Molecular dynamics simulation of the cyclic decapeptide antibiotic, Gramicidin S, in dimethyl sulfoxide solution

Article Abstract:

The cyclic peptide antibiotic Gramicidin S is characterized by the sequence cyclo-(Leu-D-Phe-Pro-Val-Orn)sub 2. To shed light on its molecular dynamics, a simulation of Gramicidin S in dimethyl sulfoxide solution is done. Throughout the simulation, the backbone ring is shown to maintain an antiparallel beta-pleated sheet conformation with two-type II beta-turns. The backbone dihedrals are also shown to be relatively inflexible as they do not undergo any conformational transitions.

Antibiotics, Solution (Chemistry), Solutions (Chemistry)

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Role of ions on structure and stability of a synthetic gramicidin ion channel solution. A molecular dynamics study

Article Abstract:

A molecular dynamics (MD) simulation for the structure and stability of a synthetic gramicidin-like peptide in solution with and without ions is performed. The result reveals the Cs+ ions bind in the channel formed by the monomeric gramicidin-like peptide using implicit solvent and explicit ions with a concentration of 2 M.

Radicals (Chemistry)

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Binding of organic cations to gramicidin A channel studied with autodock and molecular dynamics simulations

Article Abstract:

The application of AutoDock program designed by binding of organic cations to the gramicidin A channel, to obtain accurate description of protein-ligand binding energies and configurations is described.

Usage, Ligands (Biochemistry), Chemical properties

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