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Quelhas D, Carneiro J, Lopes-Marques M, Jaeken J, Martins E, Rocha JF, Teixeira Carla SS, Ferreira CR, Sousa SF, Azevedo L. Assessing the effects of PMM2 variants on protein stability. Mol Genet Metab 2021; 134:344-352. [PMID: 34863624 DOI: 10.1016/j.ymgme.2021.11.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/30/2021] [Accepted: 11/02/2021] [Indexed: 11/16/2022]
Abstract
Phosphomannomutase 2 deficiency, PMM2-CDG, is the most frequent disorder of protein N-glycosylation. It is an autosomal recessive disease with a broad clinical and biochemical phenotype. Trying to predict the impact of novel variants is often a challenge due to the high number of variants and the difficulty to establish solid genotype-phenotype correlations. A potential useful strategy is to use computational chemistry calculations as a tool from which relevant information on the structural impact of novel variants may be deduced. Here we present our analyses based on four well-known PMM2 deleterious variants (p.(Leu32Arg), p.(Asp65Tyr), p.(Phe119Leu), p.(Arg141His)) and the polymorphic p.(Glu197Ala) for which we have predicted the effect on protein stability. Our work predicts the effect of different amino acid residues on the conformation and stability of PMM2. These computational simulations are, therefore, an extremely useful methodology which, in combination with routinely used in silico methods of pathogenicity prediction, may help to reveal the structural impact of novel variants at the protein level, potentially leading to a better understanding of target biological molecules.
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Affiliation(s)
- D Quelhas
- Unidade de Bioquímica Genética, Centro de Genética Médica, Centro Hospitalar Universitário do Porto, Porto, Portugal; Unit for Multidisciplinary Research in Biomedicine, ICBAS, UP, Porto, Portugal; Centro Referência Doenças Hereditárias do Metabolismo, Centro Hospitalar Universitário do Porto, Porto, Portugal.
| | - J Carneiro
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, Matosinhos, Portugal
| | - M Lopes-Marques
- i3S- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal; IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal; FCUP-Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - J Jaeken
- Center for Metabolic Diseases, KU Leuven, Leuven, Belgium
| | - E Martins
- Unit for Multidisciplinary Research in Biomedicine, ICBAS, UP, Porto, Portugal; Centro Referência Doenças Hereditárias do Metabolismo, Centro Hospitalar Universitário do Porto, Porto, Portugal
| | - J F Rocha
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal; UCIBIO - Applied Molecular Biosciences Unit, BioSIM - Department of Biomedicine, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
| | - S S Teixeira Carla
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal; UCIBIO - Applied Molecular Biosciences Unit, BioSIM - Department of Biomedicine, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
| | - C R Ferreira
- Skeletal Genomics Unit, Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - S F Sousa
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal; UCIBIO - Applied Molecular Biosciences Unit, BioSIM - Department of Biomedicine, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
| | - L Azevedo
- i3S- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal; IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal; FCUP-Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
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