A Simulated Annealing - Molecular Dynamic Approach for Conformational Sampling of full-length Amyloid-beta Peptide

Intrinsically disordered proteins (IDPs) with relatively flat energy landscapes have flexiblestructures and do not fold to unique conformations. Therefore, these proteins sample arelatively large and diverse set of conformations under native conditions and must bedescribed as ensembles of interconverting conformations [1,2].Unfortunately, conventional molecular dynamic (CMD) simulations tend to producedisordered-state ensembles that are structurally too compact relative to experiments [3]. Toovercome this problem, we introduce a new conformation sampling protocol - a MDsimulation inspired from simulated annealing (SA) method [4]. We show that simulations ofan IDP (Amyloid-beta (Aβ) in this report) using this new protocol result in disordered statesthat are substantially more expanded and in better agreement with experiment.