(340l) Studying the Effects of Mutations on the Structures and Binding of Therapeutic Proteins Towards Improving the Engineering of Protein Functions

The high effectiveness of proteins in biological systems is a result of their mutational histories. A single amino acid substitution, the most frequent of changes in proteins, can alter their physiochemical properties and functions. Mutations impact protein folding and interactions, and thus their functions in a biological system. These mutations may be beneficial, and identifying them can provide insights towards improving the engineering of proteins. Alternatively, the current pandemic has shown examples of how single point mutations in pathogens, like viruses, can lead to different variants with drastic consequences to human health; some variants may spread more easily in humans or show signs of resistance to existing treatment options. Each of the projects described in this poster use computational methods to understand the effects of mutations on protein structures and functions in therapeutic contexts.

To develop a baseline understanding of how antibodies interact with protein antigens, we identified a non-redundant database of 483 complexes from the protein databank. Each complex varies from every other complex by at least five mutations in the complementary determining regions of the antibodies. Prior experimental and computational studies had indicated that antibody-antigen complexes are typically mediated through a small number of hotspot interactions, but had not quantified the extent. Analysis of our database revealed that on average 70% of binding energy is contributed by only seven antibody residues. Building from this knowledge, we then conducted a mutational analysis of the hotspot residues in both the antibodies and antigens. This was for the purpose of developing similarity matrices for protein binding. Existing similarity matrices are based on the evolutionary effects of mutations in proteins, whereas the matrices developed from this project are based on the effects of point mutations in antibody-antigen binding interfaces. The matrices were used to identify nuances and biases present in existing protein design tools and future applications include applying this knowledge towards more efficient de novo protein designs for therapeutic purposes.

With the emergence of the COVID-19 pandemic, my research shifted towards addressing questions inspired by this global health threat. Early in the pandemic it was observed that the anti-SARS antibodies S230, M396, and 80R failed to bind to the receptor binding domain of SARS-CoV-2 despite its high degree of similarity with that of SARS-CoV. Further computational analysis found that loss of binding for all three antibodies was caused by the disruption of hotspot interactions rather than the introduction of detrimental contacts. This finding motivated a study of how antigen mutations lead to loss of antibody binding. Through understanding which phenomena contribute towards the loss of binding for antibodies with mutated antigens, we hope to develop strategies to prepare in advance for and respond rapidly to future pandemics. Finally, the last project was inspired by a question of the efficacy of the current vaccines against emerging variants of the SARS-CoV-2 virus. A computational study was conducted to understand the effects on the T-cell and B-cell responses due to point mutations in the surface proteins of a virus. The study focuses on finding mutant variants that are able to “escape” immune responses and affect the body. The purpose of this study was to answer the question of the efficacy of immunity due to vaccination or previous infection against mutated variants, as well as create a framework for improving vaccine design to future emerging pandemics.

Mutational studies are extensively used to understand protein structures and functions for different purposes. Though each of these projects focus on the effect of mutations on protein functions from a unique perspective and for a unique purpose, they all contribute to the study of how point mutations can be helpful to engineer proteins to meet specific therapeutic needs.