Multiscale computational prediction of β-sheet peptide self-assembly morphology. Issue 5 (24th March 2021)

• Record Type: Journal Article
• Authors: Deng, Li; Wang, Yanting
• Is Part Of: Molecular simulation. Volume 47:Issue 5(2021)
• Page Start: 428
• Page End: 438
• Publication Date: 2021-03-24
• Subjects: Peptide self-assembly -- computer prediction -- multiscale simulation; Molecular dynamics -- Computer simulation -- Periodicals; Statistical mechanics -- Computer simulation -- Periodicals; 539.6
• DOI: 10.1080/08927022.2020.1738426
• Languages: English
• ISSNs: 0892-7022

Abstract

ABSTRACT : Although nanostructures self-assembled by short peptides are very promising in developing novel biomaterials and nanomaterials, it is still a great challenge to design the peptide molecular structure which will self-assemble into designated nanostructures. By combining elastic theory with molecular dynamics simulations, we introduce a multiscale computational approach to predict the β-sheet morphology self-assembled by short peptides in aqueous solution only based on the molecular structure of the peptide. In our approach, the gap between the elastic model and atomistic model is bridged by the simplified model, whose parameters are determined by enhanced sampling and extensive all-atom molecular dynamics simulation results at different levels. This multiscale approach is applied to two model peptides KIIIIK (KI4K) and IIIIKK (I4K2) to test its validity. The computational results, consistent with the previous experimental observations, show that KI4K with a higher ratio of inter-sheet interaction to intra-sheet interaction tends to form tube-like morphology with a larger width, while I4K2 with a lower ratio tends to form fibril with a smaller width. This methodology is anticipated to be helpful for computer-aided design of nanostructures self-assembled by short peptides.