Journal of Physical Chemistry B, Vol.103, No.9, 1586-1594, 1999
Molecular dynamics simulation of the cyclic decapeptide antibiotic, gramicidin S, in dimethyl sulfoxide solution
We report on a 5 ns molecular dynamics simulation of the decapeptide antibiotic, gramicidin S (cyclo-(Leu-lDPhe-Pro-Val-Orn)(2)) in dimethyl sulfoxide solution. Throughout the simulation the backbone ring maintains an antiparallel beta-pleated sheet conformation with two type II' beta-turns. The backbone dihedrals are relatively inflexible and do not undergo any conformational transitions. The simulation reproduces the Phi and Psi angles derived from nuclear magnetic resonance spectroscopy to within 18 degrees standard deviation on average. Correlations between the backbone dihedral angles are found. The side chain dihedrals are much more flexible, and the multiple conformational states of these are classified using a clustering technique. Side chain hydrogen-bonding involving the ornithine and phenylalanine residues is analyzed and discussed in the context of previous work.