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Relevant bibliographies by topics / Transmembrane proteins

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Academic literature on the topic 'Transmembrane proteins'

Author: Grafiati

Published: 4 June 2021

Last updated: 1 February 2022

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Journal articles on the topic "Transmembrane proteins"

1

Deane, Caitlin. "Taming transmembrane proteins." Nature Chemical Biology 12, no. 5 (April 19, 2016): 305. http://dx.doi.org/10.1038/nchembio.2073.

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Gee, Heon Yung, Jiyoon Kim, and Min Goo Lee. "Unconventional secretion of transmembrane proteins." Seminars in Cell & Developmental Biology 83 (November 2018): 59–66. http://dx.doi.org/10.1016/j.semcdb.2018.03.016.

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Ayton, Gary S., and Gregory A. Voth. "Multiscale simulation of transmembrane proteins." Journal of Structural Biology 157, no. 3 (March 2007): 570–78. http://dx.doi.org/10.1016/j.jsb.2006.10.020.

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Bourne, H. R. "G PROTEINS IN TRANSMEMBRANE SIGNALING." Pediatric Research 33 (May 1993): S1. http://dx.doi.org/10.1203/00006450-199305001-00004.

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Miller, R. Tyler. "Transmembrane signalling through G proteins." Kidney International 39, no. 3 (March 1991): 421–29. http://dx.doi.org/10.1038/ki.1991.53.

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Marsh, D. "Lipid interactions with transmembrane proteins." Cellular and Molecular Life Sciences (CMLS) 60, no. 8 (August 1, 2003): 1575–80. http://dx.doi.org/10.1007/s00018-003-3171-z.

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Chiba, Hideki, Makoto Osanai, Masaki Murata, Takashi Kojima, and Norimasa Sawada. "Transmembrane proteins of tight junctions." Biochimica et Biophysica Acta (BBA) - Biomembranes 1778, no. 3 (March 2008): 588–600. http://dx.doi.org/10.1016/j.bbamem.2007.08.017.

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Tusnády, Gábor E., László Dobson, and Peter Tompa. "Disordered regions in transmembrane proteins." Biochimica et Biophysica Acta (BBA) - Biomembranes 1848, no. 11 (November 2015): 2839–48. http://dx.doi.org/10.1016/j.bbamem.2015.08.002.

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Balda, Maria S., and Karl Matter. "Transmembrane proteins of tight junctions." Seminars in Cell & Developmental Biology 11, no. 4 (August 2000): 281–89. http://dx.doi.org/10.1006/scdb.2000.0177.

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Ryu, Hyunil, Ahmed Fuwad, Sunhee Yoon, Huisoo Jang, Jong Lee, Sun Kim, and Tae-Joon Jeon. "Biomimetic Membranes with Transmembrane Proteins: State-of-the-Art in Transmembrane Protein Applications." International Journal of Molecular Sciences 20, no. 6 (March 21, 2019): 1437. http://dx.doi.org/10.3390/ijms20061437.

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In biological cells, membrane proteins are the most crucial component for the maintenance of cell physiology and processes, including ion transportation, cell signaling, cell adhesion, and recognition of signal molecules. Therefore, researchers have proposed a number of membrane platforms to mimic the biological cell environment for transmembrane protein incorporation. The performance and selectivity of these transmembrane proteins based biomimetic platforms are far superior to those of traditional material platforms, but their lack of stability and scalability rule out their commercial presence. This review highlights the development of transmembrane protein-based biomimetic platforms for four major applications, which are biosensors, molecular interaction studies, energy harvesting, and water purification. We summarize the fundamental principles and recent progress in transmembrane protein biomimetic platforms for each application, discuss their limitations, and present future outlooks for industrial implementation.

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Dissertations / Theses on the topic "Transmembrane proteins"

1

Kulman, John David. "Transmembrane Gla proteins /." Thesis, Connect to this title online; UW restricted, 2001. http://hdl.handle.net/1773/9271.

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Doak, David G. "Peptide models of transmembrane proteins." Thesis, University of Oxford, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.359445.

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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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Garrow, Andrew Gordon. "Search algorithms for transmembrane beta-barrel proteins." Thesis, University of Leeds, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.427773.

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Peters, Christoph. "Topology Prediction of α-Helical Transmembrane Proteins." Doctoral thesis, Stockholms universitet, Institutionen för biokemi och biofysik, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-129061.

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Membrane proteins fulfil a number of tasks in cells, including signalling, cell-cell interaction, and the transportation of molecules. The prominence of these tasks makes membrane proteins an important target for clinical drugs. Because of the decreasing price of sequencing, the number of sequences known is increasing at such a rate that manual annotations cannot compete. Here, topology prediction is a way to provide additional information. It predicts the location and number of transmembrane helices in the protein and the orientation inside the membrane. An important factor to detect transmembrane helices is their hydrophobicity, which can be calculated using dedicated scales. In the first paper, we studied the difference between several hydrophobicity scales and evaluated their performance. We showed that while they appear to be similar, their performance for topology prediction differs significantly. The better performing scales appear to measure the probability of amino acids to be within a transmembrane helix, instead of just being located in a hydrophobic environment. Around 20% of the transmembrane helices are too hydrophilic to explain their insertion with hydrophobicity alone. These are referred to as marginally hydrophobic helices. In the second paper, we studied three of these helices experimentally and performed an analysis on membrane proteins. The experiments show that for all three helices positive charges on the N-terminal side of the subsequent helix are important to insert, but only two need the subsequent helix. Additionally, the analysis shows that not only the N-terminal helices are more hydrophobic, but also the C-terminal transmembrane helices. In Paper III, the finding from the second paper was used to improve the topology prediction. By extending our hidden Markov model with N- and C-terminal helix states, we were able to set stricter cut-offs. This improved the general topology prediction and in particular miss-prediction in large N- and C-terminal domains, as well the separation between transmembrane and non-transmembrane proteins. Lastly, we contribute several new features to our consensus topology predictor, TOPCONS. We added states for the detection of signal peptides to its hidden Markov model and thus reduce the over-prediction of transmembrane helices. With a new method for the generation of profile files, it is possible to increase the size of the database used to find homologous proteins and decrease the running time by 75%.

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Batrakou, Dzmitry G. "Nuclear envelope transmembrane proteins in differentiation systems." Thesis, University of Edinburgh, 2012. http://hdl.handle.net/1842/9981.

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Historically, our perception of the nuclear envelope has evolved from a simple barrier isolating the genome from the rest of a cell to a complex system that regulates functions including transcription, splicing, DNA replication and repair and development. Several recent proteomic studies uncovered a great variety of nuclear envelope transmembrane proteins (NETs). Diseases associated with several nuclear envelope proteins, mostly NETs, affect many tissues e.g. muscle, adipose tissue, skin, bones. Many NETs of the inner nuclear membrane have been shown to interact with chromatin, suggesting that their influencing gene expression might explain NET roles in disease. This work is focused on finding novel interactions of NETs with chromatin. First, SUN2 post-translational modifications were analysed and the effect of phosphomimetic and phospho-null mutants on heterochromatin and the cytoskeleton was tested by overexpression. However, no obvious changes were found. Second, several tissue-preferential NETs were tested in an adipocyte differentiation system. NET29 changed chromosome 6 position in pre-adipocytes. This matched changes in chromosome positioning that occur during adipocyte differentiation when NET29 is normally induced. Post-translational modifications of NET29 are likely to play a vital role in this process because a phospho-null mutant dominantly blocked chromosome repositioning. The effect of over-expression and down-regulation of NET29 on transcription was tested and results suggest that NET29 negatively regulates expression of myogenic genes during adipogenesis. This thesis is split into six chapters. Chapter I is an overview of the nuclear envelope, adipogenesis and chromatin remodelling, Chapter II is a detailed description of methods used in this study. Chapter III focuses on post-translational modifications of SUN2, as well as trials to identify novel partners of SUN2. Chapter IV and V deal with a novel nuclear envelope transmembrane protein and its role in adipogenesis. Finally, the last chapter includes a discussion and recommended future directions.

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Kelm, Sebastian. "Structural modelling of transmembrane domains." Thesis, University of Oxford, 2011. http://ora.ox.ac.uk/objects/uuid:b4c9fba9-ee25-469b-8baf-b7c1d70c9d05.

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Membrane proteins represent about one third of all known vertebrate proteins and over half of the current drug targets. Knowledge of their three-dimensional (3D) structure is worth millions of pounds to the pharmaceutical industry. Yet experimental structure elucidation of membrane proteins is a slow and expensive process. In the absence of experimental data, computational modelling tools can be used to close the gap between the numbers of known protein sequences and structures. However, currently available structure prediction tools were developed with globular soluble proteins in mind and perform poorly on membrane proteins. This thesis describes the development of a modelling approach able to predict accurately the structure of transmembrane domains of proteins. In this thesis we build a template-based modelling framework especially for membrane proteins, which uses membrane protein-specific information to inform the modelling process.Firstly, we develop a tool to accurately determine a given membrane protein structure's orientation within the membrane. We offer an analysis of the preferred substitution patterns within the membrane, as opposed to non-membrane environments, and how these differences influence the structures observed. This information is then used to build a set of tools that produce better sequence alignments of membrane proteins, compared to previously available methods, as well as more accurate predictions of their 3D structures. Each chapter describes one new piece of software or information and uses the tools and knowledge described in previous chapters to build up to a complete accurate model of a transmembrane domain.

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Crick, Duncan James. "Solution NMR studies of seven-transmembrane helix proteins." Thesis, University of Cambridge, 2015. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.708906.

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Berthoumieu, Olivia. "Single molecule studies of seven transmembrane domain proteins." Thesis, University of Oxford, 2011. http://ora.ox.ac.uk/objects/uuid:ff7ae71d-5481-4523-812b-2128fe32f5fc.

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This work aimed at studying biophysical properties of two membrane proteins, one of potential nanotechnological use, bacteriorhodopsin, and one potential drug target, the NTS1 neurotensin receptor, at the single molecule scale. Bacteriorhodopsin (BR) is the only protein in the purple membrane (PM) of the halophilic organism Halobacterium salinarium. It is a light-driven proton pump converting light into a transmembrane proton gradient through isomerization of its retinal chromophore. Its stability, as well as its photoactivity remaining in dry protein layers, has made BR an attractive material for biomolecular devices. Numerous studies have been published on this topic; however, they have all used BR within the PM, on relatively large (µm-wide) surfaces. Here, conducting-probe atomic force microscopy (C-AFM) analysis was performed after removing most of the membrane lipids. For the first time, it was shown that the molecular conductance of BR can be reversibly photoswitched with predictable wavelength sensitivity. Intimate and robust coupling to gold electrodes was achieved by using a strategically engineered cysteine which, combined with partial delipidation, generated protein trimers homogenously orientated on the surface. Numerous controls using biophysical (SPR, ellipsometry, Kelvin-probe AFM) and chemical (photocurrent, cyclic voltammetry) techniques confirmed the wavelength specificity of the photoswitch, the anchoring role of the mutation and the homogenous orientation of the protein on the gold surface. Neurotensin is a brain and gastrointestinal 13 amino acid peptide acting as a neuromodulator in the central nervous system and as a hormone in the periphery. Its wide range of biological activities is primarily mediated through its binding to the neurotensin type 1 receptor (NTS1). NTS1 expressed in E.coli was purified and inserted into 100 nm brain polar lipid liposomes in a conformation which retained its ligand-binding capabilities. Initial AFM characterisation was performed as a prelude for ligand-receptor interaction studies, including high resolution imaging, force spectroscopy and solid state NMR approaches.

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Abd, Halim Khairul Bariyyah. "Molecular dynamics simulation studies of transmembrane signalling proteins." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:bc9e1e0e-433c-4adb-8374-1065eac0f37e.

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Receptor tyrosine kinases (RTKs) are a major class of cell surface receptors, important in cell signalling events associated with a variety of functions. High-throughput (HTP), coarse-grained molecular dynamics (CG-MD) simulations have been used to investigate the dimerization of the transmembrane (TM) domain of selected RTKs, including epidermal growth factor receptor (EGFR) and muscle-specific kinase (MuSK). EGFR activation requires not only a specific TM dimer interface, but also a proper orientation of its juxtamembrane (JM) domain. Phosphatidylinositol 4,5-bisphosphate (PIP₂) is known to abolish EGFR phosphorylation through interaction with basic residues within the JM domain. Here, a multiscale approach was used to investigate anionic lipid clustering around the TM-JM junction and how such clustering is modulated by the mutation of basic residues. The simulations demonstrated that PIP₂ may help stabilize the JM-A antiparallel dimer, which may in turn help stabilize TM domain helix packing of the N-terminal dimerization motif. A proximal TM domain residue has been implicated in the inhibition of ganglioside GM3 in phase-separated membranes. Here, CG simulations were used to explore the dynamic behaviour of the EGFR TM domain dimer in GM3-containing and GM3-depleted bilayers designed to resemble lipid-disordered (Ld) and phase-separated (Ld/Lo) membranes. The simulations suggest that the presence of GM3 in Ld/Lo bilayers can disrupt and destabilize the TM dimer, which helps to explain why GM3 may favour monomeric EGFR in vivo. To gain insights into the dynamic nature of the intact EGFR, a nearly complete EGFR dimer was modelled using available structural data and embedded in an asymmetric compositional complex bilayer, which resembles the mammalian plasma membrane. The results demonstrated the dynamic nature of the EGFR ectodomain and its predicted interactions with lipids in the local bilayer. Strong protein-lipid interactions, as well as lipid-lipid interactions, affect the local clustering of lipids and the diffusion of lipids in the vicinity of the protein on both leaflets.

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Books on the topic "Transmembrane proteins"

1

Bradshaw, Ralph A. Functioning of transmembrane receptors in cell signaling. Amsterdam: Academic Press, 2011.

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Chen, Yvonne Man-Yee. Expression and characterization of the transmembrane domain of phage M13 coat protein as fusion proteins. Ottawa: National Library of Canada, 1995.

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Demmers, Jeroen Adrianus Antonius. Interactions of transmembrane peptides and proteins with lipid membranes studied by mass spectrometry. [S.l: s.n.], 2002.

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Khan, Amir R. Mutational and structural analysis of second-site transmembrane region mutants of phage M13 coat protein. Ottawa: National Library of Canada, 1993.

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Quick, Michael W. Transmembrane Transporters. Wiley & Sons, Incorporated, John, 2008.

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W, Quick Michael, ed. Transmembrane transporters. New York: Wiley-Liss, 2002.

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Quick, Michael W. Transmembrane Transporters. Wiley & Sons, Incorporated, John, 2003.

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Holland, Eric C. Mechanisms for insertion of transmembrane proteins. 1986.

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Transmembrane signaling protocols. 2nd ed. Totowa, NJ: Humana Press, 2006.

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Hydar, Ali, and Haribabu Bodduluri, eds. Transmembrane signaling protocols. 2nd ed. Totowa, N.J: Humana Press, 2006.

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Book chapters on the topic "Transmembrane proteins"

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Tusnády, Gábor E., and Dániel Kozma. "Structure Prediction of Transmembrane Proteins." In Protein Modelling, 199–221. Cham: Springer International Publishing, 2014. http://dx.doi.org/10.1007/978-3-319-09976-7_9.

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Rath, Arianna, and Charles M. Deber. "Design of Transmembrane Peptides: Coping with Sticky Situations." In Membrane Proteins, 197–210. Totowa, NJ: Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-583-5_11.

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Nyman, Tomas, Jhansi Kota, and Per O. Ljungdahl. "Ancillary proteins in membrane targeting of transporters." In Molecular Mechanisms Controlling Transmembrane Transport, 207–34. Berlin, Heidelberg: Springer Berlin Heidelberg, 2004. http://dx.doi.org/10.1007/b96974.

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Randall, Arlo, and Pierre Baldi. "Transmembrane beta-barrel protein structure prediction." In Structural Bioinformatics of Membrane Proteins, 83–102. Vienna: Springer Vienna, 2010. http://dx.doi.org/10.1007/978-3-7091-0045-5_5.

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Pirovano, Walter, Sanne Abeln, K. Anton Feenstra, and Jaap Heringa. "Multiple alignment of transmembrane protein sequences." In Structural Bioinformatics of Membrane Proteins, 103–22. Vienna: Springer Vienna, 2010. http://dx.doi.org/10.1007/978-3-7091-0045-5_6.

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Spisni, A., V. Comaschi, and L. Franzoni. "The Function of Transmembrane Channels: Ion Transport Studies by 23Na NMR." In Membrane Proteins, 49–55. Berlin, Heidelberg: Springer Berlin Heidelberg, 1986. http://dx.doi.org/10.1007/978-3-642-71543-3_6.

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Hong, Heedeok, Yu-Chu Chang, and James U. Bowie. "Measuring Transmembrane Helix Interaction Strengths in Lipid Bilayers Using Steric Trapping." In Membrane Proteins, 37–56. Totowa, NJ: Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-583-5_3.

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Tome, Lydia, Dominik Steindorf, and Dirk Schneider. "Genetic Systems for Monitoring Interactions of Transmembrane Domains in Bacterial Membranes." In Membrane Proteins, 57–91. Totowa, NJ: Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-583-5_4.

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de Brevern, Alexandre G. "3D Structural Models of Transmembrane Proteins." In Methods in Molecular Biology, 387–401. Totowa, NJ: Humana Press, 2010. http://dx.doi.org/10.1007/978-1-60761-762-4_20.

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Nikravan, Mohammad Hossein, Ashwani Kumar, and Sandra Zilles. "Detecting Transmembrane Proteins Using Decision Trees." In Discovery Science, 146–60. Cham: Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-24282-8_13.

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Conference papers on the topic "Transmembrane proteins"

1

Brown, Michael C., Ross Chambers, Dale V. Onisk, Tony R. Joaquim, Lewis J. Stafford, Klaus Lindpaintner, Daniel Keter, and James W. Stave. "Abstract 4325: Monoclonal antibodies to transmembrane proteins." In Proceedings: AACR 104th Annual Meeting 2013; Apr 6-10, 2013; Washington, DC. American Association for Cancer Research, 2013. http://dx.doi.org/10.1158/1538-7445.am2013-4325.

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Tomita, Noriko, Kazuyo Abe, and Makoto Ohta. "Quantitative Analysis of Subunit Mismatch Arrangement in Staphylococcal Gamma-Hemolysin Heteroheptameric Transmembrane Pore." In ASME 2011 International Mechanical Engineering Congress and Exposition. ASMEDC, 2011. http://dx.doi.org/10.1115/imece2011-63645.

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Pore-forming cytolytic proteins distributed in a wide variety of eukaryotic and prokaryotic organisms have been intensively studied in terms of pathophysiological functions and molecular architecture of transmembrane pores. These proteins are also being developed for various analytical applications such as detector of proteins and DNA by engineering the structure of the pore. Staphylococcal gamma-hemolysin (Hlg), a pore-forming protein, which consists of two separate proteins, LukF and Hlg2, has potential to be a useful tool as a multifunctional biosensor. However, the fine structure of the Hlg pore has not been clarified. Our previous studies revealed that LukF and Hlg2 assemble alternately on the membrane in a molar ratio of 3:4 and 4:3 and form cylindrical heteroheptameric transmembrane pores. In the present study, we conducted quantitative analysis of the subunit arrangement of the pore by using two-dimensional (2-D) image analysis based on high-resolution transmission electron microscopy (TEM) images. Results of this study suggest a new aspect of the characteristic structure in two-component pore-forming protein and can contribute to the engineering of the Hlg pore.

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Das, Jishnu. "Computational design of soluble variants of transmembrane proteins." In the International Symposium. New York, New York, USA: ACM Press, 2010. http://dx.doi.org/10.1145/1722024.1722033.

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Kitsas, Ilias K., Stavros M. Panas, and Leontios J. Hadjileontiadis. "Linear discrimination of transmembrane from non-transmembrane segments in proteins using higher-order crossings." In Conference Proceedings. Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE, 2006. http://dx.doi.org/10.1109/iembs.2006.260716.

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Kitsas, Ilias K., Stavros M. Panas, and Leontios J. Hadjileontiadis. "Linear discrimination of transmembrane from non-transmembrane segments in proteins using higher-order crossings." In Conference Proceedings. Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE, 2006. http://dx.doi.org/10.1109/iembs.2006.4398780.

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Chen, Z., and Y. Xu. "Multi-scale hierarchical structure prediction of helical transmembrane proteins." In 2005 IEEE Computational Systems Bioinformatics Conference (CSB'05). IEEE, 2005. http://dx.doi.org/10.1109/csb.2005.41.

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Nadeau, Jay L., C. Annette Hollmann, Rafael M. Khatchadourian, and Samuel J. Clarke. "Nanoparticles and modified fluorescent proteins for imaging of transmembrane potential." In 2007 3rd International IEEE/EMBS Conference on Neural Engineering. IEEE, 2007. http://dx.doi.org/10.1109/cne.2007.369614.

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Kinbara, Kazushi. "Design of stimuli-responsive molecules mimicking dynamic functions of transmembrane proteins." In Molecular and Nano Machines III, edited by Zouheir Sekkat and Takashige Omatsu. SPIE, 2020. http://dx.doi.org/10.1117/12.2570681.

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Kaddur, K., F. Tranquart, P. Midoux, C. Pichon, and A. Bouakaz. "8B-3 Transmembrane Extraction of Fluorescent Proteins with Ultrasound and Microbubbles." In 2007 IEEE Ultrasonics Symposium Proceedings. IEEE, 2007. http://dx.doi.org/10.1109/ultsym.2007.170.

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Maetschke, S., M. Gallagher, and M. Boden. "A Comparison of Sequence Kernels for Localization Prediction of Transmembrane Proteins." In 2007 4th Symposium on Computational Intelligence in Bioinformatics and Computational Biology. IEEE, 2007. http://dx.doi.org/10.1109/cibcb.2007.4221246.

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Reports on the topic "Transmembrane proteins"

1

Davis, Ryan W., James A. Brozik, Susan Marie Brozik, Jason M. Cox, Gabriel P. Lopez, Todd A. Barrick, and Adrean Flores. Nanoporous microbead supported bilayers: stability, physical characterization, and incorporation of functional transmembrane proteins. Office of Scientific and Technical Information (OSTI), March 2007. http://dx.doi.org/10.2172/902211.

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Fleming, Karen G. Energetics and Structure Prediction of the Network of Homo- and Hetero-Oligomers Formed by the Transmembrane Domains of the ErbReceptor Family of Proteins. Fort Belvoir, VA: Defense Technical Information Center, June 2006. http://dx.doi.org/10.21236/ada456142.

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Young, Malin M., Kenneth L. Sale, Genetha Anne Gray, and Tamara Gibson Kolda. Optimizing an emperical scoring function for transmembrane protein structure determination. Office of Scientific and Technical Information (OSTI), October 2003. http://dx.doi.org/10.2172/918349.

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Bleecker, A. B. Biochemical and molecular analysis of a transmembrane protein kinase from Arabidopsis thaliana. Office of Scientific and Technical Information (OSTI), January 1992. http://dx.doi.org/10.2172/5176465.

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Bleecker, A. B. Biochemical and molecular analysis of a transmembrane protein kinase from Arabidopsis thaliana. Office of Scientific and Technical Information (OSTI), January 1993. http://dx.doi.org/10.2172/6592071.

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Bleecker, A. B. Biochemical and molecular analysis of a transmembrane protein kinase from Arabidopsis thaliana. Progress report. Office of Scientific and Technical Information (OSTI), July 1992. http://dx.doi.org/10.2172/10151309.

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Bleecker, A. B. Biochemical and molecular analysis of a transmembrane protein kinase from Arabidopsis thaliana. Progress report, January 1993. Office of Scientific and Technical Information (OSTI), June 1993. http://dx.doi.org/10.2172/10151596.

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