메뉴 건너뛰기




Volumn , Issue , 2006, Pages 5543-5548

Conformational heterogeneity and low-frequency vibrational modes of proteins

Author keywords

[No Author keywords available]

Indexed keywords

DIHYDROFOLATE REDUCTASE; NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE;

EID: 33751534910     PISSN: 14639076     EISSN: None     Source Type: Journal    
DOI: 10.1039/b610075a     Document Type: Article
Times cited : (27)

References (37)
  • 1
    • 0028360307 scopus 로고
    • The contribution of vibrational entropy to molecular association. The dimerization of insulin
    • B. Tidor, M. Karplus, The contribution of vibrational entropy to molecular association. The dimerization of insulin J. Mol. Biol., 1994, 238, 405-414
    • (1994) J. Mol. Biol. , vol.238 , pp. 405-414
    • Tidor, B.1    Karplus, M.2
  • 2
    • 0035940247 scopus 로고    scopus 로고
    • Dissecting the vibrational entropy change on protein/ligand binding: Burial of a water molecule in bovine pancreatic trypsin inhibitor
    • S. Fischer, J. C. Smith, C. S. Verma, Dissecting the vibrational entropy change on protein/ligand binding: burial of a water molecule in bovine pancreatic trypsin inhibitor J. Phys. Chem. B, 2001, 105, 8050-8055
    • (2001) J. Phys. Chem. B , vol.105 , pp. 8050-8055
    • Fischer, S.1    Smith, J.C.2    Verma, C.S.3
  • 3
    • 4043156208 scopus 로고    scopus 로고
    • Direct determination of vibrational density of states change on ligand binding to a protein
    • E. Balog, T. Becker, M. Oettl, R. Lechner, R. Daniel, J. Finney, J. C. Smith, Direct determination of vibrational density of states change on ligand binding to a protein Phys. Rev. Lett., 2004, 93, 028103.
    • (2004) Phys. Rev. Lett. , vol.93 , pp. 28103
    • Balog, E.1    Becker, T.2    Oettl, M.3    Lechner, R.4    Daniel, R.5    Finney, J.6    Smith, J.C.7
  • 4
    • 0003525155 scopus 로고
    • Proteins: A theoretical perspective of dynamics, structure and thermodynamics
    • C. L. Brooks III, M. Karplus, B. M. Pettitt, Proteins: a theoretical perspective of dynamics, structure and thermodynamics Adv. Chem. Phys., 1988, 71, 1-249
    • (1988) Adv. Chem. Phys. , vol.71 , pp. 1-249
    • Brooks, C.L.1    Karplus, M.2    Pettitt, B.M.3
  • 5
    • 0030553275 scopus 로고    scopus 로고
    • Low frequency motions in phosphoglycerate kinase. A normal mode analysis
    • C. Guilbert, F. Pecorari, D. Perahia, L. Mouawad, Low frequency motions in phosphoglycerate kinase. A normal mode analysis Chem. Phys., 1996, 204, 324-336
    • (1996) Chem. Phys. , vol.204 , pp. 324-336
    • Guilbert, C.1    Pecorari, F.2    Perahia, D.3    Mouawad, L.4
  • 6
    • 0028315470 scopus 로고
    • The methrotrexate story: A paradigm for development of cancer chemotherapeutic agents
    • F. M. Huennekens, The methrotrexate story: a paradigm for development of cancer chemotherapeutic agents Adv. Enzyme Regul., 1994, 34, 397-419
    • (1994) Adv. Enzyme Regul. , vol.34 , pp. 397-419
    • Huennekens, F.M.1
  • 7
    • 0022546047 scopus 로고
    • Functional role of aspartic acid-27 in dihydrofolate reductase revealed by mutagenesis
    • E. E. Howell, J. E. Villafranca, M. S. Warren, S. J. Oatley, J. Kraut, Functional role of aspartic acid-27 in dihydrofolate reductase revealed by mutagenesis Science, 1986, 231, 1123-1128
    • (1986) Science , vol.231 , pp. 1123-1128
    • Howell, E.E.1    Villafranca, J.E.2    Warren, M.S.3    Oatley, S.J.4    Kraut, J.5
  • 8
    • 0029102089 scopus 로고
    • Dynamics of the dihydrofolate reductase-folate complex: Catalytic sites and regions known to undergo conformational change exhibit diverse dynamical features
    • D. M. Epstein, S. J. Benkovic, P. E. Wright, Dynamics of the dihydrofolate reductase-folate complex: catalytic sites and regions known to undergo conformational change exhibit diverse dynamical features Biochemistry, 1995, 34, 11037-11048
    • (1995) Biochemistry , vol.34 , pp. 11037-11048
    • Epstein, D.M.1    Benkovic, S.J.2    Wright, P.E.3
  • 9
    • 0031015737 scopus 로고    scopus 로고
    • Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductase: Crystallographic evidence
    • M. R. Sawaya, J. Kraut, Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductase: crystallographic evidence Biochemistry, 1997, 36, 586-603
    • (1997) Biochemistry , vol.36 , pp. 586-603
    • Sawaya, M.R.1    Kraut, J.2
  • 10
    • 0034704984 scopus 로고    scopus 로고
    • Effect of ligand binding on the flexibility of dihydrofolate reductase as revealed by compressibility
    • T. Kamiyama, K. Gekko, Effect of ligand binding on the flexibility of dihydrofolate reductase as revealed by compressibility Biochim. Biophys. Acta, 2000, 1478, 257-266
    • (2000) Biochim. Biophys. Acta , vol.1478 , pp. 257-266
    • Kamiyama, T.1    Gekko, K.2
  • 11
    • 0000715079 scopus 로고    scopus 로고
    • Calculation of the reaction pathway for the aromatic ring flip in methrotrexate complexed to dihydrofolate reductase
    • C. S. Verma, S. Fischer, L. S. D. Caves, G. C. K. Roberts, R. E. Hubbard, Calculation of the reaction pathway for the aromatic ring flip in methrotrexate complexed to dihydrofolate reductase J. Phys. Chem., 1996, 100, 2510-2518
    • (1996) J. Phys. Chem. , vol.100 , pp. 2510-2518
    • Verma, C.S.1    Fischer, S.2    Caves, L.S.D.3    Roberts, G.C.K.4    Hubbard, R.E.5
  • 12
    • 0031557394 scopus 로고    scopus 로고
    • Domain motions in dihydrofolate reductase: A molecular dynamics study
    • C. S. Verma, L. S. D. Caves, R. E. Hubbard, G. C. K. Roberts, Domain motions in dihydrofolate reductase: a molecular dynamics study J. Mol. Biol., 1997, 266, 776-796
    • (1997) J. Mol. Biol. , vol.266 , pp. 776-796
    • Verma, C.S.1    Caves, L.S.D.2    Hubbard, R.E.3    Roberts, G.C.K.4
  • 13
    • 0001704148 scopus 로고    scopus 로고
    • Molecular dynamics and free energy perturbation study of hydrate-ion transfer step in dihydrofolate reductase using combined quantum and molecular mechanical model
    • P. L. Cummins, J. E. Gready, Molecular dynamics and free energy perturbation study of hydrate-ion transfer step in dihydrofolate reductase using combined quantum and molecular mechanical model J. Comput. Chem., 1998, 19, 977-988
    • (1998) J. Comput. Chem. , vol.19 , pp. 977-988
    • Cummins, P.L.1    Gready, J.E.2
  • 14
    • 0033955055 scopus 로고    scopus 로고
    • Protein dynamics in enzymatic catalysis: Exploration of dihydrofolate reductase
    • J. L. Radkiewicz, C. L. Brooks III, Protein dynamics in enzymatic catalysis: exploration of dihydrofolate reductase J. Am. Chem. Soc., 2000, 122, 225-231
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 225-231
    • Radkiewicz, J.L.1    Brooks, C.L.2
  • 15
    • 6344294816 scopus 로고    scopus 로고
    • The coupling of structural fluctuations to hydrate transfer in dihydrofolate reductase
    • I. F. Thorpe, C. L. Brooks III, The coupling of structural fluctuations to hydrate transfer in dihydrofolate reductase Proteins, 2004, 57, 444-457
    • (2004) Proteins , vol.57 , pp. 444-457
    • Thorpe, I.F.1    Brooks, C.L.2
  • 18
    • 0001479601 scopus 로고
    • Inelastic neutron scattering analysis of low frequency motion in proteins: A normal mode study of the bovine pancreatic trypsin inhibitor
    • J. C. Smith, S. Cusack, U. Pezzeca, B. Brooks, M. Karplus, Inelastic neutron scattering analysis of low frequency motion in proteins: A normal mode study of the bovine pancreatic trypsin inhibitor J. Chem. Phys., 1986, 85, 3636-3654
    • (1986) J. Chem. Phys. , vol.85 , pp. 3636-3654
    • Smith, J.C.1    Cusack, S.2    Pezzeca, U.3    Brooks, B.4    Karplus, M.5
  • 19
    • 0001611784 scopus 로고    scopus 로고
    • Analysis of calculated normal modes of a set of native and partially unfolded proteins
    • H. W. T. van Vlijmen, M. Karplus, Analysis of calculated normal modes of a set of native and partially unfolded proteins J. Phys. Chem. B, 1999, 103, 3009-3021
    • (1999) J. Phys. Chem. B , vol.103 , pp. 3009-3021
    • Van Vlijmen, H.W.T.1    Karplus, M.2
  • 20
    • 84943502952 scopus 로고
    • A molecular dynamics method for simulations in the canonical ensemble
    • S. Nosé, A molecular dynamics method for simulations in the canonical ensemble Mol. Phys., 1984, 52, 255-268
    • (1984) Mol. Phys. , vol.52 , pp. 255-268
    • Nosé, S.1
  • 21
    • 0001538909 scopus 로고
    • Canonical dynamics: Equilibrium phase-space distributions
    • W. G. Hoover, Canonical dynamics: Equilibrium phase-space distributions Phys. Rev. A, 1985, 31, 1695-1697
    • (1985) Phys. Rev. A , vol.31 , pp. 1695-1697
    • Hoover, W.G.1
  • 22
    • 0000961995 scopus 로고
    • Evaluation of the configurational entropy for proteins: Application to molecular dynamics simulations of an alpha-helix
    • R. M. Levy, M. Karplus, J. Kushick, D. Perahia, Evaluation of the configurational entropy for proteins: application to molecular dynamics simulations of an alpha-helix Macromolecules, 1984, 17, 1370-1374
    • (1984) Macromolecules , vol.17 , pp. 1370-1374
    • Levy, R.M.1    Karplus, M.2    Kushick, J.3    Perahia, D.4
  • 24
    • 0036193327 scopus 로고    scopus 로고
    • Temperature dependence of protein dynamics: Computer simulation analysis of neutron scattering properties
    • J. A. Hayward, J. C. Smith, Temperature dependence of protein dynamics: computer simulation analysis of neutron scattering properties Biophys. J., 2002, 82, 1216-25
    • (2002) Biophys. J. , vol.82 , pp. 1216-1225
    • Hayward, J.A.1    Smith, J.C.2
  • 25
    • 0041343122 scopus 로고    scopus 로고
    • Molecular dynamics decomposition of temperature-dependent elastic neutron scattering by a protein solution
    • J. A. Hayward, J. L. Finney, R. M. Daniel, J. C. Smith, Molecular dynamics decomposition of temperature-dependent elastic neutron scattering by a protein solution Biophys. J., 2003, 85, 679-85
    • (2003) Biophys. J. , vol.85 , pp. 679-685
    • Hayward, J.A.1    Finney, J.L.2    Daniel, R.M.3    Smith, J.C.4
  • 26
    • 0043269250 scopus 로고    scopus 로고
    • Use of computer simulation for understanding elastic neutron scattering from complex systems: A small protein in various solvents
    • J. A. Hayward, J. L. Finney, R. Daniel, J. C. Smith, Use of computer simulation for understanding elastic neutron scattering from complex systems: a small protein in various solvents Chem. Phys., 2003, 292, 389-396
    • (2003) Chem. Phys. , vol.292 , pp. 389-396
    • Hayward, J.A.1    Finney, J.L.2    Daniel, R.3    Smith, J.C.4
  • 27
    • 0037117502 scopus 로고    scopus 로고
    • Is the first hydration shell of lysozyme of higher density than bulk water?
    • F. Merzel, J. C. Smith, Is the first hydration shell of lysozyme of higher density than bulk water? Proc. Natl. Acad. Sci. U. S. A., 2002, 99, 5378-5383
    • (2002) Proc. Natl. Acad. Sci. U. S. A. , vol.99 , pp. 5378-5383
    • Merzel, F.1    Smith, J.C.2
  • 29
    • 0346216028 scopus 로고    scopus 로고
    • Principal components of the protein dynamical transition
    • A. L. Tournier, J. C. Smith, Principal components of the protein dynamical transition Phys. Rev. Lett., 2003, 91, 208106-1-208106-4
    • (2003) Phys. Rev. Lett. , vol.91 , pp. 208106-1-208106-4
    • Tournier, A.L.1    Smith, J.C.2
  • 31
    • 0032757044 scopus 로고    scopus 로고
    • Environmental dependence of the dynamics of protein hydration water
    • M. Tarek, D. J. Tobias, Environmental dependence of the dynamics of protein hydration water J. Am. Chem. Soc., 1999, 121, 9740-9741
    • (1999) J. Am. Chem. Soc. , vol.121 , pp. 9740-9741
    • Tarek, M.1    Tobias, D.J.2
  • 32
    • 19044399611 scopus 로고    scopus 로고
    • Role of protein-water hydrogen bond dynamics in the protein dynamical transition
    • M. Tarek, D. J. Tobias, Role of protein-water hydrogen bond dynamics in the protein dynamical transition Phys. Rev. Lett., 2002, 88, 138101.
    • (2002) Phys. Rev. Lett. , vol.88 , pp. 138101
    • Tarek, M.1    Tobias, D.J.2
  • 33
    • 0042861647 scopus 로고    scopus 로고
    • Translational hydration water dynamics drives the protein glass transition
    • A. L. Tournier, J. Xu, J. C. Smith, Translational hydration water dynamics drives the protein glass transition Biophys. J., 2003, 85, 1871-5
    • (2003) Biophys. J. , vol.85 , pp. 1871-1875
    • Tournier, A.L.1    Xu, J.2    Smith, J.C.3
  • 35
    • 0026320866 scopus 로고
    • The energy landscape and motions of proteins
    • H. Frauenfelder, S. G. Sligar, P. G. Wolynes, The energy landscape and motions of proteins Science, 1991, 254, 1598-1603
    • (1991) Science , vol.254 , pp. 1598-1603
    • Frauenfelder, H.1    Sligar, S.G.2    Wolynes, P.G.3
  • 36
    • 0037653186 scopus 로고    scopus 로고
    • Proteins in electric fields and pressure fields basic aspects
    • M. Koehler, J. Friedrich, J. Fidy, Proteins in electric fields and pressure fields basic aspects Biochim. Biophys. Acta, 1998, 1386, 255-288
    • (1998) Biochim. Biophys. Acta , vol.1386 , pp. 255-288
    • Koehler, M.1    Friedrich, J.2    Fidy, J.3
  • 37
    • 0030249723 scopus 로고    scopus 로고
    • Simulation evidence for experimentally detectable low-temperature vibrational inhomogeneity in a globular protein
    • A. V. Lamy, M. Souaille, J. C. Smith, Simulation evidence for experimentally detectable low-temperature vibrational inhomogeneity in a globular protein Biopolymers, 1996, 39, 471-478
    • (1996) Biopolymers , vol.39 , pp. 471-478
    • Lamy, A.V.1    Souaille, M.2    Smith, J.C.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.