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Prediction Of Protein Subcellular Localization Based On Primary Sequence DataOzarar, Mert 01 January 2003 (has links) (PDF)
Subcellular localization is crucial for determining the functions of proteins.
A system called prediction of protein subcellular localization (P2SL) that predicts
the subcellular localization of proteins in eukaryotic organisms based on the
amino acid content of primary sequences using amino acid order is designed.
The approach for prediction is to nd the most frequent motifs for each protein
in a given class based on clustering via self organizing maps and then
to use these most frequent motifs as features for classication by the help of
multi layer perceptrons. This approach allows a classication independent
of the length of the sequence. In addition to these, the use of a new encoding
scheme is described for the amino acids that conserves biological function
based on point of accepted mutations (PAM) substitution matrix. The statistical
test results of the system is presented on a four class problem. P2SL achieves
slightly higher prediction accuracy than the similar studies.
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Molecular and functional analysis of phosphatidylinositol 4 kinase type II betaJung, Gwanghyun. January 2008 (has links)
Dissertation (Ph.D.) -- University of Texas Southwestern Medical Center at Dallas, 2008. / Vita. Bibliography: p. 141-151.
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Peptide sequence assignments by probabilistic peptide profile matching to an annotated peptide database /Chen, Sharon S. January 2005 (has links)
Thesis (Ph. D.)--University of Washington, 2005. / Vita. Includes bibliographical references (p. 85-102).
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Trafficking of integral membrane proteins of the inner nuclear membrane can be mediated by the ''sorting motif'' of autographa californica nucleopolyhedrovirus odv-e66Williamson, Shawn T 30 October 2006 (has links)
The amino-terminal 33 amino acids of the baculovirus integral membrane
protein, ODV-E66, are sufficient for localization of fusion proteins to viralinduced
intranuclear microvesicles (MV) and occlusion derived virus envelopes
during infection, and has been termed the sorting motif (SM). When abundantly
expressed, SM-fusions are also detected in the inner nuclear membrane (INM),
outer nuclear membrane and endoplasmic reticulum of infected cells, suggesting
proteins with the SM use the same trafficking pathway as cellular INM proteins
to traffic to nuclear membranes. This study identifies the essential
characteristics required for sorting of the SM to the INM of uninfected cells, and
the MV and ODV envelopes of infected cells. These features are an 18 amino
acid transmembrane sequence that lacks polar and charged amino acids (a.a.)
with a cluster of charged a.a. spaced 5-11 residues from the end of the
transmembrane sequence. A comparison of the a.a. sequence of these SM
features with cellular INM proteins shows the features are conserved.
The model of INM protein sorting and localization predicts the only known
sorting event during INM protein trafficking is immobilization/retention in the INM. This study uses confocal microscopy and fluorescence recovery after
photobleaching to compare the localization and mobility of lamin B receptor
(LBR) fusions (which contain SM-like sequences) to a viral SM fusion when
expressed in either mammalian or insect cells. The results show that
immobilization is not necessarily required for accumulation of proteins in the
INM. Furthermore, the results from infected cells show that an active sorting
event, likely independent of immobilization, can distinguish the viral SM from
cellular sequences similar to the SM.
The results of this study show that sorting of proteins to the INM can be
mediated by the viral SM or INM protein SM-like sequences that can function
either independent of, or in addition to, immobilization. These data combined
with recent reports suggest that in addition to diffusion:retention a signal
mediated mechanism for sorting and localization to the INM can occur.
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The Role Of The Small GTPASE RAB14 In Apical ProteinTraffic And Maintenance Of Cell PolarityJacobson, Noelle C January 2005 (has links)
The establishment and maintenance of cell polarity during development is an active process that requires specific protein sorting and targeting to apical and basolateral regions of the cell. Our lab has identified an apical early endosomal marker, endotubin, in developing rat intestine, which we have used to label specialized apical endosomal tubules, and to probe for components of the apical sorting machinery. Studies with endotubin have implicated the small GTPase Rab14 as part of the sorting machinery for apical targeting. The current work pursues further study of the interaction between Rab14 and endotubin, as well as the role for Rab14 in the establishment of cell asymmetry. Interestingly, even nonpolarized cells may utilize polarized trafficking components for proper sorting and dynamics of endotubin.
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Predicting transmembrane topology and signal peptides with hidden Markov models /Käll, Lukas, January 2006 (has links)
Diss. (sammanfattning) Stockholm : Karol. inst., 2006. / Härtill 5 uppsatser.
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Role of the gM/gN glycoprotein complex in the final assembly and egress of the human cytomegalovirus (HCMV)Krzyzaniak, Magdalena Anna. January 2008 (has links) (PDF)
Thesis (Ph. D.)--University of Alabama at Birmingham, 2008. / Title from first page of PDF file (viewed Sept. 16, 2008). Includes bibliographical references.
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Structure and interactions of the juxtamembrane domain of the epidermal growth factor receptor /Choowongkomon, Kiattawee. January 2005 (has links)
Thesis (Ph. D.)--Case Western Reserve University, 2005. / [School of Medicine] Department of Physiology and Biophysics. Includes bibliographical references. Available online via OhioLINK's ETD Center.
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Protein sorting to the apical membrane of epithelial cells / Proteinsortierung an die apikale Membran von EpithelzellenSchuck, Sebastian 18 December 2004 (has links) (PDF)
The structure and functions of lipid rafts and the mechanisms of intracellular membrane trafficking are major topics in current cell biological research. Rafts have been proposed to act as sorting platforms during biosynthetic transport, especially along pathways that deliver proteins to the apical membrane of polarised cells. Based on this, the aim of this work was to contribute to the understanding of apical sorting in epithelial cells. The study of how lipid rafts are structured has been hampered by the scarcity of techniques for their purification. Rafts are thought to be partially resistant to solubilisation by mild detergents, which has made the isolation of detergent-resistant membranes (DRMs) the primary method to characterise them biochemically. While a growing number of detergents is being used to prepare DRMs, it is not clear what can be inferred about the native structure of cell membranes from the composition of different DRMs. This issue was addressed by an analysis of DRMs prepared with a variety of mild detergents. The protein and lipid content of different DRMs from two cell lines, Madin-Darby canine kidney (MDCK) and Jurkat cells, was compared. It was shown that the detergents differed considerably in their ability to selectively solubilise membrane proteins and lipids. These results make it unlikely that different DRMs reflect the same underlying principle of membrane organisation. Another obstacle for understanding apical sorting is that the evidence implicating certain proteins in this process has come from various disparate approaches. It would be helpful to re-examine the putative components of the apical sorting machinery in a single experimental system. To this end, a retroviral system for RNA interference (RNAi) in MDCK cells was established. Efficient suppression of thirteen genes was achieved by retroviral co-expression of short hairpin RNAs and a selectable marker. In addition, the system was extended to simultaneously target two genes, giving rise to double knockdowns.Retroviral RNAi was applied to deplete proteins implicated in apical sorting. Surprisingly, none of the knockdowns analysed caused defects in surface delivery of influenza virus hemagglutinin, a common marker protein for apical transport. Therefore, none of the proteins examined is absolutely required for transport to the apical membrane of MDCK cells. Cells may adapt to the depletion of proteins involved in membrane trafficking by activating alternative pathways. To avoid such adaptation, a visual transport assay was established. It is based on the adenoviral expression of fluorescent marker proteins whose surface transport can be followed microscopically as soon as RNAi has become effective. With this assay, it should now be possible to screen the knockdowns for defects in surface transport. Taken together, this work has provided a number of experimental tools for the study of membrane trafficking in epithelial cells. First, the biochemical analysis of DRMs highlighted that DRMs obtained with different detergents are unlikely to correspond to distinct types of membrane microdomains in cell membranes. Second, the retroviral RNAi system should be valuable for defining the function of proteins, not only in membrane transport, but also in processes like epithelial polarisation. Third, the visual assay for monitoring the surface transport of adenovirally expressed marker proteins should be suitable to detect defects in polarised sorting.
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Computational analysis of bacterial type III secreted signal sequences and in silico identification of new type III secreted proteins. / CUHK electronic theses & dissertations collectionJanuary 2011 (has links)
Wang, Yejun. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2011. / Includes bibliographical references (leaves 97-105). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese.
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