Molecular dynamics simulation of alpha-melanocyte stimulating hormone in awater-membrane model interface

The conformation of the tridecapeptide alpha-melanocyte stimulating hormone in the presence of a double water-membrane interface was studied by molecu lar dynamics simulation, using the computational package THOR. In this prog ram the solvent is represented by a continuous medium with dielectric const ant epsilon, and the interface between different media is simulated by a su rface of discontinuity of the dielectric constant. The electrostatic image method was used to write down the terms, added to the force field, that des cribe the polarisation effects induced in the interface by the atomic charg es. The program was further improved by the introduction of a second surfac e, parallel to the first one, to mimic the membrane. A conformational searc h using the software Prelude was employed to find an initial geometry for t he peptide in water. The molecular dynamics simulation performed during 10 ns showed that the peptide structure is flexible in water, without stabilis ation of any preferential conformation. In the presence of the model membra ne, the peptide moved to the medium representing the interior of the membra ne. Inside the low dielectric constant medium, the structure of the peptide showed a turn in the central sequence of amino acids and a packed conforma tion remained stabilised during more than 7.0 ns of simulation.