Diffusion of solvent around biomolecular solutes: a molecular dynamics simulation study.
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M Feig | B M Pettitt | B. Pettitt | M. Feig | V. Makarov | V A Makarov | B K Andrews | B. K. Andrews | Vladimir Makarov | Michael Feig
[1] R Abseher,et al. The influence of a protein on water dynamics in its vicinity investigated by molecular dynamics simulation , 1996, Proteins.
[2] W. L. Jorgensen,et al. Comparison of simple potential functions for simulating liquid water , 1983 .
[3] S. Swaminathan,et al. Molecular Dynamics Simulations on the Hydration, Structure and Motions of DNA Oligomers , 1993 .
[4] G. Phillips,et al. Structure and dynamics of the water around myoglobin , 1995, Protein science : a publication of the Protein Society.
[5] O. Edholm,et al. Molecular dynamics simulations of an enzyme surrounded by vacuum, water, or a hydrophobic solvent. , 1994, Biophysical journal.
[6] G. Ciccotti,et al. Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .
[7] H. Berendsen,et al. Interaction Models for Water in Relation to Protein Hydration , 1981 .
[8] P. Kollman,et al. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .
[9] A T Brünger,et al. Direct Observation of Protein Solvation and Discrete Disorder with Experimental Crystallographic Phases , 1996, Science.
[10] Michael L. Quillin,et al. High-resolution crystal structures of distal histidine mutants of sperm whale myoglobin. , 1994, Journal of molecular biology.
[11] H. Tyrrell,et al. Diffusion in liquids , 1984 .
[12] R. Mills. Diffusion in electrolytes , 1965 .
[13] K Wüthrich,et al. Hydration of proteins. A comparison of experimental residence times of water molecules solvating the bovine pancreatic trypsin inhibitor with theoretical model calculations. , 1993, Journal of molecular biology.
[14] Bernard Pettitt,et al. Peptides in ionic solutions: A comparison of the Ewald and switching function techniques , 1991 .
[15] Y. Komeiji,et al. A molecular dynamics study of solvent behavior around a protein , 1993, Proteins.
[16] Salvatore Cannistraro,et al. Anomalous and anisotropic diffusion of plastocyanin hydration water , 1997 .
[17] M Karplus,et al. Solvent effects on protein motion and protein effects on solvent motion. Dynamics of the active site region of lysozyme. , 1989, Journal of molecular biology.
[18] H. Hertz. Nuclear Magnetic Relaxation Spectroscopy , 1973 .
[19] Eric Westhof,et al. Water and Biological Macromolecules , 1993 .
[20] Lewis Stiller,et al. Computation of the mean residence time of water in the hydration shells of biomolecules , 1993, J. Comput. Chem..
[21] B. Montgomery Pettitt,et al. Efficient Ewald electrostatic calculations for large systems , 1995 .
[22] E. Jakobsson,et al. Incorporation of surface tension into molecular dynamics simulation of an interface: a fluid phase lipid bilayer membrane. , 1995, Biophysical journal.
[23] Felix Franks,et al. Water:A Comprehensive Treatise , 1972 .
[24] G. Phillips,et al. A global model of the protein-solvent interface. , 1994, Biophysical journal.
[25] M Mezei,et al. Structural chemistry of biomolecular hydration via computer simulation: the proximity criterion. , 1986, Methods in enzymology.
[26] D. Hartsough,et al. Protein dynamics and solvation in aqueous and nonaqueous environments , 1993 .
[27] M Karplus,et al. Ion transport in the gramicidin channel: molecular dynamics study of single and double occupancy. , 1995, Biophysical journal.
[28] Bizzarri,et al. Molecular dynamics simulation evidence of anomalous diffusion of protein hydration water. , 1996, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.
[29] William L. Jorgensen,et al. Molecular dynamics of proteins with the OPLS potential functions. Simulation of the third domain of silver pheasant ovomucoid in water , 1990 .
[30] B M Pettitt,et al. Reconstructing the protein-water interface. , 1998, Biopolymers.
[31] I. Muegge,et al. Heterogeneous diffusion of water at protein surfaces: application to BPTI , 1993 .
[32] A T Brünger,et al. Protein hydration observed by X-ray diffraction. Solvation properties of penicillopepsin and neuraminidase crystal structures. , 1994, Journal of molecular biology.
[33] G J Williams,et al. The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1977, Journal of molecular biology.
[34] B M Pettitt,et al. Characterizing global substates of myoglobin. , 1998, Structure.
[35] Terry R. Stouch,et al. The limiting behavior of water hydrating a phospholipid monolayer: A computer simulation study , 1993 .
[36] Wei Zu Chen,et al. Analysis of interfacial water structure and dynamics in α-maltose solution by molecular dynamics simulation , 1996 .
[37] Terry R. Stouch,et al. Effects of Switching Functions on the Behavior of Liquid Water in Molecular Dynamics Simulations , 1994 .
[38] M. Rami Reddy,et al. A molecular dynamics study of the structure and dynamics of water between dilauroylphosphatidylethanolamine bilayers , 1992 .
[39] J. Banavar,et al. Computer Simulation of Liquids , 1988 .
[40] M. Teeter,et al. Water-protein interactions: theory and experiment. , 1991, Annual review of biophysics and biophysical chemistry.
[41] O. Teleman,et al. Molecular dynamics simulation of interfacial water structure and dynamics in a parvalbumin solution , 1988 .
[42] Terry R. Stouch,et al. Computer simulation of a phospholipid monolayer‐water system: The influence of long range forces on water structure and dynamics , 1993 .
[43] Salvatore Cannistraro,et al. Water residence times around copper plastocyanin: a molecular dynamics simulation approach , 1997 .
[44] I. Muegge,et al. Residence Times and Lateral Diffusion of Water at Protein Surfaces: Application to BPTI , 1995 .
[45] Salvatore Cannistraro,et al. Origin of the anomalous diffusion observed by MD simulation at the protein-water interface , 1996 .
[46] B. Pettitt,et al. Experiment vs force fields: DNA conformation from molecular dynamics simulations , 1997 .
[47] R. Sharon,et al. Accurate simulation of protein dynamics in solution. , 1988, Proceedings of the National Academy of Sciences of the United States of America.
[48] J. Andrew McCammon,et al. Computer Simulation and the Design of New Biological Molecules , 1986 .