Source:Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes: From Bioinformatics to Molecular Quantum Mechanics, Springer International Publishing:541–558, 2019
Recent advances in computational technology have allowed us to simulate biomolecular processes on timescales that begin to reach the rates of peptide aggregation phenomena. Molecular dynamics simulations have evolved into a mature technique to the extent that they can be employed as a highly productive tool to gain meaningful insights into the structure, dynamics and molecular mechanisms of protein aggregation. In this chapter, we describe the basics of explicit solvent all-atom molecular dynamics simulations and its applications for studying early stages of aggregation processes of two short pentapeptides: KLVFF and FVFLM, related to Alzheimer's disease and preeclampsia, respectively. We focus on certain important problems in the field of protein aggregation that explicit solvent all-atom molecular dynamics simulation studies could resolve. This includes how fibril formation rates depend on a number of factors such as the presence of short peptides and population of fibril-prone conformations. Specific applications of atomistic simulations in explicit solvent to address these two issues are discussed.