메뉴 건너뛰기




Volumn 24, Issue 5, 2006, Pages 404-411

CysxHisy-Zn2+ interactions: Possibilities and limitations of a simple pairwise force field

Author keywords

Cys3His Zn2+; Force field; Molecular dynamics

Indexed keywords

ASSOCIATION REACTIONS; CHARGE TRANSFER; COMPUTER SIMULATION; DATABASE SYSTEMS; MOLECULAR DYNAMICS; PROTEINS;

EID: 33644625284     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2005.10.006     Document Type: Article
Times cited : (24)

References (47)
  • 1
    • 0001631057 scopus 로고
    • The coordination chemistry of the catalytic zinc ion in alcohol dehydrogenase studied by ab initio quantum chemical calculations
    • U. Ryde The coordination chemistry of the catalytic zinc ion in alcohol dehydrogenase studied by ab initio quantum chemical calculations Int. J. Quantum Chem. 52 1994 1229 1243
    • (1994) Int. J. Quantum Chem. , vol.52 , pp. 1229-1243
    • Ryde, U.1
  • 2
    • 0029033663 scopus 로고
    • On the role of Glu68 in alcohol dehydrogenase
    • U. Ryde On the role of Glu68 in alcohol dehydrogenase Prot. Sci. 4 1995 1124 1132
    • (1995) Prot. Sci. , vol.4 , pp. 1124-1132
    • Ryde, U.1
  • 3
    • 0034669246 scopus 로고    scopus 로고
    • Tetrahedral vs. octahedral zinc complexes with ligands of biological interest: A DFT/CDM study
    • T. Dudev, and C. Lim Tetrahedral vs. octahedral zinc complexes with ligands of biological interest: a DFT/CDM study J. Am. Chem. Soc. 122 2000 11146 11153
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 11146-11153
    • Dudev, T.1    Lim, C.2
  • 4
    • 0035525888 scopus 로고    scopus 로고
    • 2+-cysteinate complexes in proteins
    • 2+-cysteinate complexes in proteins J. Phys. Chem. B 105 2001 10709 10714
    • (2001) J. Phys. Chem. B , vol.105 , pp. 10709-10714
    • Dudev, T.1    Lim, C.2
  • 5
    • 0347652666 scopus 로고    scopus 로고
    • Ab initio calculations of proton dissociation energies of zinc ligands: Hypothesis of imidazolate as zinc ligand in proteins
    • J. El Yazal, and Y. Pang Ab initio calculations of proton dissociation energies of zinc ligands: hypothesis of imidazolate as zinc ligand in proteins J. Phys. Chem. B 103 1999 8773 8779
    • (1999) J. Phys. Chem. B , vol.103 , pp. 8773-8779
    • El Yazal, J.1    Pang, Y.2
  • 6
    • 0032578481 scopus 로고    scopus 로고
    • Reactivity of the HIV-1 nucleocapsid protein p7 zinc finger domains from the perspective of density functional theory
    • A. Maynard, M. Huang, W. Rice, and D. Covell Reactivity of the HIV-1 nucleocapsid protein p7 zinc finger domains from the perspective of density functional theory Proc. Natl. Acad. Sci. U.S.A. 95 1998 11578 11583
    • (1998) Proc. Natl. Acad. Sci. U.S.A. , vol.95 , pp. 11578-11583
    • Maynard, A.1    Huang, M.2    Rice, W.3    Covell, D.4
  • 7
    • 0026504259 scopus 로고
    • Computer simulation of the initial proton transfer step in human carbonic anhydrase I
    • J. Aqvist, and A. Warshel Computer simulation of the initial proton transfer step in human carbonic anhydrase I J. Mol. Biol. 224 1992 4 14
    • (1992) J. Mol. Biol. , vol.224 , pp. 4-14
    • Aqvist, J.1    Warshel, A.2
  • 8
    • 33751159055 scopus 로고
    • Incorporating solvation effects into density functional electronic structure calculations
    • J. Chen, L. Noodleman, D. Case, and D. Bashford Incorporating solvation effects into density functional electronic structure calculations J. Phys. Chem. 98 1994 11059 11068
    • (1994) J. Phys. Chem. , vol.98 , pp. 11059-11068
    • Chen, J.1    Noodleman, L.2    Case, D.3    Bashford, D.4
  • 9
    • 0030476749 scopus 로고    scopus 로고
    • Disruption of the active site solvent network in carbonic anhydrase II decreases the efficiency of proton transfer
    • J. Jackman, K. Merz, and C. Fierke Disruption of the active site solvent network in carbonic anhydrase II decreases the efficiency of proton transfer Biochemistry 35 1996 16421 16428
    • (1996) Biochemistry , vol.35 , pp. 16421-16428
    • Jackman, J.1    Merz, K.2    Fierke, C.3
  • 10
    • 84962352816 scopus 로고    scopus 로고
    • 2+ interactions: Thiol vs. thiolate coordination
    • 2+ interactions: thiol vs. thiolate coordination Proteins 49 2002 37 48
    • (2002) Proteins , vol.49 , pp. 37-48
    • Simonson, T.1    Calimet, N.2
  • 11
    • 0028815118 scopus 로고
    • Molecular dynamics simulations of alcohol dehydrogenase with a four- or five-coordinate catalytic zinc ion
    • U. Ryde Molecular dynamics simulations of alcohol dehydrogenase with a four- or five-coordinate catalytic zinc ion Proteins 21 1995 40 56
    • (1995) Proteins , vol.21 , pp. 40-56
    • Ryde, U.1
  • 12
    • 0029115487 scopus 로고
    • Zinc binding in proteins and in solution: A simple but accurate non-bonded representation
    • R. Stote, and M. Karplus Zinc binding in proteins and in solution: a simple but accurate non-bonded representation Proteins 23 1995 12 31
    • (1995) Proteins , vol.23 , pp. 12-31
    • Stote, R.1    Karplus, M.2
  • 13
    • 16844373030 scopus 로고    scopus 로고
    • Zn protein simulations including charge transfer and local polarization effects
    • D.V. Sakharov, and C. Lim Zn protein simulations including charge transfer and local polarization effects J. Am. Chem. Soc. 127 2005 4921 4929
    • (2005) J. Am. Chem. Soc. , vol.127 , pp. 4921-4929
    • Sakharov, D.V.1    Lim, C.2
  • 14
    • 84986432841 scopus 로고
    • 2+: An ab initio analysis of the metal-ligand interaction energy
    • 2+: an ab initio analysis of the metal-ligand interaction energy J. Comp. Chem. 16 1995 843 855
    • (1995) J. Comp. Chem. , vol.16 , pp. 843-855
    • Gresh, N.1    Stevens, W.2    Krauss, M.3
  • 15
    • 84986440367 scopus 로고
    • 2+ binding to a series of biologically relevant ligands: A molecular mechanics investigation grounded on ab initio self-consistent field supermolecular computations
    • 2+ binding to a series of biologically relevant ligands: a molecular mechanics investigation grounded on ab initio self-consistent field supermolecular computations J. Comp. Chem. 16 1995 856 882
    • (1995) J. Comp. Chem. , vol.16 , pp. 856-882
    • Gresh, N.1
  • 16
    • 0000111275 scopus 로고    scopus 로고
    • Parallel ab initio and molecular mechanics investigation of polycoordinated Zn(II) complexes with model hard and soft ligands: Variation of binding energy and its components with number and charges of ligands
    • G. Tiraboschi, N. Gresh, C. Giessner-Prettre, L. Pedersen, and D. Deerfield Parallel ab initio and molecular mechanics investigation of polycoordinated Zn(II) complexes with model hard and soft ligands: variation of binding energy and its components with number and charges of ligands J. Comp. Chem. 21 2000 1011 1039
    • (2000) J. Comp. Chem. , vol.21 , pp. 1011-1039
    • Tiraboschi, G.1    Gresh, N.2    Giessner-Prettre, C.3    Pedersen, L.4    Deerfield, D.5
  • 17
    • 0041754408 scopus 로고    scopus 로고
    • Free energy calculations
    • O. Becker A. Mackerell B. Roux M. Watanabe Jr. Marcel Dekker N.Y.
    • T. Simonson Free energy calculations O. Becker A. Mackerell B. Roux M. Watanabe Jr. Computational Biochemistry & Biophysics 2001 Marcel Dekker N.Y. (chapter 9)
    • (2001) Computational Biochemistry & Biophysics
    • Simonson, T.1
  • 18
    • 0028814905 scopus 로고
    • Molecular dynamics simulations of the glucocorticoid receptor DNA-binding domain in complex with DNA and free in solution
    • M. Eriksson, T. Härd, and L. Nilsson Molecular dynamics simulations of the glucocorticoid receptor DNA-binding domain in complex with DNA and free in solution Biophys. J. 68 1995 402 426
    • (1995) Biophys. J. , vol.68 , pp. 402-426
    • Eriksson, M.1    Härd, T.2    Nilsson, L.3
  • 19
    • 0030025260 scopus 로고    scopus 로고
    • Molecular dynamics study of glucocorticoid receptor DNA-binding
    • T. Bishop, and K. Schulten Molecular dynamics study of glucocorticoid receptor DNA-binding Proteins 24 1996 115 133
    • (1996) Proteins , vol.24 , pp. 115-133
    • Bishop, T.1    Schulten, K.2
  • 20
    • 0031577320 scopus 로고    scopus 로고
    • Calculation of the dielectric properties of a protein and its solvent: Theory and a case study
    • G. Löffler, H. Schreiber, and O. Steinhauser Calculation of the dielectric properties of a protein and its solvent: theory and a case study J. Mol. Biol. 270 1997 520 534
    • (1997) J. Mol. Biol. , vol.270 , pp. 520-534
    • Löffler, G.1    Schreiber, H.2    Steinhauser, O.3
  • 21
    • 0025197061 scopus 로고
    • a's of ionizable groups in proteins: Atomic detail from a continuum electrostatic model
    • a 's of ionizable groups in proteins: atomic detail from a continuum electrostatic model Biochemistry 29 1990 10219 10225
    • (1990) Biochemistry , vol.29 , pp. 10219-10225
    • Bashford, D.1    Karplus, M.2
  • 22
    • 0031776357 scopus 로고    scopus 로고
    • Electrostatic contributions to molecular free energies in solution
    • M. Schaefer, H.V. Vlijmen, and M. Karplus Electrostatic contributions to molecular free energies in solution Adv. Protein Chem. 51 1998 1 57
    • (1998) Adv. Protein Chem. , vol.51 , pp. 1-57
    • Schaefer, M.1    Vlijmen, H.V.2    Karplus, M.3
  • 23
    • 0032586777 scopus 로고    scopus 로고
    • a and acid pH-dependent stability estimation in proteins: Removing dielectric and counterion boundaries
    • a and acid pH-dependent stability estimation in proteins: removing dielectric and counterion boundaries Protein Sci. 8 1999 418 425
    • (1999) Protein Sci. , vol.8 , pp. 418-425
    • Warwicker, J.1
  • 24
    • 0035312551 scopus 로고    scopus 로고
    • Macromolecular electrostatics: Continuum models and their growing pains
    • T. Simonson Macromolecular electrostatics: continuum models and their growing pains Curr. Opin. Struct. Biol. 11 2001 243 252
    • (2001) Curr. Opin. Struct. Biol. , vol.11 , pp. 243-252
    • Simonson, T.1
  • 25
    • 0037529067 scopus 로고    scopus 로고
    • Electrostatics and dynamics of proteins
    • T. Simonson Electrostatics and dynamics of proteins Rep. Prog. Phys. 66 2003 737 787
    • (2003) Rep. Prog. Phys. , vol.66 , pp. 737-787
    • Simonson, T.1
  • 26
    • 84962440579 scopus 로고    scopus 로고
    • Incorporating solvation effects into density functional theory: Calculation of absolute acidities
    • W. Richardson, C. Peng, D. Bashford, L. Noodleman, and D. Case Incorporating solvation effects into density functional theory: calculation of absolute acidities Int. J. Quantum Chem. 61 1997 207 217
    • (1997) Int. J. Quantum Chem. , vol.61 , pp. 207-217
    • Richardson, W.1    Peng, C.2    Bashford, D.3    Noodleman, L.4    Case, D.5
  • 27
    • 0030457336 scopus 로고    scopus 로고
    • Retention of thiol protons in two classes of protein zinc ion coordination centers
    • D. Fabris, J. Zaia, Y. Hathout, and C. Fenselau Retention of thiol protons in two classes of protein zinc ion coordination centers J. Am. Chem. Soc. 118 1996 12242 12243
    • (1996) J. Am. Chem. Soc. , vol.118 , pp. 12242-12243
    • Fabris, D.1    Zaia, J.2    Hathout, Y.3    Fenselau, C.4
  • 28
    • 0001403961 scopus 로고    scopus 로고
    • Investigation of zinc chelation in zinc-finger arrays by electrospray mass spectrometry
    • D. Fabris, Y. Hathout, and C. Fenselau Investigation of zinc chelation in zinc-finger arrays by electrospray mass spectrometry Inorg. Chem. 38 1999 1322 1325
    • (1999) Inorg. Chem. , vol.38 , pp. 1322-1325
    • Fabris, D.1    Hathout, Y.2    Fenselau, C.3
  • 30
    • 0000189651 scopus 로고
    • Density functional thermochemistry. III. the role of exact exchange
    • A. Becke Density functional thermochemistry. III. The role of exact exchange J. Chem. Phys. 98 1993 5648
    • (1993) J. Chem. Phys. , vol.98 , pp. 5648
    • Becke, A.1
  • 31
    • 0345491105 scopus 로고
    • Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density
    • C. Lee, W. Yang, and R. Parr Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density Phys. Rev. B 37 1988 785 789
    • (1988) Phys. Rev. B , vol.37 , pp. 785-789
    • Lee, C.1    Yang, W.2    Parr, R.3
  • 32
    • 0033603838 scopus 로고    scopus 로고
    • Competitive binding in magnesium coordination chemistry: Water versus ligands of biological interest
    • T. Dudev, J. Cowan, and C. Lim Competitive binding in magnesium coordination chemistry: water versus ligands of biological interest J. Am. Chem. Soc. 121 1999 7665 7673
    • (1999) J. Am. Chem. Soc. , vol.121 , pp. 7665-7673
    • Dudev, T.1    Cowan, J.2    Lim, C.3
  • 34
    • 0028979464 scopus 로고
    • 2 activator binding domain of protein kinase C delta in complex with phorbol ester
    • 2 activator binding domain of protein kinase C delta in complex with phorbol ester Cell 81 1995 917
    • (1995) Cell , vol.81 , pp. 917
    • Zhang, G.1    Kazanietz, M.2    Blumberg, P.3    Hurley, J.4
  • 35
  • 37
    • 33846823909 scopus 로고
    • Particle Mesh Ewald: An Nlog(N) method for Ewald sums in large systems
    • T. Darden, D. York, and L. Pedersen Particle Mesh Ewald: an N log(N) method for Ewald sums in large systems J. Chem. Phys. 98 1993 10089 10092
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 38
    • 34047201363 scopus 로고    scopus 로고
    • Dynamics methods
    • O. Becker A. Mackerell B. Roux M. Watanabe Jr. Marcel Dekker N.Y.
    • O. Becker, and M. Watanabe Dynamics methods O. Becker A. Mackerell B. Roux M. Watanabe Jr. Computational Biochemistry & Biophysics 2000 Marcel Dekker N.Y. (chapter 3)
    • (2000) Computational Biochemistry & Biophysics
    • Becker, O.1    Watanabe, M.2
  • 39
    • 33646940952 scopus 로고
    • Numerical integration of the cartesian equations of motion for a system with constraints: Molecular dynamics of n-alkanes
    • J. Ryckaert, G. Ciccotti, and H. Berendsen Numerical integration of the cartesian equations of motion for a system 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.1    Ciccotti, G.2    Berendsen, H.3
  • 40
    • 84986512474 scopus 로고
    • Charmm: A program for macromolecular energy, minimization, and molecular dynamics calculations
    • B. Brooks, R. Bruccoleri, B. Olafson, D. States, S. Swaminathan, and M. Karplus Charmm: a program for macromolecular energy, minimization, and molecular dynamics calculations J. Comp. Chem. 4 1983 187 217
    • (1983) J. Comp. Chem. , vol.4 , pp. 187-217
    • Brooks, B.1    Bruccoleri, R.2    Olafson, B.3    States, D.4    Swaminathan, S.5    Karplus, M.6
  • 43
    • 0027393609 scopus 로고
    • Zinc- and sequence-dependent binding to nucleic acids by the N-terminal zinc finger domain of the HIV nucleocapsid protein: NMR structure of the complex with the psi-site analog, dACGCC
    • T. South, and M. Summers Zinc- and sequence-dependent binding to nucleic acids by the N-terminal zinc finger domain of the HIV nucleocapsid protein: NMR structure of the complex with the psi-site analog, dACGCC Protein Sci. 2 1993 3
    • (1993) Protein Sci. , vol.2 , pp. 3
    • South, T.1    Summers, M.2
  • 44
    • 0032964122 scopus 로고    scopus 로고
    • DNA-binding mechanism of the monomeric orphan nuclear receptor NGFI-B
    • G. Meinke, and P. Sigler DNA-binding mechanism of the monomeric orphan nuclear receptor NGFI-B Nat. Struct. Biol. 6 1999 471
    • (1999) Nat. Struct. Biol. , vol.6 , pp. 471
    • Meinke, G.1    Sigler, P.2
  • 45
    • 0028305457 scopus 로고
    • Prediction of pH dependent properties of proteins
    • J. Antosiewicz, J. McCammon, and M. Gilson Prediction of pH dependent properties of proteins J. Mol. Biol. 238 1994 415 436
    • (1994) J. Mol. Biol. , vol.238 , pp. 415-436
    • Antosiewicz, J.1    McCammon, J.2    Gilson, M.3
  • 46
    • 0000882945 scopus 로고    scopus 로고
    • Importance of charge transfer and polarization effects for the modelling of uranyl-cation complexes
    • L. Hemmingsen, P. Amara, E. Ansoborio, and M. Field Importance of charge transfer and polarization effects for the modelling of uranyl-cation complexes J. Phys. Chem. A 104 2000 4095 4101
    • (2000) J. Phys. Chem. a , vol.104 , pp. 4095-4101
    • Hemmingsen, L.1    Amara, P.2    Ansoborio, E.3    Field, M.4
  • 47
    • 80053073402 scopus 로고    scopus 로고
    • The dielectric constant of cytochrome c from simulations in a water droplet including all electrostatic interactions
    • T. Simonson The dielectric constant of cytochrome c from simulations in a water droplet including all electrostatic interactions J. Am. Chem. Soc. 120 1998 4875 4876
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 4875-4876
    • Simonson, T.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.