1
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Gil-Martínez J, Bernardo-Seisdedos G, Mato JM, Millet O. The use of pharmacological chaperones in rare diseases caused by reduced protein stability. Proteomics 2022; 22:e2200222. [PMID: 36205620 DOI: 10.1002/pmic.202200222] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/26/2022] [Accepted: 09/29/2022] [Indexed: 11/05/2022]
Abstract
Rare diseases are most often caused by inherited genetic disorders that, after translation, will result in a protein with altered function. Decreased protein stability is the most frequent mechanism associated with a congenital pathogenic missense mutation and it implies the destabilization of the folded conformation in favour of unfolded or misfolded states. In the cellular context and when experimental data is available, a mutant protein with altered thermodynamic stability often also results in impaired homeostasis, with the deleterious accumulation of protein aggregates, metabolites and/or metabolic by-products. In the last decades, a significant effort has enabled the characterization of rare diseases associated to protein stability defects and triggered the development of innovative therapeutic intervention lines, say, the use of pharmacological chaperones to correct the intracellular impaired homeostasis. Here, we review the current knowledge on rare diseases caused by reduced protein stability, paying special attention to the thermodynamic aspects of the protein destabilization, also focusing on some examples where pharmacological chaperones are being tested.
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Affiliation(s)
- Jon Gil-Martínez
- Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia, Spain
| | | | - José M Mato
- Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| | - Oscar Millet
- Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia, Spain.,ATLAS Molecular Pharma, Bizkaia, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
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2
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Loss of stability and unfolding cooperativity in hPGK1 upon gradual structural perturbation of its N-terminal domain hydrophobic core. Sci Rep 2022; 12:17200. [PMID: 36229482 PMCID: PMC9561527 DOI: 10.1038/s41598-022-22088-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 10/10/2022] [Indexed: 01/06/2023] Open
Abstract
Phosphoglycerate kinase has been a model for the stability, folding cooperativity and catalysis of a two-domain protein. The human isoform 1 (hPGK1) is associated with cancer development and rare genetic diseases that affect several of its features. To investigate how mutations affect hPGK1 folding landscape and interaction networks, we have introduced mutations at a buried site in the N-terminal domain (F25 mutants) that either created cavities (F25L, F25V, F25A), enhanced conformational entropy (F25G) or introduced structural strain (F25W) and evaluated their effects using biophysical experimental and theoretical methods. All F25 mutants folded well, but showed reduced unfolding cooperativity, kinetic stability and altered activation energetics according to the results from thermal and chemical denaturation analyses. These alterations correlated well with the structural perturbation caused by mutations in the N-terminal domain and the destabilization caused in the interdomain interface as revealed by H/D exchange under native conditions. Importantly, experimental and theoretical analyses showed that these effects are significant even when the perturbation is mild and local. Our approach will be useful to establish the molecular basis of hPGK1 genotype-phenotype correlations due to phosphorylation events and single amino acid substitutions associated with disease.
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3
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Liu H, Wang X, Shen P, Ni Y, Han X. The basic functions of phosphoglycerate kinase 1 and its roles in cancer and other diseases. Eur J Pharmacol 2022; 920:174835. [DOI: 10.1016/j.ejphar.2022.174835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 02/15/2022] [Indexed: 01/17/2023]
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4
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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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5
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Therapeutic Benefit of Blood Transfusion in a Patient With Novel PGK1 Mutation (c.461T>C [p.L154P]). J Pediatr Hematol Oncol 2020; 42:e228-e230. [PMID: 30951021 DOI: 10.1097/mph.0000000000001463] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Phosphoglycerate kinase (PGK) is glycolytic enzyme critical in the creation of adenosine triphosphate. Mutations in the gene for this enzyme, PGK1, are associated with PGK deficiency, which is characterized by neurologic symptoms, nonhereditary spherocytic hemolytic anemia, and myopathy. We present a 20-year-old male with a novel c.461T>C (p.L154P) PGK1 mutation and clinical disease complicated by anemia and neurological symptoms. There is no recommended treatment for PGK deficiency. Because of our patient's advanced disease progression, we initiated serial blood transfusions and report significant subjective improvement in the patient's physical condition before his passing from PGK deficiency-related complications.
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6
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Garcia-Solaesa V, Serrano-Lorenzo P, Ramos-Arroyo MA, Blázquez A, Pagola-Lorz I, Artigas-López M, Arenas J, Martín MA, Jericó-Pascual I. A Novel Missense Variant Associated with A Splicing Defect in A Myopathic Form of PGK1 Deficiency in The Spanish Population. Genes (Basel) 2019; 10:genes10100785. [PMID: 31658606 PMCID: PMC6826351 DOI: 10.3390/genes10100785] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/04/2019] [Accepted: 10/08/2019] [Indexed: 11/16/2022] Open
Abstract
Phosphoglycerate kinase (PGK)1 deficiency is an X-linked inherited disease associated with different clinical presentations, sometimes as myopathic affectation without hemolytic anemia. We present a 40-year-old male with a mild psychomotor delay and mild mental retardation, who developed progressive exercise intolerance, cramps and sporadic episodes of rhabdomyolysis but no hematological features. A genetic study was carried out by a next-generation sequencing (NGS) panel of 32 genes associated with inherited metabolic myopathies. We identified a missense variant in the PGK1 gene c.1114G > A (p.Gly372Ser) located in the last nucleotide of exon 9. cDNA studies demonstrated abnormalities in mRNA splicing because this change abolishes the exon 9 donor site. This novel variant is the first variant associated with a myopathic form of PGK1 deficiency in the Spanish population.
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Affiliation(s)
- Virginia Garcia-Solaesa
- Department of Medical Genetics, Complejo Hospitalario de Navarra, IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain, (M.A.R.-A.).
| | - Pablo Serrano-Lorenzo
- Laboratorio de Enfermedades Mitocondriales y Neurometabólicas. Instituto de Investigación Hospital 12 de Octubre, 28041 Madrid, Spain, (P.S.-L.).
| | - Maria Antonia Ramos-Arroyo
- Department of Medical Genetics, Complejo Hospitalario de Navarra, IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain, (M.A.R.-A.).
| | - Alberto Blázquez
- Laboratorio de Enfermedades Mitocondriales y Neurometabólicas. Instituto de Investigación Hospital 12 de Octubre, 28041 Madrid, Spain, (P.S.-L.).
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28041 Madrid, Spain.
| | - Inmaculada Pagola-Lorz
- Department of Neurology, Complejo Hospitalario de Navarra, IdiSNA (Navarra Institute for Health Research), 31008 Pamplona, Spain, (I.P.-L.).
| | - Mercè Artigas-López
- Department of Medical Genetics, Complejo Hospitalario de Navarra, IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain, (M.A.R.-A.).
| | - Joaquín Arenas
- Laboratorio de Enfermedades Mitocondriales y Neurometabólicas. Instituto de Investigación Hospital 12 de Octubre, 28041 Madrid, Spain, (P.S.-L.).
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28041 Madrid, Spain.
| | - Miguel A Martín
- Laboratorio de Enfermedades Mitocondriales y Neurometabólicas. Instituto de Investigación Hospital 12 de Octubre, 28041 Madrid, Spain, (P.S.-L.).
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28041 Madrid, Spain.
| | - Ivonne Jericó-Pascual
- Department of Neurology, Complejo Hospitalario de Navarra, IdiSNA (Navarra Institute for Health Research), 31008 Pamplona, Spain, (I.P.-L.).
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7
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Echaniz-Laguna A, Nadjar Y, Béhin A, Biancalana V, Piraud M, Malfatti E, Laforêt P. Phosphoglycerate kinase deficiency: A nationwide multicenter retrospective study. J Inherit Metab Dis 2019; 42:803-808. [PMID: 30887539 DOI: 10.1002/jimd.12087] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 03/14/2019] [Indexed: 11/11/2022]
Abstract
Phosphoglycerate kinase (PGK) deficiency is a rare X-linked metabolic disorder caused by mutations in the PGK1 gene. Patients usually develop various combinations of nonspherocytic hemolytic anemia (NSHA), myopathy, and central nervous system disorders. In this national multicenter observational retrospective study, we recorded all known French patients with PGK deficiency, and 3 unrelated patients were identified. Case 1 was a 32-year-old patient with severe chronic axonal sensorimotor polyneuropathy resembling Charcot-Marie-Tooth (CMT) disease, mental retardation, microcephaly, ophthalmoplegia, pes cavus, and the new c.323G > A PGK1 hemizygous mutation. Case 2 was a 71-year-old patient with recurrent exertional rhabdomyolysis, and a c.943G > A PGK1 hemizygous mutation. Case 3 was a 48-year-old patient with NSHA, retinitis pigmentosa, mental retardation, seizures, stroke, parkinsonism, and a c.491A > T PGK1 hemizygous mutation. This study confirms that PGK deficiency is an extremely rare disorder with a wide phenotypic spectrum, and demonstrates for the first time that PGK deficiency may affect the peripheral nervous system and present as a CMT-like disorder.
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Affiliation(s)
- Andoni Echaniz-Laguna
- Department of Neurology, APHP, Bicêtre University Hospital, Le Kremlin Bicêtre, France
- French National Reference Center for Rare Neuropathies (NNERF), Le Kremlin Bicêtre, France
- INSERM U1195 & Paris-Sud University, Le Kremlin Bicêtre, France
| | - Yann Nadjar
- Neurology Department, Hôpital Pitié-Salpêtrière, Paris, France
| | - Anthony Béhin
- Neurology Department, Hôpital Pitié-Salpêtrière, Paris, France
| | - Valérie Biancalana
- Laboratoire Diagnostic Génétique, CHR, Strasbourg, France
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR 7104, Fédération de Médecine Translationnelle de Strasbourg, Université de Strasbourg, Illkirch, France
| | - Monique Piraud
- Laboratoire des Maladies Héréditaires du Métabolisme et dépistage Néonatal, Centre de Biologie et de Pathologie Est, Hospices Civils de Lyon, Bron, France
| | | | - Pascal Laforêt
- Neurology Department, Hôpital Raymond Poincaré, Paris, France
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8
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Morel B, Conejero-Lara F. Early mechanisms of amyloid fibril nucleation in model and disease-related proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:140264. [PMID: 31437584 DOI: 10.1016/j.bbapap.2019.140264] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/18/2019] [Accepted: 08/12/2019] [Indexed: 02/06/2023]
Abstract
Protein amyloid aggregation is a hallmark in neuropathologies and other diseases of tremendous impact such as Alzheimer's or Parkinson's diseases. During the last decade, it has become increasingly evident that neuronal death is mainly induced by proteinaceous oligomers rather than the mature amyloid fibrils. Therefore, the earliest molecular events occurring during the amyloid aggregation cascade represent a growing interest of study. Important breakthroughs have been achieved using experimental data from different proteins, used as models, as well as systems related to diseases. Here, we summarize the structural properties of amyloid oligomeric and fibrillar aggregates and review the recent advances on how biophysical techniques can be combined with quantitative kinetic analysis and theoretical models to study the detailed mechanism of oligomer formation and nucleation of fibrils. These insights into the mechanism of early oligomerization and amyloid nucleation are of relevant interest in drug discovery and in the design of preventive strategies against neurodegenerative diseases.
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Affiliation(s)
- Bertrand Morel
- Departamento de Química Física e Instituto de Biotecnología, Universidad de Granada, 18071 Granada, Spain.
| | - Francisco Conejero-Lara
- Departamento de Química Física e Instituto de Biotecnología, Universidad de Granada, 18071 Granada, Spain
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9
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Lin CY, Wu CL, Lee KZ, Chen YJ, Zhang PH, Chang CY, Harn HJ, Lin SZ, Tsai HJ. Extracellular Pgk1 enhances neurite outgrowth of motoneurons through Nogo66/NgR-independent targeting of NogoA. eLife 2019; 8:49175. [PMID: 31361595 PMCID: PMC6667276 DOI: 10.7554/elife.49175] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 07/05/2019] [Indexed: 12/11/2022] Open
Abstract
NogoA inhibits neurite outgrowth of motoneurons (NOM) through interaction with its receptors, Nogo66/NgR. Inhibition of Nogo receptors rescues NOM, but not to the extent exhibited by NogoA-knockout mice, suggesting the presence of other pathways. We found that NogoA-overexpressing muscle cells reduced phosphoglycerate kinase 1 (Pgk1) secretion, resulting in inhibiting NOM. Apart from its glycolytic role and independent of the Nogo66 pathway, extracellular Pgk1 stimulated NOM by triggering a reduction of p-Cofilin-S3, a growth cone collapse marker, through decreasing a novel Rac1-GTP/p-Pak1-T423/p-P38-T180/p-MK2-T334/p-Limk1-S323/p-Cofilin-S3 molecular pathway. Not only did supplementary Pgk1 enhance NOM in defective cells, but injection of Pgk1 rescued denervation in muscle-specific NogoA-overexpression of zebrafish and an Amyotrophic Lateral Sclerosis mouse model, SOD1 G93A. Thus, Pgk1 secreted from muscle is detrimental to motoneuron neurite outgrowth and maintenance.
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Affiliation(s)
- Cheng Yung Lin
- Institute of Biomedical Sciences, Mackay Medical College, New Taipei City, Taiwan
| | - Chia Lun Wu
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
| | - Kok Zhi Lee
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
| | - You Jei Chen
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
| | - Po Hsiang Zhang
- Institute of Biomedical Sciences, Mackay Medical College, New Taipei City, Taiwan
| | - Chia Yu Chang
- Bioinnovation Center, Buddhist Tzu Chi Medical Foundation, Hualien City, Taiwan.,Department of Medical Research and Neuroscience Center, Buddhist Tzu Chi General Hospital, Hualien City, Taiwan
| | - Horng Jyh Harn
- Bioinnovation Center, Buddhist Tzu Chi Medical Foundation, Hualien City, Taiwan.,Department of Pathology, Buddhist Tzu Chi General Hospital and Tzu Chi University, Hualien City, Taiwan
| | - Shinn Zong Lin
- Bioinnovation Center, Buddhist Tzu Chi Medical Foundation, Hualien City, Taiwan.,Department of Neurosurgery, Buddhist Tzu Chi General Hospital, Hualien City, Taiwan
| | - Huai Jen Tsai
- Institute of Biomedical Sciences, Mackay Medical College, New Taipei City, Taiwan
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10
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Behlmann AM, Goyal NA, Yang X, Chen PH, Ankala A. A Hemizygous Deletion Within the PGK1 Gene in Males with PGK1 Deficiency. JIMD Rep 2018; 45:105-110. [PMID: 30570712 PMCID: PMC6336546 DOI: 10.1007/8904_2018_147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 08/24/2018] [Accepted: 09/25/2018] [Indexed: 02/05/2023] Open
Abstract
Phosphoglycerate kinase-1 (PGK1) deficiency is a rare X-linked disorder caused by pathogenic variants in the PGK1 gene. Complete loss-of-function variants have not been reported in this gene, indicating that residual enzyme function is critical for viability in males. Therefore, copy number variants (CNVs) that include single exon or multiple exon deletions or duplications are generally not expected in individuals with PGK1 deficiency. Here we describe a 64-year-old male presenting with a family history (three additional affected males) and a personal history of childhood-onset metabolic myopathy that involves episodes of muscle pain, stiffness after activity, exercise intolerance, and myoglobinuria after exertion. Biochemical analysis on a muscle biopsy indicated significantly reduced activity (15% compared to normal) for phosphoglycerate kinase (PGK1), a glycolytic enzyme encoded by PGK1. A diagnosis of PGK1 deficiency was established by molecular analysis which detected an approximately 886 kb deletion involving the polyadenylation site in the 3'UTR of the PGK1 gene. RNA analysis showed significantly reduced PGK1 transcript levels (30% compared to normal). This is the first deletion reported in the PGK1 gene and is the first pathogenic variant involving the 3'UTR polyadenylation site of this gene. Our report emphasizes the role of 3'UTR variants in human disorders and underscores the need for exploring noncoding regions of disease-associated genes when seeking a molecular diagnosis.
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Affiliation(s)
- Andrea Medrano Behlmann
- grid.189967.80000 0001 0941 6502Department of Human Genetics, Emory University School of Medicine, Atlanta, GA USA
| | - Namita A. Goyal
- grid.266093.80000 0001 0668 7243Department of Neurology, University of California, Irvine, CA USA
| | - Xiaoyu Yang
- grid.189967.80000 0001 0941 6502Department of Cell Biology, Emory University School of Medicine, Atlanta, GA USA
| | - Ping H. Chen
- grid.189967.80000 0001 0941 6502Department of Cell Biology, Emory University School of Medicine, Atlanta, GA USA
| | - Arunkanth Ankala
- grid.189967.80000 0001 0941 6502Department of Human Genetics, Emory University School of Medicine, Atlanta, GA USA ,EGL Genetic Diagnostics LLC, Tucker, GA USA
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11
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Pey AL. Biophysical and functional perturbation analyses at cancer-associated P187 and K240 sites of the multifunctional NADP(H):quinone oxidoreductase 1. Int J Biol Macromol 2018; 118:1912-1923. [PMID: 30009918 DOI: 10.1016/j.ijbiomac.2018.07.051] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 07/10/2018] [Accepted: 07/11/2018] [Indexed: 12/14/2022]
Abstract
Once whole-genome sequencing has reached the clinical practice, a main challenge ahead is the high-throughput and accurate prediction of the pathogenicity of genetic variants. However, current prediction tools do not consider explicitly a well-known property of disease-causing mutations: their ability to affect multiple functional sites distant in the protein structure. Here we carried out an extensive biophysical characterization of fourteen mutant variants at two cancer-associated sites of the enzyme NQO1, a paradigm of multi-functional protein. We showed that the magnitude of destabilizing effects, their molecular origins (structural vs. dynamic) and their efficient propagation through the protein structure gradually led to functional perturbations at different sites. Modulation of these structural perturbations also led to switches between molecular phenotypes. Our work supports that experimental and computational perturbation analyses would improve our understanding of the molecular basis of many loss-of-function genetic diseases as well as our ability to accurately predict the pathogenicity of genetic variants in a high-throughput fashion.
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Affiliation(s)
- Angel L Pey
- Department of Physical Chemistry, University of Granada, Av. Fuentenueva S/N, 18071 Granada, Spain.
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12
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Medina-Carmona E, Neira JL, Salido E, Fuchs JE, Palomino-Morales R, Timson DJ, Pey AL. Site-to-site interdomain communication may mediate different loss-of-function mechanisms in a cancer-associated NQO1 polymorphism. Sci Rep 2017; 7:44532. [PMID: 28291250 PMCID: PMC5349528 DOI: 10.1038/srep44532] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 02/10/2017] [Indexed: 12/27/2022] Open
Abstract
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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Affiliation(s)
- Encarnación Medina-Carmona
- Department of Physical Chemistry, Faculty of Sciences, University of Granada, Av. Fuentenueva s/n, 18071, Granada, Spain
| | - Jose L. Neira
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Avda. del Ferrocarril s/n, 03202, Elche, Alicante, Spain
- Instituto de Biocomputación y Física de los Sistemas Complejos (BIFI), 50009, Zaragoza, Spain
| | - Eduardo Salido
- Hospital Universitario de Canarias, Centre for Biomedical Research on Rare Diseases (CIBERER), Tenerife, Spain
| | - Julian E. Fuchs
- Institute of General, Inorganic and Theoretical Chemistry, Faculty of Chemistry and Pharmacy, University of Innsbruck, Innsbruck, Austria
| | - Rogelio Palomino-Morales
- Department of Biochemistry and Molecular Biology I, Faculty of Sciences, University of Granada, Av. Fuentenueva s/n, 18071, Granada, Spain
| | - David J. Timson
- School of Pharmacy and Biomolecular Sciences, The University of Brighton, Brighton, UK
| | - Angel L. Pey
- Department of Physical Chemistry, Faculty of Sciences, University of Granada, Av. Fuentenueva s/n, 18071, Granada, Spain
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13
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Fuchs JE, Schilling O, Liedl KR. Determinants of Macromolecular Specificity from Proteomics-Derived Peptide Substrate Data. Curr Protein Pept Sci 2017; 18:905-913. [PMID: 27455965 PMCID: PMC5898033 DOI: 10.2174/1389203717666160724211231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 03/30/2017] [Accepted: 04/15/2017] [Indexed: 11/22/2022]
Abstract
BACKGROUND Recent advances in proteomics methodologies allow for high throughput profiling of proteolytic cleavage events. The resulting substrate peptide distributions provide deep insights in the underlying macromolecular recognition events, as determinants of biomolecular specificity identified by proteomics approaches may be compared to structure-based analysis of corresponding protein-protein interfaces. METHOD Here, we present an overview of experimental and computational methodologies and tools applied in the area and provide an outlook beyond the protein class of proteases. RESULTS AND CONCLUSION We discuss here future potential, synergies and needs of the emerging overlap disciplines of proteomics and structure-based modelling.
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Affiliation(s)
- Julian E. Fuchs
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, CambridgeCB2 1EW, United Kingdom
| | - Oliver Schilling
- Institute of Molecular Medicine and Cell Research, University of Freiburg, Stefan-Meier-Str. 17, D-79104 Freiburg, Germany and BIOSS Centre for Biological Signaling Studies, University of Freiburg, D-79104Freiburg, Germany
| | - Klaus R. Liedl
- Institute of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, A-6020Innsbruck, Austria
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Modulating Mobility: a Paradigm for Protein Engineering? Appl Biochem Biotechnol 2016; 181:83-90. [PMID: 27449223 DOI: 10.1007/s12010-016-2200-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 07/17/2016] [Indexed: 12/30/2022]
Abstract
Proteins are highly mobile structures. In addition to gross conformational changes occurring on, for example, ligand binding, they are also subject to constant thermal motion. The mobility of a protein varies through its structure and can be modulated by ligand binding and other events. It is becoming increasingly clear that this mobility plays an important role in key functions of proteins including catalysis, allostery, cooperativity, and regulation. Thus, in addition to an optimum structure, proteins most likely also require an optimal dynamic state. Alteration of this dynamic state through protein engineering will affect protein function. A dramatic example of this is seen in some inherited metabolic diseases where alternation of residues distant from the active site affects the mobility of the protein and impairs function. We postulate that using molecular dynamics simulations, experimental data or a combination of the two, it should be possible to engineer the mobility of active sites. This may be useful in, for example, increasing the promiscuity of enzymes. Thus, a paradigm for protein engineering is suggested in which the mobility of the active site is rationally modified. This might be combined with more "traditional" approaches such as altering functional groups in the active site.
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Recurrent episodes of myoglobinuria, mental retardation and seizures but no hemolysis in two brothers with phosphoglycerate kinase deficiency. Neuromuscul Disord 2016; 26:207-10. [PMID: 26883264 DOI: 10.1016/j.nmd.2015.11.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Revised: 09/24/2015] [Accepted: 11/23/2015] [Indexed: 11/21/2022]
Abstract
We report two brothers with mild intellectual deficiency, exercise intolerance, rhabdomyolysis, seizures and no hemolysis. Phosphoglycerate kinase (PGK) activity was strongly decreased in their red blood cells. Subsequent molecular analysis of PGK1 revealed hemizygosity for a novel mutation c.756 + 3A > G, in intron 7. Analysis of the effect of this mutation on pre-mRNA processing demonstrated markedly decreased levels of normal PGK1 mRNA. In addition, the c.756 + 3A > G change resulted in abnormally spliced transcripts. If translated, these transcripts mostly encode for C-terminally truncated proteins. The consequences of the c.756 + 3A > G mutation is discussed, as well as the genotype-to-phenotype correlation with regard to previously described mutations (PGK Fukuroi and PGK Antwerp), which also result in C-terminal truncated proteins.
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Fuchs JE, Muñoz IG, Timson DJ, Pey AL. Experimental and computational evidence on conformational fluctuations as a source of catalytic defects in genetic diseases. RSC Adv 2016. [DOI: 10.1039/c6ra05499d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Catalytic mutants causing inherited type III galactosemia alter active site structural dynamics and shift the native conformational equilibrium towards inactive conformations.
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Affiliation(s)
- Julian E. Fuchs
- Institute of General, Inorganic and Theoretical Chemistry
- Faculty of Chemistry and Pharmacy
- University of Innsbruck
- Innsbruck
- Austria
| | - Inés G. Muñoz
- Crystallography and Protein Engineering Unit
- Structural Biology and Biocomputing Programme
- Spanish National Cancer Research Centre (CNIO)
- Madrid
- Spain
| | - David J. Timson
- School of Pharmacy and Biomolecular Sciences
- The University of Brighton
- Brighton
- UK
| | - Angel L. Pey
- Department of Physical Chemistry
- Faculty of Sciences
- University of Granada
- Granada
- Spain
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Timson DJ. Value of predictive bioinformatics in inherited metabolic diseases. World J Med Genet 2015; 5:46-51. [DOI: 10.5496/wjmg.v5.i3.46] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 04/28/2015] [Accepted: 05/18/2015] [Indexed: 02/06/2023] Open
Abstract
Typically, inherited metabolic diseases arise from point mutations in genes encoding metabolic enzymes. Although some of these mutations directly affect amino acid residues in the active sites of these enzymes, the majority do not. It is now well accepted that the majority of these disease-associated mutations exert their effects through alteration of protein stability, which causes a reduction in enzymatic activity. This finding suggests a way to predict the severity of newly discovered mutations. In silico prediction of the effects of amino acid sequence alterations on protein stability often correlates with disease severity. However, no stability prediction tool is perfect and, in general, better results are obtained if the predictions from a variety of tools are combined and then interpreted. In addition to predicted alterations to stability, the degree of conservation of a particular residue can also be a factor which needs to be taken into account: alterations to highly conserved residues are more likely to be associated with severe forms of the disease. The approach has been successfully applied in a variety of inherited metabolic diseases, but further improvements are necessary to enable robust translation into clinically useful tools.
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Mesa-Torres N, Salido E, Pey AL. The lower limits for protein stability and foldability in primary hyperoxaluria type I. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:2355-65. [PMID: 25461797 DOI: 10.1016/j.bbapap.2014.10.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 09/29/2014] [Accepted: 10/10/2014] [Indexed: 01/12/2023]
Abstract
Mutational effects on protein stability and foldability are important to understand conformational diseases and protein evolution. In this work, we perform a comprehensive investigation on the energetic basis underlying mutational effects on the stability of human alanine:glyoxylate aminotransferase (AGT). We study twenty two variants whose kinetic stabilities span over eleven orders of magnitude and are classified into two groups: i) ten naturally-occurring variants, including the most common mutations causing primary hyperoxaluria type I (PH1); and ii) twelve consensus variants obtained by sequence-alignment statistics. We show that AGT dimer stability determines denaturation rates, and mutations modulate stability by changes in the effective thermodynamic stability, the aggregation propensity of partially/globally unfolded states and subtle energetic changes in the rate-limiting denaturation step. In combination with our previous expression analyses in eukaryotic cells, we propose the existence of two lower limits for AGT stability, one linked to optimal folding efficiency (close to the major allele stability) and the other setting a minimal efficiency compatible with glyoxylate detoxification in vivo (close to the minor allele stability). These lower limits could explain the high prevalence of misfolding as a disease mechanism in PH1 and support the use of pharmacological ligands aimed to increase AGT stability as therapies for this disease.
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Affiliation(s)
- Noel Mesa-Torres
- Departamento de Química-Física, Facultad de Ciencias, Universidad de Granada, E-18071 Granada, Spain
| | - Eduardo Salido
- Hospital Universitario de Canarias, Universidad La Laguna, Centre for Biomedical Research on Rare Diseases (CIBERER), Tenerife E-38320, Spain
| | - Angel L Pey
- Departamento de Química-Física, Facultad de Ciencias, Universidad de Granada, E-18071 Granada, Spain.
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