Graphical visualization of mean hydration from molecular dynamics simulations.
How does one characterize water solvating a complex solute? Specific hydration of proteins and nucleic acids plays a key role in many biological processes. However, traditional pairwise descriptions of solvent structure (radial distribution functions, etc.) are incapable of adequately describing the hydration of these complex solutes. We have developed methods to visualize the average three-dimensional water structure surrounding a solute, as seen in a molecular dynamics (MD) simulation. Applications to simple solutes [sodium ion, N-methyl acetamide, 18-crown-6, (hydroxymethyl)phenols] are presented, and the extension of the method to larger molecules of biochemical interest is discussed.
Graduate Group in Biophysics, University of California, San Francisco 94143, USA.
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Pitera
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Kollman
D000081:Acetamides / Q000737:chemistry; D002414:Cations, Monovalent / Q000737:chemistry; D003196:Computer Graphics; D003198:Computer Simulation; D043844:Crown Ethers; D004988:Ethers, Cyclic / Q000737:chemistry; D008958:Models, Molecular; D011336:Probability; D012964:Sodium / Q000737:chemistry; D014867:Water / Q000737:chemistry*
D000081:Acetamides; D002414:Cations, Monovalent; D043844:Crown Ethers; D004988:Ethers, Cyclic; D014867:Water; C015762:18-crown-6; D012964:Sodium; C018595:N-methylacetamide