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| Title
| - Molecular Dynamics Simulation of the Cyclic Decapeptide Antibiotic, Gramicidin S, inDimethyl Sulfoxide Solution
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| Abstract
| - We report on a 5 ns molecular dynamics simulation of the decapeptide antibiotic, gramicidin S (cyclo-(Leu-DPhe-Pro-Val-Orn)2) in dimethyl sulfoxide solution. Throughout the simulation the backbone ring maintainsan antiparallel β-pleated sheet conformation with two type II‘ β-turns. The backbone dihedrals are relativelyinflexible and do not undergo any conformational transitions. The simulation reproduces the Φ and Ψ anglesderived from nuclear magnetic resonance spectroscopy to within 18° standard deviation on average. Correlationsbetween the backbone dihedral angles are found. The side chain dihedrals are much more flexible, and themultiple 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 previouswork.
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