In Silico And In Vivo Analysis Of Otu Deubiquitinases Otub1, Otub2 And Otulin Protein-protein Interactions

In this post-genomic era, proteomic and interactomic data are important sources for understanding the molecular basis of cell functional diversity. Research in these fields is still progressing, with at least 90% of proteins annotated so far and many more interactions to be uncovered to complete the...

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Main Author:	Zulkifli, Nur Wahida
Format:	Thesis
Language:	English
Published:	2023
Subjects:	R5-920 Medicine (General)
Online Access:	http://eprints.usm.my/60686/1/NUR%20WAHIDA%20BINTI%20ZULKIFLI%20-%20TESIS24.pdf
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id	my-usm-ep.60686
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spelling	my-usm-ep.606862024-05-31T08:40:44Z In Silico And In Vivo Analysis Of Otu Deubiquitinases Otub1, Otub2 And Otulin Protein-protein Interactions 2023-09 Zulkifli, Nur Wahida R5-920 Medicine (General) In this post-genomic era, proteomic and interactomic data are important sources for understanding the molecular basis of cell functional diversity. Research in these fields is still progressing, with at least 90% of proteins annotated so far and many more interactions to be uncovered to complete the proteome and interactome maps. The purpose of this study is to contribute to the expansion of human interactome data by focusing on the deubiquitinating enzymes (DUBs) protein-protein interaction (PPI) using several in silico and in vivo approaches. First, a DUBs interactome was built on Cytoscape ver 3.9.1 using data from IMEx database and analysed using various graph theory algorithms. The DUBs interactome consisted of 3,406 nodes and 4,982 edges, whereas a cancer protein subnetwork extracted from the interactome revealed that DUBs are significant in cancer biology. Concluding the interactome study, OTUB1, one of the proteins with strong network characteristics, along with its closest homologue OTUB2, and the newest family member OTULIN, were selected for yeast two-hybrid (Y2H) screening against human cDNA library derived from HEK293. Y2H bait and cDNA library prey vectors were generated using Gateway technology, first in donor vector TOPO/pDONR222 before being shuffled into destination vector pDEST32/22. The bait vector is sequence-verified, and the prey vector is of sufficient quality and quantity to represent human cDNA with total clones of 6.8×106 cfu. Both vectors were transformed into MaV203 S. cerevisiae strain for Y2H screening to identify putative interacting proteins 2023-09 Thesis http://eprints.usm.my/60686/ http://eprints.usm.my/60686/1/NUR%20WAHIDA%20BINTI%20ZULKIFLI%20-%20TESIS24.pdf application/pdf en public phd doctoral Universiti Sains Malaysia Institut Perubatan & Pergigian Termaju
institution	Universiti Sains Malaysia
collection	USM Institutional Repository
language	English
topic	R5-920 Medicine (General)
spellingShingle	R5-920 Medicine (General) Zulkifli, Nur Wahida In Silico And In Vivo Analysis Of Otu Deubiquitinases Otub1, Otub2 And Otulin Protein-protein Interactions
description	In this post-genomic era, proteomic and interactomic data are important sources for understanding the molecular basis of cell functional diversity. Research in these fields is still progressing, with at least 90% of proteins annotated so far and many more interactions to be uncovered to complete the proteome and interactome maps. The purpose of this study is to contribute to the expansion of human interactome data by focusing on the deubiquitinating enzymes (DUBs) protein-protein interaction (PPI) using several in silico and in vivo approaches. First, a DUBs interactome was built on Cytoscape ver 3.9.1 using data from IMEx database and analysed using various graph theory algorithms. The DUBs interactome consisted of 3,406 nodes and 4,982 edges, whereas a cancer protein subnetwork extracted from the interactome revealed that DUBs are significant in cancer biology. Concluding the interactome study, OTUB1, one of the proteins with strong network characteristics, along with its closest homologue OTUB2, and the newest family member OTULIN, were selected for yeast two-hybrid (Y2H) screening against human cDNA library derived from HEK293. Y2H bait and cDNA library prey vectors were generated using Gateway technology, first in donor vector TOPO/pDONR222 before being shuffled into destination vector pDEST32/22. The bait vector is sequence-verified, and the prey vector is of sufficient quality and quantity to represent human cDNA with total clones of 6.8×106 cfu. Both vectors were transformed into MaV203 S. cerevisiae strain for Y2H screening to identify putative interacting proteins
format	Thesis
qualification_name	Doctor of Philosophy (PhD.)
qualification_level	Doctorate
author	Zulkifli, Nur Wahida
author_facet	Zulkifli, Nur Wahida
author_sort	Zulkifli, Nur Wahida
title	In Silico And In Vivo Analysis Of Otu Deubiquitinases Otub1, Otub2 And Otulin Protein-protein Interactions
title_short	In Silico And In Vivo Analysis Of Otu Deubiquitinases Otub1, Otub2 And Otulin Protein-protein Interactions
title_full	In Silico And In Vivo Analysis Of Otu Deubiquitinases Otub1, Otub2 And Otulin Protein-protein Interactions
title_fullStr	In Silico And In Vivo Analysis Of Otu Deubiquitinases Otub1, Otub2 And Otulin Protein-protein Interactions
title_full_unstemmed	In Silico And In Vivo Analysis Of Otu Deubiquitinases Otub1, Otub2 And Otulin Protein-protein Interactions
title_sort	in silico and in vivo analysis of otu deubiquitinases otub1, otub2 and otulin protein-protein interactions
granting_institution	Universiti Sains Malaysia
granting_department	Institut Perubatan & Pergigian Termaju
publishDate	2023
url	http://eprints.usm.my/60686/1/NUR%20WAHIDA%20BINTI%20ZULKIFLI%20-%20TESIS24.pdf
_version_	1804888985945767936

In Silico And In Vivo Analysis Of Otu Deubiquitinases Otub1, Otub2 And Otulin Protein-protein Interactions

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