1
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Vankova P, Pacheco-Garcia JL, Loginov DS, Gómez-Mulas A, Kádek A, Martín-Garcia JM, Salido E, Man P, Pey AL. Insights into the pathogenesis of primary hyperoxaluria type I from the structural dynamics of alanine:glyoxylate aminotransferase variants. FEBS Lett 2024; 598:485-499. [PMID: 38243391 DOI: 10.1002/1873-3468.14800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/06/2023] [Accepted: 12/20/2023] [Indexed: 01/21/2024]
Abstract
Primary hyperoxaluria type I (PH1) is caused by deficient alanine:glyoxylate aminotransferase (AGT) activity. PH1-causing mutations in AGT lead to protein mistargeting and aggregation. Here, we use hydrogen-deuterium exchange (HDX) to characterize the wild-type (WT), the LM (a polymorphism frequent in PH1 patients) and the LM G170R (the most common mutation in PH1) variants of AGT. We provide the first experimental analysis of AGT structural dynamics, showing that stability is heterogeneous in the native state and providing a blueprint for frustrated regions with potentially functional relevance. The LM and LM G170R variants only show local destabilization. Enzymatic transamination of the pyridoxal 5-phosphate cofactor bound to AGT hardly affects stability. Our study, thus, supports that AGT misfolding is not caused by dramatic effects on structural dynamics.
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Affiliation(s)
- Pavla Vankova
- Institute of Biotechnology - BioCeV, Academy of Sciences of the Czech Republic, Vestec, Czech Republic
| | | | - Dmitry S Loginov
- Institute of Microbiology - BioCeV, Academy of Sciences of the Czech Republic, Vestec, Czech Republic
| | | | - Alan Kádek
- Institute of Microbiology - BioCeV, Academy of Sciences of the Czech Republic, Vestec, Czech Republic
| | - José Manuel Martín-Garcia
- Department of Crystallography & Structural Biology, Institute of Physical Chemistry Blas Cabrera, Spanish National Research Council (CSIC), Madrid, Spain
| | - Eduardo Salido
- Center for Rare Diseases (CIBERER), Hospital Universitario de Canarias, Universidad de la Laguna, Tenerife, Spain
| | - Petr Man
- Institute of Microbiology - BioCeV, Academy of Sciences of the Czech Republic, Vestec, Czech Republic
| | - Angel L Pey
- Departamento de Química Física, Unidad de Excelencia en Química Aplicada a Biomedicina y Medioambiente e Instituto de Biotecnología, Universidad de Granada, Spain
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2
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Yuhan L, Khaleghi Ghadiri M, Gorji A. Impact of NQO1 dysregulation in CNS disorders. J Transl Med 2024; 22:4. [PMID: 38167027 PMCID: PMC10762857 DOI: 10.1186/s12967-023-04802-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 12/12/2023] [Indexed: 01/05/2024] Open
Abstract
NAD(P)H Quinone Dehydrogenase 1 (NQO1) plays a pivotal role in the regulation of neuronal function and synaptic plasticity, cellular adaptation to oxidative stress, neuroinflammatory and degenerative processes, and tumorigenesis in the central nervous system (CNS). Impairment of the NQO1 activity in the CNS can result in abnormal neurotransmitter release and clearance, increased oxidative stress, and aggravated cellular injury/death. Furthermore, it can cause disturbances in neural circuit function and synaptic neurotransmission. The abnormalities of NQO1 enzyme activity have been linked to the pathophysiological mechanisms of multiple neurological disorders, including Parkinson's disease, Alzheimer's disease, epilepsy, multiple sclerosis, cerebrovascular disease, traumatic brain injury, and brain malignancy. NQO1 contributes to various dimensions of tumorigenesis and treatment response in various brain tumors. The precise mechanisms through which abnormalities in NQO1 function contribute to these neurological disorders continue to be a subject of ongoing research. Building upon the existing knowledge, the present study reviews current investigations describing the role of NQO1 dysregulations in various neurological disorders. This study emphasizes the potential of NQO1 as a biomarker in diagnostic and prognostic approaches, as well as its suitability as a target for drug development strategies in neurological disorders.
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Affiliation(s)
- Li Yuhan
- Epilepsy Research Center, Münster University, Münster, Germany
- Department of Breast Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | | | - Ali Gorji
- Epilepsy Research Center, Münster University, Münster, Germany.
- Department of Neurosurgery, Münster University, Münster, Germany.
- Shefa Neuroscience Research Center, Khatam Alanbia Hospital, Tehran, Iran.
- Neuroscience Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
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3
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Pintado-Grima C, Bárcenas O, Ventura S. Expanding the Landscape of Amyloid Sequences with CARs-DB: A Database of Polar Amyloidogenic Peptides from Disordered Proteins. Methods Mol Biol 2024; 2714:171-185. [PMID: 37676599 DOI: 10.1007/978-1-0716-3441-7_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
Several databases collecting amyloidogenic regions have been released to provide information on protein sequences able to form amyloid fibrils. However, most of these resources are built with data from experiments that detect highly hydrophobic stretches located within transiently exposed protein segments. We recently demonstrated that cryptic amyloidogenic regions (CARs) of polar nature have the potential to form amyloid fibrils in vitro. Given the underrepresentation of these types of sequences in current amyloid databases, we developed CARs-DB, the first repository that collects thousands of predicted CARs from intrinsically disordered regions. This protocol chapter describes how to use CARs-DB to search for sequences of interest that might be connected to disease or functional protein-protein interactions. In addition, we provide study cases to illustrate the database's features to users. The CARs-DB is readily accessible at http://carsdb.ppmclab.com/ .
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Affiliation(s)
- Carlos Pintado-Grima
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Oriol Bárcenas
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain.
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4
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Gatticchi L, Dindo M, Pampalone G, Conter C, Cellini B, Takayama T. Biochemical and cellular effects of a novel missense mutation of the AGXT gene associated with Primary Hyperoxaluria Type 1. Biochem Biophys Res Commun 2023; 645:118-123. [PMID: 36682331 DOI: 10.1016/j.bbrc.2023.01.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 01/14/2023] [Indexed: 01/15/2023]
Abstract
Primary Hyperoxaluria Type 1 (PH1) is a rare autosomal disease caused by mutations in AGXT that lead to the deficiency of alanine:glyoxylate aminotransferase (AGT). AGT is a liver pyridoxal 5'-phosphate (PLP)-dependent enzyme that detoxifies glyoxylate inside peroxisomes. The lack of AGT activity results in a build-up of glyoxylate that is oxidized to oxalate, then culminating in hyperoxaluria often leading to kidney failure. Most pathogenic mutations reduce AGT specific activity because of catalytic defects, improper folding, mistargeting to mitochondria, reduced intracellular stability, dimerization, and/or aggregation. Administration of pyridoxine (PN), a precursor of PLP, is a therapeutic option available for PH1 patients carrying responsive genotypes through the ability of the coenzyme to behave as a chaperone. Here, we report the clinical and biochemical characterization of the novel mutation c.1093G > T (p.Gly365Cys) identified in a Japanese patient. In silico studies predict that the p.Gly365Cys mutation causes a steric clash resulting in a local rearrangement of the region surrounding the active site, thus possibly affecting PLP binding and catalysis. Indeed, the purified p.Gly365Cys mutant displays proper folding but shows an extensive decrease of catalytic efficiency due to an altered PLP-binding. When expressed in AGXT1-KO HepG2 cells the variant shows reduced specific activity and protein levels in comparison with wild type AGT that cannot be rescued by PN treatment. Overall, our data indicate that the mutation of Gly365 induces a conformational change at the AGT active site translating into a functional and structural defect and allow to predict that the patients will not be responsive to vitamin B6, thus supporting the usefulness of preclinical studies to guide therapeutic decisions in the era of precision medicine.
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Affiliation(s)
- Leonardo Gatticchi
- Department of Medicine and Surgery, Physiology and Biochemistry Section, University of Perugia, 06132, Perugia, Italy.
| | - Mirco Dindo
- Department of Medicine and Surgery, Physiology and Biochemistry Section, University of Perugia, 06132, Perugia, Italy.
| | - Gioena Pampalone
- Department of Medicine and Surgery, Physiology and Biochemistry Section, University of Perugia, 06132, Perugia, Italy.
| | - Carolina Conter
- Laboratory of Biochemistry, Department of Biotechnology, University of Verona, 37134, Verona, Italy.
| | - Barbara Cellini
- Department of Medicine and Surgery, Physiology and Biochemistry Section, University of Perugia, 06132, Perugia, Italy.
| | - Tatsuya Takayama
- Department of Urology, Jichi Medical University, 329-0498, Tochigi, Japan; Department of Urology, International University of Health and Welfare Hospital, 329-2763, Tochigi, Japan.
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5
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Phenotypic Modulation of Cancer-Associated Antioxidant NQO1 Activity by Post-Translational Modifications and the Natural Diversity of the Human Genome. Antioxidants (Basel) 2023; 12:antiox12020379. [PMID: 36829939 PMCID: PMC9952366 DOI: 10.3390/antiox12020379] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 02/08/2023] Open
Abstract
Human NAD(P)H:quinone oxidoreductase 1 (hNQO1) is a multifunctional and antioxidant stress protein whose expression is controlled by the Nrf2 signaling pathway. hNQO1 dysregulation is associated with cancer and neurological disorders. Recent works have shown that its activity is also modulated by different post-translational modifications (PTMs), such as phosphorylation, acetylation and ubiquitination, and these may synergize with naturally-occurring and inactivating polymorphisms and mutations. Herein, I describe recent advances in the study of the effect of PTMs and genetic variations on the structure and function of hNQO1 and their relationship with disease development in different genetic backgrounds, as well as the physiological roles of these modifications. I pay particular attention to the long-range allosteric effects exerted by PTMs and natural variation on the multiple functions of hNQO1.
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6
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Molecular Mechanisms, Genotype-Phenotype Correlations and Patient-Specific Treatments in Inherited Metabolic Diseases. J Pers Med 2023; 13:jpm13010117. [PMID: 36675778 PMCID: PMC9864038 DOI: 10.3390/jpm13010117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023] Open
Abstract
Advances in DNA sequencing technologies are revealing a vast genetic heterogeneity in human population, which may predispose to metabolic alterations if the activity of metabolic enzymes is affected [...].
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Phosphorylation of Thr9 Affects the Folding Landscape of the N-Terminal Segment of Human AGT Enhancing Protein Aggregation of Disease-Causing Mutants. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27248762. [PMID: 36557898 PMCID: PMC9786777 DOI: 10.3390/molecules27248762] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/07/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022]
Abstract
The mutations G170R and I244T are the most common disease cause in primary hyperoxaluria type I (PH1). These mutations cause the misfolding of the AGT protein in the minor allele AGT-LM that contains the P11L polymorphism, which may affect the folding of the N-terminal segment (NTT-AGT). The NTT-AGT is phosphorylated at T9, although the role of this event in PH1 is unknown. In this work, phosphorylation of T9 was mimicked by introducing the T9E mutation in the NTT-AGT peptide and the full-length protein. The NTT-AGT conformational landscape was studied by circular dichroism, NMR, and statistical mechanical methods. Functional and stability effects on the full-length AGT protein were characterized by spectroscopic methods. The T9E and P11L mutations together reshaped the conformational landscape of the isolated NTT-AGT peptide by stabilizing ordered conformations. In the context of the full-length AGT protein, the T9E mutation had no effect on the overall AGT function or conformation, but enhanced aggregation of the minor allele (LM) protein and synergized with the mutations G170R and I244T. Our findings indicate that phosphorylation of T9 may affect the conformation of the NTT-AGT and synergize with PH1-causing mutations to promote aggregation in a genotype-specific manner. Phosphorylation should be considered a novel regulatory mechanism in PH1 pathogenesis.
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8
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Pacheco-Garcia JL, Cagiada M, Tienne-Matos K, Salido E, Lindorff-Larsen K, L. Pey A. Effect of naturally-occurring mutations on the stability and function of cancer-associated NQO1: Comparison of experiments and computation. Front Mol Biosci 2022; 9:1063620. [PMID: 36504709 PMCID: PMC9730889 DOI: 10.3389/fmolb.2022.1063620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 11/03/2022] [Indexed: 11/25/2022] Open
Abstract
Recent advances in DNA sequencing technologies are revealing a large individual variability of the human genome. Our capacity to establish genotype-phenotype correlations in such large-scale is, however, limited. This task is particularly challenging due to the multifunctional nature of many proteins. Here we describe an extensive analysis of the stability and function of naturally-occurring variants (found in the COSMIC and gnomAD databases) of the cancer-associated human NAD(P)H:quinone oxidoreductase 1 (NQO1). First, we performed in silico saturation mutagenesis studies (>5,000 substitutions) aimed to identify regions in NQO1 important for stability and function. We then experimentally characterized twenty-two naturally-occurring variants in terms of protein levels during bacterial expression, solubility, thermal stability, and coenzyme binding. These studies showed a good overall correlation between experimental analysis and computational predictions; also the magnitude of the effects of the substitutions are similarly distributed in variants from the COSMIC and gnomAD databases. Outliers in these experimental-computational genotype-phenotype correlations remain, and we discuss these on the grounds and limitations of our approaches. Our work represents a further step to characterize the mutational landscape of NQO1 in the human genome and may help to improve high-throughput in silico tools for genotype-phenotype correlations in this multifunctional protein associated with disease.
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Affiliation(s)
| | - Matteo Cagiada
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | | | - Eduardo Salido
- Center for Rare Diseases (CIBERER), Hospital Universitario de Canarias, Universidad de la Laguna, La Laguna, TenerifeTenerife, Spain
| | - Kresten Lindorff-Larsen
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | - Angel L. Pey
- Departamento de Química Física, Unidad de Excelencia en Química Aplicada a Biomedicina y Medioambiente e Instituto de Biotecnología, Universidad de Granada, Granada, Spain,*Correspondence: Angel L. Pey,
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9
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Targeting HIF-1α Function in Cancer through the Chaperone Action of NQO1: Implications of Genetic Diversity of NQO1. J Pers Med 2022; 12:jpm12050747. [PMID: 35629169 PMCID: PMC9146583 DOI: 10.3390/jpm12050747] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 04/25/2022] [Indexed: 02/04/2023] Open
Abstract
HIF-1α is a master regulator of oxygen homeostasis involved in different stages of cancer development. Thus, HIF-1α inhibition represents an interesting target for anti-cancer therapy. It was recently shown that the HIF-1α interaction with NQO1 inhibits proteasomal degradation of the former, thus suggesting that targeting the stability and/or function of NQO1 could lead to the destabilization of HIF-1α as a therapeutic approach. Since the molecular interactions of NQO1 with HIF-1α are beginning to be unraveled, in this review we discuss: (1) Structure–function relationships of HIF-1α; (2) our current knowledge on the intracellular functions and stability of NQO1; (3) the pharmacological modulation of NQO1 by small ligands regarding function and stability; (4) the potential effects of genetic variability of NQO1 in HIF-1α levels and function; (5) the molecular determinants of NQO1 as a chaperone of many different proteins including cancer-associated factors such as HIF-1α, p53 and p73α. This knowledge is then further discussed in the context of potentially targeting the intracellular stability of HIF-1α by acting on its chaperone, NQO1. This could result in novel anti-cancer therapies, always considering that the substantial genetic variability in NQO1 would likely result in different phenotypic responses among individuals.
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10
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Analysis of missense variants in the human genome reveals widespread gene-specific clustering and improves prediction of pathogenicity. Am J Hum Genet 2022; 109:457-470. [PMID: 35120630 PMCID: PMC8948164 DOI: 10.1016/j.ajhg.2022.01.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 01/11/2022] [Indexed: 12/11/2022] Open
Abstract
We used a machine learning approach to analyze the within-gene distribution of missense variants observed in hereditary conditions and cancer. When applied to 840 genes from the ClinVar database, this approach detected a significant non-random distribution of pathogenic and benign variants in 387 (46%) and 172 (20%) genes, respectively, revealing that variant clustering is widespread across the human exome. This clustering likely occurs as a consequence of mechanisms shaping pathogenicity at the protein level, as illustrated by the overlap of some clusters with known functional domains. We then took advantage of these findings to develop a pathogenicity predictor, MutScore, that integrates qualitative features of DNA substitutions with the new additional information derived from this positional clustering. Using a random forest approach, MutScore was able to identify pathogenic missense mutations with very high accuracy, outperforming existing predictive tools, especially for variants associated with autosomal-dominant disease and cancer. Thus, the within-gene clustering of pathogenic and benign DNA changes is an important and previously underappreciated feature of the human exome, which can be harnessed to improve the prediction of pathogenicity and disambiguation of DNA variants of uncertain significance.
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11
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Dindo M, Ambrosini G, Oppici E, Pey AL, O’Toole PJ, Marrison JL, Morrison IEG, Butturini E, Grottelli S, Costantini C, Cellini B. Dimerization Drives Proper Folding of Human Alanine:Glyoxylate Aminotransferase But Is Dispensable for Peroxisomal Targeting. J Pers Med 2021; 11:jpm11040273. [PMID: 33917320 PMCID: PMC8067440 DOI: 10.3390/jpm11040273] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 03/30/2021] [Accepted: 04/02/2021] [Indexed: 12/15/2022] Open
Abstract
Peroxisomal matrix proteins are transported into peroxisomes in a fully-folded state, but whether multimeric proteins are imported as monomers or oligomers is still disputed. Here, we used alanine:glyoxylate aminotransferase (AGT), a homodimeric pyridoxal 5′-phosphate (PLP)-dependent enzyme, whose deficit causes primary hyperoxaluria type I (PH1), as a model protein and compared the intracellular behavior and peroxisomal import of native dimeric and artificial monomeric forms. Monomerization strongly reduces AGT intracellular stability and increases its aggregation/degradation propensity. In addition, monomers are partly retained in the cytosol. To assess possible differences in import kinetics, we engineered AGT to allow binding of a membrane-permeable dye and followed its intracellular trafficking without interfering with its biochemical properties. By fluorescence recovery after photobleaching, we measured the import rate in live cells. Dimeric and monomeric AGT displayed a similar import rate, suggesting that the oligomeric state per se does not influence import kinetics. However, when dimerization is compromised, monomers are prone to misfolding events that can prevent peroxisomal import, a finding crucial to predicting the consequences of PH1-causing mutations that destabilize the dimer. Treatment with pyridoxine of cells expressing monomeric AGT promotes dimerization and folding, thus, demonstrating the chaperone role of PLP. Our data support a model in which dimerization represents a potential key checkpoint in the cytosol at the crossroad between misfolding and correct targeting, a possible general mechanism for other oligomeric peroxisomal proteins.
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Affiliation(s)
- Mirco Dindo
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (M.D.); (S.G.); (C.C.)
| | - Giulia Ambrosini
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy; (G.A.); (E.O.); (E.B.)
| | - Elisa Oppici
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy; (G.A.); (E.O.); (E.B.)
| | - Angel L. Pey
- Departamento de Química Física, Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain;
| | - Peter J. O’Toole
- Bioscience Technology Facility, Department of Biology, University of York, York YO23 3GE, UK; (P.J.O.); (J.L.M.); (I.E.G.M.)
| | - Joanne L. Marrison
- Bioscience Technology Facility, Department of Biology, University of York, York YO23 3GE, UK; (P.J.O.); (J.L.M.); (I.E.G.M.)
| | - Ian E. G. Morrison
- Bioscience Technology Facility, Department of Biology, University of York, York YO23 3GE, UK; (P.J.O.); (J.L.M.); (I.E.G.M.)
| | - Elena Butturini
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy; (G.A.); (E.O.); (E.B.)
| | - Silvia Grottelli
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (M.D.); (S.G.); (C.C.)
| | - Claudio Costantini
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (M.D.); (S.G.); (C.C.)
| | - Barbara Cellini
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (M.D.); (S.G.); (C.C.)
- Correspondence: ; Tel.: +39-075-585-8339
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12
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Pacheco-García JL, Cano-Muñoz M, Sánchez-Ramos I, Salido E, Pey AL. Naturally-Occurring Rare Mutations Cause Mild to Catastrophic Effects in the Multifunctional and Cancer-Associated NQO1 Protein. J Pers Med 2020; 10:E207. [PMID: 33153185 PMCID: PMC7711955 DOI: 10.3390/jpm10040207] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 10/27/2020] [Accepted: 11/02/2020] [Indexed: 12/13/2022] Open
Abstract
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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Affiliation(s)
- Juan Luis Pacheco-García
- Departamento de Química Física, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain; (J.L.P.-G.); (M.C.-M.); (I.S.-R.)
| | - Mario Cano-Muñoz
- Departamento de Química Física, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain; (J.L.P.-G.); (M.C.-M.); (I.S.-R.)
| | - Isabel Sánchez-Ramos
- Departamento de Química Física, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain; (J.L.P.-G.); (M.C.-M.); (I.S.-R.)
| | - Eduardo Salido
- Centre for Biomedical Research on Rare Diseases (CIBERER), Hospital Universitario de Canarias, 38320 Tenerife, Spain;
| | - Angel L. Pey
- Departamento de Química Física y Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
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13
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Pey AL. Towards Accurate Genotype-Phenotype Correlations in the CYP2D6 Gene. J Pers Med 2020; 10:jpm10040158. [PMID: 33049937 PMCID: PMC7711719 DOI: 10.3390/jpm10040158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 10/01/2020] [Indexed: 12/17/2022] Open
Abstract
Establishing accurate and large-scale genotype-phenotype correlations and predictions of individual response to pharmacological treatments are two of the holy grails of Personalized Medicine. These tasks are challenging and require an integrated knowledge of the complex processes that regulate gene expression and, ultimately, protein functionality in vivo, the effects of mutations/polymorphisms and the different sources of interindividual phenotypic variability. A remarkable example of our advances in these challenging tasks is the highly polymorphic CYP2D6 gene, which encodes a cytochrome P450 enzyme involved in the metabolization of many of the most marketed drugs (including SARS-Cov-2 therapies such as hydroxychloroquine). Since the introduction of simple activity scores (AS) over 10 years ago, its ability to establish genotype-phenotype correlations on the drug metabolizing capacity of this enzyme in human population has provided lessons that will help to improve this type of score for this, and likely many other human genes and proteins. Multidisciplinary research emerges as the best approach to incorporate additional concepts to refine and improve such functional/activity scores for the CYP2D6 gene, as well as for many other human genes associated with simple and complex genetic diseases.
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Affiliation(s)
- Angel L Pey
- Departamento de Química Física, Unidad de Excelencia de Química aplicada a Biomedicina y Medioambiente, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
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14
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Dindo M, Mandrile G, Conter C, Montone R, Giachino D, Pelle A, Costantini C, Cellini B. The ILE56 mutation on different genetic backgrounds of alanine:glyoxylate aminotransferase: Clinical features and biochemical characterization. Mol Genet Metab 2020; 131:171-180. [PMID: 32792227 DOI: 10.1016/j.ymgme.2020.07.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/30/2020] [Accepted: 07/30/2020] [Indexed: 01/20/2023]
Abstract
Primary Hyperoxaluria type I (PH1) is a rare disease caused by mutations in the AGXT gene encoding alanine:glyoxylate aminotransferase (AGT), a liver enzyme involved in the detoxification of glyoxylate, the failure of which results in accumulation of oxalate and kidney stones formation. The role of protein misfolding in the AGT deficit caused by most PH1-causing mutations is increasingly being recognized. In addition, the genetic background in which a mutation occurs is emerging as a critical risk factor for disease onset and/or severity. Based on these premises, in this study we have analyzed the clinical, biochemical and cellular effects of the p.Ile56Asn mutation, recently described in a PH1 patient, as a function of the residue at position 11, a hot-spot for both polymorphic (p.Pro11Leu) and pathogenic (p.Pro11Arg) mutations. We have found that the p.Ile56Asn mutation induces a structural defect mostly related to the apo-form of AGT. The effects are more pronounced when the substitution of Ile56 is combined with the p.Pro11Leu and, at higher degree, the p.Pro11Arg mutation. As compared with the non-pathogenic forms, AGT variants display reduced expression and activity in mammalian cells. Vitamin B6, a currently approved treatment for PH1, can overcome the effects of the p.Ile56Asn mutation only when it is associated with Pro at position 11. Our results provide a first proof that the genetic background influences the effects of PH1-causing mutations and the responsiveness to treatment and suggest that molecular and cellular studies can integrate clinical data to identify the best therapeutic strategy for PH1 patients.
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Affiliation(s)
- Mirco Dindo
- Department of Experimental Medicine, University of Perugia, Perugia, Italy
| | - Giorgia Mandrile
- Medical Genetics Unit, Department of Clinical and Biological Sciences, University of Torino, Orbassano (TO), Italy; Genetica e Thalassemia Unit, San Luigi University Hospital, Orbassano (TO), Italy
| | - Carolina Conter
- Department of Neurological, Biomedical, and Movement Sciences, University of Verona, Verona, Italy
| | - Rosa Montone
- Department of Neurological, Biomedical, and Movement Sciences, University of Verona, Verona, Italy
| | - Daniela Giachino
- Medical Genetics Unit, Department of Clinical and Biological Sciences, University of Torino, Orbassano (TO), Italy
| | - Alessandra Pelle
- Medical Genetics Unit, Department of Clinical and Biological Sciences, University of Torino, Orbassano (TO), Italy
| | - Claudio Costantini
- Department of Experimental Medicine, University of Perugia, Perugia, Italy
| | - Barbara Cellini
- Department of Experimental Medicine, University of Perugia, Perugia, Italy.
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15
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Anoz-Carbonell E, Timson DJ, Pey AL, Medina M. The Catalytic Cycle of the Antioxidant and Cancer-Associated Human NQO1 Enzyme: Hydride Transfer, Conformational Dynamics and Functional Cooperativity. Antioxidants (Basel) 2020; 9:E772. [PMID: 32825392 PMCID: PMC7554937 DOI: 10.3390/antiox9090772] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/11/2020] [Accepted: 08/18/2020] [Indexed: 12/11/2022] Open
Abstract
Human NQO1 [NAD(H):quinone oxidoreductase 1] is a multi-functional and stress-inducible dimeric protein involved in the antioxidant defense, the activation of cancer prodrugs and the stabilization of oncosuppressors. Despite its roles in human diseases, such as cancer and neurological disorders, a detailed characterization of its enzymatic cycle is still lacking. In this work, we provide a comprehensive analysis of the NQO1 catalytic cycle using rapid mixing techniques, including multiwavelength and spectral deconvolution studies, kinetic modeling and temperature-dependent kinetic isotope effects (KIEs). Our results systematically support the existence of two pathways for hydride transfer throughout the NQO1 catalytic cycle, likely reflecting that the two active sites in the dimer catalyze two-electron reduction with different rates, consistent with the cooperative binding of inhibitors such as dicoumarol. This negative cooperativity in NQO1 redox activity represents a sort of half-of-sites activity. Analysis of KIEs and their temperature dependence also show significantly different contributions from quantum tunneling, structural dynamics and reorganizations to catalysis at the two active sites. Our work will improve our understanding of the effects of cancer-associated single amino acid variants and post-translational modifications in this protein of high relevance in cancer progression and treatment.
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Affiliation(s)
- Ernesto Anoz-Carbonell
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, 50009 Zaragoza, Spain;
| | - David J. Timson
- School of Pharmacy and Biomolecular Sciences, The University of Brighton, Brighton BN2 4GJ, UK;
| | - Angel L. Pey
- Departamento de Química Física, Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, 50009 Zaragoza, Spain;
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16
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Gopi S, Devanshu D, Rajasekaran N, Anantakrishnan S, Naganathan AN. pPerturb: A Server for Predicting Long-Distance Energetic Couplings and Mutation-Induced Stability Changes in Proteins via Perturbations. ACS OMEGA 2020; 5:1142-1146. [PMID: 31984271 PMCID: PMC6977024 DOI: 10.1021/acsomega.9b03371] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 12/20/2019] [Indexed: 05/02/2023]
Abstract
The strength of intraprotein interactions or contact network is one of the dominant factors determining the thermodynamic stabilities of proteins. The nature and the extent of connectivity of this network also play a role in allosteric signal propagation characteristics upon ligand binding to a protein domain. Here, we develop a server for rapid quantification of the strength of an interaction network by employing an experimentally consistent perturbation approach previously validated against a large data set of 375 mutations in 19 different proteins. The web server can be employed to predict the extent of destabilization of proteins arising from mutations in the protein interior in experimentally relevant units. Moreover, coupling distances-a measure of the extent of percolation on perturbation-and overall perturbation magnitudes are predicted in a residue-specific manner, enabling a first look at the distribution of energetic couplings in a protein or its changes upon ligand binding. We show specific examples of how the server can be employed to probe for the distribution of local stabilities in a protein, to examine changes in side chain orientations or packing before and after ligand binding, and to predict changes in stabilities of proteins upon mutations of buried residues. The web server is freely available at http://pbl.biotech.iitm.ac.in/pPerturb and supports recent versions of all major browsers.
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Affiliation(s)
- Soundhararajan Gopi
- Department
of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras (IITM), Chennai 600036, India
| | - Devanshu Devanshu
- Department
of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras (IITM), Chennai 600036, India
| | - Nandakumar Rajasekaran
- Department
of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras (IITM), Chennai 600036, India
- Department
of Biology, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Sathvik Anantakrishnan
- Department
of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras (IITM), Chennai 600036, India
| | - Athi N. Naganathan
- Department
of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras (IITM), Chennai 600036, India
- E-mail:
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17
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Computational prediction and redesign of aberrant protein oligomerization. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 169:43-83. [DOI: 10.1016/bs.pmbts.2019.11.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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18
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Vankova P, Salido E, Timson DJ, Man P, Pey AL. A Dynamic Core in Human NQO1 Controls the Functional and Stability Effects of Ligand Binding and Their Communication across the Enzyme Dimer. Biomolecules 2019; 9:biom9110728. [PMID: 31726777 PMCID: PMC6921033 DOI: 10.3390/biom9110728] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/06/2019] [Accepted: 11/10/2019] [Indexed: 02/07/2023] Open
Abstract
Human NAD(P)H:quinone oxidoreductase 1 (NQO1) is a multi-functional protein whose alteration is associated with cancer, Parkinson's and Alzheimer´s diseases. NQO1 displays a remarkable functional chemistry, capable of binding different functional ligands that modulate its activity, stability and interaction with proteins and nucleic acids. Our understanding of this functional chemistry is limited by the difficulty of obtaining structural and dynamic information on many of these states. Herein, we have used hydrogen/deuterium exchange monitored by mass spectrometry (HDXMS) to investigate the structural dynamics of NQO1 in three ligation states: without ligands (NQO1apo), with FAD (NQO1holo) and with FAD and the inhibitor dicoumarol (NQO1dic). We show that NQO1apo has a minimally stable folded core holding the protein dimer, with FAD and dicoumarol binding sites populating binding non-competent conformations. Binding of FAD significantly decreases protein dynamics and stabilizes the FAD and dicoumarol binding sites as well as the monomer:monomer interface. Dicoumarol binding further stabilizes all three functional sites, a result not previously anticipated by available crystallographic models. Our work provides an experimental perspective into the communication of stability effects through the NQO1 dimer, which is valuable for understanding at the molecular level the effects of disease-associated variants, post-translational modifications and ligand binding cooperativity in NQO1.
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Affiliation(s)
- Pavla Vankova
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic;
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 128 43 Prague 2, Czech Republic
| | - Eduardo Salido
- Center for Rare Diseases (CIBERER), Hospital Universitario de Canarias, Universidad de La Laguna, 38320 Tenerife, Spain;
| | - David J. Timson
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Huxley Building, Lewes Road, Brighton BN2 4GJ, UK;
| | - Petr Man
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic;
- Correspondence: (P.M.); (A.L.P.)
| | - Angel L. Pey
- Department of Physical Chemistry and Unit of Excellence in Chemistry, University of Granada, Av. Fuentenueva s/n, E-18071 Granada, Spain
- Correspondence: (P.M.); (A.L.P.)
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19
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Beaver SK, Mesa-Torres N, Pey AL, Timson DJ. NQO1: A target for the treatment of cancer and neurological diseases, and a model to understand loss of function disease mechanisms. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:663-676. [PMID: 31091472 DOI: 10.1016/j.bbapap.2019.05.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 05/07/2019] [Accepted: 05/09/2019] [Indexed: 01/08/2023]
Abstract
NAD(P)H quinone oxidoreductase 1 (NQO1) is a multi-functional protein that catalyses the reduction of quinones (and other molecules), thus playing roles in xenobiotic detoxification and redox balance, and also has roles in stabilising apoptosis regulators such as p53. The structure and enzymology of NQO1 is well-characterised, showing a substituted enzyme mechanism in which NAD(P)H binds first and reduces an FAD cofactor in the active site, assisted by a charge relay system involving Tyr-155 and His-161. Protein dynamics play important role in physio-pathological aspects of this protein. NQO1 is a good target to treat cancer due to its overexpression in cancer cells. A polymorphic form of NQO1 (p.P187S) is associated with increased cancer risk and certain neurological disorders (such as multiple sclerosis and Alzheimer´s disease), possibly due to its roles in the antioxidant defence. p.P187S has greatly reduced FAD affinity and stability, due to destabilization of the flavin binding site and the C-terminal domain, which leading to reduced activity and enhanced degradation. Suppressor mutations partially restore the activity of p.P187S by local stabilization of these regions, and showing long-range allosteric communication within the protein. Consequently, the correction of NQO1 misfolding by pharmacological chaperones is a viable strategy, which may be useful to treat cancer and some neurological conditions, targeting structural spots linked to specific disease-mechanisms. Thus, NQO1 emerges as a good model to investigate loss of function mechanisms in genetic diseases as well as to improve strategies to discriminate between neutral and pathogenic variants in genome-wide sequencing studies.
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Affiliation(s)
- Sarah K Beaver
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Huxley Building, Lewes Road, Brighton BN2 4GJ, UK
| | - Noel Mesa-Torres
- Department of Physical Chemistry, Faculty of Sciences, University of Granada, Av. Fuentenueva s/n, 18071, Spain
| | - Angel L Pey
- Department of Physical Chemistry, Faculty of Sciences, University of Granada, Av. Fuentenueva s/n, 18071, Spain.
| | - David J Timson
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Huxley Building, Lewes Road, Brighton BN2 4GJ, UK.
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20
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Anion-specific interaction with human NQO1 inhibits flavin binding. Int J Biol Macromol 2019; 126:1223-1233. [PMID: 30615965 DOI: 10.1016/j.ijbiomac.2019.01.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 01/03/2019] [Accepted: 01/03/2019] [Indexed: 12/11/2022]
Abstract
Ion binding to biomacromolecules can modulate their activity and stability in vivo. It is of particular interest to understand the structural and energetic basis of anion binding to functional sites of biomacromolecules. In this work, binding of anions to the FAD binding pocket of human NAD(P)H:quinone oxidoreductase 1 (NQO1), a flavoprotein associated with cancer due to a common polymorphism causing a P187S amino acid substitution, was investigated. It is known that NQO1 stability in vivo is strongly modulated by binding of its flavin cofactor. Herein, binding and protein stability analyses were carried out to show that anion binding to the apo-state of NQO1 P187S inhibits FAD binding with increasing strength following the chaotropic behavior of anions. These inhibitory effects were significant for some anions even at low millimolar concentrations. Additional pH dependent analyses suggested that protonation of histidine residues in the FAD binding pocket was not critical for anion or flavin binding. Overall, this detailed biophysical analysis helps to understanding how anions modulate NQO1 functionality in vitro, thus allowing hypothesize that NQO1 stability in vivo could be modulated by differential anion binding and subsequent inhibition of FAD binding.
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