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Volumn 74, Issue 3, 1998, Pages 1241-1250

Calculation of electron transfer reorganization energies using the finite difference Poisson-Boltzmann model

Author keywords

[No Author keywords available]

Indexed keywords

CYTOCHROME B; CYTOCHROME C; HEMOPROTEIN; MYOGLOBIN;

EID: 0031886681     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(98)77838-5     Document Type: Article
Times cited : (77)

References (55)
  • 1
    • 0028305457 scopus 로고
    • Prediction of pH-dependent properties of proteins
    • Antosiewicz, J., J. A. McCammon and M. K. Gilson. 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
  • 2
    • 0024293244 scopus 로고
    • Electrostatic effects of charge perturbations introduced by metal oxidation in proteins: A theoretical analysis
    • Bashford, D., M. Karplus, and G. W. Canters. 1988. Electrostatic effects of charge perturbations introduced by metal oxidation in proteins: a theoretical analysis. J. Mol. Biol. 203:507-510.
    • (1988) J. Mol. Biol. , vol.203 , pp. 507-510
    • Bashford, D.1    Karplus, M.2    Canters, G.W.3
  • 4
    • 0000682989 scopus 로고    scopus 로고
    • Finite difference Poisson-Boltzmann electrostatic calculations: Increased accuracy achieved by harmonic dielectric smoothing and charge antialiasing
    • Bruccoleri, R. E., J. Novotny, K. A. Sharp, and M. E. Davis. 1996. Finite difference Poisson-Boltzmann electrostatic calculations: increased accuracy achieved by harmonic dielectric smoothing and charge antialiasing. J. Comp. Chem. 18:268-276.
    • (1996) J. Comp. Chem. , vol.18 , pp. 268-276
    • Bruccoleri, R.E.1    Novotny, J.2    Sharp, K.A.3    Davis, M.E.4
  • 5
    • 13544274971 scopus 로고
    • High driving force electron transfer in metalloproteins
    • Chang, I. J., H. B. Gray, and J. Winkler. 1991. High driving force electron transfer in metalloproteins. J. Am. Chem. Soc. 113:7056-7057.
    • (1991) J. Am. Chem. Soc. , vol.113 , pp. 7056-7057
    • Chang, I.J.1    Gray, H.B.2    Winkler, J.3
  • 6
    • 0023044641 scopus 로고
    • Control of the redox potential of cytochrome c and microscopic dielectric effects in proteins
    • Churg, A. K. and A. Warshel. 1986. Control of the redox potential of cytochrome c and microscopic dielectric effects in proteins. Biochemistry. 25:1675-1681.
    • (1986) Biochemistry , vol.25 , pp. 1675-1681
    • Churg, A.K.1    Warshel, A.2
  • 8
    • 0028957690 scopus 로고
    • Crystallographic refinement at 2.3 Å resolution and refined model of the photosynthetic reaction centre from Rhodopseudomonas viridis
    • Deisenhofer, J., O. Epp, I. Sinning, and H. Michel. 1989. Crystallographic refinement at 2.3 Å resolution and refined model of the photosynthetic reaction centre from Rhodopseudomonas viridis. J. Mol. Biol. 246: 429-457.
    • (1989) J. Mol. Biol. , vol.246 , pp. 429-457
    • Deisenhofer, J.1    Epp, O.2    Sinning, I.3    Michel, H.4
  • 9
    • 0000967631 scopus 로고
    • A comparison of perturbation method and PB electrostatic calculations for estimation of relative solvation free energies
    • Ewing, P. J., and T. P. Lybrand. 1993. A comparison of perturbation method and PB electrostatic calculations for estimation of relative solvation free energies. J. Phys. Chem. 98:1748-1752.
    • (1993) J. Phys. Chem. , vol.98 , pp. 1748-1752
    • Ewing, P.J.1    Lybrand, T.P.2
  • 11
    • 84988087911 scopus 로고
    • Calculating the electrostatic potential of molecules in solution: Method and error assessment
    • Gilson, M., K. A. Sharp, and B. Honig. 1988. Calculating the electrostatic potential of molecules in solution: method and error assessment. J. Comp. Chem. 9:327-335.
    • (1988) J. Comp. Chem. , vol.9 , pp. 327-335
    • Gilson, M.1    Sharp, K.A.2    Honig, B.3
  • 12
    • 33845185134 scopus 로고
    • Temperature and dG dependence of the electron transfer in reaction center protein from R. sphaeroides with different quinones as Qa
    • Gunner, M., and P. L. Dutton. 1989. Temperature and dG dependence of the electron transfer in reaction center protein from R. sphaeroides with different quinones as Qa. J. Am. Chem. Soc. 111:3400-3412.
    • (1989) J. Am. Chem. Soc. , vol.111 , pp. 3400-3412
    • Gunner, M.1    Dutton, P.L.2
  • 13
    • 84884906575 scopus 로고
    • Electrostatic analysis of the midpoints of the four hemes in the bound cytochrome of the reaction center of Rp. viridis
    • Ch. 2. Kluwer Academic Publishers, The Netherlands
    • Gunner, M., and B. Honig. 1990. Electrostatic analysis of the midpoints of the four hemes in the bound cytochrome of the reaction center of Rp. viridis. In Perspectives in Photosynthesis, Ch. 2. Kluwer Academic Publishers, The Netherlands.
    • (1990) Perspectives in Photosynthesis
    • Gunner, M.1    Honig, B.2
  • 14
    • 0025944990 scopus 로고
    • Electrostatic control of midpoint potentials in the cytochrome subunit of the Rhodopseudomonas viridis reaction center
    • Gunner, M. R., and B. Honig. 1991. Electrostatic control of midpoint potentials in the cytochrome subunit of the 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
  • 15
    • 0000525721 scopus 로고
    • Multigrid solution of the Poisson-Boltzmann equation
    • Holst, M., and F. Saied. 1993. Multigrid solution of the Poisson-Boltzmann equation. J. Comp. Chem. 14:105-113.
    • (1993) J. Comp. Chem. , vol.14 , pp. 105-113
    • Holst, M.1    Saied, F.2
  • 16
    • 0001656613 scopus 로고
    • Preparation, characterization and intramolecular electron transfer in pentaammineruthenium histidine-26 cytochrome b5 derivatives
    • Jacobs, B., M. Mauk, W. Funk, MacGillivray, A. G. Mauk, and H. Gray. 1991. Preparation, characterization and intramolecular electron transfer in pentaammineruthenium histidine-26 cytochrome b5 derivatives. J. Am. Chem. Soc. 113:4390-4394.
    • (1991) J. Am. Chem. Soc. , vol.113 , pp. 4390-4394
    • Jacobs, B.1    Mauk, M.2    Funk, W.3    MacGillivray4    Mauk, A.G.5    Gray, H.6
  • 17
    • 85022423714 scopus 로고
    • Electrostatic contributions to solvation energies: Comparison of free energy perturbation and continuum calculations
    • Jean-Charles, A., A. Nicholls, K. Sharp, B. Honig, A. Tempczyk, T. Hendrickson and C. Still. 1990. Electrostatic contributions to solvation energies: comparison of free energy perturbation and continuum calculations. J. Am. Chem. Soc. 113:1454-1455.
    • (1990) J. Am. Chem. Soc. , vol.113 , pp. 1454-1455
    • Jean-Charles, A.1    Nicholls, A.2    Sharp, K.3    Honig, B.4    Tempczyk, A.5    Hendrickson, T.6    Still, C.7
  • 18
    • 0000354626 scopus 로고
    • Investigation of the free energy functions for electron transfer reactions
    • King, G., and A. Warshel. 1990. Investigation of the free energy functions for electron transfer reactions. J. Chem. Phys. 93:8682-8692.
    • (1990) J. Chem. Phys. , vol.93 , pp. 8682-8692
    • King, G.1    Warshel, A.2
  • 19
  • 20
    • 5544264558 scopus 로고
    • Gaussian fluctuation formula for electrostatic free energy changes in solution
    • Levy, R. M., M. Belhadi, and D. Kitchen. 1991. Gaussian fluctuation formula for electrostatic free energy changes in solution. J. Chem. Phys. 95:3627-3633.
    • (1991) J. Chem. Phys. , vol.95 , pp. 3627-3633
    • Levy, R.M.1    Belhadi, M.2    Kitchen, D.3
  • 21
    • 0028000028 scopus 로고
    • Specific alteration of the oxidation potential of the electron donor in reaction centers from R. sphaeroides
    • Lin, X., H. Murchison, V. Nagarajan, W. Parson, J. Allen, and J. Williams. 1994. Specific alteration of the oxidation potential of the electron donor in reaction centers from R. sphaeroides. Proc. Natl. Acad. Sci. U.S.A. 91:10265-10269.
    • (1994) Proc. Natl. Acad. Sci. U.S.A. , vol.91 , pp. 10265-10269
    • Lin, X.1    Murchison, H.2    Nagarajan, V.3    Parson, W.4    Allen, J.5    Williams, J.6
  • 22
    • 33751158272 scopus 로고
    • Energetics of charge transfer reactions in solvent
    • Liu, Y., and M. Newton. 1994. Energetics of charge transfer reactions in solvent. J. Phys. Chem. 98:7162-7171.
    • (1994) J. Phys. Chem. , vol.98 , pp. 7162-7171
    • Liu, Y.1    Newton, M.2
  • 23
    • 0029354611 scopus 로고
    • Solvent reorganization and donor/ acceptor coupling in electron transfer processes: Self consistent reaction field theory and ab initio applications
    • Liu, Y. P., and M. Newton. 1995. Solvent reorganization and donor/ acceptor coupling in electron transfer processes: self consistent reaction field theory and ab initio applications. J. Phys. Chem. 99:12382-1-386.
    • (1995) J. Phys. Chem. , vol.99 , pp. 12382-11386
    • Liu, Y.P.1    Newton, M.2
  • 24
    • 0347281470 scopus 로고
    • Diabatic surfaces and the pathway for primary electron transfer in a photosynthetic reaction center
    • Marchi, M., J. Gehlen, D. Chandler, and M. Newton. 1993. Diabatic surfaces and the pathway for primary electron transfer in a photosynthetic reaction center. J. Am. Chem. Soc. 115:4178-4190.
    • (1993) J. Am. Chem. Soc. , vol.115 , pp. 4178-4190
    • Marchi, M.1    Gehlen, J.2    Chandler, D.3    Newton, M.4
  • 25
    • 0009869207 scopus 로고
    • Electrostatic free energy and other properties of states having nonequilibrium polarization. I
    • Marcus, R. 1956a. Electrostatic free energy and other properties of states having nonequilibrium polarization. I. J. Chem. Phys. 24:979-989.
    • (1956) J. Chem. Phys. , vol.24 , pp. 979-989
    • Marcus, R.1
  • 26
    • 0010884753 scopus 로고
    • On the theory of oxidation-reduction reactions involving electron transfer. I
    • Marcus, R. 1956b. On the theory of oxidation-reduction reactions involving electron transfer. I. J. Chem. Phys. 24:966-978.
    • (1956) J. Chem. Phys. , vol.24 , pp. 966-978
    • Marcus, R.1
  • 27
    • 0000378873 scopus 로고
    • Free energy of nonequilibrium polarization systems. II. Homogeneous and electrode systems
    • Marcus, R. 1963. Free energy of nonequilibrium polarization systems. II. Homogeneous and electrode systems. J. Chem. Phys. 38:1858-1862.
    • (1963) J. Chem. Phys. , vol.38 , pp. 1858-1862
    • Marcus, R.1
  • 28
    • 0022004980 scopus 로고
    • Electron transfers in chemistry and biology
    • Marcus, R., and N. Sutin. 1985. Electron transfers in chemistry and biology. Biochim. Biophys. Acta. 811:265-322.
    • (1985) Biochim. Biophys. Acta. , vol.811 , pp. 265-322
    • Marcus, R.1    Sutin, N.2
  • 29
    • 0001215319 scopus 로고
    • The x-ray crystallographic structure of calf liver cytochrome b5
    • Academic Press, New York
    • Mathews, F. S., E. W. Czerwinski, and P. Argos. 1979. The x-ray crystallographic structure of calf liver cytochrome b5. In The Porphyrins. Academic Press, New York.
    • (1979) The Porphyrins
    • Mathews, F.S.1    Czerwinski, E.W.2    Argos, P.3
  • 30
    • 0000614078 scopus 로고
    • Driving force effects on the rate of long-range electron transfer in ruthenium modified cytochrome c
    • Meade, T., H. Gray, and J. Winkler. 1989. Driving force effects on the rate of long-range electron transfer in ruthenium modified cytochrome c. J. Am. Chem. Soc. 111:4353-4356.
    • (1989) J. Am. Chem. Soc. , vol.111 , pp. 4353-4356
    • Meade, T.1    Gray, H.2    Winkler, J.3
  • 32
    • 0030828226 scopus 로고    scopus 로고
    • The reorganization energy of cytochrome-c revisited
    • Muegge, I., P. Qi, J. Wand, Z. Chu, and A. Warshel. 1997. The reorganization energy of cytochrome-c revisited. J. Phys. Chem. 101:825-836.
    • (1997) J. Phys. Chem. , vol.101 , pp. 825-836
    • Muegge, I.1    Qi, P.2    Wand, J.3    Chu, Z.4    Warshel, A.5
  • 33
    • 0001403323 scopus 로고
    • A Greens function approach to calculating electrostatic reorganization energies
    • Newton, M., and H. Friedman. 1988. A Greens function approach to calculating electrostatic reorganization energies. J. Chem. Phys. 88: 4460.
    • (1988) J. Chem. Phys. , vol.88 , pp. 4460
    • Newton, M.1    Friedman, H.2
  • 34
    • 84986486656 scopus 로고
    • A rapid finite difference algorithm utilizing successive over-relaxation to solve the Poisson-Boltzmann equation
    • Nicholls, A., and B. Honig. 1991. A rapid finite difference algorithm utilizing successive over-relaxation to solve the Poisson-Boltzmann equation. J. Comp. Chem. 12:435-445.
    • (1991) J. Comp. Chem. , vol.12 , pp. 435-445
    • Nicholls, A.1    Honig, B.2
  • 35
    • 0026319199 scopus 로고
    • Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons
    • Nicholls, A., K. A. Sharp, and H. Honig. 1991. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins. 11:281-296.
    • (1991) Proteins , vol.11 , pp. 281-296
    • Nicholls, A.1    Sharp, K.A.2    Honig, H.3
  • 36
    • 0025368499 scopus 로고
    • Electrostatic control of charge separation in bacterial photosynthesis
    • Parson, W., Z. Chu, and A. Warshel. 1990. Electrostatic control of charge separation in bacterial photosynthesis. Biochim. Biophys. Acta. 1017: 251-272.
    • (1990) Biochim. Biophys. Acta. , vol.1017 , pp. 251-272
    • Parson, W.1    Chu, Z.2    Warshel, A.3
  • 37
    • 33845281231 scopus 로고
    • A simple method for the calculation of hydration enthalpies of polar molecules with arbitrary shapes
    • Rashin, A. A., and K. Namboodiri. 1987. A simple method for the calculation of hydration enthalpies of polar molecules with arbitrary shapes. J. Phys. Chem. 91:6003-6012.
    • (1987) J. Phys. Chem. , vol.91 , pp. 6003-6012
    • Rashin, A.A.1    Namboodiri, K.2
  • 38
    • 0029038105 scopus 로고
    • Salt effects on polyelectrolyte-ligand binding: Comparison of Poisson-Boltzmann and limiting law counterion binding models
    • Sharp, K. A., R. Friedman, V. Misra, J. Hecht, and B. Honig. 1995. Salt effects on polyelectrolyte-ligand binding: comparison of Poisson-Boltzmann and limiting law counterion binding models. Biopolymers. 36:245-262.
    • (1995) Biopolymers , vol.36 , pp. 245-262
    • Sharp, K.A.1    Friedman, R.2    Misra, V.3    Hecht, J.4    Honig, B.5
  • 39
    • 0025283002 scopus 로고
    • Electrostatic interactions in macromolecules: Theory and applications
    • Sharp, K., and B. Honig. 1990. Electrostatic interactions in macromolecules: theory and applications. Annu. Rev. Biophys. Biophys. Chem. 19:301-332.
    • (1990) Annu. Rev. Biophys. Biophys. Chem. , vol.19 , pp. 301-332
    • Sharp, K.1    Honig, B.2
  • 40
    • 0029833446 scopus 로고    scopus 로고
    • Charge screening and the dielectric-constant of proteins: Insights from molecular-dynamics
    • Simonson, T., and C. L. Brooks. 1996. Charge screening 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
  • 41
    • 0000831520 scopus 로고
    • Solvation free energies estimated from a macroscopic continuum theory
    • Simonson, T., and A. Brunger. 1994. Solvation free energies estimated from a macroscopic continuum theory. J. Phys. Chem. 98:4683-4694.
    • (1994) J. Phys. Chem. , vol.98 , pp. 4683-4694
    • Simonson, T.1    Brunger, A.2
  • 42
    • 0028876827 scopus 로고
    • Internal and interfacial dielectric properties of cytochrome c from molecular dynamics in aqueous solution
    • Simonson, T., and D. Perahia. 1995. Internal and interfacial dielectric properties of cytochrome c from molecular dynamics in aqueous solution. Proc. Natl. Acad. Sci. USA. 92:1082-1086.
    • (1995) Proc. Natl. Acad. Sci. USA , vol.92 , pp. 1082-1086
    • Simonson, T.1    Perahia, D.2
  • 43
    • 32844457567 scopus 로고
    • Accurate calculation of hydration free energies using macroscopic solvent models
    • Sitkoff, D., K. Sharp, and B. Honig. 1994. 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.2    Honig, B.3
  • 44
    • 0001008706 scopus 로고
    • Dielectric properties of trypsin inhibitor and lysozyme calculated from molecular dynamics simulations
    • Smith, P., R. Brunne, A. Mark, and W. vanGunsteren. 1993. Dielectric properties of trypsin inhibitor and lysozyme calculated from molecular dynamics simulations. J. Phys. Chem. 97:2009-2014.
    • (1993) J. Phys. Chem. , vol.97 , pp. 2009-2014
    • Smith, P.1    Brunne, R.2    Mark, A.3    VanGunsteren, W.4
  • 45
    • 0000328844 scopus 로고
    • A new vertex algorithm to calculate solvent accessible surface areas
    • Sridharan, S., A. Nicholls, and B. Honig. 1992. A new vertex algorithm to calculate solvent accessible surface areas. Biophys. J. 61:995.
    • (1992) Biophys. J. , vol.61 , pp. 995
    • Sridharan, S.1    Nicholls, A.2    Honig, B.3
  • 46
    • 0028238239 scopus 로고
    • Dielectric asymmetry in the photosynthetic reaction center
    • Steffen, M., K. Lao, and S. Boxer. 1994. Dielectric asymmetry in the photosynthetic reaction center. Science. 264:810-816.
    • (1994) Science , vol.264 , pp. 810-816
    • Steffen, M.1    Lao, K.2    Boxer, S.3
  • 47
    • 0017349738 scopus 로고
    • Structure of myoglobin refined at 2.0 angstroms
    • Takano, T. 1977. Structure of myoglobin refined at 2.0 angstroms. J. Mol. Biol. 110:569-584.
    • (1977) J. Mol. Biol. , vol.110 , pp. 569-584
    • Takano, T.1
  • 48
    • 0019888623 scopus 로고
    • Conformation change of cytochrome c. I. Ferrocytochrome c structure refined at 1.5 angstroms resolution
    • Takano, T., and R. E. Dickerson. 1981. Conformation change of cytochrome c. I. Ferrocytochrome c structure refined at 1.5 angstroms resolution. J. Mol. Biol. 153:79-94.
    • (1981) J. Mol. Biol. , vol.153 , pp. 79-94
    • Takano, T.1    Dickerson, R.E.2
  • 50
    • 0026527492 scopus 로고
    • Chromophore-protein interactions and the function of the photosynthetic reaction center: A molecular dynamics study
    • Treutlein, H., K. Schulten, r. A. Brunge, M. Karplus, J. Deisenhofer, and H. Michel 1992. Chromophore-protein interactions and the function of the photosynthetic reaction center: a molecular dynamics study. Proc. Natl. Acad. Sci. USA. 89:75-79.
    • (1992) Proc. Natl. Acad. Sci. USA , vol.89 , pp. 75-79
    • Treutlein, H.1    Schulten, K.2    Brunge, R.A.3    Karplus, M.4    Deisenhofer, J.5    Michel, H.6
  • 51
    • 0031030068 scopus 로고    scopus 로고
    • Classical molecular dynamics simulation of the photoinduced electron transfer dynamics of plastocyanin
    • Ungar, L., N. Scherer, and G. Voth. 1997. Classical molecular dynamics simulation of the photoinduced electron transfer dynamics of plastocyanin. Biophys. J. 72:5-17.
    • (1997) Biophys. J. , vol.72 , pp. 5-17
    • Ungar, L.1    Scherer, N.2    Voth, G.3
  • 52
    • 0021104730 scopus 로고
    • Converting structural changes upon oxidation of cytochrome c to electrostatic reorganization energy
    • Warshel, A., and A. Churg. 1983. Converting structural changes upon oxidation of cytochrome c to electrostatic reorganization energy. J. Mol. Biol. 168:693-697.
    • (1983) J. Mol. Biol. , vol.168 , pp. 693-697
    • Warshel, A.1    Churg, A.2
  • 53
    • 33845378273 scopus 로고
    • Dependence of rate constants for photoinduced charge separation and dark charge recombination on the free energy of reaction in restricted distance porphyrin-quinone molecules
    • Wasielewski, M., M. Niemczyk, W. Svec, and E. Pewitt. 1985. Dependence of rate constants for photoinduced charge separation and dark charge recombination on the free energy of reaction in restricted distance porphyrin-quinone molecules. J. Am. Chem. Soc. 107:1080-1082.
    • (1985) J. Am. Chem. Soc. , vol.107 , pp. 1080-1082
    • Wasielewski, M.1    Niemczyk, M.2    Svec, W.3    Pewitt, E.4
  • 54
    • 0026697272 scopus 로고
    • Electron tunneling pathways in cytochrome c
    • Wuttke, D., M. Bjerrum, J. Winkler, and H. Gray. 1992. Electron tunneling pathways in cytochrome c. Science. 256:1008-1009.
    • (1992) Science , vol.256 , pp. 1008-1009
    • Wuttke, D.1    Bjerrum, M.2    Winkler, J.3    Gray, H.4
  • 55
    • 0022429751 scopus 로고
    • A new method for computing the macromolecular electric potential
    • Zauhar, R., and R. J. Morgan. 1985. A new method for computing the macromolecular electric potential. J. Mol. Biol. 186:815-820.
    • (1985) J. Mol. Biol. , vol.186 , pp. 815-820
    • Zauhar, R.1    Morgan, R.J.2


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