mtProtEvol

mtProtEvol analyzes protein evolution in vertebrate mitochondria by comparing amino acid replacement rates with residue solvent accessibility (RSA) to infer heterotachy and intra-protein epistatic interactions.

Key Features:

• RSA-Based Evolutionary Analysis: Uses residue solvent accessibility (RSA) as a proxy for protein fitness and to compare RSA changes with amino acid replacement rates.
• Heterotachy and Epistatic Interaction Detection: Identifies shifts in heterotachy driven by intra-protein epistatic interactions through RSA–replacement rate comparisons.
• Computational Efficiency via Integrated Pipeline: Implements a software pipeline that integrates RSA data and phylogenetic methods to reduce computational demands for epistasis-related analyses.
• Extensive Vertebrate Mitochondrial Dataset: Includes evolutionary analyses for 512 protein families associated with mitochondrial functions in vertebrates.
• Data Randomization for Statistical Assessment: Employs data randomization as part of its analytical approach to assess significance of RSA-related evolutionary shifts.

Scientific Applications:

• Functional Category Analysis: Assesses how functional categories of mitochondria-related proteins experience different selection pressures, for example rodents exhibit accelerated RSA evolution in enzymes of the Krebs cycle, respiratory chain, and reactive oxygen species metabolism while primates exhibit accelerated RSA evolution in stress-response, translation, and mitochondrial DNA integrity functions.
• Comparative Evolutionary Studies: Enables comparisons of evolutionary patterns between vertebrate lineages (for example, rodents and primates) to investigate the influence of metabolic rate and lifespan on protein evolution.

Methodology:

Compares evolutionary rates of amino acid replacements with RSA changes using phylogenetic approaches and data randomization within an integrated software pipeline.