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EvoMut: A Computational Framework for Engineering Oxidative Stability in Proteins.

Seyed Shahriar Arab¹, Nathan E Lewis^1,2,3

¹Center for Molecular Medicine, University of Georgia, Athens, GA 30602, United States.

Biorxiv : the Preprint Server for Biology

|April 3, 2026

Summary

This summary is machine-generated.

Identifying and engineering oxidation-vulnerable protein sites is challenging. EvoMut, a new framework, assesses oxidative risk and mutation feasibility, enabling rational design of oxidation-resistant proteins.

Keywords:

evolutionary conservation oxidative hotspot prediction oxidative stability engineering protein engineering protein oxidation structural bioinformatics

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Area of Science:

Protein engineering
Biochemistry
Computational biology

Background:

Amino acid oxidation compromises protein stability and function.
Identifying engineerable oxidation-prone sites is difficult, as not all vulnerable residues are suitable mutation targets.
Current strategies often lack consideration of functional and evolutionary constraints.

Purpose of the Study:

To present EvoMut, a residue-level analytical framework for evaluating oxidative vulnerability and mutation feasibility.
To provide a practical approach for the rational design of oxidation-resistant proteins.
To distinguish between oxidation-sensitive residues and those that are evolutionarily permissive for mutation.

Main Methods:

EvoMut integrates structural features, local functional context, chemical susceptibility, and evolutionary conservation to estimate oxidation risk.
The framework explicitly separates oxidation risk from mutation feasibility.
Candidate substitutions are evaluated after ranking high-risk residues by evolutionary substitution patterns.

Main Results:

Oxidation-prone residues exhibit varying engineering potential.
EvoMut successfully distinguishes between residues that are both oxidation-sensitive and evolutionarily permissive versus those that are chemically vulnerable but functionally constrained.
The framework provides residue-level mechanistic insights.

Conclusions:

EvoMut offers a practical framework for rational protein design to enhance oxidative stability.
The tool aids in making informed decisions for engineering proteins resistant to oxidation.
EvoMut is available as a web server at https://evomut.org.