Membrane proteins perform a variety of functions essential for the viability of the cell, including transport and signalling across the membrane. Most membrane proteins are formed from bundles of transmembrane helices. In this thesis molecular dynamics simulations have been used to investigate helix insertion into bilayers and helix association within bilayers. The potentials of mean force for the insertion of helices derived from the cystic fibrosis transmembrane conductance regulator into lipid bilayers were calculated using coarse-grained molecular dynamics simulations. The results showed that the insertion free energy increased with helix length and bilayer hydrophobic width. The insertion free energies obtained were significantly larger than comparable quantities obtained from translocon- mediated insertion experiments, consistent with a variety of previous studies. The implications of this observation for the interpretation of in vivo translocon-mediated insertion experiments, and the function of the translocon, are discussed. Coarse-grained and atomistic molecular dynamics simulations of the transmembrane region of the receptor tyrosine kinase EphA1 suggested that the transmembrane helix dimer was most stable when interacting via the glycine zipper motif, in agreement with a structure obtained by NMR spectroscopy. Coarse-grained simulations of the transmembrane region of EphA2 suggested that the dimer has two stable orientations, interacting via a glycine zipper or a heptad motif. Both structures showed right-handed dimers, although an NMR structure of the transmembrane region of EphA2 shows a left-handed dimer interacting via the heptad motif. Both structures obtained from coarse-grained simulations proved unstable when simulated at an atomistic level of detail. The potentials of mean force for dissociating the EphA1 and EphA2 dimers were calcu- lated using coarse-grained molecular dynamics calculations. Convergence of the detailed structure of the profiles was not conclusively shown, although association free energies cal- culated from the profiles were consistent over a variety of simulation times. The association free energies were slightly larger than experimental values obtained for comparable sys- tems, but consistent with similar computational calculations previously reported. However, direct comparisons are difficult owing to the influence of environmental factors on reported association free energies. The potential of mean force profiles showed that the interaction via the glycine zipper motif for EphA1 was significantly more stable than any other confor- mation. For EphA2 the potential of mean force profiles suggested that interaction via the glycine zipper and heptad motifs both provided stable or metastable conformations, with the interaction via the glycine zipper motif probably at least as stable as that via the heptad motif.

This thesis describes the development of a novel approach for prediction of the three-dimensional structure of transmembrane regions of membrane proteins directly from amino acid sequence and basic transmembrane region topology. The development rationale employed involved a knowledge-based approach. Based on determined membrane protein structures, 20x20 association matrices were generated to summarise the distance associations between amino acid side chains on different alpha helical transmembrane regions of membrane proteins. Using these association matrices, combined with a knowledge-based scale for propensity for residue orientation in transmembrane segments (kPROT) (Pilpel et al., 1999), the software predicts the optimal orientations and associations of transmembrane regions and generates a 3D structural model of a gi ven membrane protein, based on the amino acid sequence composition of its transmembrane regions. During the development, several structural and biostatistical analyses of determined membrane protein structures were undertaken with the aim of ensuring a consistent and reliable association matrix upon which to base the predictions. Evaluation of the model structures obtained for the protein sequences of a dataset of 17 membrane proteins of detennined structure based on cross-validated leave-one-out testing revealed generally high accuracy of prediction, with over 80% of associations between transmembrane regions being correctly predicted. These results provide a promising basis for future development and refinement of the algorithm, and to this end, work is underway using evolutionary computing approaches. As it stands, the approach gives scope for significant immediate benefit to researchers as a valuable starting point in the prediction of structure for membrane proteins of hitherto unknown structure.

No description available.

Wang Xiaofei. / "June 2002." / Thesis (Ph.D.)--Chinese University of Hong Kong, 2002. / Includes bibliographical references (p. 152-167). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Mode of access: World Wide Web. / Abstracts in English and Chinese.

In summary, the present findings have demonstrated the important roles of CFTR in prostatitis and cancer development, which may provide new insight into the understanding of the prostate in health and disease. The present findings may also have potential application in diagnosis and prognosis of cancer. / In the first part of the study, the possible role and a bacterial killing mechanism involving CFTR-mediated bicarbonate secretion in prostatitis were investigated in a rat prostate model. CFTR was found to be expressed in the epithelium of rat ventral prostate. Experiments using cultured rat primary prostate epithelial cells demonstrated that CFTR was involved in mediating bicarbonate extrusion across the prostate epithelium. The expression of CFTR and carbonic anhydrase II (CAII), a key enzyme involved in cellular HCO 3- production, along with several pro-inflammatory cytokines including IL-6, IL-1beta, TNF-alpha, was significantly up-regulated in the primary culture of rat prostate epithelial cells upon E.coli-LPS challenge. Inhibition of CFTR function in vitro or in vivo resulted in reduced bacterial killing by prostate epithelial cells or the prostate. High HCO3- content (>50mM), rather than alkaline pH, was found to be responsible for bacterial killing. The direct action of HCO 3- on bacterial killing was confirmed by its ability to suppress bacterial initiation factors in E coli. The relevance of the CFTR-mediated HCO3- secretion in human was demonstrated by the upregulated expression of CFTR and CAII in human prostatitis tissues. The present results have demonstrated that CFTR plays a previously undefined role in prostatitis and could be up-regulated during the inflammation in prostate as a host defense mechanism to increase bicarbonate secretion for bacterial killing. / In the second part of the study, the possible role of CFTR in prostate cancer development and the underlying mechanisms were investigated. Our results showed that the expression of CFTR and CAII in prostate was remarkably decreased in aged rat prostate. We observed that testosterone could up-regulate the expression of CFTR and CAII in vitro and in vivo , indicating that the declined male hormones during aging may be responsible for the observed age-dependent expression of CFTR. In the present study, we found that inhibition of CFTR enhanced cell proliferation/anti-apoptosis in the prostate primary epithelial cells. CFTR was detected in all examined prostate cell lines, but with relatively higher expression levels in immortalized cell lines (PZ-HPV-7, PNT1A, PNT2C2) than in cancer cell lines (PC-3, DU-145, LNCaP). Immunohistological studies showed that the expression of CFTR was dramatically reduced in prostate cancer specimens as compared to that in normal prostate tissues. Furthermore, our gain and loss of function studies showed that knockdown of CFTR profoundly enhanced cell proliferation, cell adhesion, invasion and migration, while inhibited apoptosis in prostate cancer cell lines, overexpression of CFTR dramatically suppressed tumorigenic phenotype of cancer cells. Soft agar anchorage-independent growth assay showed that knockdown of CFTR in prostate cancer cells increased the number of colonies formed in soft agar. More importantly, we demonstrated that CFTR knockdown promoted the tumor growth in vivo and forced overexpression of CFTR in prostate cancer cells and ultrasound-mediated gene transfer of CFTR inhibited xenograft tumor growth in vivo. Mechanistically, multiple mechanisms were identified to contribute to the CFTR- mediated tumor suppressive effects. Firstly, CFTR chloride channel function was implicated in the regulation of apoptosis in prostate cancer cells. Secondly, CFTR up-regulated the transcription level of miR-34a and miR-193b, both of which have been indicated as tumor suppressors in multiple cancers. Thirdly, 11 cancer-related genes were found to be up- or down-regulated by CFTR using PCR-array. These data demonstrated that CFTR may play an important role in prostate cancer development by acting as a tumor suppressor. / The cystic fibrosis transmembrane conductance regulator (CFTR) is an anion channel conducting both Cl- and HCO3 -. It is expressed in epithelial cells of a wide variety of tissues. CFTR is also known to be expressed in human prostate; however, the physiological role of CFTR in the prostate and related diseases remains largely unknown. This thesis explored the biological roles of CFTR in prostatitis and cancer development. / Xie, Chen. / Adviser: Chan LiShaw Chang. / Source: Dissertation Abstracts International, Volume: 73-02, Section: B, page: . / Thesis (Ph.D.)--Chinese University of Hong Kong, 2010. / Includes bibliographical references (leaves 175-192). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. [Ann Arbor, MI] : ProQuest Information and Learning, [201-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese.

As CFTR plays an important role in HCO3- transport, and HCO3- sensitive soluble adenylyl cyclase (sAC) has been shown to be largely responsible for the cAMP production in spermatogenetic cells, we hypothesized that CFTR-mediated HCO3- transport was important to spermatogenesis via sAC pathway in spermatogenetic and Sertoli cells. Using intracellular pH measurement, we demonstrated that CFTR is involved in HCO3- transport in Sertoli cells. RT-PCR results showed that increased HCO3- concentrations in the culture medium resulted in upregulation of CFTR expression. The results also showed that the intracellular cAMP level in Sertoli cells increased as the extracellular HCO3- concentration increased. HCO3- also caused phosphorylation of the cAMP response element binding (pCREB) proteins transcription factor on serine 133, a modification known to be required by Sertoli cells to support spermatogenesis. This phosphorylation could be inhibited by CFTR inhibitor, further lending support to the notion that CFTR is important for HCO3- transport in Sertoli cells, leading to HCO3- dependent events that are important for spermatogenesis. / CFTR is known to be widely expressed in epithelial cells of male reproductive tracts, but its expression in spermatogenic cells is less well known. We first confirmed the expression of CFTR in spermatogenic cells and mature sperm in rodents. Our study thus focused on the important role of CFTR in the processes related to male fertility including spermatogenesis and sperm capacitation. / Cystic fibrosis transmembrane conductance regulator (CFTR) is an anion channel, mutations of which cause cystic fibrosis, a disease characterized by defective Cl- and HCO3- transport. While over 95% of CF male patients are infertile because of congenital bilateral absence of the vas deferens (CBAVD), the question whether CFTR mutations are involved in other forms of male infertility is under intense debates. / In conclusion, our study has demonstrated the role of CFTR in male reproductive system. We have further elucidated its possible physiological role and the underlying molecular mechanisms. These studies may pave the way for the development of method strategies for diagnosis and treatment of CFTR related infertility in male. / Our study also detected CFTR in both human and mouse sperm. CFTR inhibitor or antibody significantly reduced sperm capacitation, and the associated HCO 3--dependent events including increases in intracellular pH, cAMP production and membrane hyperpolarization. The fertilizing capacity of the sperm obtained from heterozygous CFTR mutant mice is also significantly lower as compared to that of the wild type. These results suggest that CFTR in sperm may be involved in the transport of HCO3- important for sperm capacitation and that CFTR mutations with impaired CFTR function may lead to reduced sperm fertilizing capacity and male infertility other than CBAVD. / We further demonstrated the physiological role of CFTR in spermatogenesis using CFTR knockout mice as an in vivo model. Although TUNNEL staining showed normal percentage of apoptotic cells in seminiferous tubules, Cftr -/- mice had spermatogenetic defects in histology section and fewer number of mature sperm compared with wild type (WT) mice. Consistent with the proposed role of CFTR in spermatogenesis, RT-PCR and Western blot results showed reduced expression of spennatids specific gene, Protamine 1, Protamine 2, and CREM, which have been known to be involved in the process of spermatogenesis, in Cftr-/- mice. / Xu, Wenming. / "January 2008." / Source: Dissertation Abstracts International, Volume: 69-08, Section: B, page: 4506. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2008. / Includes bibliographical references (p. 121-138). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. [Ann Arbor, MI] : ProQuest Information and Learning, [200-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract in English and Chinese. / School code: 1307.

Gene positioning changes with respect to the nuclear periphery correlate with their activation in a number of tissues during development. However, the determination of the function this serves or the mechanism through which this was achieved has been remarkably difficult to resolve. It may now be possible to address these questions due to the recent identification of a number of tissue-specific nuclear envelope transmembrane proteins (NETs) which are capable of promoting the repositioning of specific subsets of chromosomes and concomitantly inducing changes to gene expression (Zuleger et al,. 2013). In this thesis I describe the role of NETs in the positioning of genes to the nuclear envelope (NE) during muscle differentiation and the role this activity plays in the optimisation of myogenic gene expression in as myoblasts (MTs) differentiate to myotubes (MTs). To do this I identified four NETs with the capacity to reposition a chromosome to the periphery that are present specifically in the NEs of skeletal muscle. Using a combination of genome-wide gene expression analysis and DamID I determined that depletion of these NETs disrupted myogenic gene expression and, more significantly, prevented the targeting to and silencing of normally repressed genes at the NE. I also investigated an analogous role for the blood-specific NET TAPBPL in the regulation of the critical T-cell regulator interleukin 2 (IL-2) at the NE in T-cells. Depletion of this NET caused release of the IL2 locus from the periphery and promoted its inappropriate and long-term activation. Interestingly, depletion of TAPBPL also prevented IL2 silencing following the end of T-cell activation, suggesting this genome organisation activity is critical for the maintenance of normal T-cell function. Collectively, the results discussed herein describe a new role for NETs in the regulation of gene expression through the manipulation of spatial genome organisation and may serve as an additional layer of higher order tissue-specific gene regulation in higher organisms.

DNA nanotechnology has been developed in order to construct nanostructures and nanomachines by virtue of the programmable self-assembly properties of DNA molecules. Although DNA nanotechnology initially focused on spatial arrangement of DNA strands, new horizons have been explored owing to the development of the toehold-mediated strand-displacement reaction, conferring new dynamic properties to previously static and rigid structures. A large variety of DNA reconfigurable nanostructures, stepped and autonomous nanomachines and circuits have been operated using the strand-displacement reaction. Biological systems rely on information processing to guide their behaviour and functions. Molecular computation is a branch of DNA nanotechnology that aims to construct and operate programmable computing devices made out of DNA that could interact in a biological context. Similar to conventional computers, the computational processes involved are based on Boolean logic, a propositional language that describes statements as being true or false while connecting them with logic operators. Numerous logic gates and circuits have been built with DNA that demonstrate information processing at the molecular level. However, development of new systems is called for in order to perform new tasks of higher computational complexity and enhanced reliability. The contribution of secondary structure to the vulnerability of a toehold-sequestered device to undesired triggering of inputs was examined, giving new approaches for minimizing leakage of DNA devices. This device was then integrated as a logic component in a DNA-based computer with a retrievable memory, thus implementing two essential biological functions in one synthetic device. Additionally, G-quadruplex logic gates were developed that can be switched between two topological states in a logic fashion. Their individual responses were detected simultaneously, establishing a new approach for parallel biological computing. A new AND-NOT logic circuit based on the seesaw mechanism was constructed that, in combination with the already existing AND and OR gates, form a now complete basis set that could perform any Boolean computation. This work introduces a new mode of kinetic control over the operation of such DNA circuits. Finally, the first example of a transmembrane logic gate being operated at the single-molecule level is described. This could be used as a potential platform for biosensing.

Tsang Lai-Ling Angel. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2001. / Includes bibliographical references (leaves 136-145). / Abstracts in English and Chinese. / Abstract --- p.i / 論文撮要 --- p.iv / Acknowledgment --- p.vi / Table of Content --- p.vii / List of Publications --- p.xii / List of Figures --- p.xiv / List of Tables --- p.xvii / Abbreviations --- p.xviii / Chapter Chapter1 --- Introduction --- p.1 / Chapter 1.1 --- The Human Uterus Vs Rat Uterus --- p.1 / Chapter 1.1.1 --- Myometrium --- p.1 / Chapter 1.1.2 --- Endometrium --- p.1 / Chapter 1.2 --- The Human Endometrium Vs Rat Endometrium --- p.2 / Chapter 1.2.1 --- The structure of Human Endometrium --- p.2 / Chapter 1.2.2 --- Cyclic Changes in the Endometrium --- p.4 / Chapter 1.2.3 --- Physiological Roles of the Endometrium --- p.7 / Chapter 1.2.4 --- Uterine Fluid Volume and its Composition --- p.7 / Chapter 1.2.4.1 --- Regulation of Uterine Fluid Volume and Composition --- p.7 / Chapter 1.2.4.2 --- Role of Endometrial Epithelium in the Regulation of Uterine Fluid Volume --- p.9 / Chapter 1.3 --- Epithelial Ion Channels --- p.9 / Chapter 1.3.1 --- Epithelial CI- Channels in Secretory Epithelia --- p.11 / Chapter 1.3.1.1 --- Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) --- p.13 / Chapter 1.3.2 --- Epithelial Na+ Channel (ENaC) in Absorbing Epithelia --- p.18 / Chapter 1.3.3 --- ENaC and CFTR in Endometrial Epithelia --- p.26 / Chapter 1.4 --- Hormonal Regulation of the Endometrial Epithelium --- p.29 / Chapter 1.4.1 --- Estrogen and Progesterone --- p.29 / Chapter 1.4.2 --- Aldosterone --- p.32 / Chapter 1.5 --- Aim of Study --- p.35 / Chapter Chapter2 --- Materials and Methods --- p.38 / Chapter 2.1 --- Materials --- p.38 / Chapter 2.1.1 --- Culture Medium and Enzymes --- p.38 / Chapter 2.1.2 --- Drugs --- p.38 / Chapter 2.1.3 --- Molecular Biology --- p.39 / Chapter 2.1.4 --- Experimental Tissues and Animals --- p.39 / Chapter 2.2 --- Preparations --- p.39 / Chapter 2.2.1 --- Pervious Support for Cell Growth --- p.39 / Chapter 2.2.2 --- Growth Medium --- p.40 / Chapter 2.2.3 --- Culture of Mouse Endometrium Epithelial Cells --- p.43 / Chapter 2.2.4 --- Solutions for the Short-Circuit Current Measurement --- p.44 / Chapter 2.2.5 --- Electrodes for the Short-Circuit Current Measurement --- p.44 / Chapter 2.2.6 --- Solutions for Molecular Biology Experiment --- p.44 / Chapter 2.2.6.1 --- Diethyl Pyrocarbonate (DEPC)-treated Water --- p.44 / Chapter 2.2.6.2 --- lx TAE (DNA gel electrophoresis and its running buffer) --- p.45 / Chapter 2.2.6.3 --- 5x MOPS (RNA gel electrophoresis and its running buffer) --- p.45 / Chapter 2.2.6.4 --- Formaldehyde Gel-loading Buffer --- p.45 / Chapter 2.3 --- Protocols --- p.46 / Chapter 2.3.1 --- Effect of Ovarian Hormones and Aldosterone on CFTR and ENaC Expression --- p.45 / Chapter 2.3.2 --- Possible Interaction between CFTR and ENaC upon Hormones Stimulation --- p.47 / Chapter 2.4 --- Methods of Measurement --- p.48 / Chapter 2.4.1 --- The Short-Circuit Current Technique --- p.48 / Chapter 2.4.1.1 --- The Short-Circuit Current Setup --- p.48 / Chapter 2.4.1.2 --- Experimental Procedures --- p.52 / Chapter 2.4.1.3 --- Data Analysis --- p.55 / Chapter 2.4.2 --- Reverse Transcription - Polymerase Chain Reaction (RT-PCR) --- p.55 / Chapter 2.4.2.1 --- RNA Isolation --- p.55 / Chapter 2.4.2.2 --- RNA Gel Electrophoresis --- p.56 / Chapter 2.4.2.3 --- Reverse Transcription (RT) --- p.57 / Chapter 2.4.2.4 --- Primer used for the Polymerase Chain Reaction (PCR) --- p.58 / Chapter 2.4.2.5 --- General Procedure of PCR and Competitive RT-PCR --- p.59 / Chapter 2.4.2.6 --- DNA Gel Electrophoresis --- p.61 / Chapter 2.4.3 --- Capillary Electrophoresis - Laser Induced Fluorescence (CE-LIF) --- p.62 / Chapter 2.4.3.1 --- Capillary Tube --- p.54 / Chapter 2.4.3.2 --- Detection System --- p.65 / Chapter 2.4.3.3 --- Experimental Procedures --- p.65 / Chapter 2.4.3.4 --- Data Analysis --- p.66 / Chapter 2.4.4 --- Statistical Analysis / Chapter Chapter3 --- Results --- p.68 / Chapter 3.1 --- Influence of Ovarian Hormones on Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) and Epithelial Na+ Channel (ENaC) Expression in Mouse Endometrial Epithelium --- p.68 / Chapter 3.2 --- Culture Condition on Expression and Function of Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) in Mouse Endometrial Epithelial Cells --- p.92 / Chapter 3.3 --- Expression Regulation of Endometrial Epithelial Na+ Channel (ENaC) Subunits and Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) by Na+ Diet During the Estrus Cycle in Mice --- p.98 / Chapter 3.4 --- Enhanced Epithelial Na+ Channel (ENaC) Activity in Mouse Endometrial Epithelium by Upregulation of γ-ENaC Subunit --- p.114 / Chapter Chapter4 --- General Discussion --- p.127 / Appendix --- p.132 / Chapter A. --- RNA Isolation --- p.132 / Chapter B. --- Reverse Transcription (RT) --- p.133 / Chapter C. --- Polymerase Chain Reaction (PCR) --- p.134 / Chapter D. --- Sequences and Conditions of All Primers --- p.135 / References --- p.136

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.