Elucidating Self-Assembling Peptide Aggregation via Morphoscanner: A New Tool for Protein-Peptide Structural Characterization

Abstract

Self-assembling and molecular folding are ubiquitous in Nature: they drive the organization of systems ranging from living creatures to DNA molecules. Elucidating the complex dynamics underlying these phenomena is of crucial importance. However, a tool for the analysis of the various phenomena involved in protein/peptide aggregation is still missing. Here, an innovative software is developed and validated for the identification and visualization of b-structuring and b-sheet formation in both simulated systems and crystal structures of proteins and peptides. The novel software suite, dubbed Morphoscanner, is designed to identify and intuitively represent b-structuring and b-sheet formation during molecular dynamics trajectories, paying attention to temporary strand-strand alignment, suboligomer formation and evolution of local order. Self-assembling peptides (SAPs) constitute a promising class of biomaterials and an interesting model to study the spontaneous assembly of molecular systems in vitro. With the help of coarse-grained molecular dynamics the self-assembling of diverse SAPs is simulated into molten aggregates. When applied to these systems, Morphoscanner highlights different b-structuring schemes and kinetics related to SAP sequences. It is demonstrated that Morphoscanner is a novel versatile tool designed to probe the aggregation dynamics of self-assembling systems, adaptable to the analysis of differently coarsened simulations of a variety of biomolecules.