Mutations L163P and R190C in NKX2‐5 Confer More Stability to the Protein's Binding to DNA

Abstract

The NKX2‐5 is a gene that encodes for a transcription factor containing the homeobox domain which functions mainly in heart formation and development. Mutations in this gene have been known to cause heart malformation diseases and congenital hypothyroidism. The objective of this study is to determine, through methods in computational biology, the effect of mutations on the binding affinity of NKX2‐5 to DNA and thus predict their phenotypic consequences. The mutations used were determined using UCSC Genome Browser based on regions of highest conservation. Structure‐function prediction was performed for these mutations using Polyphen‐2, Mutation Assessor, HOPE, and Mutation Taster. Molecular docking experiments for the binding of NKX2‐5 to DNA were then performed using the ZDock module of Discovery Studio (Biovia). Results include the mutations rs757605578 (p. L163P) and rs104893906 (p. R190C), which were identified from regions of high conservation (across metazoans). The functional predictions for the mutant L163P using the tools Polyphen‐2, Mutation Assessor, HOPE, and Mutation Taster are “Probably Damaging” (Score: 1.000), “Low” (Score: 1.45), “Probably Not Damaging”, and “Could Not Retrieve a Sequence”, respectively. For mutant R190C, the predictions are “Probably Damaging” (Score: 1.000), “High” (Score: 4.015), “Severity: Disease”, and “Disease Causing” (Score: 180), in the same order as the previous. Results of the docking experiments show that the best poses for the wild‐type, L163P, and R190C had structural energies of −80.2641 kJ/mol, −82.1326 kJ/mol, and −81.4704 kJ/mol, respectively. These show that the mutant NKX2‐5 proteins had more stable binding to DNA. Examination of the non‐covalent interactions formed by mutated residues compared to wild‐type reveals that there are fewer interactions in the mutated residues compared to the wild‐type. These suggest that it may be the nature of the interactions (charge interactions, H‐bonds, polar interactions, or hydrophobic interactions) and/or steric effects that are responsible for the increased stability of binding by NKX2‐5 to DNA. It is concluded that mutations L163P and R190C are functionally highly important and are predicted to be, in general, probably disease‐causing. The increased stability of binding to DNA by the mutants, therefore increased transcription factor activity, may be the mechanism by which this predicted phenotype is achieved.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.