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Volumn 33, Issue 3, 1998, Pages 417-429

Analysis of domain motions by approximate normal mode calculations

Author keywords

ATCase; Crambin; Lysozyme; Protein energy surface

Indexed keywords

ASPARTATE CARBAMOYLTRANSFERASE; CRAMBIN; LYSOZYME; PROTEIN; UNCLASSIFIED DRUG;

EID: 0032533790     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19981115)33:3<417::AID-PROT10>3.0.CO;2-8     Document Type: Article
Times cited : (663)

References (23)
  • 1
    • 0028331255 scopus 로고
    • Normal mode analysis of protein dynamics
    • Case, D.A. Normal mode analysis of protein dynamics. Curr. Opin. Struct. Biol. 4:285-290, 1994.
    • (1994) Curr. Opin. Struct. Biol. , vol.4 , pp. 285-290
    • Case, D.A.1
  • 2
    • 0020771265 scopus 로고
    • Dynamics of a small globular protein in terms of low-frequency vibrational modes
    • Go, N., Noguti, T., Nishikawa, T. Dynamics of a small globular protein in terms of low-frequency vibrational modes. Proc. Natl. Acad. Sci. USA 80:3696-3700, 1983.
    • (1983) Proc. Natl. Acad. Sci. USA , vol.80 , pp. 3696-3700
    • Go, N.1    Noguti, T.2    Nishikawa, T.3
  • 4
    • 0025292904 scopus 로고
    • Langevin modes of macromolecules: Application to Crambin and DNAhexamers
    • Kottalam, J., Case, D.A. Langevin modes of macromolecules: Application to Crambin and DNAhexamers. Biopolymers 29:1409-1421, 1990.
    • (1990) Biopolymers , vol.29 , pp. 1409-1421
    • Kottalam, J.1    Case, D.A.2
  • 5
    • 0027732618 scopus 로고
    • Effect of solvent on collective motions in globular proteins
    • Hayward, S., Kitao, A., Hirata, F., Go, N. Effect of solvent on collective motions in globular proteins. J. Mol. Biol. 234:1207-1217, 1993.
    • (1993) J. Mol. Biol. , vol.234 , pp. 1207-1217
    • Hayward, S.1    Kitao, A.2    Hirata, F.3    Go, N.4
  • 6
    • 0025753631 scopus 로고
    • Projection of Monte-Carlo and molecular dynamics trajectories onto the normal mode axes: Human lysozyme
    • Horiuchi, T., Go, N. Projection of Monte-Carlo and molecular dynamics trajectories onto the normal mode axes: Human lysozyme. Proteins 10:106-116, 1991.
    • (1991) Proteins , vol.10 , pp. 106-116
    • Horiuchi, T.1    Go, N.2
  • 7
    • 0030888546 scopus 로고    scopus 로고
    • Model-free methods of analyzing domain motions in proteins from simulations: A comparison of normal mode analysis and molecular dynamics simulation
    • Hayward, S., Kitao, A., Berendsen, H.J.C. Model-free methods of analyzing domain motions in proteins from simulations: A comparison of normal mode analysis and molecular dynamics simulation. Proteins 27:425-437, 1997.
    • (1997) Proteins , vol.27 , pp. 425-437
    • Hayward, S.1    Kitao, A.2    Berendsen, H.J.C.3
  • 8
    • 0023140044 scopus 로고
    • Multiple conformational states of proteins: A molecular dynamics analysis of myoglobin
    • Elber, R., Karplus, M. Multiple conformational states of proteins: A molecular dynamics analysis of myoglobin. Science 235:318-321, 1987.
    • (1987) Science , vol.235 , pp. 318-321
    • Elber, R.1    Karplus, M.2
  • 10
    • 0030249723 scopus 로고    scopus 로고
    • Simulation evidence for experimentally detectable low-temperature vibrational inhomogeneity in a globular protein
    • Lamy, A.V., Souaille, M., Smith, J.C. Simulation evidence for experimentally detectable low-temperature vibrational inhomogeneity in a globular protein. Biopolymers 39:471-478, 1996.
    • (1996) Biopolymers , vol.39 , pp. 471-478
    • Lamy, A.V.1    Souaille, M.2    Smith, J.C.3
  • 11
    • 0000885331 scopus 로고
    • Harmonic analysis of large systems. I. Methodology
    • Brooks, B.R., Janeøziøc, D., Karplus, M. Harmonic analysis of large systems. I. Methodology. J. Comp. Chem. 16:1522-1542, 1995.
    • (1995) J. Comp. Chem. , vol.16 , pp. 1522-1542
    • Brooks, B.R.1    Janeøziøc, D.2    Karplus, M.3
  • 12
    • 0028393405 scopus 로고
    • Analyzing the normal mode dynamics of macromolecules by the component synthesis method: Residue clustering and multiple-component approach
    • Hao, M.H., Scheraga, H.A. Analyzing the normal mode dynamics of macromolecules by the component synthesis method: Residue clustering and multiple-component approach. Biopolymers 34:321-334, 1994.
    • (1994) Biopolymers , vol.34 , pp. 321-334
    • Hao, M.H.1    Scheraga, H.A.2
  • 13
    • 0027576952 scopus 로고
    • Diagonalization in a mixed basis: A method to compute low-frequency normal modes for large macromolecules
    • Mouawad, L., Perahia, D. Diagonalization in a mixed basis: A method to compute low-frequency normal modes for large macromolecules. Biopolymers 33:599-611, 1993.
    • (1993) Biopolymers , vol.33 , pp. 599-611
    • Mouawad, L.1    Perahia, D.2
  • 14
    • 0030004936 scopus 로고    scopus 로고
    • Analysis of the low frequency normal modes of the T-state of aspartate transcarbamylase
    • Thomas, A., Field, M.J., Mouawad, L., Perahia, D. Analysis of the low frequency normal modes of the T-state of aspartate transcarbamylase. J. Mol. Biol. 257:1070-1087, 1996.
    • (1996) J. Mol. Biol. , vol.257 , pp. 1070-1087
    • Thomas, A.1    Field, M.J.2    Mouawad, L.3    Perahia, D.4
  • 16
    • 0000118827 scopus 로고
    • Harmonic and quasiharmonic descriptions of crambin
    • Teeter, M.M., Case, D.A. Harmonic and quasiharmonic descriptions of crambin. J. Phys. Chem. 94:8091-8097, 1990.
    • (1990) J. Phys. Chem. , vol.94 , pp. 8091-8097
    • Teeter, M.M.1    Case, D.A.2
  • 17
    • 0000197372 scopus 로고    scopus 로고
    • Low-amplitude elastic motions in proteins from a single-parameter atomic analysis
    • Tirion, M.M. Low-amplitude elastic motions in proteins from a single-parameter atomic analysis. Phys. Rev. Lett. 77:1905-1908, 1996.
    • (1996) Phys. Rev. Lett. , vol.77 , pp. 1905-1908
    • Tirion, M.M.1
  • 18
    • 0030623823 scopus 로고    scopus 로고
    • Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
    • Bahar, I., Atilgan, A.R., Erman, B. Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Folding Design 2:173-181, 1997.
    • (1997) Folding Design , vol.2 , pp. 173-181
    • Bahar, I.1    Atilgan, A.R.2    Erman, B.3
  • 19
    • 0006978393 scopus 로고    scopus 로고
    • The Molecular Modeling Toolkit: A case study of a large scientific application in Python
    • Hinsen, K. The Molecular Modeling Toolkit: A case study of a large scientific application in Python. Proceedings of the 6th International Python Conference. http://www. python.org/workshops/1997-10/proceedings/hinsen.html
    • Proceedings of the 6th International Python Conference
    • Hinsen, K.1
  • 20
    • 0029011701 scopus 로고
    • A second generation force field for the simulation of proteins and nucleic acids
    • Cornell, W.D., Cieplak, P., Bayly, C.I., et al. A second generation force field for the simulation of proteins and nucleic acids. J. Am. Chem. Soc. 117:5179-5197, 1995.
    • (1995) J. Am. Chem. Soc. , vol.117 , pp. 5179-5197
    • Cornell, W.D.1    Cieplak, P.2    Bayly, C.I.3
  • 21
    • 0000525633 scopus 로고
    • Effect of constraints on the dynamics of macromolecules
    • van Gunsteren, W.F., Karplus, M. Effect of constraints on the dynamics of macromolecules. Macromolecules 15:1528-1544, 1982.
    • (1982) Macromolecules , vol.15 , pp. 1528-1544
    • Van Gunsteren, W.F.1    Karplus, M.2
  • 22
    • 0028144138 scopus 로고
    • Aspartate transcarbamylase from Escherichia coli: Activity and regulation
    • Lipscomb, W.N. Aspartate transcarbamylase from Escherichia coli: Activity and regulation. Adv. Enzymol. Relat. Areas Mol. Biol. 68:67-151, 1994.
    • (1994) Adv. Enzymol. Relat. Areas Mol. Biol. , vol.68 , pp. 67-151
    • Lipscomb, W.N.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.