Composition-related structural transition of random peptides: insight into the boundary between intrinsically disordered proteins and folded proteins

Multi-scale molecular simulation of random peptide phase separation and its extended-to-compact structure transition driven by hydrophobic interactions

Intrinsically disordered proteins (IDPs) often undergo liquid-liquid phase separation (LLPS) and form membraneless organelles or protein condensates. One of the core problems is how do electrostatic repulsion and hydrophobic interactions in peptides regulate the phase separation process? To answer this question, this study uses random peptides composed of positively charged arginine (Arg, R) and hydrophobic isoleucine (Ile, I) as the model systems, and conduct large-scale simulations using all atom and coarse-grained model multi-scale simulation methods. In this article, we investigate the phase separation of different sequences using a coarse-grained model. It is found that the stronger the electrostatic repulsion in the system, the more extended the single-chain structure, and the more likely the system forms a low-density homogeneous phase. In contrast, the stronger the hydrophobic effect of the system, the more compact the single-chain structure, the easier phase separation, and the higher the critical temperature of phase separation. Overall, by taking the random polypeptides composed of two types of amino acid residues as model systems, this study discusses the relationship between the protein sequence and phase behaviour, and provides theoretical insights into the interactions within or between proteins. It is expected to provide essential physical information for the sequence design of functional IDPs, as well as data to support the diagnosis and treatment of the LLPS-associated diseases.

Oligomers, fibrils and aggregates formed by alpha-synuclein: role of solution conditions

The classical Hofmeister series orders ions into kosmotropes and chaotropes, based on their interaction with the solvent, water. The role of protein is mostly ignored probably because most of the proteins studied are natively folded and broadly follow this classification pattern. Recent reports suggest that the interaction of ions is different with solvent molecules of proximal layer and bulk. Intrinsically disordered proteins (IDPs) differ from globular proteins in the fraction of polar vis-à-vis hydrophobic amino acids and the absence of distinct secondary and tertiary structures. The kosmotrope, ammonium sulphate, increases the compactness of the polypeptide conformation, with differing effects for globular proteins and IDPs. For globular proteins, lowered flexibility corresponds to a more stable native structure. Using oligomer-specific and aggregation-specific antibodies and comparing with fibrillation results, we show for alpha-synuclein, an IDP, ammonium sulphate-induced compaction results in the formation of the aggregation-prone hydrophobic core, which combines with other similar moieties to form the fibrillar 'seed'. SEC-HPLC and SAXS analysis show the presence of the threshold oligomers. In the presence of the aggregation suppressor, arginine too, an oligomer is formed. This oligomer, however, is 'dead', and does not move further along the aggregation pathway. Thus, alpha-synuclein undergoes compaction in the presence of protein stabilisers, with differing consequences. In case of the chaotropes, KSCN and urea, aggregation of alpha-synuclein is partially inhibited. However, the amounts and types of aggregates formed are different in the two cases. Thus, the classical catalogue of molecules into protein stabilisers and destabilisers requires a relook for IDPs.Communicated by Ramaswamy H. Sarma.