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Volumn 264, Issue 3, 1996, Pages 546-555

Dynamic contributions to the DNA binding entropy of the EcoRI and EcoRV restriction endonucleases

Author keywords

EcoRI endonuclease; EcoRV endonuclease; Entropy; Molecular dynamics; Sequence specific DNA protein interactions

Indexed keywords

DNA; RESTRICTION ENDONUCLEASE;

EID: 0030573020     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0660     Document Type: Article
Times cited : (20)

References (29)
  • 2
    • 0027975255 scopus 로고
    • 10-/α-helix transition: Implications for a natural reaction coordinate
    • 10-/α-helix transition: implications for a natural reaction coordinate. J. Am. Chem. Soc. 16, 6307-6315.
    • (1994) J. Am. Chem. Soc. , vol.16 , pp. 6307-6315
    • Basu, G.1    Kitao, A.2    Hirata, F.3    Go, N.4
  • 7
    • 33846823909 scopus 로고
    • Particle mesh Ewald: An N.log(n) method for Ewald sums in large systems
    • Darden, T., York, D. & Pedersen, L. (1993). Particle mesh Ewald: an N.log(n) method for Ewald sums in large systems. J. Chem. Phys. 98, 10089-10092.
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 8
    • 0018793861 scopus 로고
    • Temperature-dependent X-ray diffraction as a probe of protein structural dynamics
    • Frauenfelder, H., Petsko, G. A. & Tsernoglou, D. (1979). Temperature-dependent X-ray diffraction as a probe of protein structural dynamics. Nature, 280, 558-563.
    • (1979) Nature , vol.280 , pp. 558-563
    • Frauenfelder, H.1    Petsko, G.A.2    Tsernoglou, D.3
  • 10
    • 0029092698 scopus 로고
    • Fluctuation and cross-correlation analysis of protein motions observed in nanosecond molecular dynamics simulations
    • Hunenberger, P. H., Mark, A. E. & van Gunsteren, W. F. (1995). Fluctuation and cross-correlation analysis of protein motions observed in nanosecond molecular dynamics simulations. J. Mol. Biol. 252, 492-503.
    • (1995) J. Mol. Biol. , vol.252 , pp. 492-503
    • Hunenberger, P.H.1    Mark, A.E.2    Van Gunsteren, W.F.3
  • 11
    • 0024276807 scopus 로고
    • Anisotropy and anharmonicity of atomic fluctuations in proteins: Implications for X-ray analysis
    • Ichiye, T. & Karplus, M. (1988). Anisotropy and anharmonicity of atomic fluctuations in proteins: implications for X-ray analysis. Biochemistry, 27, 3487-3497.
    • (1988) Biochemistry , vol.27 , pp. 3487-3497
    • Ichiye, T.1    Karplus, M.2
  • 13
    • 0000127140 scopus 로고
    • Method for estimating the configurational entropy of macromolecules
    • Karplus, M. & Kushick, J. N. (1981). Method for estimating the configurational entropy of macromolecules. Macromolecules, 14, 325-332.
    • (1981) Macromolecules , vol.14 , pp. 325-332
    • Karplus, M.1    Kushick, J.N.2
  • 14
    • 0023475026 scopus 로고
    • Configurational entropy of native proteins
    • Karplus, M., Ichiye, T. & Pettitt, B. M. (1987). Configurational entropy of native proteins. Biophys. J. 52, 1083-1085.
    • (1987) Biophys. J. , vol.52 , pp. 1083-1085
    • Karplus, M.1    Ichiye, T.2    Pettitt, B.M.3
  • 15
    • 0026717834 scopus 로고
    • Normal mode refinement: Crystallographic refinement of protein dynamic structure. II. Application to human lysozyme
    • Kidera, A., Inaka, K., Matsushima, M. & Go, N. (1992). Normal mode refinement: crystallographic refinement of protein dynamic structure. II. Application to human lysozyme. J. Mol. Biol. 225, 477-486.
    • (1992) J. Mol. Biol. , vol.225 , pp. 477-486
    • Kidera, A.1    Inaka, K.2    Matsushima, M.3    Go, N.4
  • 16
    • 0028988416 scopus 로고
    • 2+ binding to the active site of EcoRV endonuclease: A crystallographic study of complexes with substrate and product DNA at 2 Å resolution
    • 2+ binding to the active site of EcoRV endonuclease: a crystallographic study of complexes with substrate and product DNA at 2 Å resolution. Biochemistry, 34, 683-696.
    • (1995) Biochemistry , vol.34 , pp. 683-696
    • Kostrewa, D.1    Winkler, F.K.2
  • 17
    • 0028578644 scopus 로고
    • Molecular-dynamics simulations suggest that the EcoRI kink is an example of molecular strain
    • Kumar, S., Duan, Y., Kollman, P. A. & Rosenberg, J. M. (1994). Molecular-dynamics simulations suggest that the EcoRI kink is an example of molecular strain. J. Biomol. Struct. Dynam. 12, 487-525.
    • (1994) J. Biomol. Struct. Dynam. , vol.12 , pp. 487-525
    • Kumar, S.1    Duan, Y.2    Kollman, P.A.3    Rosenberg, J.M.4
  • 18
    • 0025904209 scopus 로고
    • Rigid protein motion as a model for crystallographic temperature factors
    • Kuriyan, J. & Weis, W. L. (1991). Rigid protein motion as a model for crystallographic temperature factors. Proc. Natl acad. Sci. USA, 88, 2773-2777.
    • (1991) Proc. Natl Acad. Sci. USA , vol.88 , pp. 2773-2777
    • Kuriyan, J.1    Weis, W.L.2
  • 19
    • 0023053635 scopus 로고
    • Effect of anisotropy and anharmonicity on protein crystallographic refinement. An evaluation by molecular dynamics
    • Kuriyan, J., Petsko, G. A., Levy, R. M. & Karplus, M. (1986). Effect of anisotropy and anharmonicity on protein crystallographic refinement. An evaluation by molecular dynamics. J. Mol. Biol. 190, 227-254.
    • (1986) J. Mol. Biol. , vol.190 , pp. 227-254
    • Kuriyan, J.1    Petsko, G.A.2    Levy, R.M.3    Karplus, M.4
  • 20
    • 0000927175 scopus 로고
    • Nanosecond molecular-dynamics simulations on the d(CGC-GAATTCGCG) double helix in water
    • McConnell, K. J., Nirmala, R., Young, M. A., Ravishanker, G. & Beveridge, D. L. (1994a). Nanosecond molecular-dynamics simulations on the d(CGC-GAATTCGCG) double helix in water. Biophys. J. 66, 391-391.
    • (1994) Biophys. J. , vol.66 , pp. 391-391
    • McConnell, K.J.1    Nirmala, R.2    Young, M.A.3    Ravishanker, G.4    Beveridge, D.L.5
  • 21
    • 0028052906 scopus 로고
    • A nanosecond molecular-dynamics trajectory for a B-DNA double helix-evidence for substates
    • McConnell, K. J., Nirmala, R., Young, M. A., Ravishanker, G. & Beveridge, D. L. (1994b). A nanosecond molecular-dynamics trajectory for a B-DNA double helix-evidence for substates. J. Am. Chem. Soc. 116, 4461-4462.
    • (1994) J. Am. Chem. Soc. , vol.116 , pp. 4461-4462
    • McConnell, K.J.1    Nirmala, R.2    Young, M.A.3    Ravishanker, G.4    Beveridge, D.L.5
  • 22
    • 84986440341 scopus 로고
    • SETTLE: An analytical version of the SHAKE and RATTLE algorithm for rigid water models
    • Miyamoto, S. & Kollman, P. A. (1992). SETTLE: an analytical version of the SHAKE and RATTLE algorithm for rigid water models. J. Comp. Chem. 13, 952-962.
    • (1992) J. Comp. Chem. , vol.13 , pp. 952-962
    • Miyamoto, S.1    Kollman, P.A.2
  • 25
    • 33646940952 scopus 로고
    • Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • Ryckaert, J.-P., Ciccotti, G. & Berendsen, H. J. C. (1977). Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comp. Phys. 23, 327-341.
    • (1977) J. Comp. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.-P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 26
    • 23444450909 scopus 로고
    • Coupling of local folding to site-specific binding of proteins to DNA
    • Spolar, R. S. & Record, M. T., Jr (1994). Coupling of local folding to site-specific binding of proteins to DNA. Science, 263, 777-784.
    • (1994) Science , vol.263 , pp. 777-784
    • Spolar, R.S.1    Record M.T., Jr.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.