title: In silico analysis of Single Nucleotide Polymorphisms (SNPs) in human BRAF gene.
abstract: BRAF gene mutations are frequently seen in both inherited and somatic diseases. However, the harmful mutations for BRAF gene have not been predicted in silico. Owing to the importance of BRAF gene in cell division, differentiation and secretion processes, the functional analysis was carried out to explore the possible association between genetic mutations and phenotypic variations. Genomic analysis of BRAF was initiated with SIFT followed by PolyPhen and SNPs&GO servers to retrieve the 85 deleterious non-synonymous SNPs (nsSNPs) from dbSNP. A total of 5 mutations i.e. c.406T>G (S136A), c.1446G>T (R462I), c.1556 A>G (K499E), c.1860 T>A (V600E) and c.2352 C>T (P764L) that are found to exert benign effects on the BRAF protein structure and function were chosen for further analysis. Protein structural analysis with these amino acid variants was performed by using I-Mutant, FOLD-X, HOPE, NetSurfP, Swiss PDB viewer, Chimera and NOMAD-Ref servers to check their solvent accessibility, molecular dynamics and energy minimization calculations. Our in silico analysis suggested that S136A and P764L variants of BRAF could directly or indirectly destabilize the amino acid interactions and hydrogen bond networks thus explain the functional deviations of protein to some extent. Screening for BRAF, S136A and P764Lvariants may be useful for disease molecular diagnosis and also to design the molecular inhibitors of BRAF pathways.
authors: Institute of Molecular Sciences and Bioinformatics Lahore, Pakistan. ramzan.manwar@yahoo.com
authors: Muhammad Ramzan Manwar
authors: MR
authors: Hussain
authors: Noor Ahmad
authors: NA
authors: Shaik
authors: Jumana Yousuf
authors: JY
authors: Al-Aama
authors: Hani Z
authors: HZ
authors: Asfour
authors: Fatima Subhani
authors: FS
authors: Khan
authors: Tariq Ahmad
authors: TA
authors: Masoodi
authors: Muhammad Akhtar
authors: MA
authors: Khan
authors: Nazia Sultana
authors: NS
authors: Shaik
mesh_terms: D019295:Computational Biology; D004194:Disease / Q000235:genetics*; D006801:Humans; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D009154:Mutation / Q000235:genetics*; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D011487:Protein Conformation; D048493:Proto-Oncogene Proteins B-raf / Q000235:genetics*; D013329:Structure-Activity Relationship
chemical_list: C482119:BRAF protein, human; D048493:Proto-Oncogene Proteins B-raf