Computational Compensatory Mutation Discovery Approach: Predicting a PARP1 Variant Rescue Mutation

Abstract

The prediction of protein mutations that affect function may be exploited for multiple uses. In the context of disease variants, the prediction of compensatory mutations that reestablish functional phenotypes could aid in the development of genetic therapies. In this work, we present an integrated approach that combines coevolutionary analysis and molecular dynamics (MD) simulations to discover functional compensatory mutations. This approach is employed to investigate possible rescue mutations of a poly(ADP-ribose) polymerase 1 (PARP1) variant, PARP1 V762A, associated with lung cancer and follicular lymphoma. MD simulations show PARP1 V762A exhibits noticeable changes in structural and dynamical behavior compared with wild type PARP1. Our integrated approach predicts A755E as a possible compensatory mutation based on coevolutionary information, and molecular simulations indicate that the PARP1 A755E/V762A double mutant exhibits similar structural and dynamical behavior to WT PARP1. Our methodology can be broadly applied to a large number of systems where single nucleotide polymorphisms (SNPs) have been identified as connected to disease and can shed light on the biophysical effects of such changes as well as provide a way to discover potential mutants that could restore wild type-like functionality. This can in turn be further utilized in the design of molecular therapeutics that aim to mimic such compensatory effect. Significance StatementDiscovering protein mutations with desired phenotypes can be challenging due to its combinatorial nature. Herein we employ a methodology combining gene SNP association to disease, direct coupling analysis and molecular dynamics simulations to systematically predict rescue mutations. Our workflow identifies A755E as a potential rescue for the PARP1 V762A mutation, which has been associated with cancer. This methodology is general and can be applied broadly.