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Volumn 28, Issue 7, 1999, Pages 533-551

Electrostatic models for computing protonation and redox equilibria in proteins

Author keywords

[No Author keywords available]

Indexed keywords

ACID BASE BALANCE; CONFORMATIONAL TRANSITION; ELECTRICITY; ENZYME ACTIVITY; MATHEMATICAL ANALYSIS; OXIDATION REDUCTION REACTION; PHOSPHATE METABOLISM; PROTON TRANSPORT; QUANTUM CHEMISTRY; REVIEW;

EID: 0000000699     PISSN: 01757571     EISSN: None     Source Type: Journal    
DOI: 10.1007/s002490050236     Document Type: Review
Times cited : (236)

References (135)
  • 1
    • 0030945495 scopus 로고    scopus 로고
    • Incorporating protein conformational flexibility into the calculation of pH dependent protein properties
    • Alexov EG, Gunner MR (1997) Incorporating protein conformational flexibility into the calculation of pH dependent protein properties. Biophys J 74: 2075-2093
    • (1997) Biophys J , vol.74 , pp. 2075-2093
    • Alexov, E.G.1    Gunner, M.R.2
  • 2
    • 0028305457 scopus 로고
    • Prediction of pH-dependent properties of proteins
    • Antosiewicz J, McCammon JA, Gilson MK (1994) Prediction of pH-dependent properties of proteins. J Mol Biol 238: 415-436
    • (1994) J Mol Biol , vol.238 , pp. 415-436
    • Antosiewicz, J.1    McCammon, J.A.2    Gilson, M.K.3
  • 5
    • 0030010549 scopus 로고    scopus 로고
    • Free energy computations on the shift of the special pair redox potential: Mutants of the reaction center of Rhodobacter sphaeroides
    • Apostolakis J, Muegge I, Ermler U, Fritzsch G, Knapp E (1996) Free energy computations on the shift of the special pair redox potential: mutants of the reaction center of Rhodobacter sphaeroides. J Am Chem Soc 118: 3743-3752
    • (1996) J am Chem Soc , vol.118 , pp. 3743-3752
    • Apostolakis, J.1    Muegge, I.2    Ermler, U.3    Fritzsch, G.4    Knapp, E.5
  • 6
    • 0031192417 scopus 로고    scopus 로고
    • A quantum chemical view of density functional theory
    • Baerends EJ, Gritsenko OV (1997) A quantum chemical view of density functional theory. J Phys Chem A 101: 5383-5403
    • (1997) J Phys Chem A , vol.101 , pp. 5383-5403
    • Baerends, E.J.1    Gritsenko, O.V.2
  • 7
    • 0030970305 scopus 로고    scopus 로고
    • Simulation of protein conformational freedom as a function of pH: Constant-pH molecular dynamics using implicit titration
    • Baptista AM, Martel PJ, Peters SB (1997) Simulation of protein conformational freedom as a function of pH: constant-pH molecular dynamics using implicit titration. Proteins 27: 523-544
    • (1997) Proteins , vol.27 , pp. 523-544
    • Baptista, A.M.1    Martel, P.J.2    Peters, S.B.3
  • 8
    • 0000339209 scopus 로고
    • Electrostatic effects in biological molecules
    • Bashford D (1991) Electrostatic effects in biological molecules. Curr Opin Struct Biol 1: 175-184
    • (1991) Curr Opin Struct Biol , vol.1 , pp. 175-184
    • Bashford, D.1
  • 9
    • 0026612756 scopus 로고
    • a values of ionizable groups in bacteriorhodopsin
    • a values of ionizable groups in bacteriorhodopsin. J Mol Biol 224: 473-486
    • (1992) J Mol Biol , vol.224 , pp. 473-486
    • Bashford, D.1    Gerwert, K.2
  • 10
    • 0025197061 scopus 로고
    • aS of ionizable groups in proteins: Atomic detail from a continuum electrostatic model
    • aS of ionizable groups in proteins: atomic detail from a continuum electrostatic model. Biochemistry 29: 10219-10225
    • (1990) Biochemistry , vol.29 , pp. 10219-10225
    • Bashford, D.1    Karplus, M.2
  • 11
    • 33751499830 scopus 로고
    • Multiple-site titration curves of proteins: An analysis of exact and approximate methods for their calculations
    • Bashford D, Karplus M (1991) Multiple-site titration curves of proteins: an analysis of exact and approximate methods for their calculations. J Phys Chem 95: 9557-9561
    • (1991) J Phys Chem , vol.95 , pp. 9557-9561
    • Bashford, D.1    Karplus, M.2
  • 13
    • 33748400070 scopus 로고    scopus 로고
    • Including side chain flexibility in continuum electrostatic calculations of protein titration
    • Beroza P, Case DA (1996) Including side chain flexibility in continuum electrostatic calculations of protein titration. J Phys Chem 100: 20156-20163
    • (1996) J Phys Chem , vol.100 , pp. 20156-20163
    • Beroza, P.1    Case, D.A.2
  • 14
    • 0032319206 scopus 로고    scopus 로고
    • Calculation of proton binding thermodynamics in proteins
    • Beroza P, Case DA (1998) Calculation of proton binding thermodynamics in proteins. Methods Enzymol 295: 170-189
    • (1998) Methods Enzymol , vol.295 , pp. 170-189
    • Beroza, P.1    Case, D.A.2
  • 15
    • 0001715782 scopus 로고    scopus 로고
    • as in a protein from a continuum electrostatic model: Methods and sensitivity analysis
    • as in a protein from a continuum electrostatic model: methods and sensitivity analysis. J Comput Chem 17: 1229-1244
    • (1996) J Comput Chem , vol.17 , pp. 1229-1244
    • Beroza, P.1    Fredkin, D.R.2
  • 16
    • 0026095641 scopus 로고
    • Protonation of interacting residues in a protein by a Monte Carlo method: Application to lysozyme and the photosynthetic reaction center
    • Beroza P, Fredkin DR, Okamura MY, Feher G (1991) Protonation of interacting residues in a protein by a Monte Carlo method: application to lysozyme and the photosynthetic reaction center. Proc Natl Acad Sci USA 88: 5804-5808
    • (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
  • 18
    • 84986513567 scopus 로고
    • Determining atom-centered monopoles from molecular electrostatic potentials. Need for high sampling density in formamide conformational analysis
    • Breneman CN, Wiberg KB (1990) Determining atom-centered monopoles from molecular electrostatic potentials. Need for high sampling density in formamide conformational analysis. J Comput Chem 11: 361-373
    • (1990) J Comput Chem , vol.11 , pp. 361-373
    • Breneman, C.N.1    Wiberg, K.B.2
  • 19
    • 0041140017 scopus 로고
    • Simulation of peptide conformational dynamics and thermodynamics
    • Brooks CL, Case DA (1993) Simulation of peptide conformational dynamics and thermodynamics. Chem Rev 93: 2487-2502
    • (1993) Chem Rev , vol.93 , pp. 2487-2502
    • Brooks, C.L.1    Case, D.A.2
  • 20
    • 0030180876 scopus 로고    scopus 로고
    • Calculation of proton affinities using density functional procedures: A critical study
    • Chandra AK, Goursot A (1996) Calculation of proton affinities using density functional procedures: a critical study. J Phys Chem 100: 11596-11599
    • (1996) J Phys Chem , vol.100 , pp. 11596-11599
    • Chandra, A.K.1    Goursot, A.2
  • 21
    • 33751159055 scopus 로고
    • Incorporating solvation effects into density functional electronic structure calculations
    • Chen JL, Noodleman L, Case D, Bashford D (1994) Incorporating solvation effects into density functional electronic structure calculations. J Phys Chem 98: 11059-11068
    • (1994) J Phys Chem , vol.98 , pp. 11059-11068
    • Chen, J.L.1    Noodleman, L.2    Case, D.3    Bashford, D.4
  • 24
    • 0028169692 scopus 로고
    • as of ionizable residues in proteins: An explicit solvent calculation for lysozyme
    • as of ionizable residues in proteins: an explicit solvent calculation for lysozyme. Proteins 20: 85-97
    • (1994) Proteins , vol.20 , pp. 85-97
    • Del Buono, G.S.1    Figueirisco, F.E.2    Levy, R.3
  • 26
    • 33748593093 scopus 로고    scopus 로고
    • as of ionizable groups in proteins
    • as of ionizable groups in proteins. J Phys Chem 100: 17373-17387
    • (1996) J Phys Chem , vol.100 , pp. 17373-17387
    • Demchuck, E.1    Wade, R.C.2
  • 27
    • 0032516494 scopus 로고    scopus 로고
    • as in the active site of Escherichia coli thioredoxin
    • as in the active site of Escherichia coli thioredoxin. Biochemistry 37: 10298-10306
    • (1998) Biochemistry , vol.37 , pp. 10298-10306
    • Dillet, V.1    Dyson, H.J.2    Bashford, D.3
  • 28
    • 0030970306 scopus 로고    scopus 로고
    • Self-consistent field approach to protein structure and stability. I: PH dependence of electrostatic contributions
    • Dimitrov RA, Crichton RR (1997) Self-consistent field approach to protein structure and stability. I: pH dependence of electrostatic contributions. Proteins 27: 576-596
    • (1997) Proteins , vol.27 , pp. 576-596
    • Dimitrov, R.A.1    Crichton, R.R.2
  • 30
    • 0032537485 scopus 로고    scopus 로고
    • Theoretical and experimental analysis of ionization equilibria in ovomucoid third domain
    • Forsyth WR, Gilson MK, Antosiewic J, Jaren OR, Robertson AD (1998) Theoretical and experimental analysis of ionization equilibria in ovomucoid third domain. Biochemistry 37: 8643-8652
    • (1998) Biochemistry , vol.37 , pp. 8643-8652
    • Forsyth, W.R.1    Gilson, M.K.2    Antosiewic, J.3    Jaren, O.R.4    Robertson, A.D.5
  • 33
    • 0027477251 scopus 로고
    • Multiple-site titration and molecular modelling: Two rapid methods for computing energies and forces for ionizable groups in proteins
    • Gilson MK (1993) Multiple-site titration and molecular modelling: Two rapid methods for computing energies and forces for ionizable groups in proteins. Proteins 15: 266-282
    • (1993) Proteins , vol.15 , pp. 266-282
    • Gilson, M.K.1
  • 34
    • 0029066848 scopus 로고
    • Theory of electrostatic interactions in macromolecules
    • Gilson MK (1995) Theory of electrostatic interactions in macromolecules. Curr Opin Struct Biol 5: 216-223
    • (1995) Curr Opin Struct Biol , vol.5 , pp. 216-223
    • Gilson, M.K.1
  • 35
    • 0031058541 scopus 로고    scopus 로고
    • The statistical thermodynamic basis for computation of binding affinities: A critical review
    • Gilson MK, Given JA, Bush BL, McCammon JA (1997) The statistical thermodynamic basis for computation of binding affinities: a critical review. Biophys J 72: 1047-1069
    • (1997) Biophys J , vol.72 , pp. 1047-1069
    • Gilson, M.K.1    Given, J.A.2    Bush, B.L.3    McCammon, J.A.4
  • 36
    • 0025944990 scopus 로고
    • Electrostatic control of midpoint potentials in the cytochrome subunit of Rhodopseudomonas viridis reaction center
    • Gunner MR, Honig B (1991) Electrostatic control of midpoint potentials in the cytochrome subunit of Rhodopseudomonas viridis reaction center. Proc Natl Acad Sci USA 88: 9151-9155
    • (1991) Proc Natl Acad Sci USA , vol.88 , pp. 9151-9155
    • Gunner, M.R.1    Honig, B.2
  • 37
    • 0000414723 scopus 로고    scopus 로고
    • Electrostatic potentials in Rhodopseudomonas viridis reaction centers: Implications for the driving force and directionality of the electron transfer
    • Gunner MR, Nicholls A, Honig B (1996) Electrostatic potentials in Rhodopseudomonas viridis reaction centers: implications for the driving force and directionality of the electron transfer. J Phys Chem 100: 4277-4291
    • (1996) J Phys Chem , vol.100 , pp. 4277-4291
    • Gunner, M.R.1    Nicholls, A.2    Honig, B.3
  • 38
    • 2142813682 scopus 로고
    • Computer simulation of molecular dynamics: Methodology, applications, and perspectives in chemistry
    • Gunsteren WF van, Berendsen HJC (1990) Computer simulation of molecular dynamics: methodology, applications, and perspectives in chemistry. Angew Chem Int Ed Engl 29: 992-1023
    • (1990) Angew Chem int Ed Engl , vol.29 , pp. 992-1023
    • Van Gunsteren, W.F.1    Berendsen, H.J.C.2
  • 39
    • 0024519351 scopus 로고
    • Treatment of electrostatic effects in macromolecular modelling
    • Harvey SC (1989) Treatment of electrostatic effects in macromolecular modelling. Proteins 5: 78-92
    • (1989) Proteins , vol.5 , pp. 78-92
    • Harvey, S.C.1
  • 40
    • 0029888335 scopus 로고    scopus 로고
    • Polypeptide folding with off-lattice Monte Carlo dynamics: The method
    • Hoffmann D, Knapp EW (1996a) Polypeptide folding with off-lattice Monte Carlo dynamics: the method. Eur Biophys J 24: 387-403
    • (1996) Eur Biophys J , vol.24 , pp. 387-403
    • Hoffmann, D.1    Knapp, E.W.2
  • 41
    • 0042131964 scopus 로고    scopus 로고
    • Protein dynamics with off-lattice Monte Carlo moves
    • Hoffmann D, Knapp EW (1996b) Protein dynamics with off-lattice Monte Carlo moves. Phys Rev E 53: 4221-4224
    • (1996) Phys Rev E , vol.53 , pp. 4221-4224
    • Hoffmann, D.1    Knapp, E.W.2
  • 42
    • 0031208687 scopus 로고    scopus 로고
    • Folding pathways of a helix-turn-helix model protein
    • Hoffmann D, Knapp E.-W (1997) Folding pathways of a helix-turn-helix model protein. J Phys Chem B 101: 6734-6740
    • (1997) J Phys Chem B , vol.101 , pp. 6734-6740
    • Hoffmann, D.1    Knapp, E.-W.2
  • 43
    • 0345102881 scopus 로고    scopus 로고
    • Tackling concrete problems in molecular biophysics using Monte Carlo and related methods: Glycosylation, folding, solvation
    • Grassberger P, Barkema GT, Nadler W (eds) World Scientific, Singapore
    • Hoffmann D, Washio T, Gessler K, Jacob J (1999) Tackling concrete problems in molecular biophysics using Monte Carlo and related methods: glycosylation, folding, solvation. In: Grassberger P, Barkema GT, Nadler W (eds) Monte Carlo approach to biopolymers and protein folding. World Scientific, Singapore, pp 153-170
    • (1999) Monte Carlo Approach to Biopolymers and Protein Folding , pp. 153-170
    • Hoffmann, D.1    Washio, T.2    Gessler, K.3    Jacob, J.4
  • 45
    • 84986437211 scopus 로고
    • Numerical solution of the nonlinear Poisson-Boltzmann equation: Developing more robust and efficient methods
    • Holst MJ, Saied F (1995) Numerical solution of the nonlinear Poisson-Boltzmann equation: developing more robust and efficient methods. J Comput Chem 16: 337-364
    • (1995) J Comput Chem , vol.16 , pp. 337-364
    • Holst, M.J.1    Saied, F.2
  • 46
    • 0028222670 scopus 로고
    • Treatment of electrostatic effect in proteins: Multigrid-based Newton iterative method for solution of the full nonlinear Poisson-Boltzmann equation
    • Holst MJ, Kozack RE, Saied F, Subramiam S (1994) Treatment of electrostatic effect in proteins: multigrid-based Newton iterative method for solution of the full nonlinear Poisson-Boltzmann equation. Proteins 18: 231-245
    • (1994) Proteins , vol.18 , pp. 231-245
    • Holst, M.J.1    Kozack, R.E.2    Saied, F.3    Subramiam, S.4
  • 47
    • 0029016182 scopus 로고
    • Classical electrostatics in biology and chemistry
    • Honig B, Nicholls A (1995) Classical electrostatics in biology and chemistry. Science 268: 1144-1149
    • (1995) Science , vol.268 , pp. 1144-1149
    • Honig, B.1    Nicholls, A.2
  • 48
    • 0000741414 scopus 로고    scopus 로고
    • A modification of the generalized Born theory for improved estimates of solvation energies and pK shifts
    • Jayaram B, Liu Y, Beveridge DL (1998) A modification of the generalized Born theory for improved estimates of solvation energies and pK shifts. J Chem Phys 109: 1465-1471
    • (1998) J Chem Phys , vol.109 , pp. 1465-1471
    • Jayaram, B.1    Liu, Y.2    Beveridge, D.L.3
  • 49
    • 0031237025 scopus 로고    scopus 로고
    • Calculating acid-dissociation constants of proteins using the boundary element method
    • Juffer AH, Argos P. Vogel HJ (1997) Calculating acid-dissociation constants of proteins using the boundary element method. J Phys Chem B 101: 7664-7673
    • (1997) J Phys Chem B , vol.101 , pp. 7664-7673
    • Juffer, A.H.1    Argos, P.2    Vogel, H.J.3
  • 51
    • 84961985326 scopus 로고    scopus 로고
    • a values of amines in water from quantum mechanical calculations using a polarized dielectric continuum representation of the solvent
    • a values of amines in water from quantum mechanical calculations using a polarized dielectric continuum representation of the solvent. J Phys Chem B 101: 2959-2967
    • (1997) J Phys Chem B , vol.101 , pp. 2959-2967
    • Kallies, B.1    Mitzner, R.2
  • 52
    • 0031880698 scopus 로고    scopus 로고
    • The coupling of electron transfer and proton translocation: Electrostatic calculations on Paracoccus denitrificans cytochrome c oxidase
    • Kannt A, Lancaster CRD, Michel H (1998) The coupling of electron transfer and proton translocation: electrostatic calculations on Paracoccus denitrificans cytochrome c oxidase. Biophys J 74: 708-721
    • (1998) Biophys J , vol.74 , pp. 708-721
    • Kannt, A.1    Lancaster, C.R.D.2    Michel, H.3
  • 53
    • 0025048105 scopus 로고
    • Molecular dynamics simulations in biology
    • Karplus M, Petsko GA (1990) Molecular dynamics simulations in biology. Nature 347: 631-639
    • (1990) Nature , vol.347 , pp. 631-639
    • Karplus, M.1    Petsko, G.A.2
  • 54
    • 0029018932 scopus 로고
    • A simple algorithm for the calculation of multiple site titrution curves
    • Karshikoff A (1995) A simple algorithm for the calculation of multiple site titrution curves. Protein Eng 8: 243-248
    • (1995) Protein Eng , vol.8 , pp. 243-248
    • Karshikoff, A.1
  • 56
    • 20644431615 scopus 로고
    • Theory of solution of molecules containing widely separated charges with special application to zwitterions
    • Kirkwood JG (1934) Theory of solution of molecules containing widely separated charges with special application to zwitterions. J Chem Phys 2: 351-361
    • (1934) J Chem Phys , vol.2 , pp. 351-361
    • Kirkwood, J.G.1
  • 57
    • 0345178973 scopus 로고
    • Long time dynamics of proteins: An off-lattice Monte Carlo method
    • Harms U (ed) Springer, Berlin Heidelberg New York
    • Knapp E, Irgens-Defregger A (1991) Long time dynamics of proteins: an off-lattice Monte Carlo method. In: Harms U (ed) Supercomputer and chemistry, vol 2. Springer, Berlin Heidelberg New York, pp 83-106
    • (1991) Supercomputer and Chemistry , vol.2 , pp. 83-106
    • Knapp, E.1    Irgens-Defregger, A.2
  • 58
    • 7044239742 scopus 로고
    • Free energy calculations: Applications to chemical and biochemical phenomena
    • Kollman PA (1993) Free energy calculations: applications to chemical and biochemical phenomena. Chem Rev 93: 2395-2417
    • (1993) Chem Rev , vol.93 , pp. 2395-2417
    • Kollman, P.A.1
  • 59
    • 0030030176 scopus 로고    scopus 로고
    • Calculated coupling of electron and proton transfer in the photosynthestic reaction center of Rhodopseudomonas viridis
    • Lancaster CR, Michel H, Honig B, Gunner MR (1996) Calculated coupling of electron and proton transfer in the photosynthestic reaction center of Rhodopseudomonas viridis. Biophys J 70: 2469-2492
    • (1996) Biophys J , vol.70 , pp. 2469-2492
    • Lancaster, C.R.1    Michel, H.2    Honig, B.3    Gunner, M.R.4
  • 60
    • 0015437961 scopus 로고
    • Study of protein-protein and of protein-ligand interaction by potentiometric methods
    • Laskowski M, Finkenstadt WR (1972) Study of protein-protein and of protein-ligand interaction by potentiometric methods. Methods Enzymol 26: 193-227
    • (1972) Methods Enzymol , vol.26 , pp. 193-227
    • Laskowski, M.1    Finkenstadt, W.R.2
  • 61
    • 0345453983 scopus 로고    scopus 로고
    • a values of hydrated transition metal cations by a combined density functional and continuum dielectric theory
    • a values of hydrated transition metal cations by a combined density functional and continuum dielectric theory. J Phys Chem 96: 2855-2866
    • (1996) J Phys Chem , vol.96 , pp. 2855-2866
    • Li, J.1    Fischer, C.L.2    Chen, J.L.3    Bashford, D.4    Noodleman, L.5
  • 62
    • 84962367570 scopus 로고    scopus 로고
    • Incorporating protein environments in density functional theory: A self-consistent reaction field calculation of redox potentials of [2Fe2S] clusters in ferredoxin and phthalate dioxygenase reductase
    • Li J, Nelson MR, Peng CY, Bashford D, Noodleman L (1998) Incorporating protein environments in density functional theory: a self-consistent reaction field calculation of redox potentials of [2Fe2S] clusters in ferredoxin and phthalate dioxygenase reductase. J Phys Chem A 102: 6311-6324
    • (1998) J Phys Chem A , vol.102 , pp. 6311-6324
    • Li, J.1    Nelson, M.R.2    Peng, C.Y.3    Bashford, D.4    Noodleman, L.5
  • 63
    • 33751500123 scopus 로고
    • a calculations with continuum dielectric methods
    • a calculations with continuum dielectric methods. J Phys Chem 95: 5610-5620
    • (1991) J Phys Chem , vol.95 , pp. 5610-5620
    • Lim, C.1    Bashford, D.2    Karplus, M.3
  • 65
    • 0031779284 scopus 로고    scopus 로고
    • a shifts in small molecules and HIV protease: Electrostatics and conformation
    • a shifts in small molecules and HIV protease: electrostatics and conformation. J Am Chem Soc 120: 6138-6146
    • (1998) J am Chem Soc , vol.120 , pp. 6138-6146
    • Luo, R.1    Martha, S.2    Head, J.M.3    Gilson, M.K.4
  • 68
    • 0029415109 scopus 로고
    • a values of titratable groups of an antigen-antibody complex, HyHEL-5-hen egg lysozyme
    • a values of titratable groups of an antigen-antibody complex, HyHEL-5-hen egg lysozyme. Protein Eng 8: 915-924
    • (1995) Protein Eng , vol.8 , pp. 915-924
    • McDonald, S.M.1    Willson, R.C.2    McCammon, J.A.3
  • 69
    • 0000703443 scopus 로고    scopus 로고
    • Self-consistent, free energy based approximation to calculate pH dependent electrostatic effects in proteins
    • Mehler EL (1996) Self-consistent, free energy based approximation to calculate pH dependent electrostatic effects in proteins. J Phys Chem 100: 16006-16018
    • (1996) J Phys Chem , vol.100 , pp. 16006-16018
    • Mehler, E.L.1
  • 70
    • 22244435668 scopus 로고    scopus 로고
    • Calculated gas-phase acidities using density functional theory: Is it reliable?
    • Merril GN, Kass SR (1996) Calculated gas-phase acidities using density functional theory: is it reliable? J Phys Chem 100: 17465-17471
    • (1996) J Phys Chem , vol.100 , pp. 17465-17471
    • Merril, G.N.1    Kass, S.R.2
  • 71
    • 0031272364 scopus 로고    scopus 로고
    • Multiply-protonated protein ions in the gas phase: Calculation of the electrostatic interactions between charged sites
    • Miteva M, Demirev PA, Karshikof AD (1997) Multiply-protonated protein ions in the gas phase: calculation of the electrostatic interactions between charged sites. J Phys Chem B 101: 9645-9650
    • (1997) J Phys Chem B , vol.101 , pp. 9645-9650
    • Miteva, M.1    Demirev, P.A.2    Karshikof, A.D.3
  • 73
  • 74
    • 0343028401 scopus 로고
    • Density functional Poisson-Boltzmann calculations of redox potentials for iron-sulfur clusters
    • Mousca J-M, Chen JL, Noodleman L, Bashford D, Case DA (1995) Density functional Poisson-Boltzmann calculations of redox potentials for iron-sulfur clusters. J Am Chem Soc 116: 11989-11914
    • (1995) J am Chem Soc , vol.116 , pp. 11989-111914
    • Mousca, J.-M.1    Chen, J.L.2    Noodleman, L.3    Bashford, D.4    Case, D.A.5
  • 75
    • 0030018295 scopus 로고    scopus 로고
    • Shift of the special pair redox potential: Electrostatic computations of mutants of the reaction center from Rhodobacter sphaeroides
    • Muegge I, Apostolakis J, Ermler U. Fritsch G, Lubitz W, Knapp EW (1996) Shift of the special pair redox potential: electrostatic computations of mutants of the reaction center from Rhodobacter sphaeroides. Biochemistry 35: 8359-8370
    • (1996) Biochemistry , vol.35 , pp. 8359-8370
    • Muegge, I.1    Apostolakis, J.2    Ermler, U.3    Fritsch, G.4    Lubitz, W.5    Knapp, E.W.6
  • 77
    • 0001461682 scopus 로고
    • Examination of titration behavior
    • Nozaki Y, Tanford C (1967) Examination of titration behavior. Methods Enzymol 11: 715-734
    • (1967) Methods Enzymol , vol.11 , pp. 715-734
    • Nozaki, Y.1    Tanford, C.2
  • 78
    • 0027209697 scopus 로고
    • Multigrid solution of the nonlinear Poisson-Boltzmann equation and calculation of titration curves
    • Oberoi H, Allewell N (1993) Multigrid solution of the nonlinear Poisson-Boltzmann equation and calculation of titration curves. Biophys J 65: 48-55
    • (1993) Biophys J , vol.65 , pp. 48-55
    • Oberoi, H.1    Allewell, N.2
  • 80
    • 0031719963 scopus 로고    scopus 로고
    • Calculation of protonation patterns in proteins with conformational relaxation - Application to the photosynthetic reaction center
    • Rabenstein B, Ullmann GM, Knapp EW (1998a) Calculation of protonation patterns in proteins with conformational relaxation - application to the photosynthetic reaction center. Eur Biophys J 27: 628-637
    • (1998) Eur Biophys J , vol.27 , pp. 628-637
    • Rabenstein, B.1    Ullmann, G.M.2    Knapp, E.W.3
  • 81
    • 0032562210 scopus 로고    scopus 로고
    • Energetics of the electron transfer and protonation reactions of the quinones in the photosynthetic reaction center of Rhodopseudomonas viridis
    • Rabenstein B, Ullmann GM, Knapp EW (1998b) Energetics of the electron transfer and protonation reactions of the quinones in the photosynthetic reaction center of Rhodopseudomonas viridis. Biochemistry 37: 2488-2495
    • (1998) Biochemistry , vol.37 , pp. 2488-2495
    • Rabenstein, B.1    Ullmann, G.M.2    Knapp, E.W.3
  • 84
    • 84962440579 scopus 로고    scopus 로고
    • Incorporating solvation effects into density functional theory: Calculation of absolute acidities
    • Richardson WH, Peng C, Bashford D, Noodleman L, Case DA (1997) Incorporating solvation effects into density functional theory: calculation of absolute acidities. Int J Quantum Chem 61: 207-217
    • (1997) Int J Quantum Chem , vol.61 , pp. 207-217
    • Richardson, W.H.1    Peng, C.2    Bashford, D.3    Noodleman, L.4    Case, D.A.5
  • 85
    • 0030582736 scopus 로고    scopus 로고
    • Coupling between folding and ionization equilibria: Effects of pH on the conformational preferences of polypeptides
    • Ripoll DR, Vorobjev YN, Liwo A, Vila JA, Scheraga HA (1996) Coupling between folding and ionization equilibria: effects of pH on the conformational preferences of polypeptides. J Mol Biol 264: 770-783
    • (1996) J Mol Biol , vol.264 , pp. 770-783
    • Ripoll, D.R.1    Vorobjev, Y.N.2    Liwo, A.3    Vila, J.A.4    Scheraga, H.A.5
  • 86
    • 0028218956 scopus 로고
    • Environmental effects on the protonation states of the active site residues in bacteriorhodopsin
    • Sampogna RV, Honig B (1994) Environmental effects on the protonation states of the active site residues in bacteriorhodopsin. Biophys J 66: 1341-1352
    • (1994) Biophys J , vol.66 , pp. 1341-1352
    • Sampogna, R.V.1    Honig, B.2
  • 87
    • 0030908397 scopus 로고    scopus 로고
    • a calculations along a bacteriorhodopsin molecular dynamics trajectory
    • a calculations along a bacteriorhodopsin molecular dynamics trajectory. Biophys Chem 65: 189-204
    • (1997) Biophys Chem , vol.65 , pp. 189-204
    • Sandberg, L.1    Edholm, O.2
  • 88
    • 0012289137 scopus 로고    scopus 로고
    • An energy function for dynamics simulations of polypeptides in torsion angle space
    • Sartori F, Melchers B, Böttcher H, Knapp EW (1998) An energy function for dynamics simulations of polypeptides in torsion angle space. J Chem Phys 108: 8264-8276
    • (1998) J Chem Phys , vol.108 , pp. 8264-8276
    • Sartori, F.1    Melchers, B.2    Böttcher, H.3    Knapp, E.W.4
  • 89
    • 0012227656 scopus 로고    scopus 로고
    • A comprehensive analytical treatment of continuum electrostatics
    • Schaefer M, Karplus M (1996) A comprehensive analytical treatment of continuum electrostatics. J Phys Chem 100: 1578-1599
    • (1996) J Phys Chem , vol.100 , pp. 1578-1599
    • Schaefer, M.1    Karplus, M.2
  • 90
    • 0031076776 scopus 로고    scopus 로고
    • pH-dependence of protein stability: Absolute electrostatic free energy differences between conformations
    • Schaefer M, Sommer M, Karplus M (1997) pH-dependence of protein stability: absolute electrostatic free energy differences between conformations. J Phys Chem B 101: 1663-1683
    • (1997) J Phys Chem B , vol.101 , pp. 1663-1683
    • Schaefer, M.1    Sommer, M.2    Karplus, M.3
  • 91
    • 0032484151 scopus 로고    scopus 로고
    • Solution conformations and thermodynamics of structured peptides: Molecular dynamics simulation with an implicit solvation model
    • Schaefer M, Bartels C, Karplus M (1998) Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model. J Mol Biol 284: 835-848
    • (1998) J Mol Biol , vol.284 , pp. 835-848
    • Schaefer, M.1    Bartels, C.2    Karplus, M.3
  • 92
    • 0000671518 scopus 로고    scopus 로고
    • a's of ionizable residues in proteins: Semi-microscopic and microscopic approaches
    • a's of ionizable residues in proteins: semi-microscopic and microscopic approaches. J Phys Chem B 101: 4458-4472
    • (1997) J Phys Chem B , vol.101 , pp. 4458-4472
    • Sham, Y.Y.1    Chu, Z.T.2    Warshel, A.3
  • 93
    • 0028215767 scopus 로고
    • Electrostatic interactions in macromolecules
    • Sharp KA (1994) Electrostatic interactions in macromolecules. Curr Opin Struct Biol 4: 234-239
    • (1994) Curr Opin Struct Biol , vol.4 , pp. 234-239
    • Sharp, K.A.1
  • 94
  • 95
    • 0029833446 scopus 로고    scopus 로고
    • Charge separation and the dielectric constant of proteins: Insights from molecular dynamics
    • Simonson T, Brooks CL (1996) Charge separation and the dielectric constant of proteins: insights from molecular dynamics. J Am Chem Soc 118: 8452-8458
    • (1996) J am Chem Soc , vol.118 , pp. 8452-8458
    • Simonson, T.1    Brooks, C.L.2
  • 96
    • 0028876827 scopus 로고
    • Internal and interfacial dielectric properties of cytochrome c from molecular dynamics in aqueous solution
    • Simonson T, Perahia D (1995a) Internal and interfacial dielectric properties of cytochrome c from molecular dynamics in aqueous solution. Proc Nail Acad Sci USA 92: 1082-1086
    • (1995) Proc Nail Acad Sci USA , vol.92 , pp. 1082-1086
    • Simonson, T.1    Perahia, D.2
  • 97
    • 0028983852 scopus 로고
    • Microscopic dielectric properties of cytochrome c from molecular dynamics simulation in aqueous solution
    • Simonson T, Perahia D (1995b) Microscopic dielectric properties of cytochrome c from molecular dynamics simulation in aqueous solution. J Am Chem Soc 117: 7987-8000
    • (1995) J am Chem Soc , vol.117 , pp. 7987-8000
    • Simonson, T.1    Perahia, D.2
  • 98
    • 0025847876 scopus 로고
    • Intramolecular dielectric screening in proteins
    • Simonson T, Perahia D, Bricogne G (1992) Intramolecular dielectric screening in proteins. J Mol Biol 218: 859-886
    • (1992) J Mol Biol , vol.218 , pp. 859-886
    • Simonson, T.1    Perahia, D.2    Bricogne, G.3
  • 99
    • 0028173135 scopus 로고
    • Calculation of electrostatic effects at the amino terminus of an α-helix
    • Sitkoff D, Lockhart DJ, Sharp KA, Honig B (1994a) Calculation of electrostatic effects at the amino terminus of an α-helix. Biophys J 67: 2251-2260
    • (1994) Biophys J , vol.67 , pp. 2251-2260
    • Sitkoff, D.1    Lockhart, D.J.2    Sharp, K.A.3    Honig, B.4
  • 100
    • 32844457567 scopus 로고
    • Accurate calculation of hydration free energies using macroscopic solvent models
    • Sitkoff D, Sharp KA, Honig B (1994b) Accurate calculation of hydration free energies using macroscopic solvent models. J Phys Chem 98: 1978-1988
    • (1994) J Phys Chem , vol.98 , pp. 1978-1988
    • Sitkoff, D.1    Sharp, K.A.2    Honig, B.3
  • 101
    • 0037653183 scopus 로고
    • Including solvent and counterion effects in the force fields of macromolecular mechanics: The field integrated electrostatic approach (FIESTA)
    • Beveridge DL, Lavery R (eds) Adenine Press, New York
    • Sklenar H, Eisenhaber F, Poncin M, Lavery R (1990) Including solvent and counterion effects in the force fields of macromolecular mechanics: the field integrated electrostatic approach (FIESTA). In: Beveridge DL, Lavery R (eds) Theoretical biochemistry & molecular biophysics. Adenine Press, New York, pp 317-336
    • (1990) Theoretical Biochemistry & Molecular Biophysics , pp. 317-336
    • Sklenar, H.1    Eisenhaber, F.2    Poncin, M.3    Lavery, R.4
  • 103
    • 0030781781 scopus 로고    scopus 로고
    • Electrostatic effects on electron-transfer kinetics in the cytochrome f-plastocyanin complex
    • Soriano GM, Cramer WA, Krishtalik LI (1997) Electrostatic effects on electron-transfer kinetics in the cytochrome f-plastocyanin complex. Biophys J 73: 3265-3276
    • (1997) Biophys J , vol.73 , pp. 3265-3276
    • Soriano, G.M.1    Cramer, W.A.2    Krishtalik, L.I.3
  • 104
    • 0344778061 scopus 로고
    • Semi-analytical treatment of solvation for molecular mechanics and dynamics
    • Still WC, Tempczyk A, Hawley RC, Hendrickson T (1990) Semi-analytical treatment of solvation for molecular mechanics and dynamics. J Am Chem Soc 112: 6127-6129
    • (1990) J am Chem Soc , vol.112 , pp. 6127-6129
    • Still, W.C.1    Tempczyk, A.2    Hawley, R.C.3    Hendrickson, T.4
  • 105
    • 0029644936 scopus 로고
    • Electrostatic analysis of TEM1 b-lactamase: Effect of substrate binding, steep potential gradients and consequences of site-directed mutations
    • Swaren P, Maveyraud L, Guillet V, Masson J-M, Mourey L, Samama J-P (1995) Electrostatic analysis of TEM1 b-lactamase: effect of substrate binding, steep potential gradients and consequences of site-directed mutations. Structure 3: 603-613
    • (1995) Structure , vol.3 , pp. 603-613
    • Swaren, P.1    Maveyraud, L.2    Guillet, V.3    Masson, J.-M.4    Mourey, L.5    Samama, J.-P.6
  • 107
    • 77956727554 scopus 로고
    • The interpretation of hydrogen ion titration curves of proteins
    • Tanford C (1962) The interpretation of hydrogen ion titration curves of proteins. Adv Protein Chem 17: 69-165
    • (1962) Adv Protein Chem , vol.17 , pp. 69-165
    • Tanford, C.1
  • 108
    • 0014718113 scopus 로고
    • Protein denaturation. Part C: Theoretical models for the mechanisms of denaturation
    • Tanford C (1970) Protein denaturation. Part C: theoretical models for the mechanisms of denaturation. Adv Protein Chem 25: 1-95
    • (1970) Adv Protein Chem , vol.25 , pp. 1-95
    • Tanford, C.1
  • 109
    • 33947468892 scopus 로고
    • Theory of protein titration curves
    • Tanford C, Kirkwood JG (1957) Theory of protein titration curves. J Am Chem Soc 79: 5333-5347
    • (1957) J am Chem Soc , vol.79 , pp. 5333-5347
    • Tanford, C.1    Kirkwood, J.G.2
  • 110
    • 0015520587 scopus 로고
    • Interpretation of protein titration curves. Application to lysozyme
    • Tanford C, Roxby R (1972) Interpretation of protein titration curves. Application to lysozyme. Biochemistry 11: 2192-2198
    • (1972) Biochemistry , vol.11 , pp. 2192-2198
    • Tanford, C.1    Roxby, R.2
  • 111
    • 0021103512 scopus 로고
    • 1H-NMR study on the tautomerism of the imidazole ring of histidine residues. I. Microscopic pK values and molar ratios of tautomers in histidine-containing peptides
    • 1H-NMR study on the tautomerism of the imidazole ring of histidine residues. I. Microscopic pK values and molar ratios of tautomers in histidine-containing peptides. Biochim Biophys Acta 742: 576-585
    • (1983) Biochim Biophys Acta , vol.742 , pp. 576-585
    • Tanokura, M.1
  • 112
    • 0030612614 scopus 로고    scopus 로고
    • a changes in a protein tyrosine phosphatase: Experimental and theoretical determination of electrostatic properties in a small protein
    • a changes in a protein tyrosine phosphatase: experimental and theoretical determination of electrostatic properties in a small protein. Biochemistry 39: 11984-11994
    • (1997) Biochemistry , vol.39 , pp. 11984-11994
    • Tishmack, P.A.1    Bashford, D.2    Harms, E.3    Etten, R.L.V.4
  • 113
    • 0031358013 scopus 로고    scopus 로고
    • Calculation of absolute and relative acidities of substituted imidazoles in aqueous solvent
    • Topol IA, Tawa GJ, Burt SK, Rashin AA (1997) Calculation of absolute and relative acidities of substituted imidazoles in aqueous solvent. J Phys Chem A 101: 10075-10081
    • (1997) J Phys Chem A , vol.101 , pp. 10075-10081
    • Topol, I.A.1    Tawa, G.J.2    Burt, S.K.3    Rashin, A.A.4
  • 115
    • 0012882483 scopus 로고    scopus 로고
    • Shifts of the special pair redox potential of mutants of Rhodobacter sphaeroides calculated with Delphi and Charmm energy functions
    • Michel-Beyerle EM (ed): Springer, Berlin Heidelberg New York
    • Ullmann GM, Muegge I, Knapp EW (1996) Shifts of the special pair redox potential of mutants of Rhodobacter sphaeroides calculated with Delphi and Charmm energy functions. In: Michel-Beyerle EM (ed): The reaction centers of photosynthetic bacteria. Structure and dynamics. Springer, Berlin Heidelberg New York, pp 143-155
    • (1996) The Reaction Centers of Photosynthetic Bacteria. Structure and Dynamics , pp. 143-155
    • Ullmann, G.M.1    Muegge, I.2    Knapp, E.W.3
  • 116
    • 0031041540 scopus 로고    scopus 로고
    • Computational simulation and analysis of the dynamic association between plastocyanin and cytochrome f. Consequences for the electron-transfer reaction
    • Ullmann GM, Knapp EW, Kostić NM (1997) Computational simulation and analysis of the dynamic association between plastocyanin and cytochrome f. Consequences for the electron-transfer reaction. J Am Chem Soc 119: 42-52
    • (1997) J am Chem Soc , vol.119 , pp. 42-52
    • Ullmann, G.M.1    Knapp, E.W.2    Kostić, N.M.3
  • 117
    • 0001290941 scopus 로고
    • Conformational energy calculations on polypeptides and proteins
    • Vásquez M, Némethy G, Scheraga HA (1994) Conformational energy calculations on polypeptides and proteins. Chem Rev 94: 2183-2239
    • (1994) Chem Rev , vol.94 , pp. 2183-2239
    • Vásquez, M.1    Némethy, G.2    Scheraga, H.A.3
  • 119
    • 33748641995 scopus 로고    scopus 로고
    • Effect of ionic strength on the protonation of various amino acids analysed by the mean sperical approximation
    • Vilaiño T, Fiol S, Armesto XL, Brandariz I, Saraste de Vicente ME (1997) Effect of ionic strength on the protonation of various amino acids analysed by the mean sperical approximation. J Chem Soc Faraday Trans 93: 413-417
    • (1997) J Chem Soc Faraday Trans , vol.93 , pp. 413-417
    • Vilaiño, T.1    Fiol, S.2    Armesto, X.L.3    Brandariz, I.4    De Saraste Vicente, M.E.5
  • 120
    • 0032536161 scopus 로고    scopus 로고
    • Titration calculations of foot-and-mouth disease virus capsids and their stabilities as a function of pH
    • Vlijmen HWT van, Curry S, Schaefer M, Karplus M (1998) Titration calculations of foot-and-mouth disease virus capsids and their stabilities as a function of pH. J Mol Biol 275: 295-308
    • (1998) J Mol Biol , vol.275 , pp. 295-308
    • Van Vlijmen, H.W.T.1    Curry, S.2    Schaefer, M.3    Karplus, M.4
  • 121
    • 0025891413 scopus 로고
    • Electrostatic energy and macromolecular function
    • Warshel A, Åqvist J (1991) Electrostatic energy and macromolecular function. Annu Rev Biophys Biophys Chem 20: 267-298
    • (1991) Annu Rev Biophys Biophys Chem , vol.20 , pp. 267-298
    • Warshel, A.1    Åqvist, J.2
  • 122
    • 0032054517 scopus 로고    scopus 로고
    • Electrostatic effects in macromolecules: Fundamental concepts and practical modeling
    • Warshel A, Papazyan A (1998) Electrostatic effects in macromolecules: fundamental concepts and practical modeling. Curr Opin Struct Biol 8: 211-217
    • (1998) Curr Opin Struct Biol , vol.8 , pp. 211-217
    • Warshel, A.1    Papazyan, A.2
  • 123
    • 0021476470 scopus 로고
    • Calculations of electrostatic interaction in biological systems and in solution
    • Warshel A, Russel ST (1984) Calculations of electrostatic interaction in biological systems and in solution. Q Rev Biophys 17: 283-422
    • (1984) Q Rev Biophys , vol.17 , pp. 283-422
    • Warshel, A.1    Russel, S.T.2
  • 125
    • 0001926107 scopus 로고
    • Electrochemical studies of porphyrin redox reactions as cytochrome models
    • Wilson GS (1983) Electrochemical studies of porphyrin redox reactions as cytochrome models. Bioelectrochem Bioenerg 1: 172-179
    • (1983) Bioelectrochem Bioenerg , vol.1 , pp. 172-179
    • Wilson, G.S.1
  • 126
    • 0031052519 scopus 로고    scopus 로고
    • Prediction of titration properties of structures of a protein derived from molecular dynamics trajectories
    • Wlodek ST, Antosiewicz J, McCammon JA (1997) Prediction of titration properties of structures of a protein derived from molecular dynamics trajectories. Protein Sci 6: 373-382
    • (1997) Protein Sci , vol.6 , pp. 373-382
    • Wlodek, S.T.1    Antosiewicz, J.2    McCammon, J.A.3
  • 127
    • 67650040559 scopus 로고
    • Linked functions and reciprocal effects in hemoglobin: A second look
    • Wyman J (1964) Linked functions and reciprocal effects in hemoglobin: a second look. Adv Protein Chem 19: 223-286
    • (1964) Adv Protein Chem , vol.19 , pp. 223-286
    • Wyman, J.1
  • 128
    • 0000364298 scopus 로고
    • The binding potential, a neglected linkage concept
    • Wyman J (1965) The binding potential, a neglected linkage concept. J Mol Biol 11: 631-644
    • (1965) J Mol Biol , vol.11 , pp. 631-644
    • Wyman, J.1
  • 129
    • 0014096443 scopus 로고
    • The proton dissociation constant of pyrrole, indole and related compounds
    • Yagil G (1967) The proton dissociation constant of pyrrole, indole and related compounds. Tetrahedron 23: 2855-2861
    • (1967) Tetrahedron , vol.23 , pp. 2855-2861
    • Yagil, G.1
  • 130
    • 0027231258 scopus 로고
    • On the pH dependence of protein stability
    • Yang A-S, Honig B (1993) On the pH dependence of protein stability. J Mol Biol 231: 459-474
    • (1993) J Mol Biol , vol.231 , pp. 459-474
    • Yang, A.-S.1    Honig, B.2
  • 132
    • 0028859420 scopus 로고
    • Conformation and hydrogen ion titration of proteins: A continuum electrostatic model with conformational flexibility
    • You T, Bashford D (1995) Conformation and hydrogen ion titration of proteins: a continuum electrostatic model with conformational flexibility. Biophys J 69: 1721-1733
    • (1995) Biophys J , vol.69 , pp. 1721-1733
    • You, T.1    Bashford, D.2
  • 133
    • 84962420696 scopus 로고    scopus 로고
    • A fast and space-efficient boundary element method for computing electrostatic and hydration effects in large molecules
    • Zauhar RY, Varnek A (1996) A fast and space-efficient boundary element method for computing electrostatic and hydration effects in large molecules. J Comput Chem 17: 864-877
    • (1996) J Comput Chem , vol.17 , pp. 864-877
    • Zauhar, R.Y.1    Varnek, A.2
  • 135
    • 0344791553 scopus 로고
    • Approximate density functional theory as a practical tool in molecular energetics and dynamics
    • Ziegler T (1991) Approximate density functional theory as a practical tool in molecular energetics and dynamics. Chem Rev 91: 651-667
    • (1991) Chem Rev , vol.91 , pp. 651-667
    • Ziegler, T.1


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