This Article Full Text Full Text (PDF) All Versions of this Article: biophysj.104.054130v1 89/3/1433    most recent Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Dadarlat, V. M. Search for Related Content PubMed PubMed Citation Articles by Dadarlat, V. M.

Potentials of Mean Force for the Interaction of Blocked Alanine Dipeptide Molecules in Water and Gas Phase from MD Simulations

Department of Chemistry, Purdue University, West Lafayette, Indiana 47907

Correspondence: Address reprint requests to Voichita M. Dadarlat, Tel.: 765-496-3361; Fax: 765-494-5489; E-mail: voichi{at}purdue.edu.

We calculate potentials of mean force (PMFs) for the intermolecular interaction of two blocked alanine dipeptide (AcAlaNHMe) molecules in water and gas phase at two temperatures, 278 and 300 K, from all-atom molecular dynamics simulations. Simple models based on buried solvent accessible surface and one-dimensional potentials derived from distance-based radial distribution functions are not capable of expressing the short- and long-range complexity of the solute-solute interactions in water. Instead, radial and angular variations in the PMFs are observed with the two-dimensional potentials. The strength of the interactions for specific relative orientations of the molecules in the two-dimensional PMFs is more than double that observed in the one-dimensional PMFs. The populations of specific blocked alanine dipeptide conformations in water, such as _R and PPII, vary with temperature, and most significantly, with the distance between the centers of mass. A preference for helical conformations is observed at close encounter between molecules.

This article has been cited by other articles:

				V. M. Dadarlat and C. B. Post Decomposition of Protein Experimental Compressibility into Intrinsic and Hydration Shell Contributions Biophys. J., December 15, 2006; 91(12): 4544 - 4554. [Abstract] [Full Text] [PDF]