Computational analysis on missense mutation of ornithine transcarbamylase (OTCase) enzyme / Ernie Zuraida Ali

Missense mutations occur close to the binding pocket of ornithine transcarbamylase (OTCase) enzyme associated with a severe form of ornithine transcarbamylase deficiency (OTCD), an X-linked disorder. These mutations affect the functions of OTCase enzyme in the body that can lead to acute clinical sy...

Full description

Saved in:

Bibliographic Details
Main Author:	Ali, Ernie Zuraida
Format:	Thesis
Language:	English
Published:	2020
Subjects:	Biomedical engineering Administration
Online Access:	https://ir.uitm.edu.my/id/eprint/32494/1/32494.pdf
Tags:	Add Tag No Tags, Be the first to tag this record!

id	my-uitm-ir.32494
record_format	uketd_dc
spelling	my-uitm-ir.324942022-06-08T07:58:04Z Computational analysis on missense mutation of ornithine transcarbamylase (OTCase) enzyme / Ernie Zuraida Ali 2020 Ali, Ernie Zuraida Biomedical engineering Clinical pathology. Laboratory technique Administration Missense mutations occur close to the binding pocket of ornithine transcarbamylase (OTCase) enzyme associated with a severe form of ornithine transcarbamylase deficiency (OTCD), an X-linked disorder. These mutations affect the functions of OTCase enzyme in the body that can lead to acute clinical symptoms. Early diagnosis and intervention is crucial for effective decision on managing patients and reducing mortality rate. However, the current diagnosis and biochemical analyses being used are still time consuming, labour intensive and costly. Therefore, in this work, three (3) stages of computational approaches (mutation prediction servers, molecular docking, molecular dynamics simulations) are explored and implemented to predict the severity of the missense mutations in OTCD. The findings are based on two novels, Q171H and N199H, and 30 other known missense mutations located in the OTCase ligand binding pocket. The novel mutations were obtained from the nucleotide sequencing results from two OTCD Malaysian patients, while the other 30 known mutations were collected from HGMD and 1000G browser databases. The consensus prediction of five mutation prediction servers concluded all 32 mutations are disease-causing. Further study using docking of PALO ligand, an analog of N-phosphonacetyl-Lornithine resulted in binding of the ligand to the mutant OTCase structures with slightly differently conformation when compared to the wild type structure. In the final stage, MD simulations of the mutant complexes (Q171H-PALO, N199H-PALO, R92P-PALO and H168R-PALO) confirmed the conformational instability due to the disruption of intermolecular interactions between PALO and OTCase. The missense mutations disrupted hydrogen bond interactions with the neighbouring residues (S267, M268, D263, C303, R330 and E326), including residues involved in the catalytic mechanism (C303, D263 and R330). In addition, the role of SMG loop as a second ligand recognition site was observed during the simulations. Application of computational approaches successfully revealed the mutations potentially disturb catalytic efficiency contributing to the occurrence of various OTCD symptoms. In conclusion, computational approaches can potentially be used as preliminary screening and rapid diagnosis for new mutation as it can provide the fast result, save time and cost. 2020 Thesis https://ir.uitm.edu.my/id/eprint/32494/ https://ir.uitm.edu.my/id/eprint/32494/1/32494.pdf text en public phd doctoral Universiti Teknologi MARA Faculty of Pharmacy Jusoh, Siti Azma (Dr.)
institution	Universiti Teknologi MARA
collection	UiTM Institutional Repository
language	English
advisor	Jusoh, Siti Azma (Dr.)
topic	Biomedical engineering Biomedical engineering Administration
spellingShingle	Biomedical engineering Biomedical engineering Administration Ali, Ernie Zuraida Computational analysis on missense mutation of ornithine transcarbamylase (OTCase) enzyme / Ernie Zuraida Ali
description	Missense mutations occur close to the binding pocket of ornithine transcarbamylase (OTCase) enzyme associated with a severe form of ornithine transcarbamylase deficiency (OTCD), an X-linked disorder. These mutations affect the functions of OTCase enzyme in the body that can lead to acute clinical symptoms. Early diagnosis and intervention is crucial for effective decision on managing patients and reducing mortality rate. However, the current diagnosis and biochemical analyses being used are still time consuming, labour intensive and costly. Therefore, in this work, three (3) stages of computational approaches (mutation prediction servers, molecular docking, molecular dynamics simulations) are explored and implemented to predict the severity of the missense mutations in OTCD. The findings are based on two novels, Q171H and N199H, and 30 other known missense mutations located in the OTCase ligand binding pocket. The novel mutations were obtained from the nucleotide sequencing results from two OTCD Malaysian patients, while the other 30 known mutations were collected from HGMD and 1000G browser databases. The consensus prediction of five mutation prediction servers concluded all 32 mutations are disease-causing. Further study using docking of PALO ligand, an analog of N-phosphonacetyl-Lornithine resulted in binding of the ligand to the mutant OTCase structures with slightly differently conformation when compared to the wild type structure. In the final stage, MD simulations of the mutant complexes (Q171H-PALO, N199H-PALO, R92P-PALO and H168R-PALO) confirmed the conformational instability due to the disruption of intermolecular interactions between PALO and OTCase. The missense mutations disrupted hydrogen bond interactions with the neighbouring residues (S267, M268, D263, C303, R330 and E326), including residues involved in the catalytic mechanism (C303, D263 and R330). In addition, the role of SMG loop as a second ligand recognition site was observed during the simulations. Application of computational approaches successfully revealed the mutations potentially disturb catalytic efficiency contributing to the occurrence of various OTCD symptoms. In conclusion, computational approaches can potentially be used as preliminary screening and rapid diagnosis for new mutation as it can provide the fast result, save time and cost.
format	Thesis
qualification_name	Doctor of Philosophy (PhD.)
qualification_level	Doctorate
author	Ali, Ernie Zuraida
author_facet	Ali, Ernie Zuraida
author_sort	Ali, Ernie Zuraida
title	Computational analysis on missense mutation of ornithine transcarbamylase (OTCase) enzyme / Ernie Zuraida Ali
title_short	Computational analysis on missense mutation of ornithine transcarbamylase (OTCase) enzyme / Ernie Zuraida Ali
title_full	Computational analysis on missense mutation of ornithine transcarbamylase (OTCase) enzyme / Ernie Zuraida Ali
title_fullStr	Computational analysis on missense mutation of ornithine transcarbamylase (OTCase) enzyme / Ernie Zuraida Ali
title_full_unstemmed	Computational analysis on missense mutation of ornithine transcarbamylase (OTCase) enzyme / Ernie Zuraida Ali
title_sort	computational analysis on missense mutation of ornithine transcarbamylase (otcase) enzyme / ernie zuraida ali
granting_institution	Universiti Teknologi MARA
granting_department	Faculty of Pharmacy
publishDate	2020
url	https://ir.uitm.edu.my/id/eprint/32494/1/32494.pdf
_version_	1783734168057806848

Computational analysis on missense mutation of ornithine transcarbamylase (OTCase) enzyme / Ernie Zuraida Ali

Similar Items