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Volumn 85, Issue 5, 2003, Pages 2818-2829

Prediction of Reduction Potential Changes in Rubredoxin: A Molecular Mechanics Approach

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE; RUBREDOXIN; VALINE;

EID: 0242290877     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(03)74705-5     Document Type: Article
Times cited : (22)

References (29)
  • 1
    • 0031723935 scopus 로고    scopus 로고
    • Crystal structure of rubredoxin from Pyrococcus furiosus at 0.95 Å resolution, and the structures of N-terminal methionine and formylmethionine variants of Pf Rd. Contributions of N-terminal interactions to thermostability
    • Bau, R., D. C. Rees, J. Kurtz, M. Donald, R. A. Scott, H. Huang, M. W. W. Adams, and M. K. Eidsness. 1998. Crystal structure of rubredoxin from Pyrococcus furiosus at 0.95 Å resolution, and the structures of N-terminal methionine and formylmethionine variants of Pf Rd. Contributions of N-terminal interactions to thermostability. J. Biol. Inorg. Chem. 3:484-493.
    • (1998) J. Biol. Inorg. Chem. , vol.3 , pp. 484-493
    • Bau, R.1    Rees, D.C.2    Kurtz, J.3    Donald, M.4    Scott, R.A.5    Huang, H.6    Adams, M.W.W.7    Eidsness, M.K.8
  • 2
    • 0034906470 scopus 로고    scopus 로고
    • Sequence determination of reduction potential by cysteinyl hydrogen bonds and peptide dipoles in [4Fe-4S] Ferredoxin
    • Beck, B. W., Q. Xie, and T. Ichiye. 2001. Sequence determination of reduction potential by cysteinyl hydrogen bonds and peptide dipoles in [4Fe-4S] Ferredoxin. Biophys. J. 81:601-613.
    • (2001) Biophys. J. , vol.81 , pp. 601-613
    • Beck, B.W.1    Xie, Q.2    Ichiye, T.3
  • 4
    • 0029787099 scopus 로고    scopus 로고
    • Zinc- and iron-rubredoxins from Clostridium pasteurianum at atomic resolution: A high-precision model of a ZnS4 coordination unit in a protein
    • Dauter, Z., K. S. Wilson, L. C. Sieker, J. M. Moulis, and J. Meyer. 1996. Zinc- and iron-rubredoxins from Clostridium pasteurianum at atomic resolution: a high-precision model of a ZnS4 coordination unit in a protein. Proc. Natl. Acad. Sci. USA. 93:8836-8840.
    • (1996) Proc. Natl. Acad. Sci. USA , vol.93 , pp. 8836-8840
    • Dauter, Z.1    Wilson, K.S.2    Sieker, L.C.3    Moulis, J.M.4    Meyer, J.5
  • 6
    • 0030808566 scopus 로고    scopus 로고
    • Dissecting contributions to the thermostability of Pyrococcus furiosus rubredoxin: β-sheet chimeras
    • Eidsness, M. K., K. A. Richie, A. E. Burden, and D. M. Kurtz, Jr. 1997. Dissecting contributions to the thermostability of Pyrococcus furiosus rubredoxin: β-sheet chimeras. Biochemistry. 36:10406-10413.
    • (1997) Biochemistry , vol.36 , pp. 10406-10413
    • Eidsness, M.K.1    Richie, K.A.2    Burden, A.E.3    Kurtz D.M., Jr.4
  • 7
    • 0013033198 scopus 로고
    • Water structure of crystallized proteins: High-resolution studies
    • E. Westhof, editor. CRC Press, Boca Raton
    • Frey, M. 1993. Water structure of crystallized proteins: high-resolution studies. In Water and Biological Macromolecules. E. Westhof, editor. CRC Press, Boca Raton. 98-147.
    • (1993) Water and Biological Macromolecules , pp. 98-147
    • Frey, M.1
  • 8
    • 0027054423 scopus 로고
    • Mutation of conserved residues in Escherichia coli thioredoxin: Effects on stability and function
    • Gleason, F. K. 1992. Mutation of conserved residues in Escherichia coli thioredoxin: effects on stability and function. Prot. Sci. 1:609-616.
    • (1992) Prot. Sci. , vol.1 , pp. 609-616
    • Gleason, F.K.1
  • 9
    • 0001025176 scopus 로고    scopus 로고
    • Non-linear response in ionic solvation: A theoretical investigation
    • Hyun, J.-K., and T. Ichiye. 1998. Non-linear response in ionic solvation: a theoretical investigation. J. Chem. Phys. 109:1074-1083.
    • (1998) J. Chem. Phys. , vol.109 , pp. 1074-1083
    • Hyun, J.-K.1    Ichiye, T.2
  • 10
    • 0242336075 scopus 로고    scopus 로고
    • Simulations of electron transfer proteins
    • O. M. Becker, A. D. MacKerell Jr., B. Roux, and M. Watanabe, editors. Marcel Dekker, Inc., New York, NY
    • Ichiye, T. 2001. Simulations of electron transfer proteins. In Computational Biochemistry and Biophysics. O. M. Becker, A. D. MacKerell Jr., B. Roux, and M. Watanabe, editors. Marcel Dekker, Inc., New York, NY. 393-415.
    • (2001) Computational Biochemistry and Biophysics , pp. 393-415
    • Ichiye, T.1
  • 12
    • 0026244229 scopus 로고
    • MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
    • Kraulis, P. J. 1991. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24:946-950.
    • (1991) J. Appl. Crystallogr. , vol.24 , pp. 946-950
    • Kraulis, P.J.1
  • 13
    • 0015222647 scopus 로고
    • The interpretation of protein structures: Estimation of static accessibility
    • Lee, B., and F. M. Richards. 1971. The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55:379-400.
    • (1971) J. Mol. Biol. , vol.55 , pp. 379-400
    • Lee, B.1    Richards, F.M.2
  • 14
    • 0013788501 scopus 로고
    • Rubredoxin: A new electron transfer protein from Clostridium pasteurianum
    • Lovenberg, W., and B. Sobel. 1965. Rubredoxin: a new electron transfer protein from Clostridium pasteurianum. Proc. Natl. Acad. Sci. USA. 54:193-199.
    • (1965) Proc. Natl. Acad. Sci. USA , vol.54 , pp. 193-199
    • Lovenberg, W.1    Sobel, B.2
  • 16
    • 0028057108 scopus 로고
    • RASTER3D version 2.0: A program for photorealistic molecular graphics
    • Merritt, E. A., and M. E. P. Murphy. 1994. RASTER3D version 2.0: a program for photorealistic molecular graphics. Acta Crystallogr. D50:869-873.
    • (1994) Acta Crystallogr. D , vol.50 , pp. 869-873
    • Merritt, E.A.1    Murphy, M.E.P.2
  • 17
    • 0020851111 scopus 로고
    • Correlation between rate constant for reduction and redox potential as a basis for systematic investigation of reaction mechanisms of electron transfer proteins
    • Meyer, T. E., J. A. Prezysiecki, J. A. Watkins, A. Bhattacharyya, R. P. Simondsen, M. A. Cusanovich, and G. Tollin. 1983. Correlation between rate constant for reduction and redox potential as a basis for systematic investigation of reaction mechanisms of electron transfer proteins. Proc. Natl. Acad. Sci. USA. 80:6740-6744.
    • (1983) Proc. Natl. Acad. Sci. USA , vol.80 , pp. 6740-6744
    • Meyer, T.E.1    Prezysiecki, J.A.2    Watkins, J.A.3    Bhattacharyya, A.4    Simondsen, R.P.5    Cusanovich, M.A.6    Tollin, G.7
  • 18
    • 0035100426 scopus 로고    scopus 로고
    • Water gates and other structural modulators in the reduction of Clostridium pasteurianum rubredoxin
    • Min, T., C. E. Ergenekan, M. K. Eidsness, T. Ichiye, and C. Kang. 2001. Water gates and other structural modulators in the reduction of Clostridium pasteurianum rubredoxin. Prot. Sci. 10:613-621.
    • (2001) Prot. Sci. , vol.10 , pp. 613-621
    • Min, T.1    Ergenekan, C.E.2    Eidsness, M.K.3    Ichiye, T.4    Kang, C.5
  • 19
    • 0018569234 scopus 로고
    • Redox studies on rubredoxin from sulphate and sulphur reducing bacteria
    • Moura, I., J. G. Moura, M. H. Santos, A. V. Xavier, and J. LeGall. 1979. Redox studies on rubredoxin from sulphate and sulphur reducing bacteria. FEBS Lett. 107:419-421.
    • (1979) FEBS Lett. , vol.107 , pp. 419-421
    • Moura, I.1    Moura, J.G.2    Santos, M.H.3    Xavier, A.V.4    LeGall, J.5
  • 20
    • 33646940952 scopus 로고
    • Numerical integration of the Cartesian equation of motion of a system with constraints: Molecular dynamics of n-alkanes
    • Rychaert, J. P., G. Ciccotti, and H. J. C. Berendsen. 1977. Numerical integration of the Cartesian equation of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comp. Phys. 23:327-341.
    • (1977) J. Comp. Phys. , vol.23 , pp. 327-341
    • Rychaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 23
    • 0027490297 scopus 로고
    • Influence of protein flexibility on the redox potential of rubredoxin: Energy minimization studies
    • Shenoy, V. S., and T. Ichiye. 1993. Influence of protein flexibility on the redox potential of rubredoxin: energy minimization studies. Proteins. 17:152-160.
    • (1993) Proteins , vol.17 , pp. 152-160
    • Shenoy, V.S.1    Ichiye, T.2
  • 24
    • 84986534166 scopus 로고
    • New spherical-cutoff methods for long-range forces in macromolecular simulation
    • Steinbach, P. J., and B. R. Brooks. 1994. New spherical-cutoff methods for long-range forces in macromolecular simulation. J. Comp. Chem. 15: 667-683.
    • (1994) J. Comp. Chem. , vol.15 , pp. 667-683
    • Steinbach, P.J.1    Brooks, B.R.2
  • 25
    • 0029753015 scopus 로고    scopus 로고
    • Structural origins of redox potential in iron-sulfur proteins: Electrostatic potentials of crystal structures
    • Swartz, P. D., B. W. Beck, and T. Ichiye. 1996. Structural origins of redox potential in iron-sulfur proteins: electrostatic potentials of crystal structures. Biophys. J. 71:2958-2969.
    • (1996) Biophys. J. , vol.71 , pp. 2958-2969
    • Swartz, P.D.1    Beck, B.W.2    Ichiye, T.3
  • 26
    • 0019325181 scopus 로고
    • Crystallographic refinement of rubredoxin at 1.2 Å resolution
    • Watenpaugh, K., L. C. Sieker, and L. H. Jensen. 1980. Crystallographic refinement of rubredoxin at 1.2 Å resolution. J. Mol. Biol. 138:615-633.
    • (1980) J. Mol. Biol. , vol.138 , pp. 615-633
    • Watenpaugh, K.1    Sieker, L.C.2    Jensen, L.H.3
  • 27
    • 0028998016 scopus 로고
    • Molecular dynamics simulations of rubredoxin from Clostridium pasteurianum: Changes in structure and electrostatic potential during redox reactions
    • Yelle, R. B., N.-S. Park, and T. Ichiye. 1995. Molecular dynamics simulations of rubredoxin from Clostridium pasteurianum: changes in structure and electrostatic potential during redox reactions. Proteins. 22:154-167.
    • (1995) Proteins , vol.22 , pp. 154-167
    • Yelle, R.B.1    Park, N.-S.2    Ichiye, T.3
  • 28
    • 0034001668 scopus 로고    scopus 로고
    • Mutation of the surface valine residues 8 and 44 in the rubredoxin from Clostridium pasteurianum: Solvent access versus structural changes as determinants of reversible potential
    • Xiao, Z., M. J. Maher, M. Cross, C. S. Bond, J. M. Guss, and A. G. Wedd. 2000. Mutation of the surface valine residues 8 and 44 in the rubredoxin from Clostridium pasteurianum: solvent access versus structural changes as determinants of reversible potential. J. Biol. Inorg. Chem. 5:75-84.
    • (2000) J. Biol. Inorg. Chem. , vol.5 , pp. 75-84
    • Xiao, Z.1    Maher, M.J.2    Cross, M.3    Bond, C.S.4    Guss, J.M.5    Wedd, A.G.6
  • 29
    • 0001751647 scopus 로고    scopus 로고
    • Protein determinants of metal site reduction potentials. Site directed mutagenesis studies of Clostridium pasteurianum rubredoxin
    • Zeng, Q., E. T. Smith, D. M. Kurtz, and R. A. Scott. 1996. Protein determinants of metal site reduction potentials. Site directed mutagenesis studies of Clostridium pasteurianum rubredoxin. Inorg. Chim. Acta. 242:245-251.
    • (1996) Inorg. Chim. Acta , vol.242 , pp. 245-251
    • Zeng, Q.1    Smith, E.T.2    Kurtz, D.M.3    Scott, R.A.4


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