Searching the global minimum of a peptide/bilayer potential energy surface by fast heating and cooling cycles of simulated annealing

Abstract

ABSTRACT:The total time reached by molecular dynamics simulation in the study of the interactions between hydrated bilayers and peptides is still very short. A scheme of fast heating and cooling cycles of simulated annealing (FHCCSA) is proposed to improve the efficiency of the search for the global minimum of the peptide/bilayer potential energy surface. In FHCCSA, the high temperatures facilitate the transitions between stable configurations; i.e., heating and cooling cycles make easier the escape of the system outside the local energy minimum. The FHCCSA efficiency is confirmed by comparing its results with conventional NpT simulations. The new scheme saves more than 90% of the total cpu time compared with ordinary NpT simulations.

Transmembrane Structures for Alzheimer’s Aβ1−42 Oligomers

“…Basin-hopping techniques have already been used to explore amyloid assembly for short peptide sequences, for instance for the KFFE peptide ,− and Aβ 16−22 . , The current study is, to the best of our knowledge, the first one to search for the global minimum of a longer amyloidogenic peptide, such as Aβ 1−42 , and its oligomers in a membrane environment. In a recent study, simulated annealing was employed to search for the global minimum of a peptide/bilayer system . The BH global optimization approach should enable us to locate low-lying structures much faster and more reliably.…”

“…In a recent study, simulated annealing was employed to search for the global minimum of a peptide/bilayer system. 100 The BH global optimization approach should enable us to locate low-lying structures much faster and more reliably.…”

Structural Bioinformatics for Protein Engineering

“…For each system, an initial simulation was performed for 0.5 ns applying restrictions to the peptides and bilayer atomic coordinates to equilibrate the systems using a dt = 0.5 fs. The restrictions were removed and the systems were initially simulated by 30 fast heating and cooling cycles of simulated annealing (Fuzo et al, 2008) with dt =2 fs. In the next stage, the systems were submitted to 20 ns NpT simulations with dt of 2 fs, with 50 ns total simulation time for each system.…”

Study of the antimicrobial peptide indolicidin and a mutant in micelle medium by molecular dynamics simulation

“…Although, details of peptide insertion and positioning in the membranes are of particular interest so that more realistic models concerning the action of AMPs can be achieved, knowledge about models of interactions between AMPs and membranes is still subject to the limited information obtained from experiments. In this sense, computational techniques have been used to solve many problems concerning biological systems and to complement experimental observations (Murakami et al, 2005;Brancaleoni et al, 2006;Mazzé et al, 2007;Fuzo et al, 2008). Among the various computational techniques, molecular dynamics simulation (Alder and Wainwright, 1957) is a powerful tool that provides detailed configurational and dynamic information at the atomic level.…”