Abstract
Maturity-onset diabetes of the young type 3 (MODY3) is a non-ketotic form of diabetes associated with poor insulin secretion. Over the past years, several studies have reported the association of missense mutations in the Hepatocyte Nuclear Factor 1 Alpha (HNF1A) with MODY3. Missense mutations in the POU homeodomain (POUH) of HNF1A hinder binding to the DNA, thereby leading to a dysfunctional protein. Missense mutations of the HNF1A were retrieved from public databases and subjected to a three-step computational mutational analysis to identify the underlying mechanism. First, the pathogenicity and stability of the mutations were analyzed to determine whether they alter protein structure and function. Second, the sequence conservation and DNA-binding sites of the mutant positions were assessed; as HNF1A protein is a transcription factor. Finally, the biochemical properties of the biological system were validated using molecular dynamic simulations in Gromacs 4.6.3 package. Two arginine residues (131 and 203) in the HNF1A protein are highly conserved residues and contribute to the function of the protein. Furthermore, the R131W, R131Q, and R203C mutations were predicted to be highly deleterious by in silico tools and showed lower binding affinity with DNA when compared to the native protein using the molecular docking analysis. Triplicate runs of molecular dynamic (MD) simulations (50ns) revealed smaller changes in patterns of deviation, fluctuation, and compactness, in complexes containing the R131Q and R131W mutations, compared to complexes containing the R203C mutant complex. We observed reduction in the number of intermolecular hydrogen bonds, compactness, and electrostatic potential, as well as the loss of salt bridges, in the R203C mutant complex. Substitution of arginine with cysteine at position 203 decreases the affinity of the protein for DNA, thereby destabilizing the protein. Based on our current findings, the MD approach is an important tool for elucidating the impact and affinity of mutations in DNA-protein interactions and understanding their function.
Highlights
Maturity-onset diabetes of the young (MODY) is a hereditary monogenic form of diabetes, with eleven different forms caused by changes in eleven different genes, of the eleven forms, MODY2 and Maturity-onset diabetes of the young type 3 (MODY3) are the most common; with frequent mutations in the GCK and Hepatocyte Nuclear Factor 1 Alpha (HNF1A) genes [1,2,3,4]
The effects of mutations associated with the HNF1A protein are of substantial clinical importance because they are known to be associated with MODY3 [47]
All HNF1A missense mutations were retrieved from the dbSNP, UniProt, and Human Gene Mutation Database (HGMD) databases. 219 missense mutations were analyzed with various in silico prediction tools to measure their effects on pathogenicity and stability
Summary
Maturity-onset diabetes of the young (MODY) is a hereditary monogenic form of diabetes, with eleven different forms caused by changes in eleven different genes, of the eleven forms, MODY2 and MODY3 are the most common; with frequent mutations in the GCK and HNF1A genes [1,2,3,4]. Patients with MODY3 are known to develop late-onset microvascular complications [5, 6]. Heterozygous mutations in the HNF1A gene are further transcribed to produce the protein (transcription factor), leading to a confirmed disease condition [7]. The HNF1Agene is located on chromosome (12q24.2), spanning 23,790 bp, and it encodes a 631 amino acid-long protein consisting of an amino-terminal dimerization domain (residues 1–32), a DNA-binding motif containing a typical homeodomain (residues 203–276), and a carboxyl-terminal transactivation domain (residues 281–631) [11]. POUs is an integral part of HNF1A that helps in maintaining the stability of the protein, whereas the POUH domain of the transcription factor acts as a crucial interface initiating the interaction between the protein and DNA[12,15]
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