Estimation of varicocele associated human ARG2 and NOS1 proteins and computational analysis on the effect of its nsSNPs.

One of the major causes of varicocele is nitrosative stress. Two genes namely arginase 2 (ARG2) and nitric oxide synthase 1 (NOS1) are important in the mechanism of nitric oxide (NO) in the body. Semen samples from three different categories were taken, fertile (n = 20), Infertile (n = 20), and unilateral varicocele (n = 15). Quantitative estimation of ARG2 and NOS1 was carried out through the ELISA kit method. t-Test and ANOVA were calculated using Graphpad Prism. For the in silico analysis, the sequence of the proteins obtained from dbSNP was used in online tools such as nsSNPAnalyzer, PolyPhen-2, Fathmm, I-Mutant 2.0, SNPs&GO, PhD-SNP, PANTHER, SNAP2, PROVEAN, SIFT, and SNPeffect for screening deleterious mutants. These mutants were further evaluated with Swiss PDB and PyMOL for recording energy minimization, Root mean square deviation (RMSD) value, TM score, Hydrogen bonding, and Comparative modeling. Further, ConSurf, Netsurf, and STRING tools were used for evaluating conserved regions, stability, and protein-protein interactions respectively. The results of ARG2 protein were, fertile = 0.168 ± 0.007 U/ml, infertile = 0.201 ± 0.004 U/ml and, varicocele = 0.092 ± 0.002 U/ml. Results of NOS1 protein were fertile = 32.61 ± 2.8 nM/mg, infertile = 19.33 ± 3.7 nM/mg and, varicocele = 54.74 ± 4.8 nM/mg. From statistical analysis, the parameters were highly significant. From the in silico retrieved data, there were 130 and 499 nsSNPs (non-synonymous SNP) in ARG2 and NOS1 respectively. After screening with online tools, 6 deleterious nsSNPs each of ARG2 and NOS1 were considered for analysis through Swiss PDB. FoldX result of A52P mutant (ConSurf score = 9) of ARG2 was found to severely affect protein stability and that of A363T mutant (ConSurf score = 9) of NOS1 revealed a structural change. A52P had a higher RMSD value and A363T of NOS1 developed a new H-bond with 580th position. In varicocele cases, the ARG2 protein is found in lower quantity. The A52P variant of this protein can cause dysfunction and induce nitrosative stress. However, in infertile cases, NOS1 protein is found in lower quantity and the A363T variant can result in a decrease in NO leading to other forms of infertility.