title: Identification of Deleterious SNPs and Their Effects on Structural Level in CHRNA3 Gene.
abstract: The aim of our study is to identify probable deleterious genetic variations that can alter the expression and the function of the CHRNA3 gene using in silico methods. Of the 2305 SNPs identified in the CHRNA3 gene, 115 were found to be non-synonymous and 12 and 15 nsSNPs were found to be in the 5' and 3' UTRs, respectively. Further, out of the 115 nsSNPs investigated, eight were predicted to be deleterious by both SIFT and PredictSNP servers. The major mutations predicted to affect the structure of the protein are phenylalanine to valine (Y43V) and lysine to asparagine (K216N) as shown by the trajectory run in molecular dynamics studies. The random transition of the protein structures over the simulation period caused by these mutations hints at how the native state is distorted which could lead to the loss of structural stability and functionality of the nicotinic acetylcholine receptors subunit α-3 protein. Based on this work, we propose that the nsSNP with SNP id of rs75495285 and rs76821682 will have comparatively more deleterious effects than the other predicted mutations in destabilizing the protein structure.
authors.affiliation: Department of Biotechnology, Siddaganga Institute of Technology, Tumkur, 572013, Karnataka, India, vivek.bioinf@gmail.com.
authors.forename: Vivek
authors.initials: V
authors.lastname: Chandramohan
authors.forename: Navya
authors.initials: N
authors.lastname: Nagaraju
authors.forename: Shrikant
authors.initials: S
authors.lastname: Rathod
authors.forename: Anubhav
authors.initials: A
authors.lastname: Kaphle
authors.forename: Uday
authors.initials: U
authors.lastname: Muddapur
mesh_terms: D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D000595:Amino Acid Sequence; D001483:Base Sequence; D019295:Computational Biology; D003198:Computer Simulation; D030562:Databases, Protein; D006801:Humans; D008958:Models, Molecular; D020641:Polymorphism, Single Nucleotide; D011487:Protein Conformation; D055550:Protein Stability; D011978:Receptors, Nicotinic / Q000737:chemistry / Q000235:genetics*; D017384:Sequence Deletion; D012984:Software
chemical_list: D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D011978:Receptors, Nicotinic