A further implementation of the rotational symmetry boundary conditions for calculations of P43212 symmetry crystals

Journal of Molecular Graphics and Modelling

Volumn 15, Issue 4, 1997, Pages 233-237

  Yoneda, Shigetaka ^a  

^a KITASATO UNIVERSITY   (Japan)

Author keywords

Glycogen phosphorylase b; Molecular dynamics simulation; Protein assembly; Protein crystal; Rotational symmetry boundary condition

Indexed keywords

GLYCOGEN PHOSPHORYLASE B; PROTEIN;

ARTICLE; CRYSTAL STRUCTURE; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN ASSEMBLY; SIMULATION;

COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; MODELS, MOLECULAR; PHOSPHORYLASE B;

EID: 0031410843     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1093-3263(97)00081-8     Document Type: Article

References (15)

1. Kitson D.H., Avbelj F., Moult J., Nguyen D.T., Mertz J.E., Hadzi D., Hagler A.T. On achieving better than 1-Å accuracy in a simulation of a large protein Streptomyces griseus protease A . Proc. Natl. Acad. Sci. U.S.A. 90:1993;8920-8924.
2. Mathiowetz A.M., Jain A., Karasawa N., Goddard W.A. III. Protein simulations using techniques suitable for very large systems The cell multipole method for nonbond interactions and the Newton-Euler inverse mass operator method for internal coordinate dynamics . Proteins. 20:1994;227-247.
3. Saito M. Molecular dynamics simulations of proteins in solution Artifacts caused by the cutoff approximation . J. Chem. Phys. 101:1994;4055-4061.
4. York D.M., Wlodawer A., Pedersen L.G., Darden T.A. Atomic-level accuracy in simulations of large protein crystals. Proc. Natl. Acad. Sci. U.S.A. 91:1994;8715-8718.
5. Cheatham T.E. III, Miller J.L., Fox T., Darden T.A., Kollman P.A. Molecular dynamics simulations on solvated biomolecular systems The particle mesh Ewald method leads to stable trajectories of DNA, RNA, and proteins . J. Am. Chem. Soc. 117:1995;4193-4194.
6. Cagin T., Holder M., Pettitt B.M. A method for modeling icosahedral virions Rotational symmetry boundary conditions . J. Comput. Chem. 12:1991;627-634.
7. Yoneda S., Umeyama H. Free energy perturbation calculations on multiple mutation bases. J. Chem. Phys. 97:1992;6730-6736.
8. Yoneda S., Kitazawa M., Umeyama H. Molecular dynamics simulation of a rhinovirus capsid under rotational symmetry boundary conditions. J. Comput. Chem. 17:1996;191-203.
9. Barford D., Hu S.-H., Johnson L.N. Structural mechanism for glycogen phosphorylase control by phosphorylation and AMP. J. Mol. Biol. 218:1991;233-260.
10. Bernstein F.C., Koetzle T.F., Williams G.J.B., Meyer E.F. Jr, Brice M.D., Rodgers J.R., Kennard O., Shimanouchi T., Tasumi M. The Protein Data Bank A computer-based archival file for macromolecular structures . J. Mol. Biol. 112:1977;535-542.
11. Weiner S.J., Kollman P.A., Case D.A., Singh U.C., Ghio C., Alagona G., Profeta S. Jr., Weiner P. A new force field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem. Soc. 106:1984;765-784.
12. Wampler J.E. Electrostatic potential derived charges for enzyme cofactors Methods, correlations, and scaling for organic cofactors . J. Chem. Inf. Comput. Sci. 35:1995;617-632.
13. van Gunsteren W.F., Berendsen H.J.C. Algorithms for macromolecular dynamics and constraint dynamics. Mol. Phys. 34:1977;1311-1327.
14. Sayle R.A., Milner-White E.J. RASMOL Biomolecuar graphics for all . Trends Biochem. Sci. 20:1995;374-376.
15. York D.M., Darden T.A., Pedersen L.G., Anderson M.W. Molecular dynamics simulation of HIV-1 protease in a crystalline environment and in solution. Biochemistry. 32:1993;1443-1453.