Potentials of Mean Force (PMFs) for the interaction of blocked alanine dipeptide molecules in water and vacuum from MD simulations

¹ Purdue University

^* To whom correspondence should be addressed. E-mail: voichi{at}purdue.edu.

Submitted on October 12, 2004
Revised on November 30, 2004
Accepted on 4 April 2005

	Abstract

We calculate potentials of mean force (PMFs) for the intermolecular interaction of two blocked alanine dipeptide (AcAlaNHMe) molecules in water and vacuum at two temperatures, 278 and 300 K, from all atom MD simulations. Simple models based on buried solvent accessible surface and one dimensional potentials derived from distance based radial distribution functions (RDFs) 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 2D potentials. The strength of the interactions for specific relative orientations of the molecules in the 2D PMFs is more than double that observed in the 1D PMFs. The populations of specific blocked alanine dipeptide (bAdp) conformations in water, such as alpha helix 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.

Key Words: 1D and 2D PMF, alpha helix promotion, angular dependence, blocked alanine dipeptide, potentials of mean force, solute-solute interaction

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