Active Site-Induced Evolutionary Constraints Follow Fold Polarity Principles in Soluble Globular Enzymes

Abstract

A recent analysis of evolutionary rates in >500 globular soluble enzymes revealed pervasive conservation gradients toward catalytic residues. By looking at amino acid preference profiles rather than evolutionary rates in the same data set, we quantified the effects of active sites on site-specific constraints for physicochemical traits. We found that conservation gradients respond to constraints for polarity, hydrophobicity, flexibility, rigidity and structure in ways consistent with fold polarity principles; while sites far from active sites seem to experience no physicochemical constraint, rather being highly variable and favoring amino acids of low metabolic cost. Globally, our results highlight that amino acid variation contains finer information about protein structure than usually regarded in evolutionary models, and that this information is retrievable automatically with simple fits. We propose that analyses of the kind presented here incorporated into models of protein evolution should allow for better description of the physical chemistry that underlies molecular evolution.

The Natterin Proteins Diversity: A Review on Phylogeny, Structure, and Immune Function

“…Then, we found that the two hydroxylated amino acid residues of threonine (T) and serine (S) that flanked the AGIP motif located in the insertion membrane of Natterin-1 and Natterin-2 was conserved in all sequences, except in Natterin-like sequences of Acanthochromis polyacanthus that was replaced by lysine (K) and glutamic acid (E) residues, which demonstrated low and intermediate flexibility features, respectively [ 81 ]. In comparison to Natterin-4, the threonine (T) residues were replaced by serine (S) in seven Natterin-like sequences of T. amazonica and one sequence of Paramormyrops kingsleyae .…”

“…Mayorov, Dal Peraro and Abriata [ 81 ] demonstrated that sites that favor flexibility display variable degrees of solvent exposure and intermediate to high conservation, suggesting their relevance for protein fitness. Flexibility might be required to modulate receptor selectivity, and binding stabilized by hydrophobic contacts and rigid amino acids.…”

Understanding the origins of loss of protein function by analyzing the effects of thousands of variants on activity and abundance

“…The relatively tight confinement of these low-activity/high-abundance positions may also explain why predictions of changes in protein stability can be used to predict a substantial number of disease variants: At least in NUDT15 and PTEN the number of positions where substitutions typically cause loss of abundance (and thereby activity) is greater than the number of positions where substitutions cause loss of activity while retaining protein abundance. Indeed, while functional sites induce substantial constraints on amino acid variation during evolution, the strongest effects are those closest to the active sites ( Jack et al, 2016 ; Mayorov et al, 2019 ). Our ability to predict these sites by combining evolutionary analysis and stability calculations also suggest an approach for discovering new functionally-important sites using a combined analysis of protein structure and sequences.…”

Counterintuitive structural and functional effects due to naturally occurring mutations targeting the active site of the disease‐associated NQO1 enzyme*

“…Based on different bioinformatic predictive tools, all mutations are expected to be largely deleterious except p.H162N (Table 1). Since the mutated sites are highly conserved, this set of naturally occurring mutations in the active site of NQO1 should affect function mostly due to the changes in charge, polarity and hydrophobicity [24].…”