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

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.

Figure 1

Plan of work.

Figure 2

Outcomes of the ConSurf study in terms of residue conservation. The amount of confidence in the sequence conservation is shown by a range of colors in the ConSurf results. The sky-blue color in this color scheme stands in for variable residues, while the dark purple color stands in for highly conserved residues.

Figure 3

Simulation of the temperature changes over time for the α-syn protein wildtype and mutant versions. The simulation was performed using the GROMACS 5.1.2. The color black is used to symbolize the wildtype, whereas the colors red, blue, and yellow are used to represent the V82A mutant, K80E mutant, and yellow to represent the E46K mutant.

Figure 4

Simulation of the pressure changes over time for the α-Syn wildtype and mutant versions. The simulation was performed using the GROMACS program. The color black is used to symbolize the wildtype, whereas the colors red, blue, and yellow are used to represent the V82A mutant, K80E mutant, and yellow to represent the E46K mutant.

Figure 5

Simulation of the density changes over time for the α-syn protein wildtype and mutant versions. The simulation was performed using the GROMACS 5.1.2 program. The color black is used to symbolize the wildtype, whereas the colors red, blue, and yellow are used to represent the V82A mutant, K80E mutant and yellow to represent the E46K mutant.

Figure 6

Difference between the root-mean-square deviation (RMSD) (A), and the root-mean-square fluctuation (RMSF) (B). For the backbone atoms of the α-Syn protein wildtype and mutant forms, graphs were created. The simulations were carried out with GROMACS 5.1.2. Black for to represent the wildtype, while red, blue, and yellow for the V82A, K80E, and E46K mutants, respectively.

Figure 7

The Rg of C atoms in native and mutant α-Syn protein types. The wildtype (a), the V82A (b), the K80E (c), and the E46K (d).

Figure 8

Solvent accessible surface area (SASA) of wildtype and mutant forms of α-Syn protein. Wildtype (a), V82A (b), K80E (c), and E46K (d) mutants.

Figure 9

The three-dimensional structure of the α-syn protein (PDB ID:1XQ8), the sites of the mutations are shown in surface presentation and red color. This figure is prepared using YASARA view.