Dissertations / Theses: 'Membrane bound proteins'

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Whitehead, L. "Computer simulation of biological membranes and membrane bound proteins." Thesis, University of Southampton, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.297412.

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Adcock, Stewart Alan. "Computer simulation of membrane bound molecules." Thesis, University of Oxford, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.249194.

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Höglund, Pär J. "Identification, Characterization and Evolution of Membrane-bound Proteins /." Uppsala : Acta Universitatis Upsaliensis Acta Universitatis Upsaliensis, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-9329.

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Höglund, Pär J. "Identification, Characterization and Evolution of Membrane-bound Proteins." Doctoral thesis, Uppsala universitet, Institutionen för neurovetenskap, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-9329.

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Membrane proteins constitute approximately 30% of all genes in the human genome and two large families of membrane proteins are G protein-coupled receptors (GPCRs) and Solute Carriers (SLCs) with about 800 and 380 human genes, respectively. In Papers I, II and IV, we report 16 novel human Adhesion GPCRs found by searches in NCBI and Celera databases. In Paper I, we report eight novel human GPCRs, and six in Paper II. We identified two new human Adhesion GPCRs and 17 mouse orthologs in Paper IV. Phylogenetic analysis demonstrates that the 16 novel human genes are additional members of the Adhesion GPCR family and can be divided into eight phylogenetic groups. EST expression charts for the entire repertoire of Adhesions in human and mouse were established, showing widespread distribution in both central and peripheral tissues. Different domains were found in their N-terminus, some, such as pentraxin in GPR112, indicates that they take part in immunological processes. In Paper III, we discovered seven new human Rhodopsin GPCRs. In Paper V, we present the identification of two new human genes, termed SLC6A17 and SLC6A18 from the Solute Carriers family 6 (SLC6). We also identified the corresponding orthologs and additional genes from the mouse and rat genomes. We analysed, in total, 430 unique SLC6 proteins from 10 animal, one plant, two fungi and 196 bacterial genomes. In Paper VI, we provide the first systematic analysis of the evolutionary history of the different SLC families in Eukaryotes. In all, we analysed 2403 sequences in eight species and we delineate the evolutionary history of each of the 46 SLC families.

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Chandler, Becky. "Interrelationships between HIV, antiretroviral therapy and membrane bound proteins." Thesis, University of Liverpool, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.402412.

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Witkowski, Thomas, Rainer Backofen, and Axel Voigt. "The influence of membrane bound proteins on phase separation and coarsening in cell membranes." Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2014. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-139226.

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A theoretical explanation of the existence of lipid rafts in cell membranes remains a topic of lively debate. Large, micrometer sized rafts are readily observed in artificial membranes and can be explained using thermodynamic models for phase separation and coarsening. In live cells such domains are not observed and various models are proposed to describe why the systems do not coarsen. We review these attempts critically and show within a phase field approach that membrane bound proteins have the potential to explain the different behaviour observed in vitro and in vivo. Large scale simulations are performed to compute scaling laws and size distribution functions under the influence of membrane bound proteins and to observe a significant slow down of the domain coarsening at longer times and a breakdown of the self-similarity of the size-distribution function
Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich

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Witkowski, Thomas, Rainer Backofen, and Axel Voigt. "The influence of membrane bound proteins on phase separation and coarsening in cell membranes." Royal Society of Chemistry, 2012. https://tud.qucosa.de/id/qucosa%3A27814.

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A theoretical explanation of the existence of lipid rafts in cell membranes remains a topic of lively debate. Large, micrometer sized rafts are readily observed in artificial membranes and can be explained using thermodynamic models for phase separation and coarsening. In live cells such domains are not observed and various models are proposed to describe why the systems do not coarsen. We review these attempts critically and show within a phase field approach that membrane bound proteins have the potential to explain the different behaviour observed in vitro and in vivo. Large scale simulations are performed to compute scaling laws and size distribution functions under the influence of membrane bound proteins and to observe a significant slow down of the domain coarsening at longer times and a breakdown of the self-similarity of the size-distribution function.
Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.

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O'Ryan, Liam. "Studies on the structure of membrane bound and membrane associated proteins using scattering techniques." Thesis, University of Manchester, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.518435.

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Doughty, Stephen William. "Molecular modelling of voltage-gated calcium channels." Thesis, University of Oxford, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.362014.

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Ladomery, Michael R. "Analysis of proteins bound to stored messenger RNA in Xenopus oocytes." Thesis, University of St Andrews, 1996. http://hdl.handle.net/10023/14505.

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Regulation at the post-transcriptional level is gaining significance at a rapid pace. One example is the storage of messenger mRNA molecules in a translationally quiescent state, the so-called "masked messengers". Their existence has been known since the 1960s, but many details of their composition and structure have not yet been resolved. Masked messenger RNAs are particularly abundant in the oocytes of the African clawed toad Xenopus laevis. The aim of this study has been to examine the proteins bound to stored mRNAs in the oocytes, by focussing on the Y-box proteins which had already been identified as major components in mRNA masking, and by analyzing some of the other unidentified mRNP proteins. The YB proteins were studied in greater detail, gaining fresh information about their RNA-binding properties, defining distinct binding domains. The presence of an mRNP-associated protein kinase was confirmed, and binding assays suggested that phosphorylation influences the ability of the YB proteins to bind to mRNA. cDNA expression libraries were screened both with an RNA-binding assay and with an immunoscreening method, isolating a variety of known and novel cDNAs. Peptide sequencing of mRNP proteins revealed the presence of an RNA helicase distinct from the translation initiation factor eIF4A. It is postulated that the RNA helicase, in addition to the YB proteins, will be seen to have an important role in the formation and activity of the masked messenger RNA particles.

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Hartshorn, Christopher M. "Studies of the molecular effects of a solid support upon lipid membranes and membrane bound proteins." Pullman, Wash. : Washington State University, 2009. http://www.dissertations.wsu.edu/Dissertations/Fall2009/c_Hartshorn_101209.pdf.

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Sengupta, Durba. "Insights into the energetics of membrane-bound peptides towards an understanding of the structural organisation of membrane proteins /." [S.l. : s.n.], 2005. http://deposit.ddb.de/cgi-bin/dokserv?idn=976744465.

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McKnight, Holly A. "PROTEOMIC ANALYSIS OF MEMBRANE BOUND AND ASSOCIATED PROTEINS OF HUMAN GINGIVAL FIBROBLASTS AND PERIODONTAL LIGAMENT FIBROBLASTS." The Ohio State University, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=osu1338325450.

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Münzberg, Eileen [Verfasser], and Dieter [Gutachter] Schinzer. "Of proteins and lipids : a molecular dynamics study of membrane-bound Rab5 / Eileen Münzberg ; Gutachter: Dieter Schinzer." Magdeburg : Universitätsbibliothek Otto-von-Guericke-Universität, 2019. http://d-nb.info/1219937762/34.

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Tian, Xuefei. "Modulation of the conformaiton [sic] and function of membrane-bound anti-apoptotic Bcl-2 by potential anti-cancer drugs." Oklahoma City : [s.n.], 2008.

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Västermark, Åke. "Evolution of Membrane Bound Proteins and their Ligands : The Melanocortin (MC) Receptor Inverse Agonists AgRP2, ASIP2, Drug/Metabolite Transporters, and SPNS1." Doctoral thesis, Uppsala universitet, Funktionell farmakologi, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-177650.

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Integral membrane proteins play a key role hormonal and neuronal signaling. Transmembrane helix (TM) proteins form about 27% of the human proteome. Furthermore, 44% of the human drug targets are receptors, and 19% of these are seven-transmembrane domain receptors (GPCRs), which constitute 4% of the entire protein-coding genome. After receptors, solute carriers (SLCs) constitute the second largest superfamily of TM proteins. Three of the largest SLC families contain protein domains that are members of the drug/metabolite transporter clan. We present evidence that the drug/metabolite transporter (DMT) families have evolved from a domain duplication event before the radiation of Viridiplantae in the EamA family (previously called domain unknown function 6). We present evidence that the family called fatty acid elongases are homologous to transporters, not enzymes as had previously been thought. We renamed several transporters, and introduced the new HGNC-approved nomenclature of SLC35G1 – 6. We show the presence of AgRP and ASIP in elephant shark, a cartilaginous fish belonging to the subclass of Holocephali. However, we do not find any of these genes in lamprey or lancelet, suggesting that the MCA and MCB receptors function without antagonists in lamprey. We report that a venom peptide in Plectreurys tristis has the same cysteine knot structure as fish AgRP2, a higher similarity than previously known. Here we suggest that the Agouti-like peptide genes were formed through classical subsequent gene duplications where the AgRP is likely to be the most ancestral, first splitting from a common ancestor to ASIP and A2. We introduce a new technique for synteny detection, sinusoidal Hough transform. We found that the known obesity SNPs in SH2B1, rs4788102 (p=0.0023) and rs7498665 (p=0.0018) were associated with triglyceride levels in the North Swedish Population Health Study (NSPHS) cohort, consisting of 719 individuals from the Karesuando parish in northern Sweden. To account for kinship, the SH2B1 SNPs, and four SNPs in the expanded region were analyzed for association with triglyceride levels using SOLAR. We found a stronger signal (p=0.0009) for a SNP, near SH2B1, rs8045689, located in an intron of SPNS1 which is structurally similar to a sphingolipid transporter.

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Warnau, Judith [Verfasser], Ville [Akademischer Betreuer] Kaila, Ville [Gutachter] Kaila, and Gerhard [Gutachter] Hummer. "Computational Studies of Membrane-bound Proteins Na+/H+ -Antiporter and Respiratory Complex I / Judith Warnau ; Gutachter: Ville Kaila, Gerhard Hummer ; Betreuer: Ville Kaila." München : Universitätsbibliothek der TU München, 2019. http://d-nb.info/1213025931/34.

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Geiss, Frank Andreas [Verfasser]. "Proteo-Lipobeads : a novel platform to investigate strictly oriented membrane proteins in their functionally active form. Bio-UV-SPR: exploring the ultraviolet spectral range for water-bound analytes in surface plasmon resonance spectroscopy / Frank Andreas Geiss." Mainz : Universitätsbibliothek Mainz, 2019. http://d-nb.info/1175027928/34.

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Morton, J. D. "The effect on protein synthesis in barley of infection with P. hordei." Lincoln College, University of Canterbury, 1989. http://hdl.handle.net/10182/1950.

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Infection of barley (Hordeum vulgare) leaves with the rust fungus, Puccinia hordei, causes changes in the host protein synthesis. This thesis analyses these changes in the barley cultivar Triumph following inoculation of 7-day-old leaves with either a virulent or an avirulent race of P. hordei. The initial approach was to isolate membrane-bound polysomes from infected leaves, translate them in vitro and analyse the translation products. These products include the integral membrane proteins which were expected to be involved in the response of the host to the pathogen. A method based on differential centrifugation in the presence of a ribonuclease-inhibiting buffer was developed for separating membrane-bound polysomes from the rest of the cytoplasmic polysomes. Membrane-bound polysomes were found to comprise one fifth of the total polysomes in the leaves. Analysis of the translation products of membrane-bound polysomes by SDS-PAGE showed them to be of higher average molecular weight than those from free polysomes. Comparison of polypeptides produced by membrane-bound polysomes from healthy and inoculated plants showed some differences however the low yield of membrane-bound polysomes made it difficult to obtain conclusive results. Thus it was decided to isolate total polysomes by including 1% Triton X-100 in the extraction buffer. Polysomes were extracted from 12 to 72 h after inoculation. Infection caused a decline in yield of polysomes during this period when compared with healthy leaves of the same age. Polysomes isolated 16 h after inoculation with the virulent race were 20% less efficient at translation than polysomes from control leaves. In contrast polysome isolated from leaves inoculated with the avirulent race were 20% more efficient. Analysis of the labelled translation products by SDS-PAGE and fluorography showed relative increases in the synthesis of some proteins by 16 h after inoculation with either race when compared to products from healthy leaves. Protein synthesis in the infected plants was further analysed by in vivo labelling and one- and two-dimensional PAGE. The fluorographs revealed increased synthesis of a group of proteins from 58 to 116 kDa starting 12 h after inoculation with either race of P. hordei; confirming the results from the polysome translations. Two polypeptides with molecular weights of about 66 kDa were found to increase following infection only with the virulent race. By three days after inoculation with either fungal race the most obvious change in protein synthesis was a marked decrease in the synthesis of the two most prominent polypeptides with molecular weights of 15 and 51 kDa which were considered to be the subunits of ribulose bisphosphate carboxylase. The elicitor hypothesis, in attempting to explain cultivar-specific resistance in plants, postulates that resistance is controlled by the interaction of specific fungal elicitors and plant receptors and that this interaction which only occurs between resistant hosts and avirulent pathogens triggers specific gene expression leading to resistance. This hypothesis does not fit the situation in the barley-P. hordei interaction as protein synthesis showed similar changes following infection with either a virulent or an avirulent race.

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Blowers, David Peter. "Regulation of membrane bound protein kinase activity in Pisum sativum L." Thesis, University of Edinburgh, 1986. http://hdl.handle.net/1842/10833.

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Herbert, Andrew S. "Cytokine-bearing Influenza Vaccine: Adjuvant Potential of Membrane-bound Immunomodulators." Diss., Virginia Tech, 2009. http://hdl.handle.net/10919/27660.

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Influenza epidemics continue to cause morbidity and mortality within the human population despite widespread vaccination efforts. This, along with the ominous threat of an avian influenza pandemic (H5N1), demonstrates the need for a much improved, more sophisticated influenza vaccine. Our group has developed an in vitro model system for producing a membrane-bound Cytokine-bearing Influenza Vaccine (CYT-IVAC). Numerous cytokines are involved in directing both innate and adaptive immunity and it is our goal to utilize the properties of individual cytokines and other immunomodulatory proteins to create a more immunogenic vaccine. Here we report methodologies for the construction of membrane-bound cytokine fusion constructs in which our cytokine of interest (mouse GM-CSF, mouse IL-2, mouse IL-4) was fused to the membrane anchoring regions of viral Hemagglutinin (HA). Progeny virions, produced from influenza infected MDCK cells expressing membrane-bound cytokines, readily incorporated membrane-bound cytokines during budding and these cytokines on the virus particles retained bioactivity following viral inactivation. In vivo vaccination studies in mice showed enhanced antibody titers and improved protection following lethal challenge in those mice vaccinated with IL-2 and IL-4-bearing CYT-IVACâ s compared to the conventional wild-type vaccine without membrane-bound cytokines. In addition, the immune response induced by IL-2 and IL-4-bearing CYT-IVACs was skewed toward Th1 (cellular) mediated immunity compared to the Th2 (humoral) dominated response induced with wild-type vaccination. Cellular mediated immunity afforded by IL-2 and IL-4 CYT-IVACs was manifested as enhanced influenza specific T cell proliferation and activation. In conclusion, we have developed a novel methodology to introduce bioactive membrane-bound cytokines directly into virus particles in order to augment the immunogenicity of inactivated, whole virus influenza vaccines.
Ph. D.

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Wickles, Stephan. "A structural model of the active ribosome-bound membrane protein insertase YidC." Diss., Ludwig-Maximilians-Universität München, 2015. http://nbn-resolving.de/urn:nbn:de:bvb:19-180793.

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Zhang, Yifeng. "Association of Protein Disulfide Isomerase and ATP Synthase β Subunit with Membrane-Bound P-Glycoprotein." Thesis, The University of Arizona, 2014. http://hdl.handle.net/10150/322110.

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Jain, Surbhi. "Role of Disulfide Bond Rearrangement in Newcastle Disease Virus Entry: A Dissertation." eScholarship@UMMS, 2008. https://escholarship.umassmed.edu/gsbs_diss/379.

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Newcastle disease virus (NDV), an avian paramyxovirus, enters the host cell by fusion of viral and host cell membranes. The fusion of two membranes is mediated by the viral fusion (F) protein. The F protein, like other class I fusion proteins, is thought to undergo major conformational changes during the fusion process. The exact mechanism that leads to major refolding of F protein is not clear. Recently, it has been proposed that disulfide bond reduction in the fusion protein of some viruses may be involved in the conformational changes in fusion proteins. In some viruses, the reduction of disulfide bonds in the fusion protein is mediated by host cell disulfide isomerases belonging to the protein disulfide isomerase (PDI) family. In this study, the role of disulfide bond isomerization in the entry of NDV was analyzed. Using inhibitors of thiol-disulfide isomerases, we found that blocking the reduction of disulfide bonds in the fusion protein inhibited cell-cell fusion as well as virus entry into the host cell. Also, over-expression of isomerases belonging to the PDI family significantly enhanced cell-cell fusion. Taken together, these results suggest that free thiols play an important role in fusion mediated by NDV glycoproteins. Using a thiol specific, membrane impermeable biotin, MPB, we found that free thiols are produced in cell surface-expressed NDV F protein. The production of free thiols was inhibited by inhibitors of thiol-disulfide isomerases. Over-expression of isomerases belonging to the PDI family enhanced detection of free thiols in F protein. In F protein, present in virions or in virus-like particles, free thiols were detected only after the particles were attached to target cells. Taken together, these results suggest that free thiols are produced in F protein and the production of free thiols is mediated by host cell thiol-disulfide isomerases. Using conformation sensitive antibodies, we also studied the conformation of cell surface-expressed F protein in the presence ofthiol-disulfide isomerase inhibitors or in cells over-expressing thiol-disulfide isomerases. In the presence of thiol-disulfide isomerase inhibitors, the cell surface-expressed F protein was in a prefusion conformation while in cells over-expressing thiol-disulfide isomerases the F protein was in a post-fusion conformation. We also correlated the production of free thiols to the conformational changes in F protein. Using temperature-arrested intermediates or F protein with mutations in heptad repeat domains, which are defective in attaining intermediate conformations, we found that free thiols are produced before any of the proposed conformational changes in F protein. Also, the production of free thiols in F protein was found to be independent of its activation by hemagglutinin-neuraminidase (HN) protein. These results suggest that free thiols are probably required for the activation of F protein during membrane fusion.

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Svahn, Emelie. "Molecular machinery of a membrane-bound proton pump : Studies of charge transfer reactions in cytochrome c oxidase." Doctoral thesis, Stockholms universitet, Institutionen för biokemi och biofysik, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-108335.

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In cellular respiration, electron transfer from the breakdown of foodstuff is coupled to the formation of an electrochemical proton gradient. This is accomplished through proton translocation by respiratory complexes, and the proton gradient is subsequently used e.g. to drive ATP production. Consequently, proton- and electron-transfer reactions through the hydrophobic interior of membrane proteins are central to cellular respiration. In this thesis, proton- and electron transfer through an aa3-type terminal oxidase, cytochrome c oxidase (CytcO) from Rhodobacter sphaeroides, have been studied with the aim of understanding the molecular proton-transfer machinery of this proton pump. In the catalytic site of CytcO the electrons combine with protons and the terminal electron acceptor O2 to form water in an exergonic reaction that drives proton pumping. Therefore, CytcO must transfer both protons that are pumped and protons for the oxygen chemistry through its interior. This is done through its two proton-transfer pathways, termed the D pathway and the K pathway. Our studies have shown that the protons pumped during oxidation of CytcO are taken through the D pathway, and that this process does not require a functional K pathway. Furthermore, our data suggests that the K pathway is used for charge compensation of electron transfer to the catalytic site, but only in the A2 → P3 state transition. Our data also show that the water molecules identified in the crystal structures of CytcO play an important role in proton transfer through the D pathway. Finally, the effects of liposome reconstitution of CytcO on D-pathway proton transfer were investigated. The results suggest that the membrane modulates the rates of proton transfer through the D pathway, and also influences the extent of electron transfer between redox-active sites CuA and heme a.

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Kakio, Atsuko. "Formation Mechanisms and Properties of Ganglioside-Bound Altzheimer's Amyloid β-Protein in Raft-Like Membranes." 京都大学 (Kyoto University), 2003. http://hdl.handle.net/2433/148530.

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Perland, Emelie. "Atypical Solute Carriers : Identification, evolutionary conservation, structure and histology of novel membrane-bound transporters." Doctoral thesis, Uppsala universitet, Institutionen för neurovetenskap, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-324206.

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Solute carriers (SLCs) constitute the largest family of membrane-bound transporter proteins in humans, and they convey transport of nutrients, ions, drugs and waste over cellular membranes via facilitative diffusion, co-transport or exchange. Several SLCs are associated with diseases and their location in membranes and specific substrate transport makes them excellent as drug targets. However, as 30 % of the 430 identified SLCs are still orphans, there are yet numerous opportunities to explain diseases and discover potential drug targets. Among the novel proteins are 29 atypical SLCs of major facilitator superfamily (MFS) type. These share evolutionary history with the remaining SLCs, but are orphans regarding expression, structure and/or function. They are not classified into any of the existing 52 SLC families. The overall aim in this thesis was to study the atypical SLCs with a focus on their phylogenetic clustering, evolutionary conservation, structure, protein expression in mouse brains and if and how their gene expressions were affected upon changed food intake. In Papers I-III, the focus was on specific proteins, MFSD5 and MFSD11 (Paper I), MFSD1 and MFSD3 (Paper II), and MFSD4A and MFSD9 (Paper III). They all shared neuronal expression, and their transcription levels were altered in several brain areas after subjecting mice to food deprivation or a high-fat diet. In Paper IV, the 29 atypical SLCs of MFS type were examined. They were divided into 15 families, based on phylogenetic analyses and sequence identities, to facilitate functional studies. Their sequence relationships with other SLCs were also established. Some of the proteins were found to be well conserved with orthologues down to nematodes and insects, whereas others emerged at first in vertebrates. The atypical SLCs of MFS type were predicted to have the common MFS structure, composed of 12 transmembrane segments. With single-cell RNA sequencing and in situ proximity ligation assay, co-expression of atypical SLCs was analysed to get a comprehensive understanding of how membrane-bound transporters interact. In conclusion, the atypical SLCs of MFS type are suggested to be novel SLC transporters, involved in maintaining nutrient homeostasis through substrate transport.

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Wickles, Stephan [Verfasser], and Roland [Akademischer Betreuer] Beckmann. "A structural model of the active ribosome-bound membrane protein insertase YidC / Stephan Wickles. Betreuer: Roland Beckmann." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2015. http://d-nb.info/1069491403/34.

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Rosário, Ana Lúcia Rebelo do. "Functional and structural studies of two enzymes: membrane bound kinase and Z-DNA/Z-RNA-binding protein." Doctoral thesis, Faculdade de Ciências e Tecnologia, 2013. http://hdl.handle.net/10362/11445.

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Dissertação para obtenção do Grau de Doutor em Sistemas de Bioengenharia
The neocortex is a unique structure designed for higher cognitive and associative functions. Herein, we will refer to the work performed to assess the role of TAOK2α, a specific membrane bound kinase, in the mammalian neocortical development. The results obtained, delineate a pathway whereby Semaphorin3A and Neuropilin1 transduce signals through TAOK2α and c-Jun N-terminal Kinase to regulate basal dendrite development and migration in cortical neurons. This work represents the first approach aimed at understanding the mechanisms responsible for the delineation of basal and apical dendrites during pyramidal neuron development in the embryo, and how such mechanism may evolve to neocortical disconnection disorders. Additional work performed on humanTAOK2α focused at the determination of its three-dimensional structure by X-ray crystallography to elucidate its regulatory mechanism. The 20th century exciting discovery of the DNA left-handed conformation, and the fact it binds to certain classes of proteins with high affinity and specificity, indicated a biological role to it. However, a full function is still to be elucidated. The human double-stranded RNA adenosine deaminase (ADAR1) is the best characterized of all Z-DNA binding proteins, where Zα domain binds and stabilizes Z-DNA/Z-RNA forms upon binding. The second part of this thesis describes the work on the ZαADAR1 domain that binds to Z-RNA/Z-DNA. When a section of a DNA or RNA molecule forms a left-handed Z-DNA/Z-RNA segment, two B-Z/A-Z junctions are formed. Herein, we describe the study carried out on the formation of Z-Z junctions from DNA and, also, the approach on trying to describe the Z-Z junction for RNA when interacting with ZαADAR1. The structure of the Z-Z-DNA junction consists of a single base pair that leads to partial or full disruption of the helical stacking. The junction region allows intercalating agents to insert themselves into the left-handed helix, which is otherwise resistant to intercalation.
Fundação para a Ciência e Tecnologia - PhD grant reference SFRH / BD / 37676 / 2007

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Sheremet, Andriy. "Bioinspired polyethersulfone-based hollow fiber membranes as the scaffolds in renal assist device for protein-bound toxins removal from blood." Master's thesis, Faculdade de Ciências e Tecnologia, 2014. http://hdl.handle.net/10362/13308.

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Dissertation for obtaining the Master degree in Membrane Engineering
Erasmus Mundus Master in Membrane Engineering
Using bioartificial kidney is the promising approach for removal of non-dializable, proteinbound uremic toxins, which are responsible for high mortality and morbidity in treating kidney failure related conditions. Additionaly, bioartificial kidney device could perform the physiological roles of the kidney such as metabolic replacement, endocrine function and immunomodulation. In the current work two commercial polyethersulfone-based membranes, Gambro HCO 1100 and Membrana MicroPES TF10 used in haemofiltration and plasma separation applications respectively were investigated. To provide adequate cytocompatibility of the membrane biomimetic, biomimetic double layer coating was developed. First, the membranes were coated with musselinspired synthetic polydopamine film, following with the coating of Collagen Type IV. Transport properties of the coated and native membranes were investigated. Increase in pure water permeability of the coated HCO 1100 membranes was observed. Membrane surface hydrophilization was assumed as the major factor responsible for the effect. Membrane permeabilities for bovine serum albumin and immunoglobulin G solutions were studied. Significant increase in protein rejection was observed for double coated HCO 1100 membranes with small or no effect of the double coated MicroPES TF10 membranes. Next, formation of confluent monolayers of the renal epithelial cells on the membrane scaffolds was studied. Cell seeding strategy was developed and two seeding conditions were tested. Specifically, the cells were allowed to adhere to the biomimetic membranes passively, and the negative pressure was applied to facilitate cell adhesion. After cultivation in semi-batch conditions the monolayer formation was examined. Confluent monolayers were observed for the conditions with passive cell adherence for the both membranes. Cell contacts formation and cell polarization were confirmed with the staining for ZO-1 protein. Applying the pressure to facilitate cell adhesion, on the contrary, resulted in the loss of cell ability to form functional monolayers.
EM3E Master is an Education Programme supported by the European Commission, the European Membrane Society (EMS), the European Membrane House (EMH), and a large international network of industrial companies, research centres and universities

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Acharya, Kalpana D. Ms. "ROLE OF MEMBRANE BOUND G-PROTEIN COUPLED ESTROGEN RECEPTOR GPR30 AND Z-LINKED RIBOSOMAL GENE S6 (RPS6) IN SEXUALLY DIMORPHIC DEVELOPMENT OF THE ZEBRA FINCH BRAIN." Kent State University / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=kent1341338394.

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Tan, Yi Lei. "Structural and Biophysical Characterisation of Denatured States and Reversible Unfolding of Sensory Rhodopsin II." Thesis, University of Cambridge, 2019. https://www.repository.cam.ac.uk/handle/1810/289718.

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Our understanding of the folding of membrane proteins lags behind that of soluble proteins due to the challenges posed by the exposure of hydrophobic regions during in vitro chemical denaturation and refolding experiments. While different folding models are accepted for soluble proteins, only the two-stage model and the long-range interactions model have been proposed so far for helical membrane proteins. To address our knowledge gap on how different membrane proteins traverse their folding landscapes, Chapter 2 investigates the structural features of SDS-denatured states and the kinetics for reversible unfolding of sensory rhodopsin II (pSRII), a retinal-binding photophobic receptor from Natronomonas pharaonis. pSRII is difficult to denature, and only SDS can dislodge the retinal chromophore without rapid aggregation. Even in 30% SDS (0.998 $\mathit{\Chi}_{SDS}$), pSRII retains the equivalent of six out of seven transmembrane helices, while the retinal binding pocket is disrupted, with transmembrane residues becoming more solvent-exposed. Folding of pSRII from an SDS-denatured state harbouring a covalently-bound retinal chromophore shows deviations from an apparent two-state behaviour. SDS denaturation to form the sensory opsin apo-protein is reversible. This chapter establishes pSRII as a new model protein which is suitable for membrane protein folding studies and has a unique folding mechanism that differs from those of bacteriorhodopsin and bovine rhodopsin. In Chapter 3, SDS-denatured pSRII, acid-denatured pSRII and sensory opsin obtained by hydroxylamine-mediated bleaching of pSRII were characterised by solution state NMR. 1D $^1$H and $^{19}$F NMR were first used to characterise global changes in backbone amide protons and tryptophan side-chains. Residue-specific changes in backbone amide chemical shifts and peak intensities in 2D [$^1$H,$^{15}$N]-correlation spectra were analysed. While only small changes in the chemical environment of backbone amides were detected, changes in backbone amide dynamics were identified as an important feature of SDS- and acid-denatured pSRII and sensory opsin. $^{15}$N relaxation experiments were performed to study the backbone amide dynamics of SDS-denatured pSRII, reflecting motions on different timescales, including fast fluctuations of NH bond vectors on the ps-ns timescale and the lack of exchange contributions on the µs timescale. These studies shed insight on differences in the unfolding pathways under different denaturing conditions and the crucial role of the retinal chromophore in governing the structural integrity and dynamics of the pSRII helical bundle. Hydrogen bonds play fundamental roles in stabilising protein secondary and tertiary structure, and regulating protein function. Successful detection of hydrogen bonds in denatured states and during protein folding would contribute towards our understanding on the unfolding and folding pathways of the protein. Previous studies have demonstrated residue-specific detection of stable and transient hydrogen bonds in small globular proteins by measuring $^1{\it J}_{NH}$ scalar coupling constants using NMR. In Chapter 4, different methods for measuring $^1{\it J}_{NH}$ scalar coupling were explored using RalA, a small GTPase with a mixed alpha/beta fold, as proof-of-concept. Detection of hydrogen bonds was then attempted with OmpX, a beta-barrel membrane protein, both in its folded state in DPC micelles and in the urea-denatured state. While $^1{\it J}_{NH}$ measurement holds promise for studying hydrogen bond formation, further optimisation of NMR experiments and utilisation of perdeuterated samples are required to improve the precision of such measurements in large detergent-membrane protein complexes. Naturally occurring split inteins can mediate spontaneous trans-splicing both in vivo and in vitro. Previous studies have demonstrated successful assembly of proteorhodopsin from two separate fragments consisting of helices A-B and helices C-G via a splicing site in the BC loop. To complement the in vitro unfolding/folding studies, pSRII assembly in vivo was attempted by introducing a splicing site in the loop region of the beta-hairpin constituting the BC loop of pSRII. The expression conditions for the N- and C-terminal pSRII-intein segments were optimised, and the two segments co-expressed. However, the native chromophore was not observed. Further optimisation is required for successful in vivo trans-splicing of pSRII and application of this approach towards understanding the roles of helices and loops in the folding of pSRII.

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33

Sung, Yu-Ling, and 宋浴玲. "Characterization of soluble and membrane-bound XpsG proteins in Xanthomonas campestris." Thesis, 1999. http://ndltd.ncl.edu.tw/handle/18329985056070903478.

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碩士
中山醫學院
生物化學研究所
87
Abstract The protein translocation machinery in Gram-negative bacteria are classified into three types. The type II pathway or the so-called general secretion pathway (GSP) is the most common one. The outer membrane GSP secretion machinery is composed of twelve to thirteen gene products designated as GspCDEFGHIJKLMNO. The N-termini of GspGHIJ are highly homologous to the N-terminus of PilA pilus, and were considered as the same family. However, the pili structure of GspGHIJ structure had never been identified or isolated. In this study, we used biochemical and genetic methods to systematically investigate the GspGHIJ pili structure in the outer membrane protein secretion system of Xanthomonas campestris. We had prepared anti-XpsG antibody and xpsG knockout mutant strain. XpsG protein was found to present in the soluble and insoluble fraction of lysed cells. Gel filtration chromatography analysis showed that the XpsG from membrane fraction was in the dimer form and from soluble fraction was in a higher order form. In the presence of high concentration of detergent DOC, the higher-order form dissociated to dimers. Second gel filtration analysis of the dissociated dimer in the absence of DOC revealed that the proteins could not revert to the higher-order form, indicating that the formation of the higher order from might require the participation of other factors. The soluble high-order form was stable at 80℃ and did not be dissociated. Under low concentration of DOC, the structure did not dissociate at pH 8 but dissociated at pH10.3. The XpsG-containing, high-order structures observed in this study could be the pilus-like structure proposed for the pilin-like protein family. The five-conserved aspartate residues of XpsG protein at the 70, 103, 121, 128 and 139 positions were substituted to glutamate by site-directed mutagenesis. By -amylase secretion function assay, only mutant D103E was found that could not compensate the secretion ability of XC1713 and could interfere the secretion ability of XC1701. Using gel filtration chromatography analyses, no difference of elution profiles were found between wild type and mutant XpsG proteins in soluble and membrane forms. These results indicated that D103 of XpsG protein might be play a special function on protein secretion mechanism and this function was not related to the multimer function. In conclusion of this study, XpsG protein might form pilus-like structure, and the soluble higher-order form of XpsG protein might be cleavaged from membrane pilus-like structure.

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34

Sengupta, Durba [Verfasser]. "Insights into the energetics of membrane-bound peptides : towards an understanding of the structural organisation of membrane proteins / presented by Durba Sengupta." 2005. http://d-nb.info/976744465/34.

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Williamson, Ritchie, A. Usardi, D. P. Hanger, and B. H. Anderton. "Membrane-bound beta-amyloid oligomers are recruited into lipid rafts by a fyn-dependent mechanism." 2008. http://hdl.handle.net/10454/6237.

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Recently published research indicates that soluble oligomers of beta-amyloid (Abeta) may be the key neurotoxic species associated with the progression of Alzheimer's disease (AD) and that the process of Abeta aggregation may drive this event. Furthermore, soluble oligomers of Abeta and tau accumulate in the lipid rafts of brains from AD patients through an as yet unknown mechanism. Using cell culture models we report a novel action of Abeta on neuronal plasma membranes where exogenously applied Abeta in the form of ADDLs can be trafficked on the neuronal membrane and accumulate in lipid rafts. ADDL-induced dynamic alterations in lipid raft protein composition were found to facilitate this movement. We show clear associations between Abeta accumulation and redistribution on the neuronal membrane and alterations in the protein composition of lipid rafts. In addition, our data from fyn(-/-) transgenic mice show that accumulation of Abeta on the neuronal surface was not sufficient to cause cell death but that fyn is required for both the redistribution of Abeta and subsequent cell death. These results identify fyn-dependent Abeta redistribution and accumulation in lipid rafts as being key to ADDL-induced cell death and defines a mechanism by which oligomers of Abeta and tau accumulate in lipid rafts.

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Adigüzel, Yekbun [Verfasser]. "ATR-FTIR spectroscopy of membrane-bound Ras protein / written by Yekbun Adigüzel." 2008. http://d-nb.info/989596451/34.

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37

Chung, Sung Fan, and 宋範強. "Effective High-throughput Identification on The Global Cytoplasmic Membrane Protein-bound Oilgopeptides." Thesis, 2003. http://ndltd.ncl.edu.tw/handle/68585291042463457148.

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碩士
中國文化大學
生物科技研究所
91
Abstract This research establishes the high-throughput screening ( HTS ) technology platform to operate selection of the candidate oligopeptide at automatic equipments and high speed processes. The candidate oligopepetide can become the lead drug by employed binding to cytoplasmic membrane protein, because many studies show the important art of cytoplasmic membrane proteins in cancer cells consider with apoptopsis or signal transduction. But then we integrated the combinatorial library which synthetic randomly tri-, tetra-, and penta-oligopeptides via the strategy of mix-and-select method in times before. It is better using combinatorial chemistry is advances in drug discovery than find complex mixture of natural product such as plant and animal extracts in traditional drug discovery. So we really find some of acute myeloid leukemia ( AML ) of cytoplsmic membrane protein-bound oligopeptides such as HER, SGMR, and NLGR etc. binding to AML's bone marrow specimen and TMR, VAVK, DGNK etc. binding to AML's peripheral blood lymphocyte specimen could become important anti-cancer agents. In the last few years, the human genomic project increase annotation of the genome functions. But all of know protein that is the genetic product process the cell growth and metabolism. This research focus to integrate proteomic technology, because of it is big engineering to analye the 10,000 — 20,000 proteins expressed in a mammalian cells. However, proteomic and mass manipulation provide simple and convenient methods which can review the profile of the mammalian cell proteome. In this study, we firstly assess two-dimensional gel electrophorsesis ( 2-DE ) of cytoplasmic membrane protein variability of the AML in pretreatment and posttreatment by chemical therapy. We hope find specific spots on the 2-DE for future progess in theranostic agents. Now we can to do appling the candidate oligopeptides screen these specific spots which seek to binding correlation between response to specific candidate, and maybe will lucrative new drugs or diagnostics probes.

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YEN, SHIH-CHIEH, and 顏士傑. "Studies on Electrospun Carbon Nanotube-Conducting Polymer Composite Nanofiber Membranes for Efficient Removal of Protein-bound Uremic Toxins." Thesis, 2018. http://ndltd.ncl.edu.tw/handle/9bvn57.

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碩士
明志科技大學
材料工程系碩士班
106
Herein we have developed an integrated electrospinning approach for producing a wide-range of high quality three-dimensional (3D) carbon nanotube/conducting polymer composite nanofiber mats as the bioelectronic interfaces (BEIs), which can be further assembled on ultrafiltration membranes for efficient removal of uremic toxin. We use the multiwalled carbon nanotubes (MWCNT)-poly(ethylene oxide) (PEO)- poly(3,4-ethylenedioxythiophene): poly(styrenesulfonate) (PEDOT:PSS) quaternary blends made of nanofiber membranes. By a condensation reaction between poly (styrenesulfonate) PSS and poly (ethylene oxide) (PEO) under a high temperature treatment (130 oC for 6 hours) to form a chemical crosslinking reaction, Nanofiber mats to improve long term wet stability in PBS buffer. Finally, we integrated the nanofiber-based samples on the dialysis membrane and further assembled into a hemodialysis (HD) bioelectronic device with the use of peristaltic pump for evaluating the influence of various MWCNT additives on the removal efficiency of uremic toxins.

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39

Wu, Hsin-Yi, and 吳欣怡. "The investigation of the effect and molecular mechanism on the invasion of colon cancer cells for membrane-bound Heat Shock Protein 27 complex." Thesis, 2018. http://ndltd.ncl.edu.tw/handle/2m5789.

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Dissertations / Theses on the topic 'Membrane bound proteins'

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