Experimental and computational evidence on conformational fluctuations as a source of catalytic defects in genetic diseases

Fuchs, Julian E.; Muñoz, Inés G.; Timson, David J.; Pey, Ángel L.

doi:10.1039/c6ra05499d

Cited by 8 publications

(7 citation statements)

References 57 publications

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“…The analyses described so far with NQO1 and AGT suggest that recent divergence (over the last 50 Myr) in key consensus amino acids may have rendered these two proteins more vulnerable against disease-associated mutations. Similar consensus analyses, not yet experimentally verified, point to a similar scenario for human UDP-glucose 4-epimerase (GALE) ( Figure 5 ), a metabolic enzyme associated with LOF inherited galactosemia due to structural destabilization and altered protein dynamics [ 78 , 79 , 80 ]. It must be emphasized that divergence from the consensus state at these sites in human NQO1 and AGT had no large effects on many traits of these proteins, including intracellular activity, folding, stability, trafficking or protein:protein interactions [ 21 , 74 ].…”

Section: Evolutionary Divergence In Key Compensatory Consensus Amimentioning

confidence: 62%

Evolutionary Divergent Suppressor Mutations in Conformational Diseases

Mesa‐Torres

Betancor-Fernández

Oppici

et al. 2018

Genes

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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.

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Section: Evolutionary Divergence In Key Compensatory Consensus Amimentioning

confidence: 62%

Evolutionary Divergent Suppressor Mutations in Conformational Diseases

Mesa‐Torres

Betancor-Fernández

Oppici

et al. 2018

Genes

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“…The decay of the full-length protein was fitted using a single exponential function to provide the first-order kinetic constant k obs , whereas the second-order rate constant k prot was determined by calculating the slope of the linear fit of k obs vs. thermolysin concentration. Changes in local stability of the primary cleavage site upon mutation ∆∆G prot(WT-mut) were determined by the following equation [73]:…”

Section: In Vitro Characterization Of Purified Proteinsmentioning

confidence: 99%

Naturally-Occurring Rare Mutations Cause Mild to Catastrophic Effects in the Multifunctional and Cancer-Associated NQO1 Protein

Pacheco-García

Cano-Muñoz

Sánchez-Ramos

et al. 2020

JPM

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The functional and pathological implications of the enormous genetic diversity of the human genome are mostly unknown, primarily due to our unability to predict pathogenicity in a high-throughput manner. In this work, we characterized the phenotypic consequences of eight naturally-occurring missense variants on the multifunctional and disease-associated NQO1 protein using biophysical and structural analyses on several protein traits. Mutations found in both exome-sequencing initiatives and in cancer cell lines cause mild to catastrophic effects on NQO1 stability and function. Importantly, some mutations perturb functional features located structurally far from the mutated site. These effects are well rationalized by considering the nature of the mutation, its location in protein structure and the local stability of its environment. Using a set of 22 experimentally characterized mutations in NQO1, we generated experimental scores for pathogenicity that correlate reasonably well with bioinformatic scores derived from a set of commonly used algorithms, although the latter fail to semiquantitatively predict the phenotypic alterations caused by a significant fraction of mutations individually. These results provide insight into the propagation of mutational effects on multifunctional proteins, the implementation of in silico approaches for establishing genotype-phenotype correlations and the molecular determinants underlying loss-of-function in genetic diseases.

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“…mutations and polymorphisms) affect protein activity, regulation and stability 17 18 19 20 21 22 . However, allosteric site-to-site communication underlying loss-of-function genetic variations has rarely been investigated in multi-domain oligomeric proteins 23 24 25 . Here, we hypothesize that the cancer-associated single nucleotide polymorphism p.P187S (rs1800566/c.C609T) in the NADP(H):quinone oxidoreductase 1 (NQO1; EC 1.6.5.2) mediates enzyme loss-of-function through long-range site-to-site effects originating at the p.P187S site and communicated to distant functional sites through a hypothetical allosteric interaction network ( Fig.…”

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confidence: 99%

Site-to-site interdomain communication may mediate different loss-of-function mechanisms in a cancer-associated NQO1 polymorphism

Medina‐Carmona

Neira

Salido

et al. 2017

Sci Rep

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Disease associated genetic variations often cause intracellular enzyme inactivation, dysregulation and instability. However, allosteric communication of mutational effects to distant functional sites leading to loss-of-function remains poorly understood. We characterize here interdomain site-to-site communication by which a common cancer-associated single nucleotide polymorphism (c.C609T/p.P187S) reduces the activity and stability in vivo of NAD(P)H:quinone oxidoreductase 1 (NQO1). NQO1 is a FAD-dependent, two-domain multifunctional stress protein acting as a Phase II enzyme, activating cancer pro-drugs and stabilizing p53 and p73α oncosuppressors. We show that p.P187S causes structural and dynamic changes communicated to functional sites far from the mutated site, affecting the FAD binding site located at the N-terminal domain (NTD) and accelerating proteasomal degradation through dynamic effects on the C-terminal domain (CTD). Structural protein:protein interaction studies reveal that the cancer-associated polymorphism does not abolish the interaction with p73α, indicating that oncosuppressor destabilization largely mirrors the low intracellular stability of p.P187S. In conclusion, we show how a single disease associated amino acid change may allosterically perturb several functional sites in an oligomeric and multidomain protein. These results have important implications for the understanding of loss-of-function genetic diseases and the identification of novel structural hot spots as targets for pharmacological intervention.

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Experimental and computational evidence on conformational fluctuations as a source of catalytic defects in genetic diseases

Cited by 8 publications

References 57 publications

Evolutionary Divergent Suppressor Mutations in Conformational Diseases

Evolutionary Divergent Suppressor Mutations in Conformational Diseases

Naturally-Occurring Rare Mutations Cause Mild to Catastrophic Effects in the Multifunctional and Cancer-Associated NQO1 Protein

Site-to-site interdomain communication may mediate different loss-of-function mechanisms in a cancer-associated NQO1 polymorphism

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