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Volumn 73, Issue 4, 1997, Pages 2138-2148

A molecular dynamics study of Fe2S2 putidaredoxin: Multiple conformations of the C-terminal region

Author keywords

[No Author keywords available]

Indexed keywords

CYTOCHROME P450; FERREDOXIN; FLAVINE ADENINE NUCLEOTIDE; IRON SULFUR PROTEIN;

EID: 0030762329     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(97)78244-4     Document Type: Article
Times cited : (7)

References (45)
  • 2
    • 0028932743 scopus 로고
    • Analysis of the hyperfine-shifted N-15 resonances of the oxidized form of anabaena 7210 heterocyst ferredoxin
    • Chae, Y., and J. Markley. 1995. Analysis of the hyperfine-shifted N-15 resonances of the oxidized form of anabaena 7210 heterocyst ferredoxin. Biochemistry. 34:188-193.
    • (1995) Biochemistry , vol.34 , pp. 188-193
    • Chae, Y.1    Markley, J.2
  • 3
    • 0023865160 scopus 로고
    • Theoretical study of the product specificity in the hydroxylation of camphor, norcamphor, 5,5-difluorocamphor and pericyclocamphanone by cytochrome P450cam
    • Collins, J., and G. Loew. 1988. Theoretical study of the product specificity in the hydroxylation of camphor, norcamphor, 5,5-difluorocamphor and pericyclocamphanone by cytochrome P450cam. J. Biol. Chem. 263: 3164-3170.
    • (1988) J. Biol. Chem. , vol.263 , pp. 3164-3170
    • Collins, J.1    Loew, G.2
  • 5
    • 33846823909 scopus 로고
    • Particle mesh Ewald: An n log(n) method for Ewald sums in large systems
    • Darden, T., D. York, and L. Pedersen. 1993. Particle mesh Ewald: an n log(n) method for Ewald sums in large systems. J. Chem. Phys. 98: 10089-10092.
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 6
    • 0026442895 scopus 로고
    • Genetic variants in the putidaredoxin-cytochrome P450cam electron-transfer complex: Identification of the residue responsible for redox-state-dependent conformers
    • Davies, M., and S. Sligar. 1992. Genetic variants in the putidaredoxin-cytochrome P450cam electron-transfer complex: identification of the residue responsible for redox-state-dependent conformers. Biochemistry. 31:11383-11389.
    • (1992) Biochemistry , vol.31 , pp. 11383-11389
    • Davies, M.1    Sligar, S.2
  • 7
    • 0025600834 scopus 로고
    • Enhanced sampling in molecular dynamics: Use of the time-dependent hartree approximation for a simulation of carbon monoxide diffusion through myoglobin
    • Elber, R., and M. Karplus. 1990. Enhanced sampling in molecular dynamics: use of the time-dependent hartree approximation for a simulation of carbon monoxide diffusion through myoglobin. J. Am. Chem. Soc. 112:9161.
    • (1990) J. Am. Chem. Soc. , vol.112 , pp. 9161
    • Elber, R.1    Karplus, M.2
  • 8
    • 0028190993 scopus 로고
    • Thioanisole sulfoxidation by cytochrome P450cam(CYP101): Experimental and calculated absolute stereochemistries
    • Fruetel, J., Y. Chang, J. Collins, G. Loew, and P. Ortiz de Montellano. 1994. Thioanisole sulfoxidation by cytochrome P450cam(CYP101): experimental and calculated absolute stereochemistries. J. Am. Chem. Soc. 116:11643-11648.
    • (1994) J. Am. Chem. Soc. , vol.116 , pp. 11643-11648
    • Fruetel, J.1    Chang, Y.2    Collins, J.3    Loew, G.4    Ortiz De Montellano, P.5
  • 9
    • 0000370697 scopus 로고
    • Calculated and experimental absolute stereochemistry of the styrene and beta-methylstyrene epoxides formed by cytochrome P450cam
    • Fruetel, J., J. Collins, D. Camper, G. Loew, and P. Ortiz de Montellano. 1992. Calculated and experimental absolute stereochemistry of the styrene and beta-methylstyrene epoxides formed by cytochrome P450cam. J. Am. Chem. Soc. 114:6987-6993.
    • (1992) J. Am. Chem. Soc. , vol.114 , pp. 6987-6993
    • Fruetel, J.1    Collins, J.2    Camper, D.3    Loew, G.4    Ortiz De Montellano, P.5
  • 10
    • 0026724952 scopus 로고
    • Resonance Raman and magnetic circular dichroism studies of reduced [2Fe-2S] proteins
    • Fu, W., P. Drozdzewski, M. Davies, S. Sligar, and M. Johnson. 1992. Resonance Raman and magnetic circular dichroism studies of reduced [2Fe-2S] proteins. J. Biol. Chem. 267:15502-15510.
    • (1992) J. Biol. Chem. , vol.267 , pp. 15502-15510
    • Fu, W.1    Drozdzewski, P.2    Davies, M.3    Sligar, S.4    Johnson, M.5
  • 11
    • 0020480125 scopus 로고
    • Stereochemistry and deuterium isotope effects in camphor hydroxylation by the cytochrome P450 cam monoxygenase system
    • Gelb, M., O. Malkonen, and S. Sligar. 1982. Stereochemistry and deuterium isotope effects in camphor hydroxylation by the cytochrome P450 cam monoxygenase system. Biochem. Biophys. Res. Commun. 104: 853-858.
    • (1982) Biochem. Biophys. Res. Commun. , vol.104 , pp. 853-858
    • Gelb, M.1    Malkonen, O.2    Sligar, S.3
  • 14
    • 0000088314 scopus 로고
    • 2H substitution: Coupling of the Fe-S stretching with S-C-C bending modes
    • 2H substitution: coupling of the Fe-S stretching with S-C-C bending modes. J. Am. Chem. Soc. 111:3496-3504.
    • (1989) J. Am. Chem. Soc. , vol.111 , pp. 3496-3504
    • Han, S.1    Czernuszewicz, R.2    Spiro, R.3
  • 15
    • 0030869074 scopus 로고    scopus 로고
    • Probing the interactions of putidaredoxin with redox partners in camphor P450 5-monooxygenase by mutagenesis of surface residues
    • Holden, M., M. Mayhew, D. Bunk, A. Roitberg, and V. Vilker. 1997. Probing the interactions of putidaredoxin with redox partners in camphor P450 5-monooxygenase by mutagenesis of surface residues. J. Biol. Chem. 272:21720-21725.
    • (1997) J. Biol. Chem. , vol.272 , pp. 21720-21725
    • Holden, M.1    Mayhew, M.2    Bunk, D.3    Roitberg, A.4    Vilker, V.5
  • 16
    • 0030200476 scopus 로고    scopus 로고
    • Optimization methods for conformational sampling using a Boltzmann-weighted mean field approach
    • Huber, T., A. E. Torda, and W. F. van Gunsteren. 1996. Optimization methods for conformational sampling using a Boltzmann-weighted mean field approach. Biopolymers. 39:103-114.
    • (1996) Biopolymers , vol.39 , pp. 103-114
    • Huber, T.1    Torda, A.E.2    Van Gunsteren, W.F.3
  • 17
    • 0021096858 scopus 로고
    • Fluorescence depolarization of tryptophan residues in proteins: A molecular dynamics study
    • Ichiye, T., and M. Karplus. 1983. Fluorescence depolarization of tryptophan residues in proteins: a molecular dynamics study. Biochemistry. 22:2884-2893.
    • (1983) Biochemistry , vol.22 , pp. 2884-2893
    • Ichiye, T.1    Karplus, M.2
  • 19
    • 0001385119 scopus 로고
    • The binding and regioselectivity of reaction of (R)- and (S)-nicotine with cytochrome P-450cam: Parallel experimental and theoretical studies
    • Jones, J., W. Trager, and T. Carlson. 1993. The binding and regioselectivity of reaction of (R)- and (S)-nicotine with cytochrome P-450cam: parallel experimental and theoretical studies. J. Am. Chem. Soc. 115: 381-387.
    • (1993) J. Am. Chem. Soc. , vol.115 , pp. 381-387
    • Jones, J.1    Trager, W.2    Carlson, T.3
  • 20
    • 26444479778 scopus 로고
    • Optimization by simulated annealing
    • Kirkpatrick, S., C. Gelatt, and M. Vecchi. 1983. Optimization by simulated annealing. Science. 220:671-680.
    • (1983) Science , vol.220 , pp. 671-680
    • Kirkpatrick, S.1    Gelatt, C.2    Vecchi, M.3
  • 21
    • 0027136634 scopus 로고
    • Dehalogenation by cytochrome-p-450(cam) - Effect of oxygen level on the decomposition of 1,2-dibromo-3-chloropropane
    • Koe, G., and V. Vilker. 1993. Dehalogenation by cytochrome-p-450(cam) - effect of oxygen level on the decomposition of 1,2-dibromo-3-chloropropane. Biotechnol. Prog. 9:608-614.
    • (1993) Biotechnol. Prog. , vol.9 , pp. 608-614
    • Koe, G.1    Vilker, V.2
  • 22
    • 0028343413 scopus 로고
    • Application of a self-consistent mean-field theory to predict protein side-chains conformation and estimate their conformational entropy
    • Koehl, P., and M. DeLaruc. 1994. Application of a self-consistent mean-field theory to predict protein side-chains conformation and estimate their conformational entropy. J. Mol. Biol. 239:249-275.
    • (1994) J. Mol. Biol. , vol.239 , pp. 249-275
    • Koehl, P.1    DeLaruc, M.2
  • 23
    • 0029170114 scopus 로고
    • Molecular-dynamics simulations on solvated biomolecular systems - The particle mesh Ewald method leads to stable trajectories of DNA, RNA, and proteins
    • Kollman, P., T. Cheatham, III, and J. Miller. 1995. Molecular-dynamics simulations on solvated biomolecular systems - the particle mesh Ewald method leads to stable trajectories of DNA, RNA, and proteins. J. Am. Chem. Soc. 117(14):4193-4194.
    • (1995) J. Am. Chem. Soc. , vol.117 , Issue.14 , pp. 4193-4194
    • Kollman, P.1    Cheatham T. III2    Miller, J.3
  • 24
    • 0027487141 scopus 로고
    • Reductive dehalogenation by cytochrome p450(cam) - Substrate-binding and catalysis
    • Li, S., and L. Wackett. 1993. Reductive dehalogenation by cytochrome p450(cam) - substrate-binding and catalysis. Biochemistry. 32: 9355-9361.
    • (1993) Biochemistry , vol.32 , pp. 9355-9361
    • Li, S.1    Wackett, L.2
  • 25
    • 0028909989 scopus 로고
    • Stereoselective hydroxylation of norcamphor by cytochrome p450(cam) - Experimental verification of molecular dynamics simulations
    • Loida, P., S. Sligar, M. Paulsen, G. Arnold, and R. Ornstein. 1995. Stereoselective hydroxylation of norcamphor by cytochrome p450(cam) - experimental verification of molecular dynamics simulations. J. Biol. Chem. 270:5326-5330.
    • (1995) J. Biol. Chem. , vol.270 , pp. 5326-5330
    • Loida, P.1    Sligar, S.2    Paulsen, M.3    Arnold, G.4    Ornstein, R.5
  • 26
    • 0029983732 scopus 로고    scopus 로고
    • Redox-dependent dynamics of putidaredoxin characterized by amide proton exchange
    • Lyons, T., G. Ratnaswamy, and T. Pochapsky. 1996. Redox-dependent dynamics of putidaredoxin characterized by amide proton exchange. Protein Sci. 5:627-639.
    • (1996) Protein Sci. , vol.5 , pp. 627-639
    • Lyons, T.1    Ratnaswamy, G.2    Pochapsky, T.3
  • 27
    • 0027126572 scopus 로고
    • 1H NMR sequential assignments and identification of secondary structural elements in oxidized putidaredoxin, an electron-transfer protein from Pseudomonas
    • 1H NMR sequential assignments and identification of secondary structural elements in oxidized putidaredoxin, an electron-transfer protein from Pseudomonas. Biochemistry. 31:1961-1968.
    • (1992) Biochemistry , vol.31 , pp. 1961-1968
    • Mei, X.1    Pochapsky, T.2    Pochapsky, S.3
  • 28
    • 0025916872 scopus 로고
    • Functionality maps of binding sites: A multiple copy simultaneous search method
    • Miranker, A., and M. Karplus. 1991. Functionality maps of binding sites: a multiple copy simultaneous search method. Proteins. 11:2934.
    • (1991) Proteins , vol.11 , pp. 2934
    • Miranker, A.1    Karplus, M.2
  • 29
    • 0000318315 scopus 로고
    • Density functional/poisson-Boltzmann calculations of redox potentials for iron-sulfur clusters
    • Mouesca, J.-M., J. Chen, L. Noodleman, D. Bashford, and D. 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.2    Noodleman, L.3    Bashford, D.4    Case, D.5
  • 30
    • 2442460927 scopus 로고
    • Molecular dynamics analysis of NMR relaxation in a zinc-finger peptide
    • Palmer, A., and D. Case. 1992. Molecular dynamics analysis of NMR relaxation in a zinc-finger peptide. J. Am. Chem. Soc. 114:9059-9067.
    • (1992) J. Am. Chem. Soc. , vol.114 , pp. 9059-9067
    • Palmer, A.1    Case, D.2
  • 31
    • 0029633186 scopus 로고
    • Amber, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules
    • Pearlman, D., D. Case, J. Caldwell, W. Ross, T. Cheatham, III, S. DeBolt, D. Ferguson, G. Seibel, and P. Kollman. 1995. Amber, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Comp. Phys. Comm. 91:1-41.
    • (1995) Comp. Phys. Comm. , vol.91 , pp. 1-41
    • Pearlman, D.1    Case, D.2    Caldwell, J.3    Ross, W.4    Cheatham T. III5    DeBolt, S.6    Ferguson, D.7    Seibel, G.8    Kollman, P.9
  • 32
    • 0030457189 scopus 로고    scopus 로고
    • A structure-based model for cytochrome P450(cam)-putidaredoxin interactions
    • Pochapsky, T., T. Lyons, K. Kazanis, T. Arakaki, and G. Ratnaswamy. 1996. A structure-based model for cytochrome P450(cam)-putidaredoxin interactions. Biochimie. 78(8-9):723-733.
    • (1996) Biochimie , vol.78 , Issue.8-9 , pp. 723-733
    • Pochapsky, T.1    Lyons, T.2    Kazanis, K.3    Arakaki, T.4    Ratnaswamy, G.5
  • 33
    • 0025922527 scopus 로고
    • 1H NMR identification of a beta-sheet structure and description of folding topology in putidaredoxin
    • 1H NMR identification of a beta-sheet structure and description of folding topology in putidaredoxin. Biochemistry. 30:3850-3856.
    • (1991) Biochemistry , vol.30 , pp. 3850-3856
    • Pochapsky, T.1    Mei, X.2
  • 34
    • 0028307538 scopus 로고
    • An NMR-derived model for the solution structure of oxidized putidaredoxin, a 2-Fe, 2-S ferredoxin from Pseudomonas
    • Pochapsky, T., X. Mei, G. Ratnaswamy, and T. Lyons. 1994. An NMR-derived model for the solution structure of oxidized putidaredoxin, a 2-Fe, 2-S ferredoxin from Pseudomonas. Biochemistry. 33:6424-6432.
    • (1994) Biochemistry , vol.33 , pp. 6424-6432
    • Pochapsky, T.1    Mei, X.2    Ratnaswamy, G.3    Lyons, T.4
  • 36
    • 0023645035 scopus 로고
    • High resolution crystal structure of cytochrome P450cam
    • Poulos, T., B. Finzel, and A. Howard. 1987. High resolution crystal structure of cytochrome P450cam. J. Mol. Biol. 195:687-700.
    • (1987) J. Mol. Biol. , vol.195 , pp. 687-700
    • Poulos, T.1    Finzel, B.2    Howard, A.3
  • 37
    • 36449006131 scopus 로고
    • Modeling side-chains in peptides and proteins: Application of the locally enhanced sampling and the simulated annealing methods to find minimum energy conformations
    • Roitberg, A., and R. Elber. 1992. Modeling side-chains in peptides and proteins: application of the locally enhanced sampling and the simulated annealing methods to find minimum energy conformations. J. Chem. Phys. 95:9277-9287.
    • (1992) J. Chem. Phys. , vol.95 , pp. 9277-9287
    • Roitberg, A.1    Elber, R.2
  • 38
    • 0027135804 scopus 로고
    • Computing the structure of bound peptides - Application to antigen recognition by class-i major histocompatibility complex receptors
    • Rosenfeld, R., Q. Zheng, S. Vajda, and C. DeLisi. 1993. Computing the structure of bound peptides - application to antigen recognition by class-i major histocompatibility complex receptors. J. Mol. Biol. 234: 515-521.
    • (1993) J. Mol. Biol. , vol.234 , pp. 515-521
    • Rosenfeld, R.1    Zheng, Q.2    Vajda, S.3    Delisi, C.4
  • 39
    • 33646940952 scopus 로고    scopus 로고
    • Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • Ryckaert, J.-P., G. Ciccotti, and H. Berendsen. 1997. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comp. Phys. 23:327-341.
    • (1997) J. Comp. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.-P.1    Ciccotti, G.2    Berendsen, H.3
  • 40
    • 0028150192 scopus 로고
    • Hydrophobic collapse in a cyclic hexapeptide - Computer-simulations of CHDLFC and CAAAAC in water
    • Simmerling, C. L., and R. Elber. 1994. Hydrophobic collapse in a cyclic hexapeptide - computer-simulations of CHDLFC and CAAAAC in water. J. Am. Chem. Soc. 116:2534-2547.
    • (1994) J. Am. Chem. Soc. , vol.116 , pp. 2534-2547
    • Simmerling, C.L.1    Elber, R.2
  • 41
    • 0028943629 scopus 로고
    • Computer determination of peptide conformations in water - Different roads to structure
    • Simmerling, C. L., and R. Elber. 1995. Computer determination of peptide conformations in water - different roads to structure. Proc. Natl. Acad. Sci. USA. 92:3190-3193.
    • (1995) Proc. Natl. Acad. Sci. USA , vol.92 , pp. 3190-3193
    • Simmerling, C.L.1    Elber, R.2
  • 42
    • 0003023614 scopus 로고
    • Moil-view, a program for visualization of structure and dynamics of biomolecules, and sto, a program for computing stochastic paths
    • A. Pullman, editor. Kluwer, Dordrecht, the Netherlands
    • Simmerling, C., R. Elber, and J. Zhang. 1995. Moil-view, a program for visualization of structure and dynamics of biomolecules, and sto, a program for computing stochastic paths. In Modelling of Biomolecular Structure and Mechanisms. A. Pullman, editor. Kluwer, Dordrecht, the Netherlands. 241-265.
    • (1995) Modelling of Biomolecular Structure and Mechanisms , pp. 241-265
    • Simmerling, C.1    Elber, R.2    Zhang, J.3
  • 44
    • 0025907553 scopus 로고
    • Structural microheterogeneity of a tryptophan residue required for efficient biological electron transfer between putidaredoxin and cytochrome P450cam
    • Stayton, P., and S. Sligar. 1991. Structural microheterogeneity of a tryptophan residue required for efficient biological electron transfer between putidaredoxin and cytochrome P450cam. Biochemistry. 30:1845-1851.
    • (1991) Biochemistry , vol.30 , pp. 1845-1851
    • Stayton, P.1    Sligar, S.2
  • 45
    • 0028038332 scopus 로고
    • Multiple copy sampling - Rigid versus flexible protein
    • Zheng, Q., and D. J. Kyle. 1994. Multiple copy sampling - rigid versus flexible protein. Proteins. 19:324-329.
    • (1994) Proteins , vol.19 , pp. 324-329
    • Zheng, Q.1    Kyle, D.J.2


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