Comparative analysis of sequence covariation methods to mine evolutionary hubs: Examples from selected GPCR families

Abstract

Covariation between positions in a multiple sequence alignment may reflect structural, functional, and/or phylogenetic constraints and can be analyzed by a wide variety of methods. We explored several of these methods for their ability to identify covarying positions related to the divergence of a protein family at different hierarchical levels. Specifically, we compared seven methods on a model system composed of three nested sets of G-protein-coupled receptors (GPCRs) in which a divergence event occurred. The covariation methods analyzed were based on: χ2 test, mutual information, substitution matrices, and perturbation methods. We first analyzed the dependence of the covariation scores on residue conservation (measured by sequence entropy), and then we analyzed the networking structure of the top pairs. Two methods out of seven--OMES (Observed minus Expected Squared) and ELSC (Explicit Likelihood of Subset Covariation)--favored pairs with intermediate entropy and a networking structure with a central residue involved in several high-scoring pairs. This networking structure was observed for the three sequence sets. In each case, the central residue corresponded to a residue known to be crucial for the evolution of the GPCR family and the subfamily specificity. These central residues can be viewed as evolutionary hubs, in relation with an epistasis-based mechanism of functional divergence within a protein family.

Applications of sequence coevolution in membrane protein biochemistry

“…MI can reveal residue pairs and networks with functional importance, such as protein-protein interaction interfaces and catalytic sites [49-53]. For example, a structure-based correlated mutation analysis (SCMA) approach, using MI to score coevolving residue pairs, identified the retinal binding site residues in the G-protein coupled receptor rhodopsin [54].…”

Effect of hepatitis B virus (HBV) surface‐gene variability on markers of replication during treated human immunodeficiency virus‐HBV infection in Western Africa

“…From aligned sequences, covariation between pairs of S ‐gene aa was calculated using McLauchlan‐Based Substitution Correlation (McBASC) method from the “Bios2cor” package in R (v3.4.1, R Foundation for Statistical Computing, Vienna, Austria). This method was chosen over other covariation estimation methods due to the suspected low connectivity of aa pairs and lack of a central residue . Highly covarying aa pairs were identified as having a McBASC ≥|1| and were further used to examine networks of mutations using Cytoscape v3.6.1 .…”

“…If an aa at a given position was different than the consensus sequence, a mutation was considered present at this position. Antiviral resistance mutations on the pol-gene were defined in function of associated agent: LAM (rtV173L, rtL180M, rtM204V/I); adefovir (rtA181T/V, rtN236T); en- 21 Highly covarying aa pairs were identified as having a McBASC ≥|1| and were further used to examine networks of mutations using Cytoscape v3.6.1. 22 Clusters of highly correlated mutation networks were derived using the clusterMaker2 app v1.2.1 available in Cytoscape.…”

Functional roles of evolutionary conserved motifs and residues in vertebrate chemokine receptors

“…Recently, covarying residues that are related to the diversification of the chemokine receptor family have been identified by analyzing a multiple sequence alignment of the human chemokine receptors [56]. The residue at 2.49, Ala or Ser, is a central residue working as a "hub" in the network of covarying residues.…”

“…The residue at 2.49 thus differentiates the chemokine receptors into 2 groups. The residue covaries with 9 residues with high connectivity, 6 of them residing in TM-III [56], which plays a key role in the structural rearrangements of the helix bundle during the receptor activation [57]. Although Cys6.47 and Trp6.48 are not included in the 9 residues, both residues are among the network containing the 9 covarying residues.…”