Improvements to the molecular dynamics simulated annealing procedures: conformational search of the elastin tetrapeptide Boc-Gly-Leu-Gly-Gly-NMe

Add time:08/08/2019    Source:sciencedirect.com

Molecular dynamics simulated annealing strategies have been developed in order to perform the conformational search for complex systems. The highly flexible tetrapeptide Boc-Gly-Leu-Gly-Gly-NMe, a sequence present many times in the protein elastin, has been studied. The control parameters (heat bath reference temperatures, period and rate of processes, initial configurations, overall molecular motions) have been carefully optimized and heuristic criteria established.Two strategies have been developed. The simple-procedure consists fundamentally of initialization, heating and annealing stages. The macro procedure is a succession of simple procedures obtained by first increasing and then decreasing systematically the heat bath reference temperature.In the initialization stage, minimized structures beginning at rest have been considered, avoiding the use of arbitrary and inadequate Maxwellian velocities. During the heating and annealing processes, the thermalization of the system is performed according to classical dynamics with adiabatic variation, allowing large and anticorrelated fluctuations of kinetic and potential energy. During the annealing stage the reference temperature is set to 0 K and a screening of cooling rate is performed.The procedures are able to locate efficiently the molecular global minimum in multidimensional space when operating with only the internal degrees of freedom. When the overall molecular motions are considered a less folded structure, that could model the solvated conformations, is obtained. The procedure does not suffer from memory effects of the initial conditions.From the results, some hypotheses on the mechanism of the cooling process are proposed.

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