mtProtEvol: the resource presenting molecular evolution analysis of proteins involved in the function of Vertebrate mitochondria

BMC Evolutionary Biology
Anastasia A KuzminkovaKonstantin V Gunbin

Abstract

Heterotachy is the variation in the evolutionary rate of aligned sites in different parts of the phylogenetic tree. It occurs mainly due to epistatic interactions among the substitutions, which are highly complex and make it difficult to study protein evolution. The vast majority of computational evolutionary approaches for studying these epistatic interactions or their evolutionary consequences in proteins require high computational time. However, recently, it has been shown that the evolution of residue solvent accessibility (RSA) is tightly linked with changes in protein fitness and intra-protein epistatic interactions. This provides a computationally fast alternative, based on comparison of evolutionary rates of amino acid replacements with the rates of RSA evolutionary changes in order to recognize any shifts in epistatic interaction. Based on RSA information, data randomization and phylogenetic approaches, we constructed a software pipeline, which can be used to analyze the evolutionary consequences of intra-protein epistatic interactions with relatively low computational time. We analyzed the evolution of 512 protein families tightly linked to mitochondrial function in Vertebrates and created "mtProtEvol", the web resour...Continue Reading

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Citations

Aug 1, 2019·Systematic Biology·Stephen M CrottyArndt Von Haeseler
Mar 1, 2019·BMC Evolutionary Biology·Yuriy L OrlovLeonid L Moroz

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Methods Mentioned

BETA
protein folding
RSA
PAA

Software Mentioned

Archaeopteryx
SCRATCH
STRING
PhyML
Primata
Apache server
ENSEMBL
MySQL
Procov
MSAViewer

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