 , pp. 10576-10583
    • Dupureur, C.M.1    Yu, B.Z.2    Tsai, M.D.3
  • 75
    • 33644874615 scopus 로고    scopus 로고
    • ProTherm and ProNIT: Thermodynamic databases for proteins and protein-nucleic acid interactions
    • M.D.S. Kumar, and K.A. Bava A. Sarai ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions Nucleic Acids Res. 34 Database issue 2006 D204 D206
    • (2006) Nucleic Acids Res. , vol.34 , Issue.DATABASE ISSUE
    • Kumar, M.D.S.1    Bava, K.A.2    Sarai, A.3
  • 76
    • 77749298172 scopus 로고    scopus 로고
    • Current status of the AMOEBA polarizable force field
    • J.W. Ponder, and C. Wu T. Head-Gordon Current status of the AMOEBA polarizable force field J. Phys. Chem. B 114 2010 2549 2564
    • (2010) J. Phys. Chem. B , vol.114 , pp. 2549-2564
    • Ponder, J.W.1    Wu, C.2    Head-Gordon, T.3
  • 77
    • 77952415408 scopus 로고    scopus 로고
    • Prediction of absolute solvation free energies using molecular dynamics free energy perturbation and the OPLS force field
    • D. Shivakumar, and J. Williams W. Sherman Prediction of absolute solvation free energies using molecular dynamics free energy perturbation and the OPLS force field J. Chem. Theory Comput. 6 2010 1509 1519
    • (2010) J. Chem. Theory Comput. , vol.6 , pp. 1509-1519
    • Shivakumar, D.1    Williams, J.2    Sherman, W.3
  • 79
    • 1942456697 scopus 로고    scopus 로고
    • Recent advances in the development and application of implicit solvent models in biomolecule simulations
    • M. Feig, and C.L. Brooks 3rd Recent advances in the development and application of implicit solvent models in biomolecule simulations Curr. Opin. Struct. Biol. 14 2004 217 224
    • (2004) Curr. Opin. Struct. Biol. , vol.14 , pp. 217-224
    • Feig, M.1    Brooks III, C.L.2
  • 80
    • 41949100049 scopus 로고    scopus 로고
    • Recent advances in implicit solvent-based methods for biomolecular simulations
    • J. Chen, C.L. Brooks 3rd, and J. Khandogin Recent advances in implicit solvent-based methods for biomolecular simulations Curr. Opin. Struct. Biol. 18 2008 140 148
    • (2008) Curr. Opin. Struct. Biol. , vol.18 , pp. 140-148
    • Chen, J.1    Brooks III, C.L.2    Khandogin, J.3
  • 81
    • 0038792211 scopus 로고    scopus 로고
    • New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations
    • M.S. Lee, and M. Feig C.L. Brooks 3rd New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations J. Comput. Chem. 24 2003 1348 1356
    • (2003) J. Comput. Chem. , vol.24 , pp. 1348-1356
    • Lee, M.S.1    Feig, M.2    Brooks III, C.L.3
  • 82
    • 0141956090 scopus 로고    scopus 로고
    • Generalized Born model with a simple smoothing function
    • W. Im, M.S. Lee, and C.L. Brooks 3rd Generalized Born model with a simple smoothing function J. Comput. Chem. 24 2003 1691 1702
    • (2003) J. Comput. Chem. , vol.24 , pp. 1691-1702
    • Im, W.1    Lee, M.S.2    Brooks III, C.L.3
  • 83
    • 40549111613 scopus 로고    scopus 로고
    • FACTS: Fast analytical continuum treatment of solvation
    • U. Haberthür, and A. Caflisch FACTS: Fast analytical continuum treatment of solvation J. Comput. Chem. 29 2008 701 715
    • (2008) J. Comput. Chem. , vol.29 , pp. 701-715
    • Haberthür, U.1    Caflisch, A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.