메뉴 건너뛰기




Volumn 88, Issue 4, 2005, Pages 2875-2882

Experimental and simulative dissociation of dimeric Cu,Zn superoxide dismutase doubly mutated at the intersubunit surface

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL ENZYME; COPPER ZINC SUPEROXIDE DISMUTASE; DIMER; MOLECULAR MOTOR; MONOMER; MUTANT PROTEIN; TRYPTOPHAN;

EID: 22144436201     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.104.057638     Document Type: Article
Times cited : (3)

References (45)
  • 1
    • 48749148224 scopus 로고
    • RATTLE: A "velocity" version of the SHAKE algorithm for molecular dynamics calculations
    • Andersen, H. C. 1983. RATTLE: a "velocity" version of the SHAKE algorithm for molecular dynamics calculations. J. Comput. Phys. 52:24-34.
    • (1983) J. Comput. Phys. , vol.52 , pp. 24-34
    • Andersen, H.C.1
  • 2
    • 0037195276 scopus 로고    scopus 로고
    • Dimeric and monomeric Bacillus subtilis RNAse P holoenzyme in the absence and presence of pre-tRNA substrates
    • Barrera, A., X. Fang, J. Jacob, E. Casey, P. Thiyagarajan, and T. Pan. 2002. Dimeric and monomeric Bacillus subtilis RNAse P holoenzyme in the absence and presence of pre-tRNA substrates. Biochemistry. 41:12986-12994.
    • (2002) Biochemistry , vol.41 , pp. 12986-12994
    • Barrera, A.1    Fang, X.2    Jacob, J.3    Casey, E.4    Thiyagarajan, P.5    Pan, T.6
  • 6
    • 0003199060 scopus 로고    scopus 로고
    • Cu,Zn superoxide dismutase in prokaryotes and eukaryotes
    • K. Wieghardt, R. Huber, T. Poulos, and A. Messerschmidt, editors. John Wiley & Sons, London, UK
    • Bordo, D., A. Pesce, M. Bolognesi, M. E. Stroppolo, M. Falconi, and A. Desideri. 2000. Cu,Zn superoxide dismutase in prokaryotes and eukaryotes. In Handbook of Metalloproteins. K. Wieghardt, R. Huber, T. Poulos, and A. Messerschmidt, editors. John Wiley & Sons, London, UK, 1284.
    • (2000) Handbook of Metalloproteins , pp. 1284
    • Bordo, D.1    Pesce, A.2    Bolognesi, M.3    Stroppolo, M.E.4    Falconi, M.5    Desideri, A.6
  • 8
    • 4243661501 scopus 로고
    • Constrained reaction coordinate dynamics for the simulation of rare events
    • Carter, E. A., G. Ciccotti, J. T. Hynes, and R. Kapral. 1989. Constrained reaction coordinate dynamics for the simulation of rare events. Chem. Phys. Lett. 156:472-477.
    • (1989) Chem. Phys. Lett. , vol.156 , pp. 472-477
    • Carter, E.A.1    Ciccotti, G.2    Hynes, J.T.3    Kapral, R.4
  • 9
    • 0037093645 scopus 로고    scopus 로고
    • Dissecting protein-protein recognition sites
    • Chakrabarti, P., and J. Janin. 2002. Dissecting protein-protein recognition sites. Proteins. 47:334-343.
    • (2002) Proteins , vol.47 , pp. 334-343
    • Chakrabarti, P.1    Janin, J.2
  • 10
    • 20444426965 scopus 로고
    • Effects of liquid structures on chemical reactions and conformational changes of non-rigid molecules in condensed phases. Faraday Discuss
    • Chandler, D. 1979. Effects of liquid structures on chemical reactions and conformational changes of non-rigid molecules in condensed phases. Faraday Discuss. Chem. Soc. 66:184-190.
    • (1979) Chem. Soc. , vol.66 , pp. 184-190
    • Chandler, D.1
  • 11
    • 33751232728 scopus 로고
    • Statistical mechanics of chemical equilibria and intramolecular structures of non-rigid molecules in condensed phases
    • Chandler, D., and L. R. Pratt. 1976. Statistical mechanics of chemical equilibria and intramolecular structures of non-rigid molecules in condensed phases. J. Chem. Phys. 65:2925-2940.
    • (1976) J. Chem. Phys. , vol.65 , pp. 2925-2940
    • Chandler, D.1    Pratt, L.R.2
  • 13
    • 0027934772 scopus 로고
    • Pressure effects on protein flexibility monomeric proteins
    • Cioni, P., and G. B. Strambini. 1994. Pressure effects on protein flexibility monomeric proteins. J. Mol. Biol. 242:291-301.
    • (1994) J. Mol. Biol. , vol.242 , pp. 291-301
    • Cioni, P.1    Strambini, G.B.2
  • 14
    • 1542287930 scopus 로고    scopus 로고
    • Constrained reaction coordinate dynamics for systems with constraints
    • Coluzza, I., M. Sprik, and G. Ciccotti. 2003. Constrained reaction coordinate dynamics for systems with constraints. Mol. Phys. 101:2885-2894.
    • (2003) Mol. Phys. , vol.101 , pp. 2885-2894
    • Coluzza, I.1    Sprik, M.2    Ciccotti, G.3
  • 15
    • 0034720474 scopus 로고    scopus 로고
    • Single mutation induces a metal dependent subunit association in dimeric Cu,Zn superoxide dismutase
    • D'Orazio, M., A. Battistoni, M. E. Stroppolo, and A. Desideri. 2000. Single mutation induces a metal dependent subunit association in dimeric Cu,Zn superoxide dismutase. Biochem. Biophys. Res. Commun. 272:81-83.
    • (2000) Biochem. Biophys. Res. Commun. , vol.272 , pp. 81-83
    • D'Orazio, M.1    Battistoni, A.2    Stroppolo, M.E.3    Desideri, A.4
  • 16
    • 11144227941 scopus 로고    scopus 로고
    • Dissociation of human copper-zinc superoxide dismutase dimers using chaotrope and reductant. Insights into the molecular basis for dimer stability
    • Doucette, P. A., L. J. Whitson, X. Cao, V. Schirf, B. Demeler, J. S. Valentine, J. C. Hansen, and P. J. Hart. 2004. Dissociation of human copper-zinc superoxide dismutase dimers using chaotrope and reductant. Insights into the molecular basis for dimer stability. J. Biol. Chem. 279:54558-54566.
    • (2004) J. Biol. Chem. , vol.279 , pp. 54558-54566
    • Doucette, P.A.1    Whitson, L.J.2    Cao, X.3    Schirf, V.4    Demeler, B.5    Valentine, J.S.6    Hansen, J.C.7    Hart, P.J.8
  • 17
    • 0025845307 scopus 로고
    • Oligomeric protein associations: Transition from stochastic to deterministic equilibrium
    • Erijman, L. G., and G. Weber. 1991. Oligomeric protein associations: transition from stochastic to deterministic equilibrium. Biochemistry. 30:1595-1599.
    • (1991) Biochemistry , vol.30 , pp. 1595-1599
    • Erijman, L.G.1    Weber, G.2
  • 19
    • 0343907214 scopus 로고    scopus 로고
    • Spectroscopic characterization of recombinant Cu,Zn superoxide dismutase from Photobacterium leiognathi expressed in Escherichia coli: Evidence for a novel catalytic copper binding site
    • Foti, D., B. Lo Curto, G. Cuzzocrea, M. E. Stroppolo, F. Polizio, M. Venanzi, and A. Desideri. 1997. Spectroscopic characterization of recombinant Cu,Zn superoxide dismutase from Photobacterium leiognathi expressed in Escherichia coli: evidence for a novel catalytic copper binding site. Biochemistry. 36:7109-7113.
    • (1997) Biochemistry , vol.36 , pp. 7109-7113
    • Foti, D.1    Lo Curto, B.2    Cuzzocrea, G.3    Stroppolo, M.E.4    Polizio, F.5    Venanzi, M.6    Desideri, A.7
  • 21
    • 0028861437 scopus 로고
    • Elusive affinities
    • Janin, J. 1995. Elusive affinities. Proteins. 21:30-39.
    • (1995) Proteins , vol.21 , pp. 30-39
    • Janin, J.1
  • 22
    • 0029421048 scopus 로고    scopus 로고
    • Protein-protein recognition
    • Janin, J. 1996. Protein-protein recognition. Prog. Biophys. Mol. Biol. 64:145-165.
    • (1996) Prog. Biophys. Mol. Biol. , vol.64 , pp. 145-165
    • Janin, J.1
  • 23
    • 0347093522 scopus 로고    scopus 로고
    • Characterization of the monomer-dimer equilibrium of human cytomegalovirus protease by kinetic methods
    • Khayat, R., R. Batra, G. A. Bebernitz, M. W. Olson, and L. Tong. 2004. Characterization of the monomer-dimer equilibrium of human cytomegalovirus protease by kinetic methods. Biochemistry. 43:316-322.
    • (2004) Biochemistry , vol.43 , pp. 316-322
    • Khayat, R.1    Batra, R.2    Bebernitz, G.A.3    Olson, M.W.4    Tong, L.5
  • 24
    • 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
  • 25
    • 0025643362 scopus 로고
    • A general method for rapid site-directed mutagenesis using the polymerase chain reaction
    • Landt, O., H. P. Grunert, and U. Hahn. 1990. A general method for rapid site-directed mutagenesis using the polymerase chain reaction. Gene. 96:125-128.
    • (1990) Gene , vol.96 , pp. 125-128
    • Landt, O.1    Grunert, H.P.2    Hahn, U.3
  • 26
    • 0003187567 scopus 로고    scopus 로고
    • The atomic structure of protein-protein recognition sites
    • Lo Conte, L., C. Chothia, and J. Janin. 1999. The atomic structure of protein-protein recognition sites. J. Mol. Biol. 285:2177-2198.
    • (1999) J. Mol. Biol. , vol.285 , pp. 2177-2198
    • Lo Conte, L.1    Chothia, C.2    Janin, J.3
  • 28
    • 11144256402 scopus 로고    scopus 로고
    • Effective binding force calculation in dimeric proteins
    • Maragliano, L., M. Ferrario, and G. Ciccotti. 2004. Effective binding force calculation in dimeric proteins. Mol. Sim. 30:807-816.
    • (2004) Mol. Sim. , vol.30 , pp. 807-816
    • Maragliano, L.1    Ferrario, M.2    Ciccotti, G.3
  • 29
    • 0016272750 scopus 로고
    • Involvement of the superoxide anion radical in the autoxidation of pyrogallol and a convenient assay for superoxide dismutase
    • Marklund, S., and G. Marklund. 1974. Involvement of the superoxide anion radical in the autoxidation of pyrogallol and a convenient assay for superoxide dismutase. Eur. J. Biochem. 47:469-474.
    • (1974) Eur. J. Biochem. , vol.47 , pp. 469-474
    • Marklund, S.1    Marklund, G.2
  • 31
    • 0000920304 scopus 로고    scopus 로고
    • Atomic stress isobaric scaling for systems subjected to holonomic constraints
    • Melchionna, S., and G. Ciccotti. 1997. Atomic stress isobaric scaling for systems subjected to holonomic constraints. J. Chem. Phys. 106:195-200.
    • (1997) J. Chem. Phys. , vol.106 , pp. 195-200
    • Melchionna, S.1    Ciccotti, G.2
  • 33
    • 84943502952 scopus 로고
    • A molecular dynamics method for simulations in the canonical ensemble
    • Nosè, S. 1984. A molecular dynamics method for simulations in the canonical ensemble. Mol. Phys. 52:255-268.
    • (1984) Mol. Phys. , vol.52 , pp. 255-268
    • Nosè, S.1
  • 34
    • 0042347713 scopus 로고    scopus 로고
    • Structure-based thermodynamic analysis of caspases reveals key dimerization and activity
    • Piana, S., M. Sulpizi, and U. Rothlisberger. 2003. Structure-based thermodynamic analysis of caspases reveals key dimerization and activity. Biochemistry. 42:8720-8728.
    • (2003) Biochemistry , vol.42 , pp. 8720-8728
    • Piana, S.1    Sulpizi, M.2    Rothlisberger, U.3
  • 35
    • 0037195275 scopus 로고    scopus 로고
    • Reversible ligand-induced dissociation of a tryptophan-shift mutant of phosphofructokinase from Bacillus stearothermophilus
    • Riley-Lovingshimer, M. R., D. R. Ronning, J. C. Sacchettini, and G. D. Reinhart. 2002. Reversible ligand-induced dissociation of a tryptophan-shift mutant of phosphofructokinase from Bacillus stearothermophilus. Biochemistry. 41:12967-12974.
    • (2002) Biochemistry , vol.41 , pp. 12967-12974
    • Riley-Lovingshimer, M.R.1    Ronning, D.R.2    Sacchettini, J.C.3    Reinhart, G.D.4
  • 36
    • 0024963668 scopus 로고
    • Hysteresis and conformational drift of pressure-dissociated glyceraldehydepbosphate dehydrogenase
    • Ruan, K., and G. Weber. 1989. Hysteresis and conformational drift of pressure-dissociated glyceraldehydepbosphate dehydrogenase. Biochemistry. 28:2144-2153.
    • (1989) Biochemistry , vol.28 , pp. 2144-2153
    • Ruan, K.1    Weber, G.2
  • 37
    • 33646940952 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 G. Berendsen. 1977. Numerical integration of the Cartesian equations 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
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, G.3
  • 38
    • 0037041734 scopus 로고    scopus 로고
    • Effective binding force calculation in a dimeric protein by molecular dynamics simulation
    • Sergi, A., G. Ciccotti, M. Falconi, A. Desideri, and M. Ferrario. 2002. Effective binding force calculation in a dimeric protein by molecular dynamics simulation. J. Chem. Phys. 116:6329-6338.
    • (2002) J. Chem. Phys. , vol.116 , pp. 6329-6338
    • Sergi, A.1    Ciccotti, G.2    Falconi, M.3    Desideri, A.4    Ferrario, M.5
  • 39
  • 40
    • 0036286654 scopus 로고    scopus 로고
    • Free energy simulations come of age: Protein-ligand recognition
    • Simonson, T., G. Archontis, and M. Karplus. 2002. Free energy simulations come of age: protein-ligand recognition. Acc. Chem. Res. 35:430-437.
    • (2002) Acc. Chem. Res. , vol.35 , pp. 430-437
    • Simonson, T.1    Archontis, G.2    Karplus, M.3
  • 41
    • 0001702831 scopus 로고    scopus 로고
    • Free energy from constrained molecular dynamics
    • Sprik, M., and G. Ciccotti. 1998. Free energy from constrained molecular dynamics. J. Chem. Phys. 109:7737-7744.
    • (1998) J. Chem. Phys. , vol.109 , pp. 7737-7744
    • Sprik, M.1    Ciccotti, G.2
  • 42
    • 0347949637 scopus 로고    scopus 로고
    • Revisiting free energy calculations: A theoretical connection to MM/PBSA and direct calculation of the association free energy
    • Swanson, J., R. H. Henchman, and J. A. McCammon. 2004. Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy. Biophys. J. 86:67-74.
    • (2004) Biophys. J. , vol.86 , pp. 67-74
    • Swanson, J.1    Henchman, R.H.2    McCammon, J.A.3
  • 43
    • 0028360307 scopus 로고
    • The contribution of vibrational entropy to molecular association. The dimerization of insulin
    • Tidor, B., and M. Karplus. 1994. The contribution of vibrational entropy to molecular association. The dimerization of insulin. J. Mol. Biol. 238:405-414.
    • (1994) J. Mol. Biol. , vol.238 , pp. 405-414
    • Tidor, B.1    Karplus, M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.