Biophysics of disease and evolution : molecules to organisms

This thesis describes applications of computer simulation and bioinformatics techniques in conjunction with experiments to understand various biological systems. In Chapter 2, we used molecular dynamics simulations to uncover the structural details of an experimentally observed interaction between the ALS-associated protein superoxide dismutase 1 (SOD1), and TNF receptor-associated factor 6. Residues present in their heterodimer binding interface were predicted through unbiased and metadynamics simulations and tested in cultured cells. In Chapter 3, we used a quick computational scan to identify two de novo mutations of SOD1, A89R and K128N that were expected to be destabilizing and stabilizing respectively. Expression in cell cultures and zebrafish confirmed that A89R produces pathologies similar to the ALS-associated mutant A4V, and that K128N is WT-like. Interestingly, unlike WT-SOD1, K128N rescued the aberrant phenotype of zebrafish motor neurons when coinjected with A4V-SOD1. To explain this, we used computational alchemy to calculate heterodimerization free energies for A4V-SOD1 with WT-SOD1 and K128N-SOD1, but could not confirm a "heterodimer-rescue" mechanism. In Chapter 4, we studied the conformational landscape of the SARS-CoV-2 spike protein. The conserved residues 980-990, normally buried under the receptor binding domain, have been reported to be transiently accessible to antibodies. Through umbrella sampling simulations we found that direct exposure of the epitope through dynamic motions is not a likely mechanism for this accessibility. Further, glycans play an important role in preventing such dynamics. During its normal function, this epitope undergoes a large-scale conformational change from a bent to an extended state. To aid development of a vaccine antigen containing the conserved fragment, we studied the free energy cost of this change and found that a bent pre-fusion-like conformation is preferred. Moving on from protein studies, in Chapter 5 we were interested in the biophysics of genome organization, and its evolution in early ancestors of all animals. The basal metazoan Mnemiopsis leidyi is well-suited for such studies but has not been standardized as a model organism. We developed protocols for laboratory culture of this organism, and obtained a highly contiguous reference genome for an inbred lineage.Science, Faculty ofPhysics and Astronomy, Department ofGraduat