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Volumn 27, Issue 4, 1997, Pages 576-596

Self-consistent field approach to protein structure and stability. I: pH dependence of electrostatic contribution

Author keywords

free energy minimization; local dielectric constant; local packing density; molecular field theory; titration curves

Indexed keywords

APROTININ; LYSOZYME; RIBONUCLEASE A; RIBONUCLEASE T1; SUBTILISIN;

EID: 0030970306     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(199704)27:4<576::AID-PROT10>3.0.CO;2-H     Document Type: Article
Times cited : (20)

References (63)
  • 2
    • 0025271463 scopus 로고
    • pH Dependence of the urea and guanidine hydrochloride denaturation of ribonuclease a and ribonuclease T1
    • Pace, C.N., Laurents, D.V., Thomson, J.A. pH Dependence of the urea and guanidine hydrochloride denaturation of ribonuclease A and ribonuclease T1. Biochemistry 29:2564-2572, 1990.
    • (1990) Biochemistry , vol.29 , pp. 2564-2572
    • Pace, C.N.1    Laurents, D.V.2    Thomson, J.A.3
  • 4
    • 0024086838 scopus 로고
    • A theoretical study of the dielectric constant of protein
    • Nakamura, H., Sakamoto, T., Wasa, A. A theoretical study of the dielectric constant of protein. Prot. Eng. 2:177-185, 1988.
    • (1988) Prot. Eng. , vol.2 , pp. 177-185
    • Nakamura, H.1    Sakamoto, T.2    Wasa, A.3
  • 5
    • 0022816745 scopus 로고
    • The dielectric constant of a folded protein
    • Gilson, M.K., Honig, B.H. The dielectric constant of a folded protein. Biopolymers 25:2097-2119, 1986.
    • (1986) Biopolymers , vol.25 , pp. 2097-2119
    • Gilson, M.K.1    Honig, B.H.2
  • 6
    • 20644431615 scopus 로고
    • Theory of solutions of molecules containing widdely separated charges with special applications to zwiterions
    • Kirkwood, J.G. Theory of solutions of molecules containing widdely separated charges with special applications to zwiterions. J. Chem. Phys. 2:351-361, 1934.
    • (1934) J. Chem. Phys. , vol.2 , pp. 351-361
    • Kirkwood, J.G.1
  • 7
    • 33947468892 scopus 로고
    • Theory of protein titration curves. I. General equations for impenetrable spheres
    • Tanford, C., Kirkwood, J.G. Theory of protein titration curves. I. General equations for impenetrable spheres. J. Am. Chem. Soc. 79:5333-5339, 1957.
    • (1957) J. Am. Chem. Soc. , vol.79 , pp. 5333-5339
    • Tanford, C.1    Kirkwood, J.G.2
  • 8
    • 0016207302 scopus 로고
    • Electrostatic Effects in myoglobin: Hydrogen ion equilibria in sperm whale ferrimyoglobin
    • Shire, S.J., Hanania, G.I.H., Gurd, F.R.N. Electrostatic Effects in myoglobin: Hydrogen ion equilibria in sperm whale ferrimyoglobin. Biochemistry 13:2967-2974, 1974.
    • (1974) Biochemistry , vol.13 , pp. 2967-2974
    • Shire, S.J.1    Hanania, G.I.H.2    Gurd, F.R.N.3
  • 9
    • 0018793931 scopus 로고
    • Electrostatic stabilization in myoglobin: pH dependence of summed electrostatic contributions
    • Friend, S.H., Gurd, F.R.M. Electrostatic stabilization in myoglobin: pH dependence of summed electrostatic contributions. Biochemistry 18:4612-4619, 1979.
    • (1979) Biochemistry , vol.18 , pp. 4612-4619
    • Friend, S.H.1    Gurd, F.R.M.2
  • 10
    • 0015222647 scopus 로고
    • The interpretation of protein structures: Estimation of static accessibility
    • Lee, B., Richards, F.M. The interpretation of protein structures: Estimation of static accessibility. J. Mol. Biol. 55:379-400, 1971.
    • (1971) J. Mol. Biol. , vol.55 , pp. 379-400
    • Lee, B.1    Richards, F.M.2
  • 11
    • 0022248941 scopus 로고
    • Calculations of electrostatic energies in proteins: The energetics of ionized groups in bovine pancreatic trypsin inhibitor
    • Russell, S.T., Warshel, A. Calculations of electrostatic energies in proteins: The energetics of ionized groups in bovine pancreatic trypsin inhibitor. J. Mol. Biol. 185:389-404, 1985.
    • (1985) J. Mol. Biol. , vol.185 , pp. 389-404
    • Russell, S.T.1    Warshel, A.2
  • 12
    • 0039183749 scopus 로고
    • Extention of the Kirkwood-Westheimer model of substituent effects to general shapes, charges, and polarizabilities: Application to the substituted bicyclo[2.2.2]octanes
    • Orttung, W.H. Extention of the Kirkwood-Westheimer model of substituent effects to general shapes, charges, and polarizabilities: Application to the substituted bicyclo[2.2.2]octanes. J. Am. Chem. Soc. 100:4369-4375, 1978.
    • (1978) J. Am. Chem. Soc. , vol.100 , pp. 4369-4375
    • Orttung, W.H.1
  • 13
    • 0020475509 scopus 로고
    • Calculation of the electricpotential in the active site cleft due to α-helix dipoles
    • Warwicker, J., Watson, J.H.C. Calculation of the electricpotential in the active site cleft due to α-helix dipoles. J. Mol. Biol. 157:671-679, 1982.
    • (1982) J. Mol. Biol. , vol.157 , pp. 671-679
    • Warwicker, J.1    Watson, J.H.C.2
  • 14
    • 0022964504 scopus 로고
    • Focusing of electric fields in the active site of Cu-Zn Superoxide dismutase: Effects of ionic strength and amino-acid modification
    • Klapper, I., Magstrom, R., Fine, R., Sharp, K., Honig, B. Focusing of electric fields in the active site of Cu-Zn Superoxide dismutase: Effects of ionic strength and amino-acid modification. Proteins 1:47-51, 1986.
    • (1986) Proteins , vol.1 , pp. 47-51
    • Klapper, I.1    Magstrom, R.2    Fine, R.3    Sharp, K.4    Honig, B.5
  • 16
    • 0022429751 scopus 로고
    • A new method for computing the macromolecular electric potential
    • Zauhar, R.J., Morgan, R.S. A new method for computing the macromolecular electric potential. J. Mol. Biol. 186: 815-820, 1985.
    • (1985) J. Mol. Biol. , vol.186 , pp. 815-820
    • Zauhar, R.J.1    Morgan, R.S.2
  • 17
    • 0028305457 scopus 로고
    • Prediction of pH-dependent properties of proteins
    • Antosiewicz, J., McCammon J.A., Gilson, M.K. Prediction of pH-dependent properties of proteins. J. Mol. Biol. 238:415-436, 1994.
    • (1994) J. Mol. Biol. , vol.238 , pp. 415-436
    • Antosiewicz, J.1    McCammon, J.A.2    Gilson, M.K.3
  • 18
    • 0023899747 scopus 로고
    • Energetics of charge-charge interactions in proteins
    • Gilson, M.K., Honig, B. Energetics of charge-charge interactions in proteins. Proteins 3:32-52, 1988.
    • (1988) Proteins , vol.3 , pp. 32-52
    • Gilson, M.K.1    Honig, B.2
  • 19
    • 0343416104 scopus 로고
    • a's of ionizable groups in proteins: Atomic detail from a continuum electrostatic model
    • a's of ionizable groups in proteins: Atomic detail from a continuum electrostatic model. Biochemistry 9:327-335, 1990.
    • (1990) Biochemistry , vol.9 , pp. 327-335
    • Bashford, D.1    Karplus, M.2
  • 20
    • 0027231258 scopus 로고
    • On the pH dependence of protein stability
    • Yang, An-S., Honig, B. On the pH dependence of protein stability. J. Mol. Biol. 231:459-474, 1993.
    • (1993) J. Mol. Biol. , vol.231 , pp. 459-474
    • Yang, A.-S.1    Honig, B.2
  • 21
    • 0027209697 scopus 로고
    • Multigrid solution of the nonlinear Poisson-Boltzmann equation and calculation of titration curves
    • Oberoi, H., Allewell, N.M. Multigrid solution of the nonlinear Poisson-Boltzmann equation and calculation of titration curves. Biophys. J. 65:48-55, 1993.
    • (1993) Biophys. J. , vol.65 , pp. 48-55
    • Oberoi, H.1    Allewell, N.M.2
  • 22
    • 0021813940 scopus 로고
    • On the calculation of electrostatic interactions in proteins
    • Gilson, M.K., Rashin, A., Fine, R., Honig, B. On the calculation of electrostatic interactions in proteins. J. Mol. Biol. 183:503-516, 1985.
    • (1985) J. Mol. Biol. , vol.183 , pp. 503-516
    • Gilson, M.K.1    Rashin, A.2    Fine, R.3    Honig, B.4
  • 23
    • 0028204490 scopus 로고
    • Do salt bridges stabilize proteins? A continuum electrostatic analysis
    • Hendsch, Z.S., Tidor, B. Do salt bridges stabilize proteins? A continuum electrostatic analysis. Prot. Sci. 3:211-226, 1994.
    • (1994) Prot. Sci. , vol.3 , pp. 211-226
    • Hendsch, Z.S.1    Tidor, B.2
  • 24
    • 0028040064 scopus 로고
    • Evaluation of the conformational free energies of loops in proteins
    • Smith, K.C., Honig, B. Evaluation of the conformational free energies of loops in proteins. Proteins 18:119-132, 1994.
    • (1994) Proteins , vol.18 , pp. 119-132
    • Smith, K.C.1    Honig, B.2
  • 25
    • 0027955787 scopus 로고
    • Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins
    • Abagian, R., Totrov, M. Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. J. Mol. Biol. 235:983-1001, 1994.
    • (1994) J. Mol. Biol. , vol.235 , pp. 983-1001
    • Abagian, R.1    Totrov, M.2
  • 26
    • 0015520587 scopus 로고
    • Interpretation of protein titration curves: Application to lysozyme
    • Tanford, C., Roxby, R. Interpretation of protein titration curves: Application to lysozyme. Biochemistry 11:2192-2198, 1972.
    • (1972) Biochemistry , vol.11 , pp. 2192-2198
    • Tanford, C.1    Roxby, R.2
  • 27
    • 33751499830 scopus 로고
    • Multiple-site titration curves of proteins: Analysis of exact and approximated methods for their calculation
    • Bashford, D., Karplus, M. Multiple-site titration curves of proteins: Analysis of exact and approximated methods for their calculation. J. Phys. Chem. 95:9556-9561, 1991.
    • (1991) J. Phys. Chem. , vol.95 , pp. 9556-9561
    • Bashford, D.1    Karplus, M.2
  • 29
    • 0027477251 scopus 로고
    • Multiple-site titration and molecular modeling: Two rapid methods for computing energies and forces for ionizable groups
    • Gilson, M.K. Multiple-site titration and molecular modeling: Two rapid methods for computing energies and forces for ionizable groups. Proteins 15:266-282, 1993.
    • (1993) Proteins , vol.15 , pp. 266-282
    • Gilson, M.K.1
  • 30
    • 0026095641 scopus 로고
    • Protonation of interacting residues in a protein by a Monte Carlo method: Application to lysozyme and the photosynthetic reaction center of Rhodobacter sphaeroides
    • Beroza, P. Fredkin, D.R., Okamura, M.Y., Feher, G. Protonation of interacting residues in a protein by a Monte Carlo method: Application to lysozyme and the photosynthetic reaction center of Rhodobacter sphaeroides. Proc. Natl. Acad. Sci. USA 88:5804-5808, 1991.
    • (1991) Proc. Natl. Acad. Sci. USA , vol.88 , pp. 5804-5808
    • Beroza, P.1    Fredkin, D.R.2    Okamura, M.Y.3    Feher, G.4
  • 31
    • 0025191376 scopus 로고
    • Charge effects on folded and unfolded proteins
    • Stitger, D., Dill, K.A. Charge effects on folded and unfolded proteins. Biochemistry 29:1262-1271, 1990.
    • (1990) Biochemistry , vol.29 , pp. 1262-1271
    • Stitger, D.1    Dill, K.A.2
  • 32
    • 0025794278 scopus 로고
    • Protein stability: Electrostatics and compact denatured states
    • Stitger, D., Alonso, D.O.V., Dill, K.A. Protein stability: Electrostatics and compact denatured states. Proc. Natl. Acad. Sci. USA 88:4176-4180, 1991.
    • (1991) Proc. Natl. Acad. Sci. USA , vol.88 , pp. 4176-4180
    • Stitger, D.1    Alonso, D.O.V.2    Dill, K.A.3
  • 37
    • 0023779259 scopus 로고
    • Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis
    • Gilson, M.K., Honig, B. Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis. Proteins 4:7-18, 1988.
    • (1988) Proteins , vol.4 , pp. 7-18
    • Gilson, M.K.1    Honig, B.2
  • 38
    • 84988087911 scopus 로고
    • Calculation the electrostatic potential of molecules in solution: Method and error assessment
    • Gilson, M.K., Sharp, K.A., Honig, B. Calculation the electrostatic potential of molecules in solution: Method and error assessment. J. Comp. Chem. 9:327-335, 1987.
    • (1987) J. Comp. Chem. , vol.9 , pp. 327-335
    • Gilson, M.K.1    Sharp, K.A.2    Honig, B.3
  • 39
    • 0001008706 scopus 로고
    • Dielectric properties of trypsin inhibitor and lysozvme calculated from molecular dynamics simulations
    • Smith, P.E., Brunne, R.M., Mark, A.E., van Gunsteren, W.F. Dielectric properties of trypsin inhibitor and lysozvme calculated from molecular dynamics simulations. J. Phys. Chem. 97:2009-2014, 1993.
    • (1993) J. Phys. Chem. , vol.97 , pp. 2009-2014
    • Smith, P.E.1    Brunne, R.M.2    Mark, A.E.3    Van Gunsteren, W.F.4
  • 40
    • 0028876827 scopus 로고
    • Internal and interfacial dielectric properties of cytohrome c from molecular dynamics in aqueous solution
    • Simonson, T., Perahia, D., Internal and interfacial dielectric properties of cytohrome c from molecular dynamics in aqueous solution. Proc. Natl. Acad. Sci. USA 92:1082-1086, 1995.
    • (1995) Proc. Natl. Acad. Sci. USA , vol.92 , pp. 1082-1086
    • Simonson, T.1    Perahia, D.2
  • 41
    • 0000176654 scopus 로고
    • Stability of "salt bridges" in membrane proteins
    • Honig, B., Hubbell, W. Stability of "salt bridges" in membrane proteins. Proc. Natl. Acad. Sci. USA 81:5412-5416, 1984.
    • (1984) Proc. Natl. Acad. Sci. USA , vol.81 , pp. 5412-5416
    • Honig, B.1    Hubbell, W.2
  • 44
    • 0000406967 scopus 로고
    • Protein volume in soluion
    • Zamyatnin, A.A. Protein volume in soluion. Prog. Biophys. Mol. 24:109-123, 1972.
    • (1972) Prog. Biophys. Mol. , vol.24 , pp. 109-123
    • Zamyatnin, A.A.1
  • 45
    • 0023660015 scopus 로고
    • Electrostatic effects on modification of charged groups in the active site cleft of subtilisin by protein engineering
    • Russell, A.J., Thomas, P.G., Fersht, A.R. Electrostatic effects on modification of charged groups in the active site cleft of subtilisin by protein engineering. J. Mol. Biol. 193:803-813, 1987.
    • (1987) J. Mol. Biol. , vol.193 , pp. 803-813
    • Russell, A.J.1    Thomas, P.G.2    Fersht, A.R.3
  • 46
    • 0022386437 scopus 로고
    • Tailoring the pH dependence of enzyme catalysis using protein engineering
    • Thomas, P.G., Russell, A.J., Fersht, A.R. Tailoring the pH dependence of enzyme catalysis using protein engineering. Nature 318:375-376, 1985.
    • (1985) Nature , vol.318 , pp. 375-376
    • Thomas, P.G.1    Russell, A.J.2    Fersht, A.R.3
  • 47
    • 0023280069 scopus 로고
    • Calculation of electrostatic potentials in an enzyme active site
    • Gilson, M.K., Honig, B.H. Calculation of electrostatic potentials in an enzyme active site. Nature 330:84, 1987.
    • (1987) Nature , vol.330 , pp. 84
    • Gilson, M.K.1    Honig, B.H.2
  • 48
    • 0015520587 scopus 로고
    • Interpretation of protein titration curves: Application to lysozyme
    • Tanford, C., Roxby, R. Interpretation of protein titration curves: Application to lysozyme. Biochemistry 11:2192-2198, 1972.
    • (1972) Biochemistry , vol.11 , pp. 2192-2198
    • Tanford, C.1    Roxby, R.2
  • 49
    • 0345455600 scopus 로고
    • Hydrogen ion equilibria of ribonuclease
    • Tanford, C., Haustein, J.D., Hydrogen ion equilibria of ribonuclease. J. Am. Chem. Soc. 78:5287-5291, 1956.
    • (1956) J. Am. Chem. Soc. , vol.78 , pp. 5287-5291
    • Tanford, C.1    Haustein, J.D.2
  • 51
    • 0009793340 scopus 로고
    • Protein model building by the use of a constrained-restrained least-squares procedure
    • Herzberg, O., Sussman, J.L. Protein model building by the use of a constrained-restrained least-squares procedure. J. Appl. Crystallogr. 16:144-150, 1983.
    • (1983) J. Appl. Crystallogr. , vol.16 , pp. 144-150
    • Herzberg, O.1    Sussman, J.L.2
  • 52
    • 0024291642 scopus 로고
    • Structure of phosphate-free ribonuclease a refined at 1.26 A
    • Wlodawer, A., Svensson, L.A., Sjolin, L., Gilliland, G.L. Structure of phosphate-free ribonuclease A refined at 1.26 A. Biochemistry 27:2705-2717, 1988.
    • (1988) Biochemistry , vol.27 , pp. 2705-2717
    • Wlodawer, A.1    Svensson, L.A.2    Sjolin, L.3    Gilliland, G.L.4
  • 53
    • 0024974064 scopus 로고
    • 1, Complexed with vanadate (V), suggests conformational change upon substrate binding
    • 1, Complexed with vanadate (V), suggests conformational change upon substrate binding. Biochemistry 28:7592-7600, 1989.
    • (1989) Biochemistry , vol.28 , pp. 7592-7600
    • Kostrewa, D.1    Choe, H.W.2    Heinemann, U.3    Saenger, W.4
  • 56
    • 0018945613 scopus 로고
    • Analysis of the acid-base titration curve of hen lysozyme
    • Kuramitsu, S., Hamaguchi, K. Analysis of the acid-base titration curve of hen lysozyme. J. Biochem. 87:1215-1219, 1980.
    • (1980) J. Biochem. , vol.87 , pp. 1215-1219
    • Kuramitsu, S.1    Hamaguchi, K.2
  • 58
    • 0017848335 scopus 로고
    • The influence of a single salt bridge on static and dynamic features of the globular solution conformation of the basic pancreatic trypsin inhibitor
    • Brown, L.R., Marco, A.D., Richarz, R., Wagner, G., Wüthrich, K. The influence of a single salt bridge on static and dynamic features of the globular solution conformation of the basic pancreatic trypsin inhibitor. Eur. J. Biochem. 88:87-95, 1978.
    • (1978) Eur. J. Biochem. , vol.88 , pp. 87-95
    • Brown, L.R.1    Marco, A.D.2    Richarz, R.3    Wagner, G.4    Wüthrich, K.5
  • 59
    • 0017902346 scopus 로고
    • 13C nuclear magnetic resonance studies at 90.5 Mhz of the basic pancreatic trypsin inhibitor
    • 13C nuclear magnetic resonance studies at 90.5 Mhz of the basic pancreatic trypsin inhibitor. Biochemistry 17:2263-2269, 1978.
    • (1978) Biochemistry , vol.17 , pp. 2263-2269
    • Richarz, R.1    Wüthrich, K.2
  • 60
    • 3743127461 scopus 로고
    • 1H NMR
    • Proceedings of the Second International Meeting, Sant Felin de Guixols, Girona, Spain, 1990." Cuchillo, C.M., de Liorens, R., Nogués, M.V., Parés, X. (eds.). Bellatrra, Spain: Department de Bioquimica i Bioilogia Molecular and Institut de Biologia Fonamental Vicent Villar Palasi, Universitat Autonomià de Barcelona
    • 1H NMR. In "Structure, Mechanism and Function of Ribonucleases. Proceedings of the Second International Meeting, Sant Felin de Guixols, Girona, Spain, 1990." Cuchillo, C.M., de Liorens, R., Nogués, M.V., Parés, X. (eds.). Bellatrra, Spain: Department de Bioquimica i Bioilogia Molecular and Institut de Biologia Fonamental Vicent Villar Palasi, Universitat Autonomià de Barcelona, pp. 9-14, 1990.
    • (1990) Structure, Mechanism and Function of Ribonucleases , pp. 9-14
    • Rico, M.1    Santoro, J.2    Gonzalez, C.3    Bruix, M.4    Neira, J.L.5
  • 62
    • 0024971012 scopus 로고
    • Conformational stability and activity of ribonuclease T1 and mutants
    • Shirley, B.A., Stanssen, P., Steyaert, J., Pace., C.N. Conformational stability and activity of ribonuclease T1 and mutants. J. Biol. Chem. 264:11621-11625, 1989.
    • (1989) J. Biol. Chem. , vol.264 , pp. 11621-11625
    • Shirley, B.A.1    Stanssen, P.2    Steyaert, J.3    Pace, C.N.4
  • 63
    • 0025234587 scopus 로고
    • pH-induced denaturation of proteins a single salt bridge contributes 3-5 kcal/mol to the free energy of folding of T4 lysozyme
    • Anderson, D.E., Becktel, W.J., Dahlquist, F.W. pH-induced denaturation of proteins a single salt bridge contributes 3-5 kcal/mol to the free energy of folding of T4 lysozyme. Biochemistry 29:2403-2408, 1990.
    • (1990) Biochemistry , vol.29 , pp. 2403-2408
    • Anderson, D.E.1    Becktel, W.J.2    Dahlquist, F.W.3


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