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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...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10529770/ https://www.ncbi.nlm.nih.gov/pubmed/37754311 http://dx.doi.org/10.3390/diseases11030115 |
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author | Elnageeb, Mohamed E. Elfaki, Imadeldin Adam, Khalid M. Ahmed, Elsadig Mohamed Elkhalifa, Elkhalifa M. Abuagla, Hytham A. Ahmed, Abubakr Ali Elamin Mohamed Ali, Elshazali Widaa Eltieb, Elmoiz Idris Edris, Ali M. |
author_facet | Elnageeb, Mohamed E. Elfaki, Imadeldin Adam, Khalid M. Ahmed, Elsadig Mohamed Elkhalifa, Elkhalifa M. Abuagla, Hytham A. Ahmed, Abubakr Ali Elamin Mohamed Ali, Elshazali Widaa Eltieb, Elmoiz Idris Edris, Ali M. |
author_sort | Elnageeb, Mohamed E. |
collection | PubMed |
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. |
format | Online Article Text |
id | pubmed-10529770 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-105297702023-09-28 In Silico Evaluation of the Potential Association of the Pathogenic Mutations of Alpha Synuclein Protein with Induction of Synucleinopathies Elnageeb, Mohamed E. Elfaki, Imadeldin Adam, Khalid M. Ahmed, Elsadig Mohamed Elkhalifa, Elkhalifa M. Abuagla, Hytham A. Ahmed, Abubakr Ali Elamin Mohamed Ali, Elshazali Widaa Eltieb, Elmoiz Idris Edris, Ali M. Diseases Article 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. MDPI 2023-09-06 /pmc/articles/PMC10529770/ /pubmed/37754311 http://dx.doi.org/10.3390/diseases11030115 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Elnageeb, Mohamed E. Elfaki, Imadeldin Adam, Khalid M. Ahmed, Elsadig Mohamed Elkhalifa, Elkhalifa M. Abuagla, Hytham A. Ahmed, Abubakr Ali Elamin Mohamed Ali, Elshazali Widaa Eltieb, Elmoiz Idris Edris, Ali M. In Silico Evaluation of the Potential Association of the Pathogenic Mutations of Alpha Synuclein Protein with Induction of 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 | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10529770/ https://www.ncbi.nlm.nih.gov/pubmed/37754311 http://dx.doi.org/10.3390/diseases11030115 |
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