메뉴 건너뛰기




Volumn 34, Issue 3, 1999, Pages 369-382

Analysis of domain motions in large proteins

Author keywords

Domain motions; Normal mode analysis; Protein dynamics

Indexed keywords

ASPARTATE CARBAMOYLTRANSFERASE; CITRATE SYNTHASE; DNA; PROTEIN; RNA DIRECTED DNA POLYMERASE;

EID: 0033557178     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19990215)34:3<369::AID-PROT9>3.0.CO;2-F     Document Type: Article
Times cited : (189)

References (27)
  • 2
    • 0000453761 scopus 로고
    • Domain motions in proteins
    • Schulz GE. Domain motions in proteins. Curr Opin Struct Biol 1991;1:883-888.
    • (1991) Curr Opin Struct Biol , vol.1 , pp. 883-888
    • Schulz, G.E.1
  • 3
    • 0029159748 scopus 로고
    • Rigid domains in proteins: An algorithmic approach to their identification
    • Nichols WL, Rose GD, Ten Eyek LF, Zimm BH. Rigid domains in proteins: An algorithmic approach to their identification. Proteins 1995;23:38-48.
    • (1995) Proteins , vol.23 , pp. 38-48
    • Nichols, W.L.1    Rose, G.D.2    Ten Eyek, L.F.3    Zimm, B.H.4
  • 4
    • 0030883755 scopus 로고    scopus 로고
    • Protein domain movements: Detection of rigid domains and visualization of hinges in comparisons of atomic coordinates
    • Wriggers W, Schulten K. Protein domain movements: Detection of rigid domains and visualization of hinges in comparisons of atomic coordinates. Proteins 1997;29:1-14.
    • (1997) Proteins , vol.29 , pp. 1-14
    • Wriggers, W.1    Schulten, K.2
  • 5
    • 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 HJC. Model-free methods of analyzing domain motions in proteins from simulations: A comparison of normal mode analysis and molecular dynamics simulation. Proteins 1997;27:425-437.
    • (1997) Proteins , vol.27 , pp. 425-437
    • Hayward, S.1    Kitao, A.2    Berendsen, H.J.C.3
  • 6
    • 0032006209 scopus 로고    scopus 로고
    • Systematic analysis of domain motions in proteins from conformational change: New results on citrate synthase and T4 lysozyme
    • Hayward S, Berendsen HJC. Systematic analysis of domain motions in proteins from conformational change: New results on citrate synthase and T4 lysozyme. Proteins 1998;30:144-154.
    • (1998) Proteins , vol.30 , pp. 144-154
    • Hayward, S.1    Berendsen, H.J.C.2
  • 7
    • 0032080528 scopus 로고    scopus 로고
    • Domain motions in bacteriophage T4 lysozyme: A comparison between molecular dynamics and crystallographic data
    • de Groot BL, Hayward S, van Aalten D, Amadei A, Berendsen HJC. Domain motions in bacteriophage T4 lysozyme: A comparison between molecular dynamics and crystallographic data. Proteins 1998;31:116-127.
    • (1998) Proteins , vol.31 , pp. 116-127
    • De Groot, B.L.1    Hayward, S.2    Van Aalten, D.3    Amadei, A.4    Berendsen, H.J.C.5
  • 8
    • 0028335096 scopus 로고
    • Structural mechanisms for domain movements in proteins
    • Gerstein M, Lesk AM, Chothia C. Structural mechanisms for domain movements in proteins. Biochemistry 1994;33:6739-6748.
    • (1994) Biochemistry , vol.33 , pp. 6739-6748
    • Gerstein, M.1    Lesk, A.M.2    Chothia, C.3
  • 9
    • 0032533790 scopus 로고    scopus 로고
    • Analysis of domain motions by approximate normal mode calculations
    • Hinsen K. Analysis of domain motions by approximate normal mode calculations. Proteins 1998;33:417-429..
    • (1998) Proteins , vol.33 , pp. 417-429
    • Hinsen, K.1
  • 10
    • 77952490184 scopus 로고
    • Tertiary structure of proteins. I. Representation and computation of the conformations
    • Nishikawa K, Ooi T, Isogai Y, Saito N. Tertiary structure of proteins. I. Representation and computation of the conformations. J Phys Soc Japan 1972;32:1331-1337.
    • (1972) J Phys Soc Japan , vol.32 , pp. 1331-1337
    • Nishikawa, K.1    Ooi, T.2    Isogai, Y.3    Saito, N.4
  • 11
    • 0027135767 scopus 로고
    • Automatic and accurate method for analysis of proteins that undergo hinge-mediated domain and loop movements
    • Huang ES, Rock EP, Subbiah S. Automatic and accurate method for analysis of proteins that undergo hinge-mediated domain and loop movements Curr Biol 1993;3:740-748.
    • (1993) Curr Biol , vol.3 , pp. 740-748
    • Huang, E.S.1    Rock, E.P.2    Subbiah, S.3
  • 12
    • 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
  • 13
    • 84948502362 scopus 로고
    • Superposition of molecular structures using quaternions
    • Kneller GR. Superposition of molecular structures using quaternions Mol Sim 1991;7:113-119.
    • (1991) Mol Sim , vol.7 , pp. 113-119
    • Kneller, G.R.1
  • 15
    • 0000997625 scopus 로고    scopus 로고
    • Representing protein and peptide structures with parallel coordinates
    • Becker OM. Representing protein and peptide structures with parallel coordinates. J Comp Chem 1997;18:1893-1902.
    • (1997) J Comp Chem , vol.18 , pp. 1893-1902
    • Becker, O.M.1
  • 16
    • 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
  • 19
    • 0029560322 scopus 로고
    • Hinge bending motion in citrate synthase arising from normal modes calculations
    • Marques O, Sanejouand YH. Hinge bending motion in citrate synthase arising from normal modes calculations. Proteins 1995; 23:557-560.
    • (1995) Proteins , vol.23 , pp. 557-560
    • Marques, O.1    Sanejouand, Y.H.2
  • 20
    • 0020483375 scopus 로고
    • Crystallographic refinement and atomic models of two different forms of citrate synthase at 2.7 and 1.7 Å resolution
    • Remington S, Wiegand G, Huber R. Crystallographic refinement and atomic models of two different forms of citrate synthase at 2.7 and 1.7 Å resolution, J Mol Biol 1982;158:111-152.
    • (1982) J Mol Biol , vol.158 , pp. 111-152
    • Remington, S.1    Wiegand, G.2    Huber, R.3
  • 21
  • 22
    • 0017411710 scopus 로고
    • The Protein Data Bank: A computer-based archival file for macromolecular structures
    • Bernstein FC, Koetzle TF, Williams GJB, et al. The Protein Data Bank: A computer-based archival file for macromolecular structures. J Mol Biol 1977;112:535-542.
    • (1977) J Mol Biol , vol.112 , pp. 535-542
    • Bernstein, F.C.1    Koetzle, T.F.2    Williams, G.J.B.3
  • 23
    • 0028360742 scopus 로고
    • The structural basis of asymmetry in the HIV-1 reverse transcriptase dimer
    • Wang J, Smerdon SJ, Jäger J, et al. The structural basis of asymmetry in the HIV-1 reverse transcriptase dimer. Proc Natl Acad Sci USA 1994;91:7242-7246.
    • (1994) Proc Natl Acad Sci USA , vol.91 , pp. 7242-7246
    • Wang, J.1    Smerdon, S.J.2    Jäger, J.3
  • 24
    • 0028774179 scopus 로고
    • Comparison of three different crystal forms shows HIV-1 reverse transcriptase displays an internal swivel motion
    • Jäger, J, Smerdon SJ, Wang J, Boisvert DC, Steitz TA. Comparison of three different crystal forms shows HIV-1 reverse transcriptase displays an internal swivel motion. Structure 1994;15:869-876.
    • (1994) Structure , vol.15 , pp. 869-876
    • Jäger, J.1    Smerdon, S.J.2    Wang, J.3    Boisvert, D.C.4    Steitz, T.A.5
  • 25
    • 0028144138 scopus 로고
    • Aspartate transcarbamylase from Escherichia coli: Activity and regulation
    • Lipscomb WN. Aspartate transcarbamylase from Escherichia coli: Activity and regulation. Adv Enzymol Relat Areas Mo. Biol 1994;68:67-151.
    • (1994) Adv Enzymol Relat Areas Mo. Biol , vol.68 , pp. 67-151
    • Lipscomb, W.N.1
  • 26
    • 0028846138 scopus 로고
    • Unlike quaternary structure transition, the tertiary structure change of the 240s loop in allosteric aspartate transcarbamoylase requires active site saturation by substrate for completion
    • Fetler L, Vachette P, Hervé G, Ladjimi MM. Unlike quaternary structure transition, the tertiary structure change of the 240s loop in allosteric aspartate transcarbamoylase requires active site saturation by substrate for completion. Biochemistry 1995;34: 15654-15660.
    • (1995) Biochemistry , vol.34 , pp. 15654-15660
    • Fetler, L.1    Vachette, P.2    Hervé, G.3    Ladjimi, M.M.4
  • 27
    • 0030004936 scopus 로고    scopus 로고
    • Analysis of the low frequency normal modes of the T-state of aspartate transcarbamylase
    • Thomas A, Field MJ, Mouawad L, Perahia D. Analysis of the low frequency normal modes of the T-state of aspartate transcarbamylase. J Mol Biol 1996;257:1070-1087.
    • (1996) J Mol Biol , vol.257 , pp. 1070-1087
    • Thomas, A.1    Field, M.J.2    Mouawad, L.3    Perahia, D.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.