메뉴 건너뛰기




Volumn 38, Issue 2, 2000, Pages 176-188

Continuum electrostatic analysis of preferred solvation sites around proteins in solution

Author keywords

Poisson Boltzmann electrostatics; Solvation free energy; T4 lysozyme; Water residence time

Indexed keywords

ARTICLE; BINDING SITE; CRYSTAL STRUCTURE; ELECTROSTATIC PRECIPITATION; ENZYME ACTIVITY; LIGAND BINDING; MACROMOLECULE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN PROTEIN INTERACTION; SOLVATION; X RAY CRYSTALLOGRAPHY;

EID: 0034141811     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(20000201)38:2<176::AID-PROT6>3.0.CO;2-O     Document Type: Article
Times cited : (17)

References (41)
  • 2
    • 0025896727 scopus 로고
    • Water-protein interactions: Theory and experiment
    • Teeter MM. Water-protein interactions: theory and experiment. Annu Rev Biophys Biophys Chem 1991;20:577-600.
    • (1991) Annu Rev Biophys Biophys Chem , vol.20 , pp. 577-600
    • Teeter, M.M.1
  • 3
    • 0027918556 scopus 로고
    • Water: Now you see it, now you don't
    • Levitt M, Park B. Water: now you see it, now you don't. Structure 1993;1:223-226.
    • (1993) Structure , vol.1 , pp. 223-226
    • Levitt, M.1    Park, B.2
  • 4
    • 0029868304 scopus 로고    scopus 로고
    • Locating and characterizing binding sites on proteins
    • Mattos C, Ringe D. Locating and characterizing binding sites on proteins. Nat Biotechnol 1996;14:595-599.
    • (1996) Nat Biotechnol , vol.14 , pp. 595-599
    • Mattos, C.1    Ringe, D.2
  • 5
    • 0026326956 scopus 로고
    • Protein hydration in aqueous solution
    • Otting G, Liepinsh E, Wuthrich K. Protein hydration in aqueous solution. Science 1991;254:974-980.
    • (1991) Science , vol.254 , pp. 974-980
    • Otting, G.1    Liepinsh, E.2    Wuthrich, K.3
  • 6
    • 0027977445 scopus 로고
    • NMR studies of protein hydration
    • Belton PS. NMR studies of protein hydration. Prog Biophys Mol Biol 1994;61:61-79.
    • (1994) Prog Biophys Mol Biol , vol.61 , pp. 61-79
    • Belton, P.S.1
  • 7
    • 0026547998 scopus 로고
    • Solvent structure in crystals of trypsin determined by X-ray and neutron diffraction
    • Finer-Moore JS, Kosiakoff AA, Hurley JH, Earnest T, Stroud RM. Solvent structure in crystals of trypsin determined by X-ray and neutron diffraction. Proteins 1992;12:203-222.
    • (1992) Proteins , vol.12 , pp. 203-222
    • Finer-Moore, J.S.1    Kosiakoff, A.A.2    Hurley, J.H.3    Earnest, T.4    Stroud, R.M.5
  • 8
    • 0024278949 scopus 로고
    • Distribution of water around amino acid residues in proteins
    • Thanki N, Thornton JM, Goodfellow JM. Distribution of water around amino acid residues in proteins. J Mol Biol 1988;202:637-657.
    • (1988) J Mol Biol , vol.202 , pp. 637-657
    • Thanki, N.1    Thornton, J.M.2    Goodfellow, J.M.3
  • 9
    • 0024094768 scopus 로고
    • Accurate simulation of protein dynamics in solution
    • Levitt M, Sharon R. Accurate simulation of protein dynamics in solution. Proc Natl Acad Sci USA 1988;85:7557-7561.
    • (1988) Proc Natl Acad Sci USA , vol.85 , pp. 7557-7561
    • Levitt, M.1    Sharon, R.2
  • 10
    • 0024354001 scopus 로고
    • Solvent effects on protein motion, and protein effects on solvent motion. Dynamics of the active site region of lysozyme
    • Brooks CL, Karplus M. Solvent effects on protein motion, and protein effects on solvent motion. Dynamics of the active site region of lysozyme. J Mol Biol 1989;208:159-181.
    • (1989) J Mol Biol , vol.208 , pp. 159-181
    • Brooks, C.L.1    Karplus, M.2
  • 11
    • 0027211701 scopus 로고
    • A molecular dynamics study of solvent behavior around a protein
    • Komeiji Y, Uebayasi M, Someya J, Yamato I. A molecular dynamics study of solvent behavior around a protein. Proteins 1993;16: 268-277.
    • (1993) Proteins , vol.16 , pp. 268-277
    • Komeiji, Y.1    Uebayasi, M.2    Someya, J.3    Yamato, I.4
  • 12
    • 0027304152 scopus 로고
    • Hydration of proteins. A comparison of experimental residence times of water molecules solvating the bovine pancreatic trypsin inhibitor with theoretical model calculations
    • Brunne RM, Liepinsh E, Otting G, Wuthrich K, van Gunsteren WF. Hydration of proteins. A comparison of experimental residence times of water molecules solvating the bovine pancreatic trypsin inhibitor with theoretical model calculations. J Mol Biol 1993;231:1040-1048.
    • (1993) J Mol Biol , vol.231 , pp. 1040-1048
    • Brunne, R.M.1    Liepinsh, E.2    Otting, G.3    Wuthrich, K.4    Van Gunsteren, W.F.5
  • 13
    • 0028144626 scopus 로고
    • A connected-cluster of hydration around myoglobin: Correlation between molecular dynamics simulations and experiments
    • Lounnas V, Pettitt BM. A connected-cluster of hydration around myoglobin: correlation between molecular dynamics simulations and experiments. Proteins 1994;18:133-147.
    • (1994) Proteins , vol.18 , pp. 133-147
    • Lounnas, V.1    Pettitt, B.M.2
  • 14
    • 0027957222 scopus 로고
    • Distribution function implied dynamics versus residence times and correlations: Solvation shells of myoglobin
    • Lounnas V, Pettitt BM. Distribution function implied dynamics versus residence times and correlations: solvation shells of myoglobin. Proteins 1994;18:148-160.
    • (1994) Proteins , vol.18 , pp. 148-160
    • Lounnas, V.1    Pettitt, B.M.2
  • 15
    • 0030605451 scopus 로고    scopus 로고
    • Analysis of interfacial water structure, and dynamics in an a-maltose solution by molecular dynamics simulation
    • Wang CX, Chen WZ, Tran V, Douillard R. Analysis of interfacial water structure, and dynamics in an a-maltose solution by molecular dynamics simulation. Chem Phys Lett 1996;251:268-274.
    • (1996) Chem Phys Lett , vol.251 , pp. 268-274
    • Wang, C.X.1    Chen, W.Z.2    Tran, V.3    Douillard, R.4
  • 16
    • 0031568141 scopus 로고    scopus 로고
    • Water residence times around copper plastocyanin: A molecular dynamics simulation approach
    • Rocchi C, Bizarri AR, Cannistraro S. Water residence times around copper plastocyanin: a molecular dynamics simulation approach. J Chem Phys 1997;214:261-276.
    • (1997) J Chem Phys , vol.214 , pp. 261-276
    • Rocchi, C.1    Bizarri, A.R.2    Cannistraro, S.3
  • 17
    • 0031807764 scopus 로고    scopus 로고
    • Diffusion of solvent around biomolecular solutes: A molecular dynamics simulation study
    • Makarov VA, Feig M, Andrews BK, Pettitt BM. Diffusion of solvent around biomolecular solutes: a molecular dynamics simulation study. Biophys J 1998;75:150-158.
    • (1998) Biophys J , vol.75 , pp. 150-158
    • Makarov, V.A.1    Feig, M.2    Andrews, B.K.3    Pettitt, B.M.4
  • 18
    • 0026498010 scopus 로고
    • The interdependence of protein surface topography and bound water molecules revealed by surface accessibility and fractal density measures
    • Kuhn LA, Siani MA, Pique ME, Fisher CL, Getzoff ED, Tainer JA. The interdependence of protein surface topography and bound water molecules revealed by surface accessibility and fractal density measures. J Mol Biol 1992;228:13-22.
    • (1992) J Mol Biol , vol.228 , pp. 13-22
    • Kuhn, L.A.1    Siani, M.A.2    Pique, M.E.3    Fisher, C.L.4    Getzoff, E.D.5    Tainer, J.A.6
  • 19
    • 0028341789 scopus 로고
    • Conservation of solvent-binding sites in 10 crystals of T4 lysozyme
    • Zhang XJ, Matthews JW. Conservation of solvent-binding sites in 10 crystals of T4 lysozyme. Protein Sci 1994;3:1031-1039.
    • (1994) Protein Sci , vol.3 , pp. 1031-1039
    • Zhang, X.J.1    Matthews, J.W.2
  • 20
    • 0031762253 scopus 로고    scopus 로고
    • Cluster analysis of consensus water sites in thrombin and trypsin shows conservation between serine proteases and contributions to ligand specificity
    • Sanschagrin PC, Kuhn LA. Cluster analysis of consensus water sites in thrombin and trypsin shows conservation between serine proteases and contributions to ligand specificity. Protein Sci 1998;7:2054-2064.
    • (1998) Protein Sci , vol.7 , pp. 2054-2064
    • Sanschagrin, P.C.1    Kuhn, L.A.2
  • 21
    • 0023779259 scopus 로고
    • Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis
    • Gilson MK, Honig B. Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis. Proteins 1988;4:7-18.
    • (1988) Proteins , vol.4 , pp. 7-18
    • Gilson, M.K.1    Honig, B.2
  • 22
    • 0029016182 scopus 로고
    • Classical electrostatics in biology and chemistry
    • Honig B, Nicholls A. Classical electrostatics in biology and chemistry. Science 1995;268:1144-1149.
    • (1995) Science , vol.268 , pp. 1144-1149
    • Honig, B.1    Nicholls, A.2
  • 23
    • 0000915619 scopus 로고
    • Grid positioning independence and the reduction of self - Energy in the solution of the poisson - Boltzmann equation
    • Bruccoleri RE. Grid positioning independence and the reduction of self - energy in the solution of the Poisson - Boltzmann equation. J Comp Chem 1993;14:1417-1422.
    • (1993) J Comp Chem , vol.14 , pp. 1417-1422
    • Bruccoleri, R.E.1
  • 24
    • 0029975683 scopus 로고    scopus 로고
    • Free energy mapping of class I MHC molecules and structural determination of bound peptides
    • Sezerman OU, Vajda S, DeLisi C. Free energy mapping of class I MHC molecules and structural determination of bound peptides. Protein Sci 1996;5:1272-1281.
    • (1996) Protein Sci , vol.5 , pp. 1272-1281
    • Sezerman, O.U.1    Vajda, S.2    DeLisi, C.3
  • 25
    • 0032981961 scopus 로고    scopus 로고
    • Free energy landscapes of encounter complexes in protein-protein association
    • Camacho CJ, Weng Z, Vajda S, DeLisi C. Free energy landscapes of encounter complexes in protein-protein association. Biophys J 1999;76:1176-1178.
    • (1999) Biophys J , vol.76 , pp. 1176-1178
    • Camacho, C.J.1    Weng, Z.2    Vajda, S.3    DeLisi, C.4
  • 26
    • 0004016501 scopus 로고
    • Comparison of simple potential functions for simulating liquid water
    • Jorgensen WL, Chandrasekhar J, Madura JD. Comparison of simple potential functions for simulating liquid water. J Chem Phys 1983;79:926-935.
    • (1983) J Chem Phys , vol.79 , pp. 926-935
    • Jorgensen, W.L.1    Chandrasekhar, J.2    Madura, J.D.3
  • 27
    • 0342440289 scopus 로고
    • Optimization
    • New York: John Wiley and Sons
    • Rao SS. Optimization. Theory and applications. New York: John Wiley and Sons; 1978.
    • (1978) Theory and Applications
    • Rao, S.S.1
  • 30
    • 0028102849 scopus 로고
    • Effect of conformational flexibility and solvation on receptor-ligand binding free energies
    • Vajda S, Weng Z, Rosenfeld R, DeLisi C. Effect of conformational flexibility and solvation on receptor-ligand binding free energies. Biochemistry 1994;33:13977-13988.
    • (1994) Biochemistry , vol.33 , pp. 13977-13988
    • Vajda, S.1    Weng, Z.2    Rosenfeld, R.3    DeLisi, C.4
  • 31
    • 0028228418 scopus 로고
    • The entropic cost of bound water in crystals and biomolecules
    • Dunitz JD. The entropic cost of bound water in crystals and biomolecules. Science 1994;264:670-670.
    • (1994) Science , vol.264 , pp. 670-670
    • Dunitz, J.D.1
  • 32
    • 0030917908 scopus 로고    scopus 로고
    • Loss of translational entropy in binding, folding, and catalysis
    • Amzel LM. Loss of translational entropy in binding, folding, and catalysis. Proteins 1997;28:144-149.
    • (1997) Proteins , vol.28 , pp. 144-149
    • Amzel, L.M.1
  • 33
    • 0029937870 scopus 로고    scopus 로고
    • Hydrophilicity of cavities in proteins
    • Zhang L, Hermans J. Hydrophilicity of cavities in proteins. Proteins 1996;24:433-438.
    • (1996) Proteins , vol.24 , pp. 433-438
    • Zhang, L.1    Hermans, J.2
  • 34
    • 0029757992 scopus 로고    scopus 로고
    • Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: A molecular dynamics free energy perturbation study
    • Roux B, Nina M, Pomes R, Smith JC. Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: a molecular dynamics free energy perturbation study. Biophys J 1996;71: 670-681.
    • (1996) Biophys J , vol.71 , pp. 670-681
    • Roux, B.1    Nina, M.2    Pomes, R.3    Smith, J.C.4
  • 35
    • 0022596727 scopus 로고
    • Solvation energy in protein folding and binding
    • Eisenberg D, McLachlan AD. Solvation energy in protein folding and binding. Nature 1986;319:199-203.
    • (1986) Nature , vol.319 , pp. 199-203
    • Eisenberg, D.1    McLachlan, A.D.2
  • 36
    • 0029414725 scopus 로고
    • Extracting hydrophobicity parameters from solute partition and protein mutation/unfolding experiments
    • Vajda S, Weng Z., DeLisi C, Extracting hydrophobicity parameters from solute partition and protein mutation/unfolding experiments. Protein Eng 1995;8:1081-1092.
    • (1995) Protein Eng , vol.8 , pp. 1081-1092
    • Vajda, S.1    Weng, Z.2    DeLisi, C.3
  • 37
    • 0000374395 scopus 로고
    • Effects of diffusion rates on chemical kinetics
    • Noyes RM. Effects of diffusion rates on chemical kinetics. Prog React Kinet 1961;1:129-160.
    • (1961) Prog React Kinet , vol.1 , pp. 129-160
    • Noyes, R.M.1
  • 38
    • 0037879754 scopus 로고    scopus 로고
    • Exploring potential solvation sites of proteins by multistart local minimization
    • Floudas CA, Pardalos PM, editors. Norwell, MA: Kluwer Academic
    • Dennis S, Camacho CJ, Vajda S. Exploring potential solvation sites of proteins by multistart local minimization. In: Floudas CA, Pardalos PM, editors. Otimization in Computational Chemistry and Molecular Biology. Norwell, MA: Kluwer Academic; 2000.
    • (2000) Otimization in Computational Chemistry and Molecular Biology
    • Dennis, S.1    Camacho, C.J.2    Vajda, S.3
  • 39
    • 0000238336 scopus 로고
    • A simplex method for function minimization
    • Nelder JA, Mead R. A simplex method for function minimization. Computer J 1964;7:308-313.
    • (1964) Computer J , vol.7 , pp. 308-313
    • Nelder, J.A.1    Mead, R.2
  • 40
    • 0029868304 scopus 로고    scopus 로고
    • Locating and characterizing binding sites on proteins
    • Mattos C, Ringe D. Locating and characterizing binding sites on proteins. Nat Biotech 1996;14:595-599.
    • (1996) Nat Biotech , vol.14 , pp. 595-599
    • Mattos, C.1    Ringe, D.2
  • 41
    • 0030965629 scopus 로고    scopus 로고
    • Organic solvents identify specific ligand binding sites of protein surfaces
    • Liepinsh E, Otting G. Organic solvents identify specific ligand binding sites of protein surfaces. Nat Biotech 1997;15:264-268.
    • (1997) Nat Biotech , vol.15 , pp. 264-268
    • Liepinsh, E.1    Otting, G.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.