In Silico Investigation of AKT2 Gene and Protein Abnormalities Reveals Potential Association with Insulin Resistance and Type 2 Diabetes

Abstract

Type 2 diabetes (T2D) develops from insulin resistance (IR) and the dysfunction of pancreatic beta cells. The AKT2 protein is very important for the protein signaling pathway, and the non-synonymous SNP (nsSNPs) in AKT2 gene may be associated with T2D. nsSNPs can result in alterations in protein stability, enzymatic activity, or binding specificity. The objective of this study was to investigate the effect of nsSNPs on the AKT2 protein structure and function that may result in the induction of IR and T2D. The study identified 20 variants that were considered to be the most deleterious based on a range of analytical tools included (SIFT, PolyPhen2, Mut-pred, SNAP2, PANTHER, PhD-SNP, SNP&Go, MUpro, Cosurf, and I-Mut). Two mutations, p.A179T and p.L183Q, were selected for further investigation based on their location within the protein as determined by PyMol. The results indicated that mutations, p.A179T and p.L183Q alter the protein stability and functional characteristics, which could potentially affect its function. In order to conduct a more in-depth analysis of these effects, a molecular dynamics simulation was performed for wildtype AKT2 and the two mutants (p.A179T and p.L183Q). The simulation evaluated various parameters, including temperature, pressure, density, RMSD, RMSF, SASA, and Region, over a period of 100 ps. According to the simulation results, the wildtype AKT2 protein demonstrated higher stability in comparison to the mutant variants. The mutations p.A179T and p.L183Q were found to cause a reduction in both protein stability and functionality. These findings underscore the significance of the effects of nsSNPs (mutations p.A179T and p.L183Q) on the structure and function of AKT2 that may lead to IR and T2D. Nevertheless, they require further verifications in future protein functional, protein-protein interaction, and large-scale case-control studies. When verified, these results will help in the identification and stratification of individuals who are at risk of IR and T2D for the purpose of prevention and treatment.

Keywords: AKT2; bioinformatics; insulin resistance; insulin signaling pathway; nsSNP; protein; type 2 diabetes.

Figure 1

Workflow of the nsSNP detection and analysis. The nucleotide sequences are retrieved in FASTA format, and SNPs are assessed whether synonymous, nonsynonymous, or nonsense. Nonsynonymous SNPs (nsSNPs) are assessed on the subject of whether they have deleterious effects on the protein encoded by the gene by molecular dynamic simulation.

Figure 2

The ConSurf analysis yielded results pertaining to the conservation of residues. The ConSurf results display a range of colours that correspond to the level of confidence regarding sequence conservation. In this colour scheme, the sky-blue colour represents variable residues, while the dark purple colour represents highly conserved residues.

Figure 3

The variations in temperature over time for both the wildtype and mutant forms of AKT2.

Figure 4

The variations in pressure over time for both the wildtype and mutant forms of AKT2.

Figure 5

The variations in density over time for the wildtype and mutant AKT2 protein.

Figure 6

The root-mean-square deviation (RMSD) (A) and root-mean-square fluctuation (RMSF) (B) graphs were generated for the backbone atoms of both the wildtype and mutant variants of the AKT2 protein. These simulations were conducted using GROMACS version 5.1.2. The wildtype is visually represented by the colour purple, while the A179T mutant is depicted in green and the L183Q mutant is depicted in blue.

Figure 7

The radius of gyration (Rg) of Cα atoms of native and mutant-type AKT2 protein. Wildtype (A) is shown in black, A179T (B) mutant is shown in blue and L183Q (C) is shown in green.

Figure 8

Solvent accessible surface area of wildtype (A) and mutant-type AKT protein. Wildtype is shown in black, A179T (B) mutant is shown in Blue and L183Q (C) is shown in green.

Figure 9

The cartoon structure of the AKT2 protein (PDB ID: 3D0E) showing the sites of the mutations p.A179T and p.L183Q with surface presentations indicated with arrows. This figure is prepared using YASARA view.