Abstract
Molecular dynamics trajectories of two dipeptides, vilon (Lys-Glu) and thymogen (Glu-Trp), were traced up to 700 ps. Both structures comprise intramolecular salt bridges which make them less conformationally flexibile. Vilon is comparatively more flexible due to the aliphatic side chain of Lys, whereas thymogen is quite a rigid structure, which is defined by the mutual arrangement of salt bridges and aromatic rings in the side chain of Trp. A probable mechanism of ligand-receptor binding of dipeptides with excitable membrane was proposed. The binding can be effected via the nitrogen and oxygen atoms forming the salt bridges.
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