Evolutionary Divergent Suppressor Mutations in Conformational Diseases

Abstract

Neutral and adaptive mutations are key players in the evolutionary dynamics of proteins at molecular, cellular and organismal levels. Conversely, largely destabilizing mutations are rarely tolerated by evolution, although their occurrence in diverse human populations has important roles in the pathogenesis of conformational diseases. We have recently proposed that divergence at certain sites from the consensus (amino acid) state during mammalian evolution may have rendered some human proteins more vulnerable towards disease-associated mutations, primarily by decreasing their conformational stability. We herein extend and refine this hypothesis discussing results from phylogenetic and structural analyses, structure-based energy calculations and structure-function studies at molecular and cellular levels. As proof-of-principle, we focus on different mammalian orthologues of the NQO1 (NAD(P)H:quinone oxidoreductase 1) and AGT (alanine:glyoxylate aminotransferase) proteins. We discuss the different loss-of-function pathogenic mechanisms associated with diseases involving the two enzymes, including enzyme inactivation, accelerated degradation, intracellular mistargeting, and aggregation. Last, we take into account the potentially higher robustness of mammalian orthologues containing certain consensus amino acids as suppressors of human disease, and their relation with different intracellular post-translational modifications and protein quality control capacities, to be discussed as sources of phenotypic variability between human and mammalian models of disease and as tools for improving current therapeutic approaches.

The Catalytic Cycle of the Antioxidant and Cancer-Associated Human NQO1 Enzyme: Hydride Transfer, Conformational Dynamics and Functional Cooperativity

“…Our understanding of the roles of the multifunctional NQO1 protein in many physiological and pathological states, particularly in those associated with oxidative insults such as cancer and neurological disorders, is growing steadily [ 1 , 2 , 4 , 16 ]. In addition, NQO1 is an excellent example of an oligomeric human protein in which functional ligands exert remarkable cooperative effects with important implications for the understanding of how human genetic variability, divergent evolution and post-translational modifications shape the complex functional chemistry of multifunctional proteins [ 2 , 28 , 31 , 34 , 42 , 50 , 51 , 54 , 55 , 56 , 57 , 83 ]. We provide here a kinetic analysis of the oxidoreductase cycle of NQO1 in unprecedented detail.…”

NAD(P)H quinone oxidoreductase (NQO1): an enzyme which needs just enough mobility, in just the right places

“…Interestingly, most of the effects of p.P187S and the suppressor mutations seem to operate through the apo-state conformational ensemble, which is characterised by low conformational stability and high conformational dynamics, suggesting that most of these mutational effects have dynamic as well as structural basis [19,81,82,84]. It is also worth noting that rodent NQO1 contains by default the suppressor amino acids Gln-247 and Arg-80, which suggested that some mammalian NQO1 orthologues (containing these consensus amino acids) would be more robust that the human enzyme towards p.P187S through the presence of these evolutionary divergent gatekeeper amino acids in conformational and dynamic terms [82,86].…”

Targeting HIF-1α Function in Cancer through the Chaperone Action of NQO1

“…The association of NQO1 activity with several human diseases with a huge social impact, particularly cancer, HIV infection and neurological and cardiovascular diseases, has attracted the attention towards the effects of naturally-occurring single amino acid changes on NQO1 and the predisposition provided by these changes towards disease [76,79,116,119,122,123,130,133,136,137,138,139,140,141]. There are 106 missense variants described in human population (ExAC and gnomAD databases; https://gnomad.broadinstitute.org/gene/ENSG00000181019?dataset=gnomad_r2_1) and 47 missense variants in the COSMIC database (https://cancer.sanger.ac.uk/cosmic/gene/analysis?ln=NQO1#variants).…”

“…This seems to be paradoxical, because P187 is fully buried in the protein structure, close to the NQO1 dimer interface and belongs to the minimally stable core of NQO1apo, and thus, a mutation to serine should have catastrophic effects on protein structure and function [129,136]. Detailed biochemical, biophysical, computational and mutational studies have shown that the effects of p.P187S are pleiotropic in the structure, function and stability of NQO1apo and NQO1holo, highlighting the critical role of propagation of the local stability effects due to p.P187S to long distances in the protein structure and affecting the dynamics and stability of critical regions of NQO1 function [78,79,90,119,120,122,131,133,136,137]. These studies on p.P187S have also supported that different functional sites located far (over 10-20 Å ) in the structure are functionally and energetically coupled, and thus, we might modify the interaction of NQO1 with its partners by using an allosteric site (i.e.…”