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

Abstract

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.

Targeting GATA4 for cardiac repair

“…Our model predicts that the interaction between GATA4 and NKX2‐5 share a conserved architecture with the DNA binding domain of nuclear receptors . Another recent study employing molecular dynamics simulations suggests an alternative protein–protein interaction model for GATA4‐NKX2‐5 complex . Conversely, experimental studies do not find support for this theoretical observation …”

“…99 Another recent study employing molecular dynamics simulations suggests an alternative protein-protein interaction model for GATA4-NKX2-5 complex. 16 Conversely, experimental studies do not find support for this theoretical observation. 93,97,99 4.2 | Compounds targeted to the GATA4-NKX2-5 interaction Based on the structural and functional data of the GATA4-NKX2-5 interaction, an extensive chemical screening project was established incorporating computational and experimental biology to uncover compounds acting on key cardiac TFs.…”

“…The human GATA4 protein contains 442 amino acids and includes two structurally stable zinc finger domains located at amino acid residues 217–241 and 271–295. The protein sequence outside of the zinc finger core domains and C‐terminal extension (residues 210–320) has no globular structure and it remains completely disordered . In addition, the C‐terminal extension of the zinc finger contains the amino acid sequence required for nuclear localization .…”

“…The protein sequence outside of the zinc finger core domains and C-terminal extension (residues 210-320) has no globular structure and it remains completely disordered. 16 In addition, the C-terminal extension of the zinc finger contains the amino acid sequence required for nuclear localization. 12 Several GATA4 single point mutations identified from humans have been shown to be linked to common developmental anomalies and mortality in new-borns.…”

Association of NKX2‐5, GATA4, and TBX5 polymorphisms with congenital heart disease in Egyptian children

“…They establish that NKX2-5-GATA4 complex, in case of mutant, had significant conformational alterations and harm of key polar interactions, which might be a reason of the pathogenic behaviour. D16N pathogenic mutation of NKX2-5 renders the structural-functional discrepancy that perhaps may lead to the diseased state (Mattapally, Singh, Murthy, Asthana, & Banerjee, 2018).…”