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Tsishyn M, Cia G, Hermans P, Kwasigroch J, Rooman M, Pucci F. FiTMuSiC: leveraging structural and (co)evolutionary data for protein fitness prediction. Hum Genomics 2024; 18:36. [PMID: 38627807 PMCID: PMC11020440 DOI: 10.1186/s40246-024-00605-9] [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: 08/01/2023] [Accepted: 04/02/2024] [Indexed: 04/19/2024] Open
Abstract
Systematically predicting the effects of mutations on protein fitness is essential for the understanding of genetic diseases. Indeed, predictions complement experimental efforts in analyzing how variants lead to dysfunctional proteins that in turn can cause diseases. Here we present our new fitness predictor, FiTMuSiC, which leverages structural, evolutionary and coevolutionary information. We show that FiTMuSiC predicts fitness with high accuracy despite the simplicity of its underlying model: it was among the top predictors on the hydroxymethylbilane synthase (HMBS) target of the sixth round of the Critical Assessment of Genome Interpretation challenge (CAGI6) and performs as well as much more complex deep learning models such as AlphaMissense. To further demonstrate FiTMuSiC's robustness, we compared its predictions with in vitro activity data on HMBS, variant fitness data on human glucokinase (GCK), and variant deleteriousness data on HMBS and GCK. These analyses further confirm FiTMuSiC's qualities and accuracy, which compare favorably with those of other predictors. Additionally, FiTMuSiC returns two scores that separately describe the functional and structural effects of the variant, thus providing mechanistic insight into why the variant leads to fitness loss or gain. We also provide an easy-to-use webserver at https://babylone.ulb.ac.be/FiTMuSiC , which is freely available for academic use and does not require any bioinformatics expertise, which simplifies the accessibility of our tool for the entire scientific community.
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Affiliation(s)
- Matsvei Tsishyn
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, 50 Roosevelt Ave, 1050, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Triumph Bvd, 1050, Brussels, Belgium
| | - Gabriel Cia
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, 50 Roosevelt Ave, 1050, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Triumph Bvd, 1050, Brussels, Belgium
| | - Pauline Hermans
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, 50 Roosevelt Ave, 1050, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Triumph Bvd, 1050, Brussels, Belgium
| | - Jean Kwasigroch
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, 50 Roosevelt Ave, 1050, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Triumph Bvd, 1050, Brussels, Belgium
| | - Marianne Rooman
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, 50 Roosevelt Ave, 1050, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Triumph Bvd, 1050, Brussels, Belgium
| | - Fabrizio Pucci
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, 50 Roosevelt Ave, 1050, Brussels, Belgium.
- Interuniversity Institute of Bioinformatics in Brussels, Triumph Bvd, 1050, Brussels, Belgium.
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2
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Bustad HJ, Christie MS, Laitaoja M, Aarsand AK, Martinez A, Jänis J, Kallio JP. One ring closer to a closure: the crystal structure of the ES 3 hydroxymethylbilane synthase intermediate. FEBS J 2024; 291:510-526. [PMID: 37863644 DOI: 10.1111/febs.16982] [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: 07/07/2023] [Revised: 09/08/2023] [Accepted: 10/17/2023] [Indexed: 10/22/2023]
Abstract
Hydroxymethylbilane synthase (HMBS), involved in haem biosynthesis, catalyses the head-to-tail coupling of four porphobilinogens (PBGs) via a dipyrromethane (DPM) cofactor. DPM is composed of two PBGs, and a hexapyrrole is built before the tetrapyrrolic 1-hydroxymethylbilane product is released. During this elongation, stable enzyme (E) intermediates are formed from the holoenzyme, with additional PBG substrates (S): ES, ES2 , ES3 and ES4 . Native PAGE and mass spectrometry of the acute intermittent porphyria (AIP)-associated HMBS variant p.Arg167Gln demonstrated an increased amount of ES3 . Kinetic parameters indicated catalytic dysfunction, however, the product release was not entirely prevented. Isolation and crystal structure analysis of the ES3 intermediate (PDB: 8PND) showed that a pentapyrrole was fully retained within the active site, revealing that polypyrrole elongation proceeds within the active site via a third interaction site, intermediate pyrrole site 3 (IPS3). The AIP-associated HMBS variant p.Arg195Cys, located on the opposite side to p.Arg167Gln in the active site, accumulated the ES4 intermediate in the presence of excess PBG, implying that product hydrolysis was obstructed. Arg167 is thus involved in all elongation steps and is a determinant for the rate of enzyme catalysis, whereas Arg195 is important for releasing the product. Moreover, by substituting residues in the vicinity of IPS3, our results indicate that a fully retained hexapyrrole could be hydrolysed in a novel site in proximity of the IPS3.
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Affiliation(s)
- Helene J Bustad
- Norwegian Porphyria Centre (NAPOS), Department for Medical Biochemistry and Pharmacology, Haukeland University Hospital, Bergen, Norway
| | - Marthe S Christie
- Norwegian Porphyria Centre (NAPOS), Department for Medical Biochemistry and Pharmacology, Haukeland University Hospital, Bergen, Norway
| | - Mikko Laitaoja
- Department of Chemistry, University of Eastern Finland, Joensuu, Finland
| | - Aasne K Aarsand
- Norwegian Porphyria Centre (NAPOS), Department for Medical Biochemistry and Pharmacology, Haukeland University Hospital, Bergen, Norway
- Norwegian Organization for Quality Improvement of Laboratory Examinations, Haraldsplass Deaconess Hospital, Bergen, Norway
| | | | - Janne Jänis
- Department of Chemistry, University of Eastern Finland, Joensuu, Finland
| | - Juha P Kallio
- Department of Biomedicine, University of Bergen, Norway
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3
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van Loggerenberg W, Sowlati-Hashjin S, Weile J, Hamilton R, Chawla A, Sheykhkarimli D, Gebbia M, Kishore N, Frésard L, Mustajoki S, Pischik E, Di Pierro E, Barbaro M, Floderus Y, Schmitt C, Gouya L, Colavin A, Nussbaum R, Friesema ECH, Kauppinen R, To-Figueras J, Aarsand AK, Desnick RJ, Garton M, Roth FP. Systematically testing human HMBS missense variants to reveal mechanism and pathogenic variation. Am J Hum Genet 2023; 110:1769-1786. [PMID: 37729906 PMCID: PMC10577081 DOI: 10.1016/j.ajhg.2023.08.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 08/15/2023] [Accepted: 08/21/2023] [Indexed: 09/22/2023] Open
Abstract
Defects in hydroxymethylbilane synthase (HMBS) can cause acute intermittent porphyria (AIP), an acute neurological disease. Although sequencing-based diagnosis can be definitive, ∼⅓ of clinical HMBS variants are missense variants, and most clinically reported HMBS missense variants are designated as "variants of uncertain significance" (VUSs). Using saturation mutagenesis, en masse selection, and sequencing, we applied a multiplexed validated assay to both the erythroid-specific and ubiquitous isoforms of HMBS, obtaining confident functional impact scores for >84% of all possible amino acid substitutions. The resulting variant effect maps generally agreed with biochemical expectations and provide further evidence that HMBS can function as a monomer. Additionally, the maps implicated specific residues as having roles in active site dynamics, which was further supported by molecular dynamics simulations. Most importantly, these maps can help discriminate pathogenic from benign HMBS variants, proactively providing evidence even for yet-to-be-observed clinical missense variants.
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Affiliation(s)
- Warren van Loggerenberg
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON M5G 1X5, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada
| | | | - Jochen Weile
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON M5G 1X5, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada
| | - Rayna Hamilton
- Advanced Academic Programs, Johns Hopkins University, Washington, DC 20036, USA
| | - Aditya Chawla
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON M5G 1X5, Canada
| | - Dayag Sheykhkarimli
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON M5G 1X5, Canada
| | - Marinella Gebbia
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON M5G 1X5, Canada
| | - Nishka Kishore
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON M5G 1X5, Canada
| | | | - Sami Mustajoki
- Research Program in Molecular Medicine, Biomedicum-Helsinki, University of Helsinki, 00290 Helsinki, Finland
| | - Elena Pischik
- Research Program in Molecular Medicine, Biomedicum-Helsinki, University of Helsinki, 00290 Helsinki, Finland
| | - Elena Di Pierro
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Unit of Medicine and Metabolic Diseases, 20122 Milano, Italy
| | - Michela Barbaro
- Porphyria Centre Sweden, Centre for Inherited Metabolic Diseases, Karolinska Institutet, Karolinska University Hospital, 17176 Stockholm, Sweden
| | - Ylva Floderus
- Porphyria Centre Sweden, Centre for Inherited Metabolic Diseases, Karolinska Institutet, Karolinska University Hospital, 17176 Stockholm, Sweden
| | - Caroline Schmitt
- Centre français des porphyries, hôpital Louis-Mourier, Assistance Publique-Hopitaux de Paris, 92701 Colombes, France; Centre de recherche sur l'inflammation, Université Paris Cité, UMR1149 INSERM, 75018 Paris, France
| | - Laurent Gouya
- Centre français des porphyries, hôpital Louis-Mourier, Assistance Publique-Hopitaux de Paris, 92701 Colombes, France; Centre de recherche sur l'inflammation, Université Paris Cité, UMR1149 INSERM, 75018 Paris, France
| | | | | | - Edith C H Friesema
- Porphyria Expertcenter Rotterdam, Center for Lysosomal and Metabolic Diseases, Department of Internal Medicine, Erasmus MC, 3015 Rotterdam, the Netherlands
| | - Raili Kauppinen
- Research Program in Molecular Medicine, Biomedicum-Helsinki, University of Helsinki, 00290 Helsinki, Finland
| | - Jordi To-Figueras
- Biochemistry and Molecular Genetics Department, Hospital Clínic, IDIBAPS, University of Barcelona, 08036 Barcelona, Spain
| | - Aasne K Aarsand
- Norwegian Porphyria Centre, Department of Medical Biochemistry and Pharmacology, Haukeland University Hospital, 5021 Bergen, Norway
| | - Robert J Desnick
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michael Garton
- Institute Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada.
| | - Frederick P Roth
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON M5G 1X5, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada.
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4
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van Loggerenberg W, Sowlati-Hashjin S, Weile J, Hamilton R, Chawla A, Gebbia M, Kishore N, Frésard L, Mustajoki S, Pischik E, Di Pierro E, Barbaro M, Floderus Y, Schmitt C, Gouya L, Colavin A, Nussbaum R, Friesema ECH, Kauppinen R, To-Figueras J, Aarsand AK, Desnick RJ, Garton M, Roth FP. Systematically testing human HMBS missense variants to reveal mechanism and pathogenic variation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.06.527353. [PMID: 36798224 PMCID: PMC9934555 DOI: 10.1101/2023.02.06.527353] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Defects in hydroxymethylbilane synthase (HMBS) can cause Acute Intermittent Porphyria (AIP), an acute neurological disease. Although sequencing-based diagnosis can be definitive, ~⅓ of clinical HMBS variants are missense variants, and most clinically-reported HMBS missense variants are designated as "variants of uncertain significance" (VUS). Using saturation mutagenesis, en masse selection, and sequencing, we applied a multiplexed validated assay to both the erythroid-specific and ubiquitous isoforms of HMBS, obtaining confident functional impact scores for >84% of all possible amino-acid substitutions. The resulting variant effect maps generally agreed with biochemical expectation. However, the maps showed variants at the dimerization interface to be unexpectedly well tolerated, and suggested residue roles in active site dynamics that were supported by molecular dynamics simulations. Most importantly, these HMBS variant effect maps can help discriminate pathogenic from benign variants, proactively providing evidence even for yet-to-be-observed clinical missense variants.
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Affiliation(s)
- Warren van Loggerenberg
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Shahin Sowlati-Hashjin
- Institute of Biomedical Engineering, University of Toronto, ON, Canada
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, ON, Canada
| | - Jochen Weile
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Rayna Hamilton
- Advanced Academic Programs, Johns Hopkins University, Washington, DC, USA
| | - Aditya Chawla
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | - Marinella Gebbia
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | - Nishka Kishore
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | | | - Sami Mustajoki
- Research Program in Molecular Medicine, Biomedicum-Helsinki, University of Helsinki
| | - Elena Pischik
- Research Program in Molecular Medicine, Biomedicum-Helsinki, University of Helsinki
| | - Elena Di Pierro
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Unit of Medicine and Metabolic Diseases, Milan, Italy
| | - Michela Barbaro
- Porphyria Centre Sweden, Centre for Inherited Metabolic Diseases, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Ylva Floderus
- Porphyria Centre Sweden, Centre for Inherited Metabolic Diseases, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Caroline Schmitt
- Centre Français des Porphyries, Hôpital Louis Mourier, Assistance Publique-Hôpitaux de Paris, Colombes and Centre de Recherche sur l’Inflammation, UMR1149 INSERM, Université Paris Cité, Paris, France
| | - Laurent Gouya
- Centre Français des Porphyries, Hôpital Louis Mourier, Assistance Publique-Hôpitaux de Paris, Colombes and Centre de Recherche sur l’Inflammation, UMR1149 INSERM, Université Paris Cité, Paris, France
| | | | | | - Edith C. H. Friesema
- Porphyria Expertcenter Rotterdam, Center for Lysosomal and Metabolic Diseases, Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, the Netherlands
| | - Raili Kauppinen
- Research Program in Molecular Medicine, Biomedicum-Helsinki, University of Helsinki
| | - Jordi To-Figueras
- Biochemistry and Molecular Genetics Department, Hospital Clínic, IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Aasne K Aarsand
- Norwegian Porphyria Centre, Department of Medical Biochemistry and Pharmacology, Haukeland University Hospital, Bergen, Norway
| | - Robert J. Desnick
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael Garton
- Institute of Biomedical Engineering, University of Toronto, ON, Canada
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, ON, Canada
| | - Frederick P. Roth
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
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5
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Christie MS, Laitaoja M, Aarsand AK, Kallio JP, Bustad HJ. Characterisation of a common hotspot variant in acute intermittent porphyria sheds light on the mechanism of hydroxymethylbilane synthase function. FEBS Open Bio 2022; 12:2136-2146. [PMID: 36115019 PMCID: PMC9714363 DOI: 10.1002/2211-5463.13490] [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: 04/25/2022] [Revised: 08/10/2022] [Accepted: 09/16/2022] [Indexed: 01/25/2023] Open
Abstract
Hydroxymethylbilane synthase (HMBS) is the third enzyme involved in haem biosynthesis, in which it catalyses the formation of tetrapyrrole 1-hydroxymethylbilane (HMB). In this process, HMBS binds four consecutive substrate molecules, creating the enzyme-intermediate complexes ES, ES2 , ES3 and ES4 . Pathogenic variants in the HMBS gene are associated with the dominantly inherited disorder acute intermittent porphyria. In this study, we have characterised the p.R26H variant to shed light on the role of Arg26 in the elongation mechanism of HMBS and to provide insights into its effect on the enzyme. With selected biophysical methods, we have been able to show that p.R26H forms a single enzyme-intermediate complex in the ES2 -state. We were also able to demonstrate that the p.R26H variant results in an inactive enzyme, which is unable to produce the HMB product.
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Affiliation(s)
- Marthe S. Christie
- Department of BiomedicineUniversity of BergenNorway,Norwegian Porphyria Centre (NAPOS), Department for Medical Biochemistry and PharmacologyHaukeland University HospitalBergenNorway
| | - Mikko Laitaoja
- Department of ChemistryUniversity of Eastern FinlandJoensuuFinland
| | - Aasne K. Aarsand
- Norwegian Porphyria Centre (NAPOS), Department for Medical Biochemistry and PharmacologyHaukeland University HospitalBergenNorway,Norwegian Organization for Quality Improvement of Laboratory ExaminationsHaraldsplass Deaconess HospitalBergenNorway
| | | | - Helene J. Bustad
- Norwegian Porphyria Centre (NAPOS), Department for Medical Biochemistry and PharmacologyHaukeland University HospitalBergenNorway
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6
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Helliwell JR. The crystal structures of the enzyme hydroxymethylbilane synthase, also known as porphobilinogen deaminase. Acta Crystallogr F Struct Biol Commun 2021; 77:388-398. [PMID: 34726177 PMCID: PMC8561815 DOI: 10.1107/s2053230x2100964x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 09/16/2021] [Indexed: 12/03/2022] Open
Abstract
The enzyme hydroxymethylbilane synthase (HMBS; EC 4.3.1.8), also known as porphobilinogen deaminase, catalyses the stepwise addition of four molecules of porphobilinogen to form the linear tetrapyrrole 1-hydroxymethylbilane. Thirty years of crystal structures are surveyed in this topical review. These crystal structures aim at the elucidation of the structural basis of the complex reaction mechanism involving the formation of tetrapyrrole from individual porphobilinogen units. The consistency between the various structures is assessed. This includes an evaluation of the precision of each molecular model and what was not modelled. A survey is also made of the crystallization conditions used in the context of the operational pH of the enzyme. The combination of 3D structural techniques, seeking accuracy, has also been a feature of this research effort. Thus, SAXS, NMR and computational molecular dynamics have also been applied. The general framework is also a considerable chemistry research effort to understand the function of the enzyme and its medical pathologies in acute intermittent porphyria (AIP). Mutational studies and their impact on the catalytic reaction provide insight into the basis of AIP and are also invaluable for guiding the understanding of the crystal structure results. Future directions for research on HMBS are described, including the need to determine the protonation states of key amino-acid residues identified as being catalytically important. The question remains - what is the molecular engine for this complex reaction? Thermal fluctuations are the only suggestion thus far.
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Affiliation(s)
- John R. Helliwell
- Department of Chemistry, University of Manchester, Manchester M13 9PL, United Kingdom
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7
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Helliwell JR. Combining X-rays, neutrons and electrons, and NMR, for precision and accuracy in structure-function studies. Acta Crystallogr A Found Adv 2021; 77:173-185. [PMID: 33944796 PMCID: PMC8127390 DOI: 10.1107/s205327332100317x] [Citation(s) in RCA: 6] [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: 02/14/2021] [Accepted: 03/25/2021] [Indexed: 02/02/2023] Open
Abstract
The distinctive features of the physics-based probes used in understanding the structure of matter focusing on biological sciences, but not exclusively, are described in the modern context. This is set in a wider scope of holistic biology and the scepticism about `reductionism', what is called the `molecular level', and how to respond constructively. These topics will be set alongside the principles of accuracy and precision, and their boundaries. The combination of probes and their application together is the usual way of realizing accuracy. The distinction between precision and accuracy can be blurred by the predictive force of a precise structure, thereby lending confidence in its potential accuracy. These descriptions will be applied to the comparison of cryo and room-temperature protein crystal structures as well as the solid state of a crystal and the same molecules studied by small-angle X-ray scattering in solution and by electron microscopy on a sample grid. Examples will include: time-resolved X-ray Laue crystallography of an enzyme Michaelis complex formed directly in a crystal equivalent to in vivo; a new iodoplatin for radiation therapy predicted from studies of platin crystal structures; and the field of colouration of carotenoids, as an effective assay of function, i.e. their colouration, when unbound and bound to a protein. The complementarity of probes, as well as their combinatory use, is then at the foundation of real (biologically relevant), probe-artefacts-free, structure-function studies. The foundations of our methodologies are being transformed by colossal improvements in technologies of X-ray and neutron sources and their beamline instruments, as well as improved electron microscopes and NMR spectrometers. The success of protein structure prediction from gene sequence recently reported by CASP14 also opens new doors to change and extend the foundations of the structural sciences.
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Affiliation(s)
- John R. Helliwell
- Department of Chemistry, University of Manchester, Manchester, M13 9PL, United Kingdom
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8
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Bustad HJ, Kallio JP, Vorland M, Fiorentino V, Sandberg S, Schmitt C, Aarsand AK, Martinez A. Acute Intermittent Porphyria: An Overview of Therapy Developments and Future Perspectives Focusing on Stabilisation of HMBS and Proteostasis Regulators. Int J Mol Sci 2021; 22:E675. [PMID: 33445488 PMCID: PMC7827610 DOI: 10.3390/ijms22020675] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 01/02/2021] [Accepted: 01/04/2021] [Indexed: 12/21/2022] Open
Abstract
Acute intermittent porphyria (AIP) is an autosomal dominant inherited disease with low clinical penetrance, caused by mutations in the hydroxymethylbilane synthase (HMBS) gene, which encodes the third enzyme in the haem biosynthesis pathway. In susceptible HMBS mutation carriers, triggering factors such as hormonal changes and commonly used drugs induce an overproduction and accumulation of toxic haem precursors in the liver. Clinically, this presents as acute attacks characterised by severe abdominal pain and a wide array of neurological and psychiatric symptoms, and, in the long-term setting, the development of primary liver cancer, hypertension and kidney failure. Treatment options are few, and therapies preventing the development of symptomatic disease and long-term complications are non-existent. Here, we provide an overview of the disorder and treatments already in use in clinical practice, in addition to other therapies under development or in the pipeline. We also introduce the pathomechanistic effects of HMBS mutations, and present and discuss emerging therapeutic options based on HMBS stabilisation and the regulation of proteostasis. These are novel mechanistic therapeutic approaches with the potential of prophylactic correction of the disease by totally or partially recovering the enzyme functionality. The present scenario appears promising for upcoming patient-tailored interventions in AIP.
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Affiliation(s)
- Helene J. Bustad
- Department of Biomedicine, University of Bergen, 5020 Bergen, Norway; (H.J.B.); (J.P.K.)
| | - Juha P. Kallio
- Department of Biomedicine, University of Bergen, 5020 Bergen, Norway; (H.J.B.); (J.P.K.)
| | - Marta Vorland
- Norwegian Porphyria Centre (NAPOS), Department for Medical Biochemistry and Pharmacology, Haukeland University Hospital, 5021 Bergen, Norway; (M.V.); (S.S.)
| | - Valeria Fiorentino
- INSERM U1149, Center for Research on Inflammation (CRI), Université de Paris, 75018 Paris, France; (V.F.); (C.S.)
| | - Sverre Sandberg
- Norwegian Porphyria Centre (NAPOS), Department for Medical Biochemistry and Pharmacology, Haukeland University Hospital, 5021 Bergen, Norway; (M.V.); (S.S.)
- Norwegian Organization for Quality Improvement of Laboratory Examinations (Noklus), Haraldsplass Deaconess Hospital, 5009 Bergen, Norway
| | - Caroline Schmitt
- INSERM U1149, Center for Research on Inflammation (CRI), Université de Paris, 75018 Paris, France; (V.F.); (C.S.)
- Assistance Publique Hôpitaux de Paris (AP-HP), Centre Français des Porphyries, Hôpital Louis Mourier, 92700 Colombes, France
| | - Aasne K. Aarsand
- Norwegian Porphyria Centre (NAPOS), Department for Medical Biochemistry and Pharmacology, Haukeland University Hospital, 5021 Bergen, Norway; (M.V.); (S.S.)
- Norwegian Organization for Quality Improvement of Laboratory Examinations (Noklus), Haraldsplass Deaconess Hospital, 5009 Bergen, Norway
| | - Aurora Martinez
- Department of Biomedicine, University of Bergen, 5020 Bergen, Norway; (H.J.B.); (J.P.K.)
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