Research Article: Determining the role of missense mutations in the POU domain of HNF1A that reduce the DNA-binding affinity: A computational approach

Date Published: April 14, 2017

Publisher: Public Library of Science

Author(s): Sneha P., Thirumal Kumar D., George Priya Doss C., Siva R., Hatem Zayed, Chandra Verma.


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.

Partial Text

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 [1–4]. The diagnosis of MODY3 is clearer during adolescence or early adulthood and also requires pharmacological treatment. Patients with MODY3 are known to develop late-onset microvascular complications [5, 6]. Furthermore, MODY3 is defined as a non-ketotic and autosomal dominantly inherited form of diabetes characterized by a severe deficiency in insulin secretion. Heterozygous mutations in the HNF1A gene are further transcribed to produce the protein (transcription factor), leading to a confirmed disease condition [7].

Missense mutations have long been known to inhibit protein activity, and tend to occur in DNA-binding regions of the protein affecting the DNA-binding affinity [18–20]. HNF1A is a transcription factor (DNA-binding protein) that regulates many liver, pancreas, and kidney-specific genes [48, 49]. The loss of function of this transcription factor leads to MODY (MODY3), which is most often known as monogenic diabetes [50]. The loss of the DNA-binding property of HNF1A due to the presence of a missense mutation at position 203 has received greater attention from researchers [12].

Transcription factors play pivotal roles in various cellular mechanisms, including regulation of cell function, growth, and differentiation, The detailed molecular structure analysis of the HNF1A presented here emphasizes the importance of the two arginine positions R131 and R203 for the HNF1A stability and function, the mutants R131Q and R203C were shown to be deleterious for the protein function and compromise its binding affinity, however our data suggested that the R203C mutant was the most deleterious leading to the loss of the protein binding affinity. The understanding of the detailed molecular structure of the mutations in HNF1A that cause MODY3 is expected to serve as a platform for developing therapeutic approaches for patients with MODY3 and drug discovery for treating diabetes, and maycreate a path toward personalized medicine for diabetic patients.




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