Residue mobility has decreased during protein evolution

TL;DR

This study analyzes how residue mobility in proteins has decreased over evolutionary time, revealing trends in flexibility changes across different structural domains and classes, with implications for understanding protein evolution.

Contribution

It provides a comprehensive analysis of residue B-Factors across multiple protein domains and classes, highlighting evolutionary trends in residue flexibility and structural constraints.

Findings

Residue mobility has decreased during protein evolution.

Flexibility trends vary among structural classes and residues.

Alpha by beta proteins show more stringent evolutionary constraints.

Abstract

Upon studying the B-Factors of all the atoms of all non-redundant proteins belonging to 76 most commonly found structural domains of all four major structural classes, it was found that the residue mobility has decreased during the course of evolution. Though increased residue-flexibility was preferred in the early stages of protein structure evolution, less flexibility is preferred in the medieval and recent stages. GLU is found to be the most flexible residue while VAL recorded to have the least flexibility. General trends in decrement of B-Factors conformed to the general trend in the order of emergence of protein structural domains. Decrement of B-Factor is observed to be most decisive (monotonic and uniform) for VAL, while evolution of CYS and LYS flexibility is found to be most skewed. Barring CYS, flexibility of all the residues is found to have increased during evolution of alpha by beta folds, however flexibility of all the residues (barring CYS) is found to have decreased during evolution of all beta folds. Only in alpha by beta folds the tendency of preferring higher residue mobility could be observed, neither alpha plus beta, nor all alpha nor all beta folds were found to support higher residue-mobility. In all the structural classes, the effect of evolutionary constraint on polar residues is found to follow an exactly identical trend as that on hydrophobic residues, only the extent of these effects are found to be different. Though protein size is found to be decreasing during evolution, residue mobility of proteins belonging to ancient and old structural domains showed strong positive dependency upon protein size, however for medieval and recent domains such dependency vanished. It is found that to optimize residue fluctuations, alpha by beta class of proteins are subjected to more stringent evolutionary constraints.