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Volumn 305, Issue , 2005, Pages 517-553

Study of Ligand-Protein Interactions by Means of Density Functional Theory and First-Principles Molecular Dynamics

Author keywords

ab initio molecular dynamics; Car Parrinello molecular dynamics; catalases; Density functional theory; molecular dynamics; oxyheme; protein ligand interactions

Indexed keywords

CATALASE; FORMIC ACID; FORMIC ACID DERIVATIVE; LIGAND; MYOGLOBIN; OXYGEN; PROTEIN;

EID: 21344450916     PISSN: 10643745     EISSN: 19406029     Source Type: Book Series    
DOI: 10.1385/1-59259-912-5:517     Document Type: Chapter
Times cited : (5)

References (95)
  • 1
    • 0002617092 scopus 로고    scopus 로고
    • Portrait of an allosteric protein
    • Freeman, New York, NY
    • Stryer, L. (1997) Portrait of an allosteric protein, in: Biochemistry, Freeman, New York, NY, pp. 147–180.
    • (1997) Biochemistry , pp. 147-180
    • Stryer, L.1
  • 6
    • 4243606192 scopus 로고
    • Unified approach for molecular dynamics and density-functional theory
    • Car, R. and Parrinello, M. (1985) Unified approach for molecular dynamics and density-functional theory. Phys. Rev. Lett. 55, 2471–2474.
    • (1985) Phys. Rev. Lett , vol.55 , pp. 2471-2474
    • Car, R.1    Parrinello, M.2
  • 7
    • 0344791553 scopus 로고
    • Approximate Density Functional Theory as a practical tool in molecular energetics and dynamics
    • Ziegler, T. (1991) Approximate Density Functional Theory as a practical tool in molecular energetics and dynamics. Chem. Rev. 91, 651–667.
    • (1991) Chem. Rev , vol.91 , pp. 651-667
    • Ziegler, T.1
  • 9
    • 0000074308 scopus 로고    scopus 로고
    • Molecular dynamics in low-spin excited states
    • Frank, I., Hutter, J., Marx, D., and Parrinello, M. (1998) Molecular dynamics in low-spin excited states. J. Chem. Phys. 108, 4060–4069.
    • (1998) J. Chem. Phys , vol.108 , pp. 4060-4069
    • Frank, I.1    Hutter, J.2    Marx, D.3    Parrinello, M.4
  • 10
    • 0032577087 scopus 로고    scopus 로고
    • Spin-restricted density functional approach to the open-shell problem
    • Filatov, M. and Shaik, S. (1998) Spin-restricted density functional approach to the open-shell problem. Chem. Phys. Lett. 288, 689–697.
    • (1998) Chem. Phys. Lett , vol.288 , pp. 689-697
    • Filatov, M.1    Shaik, S.2
  • 12
    • 0000790755 scopus 로고    scopus 로고
    • van der Waals energies in Density Functional Theory
    • Kohn, W., Meir, Y., and Makarov, D. (1998) van der Waals energies in Density Functional Theory. Phys. Rev. Lett. 80, 4153–4156.
    • (1998) Phys. Rev. Lett , vol.80 , pp. 4153-4156
    • Kohn, W.1    Meir, Y.2    Makarov, D.3
  • 13
    • 0035932162 scopus 로고    scopus 로고
    • Hydrogen bonding and stacking interactions of nucleic acid base pairs: a density-func-tional-theory based treatment
    • Eltsner, M., Hobza, P., Frauenheim, T., Suhai, S., and Kaxiras, E. (2001) Hydrogen bonding and stacking interactions of nucleic acid base pairs: a density-func-tional-theory based treatment. J. Chem. Phys. 114, 5149–5155.
    • (2001) J. Chem. Phys , vol.114 , pp. 5149-5155
    • Eltsner, M.1    Hobza, P.2    Frauenheim, T.3    Suhai, S.4    Kaxiras, E.5
  • 14
  • 15
    • 4243810035 scopus 로고
    • Simulation of enzyme reactions using valence bond force fields and other hybrid quantum/classical approaches
    • Aqvist, J. and Warshel, A. (1993) Simulation of enzyme reactions using valence bond force fields and other hybrid quantum/classical approaches. Chem. Rev. 93, 2523–2544.
    • (1993) Chem. Rev , vol.93 , pp. 2523-2544
    • Aqvist, J.1    Warshel, A.2
  • 16
    • 0037156101 scopus 로고    scopus 로고
    • A Hamiltonian electrostatic coupling scheme for hybrid Car–Parrinello molecular dynamics simulations
    • Laio, A., VandeVondele, J., and Rothlisberger, U. (2002) A Hamiltonian electrostatic coupling scheme for hybrid Car–Parrinello molecular dynamics simulations, J. Chem. Phys. 116, 6941–6947.
    • (2002) J. Chem. Phys , vol.116 , pp. 6941-6947
    • Laio, A.1    VandeVondele, J.2    Rothlisberger, U.3
  • 17
    • 0000730460 scopus 로고    scopus 로고
    • Selfconsistent order-N density-functional calculations for very large systems
    • Ordejon, P., Artacho, E., and Soler, J. M. (1996) Selfconsistent order-N density-functional calculations for very large systems. Phys. Rev. B. 53, R10441.
    • (1996) Phys. Rev. B , vol.53 , pp. R10441
    • Ordejon, P.1    Artacho, E.2    Soler, J. M.3
  • 18
    • 0041810451 scopus 로고    scopus 로고
    • Efficient exploration of reactive potential energy surfaces using Car–Parrinello molecular dynamics
    • Iannuzzi, M., Laio, A., and Parrinello, M. (2003) Efficient exploration of reactive potential energy surfaces using Car–Parrinello molecular dynamics, Phys. Rev. Lett. 90, 238–302.
    • (2003) Phys. Rev. Lett , vol.90 , pp. 238-302
    • Iannuzzi, M.1    Laio, A.2    Parrinello, M.3
  • 19
    • 0001181339 scopus 로고    scopus 로고
    • Density Functional Theory of biologically relevant metal centers
    • Siegbahn, P. E. and Blomberg, M. R. A. (1999) Density Functional Theory of biologically relevant metal centers, Annu. Rev. Phys. Chem. 50, 221–249.
    • (1999) Annu. Rev. Phys. Chem , vol.50 , pp. 221-249
    • Siegbahn, P. E.1    Blomberg, M. R. A.2
  • 20
    • 0032054613 scopus 로고    scopus 로고
    • Quantum mechanical calculations on biological systems
    • Friesner, R. A. and Beachy, M. D. (1998) Quantum mechanical calculations on biological systems. Curr. Op. Str. Biol. 8, 257–262.
    • (1998) Curr. Op. Str. Biol , vol.8 , pp. 257-262
    • Friesner, R. A.1    Beachy, M. D.2
  • 21
    • 0036286854 scopus 로고    scopus 로고
    • The role and perspective of ab initio molecular dynamics in the study of biological systems
    • Carloni, P., Röthlisberger, U., and Parrinello, M. (2002) The role and perspective of ab initio molecular dynamics in the study of biological systems. Acc. Chem. Res. 35, 45–464.
    • (2002) Acc. Chem. Res , vol.35 , pp. 45-464
    • Carloni, P.1    Röthlisberger, U.2    Parrinello, M.3
  • 22
    • 0038305457 scopus 로고    scopus 로고
    • Quantum chemical studies of radical-containing enzymes
    • Himo, F. and Siegbahn, P. E. M. (2003) Quantum chemical studies of radical-containing enzymes. Chem. Rev. 103, 242–2456.
    • (2003) Chem. Rev , vol.103 , pp. 242-2456
    • Himo, F.1    Siegbahn, P. E. M.2
  • 23
    • 0037366128 scopus 로고    scopus 로고
    • Principles governing Mg, Ca, and Zn binding and selectivity in proteins
    • Dudev, T. and Lim, C. (2003) Principles governing Mg, Ca, and Zn binding and selectivity in proteins. Chem. Rev. 103, 773–787.
    • (2003) Chem. Rev , vol.103 , pp. 773-787
    • Dudev, T.1    Lim, C.2
  • 25
    • 0035124398 scopus 로고    scopus 로고
    • The flexibility of carboxylate ligands in methane monooxygenase and ribonucleotide reductase: a density functional study
    • Torrent, M., Musaev, D. G., and Morokuma, K. (2001) The flexibility of carboxylate ligands in methane monooxygenase and ribonucleotide reductase: a density functional study. J. Phys. Chem. 105, 322–327.
    • (2001) J. Phys. Chem , vol.105 , pp. 322-327
    • Torrent, M.1    Musaev, D. G.2    Morokuma, K.3
  • 26
    • 0036306459 scopus 로고    scopus 로고
    • Role of conformational fluctuations in the enzymatic reaction of HIV-1 protease
    • Piana, S., Carloni, P., and Parrinello, M. (2002) Role of conformational fluctuations in the enzymatic reaction of HIV-1 protease. J. Mol. Biol. 319, 567–583.
    • (2002) J. Mol. Biol , vol.319 , pp. 567-583
    • Piana, S.1    Carloni, P.2    Parrinello, M.3
  • 27
    • 0037071785 scopus 로고    scopus 로고
    • Potassium permeation through the KcsA channel: a density functional study
    • Guidoni, L. and Carloni, P. (2002) Potassium permeation through the KcsA channel: a density functional study. Biochim. Biophys. Acta 1563, 1–6.
    • (2002) Biochim. Biophys. Acta , vol.1563 , pp. 1-6
    • Guidoni, L.1    Carloni, P.2
  • 28
    • 0029775587 scopus 로고    scopus 로고
    • Ab initio molecular dynamics study of proton transfer in a polyglycine analog of the ion channel gramicidin A
    • Sagnella D. E., Laasonen K., and Klein M. L. (1996) Ab initio molecular dynamics study of proton transfer in a polyglycine analog of the ion channel gramicidin A. Biophys. J. 71, 1172–1178.
    • (1996) Biophys. J , vol.71 , pp. 1172-1178
    • Sagnella, D. E.1    Laasonen, K.2    Klein, M. L.3
  • 30
    • 0035023569 scopus 로고    scopus 로고
    • How the CO in myoglobin acquired its bend: lessons in interpretation of crystallographic data
    • Stec, B. and Phillips, G. N. (2001) How the CO in myoglobin acquired its bend: lessons in interpretation of crystallographic data. Acta Cryst. D57, 751–754.
    • (2001) Acta Cryst , vol.D57 , pp. 751-754
    • Stec, B.1    Phillips, G. N.2
  • 31
    • 0001588361 scopus 로고    scopus 로고
    • Functional analogs of heme protein active sites
    • Collman, J. P. (1997). Functional analogs of heme protein active sites. Inorg.Chem. 36, 5145–5155.
    • (1997) Inorg.Chem , vol.36 , pp. 5145-5155
    • Collman, J. P.1
  • 32
    • 33748590497 scopus 로고    scopus 로고
    • Carbonyl tilting and bending potential energy surface of carbon monoxyhemes
    • Ghosh, A. and Bocian, D. F. (1996) Carbonyl tilting and bending potential energy surface of carbon monoxyhemes. J. Phys. Chem. 100, 6363–6367.
    • (1996) J. Phys. Chem , vol.100 , pp. 6363-6367
    • Ghosh, A.1    Bocian, D. F.2
  • 33
    • 0031276121 scopus 로고    scopus 로고
    • Equilibrium geometries and electronic structure of iron-porphyrin complexes: a density functional study
    • Rovira, C., Kunc, K., Hutter, J., Ballone, P., and Parrinello, M. (1997) Equilibrium geometries and electronic structure of iron-porphyrin complexes: a density functional study. J. Phys. Chem. A. 101, 8914–8925.
    • (1997) J. Phys. Chem. A , vol.101 , pp. 8914-8925
    • Rovira, C.1    Kunc, K.2    Hutter, J.3    Ballone, P.4    Parrinello, M.5
  • 34
    • 0001397162 scopus 로고    scopus 로고
    • Discordant results on FeCO deform-ability in heme proteins reconciled by density functional theory
    • Spiro, T. G. and Kozlowski, P. M. (1998) Discordant results on FeCO deform-ability in heme proteins reconciled by density functional theory. J. Am. Chem. Soc. 120, 4524–4525.
    • (1998) J. Am. Chem. Soc , vol.120 , pp. 4524-4525
    • Spiro, T. G.1    Kozlowski, P. M.2
  • 35
    • 0038296982 scopus 로고    scopus 로고
    • The structure and dynamics of the Fe–CO bond in myoglobin
    • Rovira, C. (2003) The structure and dynamics of the Fe–CO bond in myoglobin. J. Phys. Cond. Mat. 15, 1809–1822.
    • (2003) J. Phys. Cond. Mat , vol.15 , pp. 1809-1822
    • Rovira, C.1
  • 36
    • 0029647452 scopus 로고
    • Binding of CO to myoglobin from a heme pocket docking site to form nearly linear Fe–C–O
    • Lim, M., Jackson, T. A., and Anfinrud, P. A. (1995) Binding of CO to myoglobin from a heme pocket docking site to form nearly linear Fe–C–O. Science 269, 962–966.
    • (1995) Science , vol.269 , pp. 962-966
    • Lim, M.1    Jackson, T. A.2    Anfinrud, P. A.3
  • 38
    • 0000901899 scopus 로고    scopus 로고
    • 17 O NMR chemical shift and nuclear quadrupole coupling tensors in oxyheme model complexes
    • 17 O NMR chemical shift and nuclear quadrupole coupling tensors in oxyheme model complexes. J. Phys. Chem. B. 104, 5200–5208.
    • (2000) J. Phys. Chem. B , vol.104 , pp. 5200-5208
    • Kaupp, M.1    Rovira, C.2    Parrinello, M.3
  • 39
    • 0037168603 scopus 로고    scopus 로고
    • Spin-dependent mechanism for duatomic ligand binding to heme
    • 759
    • Franzen, S. (2002) Spin-dependent mechanism for duatomic ligand binding to heme. Proc. Nat. Acad. Sci. 99, 16,754–16,759.
    • (2002) Proc. Nat. Acad. Sci , vol.99 , Issue.16 , pp. 754-16
    • Franzen, S.1
  • 40
    • 0346365000 scopus 로고    scopus 로고
    • Active species of horseradish peroxidase (HRP) and cytochrome P450: two electronic chameleons
    • 788
    • De Visser, S. P., Shaik, S., Sharma, P. K., Kumar, D., and Thiel, W. (2003) Active species of horseradish peroxidase (HRP) and cytochrome P450: two electronic chameleons. J. Am. Chem. Soc. 125, 15,779–15,788.
    • (2003) J. Am. Chem. Soc , vol.125 , Issue.15 , pp. 779-15
    • De Visser, S. P.1    Shaik, S.2    Sharma, P. K.3    Kumar, D.4    Thiel, W.5
  • 41
    • 0041654852 scopus 로고    scopus 로고
    • Modulation of NO trans effect in heme proteins: implications for the activation of soluble guanylate cyclase
    • Martí, M. A., Scherlis, D. A., Doctorovich, F. A., Ordejón, P., and Estrin, D. A. (2003) Modulation of NO trans effect in heme proteins: implications for the activation of soluble guanylate cyclase. J. Biol. Inorg. Chem. 8, 595–600.
    • (2003) J. Biol. Inorg. Chem , vol.8 , pp. 595-600
    • Martí, M. A.1    Scherlis, D. A.2    Doctorovich, F. A.3    Ordejón, P.4    Estrin, D. A.5
  • 44
    • 0000519270 scopus 로고    scopus 로고
    • Combined quantum mechanical and molecular mechanical potentials
    • (Schleyer, P. R., Allinger, N. L., Clark, T., Gasteiget, J., Kollman, P. A., Schaefer III, H. F., Schreiner, P. R., eds) John Wiley & Sons, Chichester, UK
    • Amara, P. and Field, M. (1998) Combined quantum mechanical and molecular mechanical potentials, in: Encyclopedia of computational chemistry (Schleyer, P. v. R., Allinger, N. L., Clark, T., Gasteiget, J., Kollman, P. A., Schaefer III, H. F., Schreiner, P. R., eds.) John Wiley & Sons, Chichester, UK.
    • (1998) Encyclopedia of computational chemistry
    • Amara, P.1    Field, M.2
  • 45
    • 0001763714 scopus 로고    scopus 로고
    • Frontier bonds in QM/ MM methods: A comparison of different approaches
    • Reuter, N., Dejaegere, A., Maigret, B., and Karplus, M. (2000) Frontier bonds in QM/ MM methods: A comparison of different approaches. J. Phys. Chem. A 104, 1720–1735.
    • (2000) J. Phys. Chem. A , vol.104 , pp. 1720-1735
    • Reuter, N.1    Dejaegere, A.2    Maigret, B.3    Karplus, M.4
  • 46
    • 0037156101 scopus 로고    scopus 로고
    • A hamiltonian electrostatic coupling scheme for hybrid Car-Parrinello molecular dynamics simulations
    • Laio, A., VandeVondele, J., and Röthlisberger, U. (2002) A hamiltonian electrostatic coupling scheme for hybrid Car-Parrinello molecular dynamics simulations. J. Chem. Phys. 116, 6941–6947.
    • (2002) J. Chem. Phys , vol.116 , pp. 6941-6947
    • Laio, A.1    VandeVondele, J.2    Röthlisberger, U.3
  • 47
    • 0038003758 scopus 로고    scopus 로고
    • Characterization of the dizinc analogue of the synthetic diiron DF1 using an initio hybrid quantum/classical molecular dynamics simulations
    • Magistrato, A., DeGrado, W., Laio, A., Röthlisberger, U., VandeVondele, J., and Klein, M. L. (2003) Characterization of the dizinc analogue of the synthetic diiron DF1 using an initio hybrid quantum/classical molecular dynamics simulations. J. Phys. Chem. B. 107, 4182–4188.
    • (2003) J. Phys. Chem. B , vol.107 , pp. 4182-4188
    • Magistrato, A.1    DeGrado, W.2    Laio, A.3    Röthlisberger, U.4    VandeVondele, J.5    Klein, M. L.6
  • 48
    • 0034951055 scopus 로고    scopus 로고
    • Influence of the heme pocket conformation on the structure and vibrations of the Fe-CO bond in myoglobin. A QM/MM density functional study
    • Rovira. C., Schulze, B., Eichinger, M., Evanseck, J. D., and Parrinello, M. (2001) Influence of the heme pocket conformation on the structure and vibrations of the Fe-CO bond in myoglobin. A QM/MM density functional study. Biophys. J. 81, 435–445.
    • (2001) Biophys. J , vol.81 , pp. 435-445
    • Rovira., C.1    Schulze, B.2    Eichinger, M.3    Evanseck, J. D.4    Parrinello, M.5
  • 49
    • 0037055032 scopus 로고    scopus 로고
    • The elusive oxidant species of cytochrome P450 enzymes: characterization by combined quantum mechanical/molecular mechanical (QM/MM) calculations
    • Schöneboom, J. C., Lin, H., Reuter, N., Thiel, W., Cohen, S., Ogliaro, F., and Shaik, S. (2002) The elusive oxidant species of cytochrome P450 enzymes: characterization by combined quantum mechanical/molecular mechanical (QM/MM) calculations. J. Am. Chem. Soc. 124, 8142–8151.
    • (2002) J. Am. Chem. Soc , vol.124 , pp. 8142-8151
    • Schöneboom, J. C.1    Lin, H.2    Reuter, N.3    Thiel, W.4    Cohen, S.5    Ogliaro, F.6    Shaik, S.7
  • 50
    • 85194600863 scopus 로고    scopus 로고
    • CPMD program, Copyright IBM Corp. 1990–2003, Copyright MPI für Festkörperforschung, Stuttgart 1997-2001
    • CPMD program, Copyright IBM Corp. 1990–2003, Copyright MPI für Festkörperforschung, Stuttgart 1997-2001. URL: http://www.cpmd.org.
  • 51
    • 10644250257 scopus 로고
    • Inhomogeneous electron gas
    • Hohenberg, P. and Kohn, W. (1964) Inhomogeneous electron gas. Phys. Rev. B 136, 864–871.
    • (1964) Phys. Rev. B , vol.136 , pp. 864-871
    • Hohenberg, P.1    Kohn, W.2
  • 52
    • 0042113153 scopus 로고
    • Self-consistent equations including exchange and correlation effects
    • Kohn, W. and Sham, L. J. (1965) Self-consistent equations including exchange and correlation effects. Phys. Rev. A. 140, 1133–1138.
    • (1965) Phys. Rev. A , vol.140 , pp. 1133-1138
    • Kohn, W.1    Sham, L. J.2
  • 53
    • 0242314692 scopus 로고    scopus 로고
    • The quest for approximate exchange-correlation functionals
    • Wiley-VCH, Weinheim, Germany
    • Koch, W. and Holthausen, M. C. (2000) The quest for approximate exchange-correlation functionals, in: A Chemist’s Guide to Density Functional Theory, Wiley-VCH, Weinheim, Germany, pp. 65–91.
    • (2000) A Chemist’s Guide to Density Functional Theory , pp. 65-91
    • Koch, W.1    Holthausen, M. C.2
  • 55
    • 0039892284 scopus 로고
    • Density functional calculations of molecular bond energies
    • Becke, A. D. (1986) Density functional calculations of molecular bond energies. J. Chem. Phys. 84, 4524–4529.
    • (1986) J. Chem. Phys , vol.84 , pp. 4524-4529
    • Becke, A. D.1
  • 56
    • 5944261746 scopus 로고
    • Density-functional approximation for the correlation energy of the inhomogeneous electron gas
    • Perdew, J. P. (1986) Density-functional approximation for the correlation energy of the inhomogeneous electron gas. Phys. Rev. B. 33, 8822–8824.
    • (1986) Phys. Rev. B , vol.33 , pp. 8822-8824
    • Perdew, J. P.1
  • 57
    • 0345491105 scopus 로고
    • Development of the Colle–Salvetti correla-tion-energy formula into a functional of electron density
    • Lee, C., Yang, W., and Parr, R. G. (1988) Development of the Colle–Salvetti correla-tion-energy formula into a functional of electron density. Phys. Rev. B. 37, 785–789.
    • (1988) Phys. Rev. B , vol.37 , pp. 785-789
    • Lee, C.1    Yang, W.2    Parr, R. G.3
  • 58
    • 4243943295 scopus 로고    scopus 로고
    • Generalized gradient approximation made simple
    • Erratum: (1997) Phys. Rev. Lett. 78, 1396
    • Perdew, J. P., Burke, K., and Ernzerhof, M. (1996) Generalized gradient approximation made simple. Phys. Rev. Lett. 77, 3865–3868, Erratum: (1997) Phys. Rev. Lett. 78, 1396.
    • (1996) Phys. Rev. Lett , vol.77 , pp. 3865-3868
    • Perdew, J. P.1    Burke, K.2    Ernzerhof, M.3
  • 59
    • 34250817103 scopus 로고
    • A new mixing of Hartree–Fock and local density-functional theories
    • Becke, A. D. (1993) A new mixing of Hartree–Fock and local density-functional theories. J. Chem. Phys. 98, 5648–5652.
    • (1993) J. Chem. Phys , vol.98 , pp. 5648-5652
    • Becke, A. D.1
  • 60
    • 11944256577 scopus 로고
    • Iterative minimization techniques for ab initio total-energy calculations: molecular dynamics and conjugate gradients
    • Payne, M. C., Teter, M. P., Allan, D. C., Arias, T. A., and Joannopoulos, J. D. (1992) Iterative minimization techniques for ab initio total-energy calculations: molecular dynamics and conjugate gradients. Rev. Mod. Phys. 64, 1045–1097.
    • (1992) Rev. Mod. Phys , vol.64 , pp. 1045-1097
    • Payne, M. C.1    Teter, M. P.2    Allan, D. C.3    Arias, T. A.4    Joannopoulos, J. D.5
  • 61
    • 4143095330 scopus 로고
    • Electron affinities of the first-row atoms revisited. Systematic basis sets and wave functions
    • Kendall, R. A., Dunning, T. H., Jr., and Harrison, R. J. (1992) Electron affinities of the first-row atoms revisited. Systematic basis sets and wave functions. J. Chem. Phys. 96, 6796–6806.
    • (1992) J. Chem. Phys , vol.96 , pp. 6796-6806
    • Kendall, R. A.1    Dunning, T. H.2    Harrison, R. J.3
  • 62
    • 33646638059 scopus 로고
    • Pseudopotential methods in condensed matter applications
    • Pickett, W. E. (1989) Pseudopotential methods in condensed matter applications Comput. Phys. Rep. 9, 115–197.
    • (1989) Comput. Phys. Rep , vol.9 , pp. 115-197
    • Pickett, W. E.1
  • 63
    • 0000323669 scopus 로고    scopus 로고
    • Ab initio molecular dynamics: theory and implementation
    • (Grotendorst, J., ed), John von Neumann Institute for Computing, Julich, Germany
    • Marx, D. and Hutter, J. (2000) Ab initio molecular dynamics: theory and implementation, in: Modern methods and algorithms of Quantum Chemistry (Grotendorst, J., ed.), John von Neumann Institute for Computing, Julich, Germany, pp. 301–409.
    • (2000) Modern methods and algorithms of Quantum Chemistry , pp. 301-409
    • Marx, D.1    Hutter, J.2
  • 64
    • 22944467757 scopus 로고
    • Computer “experiments” on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules
    • Verlet, L. (1967) Computer “experiments” on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules. Phys. Rev. 159, 98–103.
    • (1967) Phys. Rev , vol.159 , pp. 98-103
    • Verlet, L.1
  • 65
    • 0009822387 scopus 로고
    • Comment on ”error cancelation in the molecular dynamics method for total energy calculations
    • Car, R., Parrinello, M., and Payne, M. (1991) Comment on ”error cancelation in the molecular dynamics method for total energy calculations.” J. Phys. Cond. Matt. 3, 9539–9543.
    • (1991) J. Phys. Cond. Matt , vol.3 , pp. 9539-9543
    • Car, R.1    Parrinello, M.2    Payne, M.3
  • 66
    • 84947362301 scopus 로고
    • Molecular dynamics without effective potentials via the Car–Parrinello approach
    • Remler, D. K. and Madden, P. A. (1990) Molecular dynamics without effective potentials via the Car–Parrinello approach. Mol. Phys. 70, 921–966.
    • (1990) Mol. Phys , vol.70 , pp. 921-966
    • Remler, D. K.1    Madden, P. A.2
  • 67
    • 0036025449 scopus 로고    scopus 로고
    • Ab initio molecular dynamics with density functional theory
    • Tse, J. S. (2002) Ab initio molecular dynamics with density functional theory. Annu. Rev. Phys. Chem. 53, 24–290.
    • (2002) Annu. Rev. Phys. Chem , vol.53 , pp. 24-290
    • Tse, J. S.1
  • 68
    • 0037139291 scopus 로고    scopus 로고
    • Structure and spin-state energetics of an iron–porphyrin model: An assessment of theoretical methods
    • Scherlis, D. A. and Estrin, D. A. (2002) Structure and spin-state energetics of an iron–porphyrin model: An assessment of theoretical methods. Int. J. Quant. Chem. 87, 158–166.
    • (2002) Int. J. Quant. Chem , vol.87 , pp. 158-166
    • Scherlis, D. A.1    Estrin, D. A.2
  • 69
    • 0141959727 scopus 로고    scopus 로고
    • Theoretical prediction of the Co–C bond strength in cobalamins
    • Jensen, K. and Ryde, U. (2003) Theoretical prediction of the Co–C bond strength in cobalamins. J. Phys. Chem. A. 107, 7539–7545.
    • (2003) J. Phys. Chem. A , vol.107 , pp. 7539-7545
    • Jensen, K.1    Ryde, U.2
  • 70
    • 33645426115 scopus 로고
    • Efficient pseudopotentials for plane-wave calculations
    • Troullier, M. and Martins, J. L. (1991) Efficient pseudopotentials for plane-wave calculations, Phys. ReV. B 43, 1993–2006.
    • (1991) Phys. ReV. B , vol.43 , pp. 1993-2006
    • Troullier, M.1    Martins, J. L.2
  • 71
    • 0000549623 scopus 로고
    • Non-linear ionic pseudopotentials in spin-density-functional calculations
    • Louie, S. G., Froyen, S., and Cohen, M. L. (1982) Non-linear ionic pseudopotentials in spin-density-functional calculations, Phys. Rev. B. 26, 1738–1742.
    • (1982) Phys. Rev. B , vol.26 , pp. 1738-1742
    • Louie, S. G.1    Froyen, S.2    Cohen, M. L.3
  • 72
    • 0038853525 scopus 로고    scopus 로고
    • Crystal structures of myoglobin-ligand complexes at near-atomic resolution
    • Vojtechovsky, J., Chu, K., Berendzen, J., Sweet, R. M., and Schlichting, I. (1999) Crystal structures of myoglobin-ligand complexes at near-atomic resolution. Biophys. J. 77, 2153–2174.
    • (1999) Biophys. J , vol.77 , pp. 2153-2174
    • Vojtechovsky, J.1    Chu, K.2    Berendzen, J.3    Sweet, R. M.4    Schlichting, I.5
  • 73
    • 0019942576 scopus 로고
    • The iron–oxygen bond in human oxyhaemoglobin
    • Shaanan, B. (1982) The iron–oxygen bond in human oxyhaemoglobin. Nature 296, 683–684.
    • (1982) Nature , vol.296 , pp. 683-684
    • Shaanan, B.1
  • 74
    • 0001622166 scopus 로고
    • Structure of a dyoxygen adduct of (1-methylimidazole)-meso-tetrakis(α,α,α,α−ο-pivalamidophenyl) porphinatoiron(II). An iron dioxygen model for the heme component of oxymyoglobin
    • Jameson, G. B., Rodley, G. A., Robinson, W. T., Gagne, R. R., Reed, C. A., and Collman, J. P. (1978). Structure of a dyoxygen adduct of (1-methylimidazole)-meso-tetrakis(α,α,α,α−ο-pivalamidophenyl) porphinatoiron(II). An iron dioxygen model for the heme component of oxymyoglobin. Inorg. Chem. 17, 850–857.
    • (1978) Inorg. Chem , vol.17 , pp. 850-857
    • Jameson, G. B.1    Rodley, G. A.2    Robinson, W. T.3    Gagne, R. R.4    Reed, C. A.5    Collman, J. P.6
  • 75
    • 0000564803 scopus 로고
    • Models for the active site of oxygen-binding hemoproteins. Dioxygen binding properties and the structures of (2-methylimidazole)-meso-tetra(α,α,α,α−ο−pivalamidophenyl)poprhyrinatoiron(II)-ethanol and its dioxygen adduct
    • Jameson, G. B., Molinaro, F., Ibers, J. A., Collman, J. P., Brauman, J. I., Rose, E., and Suslick, K. S. (1980) Models for the active site of oxygen-binding hemoproteins. Dioxygen binding properties and the structures of (2-methylimidazole)-meso-tetra(α,α,α,α−ο−pivalamidophenyl)poprhyrinatoiron(II)-ethanol and its dioxygen adduct. J. Am. Chem. Soc. 102, 3224–3237.
    • (1980) J. Am. Chem. Soc , vol.102 , pp. 3224-3237
    • Jameson, G. B.1    Molinaro, F.2    Ibers, J. A.3    Collman, J. P.4    Brauman, J. I.5    Rose, E.6    Suslick, K. S.7
  • 76
    • 0020749147 scopus 로고
    • O2 and CO binding to iron(II) porphyrins: a comparison of the “picket fence” and “pocket” porphyrins
    • Collman, J. P., Brauman, J. I., Iverson, B. L., Sessler, J. L., Morris, R. M., and Gibson, Q. H. (1983) O2 and CO binding to iron(II) porphyrins: a comparison of the “picket fence” and “pocket” porphyrins. J. Am. Chem. Soc. 105, 3052–3064.
    • (1983) J. Am. Chem. Soc , vol.105 , pp. 3052-3064
    • Collman, J. P.1    Brauman, J. I.2    Iverson, B. L.3    Sessler, J. L.4    Morris, R. M.5    Gibson, Q. H.6
  • 78
    • 0002424327 scopus 로고
    • Nature of the iron-oxygen bond in oxyhemoglobin
    • Weiss, J. J. (1964) Nature of the iron-oxygen bond in oxyhemoglobin. Nature (London) 202, 83–84.
    • (1964) Nature (London) , vol.202 , pp. 83-84
    • Weiss, J. J.1
  • 79
    • 37049049612 scopus 로고
    • Nature of the iron-oxygen bond in oxyhemoglobin
    • Pauling, L. (1964) Nature of the iron-oxygen bond in oxyhemoglobin. Nature (London) 203, 182–183.
    • (1964) Nature (London) , vol.203 , pp. 182-183
    • Pauling, L.1
  • 80
    • 0017902203 scopus 로고
    • 2 – coupling at the active center
    • 2 – coupling at the active center. Z. Naturforsch 33, 488–494.
    • (1978) Z. Naturforsch , vol.33 , pp. 488-494
    • Bade, D.1    Parak, F.2
  • 81
    • 3042907629 scopus 로고
    • Synthetic heme-dioxygen complexes
    • Momenteau, M. and Reed, C. A. (1994) Synthetic heme-dioxygen complexes Chem. Rev. 94, 659–698.
    • (1994) Chem. Rev , vol.94 , pp. 659-698
    • Momenteau, M.1    Reed, C. A.2
  • 82
    • 0012904850 scopus 로고
    • A theoretical investigation of the magnetic and ground-state properties of model oxyhemoglobin complexes
    • Herman, Z. S. and Loew, G. H. (1980) A theoretical investigation of the magnetic and ground-state properties of model oxyhemoglobin complexes. J. Am. Chem. Soc. 102, 1815–1821.
    • (1980) J. Am. Chem. Soc , vol.102 , pp. 1815-1821
    • Herman, Z. S.1    Loew, G. H.2
  • 83
    • 0001415426 scopus 로고
    • CASSCF calculation on dioxygen heme complex with extended basis set
    • Yamamoto, S. and Kashiwagi, H. (1993) CASSCF calculation on dioxygen heme complex with extended basis set. Chem. Phys. Lett. 205, 306–312.
    • (1993) Chem. Phys. Lett , vol.205 , pp. 306-312
    • Yamamoto, S.1    Kashiwagi, H.2
  • 84
    • 0001512013 scopus 로고    scopus 로고
    • Oxygen binding to iron-porphyrin: a Density functional study using both LSD and LSD+GC schemes
    • Rovira, C. and Parrinello, M. (1998) Oxygen binding to iron-porphyrin: a Density functional study using both LSD and LSD+GC schemes. Int. J. Quant. Chem. 70, 387–394.
    • (1998) Int. J. Quant. Chem , vol.70 , pp. 387-394
    • Rovira, C.1    Parrinello, M.2
  • 85
    • 0021027685 scopus 로고
    • Structure of human oxyhaemoglobin at 2.1 Å resolution
    • Shaanan, B. (1983). Structure of human oxyhaemoglobin at 2.1 Å resolution. J. Mol. Biol. 171, 31–59.
    • (1983) J. Mol. Biol , vol.171 , pp. 31-59
    • Shaanan, B.1
  • 86
    • 0001740216 scopus 로고
    • Mössbauer spectroscopy of hemoglobin model compounds: evidence for conformational excitation
    • Spartalian, K., Lang, G., Collman, J. P., Gagne, R. R., and Reed, C. A. (1975) Mössbauer spectroscopy of hemoglobin model compounds: evidence for conformational excitation. J. Chem. Phys. 63, 5375–5382.
    • (1975) J. Chem. Phys , vol.63 , pp. 5375-5382
    • Spartalian, K.1    Lang, G.2    Collman, J. P.3    Gagne, R. R.4    Reed, C. A.5
  • 87
    • 0039358601 scopus 로고
    • Hydrogen-bond stabilization of oxygen in hemoprotein models
    • Mispelter, J., Momenteau, M., Lavalette, D., and Lhoste, J.-M. (1983) Hydrogen-bond stabilization of oxygen in hemoprotein models. J. Am.Chem. Soc. 105, 5165–5166.
    • (1983) J. Am.Chem. Soc , vol.105 , pp. 5165-5166
    • Mispelter, J.1    Momenteau, M.2    Lavalette, D.3    Lhoste, J.-M.4
  • 89
    • 0031245896 scopus 로고    scopus 로고
    • EPR studies of the dynamics of rotation of dioxygen in model cobalt(II) hemes and cobalt-containing hybrid hemoglobins
    • Bowen, J. H., Shokhirev, N. V., Raitsimring, A. M., Buttlaire, D. H., and Walker, F. A. (1997) EPR studies of the dynamics of rotation of dioxygen in model cobalt(II) hemes and cobalt-containing hybrid hemoglobins. J. Am. Chem. Soc. 101, 8683–8691.
    • (1997) J. Am. Chem. Soc , vol.101 , pp. 8683-8691
    • Bowen, J. H.1    Shokhirev, N. V.2    Raitsimring, A. M.3    Buttlaire, D. H.4    Walker, F. A.5
  • 90
    • 35448998145 scopus 로고    scopus 로고
    • Enzymology and structure of cata-lases
    • Nicholls, P., Fita, I., and Loewen, P. C. (2001) Enzymology and structure of cata-lases, Adv. Inorg. Chem. 51, 51–106.
    • (2001) Adv. Inorg. Chem , vol.51 , pp. 51-106
    • Nicholls, P.1    Fita, I.2    Loewen, P. C.3
  • 91
    • 1542297780 scopus 로고    scopus 로고
    • The X3LYP extended density functional for accurate descriptions of nonbond interactions, spin states, and thermochemi-cal properties
    • Xu, X. and Goddard III, W. A. (2004) The X3LYP extended density functional for accurate descriptions of nonbond interactions, spin states, and thermochemi-cal properties. Proc. Nat. Acad. Sci. USA 101, 2673–2677.
    • (2004) Proc. Nat. Acad. Sci. USA , vol.101 , pp. 2673-2677
    • Xu, X.1    Goddard, W. A.2
  • 92
    • 0001161603 scopus 로고
    • Efficacious form for model pseudopotentials
    • Kleinman, L. and Bylander, D. M. (1982) Efficacious form for model pseudopotentials Phys. Rev. Lett. 48, 1425–1428.
    • (1982) Phys. Rev. Lett , vol.48 , pp. 1425-1428
    • Kleinman, L.1    Bylander, D. M.2
  • 93
    • 84986524957 scopus 로고
    • Convergence acceleration of iterative sequences. The case of scf iteration
    • Pulay, P. (1980) Convergence acceleration of iterative sequences. The case of scf iteration. Chem. Phys. Lett. 73, 393–398.
    • (1980) Chem. Phys. Lett , vol.73 , pp. 393-398
    • Pulay, P.1
  • 94
    • 20644461001 scopus 로고    scopus 로고
    • On the effect of the BSSE on intermolecular potential energy surfaces. Comparison of a priori and a poste-riori BSSE correction schemes
    • Salvador, P., Paizs, B., Duran, M., and Suhai, S. (2001) On the effect of the BSSE on intermolecular potential energy surfaces. Comparison of a priori and a poste-riori BSSE correction schemes. J. Comp. Chem. 22, 765–786.
    • (2001) J. Comp. Chem , vol.22 , pp. 765-786
    • Salvador, P.1    Paizs, B.2    Duran, M.3    Suhai, S.4
  • 95
    • 84943502952 scopus 로고
    • A molecular dynamics method for simulations in the canonical ensemble
    • Nosé. 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


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