Tesis: "Membrane proteins"

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Gill, Katrina Louise. "Protein-protein interactions in membrane proteins." Thesis, University of Newcastle Upon Tyne, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.400016.

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2

Hedin, Linnea E., Kristoffer Illergård, and Arne Elofsson. "An Introduction to Membrane Proteins." Stockholms universitet, Institutionen för biokemi och biofysik, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-69241.

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alpha-Helical membrane proteins are important for many biological functions. Due to physicochemical constraints, the structures of membrane proteins differ from the structure of soluble proteins. Historically, membrane protein structures were assumed to be more or less two-dimensional, consisting of long, straight, membrane-spanning parallel helices packed against each other. However, during the past decade, a number of the new membrane protein structures cast doubt on this notion. Today, it is evident that the structures of many membrane proteins are equally complex as for many soluble proteins. Here, we review this development and discuss the consequences for our understanding of membrane protein biogenesis, folding, evolution, and bioinformatics. authorCount :3

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3

Kota, Jhansi. "Membrane chaperones : protein folding in the ER membrane /." Stockholm : Karolinska institutet, 2007. http://diss.kib.ki.se/2007/978-91-7357-102-9/.

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4

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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5

Armstrong, James P. "Artificial membrane-binding proteins." Thesis, University of Bristol, 2014. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.686615.

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Membrane functionalization is a promising strategy for augmenting cell performance in regenerative medicine. To this end, the design, construction, characterisation and cell affinity of protein-polymer surfactant nanoconstructs are presented. Nanoconstructs of eGFP were synthesised that exhibited near-native structure and function, as well as effective and persistent membrane affinity. Human mesenchymal stem cells were labelled for up to ten days in culture, without affecting cell viability or differentiation capacity. This "cell priming" technology has been used to address the issue of hypoxia-related central necrosis during in-vitro tissue engineering. Specifically, nanoconstructs of myoglobin, with enhanced oxygen-binding affinity, were synthesised and used to prime mesenchymal stem cells prior to hyaline cartilage engineering. The myoglobin-primed cells produced tissue constructs with a 62 % increase in type II : type I collagen ratio and, significantly, a reduction in cell necrosis from 42 ± 24 % to 7 ± 6 %.

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6

Zhang, Xiao Xiao. "Identification of membrane-interacting proteins and membrane protein interactomes using Nanodiscs and proteomics." Thesis, University of British Columbia, 2011. http://hdl.handle.net/2429/39413.

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The insoluble nature of membrane proteins has complicated the identification of their interactomes. The Nanodisc has allowed the membrane and membrane proteins to exist in a soluble state. In this thesis, we combined Nanodisc and proteomics and applied the technique to discover the interactome of membrane proteins. Using the SecYEG and MalFGK membrane complex incorporated into Nanodisc, we identified, Syd, SecA, and MalE. These interactions were identified with high specificity and confidence from total soluble protein extracts. The protein YidC was also tested but no interactors were detected. Overall, these results showed that the technique can identify periplasmic and cytosolic interacting partners with high degree of specificity. In a second approach, the method was applied to detect proteins with high affinity for lipid using S. cerevisiae as a model organism. Using Nanodiscs containing different types of phospholipids, many known lipid interactors were identified, including: Ypt1, Sec4, Vps21, Osh6, and Faa1. Interestingly, Caj1 was identified as a PA specific interactor and this interaction was found to be pH dependent. Liposome sedimentation assay showed that Caj1 has affinity for acidic phospholipids. In vivo analysis confirmed the plasma membrane localization of N’-GFP-Caj1 and specifically to the yeast buds. However, pH dependent localization was not observed. Together, with the in vivo and in vitro results suggests that Caj1 is an acidic phospholipid interacting protein.

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7

Josyula, Ratnakar. "Structural studies of yeast mitochondrial peripheral membrane protein TIM44." Thesis, Birmingham, Ala. : University of Alabama at Birmingham, 2009. https://www.mhsl.uab.edu/dt/2009p/josyula.pdf.

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8

Rapp, Mikaela. "The Ins and Outs of Membrane Proteins : Topology Studies of Bacterial Membrane Proteins." Doctoral thesis, Stockholm : Department of Biochemistry and Biophysics, Stockholm University, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-1330.

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9

Berger, Bryan William. "Protein-surfactant solution thermodynamics applications to integral membrane proteins /." Access to citation, abstract and download form provided by ProQuest Information and Learning Company; downloadable PDF file 15.42 Mb., 304 p, 2006. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&res_dat=xri:pqdiss&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&rft_dat=xri:pqdiss:3200533.

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10

Keegan, Neil. "From engineered membrane proteins to self-assembling protein monolayers." Thesis, University of Newcastle Upon Tyne, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.419991.

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11

Stewart, Christine Catherine. "Toxicity of mutant membrane proteins /." Thesis, Connect to this title online; UW restricted, 1996. http://hdl.handle.net/1773/10259.

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12

Ye, Cui. "STABILITY STUDIES OF MEMBRANE PROTEINS." UKnowledge, 2014. http://uknowledge.uky.edu/chemistry_etds/33.

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The World Health Organization has identified antimicrobial resistance as one of the top three threats to human health. Gram-negative bacteria such as Escherichia coli are intrinsically more resistant to antimicrobials. There are very few drugs either on the market or in the pharmaceutical pipeline targeting Gram-negative pathogens. Two mechanisms, the protection of the outer membrane and the active efflux by the multidrug transporters, play important roles in conferring multidrug resistance to Gram-negative bacteria. My work focuses on two main directions, each aligning with one of the known multidrug resistance mechanisms. The first direction of my research is in the area of the biogenesis of the bacterial outer membrane. The outer membrane serves as a permeability barrier in Gram-negative bacteria. Antibiotics cross the membrane barrier mainly via diffusion into the lipid bilayer or channels formed by outer membrane proteins. Therefore, bacterial drug resistance is closely correlated with the integrity of the outer membrane, which depends on the correct folding of the outer membrane proteins. The folding of the outer membrane proteins has been studied extensively in dilute buffer solution. However, the cell periplasm, where the folding actually occurs, is a crowded environment. In Chapter 2, effects of the macromolecular crowding on the folding mechanisms of two bacterial outer membrane proteins (OmpA and OmpT) were examined. Our results suggested that the periplasmic domain of OmpA improved the efficiency of the OmpA maturation under the crowding condition, while refolding of OmpT was barely affected by the crowding. The second direction of my research focuses on the major multidrug efflux transporter in Gram-negative bacteria, AcrB. AcrB is an obligate trimer, which exists and functions exclusively in a trimeric state. In Chapter 3, the unfolding of the AcrB trimer was investigated. Our results revealed that sodium dodecyl sulfate induced unfolding of the trimeric AcrB started with a local structural rearrangement. While the refolding of secondary structure in individual monomers could be achieved, the re-association of the trimer might be the limiting factor to obtain folded wild type AcrB. In Chapter 4, the correlation between the AcrB trimer stability and the transporter activity was studied. A non-linear correlation was observed, in which the threshold trimer stability was required to maintain the efflux activity. Finally, in Chapter 5, the stability of another inner membrane protein, AqpZ, was studied. AqpZ was remarkably stable. Several molecular engineering approaches were tested to improve the thermal stability of the protein.

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13

Duncan, Anna Louise. "Coarse-grained molecular dynamics simulations of mitochondrial membrane proteins." Thesis, University of Cambridge, 2014. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.648455.

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14

Ulmschneider, Martin B. "Computational studies of membrane proteins." Thesis, University of Oxford, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.249198.

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15

Chalton, David Allen. "Engineering of outer membrane proteins." Thesis, University of Newcastle Upon Tyne, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.430336.

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16

Fearnley, I. M. "Studies of mitochondrial membrane proteins." Thesis, University of Cambridge, 1987. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.380262.

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17

Wahba, Karim A. "Statistical mechanics of membrane proteins." Diss., Restricted to subscribing institutions, 2009. http://proquest.umi.com/pqdweb?did=1905048771&sid=1&Fmt=2&clientId=1564&RQT=309&VName=PQD.

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18

Lee, Chongsoo. "Raman spectroscopy of supported lipid bilayers and membrane proteins." Thesis, University of Oxford, 2005. http://ora.ox.ac.uk/objects/uuid:76f4be6e-b7d3-46c5-a2a1-3dcc7a399410.

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Off-resonance unenhanced total internal reflection (TIR) Raman Spectroscopy was explored to investigate supported single lipid bilayers with incorporated membrane peptides/proteins at water/solid interface. A model membrane was formed on a planar supported lipid layer (pslb) by the fusion of the reconstituted small unilamellar vesicles (SUVs), and the intensity of bilayer was confirmed by a comparison of Raman spectral intensity in the C-H stretching modes with C16TAB. With prominent Raman sensitivity attained, we studied the 2-D phase transition of DMPC and DPPC pslbs and the temperature-dependent polarised spectra revealed a broad transition range of ca. 10 °C commencing at the calorimetric phase transition temperature. We applied polarised TIR-Raman Spectroscopy to pslbs formed by DMPC SUVs reconstituted with a model membrane-spanning peptide gramicidin D. A preferential channel structure formed by dissolution of trifluoroethanol could be probed by polarised Raman Spectroscopy qualitatively showing an antiparallel β-sheet conformation (different from "standard" one) and our Raman spectra by correlation with NMR and CD data confirmed single-stranded π6.3 β-helical channel structure in the single bilayer. We also studied the membrane-penetrating peptide indolicidin in the presence of DMPC pslb over the chain melting temperature and a β-turn structure was dominantly observed concomitant with membrane perturbation. Dynamic adsorption of DPPC to form pslb from a micellar solution of n-dodecyl-β- D-maltoside could be examined with high sensitivity of every 1-min acquisition. Finally we used polarised TIR-Raman scattering to porcine pancreatic phospholipase A2 hydrolytic activity on DPPC pslbs and revealed lipid-active conformation different from that of the enzyme alone.

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19

Guseva, Ksenia. "Formation and cooperative behaviour of protein complexes on the cell membrane." Thesis, University of Aberdeen, 2011. http://digitool.abdn.ac.uk:80/webclient/DeliveryManager?pid=203444.

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In this work we analyse aspects of dynamics and organization of biological membranes from a physical prospective [i.e. perspective]. We provide an analysis of the process of self-assembly and spatial organization of membrane proteins. We illustrate the analysis by considering a channel activated by membrane tension called mechanosensitive channels (MS), in E. coli and the twin arginine translocation system (Tat). We analyse the mechanism of formation of oligomeric protein complexes formed by identical subunits. By derivation of a mathematical approach based on Smoluchowski coagulation equation, we study the deficiency of the process of complex formation, taking into account both irreversible aggregation, as well as fragmentation. We find that a small fragmentation rate increases the efficiency of the formation process, however if the fragmentation rate vanishes the irreversible process is very inefficient. Our second aim is to determine how the spatial organization can affect the function of channels, which are regulated by elastic forces. We map these short-range interactions into a discretized system, from which we obtain the spatial distribution of the channels and its effect on the gating dynamics. We find that organized channels activate at lower membrane tensions, but possess a delay in the reaction time. In the last part we determine how the formation of transient pores on the membrane depends on the dynamics of its assembly process. We analyse the pores formed by the Tat complex, which is responsible for protein transport through the membrane. This system functions by polimerization in response to a signal of transport demand from a protein in the cell cytoplasm. The direct correlation of the size of the assembled pore and the size of the protein determines the speed of the translocation process. Using a differential equation approach we obtain that the flux of a given protein depends quadratically on its size.

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20

Stubberfield, Lisa Marie. "Interactions of Plasmodium falciparum proteins at the membrane skeleton of infected erythrocytes." Monash University, Dept. of Microbiology, 2003. http://arrow.monash.edu.au/hdl/1959.1/9433.

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21

LADHA, PARAG. "POLYMERIC MEMBRANE SUPPORTED BILAYER LIPID MEMBRANES RECONSTITUTED WITH BIOLOGICAL TRANSPORT PROTEINS." University of Cincinnati / OhioLINK, 2006. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1145901880.

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22

Cohen, Alona. "Studies of regulated membrane trafficking /." Access full-text from WCMC, 2008. http://proquest.umi.com/pqdweb?did=1634379741&sid=7&Fmt=2&clientId=8424&RQT=309&VName=PQD.

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23

Oldham, Alexis Jean. "Modulation of lipid domain formation in mixed model systems by proteins and peptides." View electronic thesis, 2008. http://dl.uncw.edu/etd/2008-1/r1/oldhama/alexisoldham.pdf.

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24

Nilsson, Johan. "Membrane protein topology : prediction, experimental mapping and genome-wide analysis /." Stockholm, 2004. http://diss.kib.ki.se/2004/91-7349-963-3/.

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25

Boulter, Jonathan Michael. "Structural and functional studies of the erythrocyte anion exchanger, band 3." Thesis, University of Oxford, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.297079.

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26

Francisco, Rafael Neves. "Solubilization of membrane proteins using ionic liquids." Master's thesis, Universidade de Aveiro, 2015. http://hdl.handle.net/10773/21537.

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Mestrado em Biotecnologia, ramo biotecnologia industrial e ambiental The main goal of this work consists on the study of the ability of ionic liquids (ILs) to extract membrane proteins from biological membranes while keeping their integrity in aqeuous solutions. Since typical surfactants are mainly used for this purpose, ILs are here investigated as a new class of extraction agents. For the evaluation of the ILs solvation ability power, four proteins were selected to be overexpressed in Escherichia coli and to be used as model proteins, namely the Outer Membrane Protein F (OmpF) and Outer Membrane Protein C (OmpC), that are β-barrel proteins, and two bacteriorhodopsins, Haloarcula marismortui (HmBRI) and Haloarcula walsbyi (HwBR), that α-helix proteins. In this work, the investigations carried out with OmpC failed during cloning and OmpF failed during the purification step. On the other hand, the two bacteriorhodopsins were expressed and purified successfully. Although some adjustments (mainly the His-tag) must be performed to improve the expression and the purification level, 1 mg/L of HmBRI and 0.1 mg/L of HwBR were purified. The protein HmBRI was then chosen as a model protein to test the extraction ability of several aqeuous solutions of ILs. Its interesting feature of producing solutions and pellets with a purple colour, and its specific absorbance at 552 nm, make of HmBRI an excellent model protein since it can be easily monotired by Vis-spectroscopy and analysis of its colour. Iimidazolium-, phosphonium-and cholinium-based ILs were investigated in several concentrations in aqueous solutions. None of the ILs studied revelaed to be able to extract HmBRI without denaturation. However, cholinium decanoate was able to extract a higher amount of protein from the biological membrane compared to the commercial detergent decyl maltoside. Mixtures using cholinium decanoate and decyl maltoside were then used to extract the HmBR altough no further improvements on the extraction were observed. Since HmBRI is reported as a good fusion tag for other membrane proteins, avian specific antibodies (polyclonal) were finally produced by immunizing quails to evaluate the performance of HmBRI as a fusion tag. O objetivo principal deste trabalho consistiu no estudo da capacidade de líquidos iónicos para extrair proteínas de membrana de membranas biológicas, assim como em manter a sua integridade em solução aquosa. Para a avaliação da capacidade de extração, foram selecionadas quatro proteínas para sobreexpressar em Escherichia coli, nomeadamente Outer Membrane Protein F (OmpF) e Outer Membrane Protein C (OmpC), que são proteínas em barril-β, e duas bacteriorodopsinas, Haloarcula marismortui (HmBRI) e Haloarcula walsbyi (HwBR), que são compostas por hélices-α. Infelizmente a produção de OmpC falhou durante o passo de clonagem enquanto que a obtenção de OmpF falhou durante o passo de purificação. Por outro lado, as duas bacteriorodopsinas foram expressas e purificadas com sucesso. Embora alguns ajustes (principalmente ao nível da His-tag) devam ainda ser realizados para melhorar a expressão e a purificação num futuro próximo, por cada litro de cultura foram purificados 1 mg de HmBRI e 0,1 mg de HwBR. A proteína HmBRI foi finalmente escolhida como proteína modelo para testar a capacidade de extração e solubilização de vários líquidos iónicos. A sua característica interessante de produzir soluções e pellets com cor roxa, assim como a sua absorvência específica a 552 nm, faz da HmBRI uma excelente proteína modelo facilmente monitorizada.Os líquidos iónicos estudados são derivados de catiões imidazólio, fosfónio e colinio. De um modo geral, nenhum líquido iónico foi capaz de extrair HmBRI sem a desnaturar. No entanto, o decanoato de colinio foi capaz de extrair mais proteínas da membrana biológica em comparação com o detergente comercial, decilo maltosideo. Por fim, foram estudadas misturas de decanoato de colina e surfactante comercial para extrair, apesar de os resultados serem semelhantes ao quando utilizando apenas líquido iónico. Uma vez que a HmBRI é uma boa proteína de fusão para outras proteínas de membrana, foram produzidos anticorpos específicos de aves (policlonais) pela imunização de codornizes, sendo estes anticorpos posteriormente purificados a partir de gema de ovo. Estes anticorpos são muito úteis na investigação de HmBRI como tag fusão.

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27

Shinohara, Elvira Maria Guerra. "Estudo das proteínas da membrana eritrocitária de mamíferos de treze ordens da classe mammalia." Universidade de São Paulo, 1996. http://www.teses.usp.br/teses/disponiveis/9/9136/tde-28042008-122838/.

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Foram estudadas as proteínas da membrana eritrocitária de quarenta e seis espécies diferentes pertencentes à treze ordens da classe Mammalia, através de eletroforese em gel de poliacrilamida. Observamos que: 1. não parece haver correlação entre as concentrações relativas de espectrinas e o volume corpuscular médio. 2. não parece haver correlação entre as concentrações relativas de banda 3 e o volume corpuscular médio. 3. parece haver uma correlação inversa entre as concentrações relativas das anquirinas e o volume corpuscular médio. Assim, a maior parte dos animais pertencentes à ordem dos Artiodacty/a estudados (girafa, cervo nobre, veado campeiro, veado catingueiro, carneiro, cabra), que apresentam volume corpuscular baixo, exibe aumento significativo da concentração das anquirinas. 4. observou-se, o aparecimento de uma banda difusa na região 4.5 no Didelphis marsupialis (gambá), Arctocephalus tropicalis e Arctocephalus australis (lobo marinho subantártico e lobo marinho das ilhas do sul) e Panthera leo (leão) quando os estromas são submetidos à ação do NEM na concentração de 200 µM, e o não encontro desta banda nas demais espécies estudadas. Este fato poderia advir da hipótese de haver, nas três espécies, sequências de aminoácidos comuns que possibilitariam a ação química direta do NEM. 5. observou-se que, nos mamíferos estudados, embora houvesse variações qualitativas e quantitativas das proteínas da membrana nas espécies estudadas, práticamente todas elas apresentaram as proteínas descritas no Homo sapiens, mostrando serem todas elas importantes na manutenção do citoesqueleto e da membrana como um todo. 6. Com exceção da cutia, que exibe provavelmente quatro formas de espectrinas, todas as demais espécies exibiram duas formas, embora com variações qualitativas e quantitativas. 7. A banda 3 foi a proteína que mais exibiu variação, seja no peso molecular, com variação desde 95 kDa (Capra hircus, cabra) até 169 kDa (Alouatta sp, bugio), seja no aspecto difuso ou bem definido. 8. Houve na região 4.1/4.2 uma variabilidade grande, seja qualitativa, seja quantitativa com aparentes ausências dê\' uma ou de outra. Alguns roedores, a cobaia, cutia, hamster exibiram somente uma banda protéica na região 4.1/4.2. 9. Entre os primatas, todas as proteínas apresentaram o mesmo padrão entre os Hominoidea (macacos antropóides, Gorilla gorilla e Pongo pygmaeus e homem, Homo sapiens) e os do Velho Mundo (Cercopithecoidea, Papio cynocephalus e Erythrocebus pata). Mas, os primatas do Novo Mundo (Ceboidea, Cebus apella, Alouatta sp e AteIes paniscus chamek) apresentaram variação do peso molecular da banda 3, apresentando no entanto o mesmo aspecto difuso dos outros primatas descritos anteriormente. 10. Com exceção do Didelphis marsupialis (gambá) e Giraffa came/opardalis (girafa), que apresentaram evidência da ação de serina-proteases sobre uma anquirina, as demais espécies não exibiram proteases intra-eritrocitárias ativas nas condições estudadas. Forty six different mammal species from thirteen regarding their erythrocyte membrane proteins, following data were observed: 1. No correlation was observed between mean corpuscular volume and spectrins concentration. 2. No correlation was observed between mean corpuscular volume and band 3 concentration. 3. It seems that there is inverse correlation between mean corpuscular volume and ankyrins concentration. Most of the studied animmals belonging to Artiodactyla, which exhibit low mean corpuscular volume, present higher ankyrin concentration. 4. A diffuse band in 4.5 region was observed among the Didelphis marsupialis, Arctocephalus tropicalis, Arctocephalus australis and Panthera leo when the ghosts were treated with 200 µM NEM, what was not found in the others species. This fact could be ascribed to hypothetical sequence of the Iysine, hystidine and cysteine which may be prone to NEM direct chemical action. 5. Although some qualitative and quantitative changes were observed among ali the studied species, ali of them seem to occur in the humans, disclosing that they are \"house-keeping\" proteins which participate as important pieces in the cytoskeleton structure and the membrane as well. 6. Ali the species presented two spectrins, with exception of Dasyprocta sp., which exhibited fours bands in the spectrins region. 7. The band 3 was the protein which showed the greatest variation, since 95 kDa in the Capra hircus up to 169 kDa in the Alouatta sp., as well as in the aspect, diffuse or well defined. 8. A great variability was observed in the 4.1/4.2 region, with apparent absence of one or another. Some Rodentia exhibited only one protein in the 4.1/4.2 region. 9. Among the Primates, the Hominoidea and the Cercopithecoidea presented an uniform pattern, but the New World monkeys (Cebus apella, Alouatta sp. and Ateies paniscus chamek) exhibited a striking molecular weight band 3 variation, although keeping the common diffuse pattern. 11. Ali the studied species did not present the evidence of protease action upon the membrane proteins, except the Didelphis marsupialis and Giraffa camelopardalis, which disclosed a proteolytic action upon the ankyrin.

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Carlisle, Glenn E. "Characterization of Mycobacterium avium cytoplasmic membrane proteins with an emphasis on the major cytoplasmic membrane protein." Thesis, Virginia Tech, 1991. http://hdl.handle.net/10919/42610.

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Proteins of the cytoplasmic membrane of Mycobacterium avium were investigated to identify those which were: (1)intrinsic or extrinsic, (2) attached to the cell wall, (3)surface accessible and (4) excreted. In addition sera containing anti-cytoplasmic membrane proteins were obtained and preliminary purification of the cytoplasmic membrane protein was attempted. The predominating cytoplasmic membrane protein of 31,000 daltons (MCMP) was found to be intrinsic, attached to the cell wall and possibly surface accessible. The MCMP was not excreted, even in media in which the MCMP is not found in the cytoplasmic membrane. Other cytoplasmic membrane proteins were also found to be intrinsic; a few were likely to be extrinsic based upon their separation from the membrane in sucrose gradients. Cytoplasmic membrane proteins of 66, 000, 115, 000 and 129 dalton were surface accessible as judged by I 125-Iodobead labeling. Antisera against the HCMP and other cytoplasmic membrane proteins was obtained and will be useful in further cytoplasmic membrane protein characterization. Acetone precipitation of a cytoplasmic membrane preparation was performed to partially purify the MCMP. The data from this study can be used for the development of serodiagnostic reagents for detecting mycobacterial infection. Master of Science

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29

Marchand, Petra. "Structure, membrane association, and processing of meprin subunits." Diss., This resource online, 1994. http://scholar.lib.vt.edu/theses/available/etd-06062008-171918/.

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30

Boban, Mirta. "Transcriptional regulation by inner nuclear membrane proteins /." Stockholm, 2007. http://diss.kib.ki.se/2007/978-91-7357-170-8/.

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31

Almqvist, Jonas. "Structural modeling of membrane transporter proteins /." Stockholm : Department of Physical, Inorganic and Structural Chemistry, Stockholm University, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-7402.

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32

Cox, Katherine L. "Molecular dynamics of outer membrane proteins." Thesis, University of Oxford, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.427881.

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33

Crooks, Kim Chantelle. "Turnover of plant plasma membrane proteins." Thesis, Oxford Brookes University, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.363720.

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34

Kulkarni, Chandrashekhar V. "In-Cubo Crystallization of Membrane Proteins." Thesis, Imperial College London, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.508495.

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35

Folea, Ioana Mihaela. "Electron microscopy of cyanobacterial membrane proteins." [S.l. : [Groningen : s.n.] ; University of Groningen] [Host], 2008. http://irs.ub.rug.nl/ppn/314679286.

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36

Boekel, Carolina. "Integration and topology of membrane proteins." Doctoral thesis, Stockholm : Department of Biochemistry and Biophysics, Stockholm University, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-8575.

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37

Lüthy, Roland. "Proteins involved in membrane transfer processes /." [S.l : s.n.], 1988. http://www.ub.unibe.ch/content/bibliotheken_sammlungen/sondersammlungen/dissen_bestellformular/index_ger.html.

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38

Kochva, Uzi. "Structural analysis of integral membrane proteins." E-thesis Full text (Hebrew University users only), 2007. http://shemer.mslib.huji.ac.il/dissertations/H/JSL/001449168.pdf.

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39

Saleem, Muhammad. "Structural studies of prokaryotic membrane proteins." Thesis, University of Manchester, 2008. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.492047.

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40

Polozov, Ivan V. "Interactions of class A and class L amphipathic helical peptides with model membranes." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1997. http://www.collectionscanada.ca/obj/s4/f2/dsk2/tape16/PQDD_0006/NQ30110.pdf.

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41

Tuan, Chik Syed Mohd Saufi. "Mixed Matrix Membrane Chromatography for Bovine Whey Protein Fractionation." Thesis, University of Canterbury. Chemical and Process Engineering, 2010. http://hdl.handle.net/10092/3647.

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Whey protein fractionation is an important industrial process that requires effective large-scale processes. Although packed bed chromatography has been used extensively, it suffers from low processing rates due to high back-pressures generated at high flow rates. Batch chromatography has been applied but generally has a low efficiency. More recently, adsorptive membranes have shown great promise for large-scale protein purification, particularly from large-volume dilute feedstocks. A new method for producing versatile adsorptive membranes by combining membrane and chromatographic resin matrices has been developed but not previously applied to whey protein fractionation. In this work, a series of mixed matrix membranes (MMMs) were developed for membrane chromatography using ethylene vinyl alcohol (EVAL) based membranes and various types of adsorbent resin. The feasibility of MMM was tested in bovine whey protein fractionation processes. Flat sheet anion exchange MMMs were cast using EVAL and crushed Lewatit® MP500 (Lanxess, Leverkusen, Germany) anion resin, expected to bind the acidic whey proteins β-lactoglobulin (β-Lac), α-lactalbumin (α-Lac) and bovine serum albumin (BSA). The MMM showed a static binding capacity of 120 mg β-Lac g⁻¹ membrane (36 mg β-Lac mL⁻¹ membrane) and 90 mg α-Lac g⁻¹ membrane (27 mg α-Lac mL⁻¹ membrane). It had a selective binding towards β-Lac in whey with a binding preference order of β-Lac > BSA > α-Lac. In batch whey fractionation, average binding capacities of 75.6 mg β-Lac g⁻¹ membrane, 3.5 mg α-Lac g⁻¹ membrane and 0.5 mg BSA g⁻¹ membrane were achieved with a β-Lac elution recovery of around 80%. Crushed SP Sepharose™ Fast Flow (GE Healthcare Technologies, Uppsala, Sweden) resin was used as an adsorbent particle in preparing cation exchange MMMs for lactoferrin (LF) recovery from whey. The static binding capacity of the cationic MMM was 384 mg LF g⁻¹membrane or 155 mg LF mL⁻¹ membrane, exceeding the capacity of several commercial adsorptive membranes. Adsorption of lysozyme onto the embedded ion exchange resin was visualized by confocal laser scanning microscopy. In LF isolation from whey, cross-flow operation was used to minimize membrane fouling and to enhance the protein binding capacity. LF recovery as high as of 91% with a high purity (as judged by the presence of a single band in gel electrophoresis) was achieved from 150 mL feed whey. The MMM preparation concept was extended, for the first time, to produce a hydrophobic interaction membrane using crushed Phenyl Sepharose™ (GE Healthcare Technologies, Uppsala, Sweden) resin and tested for the feasibility in whey protein fractionation. Phenyl Sepharose MMM showed binding capacities of 20.54 mg mL⁻¹ of β-Lac, 45.58 mg mL⁻¹ of α-Lac, 38.65 mg mL⁻¹ of BSA and 42.05 mg mL⁻¹ of LF for a pure protein solution (binding capacity values given on a membrane volume basis). In flow through whey fractionation, the adsorption performance of the Phenyl Sepharose MMM was similar to the HiTrap™ Phenyl hydrophobic interaction chromatography column. However, in terms of processing speed and low pressure drop across the column, the benefits of using MMM over a packed bed column were clear. A novel mixed mode interaction membrane was synthesized in a single membrane by incorporating a certain ratio of SP Sepharose cation resin and Lewatit MP500 anion resin into an EVAL base polymer solution. The mixed mode cation and anion membrane chromatography developed was able to bind basic and acidic proteins simultaneously from a solution. Furthermore, the ratio of the different types of adsorptive resin incorporated into the membrane matrix could be customised for protein recovery from a specific feedstream. The customized mixed mode MMM consisting of 42.5 wt% of MP500 anionic resin and 7.5 wt% SP Sepharose cationic resin showed a binding capacity of 7.16 mg α-Lac g⁻¹ membrane, 11.40 mg LF g⁻¹ membrane, 59.21 mg β-Lac g⁻¹ membrane and 6.79 mg IgG g⁻¹ membrane from batch fractionation of 1 mL LF-spiked whey. A tangential flow process using this membrane was predicted to be able to produce 125 g total whey protein per L membrane per h.

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42

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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43

Howard, Megan Wilder. "Coronavirus mediated membrane fusion /." Connect to full text via ProQuest. Limited to UCD Anschutz Medical Campus, 2008. http://proquest.umi.com/pqdweb?did=1552538711&sid=1&Fmt=6&clientId=18952&RQT=309&VName=PQD.

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Thesis (Ph.D. in Microbiology) -- University of Colorado Denver, 2008. Typescript. Includes bibliographical references (leaves 161-183). Free to UCD Anschutz Medical Campus. Online version available via ProQuest Digital Dissertations;

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44

Pothakanoori, Kapil. "A Web Service for Protein Refinement and Refinement of Membrane Proteins." ScholarWorks@UNO, 2010. http://scholarworks.uno.edu/td/102.

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The structures obtained from homology modeling methods are of intermediate resolution 1-3Ã… from true structure. Energy minimization methods allow us to refine the proteins and obtain native like structures. Previous work shows that some of these methods performed well on soluble proteins. So we extended this work on membrane proteins. Prediction of membrane protein structures is a particularly important, since they are important biological drug targets, and since their number is vanishingly small, as a result of the inherent difficulties in working with these molecules experimentally. Hence there is a pressing need for alternative computational protein structure prediction methods. This work tests the ability of common molecular mechanics potential functions (AMBER99/03) and a hybrid knowledge-based potential function (KB_0.1) to refine near-native structures of membrane proteins in vacuo. A web based utility for protein refinement has been developed and deployed based on the KB_0.1 potential to refine proteins.

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45

Krammer, André Thomas. "Computational studies of protein-membrane interactions and forced unfolding of proteins /." Thesis, Connect to this title online; UW restricted, 2000. http://hdl.handle.net/1773/9697.

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46

Cao, Liming. "Protein Separation with Ion-exchange Membrane Chromatography." Link to electronic thesis, 2005. http://www.wpi.edu/Pubs/ETD/Available/etd-050405-174109/.

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47

Björkholm, Patrik. "Protein Interactions from the Molecular to the Domain Level." Doctoral thesis, Stockholms universitet, Institutionen för biokemi och biofysik, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-101795.

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The basic unit of life is the cell, from single-cell bacteria to the largest creatures on the planet. All cells have DNA, which contains the blueprint for proteins. This information is transported in the form of messenger RNA from the genome to ribosomes where proteins are produced. Proteins are the main functional constituents of the cell, they usually have one or several functions and are the main actors in almost all essential biological processes. Proteins are what make the cell alive. Proteins are found as solitary units or as part of large complexes. Proteins can be found in all parts of the cell, the most common place being the cytoplasm, a central space in all cells. They are also commonly found integrated into or attached to various membranes. Membranes define the cell architecture. Proteins integrated into the membrane have a wide number of responsibilities: they are the gatekeepers of the cell, they secrete cellular waste products, and many of them are receptors and enzymes. The main focus of this thesis is the study of protein interactions, from the molecular level up to the protein domain level. In paper I use reoccurring local protein structures to try and predict what sections of a protein interacts with another part using only sequence information. In papers II and III we use a randomization approach on a membrane protein motif that we know interacts with a sphingomyelin lipid to find other candidate proteins that interact with sphingolipids. These are then experimentally verified as sphingolipid-binding. In the last paper, paper IV, we look at how protein domain interaction networks overlap and can be evaluated. At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 3: Manuscript.

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48

Tsui, Marco Man Kin. "Studies on yeast SNARE complex formation /." View Abstract or Full-Text, 2003. http://library.ust.hk/cgi/db/thesis.pl?BIOL%202003%20TSUI.

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Thesis (Ph. D.)--Hong Kong University of Science and Technology, 2003. Includes bibliographical references (leaves 130-138). Also available in electronic version. Access restricted to campus users.

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49

Mayol, Escuer Eduardo. "Development of bioinformatic tools for the study of membrane proteins." Doctoral thesis, Universitat Autònoma de Barcelona, 2019. http://hdl.handle.net/10803/667335.

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Las proteínas de membrana son elementos fundamentales de todas las células conocidas, que representan una cuarta parte de los genes del genoma humano, y desempeñan funciones esenciales en la biología celular. Alrededor del 50% de los medicamentos comercializados actualmente tienen una proteína de membrana como objetivo, y alrededor de un tercio de todos ellos se dirigen a los receptores acoplados a proteína G (GPCR). Las dificultades y limitaciones en el trabajo experimental necesario para los estudios microscópicos de la membrana, así como las proteínas de membrana, impulsaron el uso de métodos computacionales. El alcance de esta tesis es desarrollar nuevas herramientas bioinformáticas para el estudio de las proteínas de membrana y en particular para GPCRs que ayudan a caracterizar sus rasgos estructurales y ayudar a la comprensión de su función. Con respecto a las proteínas de membrana, una piedra angular de esta tesis ha sido la creación de dos bases de datos para las principales clases de proteínas de membrana: una para helices-α (TMalphaDB) y otra para proteínas barriles-β (TMbetaDB). Estas bases de datos son empleadas por una herramienta recientemente desarrollada para encontrar distorsiones estructurales inducidas por motivos específicos de secuencias de aminoácidos (http://lmc.uab.cat/tmalphadb y http://lmc.uab.cat/tmbetadb). También se usaron en la caracterización de las interacciones entre residuos que se producen en la región transmembrana de estas proteínas con el objetivo de favorecer la comprensión de la complejidad y las características diferenciales de las proteínas de membrana. Se encontró que las interacciones que involucran los residuos de Phe y Leu son las principales responsables de la estabilización de la región transmembrana. Además, se analizó la contribución energética de las interacciones entre los aminoácidos que contienen azufre (Met y Cys) y los residuos alifáticos o aromáticos. Estas interacciones normalmente no se tienen en gran consideración a pesar de que pueden formar interacciones más fuertes que las interacciones aromático-aromático o aromático-alifático. Asimismo, la familia de GPCRs, la más importante de proteínas de membrana, ha sido el foco de dos aplicaciones web dedicadas al análisis de conservación de aminoácidos o motivos de secuencia y correlación de pares (GPCR-SAS, http://lmc.uab.cat/gpcrsas) y para incorporar moléculas de agua internas en estructuras de estos receptores (HomolWat, http://lmc.uab.cat/HW). Estas aplicaciones web son estudios piloto que pueden extenderse a otras familias de proteínas de membrana en proyectos futuros. Todas estas herramientas y análisis pueden ayudar en el desarrollo de mejores modelos estructurales y contribuir a la comprensión de las proteínas de membrana. Membrane proteins are fundamental elements for every known cell, accounting for a quarter of genes in the Human genome, they play essential roles in cell biology. About 50% of currently marketed drugs have a membrane protein as target, and around a third of them target G-protein-coupled receptors (GPCRs). The current difficulties and limitations in the experimental work necessary for microscopic studies of the membrane as well as membrane proteins urged the use of computational methods. The scope of this thesis is to develop new bioinformatic tools for the study of membrane proteins and also for GPCRs in particular that help to characterize their structural features and understand their function. In regard to membrane proteins, a cornerstone of this thesis has been the creation of two databases for the main classes of membrane proteins: one for α-helical proteins (TMalphaDB) and another for β-barrel proteins (TMbetaDB). These databases are used by a newly developed tool to find structural distortions induced by specific amino acid sequence motifs (http://lmc.uab.cat/tmalphadb and http://lmc.uab.cat/tmbetadb) and in the characterization of inter-residue interactions that occur in the transmembrane region of membrane proteins aimed to understand the complexity and differential features of these proteins. Interactions involving Phe and Leu residues were found to be the main responsible for the stabilization of the transmembrane region. Moreover, the energetic contribution of interactions between sulfur-containing amino acids (Met and Cys) and aliphatic or aromatic residues were analyzed. These interactions are often not considered despite they can form stronger interactions than aromatic-aromatic or aromatic-aliphatic interactions. Additionally, G-protein coupled receptor family, the most important family of membrane proteins, have been the focus of two web applications tools dedicated to the analysis of conservation of amino acids or sequence motifs and pair correlation (GPCR-SAS, http://lmc.uab.cat/gpcrsas) and to allocate internal water molecules in receptor structures (HomolWat, http://lmc.uab.cat/HW). These web applications are pilot studies that can be extended to other membrane proteins families in future projects. All these tools and analysis may help in the development of better structural models and contribute to the understanding of membrane proteins.

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50

Käll, Lukas. "Predicting transmembrane topology and signal peptides with hidden Markov models /." Stockholm, 2006. http://diss.kib.ki.se/2006/91-7140-719-7/.

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