In Silico Evaluation of the Potential Association of the Pathogenic Mutations of Alpha Synuclein Protein with Induction of Synucleinopathies
Alpha synuclein (α-Syn) is a neuronal protein encoded by the SNCA gene and is involved in the development of Parkinson’s disease (PD). The objective of this study was to examine in silico the functional implications of non-synonymous single nucleotide polymorphisms (nsSNPs) in the SNCA gene. We used...
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MDPI AG
2023-09-01
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| author | Mohamed E. Elnageeb Imadeldin Elfaki Khalid M. Adam Elsadig Mohamed Ahmed Elkhalifa M. Elkhalifa Hytham A. Abuagla Abubakr Ali Elamin Mohamed Ahmed Elshazali Widaa Ali Elmoiz Idris Eltieb Ali M. Edris |
| author_facet | Mohamed E. Elnageeb Imadeldin Elfaki Khalid M. Adam Elsadig Mohamed Ahmed Elkhalifa M. Elkhalifa Hytham A. Abuagla Abubakr Ali Elamin Mohamed Ahmed Elshazali Widaa Ali Elmoiz Idris Eltieb Ali M. Edris |
| author_sort | Mohamed E. Elnageeb |
| collection | DOAJ |
| description | Alpha synuclein (α-Syn) is a neuronal protein encoded by the SNCA gene and is involved in the development of Parkinson’s disease (PD). The objective of this study was to examine in silico the functional implications of non-synonymous single nucleotide polymorphisms (nsSNPs) in the SNCA gene. We used a range of computational algorithms such as sequence conservation, structural analysis, physicochemical properties, and machine learning. The sequence of the SNCA gene was analyzed, resulting in the mapping of 42,272 SNPs that are classified into different functional categories. A total of 177 nsSNPs were identified within the coding region; there were 20 variants that may influence the α-Syn protein structure and function. This identification was made by employing different analytical tools including SIFT, PolyPhen2, Mut-pred, SNAP2, PANTHER, PhD-SNP, SNP&Go, MUpro, Cosurf, I-Mut, and HOPE. Three mutations, V82A, K80E, and E46K, were selected for further examinations due to their spatial positioning within the α-Syn as determined by PyMol. Results indicated that these mutations may affect the stability and function of α-Syn. Then, a molecular dynamics simulation was conducted for the SNCA wildtype and the four mutant variants (p.A18G, p.V82A, p.K80E, and p.E46K). The simulation examined temperature, pressure, density, root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), solvent-accessible surface area (SASA), and radius of gyration (Rg). The data indicate that the mutations p.V82A, p.K80E, and p.E46K reduce the stability and functionality of α-Syn. These findings highlight the importance of understanding the impact of nsSNPs on α-syn structure and function. Our results required verifications in further protein functional and case–control studies. After being verified these findings can be used in genetic testing for the early diagnosis of PD, the evaluation of the risk factors, and therapeutic approaches. |
| first_indexed | 2024-03-10T22:52:13Z |
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| id | doaj.art-7e4efb7a3b474742a149683a58dd6c02 |
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| issn | 2079-9721 |
| language | English |
| last_indexed | 2024-03-10T22:52:13Z |
| publishDate | 2023-09-01 |
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| series | Diseases |
| spelling | doaj.art-7e4efb7a3b474742a149683a58dd6c022023-11-19T10:15:28ZengMDPI AGDiseases2079-97212023-09-0111311510.3390/diseases11030115In Silico Evaluation of the Potential Association of the Pathogenic Mutations of Alpha Synuclein Protein with Induction of SynucleinopathiesMohamed E. Elnageeb0Imadeldin Elfaki1Khalid M. Adam2Elsadig Mohamed Ahmed3Elkhalifa M. Elkhalifa4Hytham A. Abuagla5Abubakr Ali Elamin Mohamed Ahmed6Elshazali Widaa Ali7Elmoiz Idris Eltieb8Ali M. Edris9Department of Basic Sciences, College of Applied Medical Sciences, University of Bisha, P.O. Box 551, Bisha 61922, Saudi ArabiaDepartment of Biochemistry, Faculty of Science, University of Tabuk, P.O. Box 741, Tabuk 71491, Saudi ArabiaDepartment of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, P.O. Box 551, Bisha 61922, Saudi ArabiaDepartment of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, P.O. Box 551, Bisha 61922, Saudi ArabiaDepartment of Anatomy, Faculty of Medicine and Health Sciences, Nile Valley University, Atbara 46611, SudanDepartment of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, P.O. Box 551, Bisha 61922, Saudi ArabiaDepartment of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, P.O. Box 551, Bisha 61922, Saudi ArabiaDepartment of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, P.O. Box 551, Bisha 61922, Saudi ArabiaDepartment of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, P.O. Box 551, Bisha 61922, Saudi ArabiaDepartment of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, P.O. Box 551, Bisha 61922, Saudi ArabiaAlpha synuclein (α-Syn) is a neuronal protein encoded by the SNCA gene and is involved in the development of Parkinson’s disease (PD). The objective of this study was to examine in silico the functional implications of non-synonymous single nucleotide polymorphisms (nsSNPs) in the SNCA gene. We used a range of computational algorithms such as sequence conservation, structural analysis, physicochemical properties, and machine learning. The sequence of the SNCA gene was analyzed, resulting in the mapping of 42,272 SNPs that are classified into different functional categories. A total of 177 nsSNPs were identified within the coding region; there were 20 variants that may influence the α-Syn protein structure and function. This identification was made by employing different analytical tools including SIFT, PolyPhen2, Mut-pred, SNAP2, PANTHER, PhD-SNP, SNP&Go, MUpro, Cosurf, I-Mut, and HOPE. Three mutations, V82A, K80E, and E46K, were selected for further examinations due to their spatial positioning within the α-Syn as determined by PyMol. Results indicated that these mutations may affect the stability and function of α-Syn. Then, a molecular dynamics simulation was conducted for the SNCA wildtype and the four mutant variants (p.A18G, p.V82A, p.K80E, and p.E46K). The simulation examined temperature, pressure, density, root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), solvent-accessible surface area (SASA), and radius of gyration (Rg). The data indicate that the mutations p.V82A, p.K80E, and p.E46K reduce the stability and functionality of α-Syn. These findings highlight the importance of understanding the impact of nsSNPs on α-syn structure and function. Our results required verifications in further protein functional and case–control studies. After being verified these findings can be used in genetic testing for the early diagnosis of PD, the evaluation of the risk factors, and therapeutic approaches.https://www.mdpi.com/2079-9721/11/3/115synucleinopathiesParkinson’s disease (PD)alpha-synuclein (α-Syn) proteinSNCA gene non-synonymous single nucleotide polymorphisms (nsSNPs)bioinformaticssynucleinopathies |
| spellingShingle | Mohamed E. Elnageeb Imadeldin Elfaki Khalid M. Adam Elsadig Mohamed Ahmed Elkhalifa M. Elkhalifa Hytham A. Abuagla Abubakr Ali Elamin Mohamed Ahmed Elshazali Widaa Ali Elmoiz Idris Eltieb Ali M. Edris In Silico Evaluation of the Potential Association of the Pathogenic Mutations of Alpha Synuclein Protein with Induction of Synucleinopathies Diseases synucleinopathies Parkinson’s disease (PD) alpha-synuclein (α-Syn) protein SNCA gene non-synonymous single nucleotide polymorphisms (nsSNPs) bioinformatics synucleinopathies |
| title | In Silico Evaluation of the Potential Association of the Pathogenic Mutations of Alpha Synuclein Protein with Induction of Synucleinopathies |
| title_full | In Silico Evaluation of the Potential Association of the Pathogenic Mutations of Alpha Synuclein Protein with Induction of Synucleinopathies |
| title_fullStr | In Silico Evaluation of the Potential Association of the Pathogenic Mutations of Alpha Synuclein Protein with Induction of Synucleinopathies |
| title_full_unstemmed | In Silico Evaluation of the Potential Association of the Pathogenic Mutations of Alpha Synuclein Protein with Induction of Synucleinopathies |
| title_short | In Silico Evaluation of the Potential Association of the Pathogenic Mutations of Alpha Synuclein Protein with Induction of Synucleinopathies |
| title_sort | in silico evaluation of the potential association of the pathogenic mutations of alpha synuclein protein with induction of synucleinopathies |
| topic | synucleinopathies Parkinson’s disease (PD) alpha-synuclein (α-Syn) protein SNCA gene non-synonymous single nucleotide polymorphisms (nsSNPs) bioinformatics synucleinopathies |
| url | https://www.mdpi.com/2079-9721/11/3/115 |
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