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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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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3
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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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4
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Dindo M, Pascarelli S, Chiasserini D, Grottelli S, Costantini C, Uechi G, Giardina G, Laurino P, Cellini B. Structural dynamics shape the fitness window of alanine:glyoxylate aminotransferase. Protein Sci 2022; 31:e4303. [PMID: 35481644 PMCID: PMC8996469 DOI: 10.1002/pro.4303] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 03/02/2022] [Accepted: 03/17/2022] [Indexed: 01/24/2023]
Abstract
The conformational landscape of a protein is constantly expanded by genetic variations that have a minimal impact on the function(s) while causing subtle effects on protein structure. The wider the conformational space sampled by these variants, the higher the probabilities to adapt to changes in environmental conditions. However, the probability that a single mutation may result in a pathogenic phenotype also increases. Here we present a paradigmatic example of how protein evolution balances structural stability and dynamics to maximize protein adaptability and preserve protein fitness. We took advantage of known genetic variations of human alanine:glyoxylate aminotransferase (AGT1), which is present as a common major allelic form (AGT-Ma) and a minor polymorphic form (AGT-Mi) expressed in 20% of Caucasian population. By integrating crystallographic studies and molecular dynamics simulations, we show that AGT-Ma is endowed with structurally unstable (frustrated) regions, which become disordered in AGT-Mi. An in-depth biochemical characterization of variants from an anticonsensus library, encompassing the frustrated regions, correlates this plasticity to a fitness window defined by AGT-Ma and AGT-Mi. Finally, co-immunoprecipitation analysis suggests that structural frustration in AGT1 could favor additional functions related to protein-protein interactions. These results expand our understanding of protein structural evolution by establishing that naturally occurring genetic variations tip the balance between stability and frustration to maximize the ensemble of conformations falling within a well-defined fitness window, thus expanding the adaptability potential of the protein.
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Affiliation(s)
- Mirco Dindo
- Protein Engineering and Evolution UnitOkinawa Institute of Science and Technology Graduate UniversityOkinawaJapan
| | - Stefano Pascarelli
- Protein Engineering and Evolution UnitOkinawa Institute of Science and Technology Graduate UniversityOkinawaJapan
| | | | - Silvia Grottelli
- Department of Medicine and SurgeryUniversity of PerugiaPerugiaItaly
| | | | - Gen‐Ichiro Uechi
- Protein Engineering and Evolution UnitOkinawa Institute of Science and Technology Graduate UniversityOkinawaJapan
| | - Giorgio Giardina
- Department of Biochemical Sciences “A. Rossi Fanelli”Sapienza University of RomeRomeItaly
| | - Paola Laurino
- Protein Engineering and Evolution UnitOkinawa Institute of Science and Technology Graduate UniversityOkinawaJapan
| | - Barbara Cellini
- Department of Medicine and SurgeryUniversity of PerugiaPerugiaItaly
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5
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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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6
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Cai R, Lin M, Chen Z, Lai Y, Huang X, Zhao G, Guo X, Xiong Z, Chen J, Chen H, Jiang Q, Liu S, Yang Y, Liang W, Zou M, Liu T, Chen W, Liu H, Peng J. Primary hyperoxaluria diagnosed after kidney transplantation failure: lesson from 3 case reports and literature review. BMC Nephrol 2019; 20:224. [PMID: 31215412 PMCID: PMC6582561 DOI: 10.1186/s12882-019-1402-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 05/28/2019] [Indexed: 12/16/2022] Open
Abstract
Background Primary hyperoxaluria (PH) is a rare inborn disorder of the metabolism of glyoxylate, which causes the hallmark production oxalate and forms insoluble calcium oxalate crystals that accumulate in the kidney and other organs. Since the manifestation of PH varies from recurrent nephrolithiasis, nephrocalcinosis, and end-stage renal disease with age at onset of symptoms ranging from infancy to the sixth decade, the disease remains undiagnosed until after kidney transplantation in some cases. Case presentation Herein, we report 3 cases of PH diagnosed after kidney transplantation failure, providing the comprehensive clinical course, the ultrasonic image of renal graft and pathologic image of the biopsy, highlighting the relevance of biopsy findings and the results of molecular genetic testing. We also focus on the treatment and the unfavorable outcome of the patients. Meanwhile, we review the literature and show the additional 10 reported cases of PH diagnosed after kidney transplantation. Additionally, we discuss the progressive molecular understanding of the mechanisms involved in PH and molecular therapy. Conclusions Overall, the necessity of preoperative screening of PH in all patients even with a minor history of nephrolithiasis and the importance of proper treatment are the lessons we learn from the 3 cases, which prompt us to avoid tragedies. Electronic supplementary material The online version of this article (10.1186/s12882-019-1402-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ruiming Cai
- Department of Organ Transplantation, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Minzhuang Lin
- Department of Organ Transplantation, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Zhiyong Chen
- Department of Organ Transplantation, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Yongtong Lai
- Department of Organ Transplantation, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Xianen Huang
- Department of Organ Transplantation, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Guozhi Zhao
- Department of Organ Transplantation, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Xuekun Guo
- Department of Organ Transplantation, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Zhongtang Xiong
- Department of Pathology, The Third Affiliated Hospital of Guangzhou Medical University, 63 Duobao Road, Guangzhou, 510150, People's Republic of China
| | - Juan Chen
- Department of Pathology, The Third Affiliated Hospital of Guangzhou Medical University, 63 Duobao Road, Guangzhou, 510150, People's Republic of China
| | - Hui Chen
- Department of Pathology, The Third Affiliated Hospital of Guangzhou Medical University, 63 Duobao Road, Guangzhou, 510150, People's Republic of China
| | - Qingping Jiang
- Department of Pathology, The Third Affiliated Hospital of Guangzhou Medical University, 63 Duobao Road, Guangzhou, 510150, People's Republic of China
| | - Shaoyan Liu
- Department of Pathology, The Third Affiliated Hospital of Guangzhou Medical University, 63 Duobao Road, Guangzhou, 510150, People's Republic of China
| | - Yuexin Yang
- Department of Pathology, The Third Affiliated Hospital of Guangzhou Medical University, 63 Duobao Road, Guangzhou, 510150, People's Republic of China
| | - Weixiang Liang
- Department of Ultrasound, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Minhui Zou
- Department of Ultrasound, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Tao Liu
- Department of Ultrasound, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Wenfang Chen
- Department of Pathology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Hongzhou Liu
- Department of Clinical Laboratory, Guangzhou Kingmed Center for Clinical Laboratory Co., Ltd, Guangzhou, 510330, China
| | - Juan Peng
- Department of Pathology, The Third Affiliated Hospital of Guangzhou Medical University, 63 Duobao Road, Guangzhou, 510150, People's Republic of China.
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7
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Fernández-Higuero JÁ, Betancor-Fernández I, Mesa-Torres N, Muga A, Salido E, Pey AL. Structural and functional insights on the roles of molecular chaperones in the mistargeting and aggregation phenotypes associated with primary hyperoxaluria type I. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2018; 114:119-152. [PMID: 30635080 DOI: 10.1016/bs.apcsb.2018.09.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
To carry out their biological function in cells, proteins must be folded and targeted to the appropriate subcellular location. These processes are controlled by a vast collection of interacting proteins collectively known as the protein homeostasis network, in which molecular chaperones play a prominent role. Protein homeostasis can be impaired by inherited mutations leading to genetic diseases. In this chapter, we focus on a particular disease, primary hyperoxaluria type 1 (PH1), in which disease-associated mutations exacerbate protein aggregation in the cell and mistarget the peroxisomal alanine:glyoxylate aminotransferase (AGT) protein to mitochondria, in part due to native state destabilization and enhanced interaction with Hsp60, 70 and 90 chaperone systems. After a general introduction of molecular chaperones and PH1, we review our current knowledge on the structural and energetic features of PH1-causing mutants that lead to these particular pathogenic mechanisms. From this perspective, and in the context of the key role of molecular chaperones in PH1 pathogenesis, we present and discuss current and future perspectives for pharmacological treatments for this disease.
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Affiliation(s)
- José Ángel Fernández-Higuero
- Biofisika Institute (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Isabel Betancor-Fernández
- Centre for Biomedical Research on Rare Diseases (CIBERER), Hospital Universitario de Canarias, ITB, University of La Laguna, Tenerife, Spain
| | - Noel Mesa-Torres
- Department of Physical Chemistry, University of Granada, Granada, Spain
| | - Arturo Muga
- Biofisika Institute (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Eduardo Salido
- Centre for Biomedical Research on Rare Diseases (CIBERER), Hospital Universitario de Canarias, ITB, University of La Laguna, Tenerife, Spain
| | - Angel L Pey
- Department of Physical Chemistry, University of Granada, Granada, Spain.
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8
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Dindo M, Conter C, Oppici E, Ceccarelli V, Marinucci L, Cellini B. Molecular basis of primary hyperoxaluria: clues to innovative treatments. Urolithiasis 2018; 47:67-78. [PMID: 30430197 DOI: 10.1007/s00240-018-1089-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 11/08/2018] [Indexed: 12/21/2022]
Abstract
Primary hyperoxalurias (PHs) are rare inherited disorders of liver glyoxylate metabolism, characterized by the abnormal production of endogenous oxalate, a metabolic end-product that is eliminated by urine. The main symptoms are related to the precipitation of calcium oxalate crystals in the urinary tract with progressive renal damage and, in the most severe form named Primary Hyperoxaluria Type I (PH1), to systemic oxalosis. The therapies currently available for PH are either poorly effective, because they address the symptoms and not the causes of the disease, or highly invasive. In the last years, advances in our understanding of the molecular bases of PH have paved the way for the development of new therapeutic strategies. They include (i) substrate-reduction therapies based on small-molecule inhibitors or the RNA interference technology, (ii) gene therapy, (iii) enzyme administration approaches, (iv) colonization with oxalate-degrading intestinal microorganisms, and, in PH1, (v) design of pharmacological chaperones. This paper reviews the basic principles of these new therapeutic strategies and what is currently known about their application to PH.
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Affiliation(s)
- Mirco Dindo
- Department of Experimental Medicine, University of Perugia, P.le Gambuli 1, 06132, Perugia, Italy
| | - Carolina Conter
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Strada le Grazie 8, 37134, Verona, VR, Italy
| | - Elisa Oppici
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Strada le Grazie 8, 37134, Verona, VR, Italy
| | - Veronica Ceccarelli
- Department of Experimental Medicine, University of Perugia, P.le Gambuli 1, 06132, Perugia, Italy
| | - Lorella Marinucci
- Department of Experimental Medicine, University of Perugia, P.le Gambuli 1, 06132, Perugia, Italy
| | - Barbara Cellini
- Department of Experimental Medicine, University of Perugia, P.le Gambuli 1, 06132, Perugia, Italy.
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9
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Medina-Carmona E, Betancor-Fernández I, Santos J, Mesa-Torres N, Grottelli S, Batlle C, Naganathan AN, Oppici E, Cellini B, Ventura S, Salido E, Pey AL. Insight into the specificity and severity of pathogenic mechanisms associated with missense mutations through experimental and structural perturbation analyses. Hum Mol Genet 2018; 28:1-15. [DOI: 10.1093/hmg/ddy323] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 09/09/2018] [Indexed: 12/21/2022] Open
Abstract
Abstract
Most pathogenic missense mutations cause specific molecular phenotypes through protein destabilization. However, how protein destabilization is manifested as a given molecular phenotype is not well understood. We develop here a structural and energetic approach to describe mutational effects on specific traits such as function, regulation, stability, subcellular targeting or aggregation propensity. This approach is tested using large-scale experimental and structural perturbation analyses in over thirty mutations in three different proteins (cancer-associated NQO1, transthyretin related with amyloidosis and AGT linked to primary hyperoxaluria type I) and comprising five very common pathogenic mechanisms (loss-of-function and gain-of-toxic function aggregation, enzyme inactivation, protein mistargeting and accelerated degradation). Our results revealed that the magnitude of destabilizing effects and, particularly, their propagation through the structure to promote disease-associated conformational states largely determine the severity and molecular mechanisms of disease-associated missense mutations. Modulation of the structural perturbation at a mutated site is also shown to cause switches between different molecular phenotypes. When very common disease-associated missense mutations were investigated, we also found that they were not among the most deleterious possible missense mutations at those sites, and required additional contributions from codon bias and effects of CpG sites to explain their high frequency in patients. Our work sheds light on the molecular basis of pathogenic mechanisms and genotype–phenotype relationships, with implications for discriminating between pathogenic and neutral changes within human genome variability from whole genome sequencing studies.
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Affiliation(s)
- Encarnación Medina-Carmona
- Department of Physical Chemistry, University of Granada, Granada, Spain
- Department of Experimental Medicine, University of Perugia, Piazzale Gambuli, Perugia
| | - Isabel Betancor-Fernández
- Centre for Biomedical Research on Rare Diseases, Hospital Universitario de Canarias, Tenerife, Spain
| | - Jaime Santos
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autónoma de Barcelona, Bellaterra, Spain
| | - Noel Mesa-Torres
- Department of Physical Chemistry, University of Granada, Granada, Spain
| | - Silvia Grottelli
- Department of Experimental Medicine, University of Perugia, Piazzale Gambuli, Perugia
| | - Cristina Batlle
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autónoma de Barcelona, Bellaterra, Spain
| | - Athi N Naganathan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras (IITM), Chennai, India
| | - Elisa Oppici
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Strada Le Grazie, Verona, Italy
| | - Barbara Cellini
- Department of Experimental Medicine, University of Perugia, Piazzale Gambuli, Perugia
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autónoma de Barcelona, Bellaterra, Spain
| | - Eduardo Salido
- Centre for Biomedical Research on Rare Diseases, Hospital Universitario de Canarias, Tenerife, Spain
| | - Angel L Pey
- Department of Physical Chemistry, University of Granada, Granada, Spain
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10
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Mesa-Torres N, Betancor-Fernández I, Oppici E, Cellini B, Salido E, Pey AL. Evolutionary Divergent Suppressor Mutations in Conformational Diseases. Genes (Basel) 2018; 9:E352. [PMID: 30011855 PMCID: PMC6071075 DOI: 10.3390/genes9070352] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 07/09/2018] [Accepted: 07/11/2018] [Indexed: 12/26/2022] Open
Abstract
Neutral and adaptive mutations are key players in the evolutionary dynamics of proteins at molecular, cellular and organismal levels. Conversely, largely destabilizing mutations are rarely tolerated by evolution, although their occurrence in diverse human populations has important roles in the pathogenesis of conformational diseases. We have recently proposed that divergence at certain sites from the consensus (amino acid) state during mammalian evolution may have rendered some human proteins more vulnerable towards disease-associated mutations, primarily by decreasing their conformational stability. We herein extend and refine this hypothesis discussing results from phylogenetic and structural analyses, structure-based energy calculations and structure-function studies at molecular and cellular levels. As proof-of-principle, we focus on different mammalian orthologues of the NQO1 (NAD(P)H:quinone oxidoreductase 1) and AGT (alanine:glyoxylate aminotransferase) proteins. We discuss the different loss-of-function pathogenic mechanisms associated with diseases involving the two enzymes, including enzyme inactivation, accelerated degradation, intracellular mistargeting, and aggregation. Last, we take into account the potentially higher robustness of mammalian orthologues containing certain consensus amino acids as suppressors of human disease, and their relation with different intracellular post-translational modifications and protein quality control capacities, to be discussed as sources of phenotypic variability between human and mammalian models of disease and as tools for improving current therapeutic approaches.
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Affiliation(s)
- Noel Mesa-Torres
- Department of Physical Chemistry, University of Granada, 18010 Granada, Spain.
| | - Isabel Betancor-Fernández
- Hospital Universitario de Canarias, Center for Rare Diseases (CIBERER), University of La Laguna, 38320 Tenerife, Spain.
| | - Elisa Oppici
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, 37134 Verona, Italy.
| | - Barbara Cellini
- Department of Experimental Medicine, University of Perugia, 06132 Perugia, Italy.
| | - Eduardo Salido
- Hospital Universitario de Canarias, Center for Rare Diseases (CIBERER), University of La Laguna, 38320 Tenerife, Spain.
| | - Angel L Pey
- Department of Physical Chemistry, University of Granada, 18010 Granada, Spain.
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11
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Oppici E, Dindo M, Conter C, Borri Voltattorni C, Cellini B. Folding Defects Leading to Primary Hyperoxaluria. Handb Exp Pharmacol 2018; 245:313-343. [PMID: 29071511 DOI: 10.1007/164_2017_59] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Protein misfolding is becoming one of the main mechanisms underlying inherited enzymatic deficits. This review is focused on primary hyperoxalurias, a group of disorders of glyoxylate detoxification associated with massive calcium oxalate deposition mainly in the kidneys. The most common and severe form, primary hyperoxaluria Type I, is due to the deficit of liver peroxisomal alanine/glyoxylate aminotransferase (AGT). Various studies performed in the last decade clearly evidence that many pathogenic missense mutations prevent the AGT correct folding, leading to various downstream effects including aggregation, increased degradation or mistargeting to mitochondria. Primary hyperoxaluria Type II and primary hyperoxaluria Type III are due to the deficit of glyoxylate reductase/hydroxypyruvate reductase (GRHPR) and 4-hydroxy-2-oxoglutarate aldolase (HOGA1), respectively. Although the molecular features of pathogenic variants of GRHPR and HOGA1 have not been investigated in detail, the data available suggest that some of them display folding defects. Thus, primary hyperoxalurias can be ranked among protein misfolding disorders, because in most cases the enzymatic deficit is due to the inability of each enzyme to reach its native and functional conformation. It follows that molecules able to improve the folding yield of the enzymes involved in each disease form could represent new therapeutic strategies.
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Affiliation(s)
- Elisa Oppici
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Strada Le Grazie 8, 37134, Verona, Italy
| | - Mirco Dindo
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Strada Le Grazie 8, 37134, Verona, Italy
| | - Carolina Conter
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Strada Le Grazie 8, 37134, Verona, Italy
| | - Carla Borri Voltattorni
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Strada Le Grazie 8, 37134, Verona, Italy.
| | - Barbara Cellini
- Department of Experimental Medicine, University of Perugia, Piazzale Gambuli 1, 06132, Perugia, Italy.
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Martin-Higueras C, Torres A, Salido E. Molecular therapy of primary hyperoxaluria. J Inherit Metab Dis 2017; 40:481-489. [PMID: 28425073 DOI: 10.1007/s10545-017-0045-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 03/20/2017] [Accepted: 04/03/2017] [Indexed: 12/19/2022]
Abstract
During the last few decades, the molecular understanding of the mechanisms involved in primary hyperoxalurias (PHs) has set the stage for novel therapeutic approaches. The availability of PH mouse models has facilitated preclinical studies testing innovative treatments. PHs are autosomal recessive diseases where the enzymatic deficit plays a central pathogenic role. Thus, molecular therapies aimed at restoring such deficit or limiting the consequences of the metabolic derangement could be envisioned, keeping in mind the specific challenges posed by the cell-autonomous nature of the deficiency. Various molecular approaches like enzyme replacement, substrate reduction, pharmacologic chaperones, and gene and cell therapies have been explored in cells and mouse models of disease. Some of these proof-of-concept studies have paved the way to current clinical trials on PH type 1, raising hopes that much needed treatments will become available for this severe inborn error of metabolism.
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Affiliation(s)
- Cristina Martin-Higueras
- Department of Pathology & Nephrology, Centre for Biomedical Research on Rare Diseases (CIBERER) Hospital Universitario Canarias, Universidad La Laguna, Tenerife, Spain
| | - Armando Torres
- Department of Pathology & Nephrology, Centre for Biomedical Research on Rare Diseases (CIBERER) Hospital Universitario Canarias, Universidad La Laguna, Tenerife, Spain
| | - Eduardo Salido
- Department of Pathology & Nephrology, Centre for Biomedical Research on Rare Diseases (CIBERER) Hospital Universitario Canarias, Universidad La Laguna, Tenerife, Spain.
- Department of Pathology, ULL School Medicine, 38320, Tenerife, Spain.
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13
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Affiliation(s)
- Barbara Cellini
- Department of Neuroscience, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Verona (VR), Italy
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14
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Montioli R, Oppici E, Dindo M, Roncador A, Gotte G, Cellini B, Borri Voltattorni C. Misfolding caused by the pathogenic mutation G47R on the minor allele of alanine:glyoxylate aminotransferase and chaperoning activity of pyridoxine. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1280-9. [DOI: 10.1016/j.bbapap.2015.07.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 07/03/2015] [Indexed: 12/22/2022]
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15
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Oppici E, Fargue S, Reid ES, Mills PB, Clayton PT, Danpure CJ, Cellini B. Pyridoxamine and pyridoxal are more effective than pyridoxine in rescuing folding-defective variants of human alanine:glyoxylate aminotransferase causing primary hyperoxaluria type I. Hum Mol Genet 2015. [DOI: 10.1093/hmg/ddv276] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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16
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Mesa-Torres N, Tomic N, Albert A, Salido E, Pey AL. Molecular recognition of PTS-1 cargo proteins by Pex5p: implications for protein mistargeting in primary hyperoxaluria. Biomolecules 2015; 5:121-41. [PMID: 25689234 PMCID: PMC4384115 DOI: 10.3390/biom5010121] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 02/05/2015] [Indexed: 01/29/2023] Open
Abstract
Peroxisomal biogenesis and function critically depends on the import of cytosolic proteins carrying a PTS1 sequence into this organelle upon interaction with the peroxin Pex5p. Recent structural studies have provided important insights into the molecular recognition of cargo proteins by Pex5p. Peroxisomal import is a key feature in the pathogenesis of primary hyperoxaluria type 1 (PH1), where alanine:glyoxylate aminotransferase (AGT) undergoes mitochondrial mistargeting in about a third of patients. Here, we study the molecular recognition of PTS1 cargo proteins by Pex5p using oligopeptides and AGT variants bearing different natural PTS1 sequences, and employing an array of biophysical, computational and cell biology techniques. Changes in affinity for Pex5p (spanning over 3–4 orders of magnitude) reflect different thermodynamic signatures, but overall bury similar amounts of molecular surface. Structure/energetic analyses provide information on the contribution of ancillary regions and the conformational changes induced in Pex5p and the PTS1 cargo upon complex formation. Pex5p stability in vitro is enhanced upon cargo binding according to their binding affinities. Moreover, we provide evidence that the rational modulation of the AGT: Pex5p binding affinity might be useful tools to investigate mistargeting and misfolding in PH1 by pulling the folding equilibria towards the native and peroxisomal import competent state.
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Affiliation(s)
- Noel Mesa-Torres
- Department of Physical Chemistry, Faculty of Sciences, University of Granada, Av. Fuentenueva s/n, 18071 Granada, Spain.
| | - Nenad Tomic
- Center for Biomedical Research on Rare Diseases (CIBERER), University Hospital of the Canary Islands and CIBICAN, University of La Laguna, 38320 Tenerife, Spain.
| | - Armando Albert
- Departamento de Cristalografía y Biología Estructural, Instituto de Química-Física "Rocasolano", Consejo Superior de Investigaciones Científicas, C/Serrano 119, 28006 Madrid, Spain.
| | - Eduardo Salido
- Center for Biomedical Research on Rare Diseases (CIBERER), University Hospital of the Canary Islands and CIBICAN, University of La Laguna, 38320 Tenerife, Spain.
| | - Angel L Pey
- Department of Physical Chemistry, Faculty of Sciences, University of Granada, Av. Fuentenueva s/n, 18071 Granada, Spain.
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