Computational modeling suggests impaired interactions between NKX2.5 and GATA4 in individuals carrying a novel pathogenic D16N NKX2.5 mutation

NKX2.5, a homeobox containing gene, plays an important role in embryonic heart development and associated mutations are linked with various cardiac abnormalities. We sequenced the NKX2.5 gene in 100 congenital heart disease (CHD) patients and 200 controls. Our analysis revealed a total of 7 mutations, 3 in intronic region, 3 in coding region and 1 in 3’ UTR. Of the above mutations, one mutation was found to be associated with tetralogy of fallot (TOF) and two (rs2277923 and a novel mutation, D16N) were strongly associated with VSD. A novel missense mutation, D16N (p-value =0.009744), located in the tinman (TN) region and associated with ventricular septal defect (VSD), is the most significant findings of this study. Computational analysis revealed that D16N mutation is pathogenic in nature. Through the molecular modeling, docking and molecular dynamics simulation studies, we have identified the location of mutant D16N in NKX2.5 and its interaction map with other partners at the atomic level. We found NKX2.5-GATA4 complex is stable, however, in case of mutant we observed significant conformational changes and loss of key polar interactions, which might be a cause of the pathogenic behavior. This study underscores the structural basis of D16N pathogenic mutation in the regulation of NKX2.5 and how this mutation renders the structural-functional divergence that possibly leading towards the diseased state.