Exploring Heterogeneous Dynamical Environment around an Ensemble of Aβ42 Peptide Monomer Conformations

Elucidating the Sluggish Water Dynamics at the Ice-Binding Surface of the Hyperactive Tenebrio molitor Antifreeze Protein

Quasi-ice-like hydration waters on the ice-binding surface (IBS) of an antifreeze protein (AFP) commonly exhibit sluggish dynamics especially at low temperatures. In this work, we have analyzed molecular dynamics (MD) simulation trajectories at two different temperatures for Tenebrio molitor antifreeze protein (TmAFP) to explore whether the unique quasi-ice-like structuring of hydration water has any impact on making their dynamics slower on the IBS of the protein. Our calculation reveals that, as translational dynamics is coupled with the conformational fluctuations, hydration water on the IBS exhibits sluggish translational motion due to reduced flexibility of the IBS compared to that on the non-ice-binding surface (NIBS) of the protein. Interestingly, it is noticed that rotational motion of hydration water is not coupled with the conformational fluctuations of the surfaces. In that case, structural relaxations of the protein-water (PW) and water-water (WW) hydrogen bonds compete with each other to make the rotational dynamics of hydration water around the IBS either faster or slower with respect to those around the NIBS. At low temperature, the slower structural relaxation of water-water hydrogen bonds dominates and imparts sluggish rotational motion of the hydration water on the IBS of the protein. The slower structural relaxation of water-water hydrogen bonds and hence the retarded rotational dynamics, despite the weak short-lived PW hydrogen bonds on the IBS, is clearly a manifestation of the rigid quasi-ice-like structure of the hydration shell on that surface.

In Silico Studies to Predict the Role of Solvent in Guiding the Conformations of Intrinsically Disordered Peptides and Their Aggregated Protofilaments

The formation of amyloids due to the self-assembly of intrinsically disordered proteins or peptides is a hallmark for different neurodegenerative diseases. For example, amyloids formed by the amyloid beta (Aβ) peptides are responsible for the most devastating neuropathological disease, namely, Alzheimer's disease, while aggregation of α-synuclein peptides causes the etiology of another neuropathological disease, Parkinson's disease. Characterization of the intermediates and the final amyloid formed during the aggregation process is, therefore, crucial for microscopic understanding of the origin behind such diseases, as well as for the development of proper therapeutics to combat those. However, most of the research activities reported in this area have been directed toward examining the early stages of the aggregation process, including probing the conformational characteristics of the responsible protein/peptide in the monomeric state or in small oligomeric forms. This is because the small soluble oligomers have been found to be more deleterious than the final insoluble amyloids. This review discusses some of the recent findings obtained from our simulation studies on Aβ and α-synuclein monomers and small preformed Aβ aggregates. A molecular-level insight of the aggregation process with a special emphasis on the role of water in inducing the aggregation process has been provided.