Membrane proteins are involved in vital cellular functions and have important implications in disease processes, drug design and therapy. However, it is difficult to obtain diffraction quality crystals to study transmembrane protein structure. Transmembrane protein topology prediction tools try to fill in the gap between abundant number of transmembrane proteins and scarce number of known membrane protein structures (3D structure and biochemically characterized topology). However, at present, the prediction accuracy is still far from perfect. TMHMM is the current state-of- the-art method for membrane protein topology prediction. In order to improve the prediction accuracy of TMHMM, based upon the method of GenomeScan, the author implemented AHMM (augmented HMM) by incorporating functional domain information externally to TMHMM. Results show that AHMM is better than TMHMM on both helix and sidedness prediction. This improvement is verified by both statistical tests as well as sensitivity and specificity studies. It is expected that when more and more functional domain predictors are available, the prediction accuracy will be further improved.

Membrane proteins are involved in vital cellular functions and have important implications in disease processes, drug design and therapy. However, it is difficult to obtain diffraction quality crystals to study transmembrane protein structure. Transmembrane protein topology prediction tools try to fill in the gap between abundant number of transmembrane proteins and scarce number of known membrane protein structures (3D structure and biochemically characterized topology). However, at present, the prediction accuracy is still far from perfect. TMHMM is the current state-of- the-art method for membrane protein topology prediction. In order to improve the prediction accuracy of TMHMM, based upon the method of GenomeScan, the author implemented AHMM (augmented HMM) by incorporating functional domain information externally to TMHMM. Results show that AHMM is better than TMHMM on both helix and sidedness prediction. This improvement is verified by both statistical tests as well as sensitivity and specificity studies. It is expected that when more and more functional domain predictors are available, the prediction accuracy will be further improved.

The hsDC2, an unknown gene, was located on chromosome 4q25. Its genetic protein product contains 149 amino acids with the molecular weight of 16.8 kDa approximately. Predicted by bioinformatics, hsDC2 might be a transmembrane protein with three transmembrane helices on the endoplasmic reticulum. Based on the results of reverse transcription-polymerase chain reaction, it revealed that hsDC2 was expressed in many tissues. It was showed that there were more mRNA expression in the cancer tissue. Using real-time quantitative PCR to analyze cancer cell lines, we found that hsDC2 might be related to differentiation status of cells. Among the well-differentiated cells such as nasopharyngeal carcinoma cell line NPC TW01, hepatoma cell line Hep3B and temperature-induced differentiated human fetal osteoblast cell line (hFOB), there were more hsDC2 mRNA expression. We also obtained some useful information from bioinformatics databases. To further elucidate the biological functions of the gene, glutathion S-transferase-hsDC2 fusion protein was used to generate anti-hsDC2 polyclonal antibody. However, we still need further research to clarify the biological function of hsDC2.

Contexte. Les protéines transmembranaires ont une importance considérable tant au niveau de la survie d'une cellule qu'au niveau de ces interactions avec les autres cellules. En raison de contraintes techniques, la cristallisation de ce type de protéine demeure très complexe, ce qui limite grandement l’exploration de leur structure. Pour contourner ces difficultés, différents outils de prédiction ont été développés,en se fondant originellement sur l'hydrophobicité des régions enfouies dans la membrane. Méthode. L'outil développé repose sur une dérivation de la moyenne d'hydrophobicité calculée sur deux ensembles de taille de fenêtres. Le premier ensemble (G1) contient des petites tailles de fenêtres ce qui correspond à des événements locaux, tandis que le second (G2) correspond à des tailles de fenêtres plus larges, adaptées à la taille des hélices formant certaines protéines transmembranaires. La variation d'hydrophobicité est obtenue en dérivant les moyennes d'hydrophobicité. Un consensus est établi pour chaque groupe, et les résultats sont comparés à un ensemble de protéines transmembranaires cristallisées. Résultats. Les variations d'hydrophobicité G2 sont liées aux extrémités des hélices transmembranaires,tandis que les variations G1 sont en relation avec la limites des structures et certaines irrégularités structurelles.Ces résultats nous ont amené à introduire une nouvelle notion : les unités transmembranaires(TMU). Les TMU consistent en un ensemble de sous-structures qui composent les structures transmembranaires. / Background. Few high-resolution structures of integral membranes proteins are available, as crystallization of such proteins needs yet to overcome too many technical limitations. Nevertheless, prediction oftheir transmembrane (TM) structure by bioinformatics tools provides interesting insights on the topology of these proteins.Method. We describe here how to extract new information from the analysis of hydrophobicity variations or hydrophobic pulses (HPulses) in the sequence of integral membrane proteins using the Hydrophobic Pulse Predictor, a new tool we developed for this purpose. To analyze the primary sequence of 70 integralmembrane proteins we defined two levels of analysis : G1-HPulses for sliding windows of n=2 to 6 andG2-HPulses for sliding windows of n=12 to 16.Results. The G2-HPulse analysis of 541 transmembrane helices allowed the definition of the new conceptof transmembrane unit (TMU) that groups together transmembrane helices and segments with potentialadjacent structures. In addition, the G1-HPulse analysis identified helix irregularities that correspondedto kinks, partial helices or unannotated structural events. These irregularities could represent key dynamicelements that are alternatively activated depending on the channel status as illustrated by the crystalstructures of the lactose permease in different conformations. Our results open a new way in the understanding of transmembrane secondary structures : hydrophobicity through hydrophobic pulses stronglyimpacts on such embedded structures and is not confined to define the transmembrane status of aminoacids.

This dissertation covers a broad range of research topics all towards the ultimate goal establishing of a novel type of biosensor in which the biocompatible membrane structure reconstituted with functional transmembrane proteins is utilized as the sensing element. It focuses on 1) examining the activity of a model transmembrane protein, bovine rhodopsin (Rho) when reconstituted into stabilized lipid membranes and 2) the instrumentation of a novel type of optical spectroscopy, plasmon waveguide resonance (PWR), which is a surface sensitive technique and its application in sensing biological events.Lipid membrane play crucial roles in cell function. Their biophysical properties affect the activity of a large amount of transmembrane receptors. They are great candidates for biosensing/ biomedical coating. However, the intrinsic instability of natural or fluid membranes prevents them to be used in a device. Studies have been done to show indirect evidence that the activity of Rho maybe maintained in polymerized membrane composed of bis-SorbPC lipids. The activity of Rho reconstituted into vesicular membranes comprised of various lipids was studied by a more direct technique, UV-Vis. It was found Rho activity was maintained to 66% of that in natural Egg PC lipid in the mixture of Egg PC:(poly)bis-SorbPC (1:1 mol:mol) as opposed to minimal values in 100 % (poly)lipids.A new type of spectral PWR was developed. The working concept, technical characterization and comparisons with similar techniques were discussed and compared in this work. A modified version of angular PWR in which lipid bilayers were formed by vesicle fusion was also developed. This method excludes possible effects from a high boiling point organic solvent on either the lipid bilayer itself or the membrane proteins associated with it. A calculating program NphaseAll for PWR was developed to do predictions of waveguide properties can be made to provide guidance for waveguide design. Theoretical calculations were done for PWR and experimental results were compared with the theoretical predictions.PWR was used to detect the formation of a biological lipid membrane, the association of alpha synuclein with membranes and the binding activity of human melanarcortin to its ligands in fluid and polymerized/dried membranes.

Members of the membrane-spanning four-domains, subfamily A (MS4A) family are small polypeptides that share the structural features of four-transmembrane domains and unevenly sized extracellular loops. The family includes CD20, FcεRIβ and HtM4, plus a number of relatively uncharacterised proteins / predicted proteins. MS4A proteins are discussed in relation to other protein families, such as the tetraspanins, that are also characterised by four-transmembrane domains. The aim of this study was to identify the cell and tissue distribution, subcellular localisation, and function of a newly discovered member of the MS4A family, hepatocellular carcinoma-associated antigen 112 (HCA112). At a subcellular level, HCA112 was found on the plasma membrane of transfected COS-7 cells, and also within the Golgi complex, trans-Golgi-network, and early endosomes. The molecule is orientated such that the large loop is extracellular and the Nand C-terminal domains are cytoplasmic. The presence of HCA112 associated with components of the endocytic pathway raised the question of whether some originated from the surface membrane. Antibody was used to label a HA epitope tag engineered into the large extracellular loop of HCA112, and the bound antibody was tracked through early endosomes to the recycling compartment. Here it co-localised with internalised transferrin, indicating strongly that HCA112 is internalised via clathrin-dependent mechanisms. Several endocytic sorting motifs within the intracellular domains of HCA112 were investigated for their ability to direct internalisation of HCA112. Deletion of a di-leucine motif was found to slow but not prevent endocytosis, suggesting that it is involved in endocytosis of HCA112, although not essential for the process. When HCA112 expression constructs featuring N- and C-terminal domain truncations were examined, it was found that the N-terminal tail does not affect the subcellular localisation or trafficking of HCA112, while deletion of the C-terminal intracellular domain resulted in retention of the mutant protein in the ER. HCA112 has a wide tissue distribution and is highly expressed in the lining/covering and parenchymal epithelium of some tissues, proximal renal tubules, ductal epithelium in a number of organs, endothelial cells, some steroidogenic endocrine cells, adipocytes, smooth muscle cells, follicular dendritic cells and macrophages. The expression of HCA112 by a wide range of cell types suggests that its function(s) has general importance and is not limited to any specific cell type(s). After reflection on the functions of the HCA112-expressing cells, a common theme that emerged was one of endocytic activity. This lead to speculate that one function of HCA112 might be related to uptake of macromolecules, for instance, in antigen processing and presentation. This might be a general function, such as facilitating uptake of other cell membrane proteins, or directing the traffic of endocytic vesicles. It was noted that HCA112 has a similar cell and tissue distribution to the scavenger receptor and fatty acid translocase FAT/CD36 (Zhang et al., 2003). Furthermore, in cells co-transfected with HCA112 and FAT/CD36, the two molecules co-localise in early endosomes and co-immunoprecipitate, suggesting that the molecules physically and spatially associate. Thus, HCA112 could be involved with (or complement) FAT/CD36 in its functions as a long chain fatty acid transporter and scavenger receptor. A proteomics study of proteins that co-immunoprecipitated with HCA112 detected putative interactions with a number of proteins. These included LR8, transferrin receptor, interferon induced transmembrane proteins 2 and 3, Calpain-6, stomatin, PDGF α receptor, and heat shock 70 kDa protein 8 (HSPA8, formerly known as clathrin un-coating ATPase). Of these, LR8 and the transferrin receptor were investigated in more detail. The results provide strong evidence that HCA112 forms a novel complex with LR8, and that this may be involved in macromolecule internalisation or trafficking of membrane proteins, such as FAT/CD36 or the transferrin receptor. In the case of the transferrin receptor, this traffic appears to involve the clathrin-dependent pathway, but it is possible that when HCA112 is associated with FAT/CD36, it functions within lipid raft domains. / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1375454 / Thesis (Ph.D.) -- University of Adelaide, School of Molecular and Biomedical Science, 2009

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Osteosarcoma is the most common primary malignancy of bone. 5-year survival has remained stable at around 60-70% for 40 years. However, a number of patients will suffer from recurrent and/or metastatic disease representing a large unmet clinical need. CSPG4 is a transmembrane protein which is expressed on a number of progenitor cells and tumour types. Preliminary work had found CSPG4 present in osteosarcoma tumour samples. In this study, CSPG4 mRNA and protein expression was demonstrated in clinical samples and model cell lines. CSPG4 mRNA is overexpressed in osteosarcoma samples compared to mature osteoblast cells, the putative cell of origin for osteosarcoma. In a cohort of patients, CSPG4 protein expression was found on 86% of samples. Furthermore, CSPG4 expression was demonstrated in U2OS, MG63, HOS, HOS-MNNG and 143B osteosarcoma cell lines. CSPG4 protein expression was successfully deleted in 143B cells using CRISPR/Cas9 technology. Two stable CSPG4-negative cell lines were produced. CSPG4 expression was then reintroduced into negative cell lines, as well as the parental 143B cell line. This created a panel of 6 cell lines with differing CSPG4 expression. Furthermore, siRNA treatment of U2OS, MG63, 143B and U87MG cell lines reduced CSPG4 expression. These cells provided another panel with varying CSPG4 expression for in vitro investigation. In vitro experiments failed to demonstrate a role for CSPG4 in osteosarcoma tumorigenesis. The CRISPR/Cas9 cell panel found that CSPG4 expression did not influence cell proliferation, adhesion and spreading on fibronectin or collagen-I, cell migration, chemosensitivity or anchorage-independent growth. Similarly, the siRNA cell panel found that CSPG4 expression did not influence cell proliferation or anchorage-independent growth. In vivo experimentation did not demonstrate a role for CSPG4 in mediating osteosarcoma tumour growth or metastatic spread. Treatment with a sc-Fv antibody fragment failed to demonstrate specific toxicity of CSPG4-positive cell lines. These results indicate that CSPG4 plays no role in osteosarcoma tumour cell behaviour. However, due to its wide expression pattern it represents a viable therapeutic option for drug targeting.

No description available.

No description available.