Rapid transition of beta barrel from arbitrary strands: A molecular dynamics observation

Abstract

A fast molecular dynamics simulation protocol for a parallel beta barrel formation from an aribitrary tetrameric strands was discussed, using charmm-27 forcefield based NAMD molecular dynamics. In this work, we employed a tetramer unit of alanine beta strands and other amino acid mutations to investigate the folding kinetics, ionic strength, shear number, entropy, C=O-H-N bonding of barrel geometry. The results were consistent with an initial model in which oxygen placed in a rectangular like shape favours the barrel formation rather than the one with a square like oxygen topology, additionally, we confirmed the formation of simple small barrels like geometries for different permutations and combinations of amino acids of tetramer sub units. Also, we confirmed the stability of such barrels upon solvent exposed environment using 20 ns of molecular dynamics. This approach allow us to compute the barrel formation trends in neurotoxic and ion channel proteins. Our simulation supports the theoretical findings reported by Chothia and coworkers [1], and significantly well in accordance with the observation of single-walled carbon nanotube induced beta-barrel formation of the Alzheimer's Abeta 25-35 oligomers.