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Volumn 28, Issue 3, 2009, Pages 270-277

Conformational flexibility decreased due to Y67F and F82H mutations in cytochrome c: Molecular dynamics simulation studies

Author keywords

Conformational flexibility; Cytochrome c; Essential dynamics; Molecular dynamics; Mutants

Indexed keywords

APOPTOSIS; APOPTOTIC; CASPASE ACTIVATION; CONFORMATIONAL FLEXIBILITY; CYTOCHROME C; CYTOSOLS; DUAL FUNCTION; DYNAMIC BEHAVIORS; EIGENVECTORS; ENERGETIC METABOLISM; ESSENTIAL DYNAMICS; FORCE FIELDS; GROMOS96; MD SIMULATION; MITOCHONDRIAL PROTEIN; MOLECULAR DYNAMICS SIMULATIONS; MUTANTS; PEROXIDASE ACTIVITIES; PROGRAMMED CELL DEATHS; STATIC STRUCTURES; TRANSFER PROCESS; WILD TYPES;

EID: 70349543985     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2009.08.005     Document Type: Article
Times cited : (13)

References (37)
  • 3
    • 0037388040 scopus 로고    scopus 로고
    • Biological inorganic chemistry at the beginning of the 21st century
    • Gray H.B. Biological inorganic chemistry at the beginning of the 21st century. Proc. Natl. Acad. Sci. U.S.A. 100 (2003) 3563-3568
    • (2003) Proc. Natl. Acad. Sci. U.S.A. , vol.100 , pp. 3563-3568
    • Gray, H.B.1
  • 4
    • 0035039678 scopus 로고    scopus 로고
    • Structural view of mitochondria-mediated apoptosis
    • Shi Y.A. Structural view of mitochondria-mediated apoptosis. Nat. Struct. Biol. 8 (2001) 394-401
    • (2001) Nat. Struct. Biol. , vol.8 , pp. 394-401
    • Shi, Y.A.1
  • 5
    • 0025007598 scopus 로고
    • High-resolution three dimensional Structure of horse heart Cytochrome c
    • Bushnell G.W., Louie G.V., and Brayer G.D. High-resolution three dimensional Structure of horse heart Cytochrome c. J. Mol. Biol. 214 (1990) 585-595
    • (1990) J. Mol. Biol. , vol.214 , pp. 585-595
    • Bushnell, G.W.1    Louie, G.V.2    Brayer, G.D.3
  • 6
    • 0042322523 scopus 로고    scopus 로고
    • Vibrational frequency shifts and relaxation rates for a selected vibrational mode in cytochrome c
    • Bu L., and Straub J.E. Vibrational frequency shifts and relaxation rates for a selected vibrational mode in cytochrome c. Biophys. J. 85 (2003) 1429-1439
    • (2003) Biophys. J. , vol.85 , pp. 1429-1439
    • Bu, L.1    Straub, J.E.2
  • 7
    • 0029983732 scopus 로고    scopus 로고
    • Redox-dependent dynamics of putidaredoxin characterized by amide proton exchange
    • Lyons T.A., Ratnaswamy G., and Pochapsky T.C. Redox-dependent dynamics of putidaredoxin characterized by amide proton exchange. Protein Sci. 5 (1996) 627-639
    • (1996) Protein Sci. , vol.5 , pp. 627-639
    • Lyons, T.A.1    Ratnaswamy, G.2    Pochapsky, T.C.3
  • 8
    • 33746907105 scopus 로고    scopus 로고
    • Native-state dynamics of the ubiquitin family: implications for function and evolution
    • Marianayagam N.J., and Jackson S.E. Native-state dynamics of the ubiquitin family: implications for function and evolution. J. Roy. Soc. Interface 2 (2005) 47-54
    • (2005) J. Roy. Soc. Interface , vol.2 , pp. 47-54
    • Marianayagam, N.J.1    Jackson, S.E.2
  • 10
    • 44749084371 scopus 로고
    • Semisynthesis of axial-ligand (position 80) mutants of cytochrome c
    • Raphael A.L., and Gray H.B. Semisynthesis of axial-ligand (position 80) mutants of cytochrome c. J. Am. Chem. Soc. 113 (1991) 1038-1040
    • (1991) J. Am. Chem. Soc. , vol.113 , pp. 1038-1040
    • Raphael, A.L.1    Gray, H.B.2
  • 11
    • 0024814209 scopus 로고
    • Axial ligand replacement in horse heart cytochrome c by semisynthesis
    • Raphael A.L., and Gray H.B. Axial ligand replacement in horse heart cytochrome c by semisynthesis. Proteins Struct. Funct. Genet. 6 (1989) 338-340
    • (1989) Proteins Struct. Funct. Genet. , vol.6 , pp. 338-340
    • Raphael, A.L.1    Gray, H.B.2
  • 12
    • 0030816577 scopus 로고    scopus 로고
    • Identification of the predominant non-native histidine ligand in unfolded cytochrome c
    • Colón W., Wakem L.P., Sherman F., and Roder H. Identification of the predominant non-native histidine ligand in unfolded cytochrome c. Biochemistry 36 (1997) 12535-12541
    • (1997) Biochemistry , vol.36 , pp. 12535-12541
    • Colón, W.1    Wakem, L.P.2    Sherman, F.3    Roder, H.4
  • 13
    • 0034801588 scopus 로고    scopus 로고
    • Direct observation of protein vibrations by selective incorporation of spectroscopically observable carbon-deuterium bonds in cytochrome c
    • Chin J.K., Jimenez R., and Romesberg F.E. Direct observation of protein vibrations by selective incorporation of spectroscopically observable carbon-deuterium bonds in cytochrome c. J. Am. Chem. Soc. 123 (2001) 2426-2427
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 2426-2427
    • Chin, J.K.1    Jimenez, R.2    Romesberg, F.E.3
  • 15
    • 0029633168 scopus 로고
    • GROMACS: a message-passing parallel molecular dynamics implementation
    • Berendsen H.J.C., van der Spoel D., and van Drunen R. GROMACS: a message-passing parallel molecular dynamics implementation. Comp. Phys. Commun. 91 (1995) 45-56
    • (1995) Comp. Phys. Commun. , vol.91 , pp. 45-56
    • Berendsen, H.J.C.1    van der Spoel, D.2    van Drunen, R.3
  • 16
    • 0035789518 scopus 로고    scopus 로고
    • GROMACS 3.0 a package for molecular simulation and trajectory analysis
    • Lindahl E., Hess B., and van der Spoel D. GROMACS 3.0 a package for molecular simulation and trajectory analysis. J. Mol. Model. 7 (2001) 306-317
    • (2001) J. Mol. Model. , vol.7 , pp. 306-317
    • Lindahl, E.1    Hess, B.2    van der Spoel, D.3
  • 19
    • 4444240014 scopus 로고    scopus 로고
    • Classical force field parameters for the heme prosthetic group of cytochrome c
    • Autenrieth F., Tajkhorshid E., Baudry J., and Luthey-Schulten Z. Classical force field parameters for the heme prosthetic group of cytochrome c. J. Comp. Chem. 25 (2004) 1613-1622
    • (2004) J. Comp. Chem. , vol.25 , pp. 1613-1622
    • Autenrieth, F.1    Tajkhorshid, E.2    Baudry, J.3    Luthey-Schulten, Z.4
  • 22
    • 33646940952 scopus 로고
    • Numerical integration of the Cartesian equations of motions of systems with constraints: molecular dynamics of n-alkanes
    • Ryckaert J.P., Ciccotti G., and Berendsen H.J.C. Numerical integration of the Cartesian equations of motions of systems with constraints: molecular dynamics of n-alkanes. J. Comp. Phys. 23 (1977) 327-341
    • (1977) J. Comp. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 23
    • 84986440341 scopus 로고
    • SETTLE: an analytical version of the SHAKE and RATTLE algorithms for rigid water molecules
    • Miyamoto S., and Kollman P.A. SETTLE: an analytical version of the SHAKE and RATTLE algorithms for rigid water molecules. J. Comp. Chem. 13 (1992) 952-962
    • (1992) J. Comp. Chem. , vol.13 , pp. 952-962
    • Miyamoto, S.1    Kollman, P.A.2
  • 24
    • 0035869698 scopus 로고    scopus 로고
    • Concerted motions in copper plastocyanin and azurin: an essential dynamics study
    • Arcangeli C., Rita Bizzarri A., and Cannistraro S. Concerted motions in copper plastocyanin and azurin: an essential dynamics study. Biophys. Chem. 90 (2001) 45-56
    • (2001) Biophys. Chem. , vol.90 , pp. 45-56
    • Arcangeli, C.1    Rita Bizzarri, A.2    Cannistraro, S.3
  • 26
    • 84986483798 scopus 로고
    • The double cube lattice method: efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies
    • Eisenhaber F., Lijnzaad P., Argos P., Sander C., and Scharf M. The double cube lattice method: efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies. J. Comp. Chem. 16 (1995) 273-284
    • (1995) J. Comp. Chem. , vol.16 , pp. 273-284
    • Eisenhaber, F.1    Lijnzaad, P.2    Argos, P.3    Sander, C.4    Scharf, M.5
  • 27
    • 0022596727 scopus 로고
    • Solvation energy in protein folding and binding
    • Eisenberg D., and McLachlan A.D. Solvation energy in protein folding and binding. Nature 319 (1986) 199-203
    • (1986) Nature , vol.319 , pp. 199-203
    • Eisenberg, D.1    McLachlan, A.D.2
  • 28
    • 0037339403 scopus 로고    scopus 로고
    • Selective excitations of natural fluctuations during thermal unfolding simulations: horse heart cytochrome c as a case study
    • Roccatano D., Daidone I., Ceruso M.A., Bossa C., and Di Nola A. Selective excitations of natural fluctuations during thermal unfolding simulations: horse heart cytochrome c as a case study. Biophys. J. 84 (2003) 1876-1883
    • (2003) Biophys. J. , vol.84 , pp. 1876-1883
    • Roccatano, D.1    Daidone, I.2    Ceruso, M.A.3    Bossa, C.4    Di Nola, A.5
  • 29
    • 0023818581 scopus 로고
    • Differences in the solution structures of oxidized and reduced cytochrome c measured by small- angle X-ray scattering
    • Trewhella J., Carlson V.A.P., Curtis E.H., and Heidorn D.B. Differences in the solution structures of oxidized and reduced cytochrome c measured by small- angle X-ray scattering. Biochemistry 27 (1988) 1121-1125
    • (1988) Biochemistry , vol.27 , pp. 1121-1125
    • Trewhella, J.1    Carlson, V.A.P.2    Curtis, E.H.3    Heidorn, D.B.4
  • 30
    • 0026608669 scopus 로고
    • Oxidation state conformational changes in cytochrome c
    • Berghuis A.M., and Brayer G.D. Oxidation state conformational changes in cytochrome c. J. Mol. Biol. 223 (1992) 959-976
    • (1992) J. Mol. Biol. , vol.223 , pp. 959-976
    • Berghuis, A.M.1    Brayer, G.D.2
  • 31
    • 0026529046 scopus 로고
    • Redox-dependent changes in β-extended chain and turn structures of cytochrome c in water solution determined by second derivative amide I infrared spectra
    • Dong A., Huang P., and Caughey W.S. Redox-dependent changes in β-extended chain and turn structures of cytochrome c in water solution determined by second derivative amide I infrared spectra. Biochemistry 31 (1992) 182-189
    • (1992) Biochemistry , vol.31 , pp. 182-189
    • Dong, A.1    Huang, P.2    Caughey, W.S.3
  • 33
    • 0034013699 scopus 로고    scopus 로고
    • Circular dichroism and resonance Raman comparative studies of WT cytochrome c and F82H mutant
    • Zheng J., Ye S., Lu T., Cotton T.M., and Chunanov G. Circular dichroism and resonance Raman comparative studies of WT cytochrome c and F82H mutant. Biospectroscopy 57 2 (2000) 77-84
    • (2000) Biospectroscopy , vol.57 , Issue.2 , pp. 77-84
    • Zheng, J.1    Ye, S.2    Lu, T.3    Cotton, T.M.4    Chunanov, G.5
  • 34
    • 0015803893 scopus 로고
    • The structure of ferrocytochrome c at 2.45 A resolution
    • Takano T., Kallai O.B., Swanson R., and Dickerson R.E. The structure of ferrocytochrome c at 2.45 A resolution. J. Biol. Chem. 248 (1973) 5234-5255
    • (1973) J. Biol. Chem. , vol.248 , pp. 5234-5255
    • Takano, T.1    Kallai, O.B.2    Swanson, R.3    Dickerson, R.E.4
  • 36
    • 0028352044 scopus 로고
    • Kinetic mechanism of cytochrome c folding: involvement of the heme and its ligands
    • Elöve G.A., Bhuyan A.K., and Roder H. Kinetic mechanism of cytochrome c folding: involvement of the heme and its ligands. Biochemistry 33 (1994) 6925-6935
    • (1994) Biochemistry , vol.33 , pp. 6925-6935
    • Elöve, G.A.1    Bhuyan, A.K.2    Roder, H.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.