# Analysis of Correlation Effects of Double Mutations in Enzymes: A Revised Residual-Contact Network Clique Model

## TL;DR

This paper introduces a revised model to study how double mutations in enzymes affect their activity, showing that mutation additivity depends on structural and chemical properties.

## Contribution

A revised residual-contact network clique model is proposed to better understand and predict the effects of double mutations in enzymes.

## Key findings

- The model successfully identified over 90% of additive double mutations in three enzymes.
- Non-additive double mutations are often found in irregular secondary structure regions.
- Mutation additivity is strongly influenced by the topology and physicochemical properties of the mutation sites.

## Abstract

The relationship between amino acid mutations and enzyme bioactivity is a significant challenge in modern bio-industrial applications. Despite many successful designs relying on complex correlations among mutations at different enzyme sites, the underlying mechanisms of these correlations still need to be explored. In this study, we introduced a revised version of the residual-contact network clique model to investigate the additive effect of double mutations based on the mutation occurrence topology, secondary structures, and physicochemical properties. The model was applied to a set of 182 double mutations reported in three extensively studied enzymes, and it successfully identified over 90% of additive double mutations and a majority of non-additive double mutations. The calculations revealed that the mutation additivity depends intensely on the studied mutation sites’ topology and physicochemical properties. For example, double mutations on irregular secondary structure regions tend to be non-additive. Our method provides valuable tools for facilitating enzyme design and optimization. The code and relevant data are available at Github.