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Non-catalytic binding sites induce weaker long-range evolutionary rate gradients than catalytic sites in enzymes

By Avital Sharir-Ivry, Yu Xia

Posted 19 Feb 2019
bioRxiv DOI: 10.1101/554436 (published DOI: 10.1016/j.jmb.2019.07.019)

Enzymes exhibit strong long-range evolutionary constraint that extends from their catalytic site and affects even distant sites, yet it remains unclear how the biological function of different sites affects the magnitude of evolutionary rate gradients they induce. Here, we calculate the evolutionary rate (dN/dS) of sites as a function of distance from different binding sites: catalytic sites, non-catalytic ligand binding sites, allosteric binding sites and protein-protein interaction sites. We show that catalytic sites induce significantly stronger evolutionary rate gradient than all other functional sites. Notably, weak long-range evolutionary rate gradients from non-catalytic binding sites on enzymes resemble those from ligand binding sites on non-enzymes. Our results suggest that enzymes and non-enzymes share similar evolutionary constraints only when examined from the perspective of non-catalytic functional sites, and that the unique evolutionary rate gradient from catalytic sites is likely driven by the optimization of catalysis rather than ligand binding and allosteric functions.

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