On the Approximation of Solvent Effects on the Conformation and Dynamics of Cyclosporin A by Stochastic Dynamics Simulation Techniques

References

• Cicotti , G. and Hoover , W. G. , eds. Molecular Dynamics of Statistical Mechanical Systems . Proceedings of the International School of Physics Enrico Fermi . Amsterdam : North-Holland . course 97
   Google Scholar
• Berendson , H. J. C. and van Gunsteren , W. F. 1984 . “ Molecular dynamics simulations: techniques and approaches ” . In Molecular Liquids-Dynamics and Interactions , NATO ASI Series C135 Edited by: Barnes , A. J. 475 – 500 . Reidel .
   Google Scholar
• van Gunsteren , W. F. and Berendson , H. J. C. 1984 . Computer simulation as a tool for tracing the conformational differences between proteins in solution and in the crystalline state . J. Molec. Biol. , 176 : 559
   PubMed Web of Science ®Google Scholar
• van Gunsteren , W. F. , Berendson , H. J. C. , Geurtsen , R. G. and Zwinderman , H. R. J. 1986 . A Molecular Dynamics Computer Simulation of an Eight-Base-Pair DNA Fragment in Aqueous Solution: Comparison with Experimental Two-Dimensional NMR Data . Ann, New York Acad. Sci. , 482 : 287
   PubMedGoogle Scholar
• Pangali , C. , Rao , M. and Berne , B. J. 1979 . Hydrophobic hydration around a pair of apolar species in water . J. Chem. Phys. , 71 : 2982
   Web of Science ®Google Scholar
• Pratt , L. R. , Hsu , C. S. and Chandler , D. 1978 . Statistical mechanics of small chain molecules in liquids. I. Effects of liquid packing on conformational structures . J. Chem. Phys. , 68 : 4202
   Web of Science ®Google Scholar
• Chandler , D. 1978 . Effects of Liquid Structures on Chemical Reactions and Conformational Changes of Non-rigid Molecules in Condensed Phases . Faraday Discuss. Chem Soc. , 66 : 184
   Google Scholar
• van Gunsteren , W. F. , Berendson , H. J. C. and Rullman , J. A. C. 1981 . Stochastic dynamics for molecules with constraints: Brownian dynamics of n-alkanes . Molec. Phys. , 44 : 69
   Web of Science ®Google Scholar
• Hodes , Z. I. , Nemethy , G. and Scheraga , H. A. 1979 . Model for the Conformational Analysis of Hydrated Peptides. Effect of Hydration on the Conformational Stability of the Terminally Blocked Residues of the 20 Naturally Occurring Amino Acids . Biopolymers , 18 : 1565
   Web of Science ®Google Scholar
• Paterson , Y. , Nemethy , G. and Scheraga , H. A. 1982 . An Empirical Potential Function for the Interaction Between Univalent Ions in Water . J. Solution Chem. , 11 : 831
   Google Scholar
• Eisenberg , D. and McLachlan , A. D. 1986 . Solvation energy in protein folding and binding . Nature , 319 : 199
   PubMed Web of Science ®Google Scholar
• Kubo , R. 1966 . The fluctuation-dissipation theorem . Rep. Progr. Phys. , 29 : 255
   Web of Science ®Google Scholar
• Allen , M. P. 1980 . Brownian dynamics simulation of a chemical reaction in solution . Molec. Phys. , 40 : 1073
   Web of Science ®Google Scholar
• van Gunsteren , W. F. and Berendson , H. J. C. 1982 . Algorithms for Brownian dynamics . Molec. Phys. , 45 : 637
   Web of Science ®Google Scholar
• van Gunsteren , W. F. and Berendson , H. J. C. 1987 . A leap-frog algorithm for stochastic dynamics . Molec. Simul. , in press
   Google Scholar
• Levy , R. M. , Karplus , M. and McCammon , J. A. 1979 . Diffusive Langevin dynamics of model alkanes . Chem. Phys. Lett. , 65 : 4
   Web of Science ®Google Scholar
• Wenger , R. M. , Payne , T. G. and Schreier , M. H. 1986 . Cyclosporin: Chemistry, Structure-Activity Relationship and Mode of Action . Progr. Clin. Biochem. Medicine , 3 : 157
   Google Scholar
• Lautz , J. , Kessler , H. , Kaptein , R. and van Gunsteren , W. F. 1987 . “ Molecular Dynamics Simulations of the Crystal and Dynamic Modelling of the Solution Structure of Cyclosporin A based on NMR Data ” . In Computational Methods in Chemical Design , Edited by: Stetzowsky , J. Oxford University Press . in press
   Google Scholar
• Lautz , J. , Kessler , H. , van Gunsteren , W. F. , Weber , H. P. and Wenger , R. M. 1987 . On the dependence of molecular conformation on the type of solvent environment: a molecular dynamics study of cyclosporin A to be submitted
   Google Scholar
• Lautz , J. , Kessler , H. , Kaptein , R. and van Gunsteren , W. F. 1987 . Molecular Dynamics Simulations of Cyclosporin A: The Crystal Structure and Dynamic Modelling of the Solution Structure Based on NMR Data . J. Comp.-Aided Molec. Design , 1 : 219
   PubMedGoogle Scholar
• Loosli , H. R. , Kessler , H. , Oschkinat , H. , Weber , H. P. , Petcher , T. J. and Widmer , A. 1985 . Peptide Conformations, part 31. The Conformation of Cyclosporin A in the Crystal and in Solution . Helv. Chim. Acta. , 68 : 682
   Web of Science ®Google Scholar
• van Gunsteren , W. F. and Berendson , H. J. C. 1987 . Groningen Molecular Simulation (GROMOS) Library manual , The Netherlands : Groningen . Biomos. Nijenborgh 16
   Google Scholar
• Ryckaert , J. P. , Ciccotti , G. and Berendson , H. J. C. 1977 . Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes . J. Comput. Phys. , 23 : 327
   Web of Science ®Google Scholar
• van Gunsteren , W. F. and Berendsen , H. J. C. 1979 . Algorithms for macromolecular dynamics and constraint dynamics . Molec. Phys. , 34 : 1311
   Google Scholar
• Hermans , J. , Berendsen , H. J. C. , van Gunsteren , W. F. and Postma , J. P. M. 1984 . A Consistent Empirical Potential for Water-Protein Interactions . Biopolymers , 23 : 1513
   Web of Science ®Google Scholar
• Rebertus , D. W. , Berne , B. J. and Chandler , D. 1979 . A molecular dynamics and Monte Carlo study of solvent effects on the conformational equilibrium of n-butane in CCl4 . J. Chem. Phys. , 70 : 3395
   Web of Science ®Google Scholar
• Berendsen , H. J. C. , Postma , J. P. M. , van Gunsteren , W. F. and Hermans , J. 1981 . “ Interaction models for water in relation to protein hydration ” . In Intermolecular forces , Edited by: Pullman , B. 331 – 342 . Reidel .
   Google Scholar
• Berendsen , H. J. C. , Postma , J. P. M. , van Gunsteren , W. F. , DiNola , A. and Haak , J. R. 1984 . Molecular dynamics with coupling to an external bath . J. Chem. Phys. , 81 : 3684
   Web of Science ®Google Scholar
• Weast , R. C. , ed. 1976 . Handbook of Chemistry and Physics , 56th edition , CRC Press .
   Google Scholar
• van Gunsteren , W. F. and Karplus , M. 1982 . The effect of constraints on the dynamics of macromolecules . Macromolecules , 15 : 1528
   Web of Science ®Google Scholar
• Lee , B. and Richards , F. M. 1971 . The Interpretation of Protein Structures: Estimation of Static Accessibility . J. Molec. Biol. , 55 : 379
   PubMed Web of Science ®Google Scholar
• Richmond , T. J. 1984 . Solvent Accessible Surface Area and Excluded Volume in Protein . J. Molec. Biol. , 178 : 63
   PubMed Web of Science ®Google Scholar
• Kessler , H. , Loosli , H. R. and Oschkinat , H. 1985 . Peptide Conformations. Part 30. Assignment of the 1H-, 13C-, and 13N-NMR Spectra of Cyclosporin A in CDC13 and C6D6 by a Combination of Homo- and Heteronuclear Two-dimensional Techniques . Helv. Chim. Acta , 60 : 661
   Google Scholar