Functional Plasticity and Evolutionary Adaptation of Allosteric Regulation

Abstract

Allostery is a fundamental regulatory mechanism of protein function. Despite notable advances, understanding the molecular determinants of allostery remains an elusive goal. Our current knowledge of allostery is principally shaped by a structure-centric view which makes it difficult to understand the decentralized character of allostery. We present a function-centric approach using deep mutational scanning to elucidate the molecular basis and underlying functional landscape of allostery. We show that allosteric signaling exhibits a high-degree of functional plasticity and redundancy through myriad mutational pathways. Residues critical for allosteric signaling are surprisingly poorly conserved while those required for structural integrity are highly conserved, suggesting evolutionary pressure to preserve fold over function. Our results suggest multiple solutions to the thermodynamic conditions of cooperativity, in contrast to the common view of a finely-tuned allosteric residue network maintained under selection.

The genotype‐phenotype landscape of an allosteric protein

“…Only 0.57% (12 of 2,101) of double amino acid substitutions in the measured data have EC 50 values that differ from the log‐additive effects of the single substitutions by more than 2.5‐fold (Fig 4). This result, combined with the wide distribution of residues that affect EC 50 , reinforces the view that allostery is a distributed biophysical phenomenon controlled by a free energy balance with additive contributions from many residues and interactions, a mechanism proposed previously (Marzen et al, 2013; Motlagh et al, 2014) and supported by other recent studies (Leander et al, 2020), rather than a process driven by the propagation of local, contiguous structural rearrangements along a defined pathway.…”

“…Only 0.57% (12 of 2,101) of double amino acid substitutions in the measured data have EC 50 values that differ from the log-additive effects of the single substitutions by more than 2.5-fold (Fig 4). This result, combined with the wide distribution of residues that affect EC 50 , reinforces the view that allostery is a distributed biophysical phenomenon controlled by a free energy balance with additive contributions from many residues and interactions, a mechanism proposed previously (Marzen et al, 2013;Motlagh et al, 2014) and supported by other recent studies (Leander et al, 2020), rather than a process driven by the propagation of local, contiguous structural rearrangements along a defined pathway. The log-additive EC 50 for double-substitution LacI variants (i.e., two amino acid substitutions) was calculated assuming log-additivity of the effect of each single substitution on the EC 50 relative to wild-type LacI: log(EC 50,AB / EC 50,wt ) = log(EC 50,A /EC 50,wt ) + log(EC 50,B /EC 50,wt ), where "wt" indicates the wild type, "A" and "B" indicate the single-substitution variants, and "AB" indicates the double-substitution variant.…”

“…However, in the absence of data, the effect of any particular substitution on the biophysical parameters is unpredictable. Furthermore, substitutions distal to the active sites of a biomolecule can strongly affect allosteric function (Taylor et al, 2016; Leander et al, 2020). Consequently, to develop a more predictive understanding of allostery will require large‐scale, quantitative measurements of changes to an allosteric dose‐response curve resulting from wide‐spread substitutions.…”

Comparative Perturbation-Based Modeling of the SARS-CoV-2 Spike Protein Binding with Host Receptor and Neutralizing Antibodies : Structurally Adaptable Allosteric Communication Hotspots Define Spike Sites Targeted by Global Circulating Mutations

“…These results bear some significance and support the latest illuminating study suggesting a model functional plasticity and evolutionary adaptation of allosteric regulation. 156 This function-centric model of allostery revealed a remarkable functional plasticity of allosteric switches allowing modulate and restore regulatory activity antibodies were built using a graph-based representation of protein structures in which residue nodes are interconnected through both dynamic 134 and coevolutionary correlations. 135 Using community decomposition, the residue interaction networks were further divided into local stable interaction modules in which residues are densely interconnected and highly correlated during simulations, while different communities are connected through long-range couplings.…”

Structurally Distributed Surface Sites Tune Allosteric Regulation

“…Given the finding that stabilizing mutations can often improve protein evolvability [53][54][55], it would be interesting to examine how the distribution of mutational effects on both DL121 function and allostery would change in the background of a stability (and/or activity) enhancing mutation to DL121. [56]. In that study a "disrupt-and-restore" strategy was used:…”