scholarly journals Molecular insights into the role of genetic determinants of congenital hypothyroidism

2021 ◽  
Vol 19 (3) ◽  
pp. e29
Author(s):  
Yedukondalu Kollati ◽  
Radha Rama Devi Akella ◽  
Shaik Mohammad Naushad ◽  
Rajesh K. Patel ◽  
G. Bhanuprakash Reddy ◽  
...  
Keyword(s):  
Thyroid Hormones ◽  
Congenital Hypothyroidism ◽  
In Silico ◽  
In Silico Analysis ◽  
Thyroid Stimulating Hormone ◽  
Binding Energies ◽  
Thyroid Peroxidase ◽  
Transcriptional Level ◽  
Missense Mutations ◽  
Wild Type

In our previous studies, we have demonstrated the association of certain variants of the thyroid-stimulating hormone receptor (TSHR), thyroid peroxidase (TPO), and thyroglobulin (TG) genes with congenital hypothyroidism. Herein, we explored the mechanistic basis for this association using different in silico tools. The mRNA 3'-untranslated region (3'-UTR) plays key roles in gene expression at the post-transcriptional level. In TSHR variants (rs2268477, rs7144481, and rs17630128), the binding affinity of microRNAs (miRs) (hsa-miR-154-5p, hsa-miR-376a-2-5p, hsa-miR-3935, hsa-miR-4280, and hsa-miR-6858-3p) to the 3'-UTR is disrupted, affecting post-transcriptional gene regulation. TPO and TG are the two key proteins necessary for the biosynthesis of thyroid hormones in the presence of iodide and H2O2. Reduced stability of these proteins leads to aberrant biosynthesis of thyroid hormones. Compared to the wild-type TPO protein, the p.S398T variant was found to exhibit less stability and significant rearrangements of intra-atomic bonds affecting the stoichiometry and substrate binding (binding energies, ΔG of wild-type vs. mutant: ‒15 vs. ‒13.8 kcal/mol; and dissociation constant, Kd of wild-type vs. mutant: 7.2E-12 vs. 7.0E-11 M). The missense mutations p.G653D and p.R1999W on the TG protein showed altered ΔG (0.24 kcal/mol and 0.79 kcal/mol, respectively). In conclusion, an in silico analysis of TSHR genetic variants in the 3'-UTR showed that they alter the binding affinities of different miRs. The TPO protein structure and mutant protein complex (p.S398T) are less stable, with potentially deleterious effects. A structural and energy analysis showed that TG mutations (p.G653D and p.R1999W) reduce the stability of the TG protein and affect its structure-functional relationship.

scholarly journals 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

2019 ◽  
Vol 2019 ◽  
pp. 1-18 ◽  
Author(s):  
Mst. Noorjahan Begum ◽  
Md Tarikul Islam ◽  
Shekh Rezwan Hossain ◽  
Golam Sarower Bhuyan ◽  
Mohammad A. Halim ◽  
...  
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Homology Modelling ◽  
Structural Features ◽  
Binding Energies ◽  
Thyroid Peroxidase ◽  
Wild Type ◽  
Protein Activity ◽  
Prosthetic Group ◽  
Thyroid Dyshormonogenesis

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.

scholarly journals Screening and Functional Analysis of TPO Gene Mutations in a Cohort of Chinese Patients With Congenital Hypothyroidism

2021 ◽  
Vol 12 ◽  
Author(s):  
Huijjuan Wang ◽  
Wenxia Wang ◽  
Xi Chen ◽  
Hailong Shi ◽  
Yinmin Shi ◽  
...  
Keyword(s):  
Congenital Hypothyroidism ◽  
High Throughput Sequencing ◽  
Biological Function ◽  
Northwest China ◽  
Chinese Patients ◽  
Thyroid Peroxidase ◽  
Missense Mutations ◽  
Wild Type ◽  
Hormone Synthesis

BackgroundsAs a crucial enzyme in thyroid hormone synthesis, the genetic defective thyroid peroxidase (TPO) was one of the main genetic factors leading to congenital hypothyroidism (CH).MethodsMutations in the TPO gene were screened and identified in 219 patients with CH from northwest China by using high-throughput sequencing and bioinformatics analysis. The biological function of detected variants was studied by in vitro experiments and homology modeling.ResultsNineteen rare variants, including seven novel ones, were detected in 17 of 219 patients (7.8%). Most cases were detected with one single heterozygous variant, and only two patients were detected with multiple variants, i.e., compounds for (1) IVS7-1G>A, p.Ala443Val, and p.Arg769Trp and (2) p.Asn592Ser and p.Asn798Lys. The biological function of the four missense mutations (i.e., p.Ala443Val, p.Arg769Trp, p.Asn592Ser, and p.Asn798Lys) they carried were further studied. Experimental data showed that these four mutations did not affect the protein expression level of the TPO gene but remarkably reduced the peroxidase activity toward guaiacol oxidation, retaining 8–32% of activity of the wild-type protein. The comparison of the predicted 3-D structures of wild-type and mutant TPO proteins showed that these four amino acid substitutions changed the non-covalent interactions of studied residues that might alter the structure and function of the TPO protein.ConclusionThis study was the first to analyze the TPO mutation spectrum of patients with CH in northwest China. Our data indicated that the TPO mutation was not a common reason to cause CH in China. The functional data may help to clarify the structure-function relationship of the TPO protein and provide further evidence for the elucidation of the genetic etiology of CH.

scholarly journals Mutation screening of the thyroid peroxidase gene in a cohort of 55 Portuguese patients with congenital hypothyroidism

2005 ◽  
Vol 152 (2) ◽  
pp. 193-198 ◽  
Author(s):  
Carina Rodrigues ◽  
Paula Jorge ◽  
José Pires Soares ◽  
Isaura Santos ◽  
Regina Salomão ◽  
...  
Keyword(s):  
Congenital Hypothyroidism ◽  
Mutation Screening ◽  
Gene Mutations ◽  
Human Thyroid ◽  
Thyroid Peroxidase ◽  
Molecular Testing ◽  
Missense Mutations ◽  
Human Thyroid Peroxidase ◽  
Iodide Organification Defect ◽  
Organification Defect

Objective: Defects in the human thyroid peroxidase (TPO) gene are reported to be one of the causes of congenital hypothyroidism (CH) due to a total iodide organification defect. The aim of the present study was to determine the nature and frequency of TPO gene mutations in patients with CH, characterised by elevated TSH levels and orthotopic thyroid gland, identified in the Portuguese National Neonatal Screening Programme. Subjects and methods: The sample comprised 55 patients, from 53 unrelated families, with follow-up in the endocrinology clinics of the treatment centres of Porto and Lisbon. Mutation screening in the TPO gene (exons 1–17) was performed by single-strand conformational analysis followed by sequencing of fragments with abnormal migration patterns. Results: Eight different mutations were detected in 13 patients (seven homozygotes and six compound heterozygotes). Novel mutations included three missense mutations, namely 391T > C (S131P), 1274A > G (N425S) and 2512T > A (C838S), as well as the predictable splice mutation 2748G > A (Q916Q/spl?). The undocumented polymorphism 180-47A > C was also detected. Conclusion: The results are in accordance with previous observations confirming the genetic heterogeneity of TPO defects. The proportion of patients in which the aetiology was determined justifies the implementation of this molecular testing in our CH patients with dyshormonogenesis.

scholarly journals Analysis of phage-resistant mechanisms inStaphylococcus aureusSA003 reveals a different binding mechanism for the closely related Twort-like phages ϕSA012 and ϕSA039

2018 ◽  
Author(s):  
Aa Haeruman Azam ◽  
Fumiya Hoshiga ◽  
Ippei Takeuchi ◽  
Kazuhiko Miyanaga ◽  
Yasunori Tanji
Keyword(s):  
Teichoic Acid ◽  
Point Mutations ◽  
In Silico Analysis ◽  
Close Relative ◽  
Phenotypic Change ◽  
Missense Mutations ◽  
Wild Type ◽  
Wall Teichoic Acid ◽  
Whole Genome Analysis ◽  
Specific Phage

ABSTRACTWe have previously generated strains ofStaphylococcus aureusSA003 resistant to its specific phage ϕSA012 through long-term coevolution experiment. However, the DNA mutations responsible for the phenotypic change of phage resistance are unknown. Whole-genome analysis revealed six genes that acquired unique point mutations: five missense mutations and one nonsense mutation. Moreover, one deletion, 1.779-bp, resulted in the deletion of the genes encoding glycosyltransferase, TarS, and iron-sulfure repair protein, ScdA. The deletion occurred from the second round of coculture (SA003R2) and remained through the last round. The ϕSA012 infection toward SA003R2 had decreased to 79.77±7.50% according to plating efficiency. Complementation of the phage-resistant strain by the wild-type allele showed two mutated host genes were linked to the inhibition of post-adsorption, and five genes were linked to phage adsorption of ϕSA012. Unlike ϕSA012, infection by ϕSA039, a close relative of ϕSA012, onto SA003R2 was impaired drastically. Complementation of SA003R2 by wild-typetarSrestores the infectivity of ϕSA039. Thus, we concluded that ϕSA039 requires β-GlcNAc in Wall Teichoic Acid (WTA) for its binding. In silico analysis of the ϕSA039 genome revealed that several proteins in the tail and baseplate region were different from ϕSA012; notably the partial deletion oforf96of ϕSA039, a homolog oforf99of ϕSA012.Orf100of ϕSA039, a homolog ofOrf103of ϕSA012, a previously reported receptor binding protein (RBP), had low similarity (86%) to that of ϕSA012. The difference in tail and baseplate proteins might be the factor for specificity difference between ϕSA012 and ϕSA039.

scholarly journals In silico analysis of missense mutations in exons 1–5 of the F9 gene that cause hemophilia B

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Lennon Meléndez-Aranda ◽  
Ana Rebeca Jaloma-Cruz ◽  
Nina Pastor ◽  
Marina María de Jesús Romero-Prado
Keyword(s):  
In Silico ◽  
In Silico Analysis ◽  
Hemophilia B ◽  
Missense Mutations ◽  
Silico Analysis

scholarly journals Molecular Modeling and Structural Stability of Wild-Type and Mutant CYP51 from Leishmania major: In Vitro and In Silico Analysis of a Laboratory Strain

Molecules ◽  
2018 ◽  
Vol 23 (3) ◽  
pp. 696 ◽  
Author(s):  
Masoud Keighobadi ◽  
Saeed Emami ◽  
Milad Lagzian ◽  
Mahdi Fakhar ◽  
Alireza Rafiei ◽  
...  
Keyword(s):  
Molecular Modeling ◽  
Structural Stability ◽  
In Silico ◽  
Leishmania Major ◽  
In Silico Analysis ◽  
Laboratory Strain ◽  
Wild Type ◽  
Silico Analysis

A novel missense mutation in the FGB gene (p.Gly302Arg) leading to afibrinogenemia

2016 ◽  
Vol 36 (S 02) ◽  
pp. S34-S37 ◽  
Author(s):  
H. Rühl ◽  
G. Detarsio ◽  
A. Biswas ◽  
S. Gupta ◽  
M. Davoli ◽  
...  
Keyword(s):  
Missense Mutation ◽  
In Silico ◽  
In Silico Analysis ◽  
Missense Mutations ◽  
The Novel ◽  
Beta Chain ◽  
The Core ◽  
And Function ◽  
Flanking Regions ◽  
Positively Charged

SummaryAfibrinogenemia represents the rarest form of fibrinogen deficiency. Causative missense mutations occur rarely and may improve the understanding of fibrinogen structure and function. Patients and methods: The propositus was a 26-year-old Argentinian with afibrinogenemia. FGA, FGB and FGG exons and flanking regions were screened by sequencing and the mutant protein was analyzed in silico. Results: A novel missense mutation in the FGB gene (Bbeta Gly272Arg, p.Gly302Arg) was identified. In silico analysis revealed its location in a highly conserved region, which preserves the core fold of the C-terminal beta-chain and is important for proper secretion. A substitution by a positively charged large Arg residue in this area would most likely disturb the core fold by additional interactions with adjacent residues (p.Asp291, p.Asp297, p.Asp311), or by forming of non-native interactions with other proteins, thereby hindering the action of molecular chaperones. Both alternatives would disturb the regular secretion of the beta-chain. Conclusions: The novel mis-sense mutation in the FGB gene causes afibrinogenemia most probably by affecting the secretion of the fibrinogen beta-chain.

Comparison of the sonography index of thyroid gland with serum level of Anti-thyroid peroxidase, Anti-thyroglobulin and thyroid function test in patients with Hashimoto thyroiditis

2021 ◽  
Author(s):  
Fatemeh Eftekharian ◽  
Gholamhossein Ranjbar Omrani ◽  
Mohammad Hossein Dabbaghmanesh ◽  
Reza Sahraei ◽  
Marzieh Bakhshayeshkaram ◽  
...  
Keyword(s):  
Thyroid Hormones ◽  
Hashimoto’S Thyroiditis ◽  
Thyroid Volume ◽  
Thyroid Function Test ◽  
Serum Levels ◽  
Significant Negative Correlation ◽  
Thyroid Stimulating Hormone ◽  
Hashimoto's Thyroiditis ◽  
Thyroid Peroxidase ◽  
Antibody Titers

Abstract Background The purpose of this study was to determine the association of sonographic parameters with the serum levels of anti-thyroid peroxidase (TPO), anti-thyroglobulin (Tg), and thyroid hormones in patients with Hashimoto's thyroiditis. Methods 149 patients (118 females, 31 males; aged 18–60 years; mean age: 38.60 ± 8.03 years) who were diagnosed with Hashimoto's thyroiditis were enrolled in the study. Blood sample was taken to measure the serum levels of free T3 and T4, thyroid stimulating hormone (TSH), anti-TPO antibody titers, and anti-Tg antibody titers. The thyroid sonography of each patient was classified into one of the five grades by real-time ultrasonography (US) based on echogenicity, thyroid size, and thyroid pattern. We evaluated whether a correlation existed between thyroid characteristics on US and serum levels of thyroid hormones, anti-TPO and anti-Tg. Results Nodular structures were detected in 54 (36.2%) patients (38 micronodular and 16 macros nodular). Echogenicity was recorded as isoechoic in 15 (10.07%) and hypoechoic in 119 (79.87%) subjects. Euthyroid ‎subjects had significantly thicker isthmus than overt and subclinical hypothyroid patients (p = 0.018). Mean serum TSH, anti-Tg and anti-TPO titers was significantly higher in patients with micronodules than those with micronodules and subjects without nodules (P < 0.05). Isthmus thickness had a significant negative correlation with FT4 and FT3 (P = 0.046; r = 0.11& P = 0.017; r = 0.15, respectively). Thyroid autoantibodies had positive significant correlations with different parameters of the thyroid volume (P < 0.05). Conclusions Thyroid’s US findings in addition to serum levels of anti-Tg and anti-TPO titers would be useful in diagnosis and evaluation of the severity and extent of Hashimoto's thyroiditis, but further evaluations are needed. Trial registration: Trial registry identifier IR.SUMS.REC.1395.S161 (2015/11/30).

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