Mutation Spectrum in TPO Gene of Bangladeshi Patients with Thyroid Dyshormonogenesis and Analysis of the Effects of Different Mutations on the Structural Features and Functions of TPO Protein through In Silico Approach

Abstract

Although thyroid dyshormonogenesis (TDH) accounts for 10-20% of congenital hypothyroidism (CH), the molecular etiology of TDH is unknown in Bangladesh. Thyroid peroxidase (TPO) is most frequently associated with TDH and the present study investigated the spectrum of TPO mutations in Bangladeshi patients and analyzed the effects of mutations on TPO protein structure through in silico approach. Sequencing-based analysis of TPO gene revealed four mutations in 36 diagnosed patients with TDH including three nonsynonymous mutations, namely, p.Ala373Ser, p.Ser398Thr, and p.Thr725Pro, and one synonymous mutation p.Pro715Pro. Homology modelling-based analysis of predicted structures of MPO-like domain (TPO142-738) and the full-length TPO protein (TPO1-933) revealed differences between mutant and wild type structures. Molecular docking studies were performed between predicted structures and heme. TPO1-933 predicted structure showed more reliable results in terms of interactions with the heme prosthetic group as the binding energies were -11.5 kcal/mol, -3.2 kcal/mol, -11.5 kcal/mol, and -7.9 kcal/mol for WT, p.Ala373Ser, p.Ser398Thr, and p.Thr725Pro, respectively, implying that p.Ala373Ser and p.Thr725Pro mutations were more damaging than p.Ser398Thr. However, for the TPO142-738 predicted structures, the binding energies were -11.9 kcal/mol, -10.8 kcal/mol, -2.5 kcal/mol, and -5.3 kcal/mol for the wild type protein, mutant proteins with p.Ala373Ser, p.Ser398Thr, and p.Thr725Pro substitutions, respectively. However, when the interactions between the crucial residues including residues His239, Arg396, Glu399, and His494 of TPO protein and heme were taken into consideration using both TPO1-933 and TPO142-738 predicted structures, it appeared that p.Ala373Ser and p.Thr725Pro could affect the interactions more severely than the p.Ser398Thr. Validation of the molecular docking results was performed by computer simulation in terms of quantum mechanics/molecular mechanics (QM/MM) and molecular dynamics (MD) simulation. In conclusion, the substitutions mutations, namely, p.Ala373Ser, p.Ser398Thr, and p.Thr725Pro, had been involved in Bangladeshi patients with TDH and molecular docking-based study revealed that these mutations had damaging effect on the TPO protein activity.

Longitudinal Associations Between TPO Gene Variants and TPOAb Seroconversion in a Population Based Study: Tehran Thyroid Study (TTS)

“…Rs732609 has previously been reported to be associated with TPOAb levels in Iranians with subclinical hypothyroidism (18). This variant is a missense mutation in exon 12 (Thr725Pro) and could affect the interactions with heme prosthetic group in the catalytic site (19). This is conceivable that slight changes in the TPO structure, occurs following single residual substitution, may trigger autoimmune reaction.…”

A Novel Homozygous Mutation of Thyroid Peroxidase Gene Abolishes a Disulfide Bond Leading to Congenital Hypothyroidism

“…For the conformational prediction of TPO, human myeloperoxidase (MPO) 3D structure was used as a template. MPO is known as the closest homolog to TPO and shares 47% sequence identity with the MPO-like domain of TPO [ 14 , 15 ]. The X-ray crystal structure of human MPO has been previously determined (PDB accession code 3F9P) [ 16 ].…”

Graves’ disease: introducing new genetic and epigenetic contributors

“…population (Huang & Jap 2015). It seems that these kinds of mutations can change TPO protein activity, its expression in serum, or even the serum levels of TPOAb, confirmed by a study introducing nonsynonymous substitutions in TPO (including p.Ala373Ser, p.Ser398Thr, and p.Thr725Pro) in Bangladeshi patients (Begum et al 2019). However, the molecular mechanisms behind the association between these variants and GD are not clearly understood.…”