Please use this identifier to cite or link to this item: http://hdl.handle.net/10603/125748
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dc.date.accessioned2017-01-18T05:42:41Z-
dc.date.available2017-01-18T05:42:41Z-
dc.identifier.urihttp://hdl.handle.net/10603/125748-
dc.description.abstractProtein domains are the functional and evolutionary units of protein structure and are independent in their functionality and folding pattern. Over millions of years, they tend to accumulate many mutations which can cause a change in their length and structure thereby increasing their functional diversity. Domain comparisons have shown that structural variation is influenced by the number, length and location of insertions and deletions of residues and these length variations can range from two-three residues to two-fold of the domain size. Length variations at the protein domain level have been known to cause functional impacts like, increasing structural stability, diversifying substrate specificity etc. In this thesis, I have studied length variations within protein domains from sequence, structure and dynamics perspective. Starting from a seed set of PASS2 database, which contains alignments of distantly related protein domains (grouped as protein superfamilies as per SCOP hierarchy), homologous sequences of the seed set were collected from the sequence space systematically. For running this automated search over 731 superfamilies (~7500 protein domains), a pipeline was developed which gathered and validated homologues having length variations. These when processed led to identifying indels and in creation of a comprehensive resource of length variant protein domains at superfamily level which will help users trace length variations/indels in their protein domain of interest. The structural significance of a twenty residue insert in a DNA polymerase, terminal deoxynucleotidyl transferase, was investigated using modeling and molecular dynamics simulation for an in-depth perspective on effect of length variation at functional level of protein. This thesis attempts to create a knowledgebase and provide pointers regarding presence of indels across various protein domain superfamilies, their effects on the structure and function of proteins which can further help in protein engineering and drug targeting.
dc.format.extentxvii,199
dc.languageEnglish
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dc.rightsself
dc.titleLength variation analysis of protein domain superfamilies amongst sequence homologues
dc.title.alternative
dc.creator.researcherEshita Mutt
dc.subject.keywordindels
dc.subject.keywordlength variation
dc.subject.keywordprotein domains
dc.subject.keywordSCOP
dc.subject.keywordTerminal Deoxynucleotidyl Transferase
dc.description.note
dc.contributor.guideProf. Abhijit Mitra
dc.publisher.placeHyderabad
dc.publisher.universityInternational Institute of Information Technology, Hyderabad
dc.publisher.institutionComputational Natural Sciences
dc.date.registered31-12-2009
dc.date.completed06/11/2014
dc.date.awarded31/12/2014
dc.format.dimensions
dc.format.accompanyingmaterialNone
dc.source.universityUniversity
dc.type.degreePh.D.
Appears in Departments:Computational Natural Sciences

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02_copyright.pdf25.45 kBAdobe PDFView/Open
03_certificate.pdf26.34 kBAdobe PDFView/Open
04_acknowledgement.pdf38.1 kBAdobe PDFView/Open
05_abstract.pdf30.37 kBAdobe PDFView/Open
06_contents.pdf42.28 kBAdobe PDFView/Open
07_list of tables and figures.pdf43.71 kBAdobe PDFView/Open
08_abbreviations.pdf26.54 kBAdobe PDFView/Open
09_chapter 1.pdf1.04 MBAdobe PDFView/Open
10_chapter 2.pdf3 MBAdobe PDFView/Open
11_chapter 3.pdf1.6 MBAdobe PDFView/Open
12_chapter 4.pdf3.47 MBAdobe PDFView/Open
13_chapter 5.pdf2.33 MBAdobe PDFView/Open
14_chapter 6.pdf10.8 MBAdobe PDFView/Open
15_chapter 7.pdf140.3 kBAdobe PDFView/Open
16_chapter 8.pdf1.78 MBAdobe PDFView/Open
17_bibliography.pdf211.74 kBAdobe PDFView/Open
18_publications.pdf89.72 kBAdobe PDFView/Open


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