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Horri-Naceur A, Timson DJ. In Silico Analysis of the Effects of Point Mutations on α-Globin: Implications for α-Thalassemia. Hemoglobin 2020; 44:89-103. [PMID: 32420790 DOI: 10.1080/03630269.2020.1739067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Hemoglobinopathies are inherited diseases that impair the structure and function of the oxygen-carrying pigment hemoglobin (Hb). Adult Hb consists of two α and two β subunits. α-Thalassemia (α-thal) affects the genes that code for the α-globin chains, HBA1 and HBA2. Mutations can result in asymptomatic, mild or severe outcomes depending on several factors, such as mutation type, number of mutations and the location at which they occur. PredictSNP was used to estimate whether every possible single nucleotide polymorphism (SNP) would have a neutral or deleterious effect on the protein. These results were then used to create a plot of predicted tolerance to change for each residue in the protein. Tolerance to change was negatively correlated with the residue's sequence conservation score. The PredictSNP data were compared to clinical reports of 110 selected variants in the literature. There were 29 disagreements between the two data types. Some of these could be resolved by considering the role of the affected residue in binding other molecules. The three-dimensional structures of some of these variant proteins were modeled. These models helped explain variants which affect heme binding. We predict that where a point mutation alters a residue that is intolerant to change, is well conserved and or involved in interactions, it is likely to be associated with disease. Overall, the data from this study could be used alongside biochemical and clinical data to assess novel α-globin variants.
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Affiliation(s)
- Agathe Horri-Naceur
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, East Sussex, UK
| | - David J Timson
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, East Sussex, UK
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Scheps KG, Hasenahuer MA, Parisi G, Targovnik HM, Fornasari MS. Curating the gnomAD database: Report of novel variants in the globin-coding genes and bioinformatics analysis. Hum Mutat 2019; 41:81-102. [PMID: 31553106 DOI: 10.1002/humu.23925] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 09/14/2019] [Accepted: 09/23/2019] [Indexed: 02/02/2023]
Abstract
Massive parallel sequencing technologies are facilitating the faster identification of sequence variants with the consequent capability of untangling the molecular bases of many human genetic syndromes. However, it is not always easy to understand the impact of novel variants, especially for missense changes, which can lead to a spectrum of phenotypes. This study presents a custom-designed multistep methodology to evaluate the impact of novel variants aggregated in the genome aggregation database for the HBB, HBA2, and HBA1 genes, by testing and improving its performance with a dataset of previously described alterations affecting those same genes. This approach scored high sensitivity and specificity values and showed an overall better performance than sequence-derived predictors, highlighting the importance of protein conformation and interaction specific analyses in curating variant databases. This study also describes the strengths and limitations of these structural studies and allows identifying residues in the globin chains more prone to tolerate substitutions.
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Affiliation(s)
- Karen G Scheps
- Departamento de Microbiología, Inmunología, Biotecnología y Genética, Cátedra de Genética, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Inmunología, Genética y Metabolismo (INIGEM), Universidad de Buenos Aires - CONICET, Buenos Aires, Argentina
| | - Marcia A Hasenahuer
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Argentina.,European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, United Kingdom.,Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Gustavo Parisi
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Héctor M Targovnik
- Departamento de Microbiología, Inmunología, Biotecnología y Genética, Cátedra de Genética, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Inmunología, Genética y Metabolismo (INIGEM), Universidad de Buenos Aires - CONICET, Buenos Aires, Argentina
| | - María S Fornasari
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Argentina
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Hoyer JD, McCormick DJ, Snow K, Kwon JH, Booth D, Duarte M, Grayson G, Kubik KS, Holmes MW, Fairbanks VF. Four new variants of the alpha2-globin gene without clinical or hematologic effects: Hb Park Ridge [alpha9(alpha7)Asn-->Lys (alpha2)], Hb Norton [alpha72(EF1)His-->Asp (alpha2)], Hb Lombard [alpha103(G10)His-->Tyr (alpha2)], and Hb San Antonio [A113(GH2)Leu-->Arg (A2)]. Hemoglobin 2002; 26:175-9. [PMID: 12144061 DOI: 10.1081/hem-120005456] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- James D Hoyer
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
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Sivaram MV, Sudha R, Roy RP. A role for the alpha 113 (GH1) amino acid residue in the polymerization of sickle hemoglobin. Evaluation of its inhibitory strength and interaction linkage with two fiber contact sites (alpha 16/23) located in the AB region of the alpha-chain. J Biol Chem 2001; 276:18209-15. [PMID: 11259442 DOI: 10.1074/jbc.m101788200] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A cluster of amino acid residues located in the AB-GH region of the alpha-chain are shown in intra-double strand axial interactions of the hemoglobin S (HbS) polymer. However, alphaLeu-113 (GH1) located in the periphery is not implicated in any interactions by either crystal structure or models of the fiber, and its role in HbS polymerization has not been explored by solution experiments. We have constructed HbS Twin Peaks (betaGlu-6-->Val, alphaLeu-113-->His) to ascertain the hitherto unknown role of the alpha113 site in the polymerization process. The structural and functional behavior of HbS Twin Peaks was comparable with HbS. HbS Twin Peaks polymerized with a slower rate compared with HbS, and its polymer solubility (C(sat)) was found to be about 1.8-fold higher than HbS. To further authenticate the participation of the alpha113 site in the polymerization process as well as to evaluate its relative inhibitory strength, we constructed HbS tetramers in which the alpha113 mutation was coupled individually with two established fiber contact sites (alpha16 and alpha23) located in the AB region of the alpha-chain: HbS(alphaLys-16-->Gln, alphaLeu-113-->His), HbS(alphaGlu-23-->Gln, alphaLeu-113-->His). The single mutants at alpha16/alpha23 sites were also engineered as controls. The C(sat) values of the HbS point mutants involving sites alpha16 or alpha23 were higher than HbS but markedly lower as compared with HbS Twin Peaks. In contrast, C(sat) values of both double mutants were comparable with or higher than that of HbS Twin Peaks. The demonstration of the inhibitory effect of alpha113 mutation alone or in combination with other sites, in quantitative terms, unequivocally establishes a role for this site in HbS gelation. These results have implications for development of a more accurate model of the fiber that could serve as a blueprint for therapeutic intervention.
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Affiliation(s)
- M V Sivaram
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
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Liebhaber SA, Cash FE, Ballas SK. Human alpha-globin gene expression. The dominant role of the alpha 2-locus in mRNA and protein synthesis. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(18)66871-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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