Computational Insights into the Unfolding of a Destabilized Superoxide Dismutase 1 Mutant.

Abstract

Simple SummaryTo function correctly, most proteins need to fold into well-defined three-dimensional structures. Destabilization of these structures may not only lead to the loss of function, but also to toxic aggregation and fibril formation. These pathological processes have been linked to a number of neurodegenerative diseases. To prevent such processes, it is important to describe factors causing protein destabilization and identify misfolded structures that are at the origin of the toxic behavior. From the experimental point of view, in many cases, it is useful to construct protein models to better investigate the issues of stability, misfolding, and aggregation. Here, indeed, we focus on a mutant model of superoxide dismutase 1, a protein implicated in amyotrophic lateral sclerosis. We apply a state-of-the-art molecular simulation method to verify whether the current computational machinery is able to describe the features of the biochemical model. Namely, our paper provides a microscopic insight into the unfolding of the superoxide dismutase 1 model while highlighting the strengths and limitations of the computational approach. Overall, our investigation opens the route to the computational study of pathological mutants of the superoxide dismutase 1 protein.In this work, we investigate the -barrel of superoxide dismutase 1 (SOD1) in a mutated form, the isoleucine 35 to alanine (I35A) mutant, commonly used as a model system to decipher the role of the full-length apoSOD1 protein in amyotrophic lateral sclerosis (ALS). It is known from experiments that the mutation reduces the stability of the SOD1 barrel and makes it largely unfolded in the cell at 37 degrees Celsius. We deploy state-of-the-art computational machinery to examine the thermal destabilization of the I35A mutant by comparing two widely used force fields, Amber a99SB-disp and CHARMM36m. We find that only the latter force field, when combined with the Replica Exchange with Solute Scaling (REST2) approach, reproduces semi-quantitatively the experimentally observed shift in the melting between the original and the mutated SOD1 barrel. In addition, we analyze the unfolding process and the conformational landscape of the mutant, finding these largely similar to those of the wildtype. Nevertheless, we detect an increased presence of partially misfolded states at ambient temperatures. These states, featuring conformational changes in the region of the -strands 46, might provide a pathway for nonnative aggregation.