%MinMax: A versatile tool for calculating and comparing synonymous codon usage and its impact on protein folding

Area of Science:

• Molecular Biology
• Bioinformatics
• Protein Engineering

Background:

• Synonymous codons are not used equally in most organisms, indicating non-random usage patterns under selection.
• Variations in codon usage can influence protein folding efficiency and impact the yield of functional proteins.
• Understanding codon usage is crucial for protein chemists, biophysicists, and structural biologists aiming for high-yield protein production.

Purpose of the Study:

• To introduce %MinMax, a web-based and downloadable codon usage calculator.
• To provide a tool for evaluating synonymous codon usage patterns against a null model.
• To offer a method for harmonizing codon usage frequencies for heterologous gene expression.

Main Methods:

• The %MinMax tool analyzes synonymous codon usage frequencies for a given protein sequence.
• It compares observed codon usage against a rigorous null model.
• The tool can utilize user-provided codon frequency tables for any genome.

Main Results:

• %MinMax evaluates codon usage patterns without assuming effects of tRNA concentrations or translation rates.
• The tool's output can predict the impact of synonymous codon substitutions on cotranslational folding.
• A calculation within %MinMax aids in harmonizing codon usage for heterologous gene expression.

Conclusions:

• %MinMax is a valuable resource for analyzing codon usage patterns relevant to protein production.
• The tool facilitates the prediction of folding efficiency changes due to codon substitutions.
• It offers practical applications for optimizing gene expression in biotechnology.