메뉴 건너뛰기




Volumn 36, Issue 2, 1999, Pages 157-174

Protein strain in blue copper proteins studied by free energy perturbations

Author keywords

Entatic state theory; Induced rack theory; Molecular dynamics; Nitrite reductase; Plastocyanin

Indexed keywords

COPPER COMPLEX; NITRITE REDUCTASE; PLASTOCYANIN;

EID: 0033180952     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19990801)36:2<157::AID-PROT3>3.0.CO;2-Y     Document Type: Article
Times cited : (50)

References (46)
  • 1
    • 0542365212 scopus 로고
    • Active-site properties of the blue copper proteins
    • Sykes AG. Active-site properties of the blue copper proteins. Adv Inorg Chem 1990;36:377-408.
    • (1990) Adv Inorg Chem , vol.36 , pp. 377-408
    • Sykes, A.G.1
  • 2
    • 0026411154 scopus 로고
    • Copper protein structures
    • Adman ET. Copper protein structures. Adv Protein Chem 1991;42: 145-197.
    • (1991) Adv Protein Chem , vol.42 , pp. 145-197
    • Adman, E.T.1
  • 3
    • 0014251790 scopus 로고
    • Metalloenzymes: The entatic nature of their active sites
    • Vallee BL, Williams RJP. Metalloenzymes: the entatic nature of their active sites. Proc Natl Acad Sci USA 1968;59:498-505.
    • (1968) Proc Natl Acad Sci USA , vol.59 , pp. 498-505
    • Vallee, B.L.1    Williams, R.J.P.2
  • 4
    • 0028822917 scopus 로고
    • Energised (entatic) states of groups and of secondary structures in proteins and metalloproteins
    • Williams RJP. Energised (entatic) states of groups and of secondary structures in proteins and metalloproteins. Eur J Biochem 1995;234:363-381.
    • (1995) Eur J Biochem , vol.234 , pp. 363-381
    • Williams, R.J.P.1
  • 5
    • 4243375336 scopus 로고
    • On the relationship between protein-forced ligand fields and the properties of blue-copper centers
    • Gray HB, Malmström BG. On the relationship between protein-forced ligand fields and the properties of blue-copper centers. Comments Inorg Chem 1983;2:203-209.
    • (1983) Comments Inorg Chem , vol.2 , pp. 203-209
    • Gray, H.B.1    Malmström, B.G.2
  • 6
    • 0027998885 scopus 로고
    • Rack-induced bonding in blue-copper proteins
    • Malmström BG. Rack-induced bonding in blue-copper proteins. Eur J Biochem 1994;223:207-216.
    • (1994) Eur J Biochem , vol.223 , pp. 207-216
    • Malmström, B.G.1
  • 7
    • 0029274711 scopus 로고
    • Electronic structure of the reduced blue copper active site: Contributions to reduction potentials and geometry
    • Guckert JA, Lowery MD, Solomon EI. Electronic structure of the reduced blue copper active site: contributions to reduction potentials and geometry. J Am Chem Soc 1995;117:2817-2844.
    • (1995) J Am Chem Soc , vol.117 , pp. 2817-2844
    • Guckert, J.A.1    Lowery, M.D.2    Solomon, E.I.3
  • 8
    • 0030606884 scopus 로고    scopus 로고
    • The cupric geometry of blue copper proteins is not strained
    • Ryde U, Olsson MHM, Pierloot K, Roos BO. The cupric geometry of blue copper proteins is not strained. J Mol Biol 1996;261:586-596.
    • (1996) J Mol Biol , vol.261 , pp. 586-596
    • Ryde, U.1    Olsson, M.H.M.2    Pierloot, K.3    Roos, B.O.4
  • 9
    • 0031944196 scopus 로고    scopus 로고
    • On the relative stability of tetragonal and trigonal Cu(II) complexes with relevance to the blue copper proteins
    • Olsson MHM, Ryde U, Roos BO, Pierloot K. On the relative stability of tetragonal and trigonal Cu(II) complexes with relevance to the blue copper proteins. J Biol Inorg Chem 1998;3:109-125.
    • (1998) J Biol Inorg Chem , vol.3 , pp. 109-125
    • Olsson, M.H.M.1    Ryde, U.2    Roos, B.O.3    Pierloot, K.4
  • 10
    • 0032561819 scopus 로고    scopus 로고
    • On the relation between the structure and spectroscopic properties of blue copper proteins
    • Pierloot K, De Kerpel JOA, Ryde U, Olsson MHM, Roos BO. On the relation between the structure and spectroscopic properties of blue copper proteins. J Am Chem Soc 1998;120:13156-13166.
    • (1998) J Am Chem Soc , vol.120 , pp. 13156-13166
    • Pierloot, K.1    De Kerpel, J.O.A.2    Ryde, U.3    Olsson, M.H.M.4    Roos, B.O.5
  • 11
    • 0029794252 scopus 로고    scopus 로고
    • Electronic structure of the perturbed blue copper site in nitrite reductase: Spectroscopic properties, bonding, and implications for the entatic/rack state
    • LaCroix LB, Shadle SE, Wang Y, et al. Electronic structure of the perturbed blue copper site in nitrite reductase: spectroscopic properties, bonding, and implications for the entatic/rack state. J Am Chem Soc 1996;118:7755-7768.
    • (1996) J Am Chem Soc , vol.118 , pp. 7755-7768
    • LaCroix, L.B.1    Shadle, S.E.2    Wang, Y.3
  • 12
    • 0011509370 scopus 로고    scopus 로고
    • Structural and functional aspects of metal sites in biology
    • Holm RH, Kennepohl P, Solomon EI. Structural and functional aspects of metal sites in biology. Chem Rev 1996;96:2239-2314.
    • (1996) Chem Rev , vol.96 , pp. 2239-2314
    • Holm, R.H.1    Kennepohl, P.2    Solomon, E.I.3
  • 14
    • 26344435738 scopus 로고
    • Fully optimized contracted gaussian basis set for atoms Li to Kr
    • Schäfer A, Horn H, Ahlrichs R. Fully optimized contracted gaussian basis set for atoms Li to Kr. J Chem Phys 1992;97:2571-2577.
    • (1992) J Chem Phys , vol.97 , pp. 2571-2577
    • Schäfer, A.1    Horn, H.2    Ahlrichs, R.3
  • 16
    • 36448998619 scopus 로고
    • Second-order perturbation theory with a complete active space self-consistent field reference function
    • Andersson K, Malmqvist P-Å, Roos BO. Second-order perturbation theory with a complete active space self-consistent field reference function. J Chem Phys 1992;96:1218-1226.
    • (1992) J Chem Phys , vol.96 , pp. 1218-1226
    • Andersson, K.1    Malmqvist, P.-Å.2    Roos, B.O.3
  • 17
    • 0038910690 scopus 로고
    • Density matrix averaged atomic narural orbital (ANO) basis sets for correlated molecular wave functions. IV. Medium size basis sets for the atoms H-Kr
    • Pierloot K, Dumez B, Widmark P-O, Roos BO. Density matrix averaged atomic narural orbital (ANO) basis sets for correlated molecular wave functions. IV. Medium size basis sets for the atoms H-Kr. Theor Chim Acta 1995;90:87-114.
    • (1995) Theor Chim Acta , vol.90 , pp. 87-114
    • Pierloot, K.1    Dumez, B.2    Widmark, P.-O.3    Roos, B.O.4
  • 20
    • 0029011701 scopus 로고
    • A second generation force field for the simulation of proteins and nucleic acids
    • Cornell WD, Cieplak P, Bayly CI, et al. A second generation force field for the simulation of proteins and nucleic acids. J Am Chem Soc 1995;117:5179-5197.
    • (1995) J Am Chem Soc , vol.117 , pp. 5179-5197
    • Cornell, W.D.1    Cieplak, P.2    Bayly, C.I.3
  • 21
    • 0024441723 scopus 로고
    • Superoxide dismutase: Fluctuations in the structure and solvation of the active site channel studied by molecular dynamics simulation
    • Shen J, Subramaniam S, Wong CF, McCammon JA. Superoxide dismutase: fluctuations in the structure and solvation of the active site channel studied by molecular dynamics simulation. Biopolymers 1990;28:2085-2096.
    • (1990) Biopolymers , vol.28 , pp. 2085-2096
    • Shen, J.1    Subramaniam, S.2    Wong, C.F.3    McCammon, J.A.4
  • 22
    • 84986519281 scopus 로고
    • Partial electronstatic charges for the active center of Cu, Zn superoxide dismutase
    • Shen J, Wong CF, Subramaniam S, Albright TA, McCammon JA. Partial electronstatic charges for the active center of Cu, Zn superoxide dismutase. J Comput Chem 1990;11:346-350.
    • (1990) J Comput Chem , vol.11 , pp. 346-350
    • Shen, J.1    Wong, C.F.2    Subramaniam, S.3    Albright, T.A.4    McCammon, J.A.5
  • 23
    • 0026338266 scopus 로고
    • Three-dimensional model for stellacyanin, a blue copper-protein
    • Fields BA, Guss JM, Freeman HC. Three-dimensional model for stellacyanin, a blue copper-protein. J Mol Biol 1991;222:1053-1065.
    • (1991) J Mol Biol , vol.222 , pp. 1053-1065
    • Fields, B.A.1    Guss, J.M.2    Freeman, H.C.3
  • 24
    • 0026675574 scopus 로고
    • Molecular dynamics studies on superoxide dismutase and its mutants: The structural and functional role of Arg 143
    • Banci L, Carloni P, La Penna G, Orioli PL. Molecular dynamics studies on superoxide dismutase and its mutants: the structural and functional role of Arg 143. J Am Chem Soc 1992;114:6994-7001.
    • (1992) J Am Chem Soc , vol.114 , pp. 6994-7001
    • Banci, L.1    Carloni, P.2    La Penna, G.3    Orioli, P.L.4
  • 25
    • 0030254837 scopus 로고    scopus 로고
    • Dimer asymmetry in superoxide dismutase studied by molecular dynamics simulation
    • Falconi M, Gallimbeni R, Paci E. Dimer asymmetry in superoxide dismutase studied by molecular dynamics simulation. J Comput Aided Mol Des 1996;10:490-498.
    • (1996) J Comput Aided Mol Des , vol.10 , pp. 490-498
    • Falconi, M.1    Gallimbeni, R.2    Paci, E.3
  • 26
    • 0009857680 scopus 로고
    • Molecular dynamics of copper plastocyanin: Simulations of structure and dynamics as a function of hydration
    • Wang CX, Bizzarri AR, Xu YW, Cannistraro S. Molecular dynamics of copper plastocyanin: simulations of structure and dynamics as a function of hydration. Chem Phys 1994;183:155-166.
    • (1994) Chem Phys , vol.183 , pp. 155-166
    • Wang, C.X.1    Bizzarri, A.R.2    Xu, Y.W.3    Cannistraro, S.4
  • 28
    • 0031030068 scopus 로고    scopus 로고
    • Classical molecular dynamics simulation of the photoinduced electron transfer dynamics of plastocyanin
    • Ungar LW, Scherer NF, Voth GA. Classical molecular dynamics simulation of the photoinduced electron transfer dynamics of plastocyanin. Biophys J 1997;72:5-17.
    • (1997) Biophys J , vol.72 , pp. 5-17
    • Ungar, L.W.1    Scherer, N.F.2    Voth, G.A.3
  • 29
    • 84986492477 scopus 로고
    • Atomic charges derived from semiempirical methods
    • Besler BH, Merz KM, Kollman PA. Atomic charges derived from semiempirical methods. J Comput Chem 1990;11:431-439.
    • (1990) J Comput Chem , vol.11 , pp. 431-439
    • Besler, B.H.1    Merz, K.M.2    Kollman, P.A.3
  • 30
    • 0000580222 scopus 로고
    • Accuracy and precision in protein crystal structure analysis: Restrained least-squares refinement of the crystal structure of poplar plastocyanin at 1.33 Å resolution
    • Guss JM, Bartunik HD, Freeman HC. Accuracy and precision in protein crystal structure analysis: restrained least-squares refinement of the crystal structure of poplar plastocyanin at 1.33 Å resolution. Acta Crystallogr 1992;B48:790-807.
    • (1992) Acta Crystallogr , vol.B48 , pp. 790-807
    • Guss, J.M.1    Bartunik, H.D.2    Freeman, H.C.3
  • 33
    • 0028815118 scopus 로고
    • Molecular dynamics simulations of alcohol dehydrogenase with a four-or five-coordinate catalytic zinc ion
    • Ryde U. Molecular dynamics simulations of alcohol dehydrogenase with a four-or five-coordinate catalytic zinc ion. Proteins 1995;21:40-56.
    • (1995) Proteins , vol.21 , pp. 40-56
    • Ryde, U.1
  • 34
    • 4243539377 scopus 로고
    • Electronic structure calculations on workstation computers: The program system TURBOMOLE
    • Ahlrichs R, Bär M, Häser M, Horn H, Kölmel C. Electronic structure calculations on workstation computers: the program system TURBOMOLE. Chem Phys Lett 1989;162:165-169.
    • (1989) Chem Phys Lett , vol.162 , pp. 165-169
    • Ahlrichs, R.1    Bär, M.2    Häser, M.3    Horn, H.4    Kölmel, C.5
  • 35
    • 0001881516 scopus 로고    scopus 로고
    • Calculations of intramolecular force fields from second-derivative tensors
    • Seminario JM. Calculations of intramolecular force fields from second-derivative tensors. Int J Quantum Chem Quantum Chem Symp 1996;30:59-65.
    • (1996) Int J Quantum Chem Quantum Chem Symp , vol.30 , pp. 59-65
    • Seminario, J.M.1
  • 36
    • 0026035371 scopus 로고
    • 2 binding to human carbonic anhydrase II
    • 2 binding to human carbonic anhydrase II. J Am Chem Soc 1991;113:406-411.
    • (1991) J Am Chem Soc , vol.113 , pp. 406-411
    • Merz, K.M.1
  • 37
    • 84986506369 scopus 로고
    • Long range nonbonded attractive constants for some charged atoms
    • Bartolotti LJ, Pedersen LG, Charifson PS. Long range nonbonded attractive constants for some charged atoms. J Comput Chem 1991;12:1125-1128.
    • (1991) J Comput Chem , vol.12 , pp. 1125-1128
    • Bartolotti, L.J.1    Pedersen, L.G.2    Charifson, P.S.3
  • 38
    • 0024578173 scopus 로고
    • Free energy via molecular simulation: Applications to chemical and biochemical systems
    • Beveridge DL, Di Capua FM. Free energy via molecular simulation: applications to chemical and biochemical systems. Annu Rev Biophys Biophys. Chem 1989;18:431-492.
    • (1989) Annu Rev Biophys Biophys. Chem , vol.18 , pp. 431-492
    • Beveridge, D.L.1    Di Capua, F.M.2
  • 39
    • 0000695598 scopus 로고
    • Free energy from simulations
    • McCammon JA. Free energy from simulations. Curr Opin Struct Biol 1991;1:196-200.
    • (1991) Curr Opin Struct Biol , vol.1 , pp. 196-200
    • McCammon, J.A.1
  • 40
    • 0000433021 scopus 로고
    • A new method for carrying out free energy perturbation calculations: Dynamically modified windows
    • Pearlman DA, Kollman PA. A new method for carrying out free energy perturbation calculations: dynamically modified windows. J Chem Phys 1989;90:2460-2470.
    • (1989) J Chem Phys , vol.90 , pp. 2460-2470
    • Pearlman, D.A.1    Kollman, P.A.2
  • 41
    • 0000288328 scopus 로고    scopus 로고
    • Theoretical study of the structural and spectroscopic properties of stellacyanin
    • De Kerpel JOA, Pierloot K, Ryde U, Roos BO. Theoretical study of the structural and spectroscopic properties of stellacyanin. J Phys Chem B 1998;102:4638-4647.
    • (1998) J Phys Chem B , vol.102 , pp. 4638-4647
    • De Kerpel, J.O.A.1    Pierloot, K.2    Ryde, U.3    Roos, B.O.4
  • 42
    • 0031042264 scopus 로고    scopus 로고
    • Theoretical study of the electronic spectrum of plastocyanin
    • Pierloot K, De Kerpel JOA, Ryde U, Roos BO. Theoretical study of the electronic spectrum of plastocyanin. J Am Chem Soc 1997;119: 218-226.
    • (1997) J Am Chem Soc , vol.119 , pp. 218-226
    • Pierloot, K.1    De Kerpel, J.O.A.2    Ryde, U.3    Roos, B.O.4
  • 43
    • 0027914978 scopus 로고
    • Electronic structure contributions to function in bioinorganic chemistry
    • Solomon EI, Lowery MD. Electronic structure contributions to function in bioinorganic chemistry. Science 1993;259:1575-1581.
    • (1993) Science , vol.259 , pp. 1575-1581
    • Solomon, E.I.1    Lowery, M.D.2
  • 44
    • 33845283303 scopus 로고
    • Spectroscopic and theoretical studies of the unusual EPR parameters of distorted tetrahedral cupric sites: Correlations to X-ray spectral features of core levels
    • Gewirth AA, Cohen SL, Schugar HJ, Solomon EI. Spectroscopic and theoretical studies of the unusual EPR parameters of distorted tetrahedral cupric sites: correlations to X-ray spectral features of core levels. Inorg Chem 1987;26:1133-1146.
    • (1987) Inorg Chem , vol.26 , pp. 1133-1146
    • Gewirth, A.A.1    Cohen, S.L.2    Schugar, H.J.3    Solomon, E.I.4
  • 45
    • 33845280170 scopus 로고
    • Electronic structure of plastocyanin: Excited state spectral features
    • Gewirth AA, Solomon EI. Electronic structure of plastocyanin: excited state spectral features. J Am Chem Soc 1988;110:3811-3819.
    • (1988) J Am Chem Soc , vol.110 , pp. 3811-3819
    • Gewirth, A.A.1    Solomon, E.I.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.