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Journal articles on the topic 'Transmembrane proteins'

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Published: 4 June 2021
Last updated: 1 February 2022

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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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2

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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3

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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4

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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5

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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6

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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7

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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8

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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9

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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10

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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11

Nicolas, F., M. C. Tiveron, J. Davoust, and H. Reggio. "GPI membrane anchor is determinant in intracellular accumulation of apical plasma membrane proteins in the non-polarized human colon cancer cell line HT-29 18." Journal of Cell Science 107, no. 10 (October 1, 1994): 2679–89. http://dx.doi.org/10.1242/jcs.107.10.2679.

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We have compared the intracellular localization of plasma membrane proteins anchored either with a transmembrane segment or with a glycosylphosphatidylinositol moiety to estimate the effects of membrane anchor on protein segregation in the non-polarized form of the human colon cancer cell line HT-29 18. We have monitored two endogenous proteins: the carcinoembryonic antigen, a glycosylphosphatidylinositol protein and the transmembrane protein dipeptidyl peptidase IV, and two transfected proteins: the glycosylphosphatidylinositol protein Thy-1 and an engineered transmembrane form of Thy-1. Using immunocytochemistry on ultra-thin cryosections and confocal microscopy, we detected a carcinoembryonic antigen-rich vesicular compartment, excluding classical pre-lysosomal and lysosomal markers such as mannose 6-phosphate receptor, lamp-1 and cathepsin D. This compartment, where carcinoembryonic antigen accumulated, excluded the transmembrane protein dipeptidyl peptidase IV and was reduced during the polarization of the cells. Moreover, the glycosylphosphatidylinositol form of Thy-1 also accumulated in the carcinoembryonic antigen-rich compartment whereas the transmembrane form of Thy-1 was excluded. We proposed that, in the non-polarized HT-29 18 cells, accumulation of glycosylphosphatidylinositol proteins independently of transmembrane proteins reveals different intracellular fates for proteins according to their anchor in the plasma membrane.
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12

XU, EMILY W., PAUL KEARNEY, and DANIEL G. BROWN. "THE USE OF FUNCTIONAL DOMAINS TO IMPROVE TRANSMEMBRANE PROTEIN TOPOLOGY PREDICTION." Journal of Bioinformatics and Computational Biology 04, no. 01 (February 2006): 109–23. http://dx.doi.org/10.1142/s0219720006001722.

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Transmembrane proteins affect vital cellular functions and pathogenesis, and are a focus of drug design. It is difficult to obtain diffraction quality crystals to study transmembrane protein structure. Computational tools for transmembrane protein topology prediction fill in the gap between the abundance of transmembrane proteins and the scarcity of known membrane protein structures. Their prediction accuracy is still inadequate: TMHMM, the current state-of-the-art method, has less than 52% accuracy in topology prediction on one set of transmembrane proteins of known topology. Based on the observation that there are functional domains that occur preferentially internal or external to the membrane, we have extended the model of TMHMM to incorporate functional domains, using a probabilistic approach originally developed for computational gene finding. Our extension is better than TMHMM in predicting the topology of transmembrane proteins. As prediction of functional domain improves, our system's prediction accuracy will likely improve as well.
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13

O. Orgel, Joseph P. "Surface-Active Helices in Transmembrane Proteins." Current Protein & Peptide Science 7, no. 6 (December 1, 2006): 553–60. http://dx.doi.org/10.2174/138920306779025666.

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14

Harrington, Susan E., and Nir Ben-Tal. "Structural Determinants of Transmembrane Helical Proteins." Structure 17, no. 8 (August 2009): 1092–103. http://dx.doi.org/10.1016/j.str.2009.06.009.

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15

Mosser, G. "Two-dimensional crystallogenesis of transmembrane proteins." Micron 32, no. 5 (July 2001): 517–40. http://dx.doi.org/10.1016/s0968-4328(00)00047-0.

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16

YAMAMOTO, Shota, and Shin MORISHITA. "Natural vibration analysis of transmembrane proteins." Proceedings of the Bioengineering Conference Annual Meeting of BED/JSME 2018.30 (2018): 2B10. http://dx.doi.org/10.1299/jsmebio.2018.30.2b10.

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17

Saier, Milton H. "Families of transmembrane sugar transport proteins." Molecular Microbiology 35, no. 4 (February 2000): 699–710. http://dx.doi.org/10.1046/j.1365-2958.2000.01759.x.

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18

Schmidt, Ulrich, and Matthias Weiss. "Anomalous diffusion of oligomerized transmembrane proteins." Journal of Chemical Physics 134, no. 16 (April 28, 2011): 165101. http://dx.doi.org/10.1063/1.3582336.

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19

Kulandaisamy, A., S. Binny Priya, R. Sakthivel, Svetlana Tarnovskaya, Ilya Bizin, Peter Hönigschmid, Dmitrij Frishman, and M. Michael Gromiha. "MutHTP: mutations in human transmembrane proteins." Bioinformatics 34, no. 13 (February 1, 2018): 2325–26. http://dx.doi.org/10.1093/bioinformatics/bty054.

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20

Cserzö, M., J. M. Bernassau, I. Simon, and B. Maigret. "New Alignment Strategy for Transmembrane Proteins." Journal of Molecular Biology 243, no. 3 (October 1994): 388–96. http://dx.doi.org/10.1006/jmbi.1994.1666.

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21

Saier, Jr., M. H. "Families of Proteins Forming Transmembrane Channels." Journal of Membrane Biology 175, no. 3 (June 1, 2000): 165–80. http://dx.doi.org/10.1007/s002320001065.

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22

Saier,, M. H. "Families of Proteins Forming Transmembrane Channels." Journal of Membrane Biology 175, no. 3 (June 2000): 165–80. http://dx.doi.org/10.1007/s00232001065.

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23

Inouye, Masayori. "Signaling by Transmembrane Proteins Shifts Gears." Cell 126, no. 5 (September 2006): 829–31. http://dx.doi.org/10.1016/j.cell.2006.08.024.

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24

Jones, D. T., and W. R. Taylor. "Towards structural genomics for transmembrane proteins." Biochemical Society Transactions 26, no. 3 (August 1, 1998): 429–38. http://dx.doi.org/10.1042/bst0260429.

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25

Hamasaki, Naotaka, Hiroyuki Kuma, Kazuhisa Ota, Masao Sakaguchi, and Katsuyoshi Mihara. "A new concept in polytopic membrane proteins following from the study of band 3 protein." Biochemistry and Cell Biology 76, no. 5 (October 1, 1998): 729–33. http://dx.doi.org/10.1139/o98-085.

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In the present communication, we introduce a novel concept in multispanning polytopic membrane proteins revealed by the study of the band 3 protein. The transmembrane domain of such proteins can be divided into three categories, that is, hydrophilic loops connecting transmembrane peptides (category 1), portions embedded by peptide-peptide interactions (category 2), and portions embedded by peptide-lipid interactions (category 3). Category 2 peptides of polytopic membrane proteins were found to stably reside in the lipid bilayer without peptide-lipid interactions that had been thought to be essential for transmembrane segments. Category 3 peptides are equivalent to single-spanning segments of bitopic membrane proteins. Three different experiments, namely proteolytic digestion, chemical modification of the band 3 protein, and cell free transcription and translation, were used to categorize the transmembrane peptides.Key words: band 3 protein, transmembrane (TM) peptide, classification of TM, category 2-TM, polytopic membrane protein.
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26

Talbert-Slagle, Kristina, Sara Marlatt, Francisco N. Barrera, Ekta Khurana, Joanne Oates, Mark Gerstein, Donald M. Engelman, Ann M. Dixon, and Daniel DiMaio. "Artificial Transmembrane Oncoproteins Smaller than the Bovine Papillomavirus E5 Protein Redefine Sequence Requirements for Activation of the Platelet-Derived Growth Factor β Receptor." Journal of Virology 83, no. 19 (July 15, 2009): 9773–85. http://dx.doi.org/10.1128/jvi.00946-09.

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ABSTRACT The bovine papillomavirus E5 protein (BPV E5) is a 44-amino-acid homodimeric transmembrane protein that binds directly to the transmembrane domain of the platelet-derived growth factor (PDGF) β receptor and induces ligand-independent receptor activation. Three specific features of BPV E5 are considered important for its ability to activate the PDGF β receptor and transform mouse fibroblasts: a pair of C-terminal cysteines, a transmembrane glutamine, and a juxtamembrane aspartic acid. By using a new genetic technique to screen libraries expressing artificial transmembrane proteins for activators of the PDGF β receptor, we isolated much smaller proteins, from 32 to 36 residues, that lack all three of these features yet still dimerize noncovalently, specifically activate the PDGF β receptor via its transmembrane domain, and transform cells efficiently. The primary amino acid sequence of BPV E5 is virtually unrecognizable in some of these proteins, which share as few as seven consecutive amino acids with the viral protein. Thus, small artificial proteins that bear little resemblance to a viral oncoprotein can nevertheless productively interact with the same cellular target. We speculate that similar cellular proteins may exist but have been overlooked due to their small size and hydrophobicity.
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27

Yu, Bin, Xian-hua Meng, Hai-jun Liu, and Yi-fei Wang. "Prediction of transmembrane helical segments in transmembrane proteins based on wavelet transform." Journal of Shanghai University (English Edition) 10, no. 4 (August 2006): 308–18. http://dx.doi.org/10.1007/s11741-006-0006-9.

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28

Valavanis, Ioannis K., Pantelis G. Bagos, and Ioannis Z. Emiris. "-Barrel transmembrane proteins: Geometric modelling, detection of transmembrane region, and structural properties." Computational Biology and Chemistry 30, no. 6 (December 2006): 416–24. http://dx.doi.org/10.1016/j.compbiolchem.2006.09.001.

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29

Martínez-Garay, Carlos A., M. Angeles Juanes, J. Carlos Igual, Ismael Mingarro, and M. Carmen Bañó. "A transmembrane serine residue in the Rot1 protein is essential for yeast cell viability." Biochemical Journal 458, no. 2 (February 14, 2014): 239–49. http://dx.doi.org/10.1042/bj20131306.

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Polar residues present in transmembrane helices influence the folding or association of membrane proteins. Rot1 is a membrane protein with a single transmembrane domain. Replacement of a serine residue in the transmembrane domain by different amino acids precluded protein function, causing cell death.
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30

Andreu-Fernández, Vicente, Mónica Sancho, Ainhoa Genovés, Estefanía Lucendo, Franziska Todt, Joachim Lauterwasser, Kathrin Funk, et al. "Bax transmembrane domain interacts with prosurvival Bcl-2 proteins in biological membranes." Proceedings of the National Academy of Sciences 114, no. 2 (December 27, 2016): 310–15. http://dx.doi.org/10.1073/pnas.1612322114.

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The Bcl-2 (B-cell lymphoma 2) protein Bax (Bcl-2 associated X, apoptosis regulator) can commit cells to apoptosis via outer mitochondrial membrane permeabilization. Bax activity is controlled in healthy cells by prosurvival Bcl-2 proteins. C-terminal Bax transmembrane domain interactions were implicated recently in Bax pore formation. Here, we show that the isolated transmembrane domains of Bax, Bcl-xL (B-cell lymphoma-extra large), and Bcl-2 can mediate interactions between Bax and prosurvival proteins inside the membrane in the absence of apoptotic stimuli. Bcl-2 protein transmembrane domains specifically homooligomerize and heterooligomerize in bacterial and mitochondrial membranes. Their interactions participate in the regulation of Bcl-2 proteins, thus modulating apoptotic activity. Our results suggest that interactions between the transmembrane domains of Bax and antiapoptotic Bcl-2 proteins represent a previously unappreciated level of apoptosis regulation.
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31

Mayol, Eduardo, Mercedes Campillo, Arnau Cordomí, and Mireia Olivella. "Inter-residue interactions in alpha-helical transmembrane proteins." Bioinformatics 35, no. 15 (December 19, 2018): 2578–84. http://dx.doi.org/10.1093/bioinformatics/bty978.

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Abstract Motivation The number of available membrane protein structures has markedly increased in the last years and, in parallel, the reliability of the methods to detect transmembrane (TM) segments. In the present report, we characterized inter-residue interactions in α-helical membrane proteins using a dataset of 3462 TM helices from 430 proteins. This is by far the largest analysis published to date. Results Our analysis of residue–residue interactions in TM segments of membrane proteins shows that almost all interactions involve aliphatic residues and Phe. There is lack of polar–polar, polar–charged and charged–charged interactions except for those between Thr or Ser sidechains and the backbone carbonyl of aliphatic and Phe residues. The results are discussed in the context of the preferences of amino acids to be in the protein core or exposed to the lipid bilayer and to occupy specific positions along the TM segment. Comparison to datasets of β-barrel membrane proteins and of α-helical globular proteins unveils the specific patterns of interactions and residue composition characteristic of α-helical membrane proteins that are the clue to understanding their structure. Availability and implementation Results data and datasets used are available at http://lmc.uab.cat/TMalphaDB/interactions.php. Supplementary information Supplementary data are available at Bioinformatics online.
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32

Yang, F. Y., Y. G. Huang, and Y. P. Tu. "Transmembrane Ca2+ gradient and function of membrane proteins." Bioscience Reports 15, no. 5 (October 1, 1995): 351–64. http://dx.doi.org/10.1007/bf01788367.

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This review will focus on the recent advance in the study of effect of transmembrane Ca2+ gradient on the function of membrane proteins. It consits of two parts: 1. Transmembrane Ca2+ gradient and sarcoplasmic reticulum Ca2+-ATPase; 2. Effect of transmembrane Ca2+ gradient on the components and coupling of cAMP signal transduction pathway. The results obtained indicate that a proper transmembrane Ca2+ gradient may play an important role in modulating the conformation and activity of SR Ca2+-ATPase and the function of membrane proteins involved in the cAMP signal transduction by mediating the physical state change of the membrane phospholipids.
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33

Serdiuk, Tetiana, Stefania A. Mari, and Daniel J. Müller. "Pull-and-Paste of Single Transmembrane Proteins." Nano Letters 17, no. 7 (June 23, 2017): 4478–88. http://dx.doi.org/10.1021/acs.nanolett.7b01844.

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34

Madsen, Jesper J., Anton V. Sinitskiy, Jianing Li, and Gregory A. Voth. "Highly Coarse-Grained Representations of Transmembrane Proteins." Journal of Chemical Theory and Computation 13, no. 2 (January 18, 2017): 935–44. http://dx.doi.org/10.1021/acs.jctc.6b01076.

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35

Truex, Nicholas L., and James S. Nowick. "Transmembrane Proteins: Amyloids Hidden in Plain Sight?" Biochemistry 56, no. 36 (August 30, 2017): 4735–36. http://dx.doi.org/10.1021/acs.biochem.7b00758.

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36

Richards, Sabine A., Christian Stutzer, Anna-Mari Bosman, and Christine Maritz-Olivier. "Transmembrane proteins – Mining the cattle tick transcriptome." Ticks and Tick-borne Diseases 6, no. 6 (September 2015): 695–710. http://dx.doi.org/10.1016/j.ttbdis.2015.06.002.

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37

Offermanns, S. "G-proteins as transducers in transmembrane signalling." Progress in Biophysics and Molecular Biology 83, no. 2 (October 2003): 101–30. http://dx.doi.org/10.1016/s0079-6107(03)00052-x.

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38

Roumia, Ahmed F., Margarita C. Theodoropoulou, Konstantinos D. Tsirigos, Henrik Nielsen, and Pantelis G. Bagos. "Landscape of Eukaryotic Transmembrane Beta Barrel Proteins." Journal of Proteome Research 19, no. 3 (February 1, 2020): 1209–21. http://dx.doi.org/10.1021/acs.jproteome.9b00740.

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39

Kohno, Kenji. "How Transmembrane Proteins Sense Endoplasmic Reticulum Stress." Antioxidants & Redox Signaling 9, no. 12 (December 2007): 2295–304. http://dx.doi.org/10.1089/ars.2007.1819.

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40

Renthal, Robert. "An Unfolding Story of Helical Transmembrane Proteins†." Biochemistry 45, no. 49 (December 2006): 14559–66. http://dx.doi.org/10.1021/bi0620454.

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41

Casey, P. J., M. P. Graziano, M. Freissmuth, and A. G. Gilman. "Role of G Proteins in Transmembrane Signaling." Cold Spring Harbor Symposia on Quantitative Biology 53 (January 1, 1988): 203–8. http://dx.doi.org/10.1101/sqb.1988.053.01.026.

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42

Hickford, Danielle, Stephen Frankenberg, Geoff Shaw, and Marilyn B. Renfree. "Evolution of vertebrate interferon inducible transmembrane proteins." BMC Genomics 13, no. 1 (2012): 155. http://dx.doi.org/10.1186/1471-2164-13-155.

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43

Waldispühl, Jérôme, Charles W. O'Donnell, Srinivas Devadas, Peter Clote, and Bonnie Berger. "Modeling ensembles of transmembrane β-barrel proteins." Proteins: Structure, Function, and Bioinformatics 71, no. 3 (November 14, 2007): 1097–112. http://dx.doi.org/10.1002/prot.21788.

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44

Renthal, Robert. "Buried water molecules in helical transmembrane proteins." Protein Science 17, no. 2 (February 2008): 293–98. http://dx.doi.org/10.1110/ps.073237508.

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45

Stevens, Timothy J., and Isaiah T. Arkin. "Substitution rates in α-helical transmembrane proteins." Protein Science 10, no. 12 (December 31, 2008): 2507–17. http://dx.doi.org/10.1110/ps.10501.

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46

Lu, Peilong, Duyoung Min, Frank DiMaio, Kathy Y. Wei, Michael D. Vahey, Scott E. Boyken, Zibo Chen, et al. "Accurate computational design of multipass transmembrane proteins." Science 359, no. 6379 (March 1, 2018): 1042–46. http://dx.doi.org/10.1126/science.aaq1739.

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47

Stevens, T. J. "Substitution rates in alpha-helical transmembrane proteins." Protein Science 10, no. 12 (November 19, 2001): 2507–17. http://dx.doi.org/10.1110/ps.ps.10501.

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48

Lio, P., and M. Vannucci. "Wavelet change-point prediction of transmembrane proteins." Bioinformatics 16, no. 4 (April 1, 2000): 376–82. http://dx.doi.org/10.1093/bioinformatics/16.4.376.

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49

Hořejší, Václav, Weiguo Zhang, and Burkhart Schraven. "Transmembrane adaptor proteins: organizers of immunoreceptor signalling." Nature Reviews Immunology 4, no. 8 (August 2004): 603–16. http://dx.doi.org/10.1038/nri1414.

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50

Bahrami, Amir Houshang, and Mir Abbas Jalali. "Vesicle deformations by clusters of transmembrane proteins." Journal of Chemical Physics 134, no. 8 (February 28, 2011): 085106. http://dx.doi.org/10.1063/1.3556669.

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