PREDICTION AND STRUCTURAL IMPACTS OF THE PATHOGENIC MISSENSE SINGLE NUCLEOTIDE POLYMORPHISMS OF IL-6 WITH IN SILICO METHODS

Abstract

Single nucleotide polymorphisms (SNPs) are known as single nucleotide changes in DNA among individuals. The most common type of SNPs is non-synonymous SNPs. Interleukin-6 (IL-6) is a pleiotropic cytokine produced by lymphoid and non-lymphoid cells with a wide range of biological functions in defense mechanism, immune response, hematopoiesis, and acute phase reactions. In this study, SNPs of IL-6 were searched in NCBI dbSNP, and there are 2530 SNPs belong to IL-6, and 227 of them are classified as missense in this database. PANTHER, SIFT, and PROVEAN bioinformatic tools were used for determining the deleterious (D), probably damaging (PRD), or possibly damaging (POD) SNPs and the HOPE tool was utilized for the detection of the structural impacts caused by these SNPs on amino acids of I-L6 protein products. SIFT and PROVEAN scores and PANTHER preservation times showed that 22 of these 227 SNPs have a category of D, PRD, or POD. According to HOPE tool results, rs11544633 (UniProt protein ids: P05231, B5MCZ3, B4DNV3, P05231, and B5MC21), rs199990564 (UniProt protein ids: P05231, B5MCZ3, B4DNV3, P05231, and B5MC21), rs201371019 (UniProt Protein ids: P05231, B5MCZ3, B4DNV3, B4DNV3, P05231, and B5MC21) causes the smaller amino acids while rs370818995 (UniProt Protein ids: P05231, B5MCZ3, and P05231) causes the bigger aminoacids in mutant types. Also, the mutant types of rs199990564 (UniProt Protein ids: P05231, B5MCZ3, B4DNV3, P05231, and B5MC21), and rs201371019 (UniProt Protein ids: P05231, B5MCZ3, B4DNV3, P05231, and B5MC21) cause more hydrophobic structure while rs370818995 (UniProt Protein ids: P05231, B5MCZ3, and P05231) causes less hydrophobic form than their wild types. In the study, this is the first time the pathogenic missense SNPs of IL-6 of its was shown with in silico methods. We think the results of this study can help for future studies about the effects of IL-6 pathogenic polymorphisms.