Paper Citing NAMD - Abstract
Ramya, L.; Gautham, N.
Effects of Hydration on the Conformational Energy Landscape of the Pentapeptide Met-Enkephalin
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 5:2180-2190, AUG 2009
We report here a study of the conformational energy landscape of the pentapeptide Met-enkephalin in the presence of explicit solvent (water) molecules. A sample of 1 500 low-energy structures of this molecule was generated using the mutually orthogonal Latin squares (MOLS) technique with the CHARMM22 force field. This technique, developed in our laboratory, allows us to sample the conformational space of a molecule in an unbiased and exhaustive manner. The study shows that inclusion of explicit solvation is important to correctly model the conformational behavior of the molecule. Structures modeled in the presence of water molecules are far more similar to the experimental structures than when the water molecules are excluded. The results also indicate that the pentapeptide Met-enkephalin prefers extended structures in an aqueous environment, as against tightly folded structures in the absence of water. Thus, the biologically relevant structure, when the molecule is not bound to the receptor, is probably the extended structure, as seen in the crystallographic and NMR experiments, rather than the GEM structures calculated by various workers.
