In Silico Evaluation of the Potential Association of the Pathogenic Mutations of Alpha Synuclein Protein with Induction of Synucleinopathies

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

doi:10.3390/diseases11030115

In Silico Evaluation of the Potential Association of the Pathogenic Mutations of Alpha Synuclein Protein with Induction of Synucleinopathies

Diseases. 2023 Sep 6;11(3):115. doi: 10.3390/diseases11030115.

Affiliations

¹ Department of Basic Sciences, College of Applied Medical Sciences, University of Bisha, P.O. Box 551, Bisha 61922, Saudi Arabia.
² Department of Biochemistry, Faculty of Science, University of Tabuk, P.O. Box 741, Tabuk 71491, Saudi Arabia.
³ Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, P.O. Box 551, Bisha 61922, Saudi Arabia.
⁴ Department of Clinical Chemistry, Faculty of Medical Laboratory Sciences, University of El Imam El Mahdi, Kosti 27711, Sudan.
⁵ Department of Anatomy, Faculty of Medicine and Health Sciences, Nile Valley University, Atbara 46611, Sudan.

Abstract

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.

Keywords: Parkinson’s disease (PD); SNCA gene non-synonymous single nucleotide polymorphisms (nsSNPs); alpha-synuclein (α-Syn) protein; bioinformatics; synucleinopathies.

Grants and funding

This research received no external funding.