메뉴 건너뛰기




Volumn 86, Issue 4, 2004, Pages 1987-2007

Theoretical Investigations on Azotobacter vinelandii Ferredoxin I: Effects of Electron Transfer on Protein Dynamics

Author keywords

[No Author keywords available]

Indexed keywords

FERREDOXIN; FERREDOXIN I; IRON SULFUR PROTEIN; UNCLASSIFIED DRUG;

EID: 1942423659     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(04)74261-7     Document Type: Article
Times cited : (15)

References (50)
  • 2
    • 5344278362 scopus 로고
    • Molecular dynamics simulations on HiPIP from Chromatium vinosum and comparison with NMR data
    • Banci, L., I. Bertini, P. Carloni, C. Luchinat, and P. L. Orioli. 1992. Molecular dynamics simulations on HiPIP from Chromatium vinosum and comparison with NMR data. J. Am. Chem. Soc. 114:10683-10689.
    • (1992) J. Am. Chem. Soc. , vol.114 , pp. 10683-10689
    • Banci, L.1    Bertini, I.2    Carloni, P.3    Luchinat, C.4    Orioli, P.L.5
  • 3
    • 4344606960 scopus 로고    scopus 로고
    • Multidimensional adaptive umbrella sampling: Applications to main chain and side chain peptide conformations
    • Bartels, C., and M. Karplus. 1997. Multidimensional adaptive umbrella sampling: applications to main chain and side chain peptide conformations. J. Comput. Chem. 18:1450-1462.
    • (1997) J. Comput. Chem. , vol.18 , pp. 1450-1462
    • Bartels, C.1    Karplus, M.2
  • 4
    • 0025743628 scopus 로고
    • Computer simulation and analysis of the reaction pathway of triosephosphate isomerase
    • Bash, P. A., M. J. Field, R. C. Davenport, G. A. Petsko, D. Ringe, and M. Karplus. 1991. Computer simulation and analysis of the reaction pathway of triosephosphate isomerase. Biochemistry. 30:5826-5832.
    • (1991) Biochemistry , vol.30 , pp. 5826-5832
    • Bash, P.A.1    Field, M.J.2    Davenport, R.C.3    Petsko, G.A.4    Ringe, D.5    Karplus, M.6
  • 5
    • 0000989147 scopus 로고    scopus 로고
    • Aconitase as iron-sulfur protein, enzyme, and iron-regulatory protein
    • Beinert, H., M. C. Kennedy, and C. D. Stout. 1996. Aconitase as iron-sulfur protein, enzyme, and iron-regulatory protein. Chem. Rev. 96:2335-2373.
    • (1996) Chem. Rev. , vol.96 , pp. 2335-2373
    • Beinert, H.1    Kennedy, M.C.2    Stout, C.D.3
  • 6
    • 84986492477 scopus 로고
    • Atomic charges derived from semiempirical methods
    • Besler, B. H., K. M. Merz, and P. A. Kollman. 1990. Atomic charges derived from semiempirical methods. J. Comp. Chem. 11:431-439.
    • (1990) J. Comp. Chem. , vol.11 , pp. 431-439
    • Besler, B.H.1    Merz, K.M.2    Kollman, P.A.3
  • 8
    • 36749119973 scopus 로고
    • Deformable stochastic boundaries in molecular dynamics
    • Brooks III, C. L., and M. Karplus. 1983. Deformable stochastic boundaries in molecular dynamics. J. Chem. Phys. 79:6312-6325.
    • (1983) J. Chem. Phys. , vol.79 , pp. 6312-6325
    • Brooks III, C.L.1    Karplus, M.2
  • 9
    • 0024354001 scopus 로고
    • Solvent effects on protein motion and protein effects on solvent motion: Dynamics of the active site region of lysozyme
    • Brooks III, C. L., and M. Karplus. 1989. Solvent effects on protein motion and protein effects on solvent motion: dynamics of the active site region of lysozyme. J. Mol. Biol. 208:159-181.
    • (1989) J. Mol. Biol. , vol.208 , pp. 159-181
    • Brooks III, C.L.1    Karplus, M.2
  • 10
    • 0024250301 scopus 로고
    • Polar hydrogen positions in proteins: Empirical energy function placement and neutron diffraction comparison
    • Brünger, A. T., and M. Karplus. 1988. Polar hydrogen positions in proteins: empirical energy function placement and neutron diffraction comparison. Proteins. 4:148-156.
    • (1988) Proteins , vol.4 , pp. 148-156
    • Brünger, A.T.1    Karplus, M.2
  • 11
    • 0026684043 scopus 로고
    • A 500 ps molecular dynamics simulation study of interleukin-1b in water: Correlation with nuclear magnetic resonance spectroscopy and crystallography
    • Chandrasekhar, I., G. M. Clore, A. Szabo, A. M. Gronenborn, and B. R. Brooks. 1992. A 500 ps molecular dynamics simulation study of interleukin-1b in water: correlation with nuclear magnetic resonance spectroscopy and crystallography. J. Mol. Biol. 226:239-250.
    • (1992) J. Mol. Biol. , vol.226 , pp. 239-250
    • Chandrasekhar, I.1    Clore, G.M.2    Szabo, A.3    Gronenborn, A.M.4    Brooks, B.R.5
  • 12
    • 0034659779 scopus 로고    scopus 로고
    • Atomically defined mechanism for proton transfer to a buried redox centre in a protein
    • Chen, K., J. Hirst, R. Camba, C. A. Bonagura, C. D. Stout, B. K. Burgess, and F. A. Armstrong. 2000. Atomically defined mechanism for proton transfer to a buried redox centre in a protein. Nature. 405:814-817.
    • (2000) Nature , vol.405 , pp. 814-817
    • Chen, K.1    Hirst, J.2    Camba, R.3    Bonagura, C.A.4    Stout, C.D.5    Burgess, B.K.6    Armstrong, F.A.7
  • 16
    • 33748381480 scopus 로고    scopus 로고
    • Proton-coupled electron transfer reactions: Evaluation of rate constants
    • Cukier, R. I. 1996. Proton-coupled electron transfer reactions: evaluation of rate constants. J. Phys. Chem. 100:15428-15443.
    • (1996) J. Phys. Chem. , vol.100 , pp. 15428-15443
    • Cukier, R.I.1
  • 17
    • 0000451307 scopus 로고
    • The gas-phase acidity and the acidic site of acetohydroxamic acid: An FT-ICR study
    • Decouzon, M., O. Exner, J.-F. Gal, and P.-C. Maria. 1990. The gas-phase acidity and the acidic site of acetohydroxamic acid: an FT-ICR study. J. Org. Chem. 55:3980-3981.
    • (1990) J. Org. Chem. , vol.55 , pp. 3980-3981
    • Decouzon, M.1    Exner, O.2    Gal, J.-F.3    Maria, P.-C.4
  • 18
    • 0028921999 scopus 로고
    • Demonstration of positionally disordered water within a protein hydrophobic cavity by NMR
    • Ernst, J. A., R. T. Clubb, H.-X. Zhou, A. M. Gronenborn, and G. M. Clore. 1995. Demonstration of positionally disordered water within a protein hydrophobic cavity by NMR. Science. 267:1813-1817.
    • (1995) Science , vol.267 , pp. 1813-1817
    • Ernst, J.A.1    Clubb, R.T.2    Zhou, H.-X.3    Gronenborn, A.M.4    Clore, G.M.5
  • 19
    • 0033578333 scopus 로고    scopus 로고
    • Binding of buried structural water increases the flexibility of proteins
    • Fischer, S., and C. S. Verma. 1999. Binding of buried structural water increases the flexibility of proteins. Proc. Natl. Acad. Sci. USA. 96:9613-9615.
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 9613-9615
    • Fischer, S.1    Verma, C.S.2
  • 21
    • 84946450438 scopus 로고
    • Algorithms for macromolecular dynamics and constraint dynamics
    • Van Gunsteren, W. V., and H. J. C. Berendsen. 1977. Algorithms for macromolecular dynamics and constraint dynamics. Mol. Phys. 34:1311-1327.
    • (1977) Mol. Phys. , vol.34 , pp. 1311-1327
    • Van Gunsteren, W.V.1    Berendsen, H.J.C.2
  • 22
    • 0034859929 scopus 로고    scopus 로고
    • Theoretical perspectives on proton-coupled electron transfer reactions
    • Hammes-Schiffer, S. 2001. Theoretical perspectives on proton-coupled electron transfer reactions. Acc. Chem. Res. 34:273-283.
    • (2001) Acc. Chem. Res. , vol.34 , pp. 273-283
    • Hammes-Schiffer, S.1
  • 23
    • 0029758487 scopus 로고    scopus 로고
    • Molecular control of vertebrate iron metabolism: MRNA-based regulatory circuits operated by iron, nitric oxide and oxidative stress
    • Hentze, M. W., and L. C. Kühn. 1996. Molecular control of vertebrate iron metabolism: mRNA-based regulatory circuits operated by iron, nitric oxide and oxidative stress. Proc. Natl. Acad. Sci. USA. 93:8175-8182.
    • (1996) Proc. Natl. Acad. Sci. USA , vol.93 , pp. 8175-8182
    • Hentze, M.W.1    Kühn, L.C.2
  • 24
    • 0032558152 scopus 로고    scopus 로고
    • Kinetics and mechanism of redox-coupled, long-range proton transfer in an iron-sulfur protein. Investigation by fast-scan protein-film voltammetry
    • Hirst, J., J. L. C. Duff, G. N. L. Jameson, M. A. Kemper, B. K. Burgess, and F. A. Armstrong. 1998. Kinetics and mechanism of redox-coupled, long-range proton transfer in an iron-sulfur protein. Investigation by fast-scan protein-film voltammetry. J. Am. Chem. Soc. 120:7085-7094.
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 7085-7094
    • Hirst, J.1    Duff, J.L.C.2    Jameson, G.N.L.3    Kemper, M.A.4    Burgess, B.K.5    Armstrong, F.A.6
  • 25
    • 0032366914 scopus 로고    scopus 로고
    • Evaluated gas phase basicities and proton affinities of molecules: An update
    • Hunter, E. P., and S. G. Lias. 1998. Evaluated gas phase basicities and proton affinities of molecules: an update. J. Phys. Chem. Ref. Data. 27:413-656.
    • (1998) J. Phys. Chem. Ref. Data , vol.27 , pp. 413-656
    • Hunter, E.P.1    Lias, S.G.2
  • 27
    • 0036570243 scopus 로고    scopus 로고
    • Theoretical investigation of large kinetic isotope effects for proton-coupled electron transfer in ruthenium polypyridil complexes
    • Iordanova, N., and S. Hammes-Schiffer. 2002. Theoretical investigation of large kinetic isotope effects for proton-coupled electron transfer in ruthenium polypyridil complexes. J. Am. Chem. Soc. 124:4848-4856.
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 4848-4856
    • Iordanova, N.1    Hammes-Schiffer, S.2
  • 28
    • 0035827120 scopus 로고    scopus 로고
    • Nonadiabatic instanton calculation of multistate electron transfer reaction rate: Interference effects in three- and four-states systems
    • Jang, S., and J. Cao. 2001. Nonadiabatic instanton calculation of multistate electron transfer reaction rate: interference effects in three- and four-states systems. J. Chem. Phys. 22:9959-9968.
    • (2001) J. Chem. Phys. , vol.22 , pp. 9959-9968
    • Jang, S.1    Cao, J.2
  • 29
    • 0032043449 scopus 로고    scopus 로고
    • Iron-sulfur proteins: New roles for old clusters
    • Johnson, M. K. 1998. Iron-sulfur proteins: new roles for old clusters. Curr. Opin. Chem. Biol. 2:173-181.
    • (1998) Curr. Opin. Chem. Biol. , vol.2 , pp. 173-181
    • Johnson, M.K.1
  • 31
    • 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., M. R. Nelson, C. Y. Peng, D. Bashford, and L. Noodleman. 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
  • 32
    • 2442609830 scopus 로고
    • Vectorial chemistry in bioenergetics: Cytochrome c oxidase as a redox-linked proton pump
    • Malmström, B. G. 1993. Vectorial chemistry in bioenergetics: cytochrome c oxidase as a redox-linked proton pump. Acc. Chem. Res. 26:332-338.
    • (1993) Acc. Chem. Res. , vol.26 , pp. 332-338
    • Malmström, B.G.1
  • 33
    • 0142212202 scopus 로고    scopus 로고
    • Theoretical investigations of Ferredoxin I: The possible role of internal water molecules on the coupled electron proton transfer reaction
    • Meuwly, M., and M. Karplus. 2003. Theoretical investigations of Ferredoxin I: the possible role of internal water molecules on the coupled electron proton transfer reaction. Faraday Discuss. 124:297-313.
    • (2003) Faraday Discuss , vol.124 , pp. 297-313
    • Meuwly, M.1    Karplus, M.2
  • 34
    • 0027082924 scopus 로고
    • Internal water molecules and H-bonding in biological macromolecules: A review of structural features with functional implications
    • Meyer, E. 1992. Internal water molecules and H-bonding in biological macromolecules: a review of structural features with functional implications. Prot. Sci. 1:1542-1562.
    • (1992) Prot. Sci. , vol.1 , pp. 1542-1562
    • Meyer, E.1
  • 35
    • 0000318315 scopus 로고
    • Density functional/Poisson-Boltzmann calculations of redox potentials for iron-sulfur clusters
    • Mouesca, J.-M., J. L. Chen, L. Noodleman, D. Bashford, and D. A. Case. 1994. Density functional/Poisson-Boltzmann calculations of redox potentials for iron-sulfur clusters. J. Am. Chem. Soc. 116:11898-11914.
    • (1994) J. Am. Chem. Soc. , vol.116 , pp. 11898-11914
    • Mouesca, J.-M.1    Chen, J.L.2    Noodleman, L.3    Bashford, D.4    Case, D.A.5
  • 36
    • 0019087876 scopus 로고
    • Iron-sulfur proteins: Spin-coupling model for three-iron clusters
    • Kent, T. A., B. H. Huynh, and E. Münck. 1980. Iron-sulfur proteins: spin-coupling model for three-iron clusters. Proc. Natl. Acad. Sci. USA. 77:6574-6576.
    • (1980) Proc. Natl. Acad. Sci. USA , vol.77 , pp. 6574-6576
    • Kent, T.A.1    Huynh, B.H.2    Münck, E.3
  • 37
    • 0001379854 scopus 로고
    • Broken symmetry analysis of spin coupling in iron-sulfur clusters
    • Noodleman, L., D. A. Case, and A. Aizman. 1988. Broken symmetry analysis of spin coupling in iron-sulfur clusters. J. Am. Chem. Soc. 110:1001-1005.
    • (1988) J. Am. Chem. Soc. , vol.110 , pp. 1001-1005
    • Noodleman, L.1    Case, D.A.2    Aizman, A.3
  • 38
    • 0031700045 scopus 로고    scopus 로고
    • Quantum chemical calculations of the reorganisation energy of blue copper proteins
    • Olsson, M. H. M., U. Ryde, and B. O. Roos. 1998. Quantum chemical calculations of the reorganisation energy of blue copper proteins. Prot. Sci. 7:2659-2668.
    • (1998) Prot. Sci. , vol.7 , pp. 2659-2668
    • Olsson, M.H.M.1    Ryde, U.2    Roos, B.O.3
  • 40
    • 0031076776 scopus 로고    scopus 로고
    • pH Dependence of protein stability: Absolute electrostatic free energy differences between conformations
    • Schaefer, M., M. Sommer, and M. Karplus. 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
  • 43
    • 84986468608 scopus 로고
    • An approach to computing electrostatic charges for molecules
    • Singh, U. C., and P. A. Kollman. 1984. An approach to computing electrostatic charges for molecules. J. Comput. Chem. 5:129-145.
    • (1984) J. Comput. Chem. , vol.5 , pp. 129-145
    • Singh, U.C.1    Kollman, P.A.2
  • 44
    • 0034248772 scopus 로고    scopus 로고
    • Derivation of rate expressions for nonadiabatic proton-coupled electron transfer reactions in solution
    • Soudackov, A., and S. Hammes-Schiffer. 2000. Derivation of rate expressions for nonadiabatic proton-coupled electron transfer reactions in solution. J. Chem. Phys. 113:2385-2396.
    • (2000) J. Chem. Phys. , vol.113 , pp. 2385-2396
    • Soudackov, A.1    Hammes-Schiffer, S.2
  • 46
    • 0032496372 scopus 로고    scopus 로고
    • 1.35 Å Structure of Azotobacter 7-Fe ferredoxin and determination of Fe-S cluster positions to 0.01 Å precision
    • Stout, C. D., E. A. Stura, and D. E. McRee. 1998. 1.35 Å Structure of Azotobacter 7-Fe ferredoxin and determination of Fe-S cluster positions to 0.01 Å precision. J. Mol. Biol. 278:629-639.
    • (1998) J. Mol. Biol. , vol.278 , pp. 629-639
    • Stout, C.D.1    Stura, E.A.2    McRee, D.E.3
  • 47
    • 84983035977 scopus 로고
    • The nature and analysis of substituent effects
    • Taft, R. W., and R. D. Topsom. 1987. The nature and analysis of substituent effects. Prog. Phys. Org. Chem. 16:1.
    • (1987) Prog. Phys. Org. Chem. , vol.16 , pp. 1
    • Taft, R.W.1    Topsom, R.D.2
  • 50
    • 0029936755 scopus 로고    scopus 로고
    • 4 cluster: Synthesis, stability, and geometric and electronic structures in a non-protein environment
    • 4 cluster: synthesis, stability, and geometric and electronic structures in a non-protein environment. J. Am. Chem. Soc. 118:1966-1980.
    • (1996) J. Am. Chem. Soc. , vol.118 , pp. 1966-1980
    • Zhou, J.1    Hu, Z.2    Münck, E.3    Holm, R.H.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.