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Journal articles on the topic 'Beta barrel membrane proteins'

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Author: Grafiati

Published: 10 December 2022

Last updated: 28 January 2023

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1

Solan, Ron, Joana Pereira, Andrei N. Lupas, Rachel Kolodny, and Nir Ben-Tal. "Gram-negative outer-membrane proteins with multiple β-barrel domains." Proceedings of the National Academy of Sciences 118, no. 31 (July 30, 2021): e2104059118. http://dx.doi.org/10.1073/pnas.2104059118.

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Outer-membrane beta barrels (OMBBs) are found in the outer membrane of gram-negative bacteria and eukaryotic organelles. OMBBs fold as antiparallel β-sheets that close onto themselves, forming pores that traverse the membrane. Currently known structures include only one barrel, of 8 to 36 strands, per chain. The lack of multi-OMBB chains is surprising, as most OMBBs form oligomers, and some function only in this state. Using a combination of sensitive sequence comparison methods and coevolutionary analysis tools, we identify many proteins combining multiple beta barrels within a single chain; combinations that include eight-stranded barrels prevail. These multibarrels seem to be the result of independent, lineage-specific fusion and amplification events. The absence of multibarrels that are universally conserved in bacteria with an outer membrane, coupled with their frequent de novo genesis, suggests that their functions are not essential but rather beneficial in specific environments. Adjacent barrels of complementary function within the same chain may allow for functions beyond those of the individual barrels.

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2

Miles, A. J., and B. A. Wallace. "Circular dichroism spectroscopy of membrane proteins." Chemical Society Reviews 45, no. 18 (2016): 4859–72. http://dx.doi.org/10.1039/c5cs00084j.

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3

Noinaj, Nicholas, Adam Kuszak, Curtis Balusek, JC Gumbart, Petra Lukacik, Hoshing Chang, Nicole Easley, Trevor Lithgow, and Susan Buchanan. "The role of BamA in the biogenesis of beta-barrel membrane proteins." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C578. http://dx.doi.org/10.1107/s2053273314094212.

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Beta-barrel membrane proteins are essential for nutrient import, signaling, motility, and survival. In Gram-negative bacteria, the beta-barrel assembly machinery (BAM) complex is responsible for the biogenesis of beta-barrel outer membrane proteins (OMPs), with homologous complexes found in mitochondria and chloroplasts. Despite their essential roles, exactly how these OMPs are formed remains unknown. The BAM complex consists of a central and essential component called BamA (an OMP itself) and four lipoproteins called BamB-E. While the structure of the lipoproteins have been reported, the structure of full length BamA has been elusive. Recently though, we described the structure of BamA from two species of bacteria: Neisseria gonorrhoeae and Haemophilus ducreyi. BamA consists of a large periplasmic domain attached to a 16-strand transmembrane beta-barrel domain. Together, our crystal structures and molecule dynamics (MD) simulations revealed several structural features which gave clues to the mechanism by which BamA catalyzes beta-barrel assembly. The first is that the interior cavity is accessible in one BamA structure and conformationally closed in the other. Second, an exterior rim of the beta-barrel has a distinctly narrowed hydrophobic surface, locally destabilizing the outer membrane. Third, the beta-barrel can undergo lateral opening, suggesting a route from the interior cavity in BamA into the outer membrane. And fourth, a surface exposed exit pore positioned above the lateral opening site which may play a role in the biogenesis of extracellular loops. In this presentation, the crystal structures and MD simulations of BamA will be presented along with our work looking at the role of these four structural features in the role of BamA within the BAM complex.

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4

Tian, Wei, Hammad Naveed, and Jie Liang. "Improving 3D Structure Prediction of Beta-Barrel Membrane Proteins." Biophysical Journal 112, no. 3 (February 2017): 55a. http://dx.doi.org/10.1016/j.bpj.2016.11.333.

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5

Lessen, Henry J., Patrick Fleming, Karen G. Fleming, and Alexander J. Sodt. "Transmembrane Beta-Barrel Proteins Rigidify the Bacterial Outer Membrane." Biophysical Journal 116, no. 3 (February 2019): 327a. http://dx.doi.org/10.1016/j.bpj.2018.11.1774.

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6

Roterman, Irena, Katarzyna Stapor, Piotr Fabian, and Leszek Konieczny. "The Functional Significance of Hydrophobic Residue Distribution in Bacterial Beta-Barrel Transmembrane Proteins." Membranes 11, no. 8 (July 30, 2021): 580. http://dx.doi.org/10.3390/membranes11080580.

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β-barrel membrane proteins have several important biological functions, including transporting water and solutes across the membrane. They are active in the highly hydrophobic environment of the lipid membrane, as opposed to soluble proteins, which function in a more polar, aqueous environment. Globular soluble proteins typically have a hydrophobic core and a polar surface that interacts favorably with water. In the fuzzy oil drop (FOD) model, this distribution is represented by the 3D Gauss function (3DG). In contrast, membrane proteins expose hydrophobic residues on the surface, and, in the case of ion channels, the polar residues face inwards towards a central pore. The distribution of hydrophobic residues in membrane proteins can be characterized by means of 1–3DG, a complementary 3D Gauss function. Such an analysis was carried out on the transmembrane proteins of bacteria, which, despite the considerable similarities of their super-secondary structure (β-barrel), have highly differentiated properties in terms of stabilization based on hydrophobic interactions. The biological activity and substrate specificity of these proteins are determined by the distribution of the polar and nonpolar amino acids. The present analysis allowed us to compare the ways in which the different proteins interact with antibiotics and helped us understand their relative importance in the development of the resistance mechanism. We showed that beta barrel membrane proteins with a hydrophobic core interact less strongly with the molecules they transport.

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7

Kazemian, Hassan B., and Cedric Maxime Grimaldi. "Cascading classifier application for topology prediction of transmembrane beta-barrel proteins." Journal of Bioinformatics and Computational Biology 18, no. 06 (October 15, 2020): 2050034. http://dx.doi.org/10.1142/s0219720020500341.

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Membrane proteins are a major focus for new drug discovery. Transmembrane beta-barrel (TMB) proteins play key roles in the translocation machinery, pore formation, membrane anchoring and ion exchange. Given their key roles and the difficulty in membrane protein structure determination, the use of computational modeling is essential. This paper focuses on the topology prediction of TMB proteins. In the field of bioinformatics, many years of research has been spent on the topology prediction of transmembrane alpha-helices. The efforts to TMB proteins topology prediction have been overshadowed and the prediction accuracy could be improved with further research. Various methodologies have been developed in the past for the prediction of TMB protein topology, however, the use of cascading classifier has never been fully explored. This research presents a novel approach to TMB topology prediction with the use of a cascading classifier. The MATLAB computer simulation results show that the proposed methodology predicts TMB proteins topologies with high accuracy for randomly selected proteins. By using the cascading classifier approach, the best overall accuracy is 76.3% with a precision of 0.831 and recall or probability of detection of 0.799 for TMB topology prediction. The accuracy of 76.3% is achieved using a two-layers cascading classifier.

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8

Jain, Sumita, and Marcia B. Goldberg. "Requirement for YaeT in the Outer Membrane Assembly of Autotransporter Proteins." Journal of Bacteriology 189, no. 14 (May 18, 2007): 5393–98. http://dx.doi.org/10.1128/jb.00228-07.

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ABSTRACT Autotransporters constitute the largest group of secreted proteins in gram-negative bacteria. Autotransporter secretion involves the insertion of a carboxy-terminal beta barrel into and the translocation of an amino-terminal domain across the outer membrane. Here, we demonstrate that secretion of autotransporters from several organisms requires the outer membrane assembly factor YaeT.

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9

Naveed, Hammad, and Jie Liang. "Weakly Stable Regions and Protein-Protein Interactions in Beta-Barrel Membrane Proteins." Current Pharmaceutical Design 20, no. 8 (March 31, 2014): 1268–73. http://dx.doi.org/10.2174/13816128113199990071.

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10

Columbus, Linda, Daniel A. Fox, and Ryan H. Lo. "Strategies for the Solution NMR Structure Determination of Beta-Barrel Membrane Proteins." Biophysical Journal 102, no. 3 (January 2012): 422a—423a. http://dx.doi.org/10.1016/j.bpj.2011.11.2311.

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11

Fischbarg, J., and J. C. Vera. "Multifunctional transporter models: lessons from the transport of water, sugars, and ring compounds by GLUTs." American Journal of Physiology-Cell Physiology 268, no. 5 (May 1, 1995): C1077—C1089. http://dx.doi.org/10.1152/ajpcell.1995.268.5.c1077.

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Facilitative glucose transporters (GLUTs) have recently been shown to be multifunctional, transporting substrates other than sugars, such as water and ring compounds as large as nitrobenzene-diazol-aminoglucose. Other membrane proteins, including transporters and cystic fibrosis transmembrane conductance regulator, have also revealed a finite permeability to water. We compare the alpha-helical and beta-barrel models for the structure of GLUTs, discuss recent evidence, and argue that a beta-barrel fold explains it better. We show a model for GLUTs consisting of a relatively rigid beta-barrel translocation unit ("channel") of diameter ample enough to allow permeation of the above substrates (approximately 20 A) but gated shut by mobile loops at both ends. Such gates would open only after aromatic interactions would lead to binding of the ring substrates for GLUTs; water would, however, traverse crevices in the closed gates. Using the insights gained from GLUTs, we propose that other transporters may share with GLUTs the motif of a beta-barrel channel and would be permeable to water due to the presence of such channels together with similarly behaving gates.

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12

McClean, Siobhan. "Eight Stranded β -Barrel and Related Outer Membrane Proteins: Role in Bacterial Pathogenesis." Protein & Peptide Letters 19, no. 10 (September 1, 2012): 1013–25. http://dx.doi.org/10.2174/092986612802762688.

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13

Rigel, Nathan W., and Thomas J. Silhavy. "Making a beta-barrel: assembly of outer membrane proteins in Gram-negative bacteria." Current Opinion in Microbiology 15, no. 2 (April 2012): 189–93. http://dx.doi.org/10.1016/j.mib.2011.12.007.

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14

Tsirigos, Konstantinos D., Arne Elofsson, and Pantelis G. Bagos. "PRED-TMBB2: improved topology prediction and detection of beta-barrel outer membrane proteins." Bioinformatics 32, no. 17 (September 1, 2016): i665—i671. http://dx.doi.org/10.1093/bioinformatics/btw444.

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15

Lithgow, Trevor. "The Assembly of Beta-Barrel Proteins into Bacterial Outer Membranes." Biophysical Journal 112, no. 3 (February 2017): 329a. http://dx.doi.org/10.1016/j.bpj.2016.11.1781.

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16

Tian, Wei, Meishan Lin, Hammad Naveed, and Jie Liang. "Efficient computation of transfer free energies of amino acids in beta-barrel membrane proteins." Bioinformatics 33, no. 11 (January 31, 2017): 1664–71. http://dx.doi.org/10.1093/bioinformatics/btx053.

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17

Naveed, Hammad, Ronald Jackups, and Jie Liang. "Accurate Ab Initio Prediction of Three Dimensional Structures of Beta-Barrel Membrane Proteins from Sequences." Biophysical Journal 98, no. 3 (January 2010): 644a. http://dx.doi.org/10.1016/j.bpj.2009.12.3529.

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18

Jacoboni, I. "Prediction of the transmembrane regions of beta-barrel membrane proteins with a neural network-based predictor." Protein Science 10, no. 4 (April 1, 2001): 779–87. http://dx.doi.org/10.1110/ps.37201.

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19

Pajón, R., D. Yero, A. Lage, A. Llanes, and C. J. Borroto. "Computational identification of beta-barrel outer-membrane proteins in Mycobacterium tuberculosis predicted proteomes as putative vaccine candidates." Tuberculosis 86, no. 3-4 (May 2006): 290–302. http://dx.doi.org/10.1016/j.tube.2006.01.005.

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20

Mizianty, Marcin J., and Lukasz Kurgan. "Improved identification of outer membrane beta barrel proteins using primary sequence, predicted secondary structure, and evolutionary information." Proteins: Structure, Function, and Bioinformatics 79, no. 1 (November 9, 2010): 294–303. http://dx.doi.org/10.1002/prot.22882.

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21

Crowet, Jean, Mehmet Nasir, Nicolas Dony, Antoine Deschamps, Vincent Stroobant, Pierre Morsomme, Magali Deleu, Patrice Soumillion, and Laurence Lins. "Insight into the Self-Assembling Properties of Peptergents: A Molecular Dynamics Simulation Study." International Journal of Molecular Sciences 19, no. 9 (September 14, 2018): 2772. http://dx.doi.org/10.3390/ijms19092772.

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By manipulating the various physicochemical properties of amino acids, the design of peptides with specific self-assembling properties has been emerging for more than a decade. In this context, short peptides possessing detergent properties (so-called “peptergents”) have been developed to self-assemble into well-ordered nanostructures that can stabilize membrane proteins for crystallization. In this study, the peptide with “peptergency” properties, called ADA8 and extensively described by Tao et al., is studied by molecular dynamic simulations for its self-assembling properties in different conditions. In water, it spontaneously forms beta sheets with a β barrel-like structure. We next simulated the interaction of this peptide with a membrane protein, the bacteriorhodopsin, in the presence or absence of a micelle of dodecylphosphocholine. According to the literature, the peptergent ADA8 is thought to generate a belt of β structures around the hydrophobic helical domain that could help stabilize purified membrane proteins. Molecular dynamic simulations are here used to image this mechanism and provide further molecular details for the replacement of detergent molecules around the protein. In addition, we generalized this behavior by designing an amphipathic peptide with beta propensity, which was called ABZ12. Both peptides are able to surround the membrane protein and displace surfactant molecules. To our best knowledge, this is the first molecular mechanism proposed for “peptergency”.

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22

Burgess, Nancy K., and Karen G. Fleming. "Beta-barrel Proteins that Reside in the E. coli Outer Membrane In Vivo Demonstrate Varied Folding Behavior In Vitro." Biophysical Journal 96, no. 3 (February 2009): 79a. http://dx.doi.org/10.1016/j.bpj.2008.12.308.

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23

Belcher Dufrisne, Meagan, and Linda M. Columbus. "Strategy for optimized expression of beta-barrel proteins from pathogenic Gram-negative bacteria to the outer membrane of Escherichia coli." Biophysical Journal 121, no. 3 (February 2022): 470a. http://dx.doi.org/10.1016/j.bpj.2021.11.432.

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24

Konovalova, Anna, and Thomas J. Silhavy. "Outer membrane lipoprotein biogenesis: Lol is not the end." Philosophical Transactions of the Royal Society B: Biological Sciences 370, no. 1679 (October 5, 2015): 20150030. http://dx.doi.org/10.1098/rstb.2015.0030.

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Bacterial lipoproteins are lipid-anchored proteins that contain acyl groups covalently attached to the N-terminal cysteine residue of the mature protein. Lipoproteins are synthesized in precursor form with an N-terminal signal sequence (SS) that targets translocation across the cytoplasmic or inner membrane (IM). Lipid modification and SS processing take place at the periplasmic face of the IM. Outer membrane (OM) lipoproteins take the localization of lipoproteins (Lol) export pathway, which ends with the insertion of the N-terminal lipid moiety into the inner leaflet of the OM. For many lipoproteins, the biogenesis pathway ends here. We provide examples of lipoproteins that adopt complex topologies in the OM that include transmembrane and surface-exposed domains. Biogenesis of such lipoproteins requires additional steps beyond the Lol pathway. In at least one case, lipoprotein sequences reach the cell surface by being threaded through the lumen of a beta-barrel protein in an assembly reaction that requires the heteropentomeric Bam complex. The inability to predict surface exposure reinforces the importance of experimental verification of lipoprotein topology and we will discuss some of the methods used to study OM protein topology.

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25

Narita, S. i., C. Masui, T. Suzuki, N. Dohmae, and Y. Akiyama. "Protease homolog BepA (YfgC) promotes assembly and degradation of -barrel membrane proteins in Escherichia coli." Proceedings of the National Academy of Sciences 110, no. 38 (September 3, 2013): E3612—E3621. http://dx.doi.org/10.1073/pnas.1312012110.

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26

Ackermann, Nikolaus, Maximilian Tiller, Gisela Anding, Andreas Roggenkamp, and Jürgen Heesemann. "Contribution of Trimeric Autotransporter C-Terminal Domains of Oligomeric Coiled-Coil Adhesin (Oca) Family Members YadA, UspA1, EibA, and Hia to Translocation of the YadA Passenger Domain and Virulence of Yersinia enterocolitica." Journal of Bacteriology 190, no. 14 (May 16, 2008): 5031–43. http://dx.doi.org/10.1128/jb.00161-08.

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ABSTRACT The Oca family is a novel class of autotransporter-adhesins with highest structural similarity in their C-terminal transmembrane region, which supposedly builds a beta-barrel pore in the outer membrane (OM). The prototype of the Oca family is YadA, an adhesin of Yersinia enterocolitica and Yersinia pseudotuberculosis. YadA forms a homotrimeric lollipop-like structure on the bacterial surface. The C-terminal regions of three YadA monomers form a barrel in the OM and translocate the trimeric N-terminal passenger domain, consisting of stalk, neck, and head region to the exterior. To elucidate the structural and functional role of the C-terminal translocator domain (TLD) and to assess its promiscuous capability with respect to transport of related passenger domains, we constructed chimeric YadA proteins, which consist of the N-terminal YadA passenger domain and C-terminal TLDs of Oca family members UspA1 (Moraxella catarrhalis), EibA (Escherichia coli), and Hia (Haemophilus influenzae). These constructs were expressed in Y. enterocolitica and compared for OM localization, surface exposure, oligomerization, adhesion properties, serum resistance, and mouse virulence. We demonstrate that all chimeric YadA proteins translocated the YadA passenger domain across the OM. Y. enterocolitica strains producing YadA chimeras or wild-type YadA showed comparable binding to collagen and epithelial cells. However, strains producing YadA chimeras were attenuated in serum resistance and mouse virulence. These results demonstrate for the first time that TLDs of Oca proteins of different origin are efficient translocators of the YadA passenger domain and that the cognate TLD of YadA is essential for bacterial survival in human serum and mouse virulence.

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27

Tian, Wei, Jie Liang, and Hammad Naveed. "Improved 3D Structure Prediction of Beta-Barrel Membrane Proteins by using Evolutionary Coupling Constraints, Reduced State Space and an Empirical Potential Function." Biophysical Journal 110, no. 3 (February 2016): 56a. http://dx.doi.org/10.1016/j.bpj.2015.11.370.

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28

Turgeson, Andrew, Lucas Morley, David Giles, and Bradley Harris. "Simulated Docking Predicts Putative Channels for the Transport of Long-Chain Fatty Acids in Vibrio cholerae." Biomolecules 12, no. 9 (September 9, 2022): 1269. http://dx.doi.org/10.3390/biom12091269.

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Fatty acids (FA) play an important role in biological functions, such as membrane homeostasis, metabolism, and as signaling molecules. FadL is the only known protein that uptakes long-chain fatty acids in Gram-negative bacteria, and this uptake has traditionally been thought to be limited to fatty acids up to 18 carbon atoms in length. Recently however, it was found Vibrio cholerae has the ability to uptake fatty acids greater than 18 carbon atoms and this uptake corresponds to bacterial survivability. Using E. coli’s FadL as a template, V. cholerae FadL homologs vc1042, vc1043, and vca0862 have been computationally folded, simulated on an atomistic level using Molecular Dynamics, and docked in silico to analyze the FadL transport channels. For the vc1042 and vc1043 homologs, these transport channels have more structural accommodations for the many rigid unsaturated bonds of long-chain polyunsaturated fatty acids, while the vca0862 homolog was found to lack transport channels within the signature beta barrel of FadL proteins.

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29

Rister, Alexander Bernhard, Thomas Gudermann, and Johann Schredelseker. "E as in Enigma: The Mysterious Role of the Voltage-Dependent Anion Channel Glutamate E73." International Journal of Molecular Sciences 24, no. 1 (December 23, 2022): 269. http://dx.doi.org/10.3390/ijms24010269.

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The voltage-dependent anion channel (VDAC) is the main passageway for ions and metabolites over the outer mitochondrial membrane. It was associated with many physiological processes, including apoptosis and modulation of intracellular Ca2+ signaling. The protein is formed by a barrel of 19 beta-sheets with an N-terminal helix lining the inner pore. Despite its large diameter, the channel can change its selectivity for ions and metabolites based on its open state to regulate transport into and out of mitochondria. VDAC was shown to be regulated by a variety of cellular factors and molecular partners including proteins, lipids and ions. Although the physiological importance of many of these modulatory effects are well described, the binding sites for molecular partners are still largely unknown. The highly symmetrical and sleek structure of the channel makes predictions of functional moieties difficult. However, one residue repeatedly sticks out when reviewing VDAC literature. A glutamate at position 73 (E73) located on the outside of the channel facing the hydrophobic membrane environment was repeatedly proposed to be involved in channel regulation on multiple levels. Here, we review the distinct hypothesized roles of E73 and summarize the open questions around this mysterious residue.

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30

van ‘t Hag, Leonie, Hsin-Hui Shen, Tsung-Wu Lin, Sally L. Gras, Calum J. Drummond, and Charlotte E. Conn. "Effect of Lipid-Based Nanostructure on Protein Encapsulation within the Membrane Bilayer Mimetic Lipidic Cubic Phase Using Transmembrane and Lipo-proteins from the Beta-Barrel Assembly Machinery." Langmuir 32, no. 47 (June 29, 2016): 12442–52. http://dx.doi.org/10.1021/acs.langmuir.6b01800.

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31

Batchelor, Eric, Don Walthers, Linda J. Kenney, and Mark Goulian. "The Escherichia coli CpxA-CpxR Envelope Stress Response System Regulates Expression of the Porins OmpF and OmpC." Journal of Bacteriology 187, no. 16 (August 15, 2005): 5723–31. http://dx.doi.org/10.1128/jb.187.16.5723-5731.2005.

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ABSTRACT We performed transposon mutagenesis of a two-color fluorescent reporter strain to identify new regulators of the porin genes ompF and ompC in Escherichia coli. Screening of colonies by fluorescence microscopy revealed numerous mutants that exhibited interesting patterns of porin expression. One mutant harbored an insertion in the gene encoding the histidine kinase CpxA, the sensor for a two-component signaling system that responds to envelope stress. The cpxA mutant exhibited increased transcription of ompC and a very strong decrease in transcription of ompF under conditions in which acetyl phosphate levels were high. Subsequent genetic analysis revealed that this phenotype is dependent on phosphorylation of the response regulator CpxR and that activation of CpxA in wild-type cells results in similar regulation of porin expression. Using DNase I footprinting, we demonstrated that CpxR binds upstream of both the ompF and ompC promoters. It thus appears that two distinct two-component systems, CpxA-CpxR and EnvZ-OmpR, converge at the porin promoters. Within the context of envelope stress, outer membrane beta-barrel proteins have generally been associated with the sigma E pathway. However, at least for the classical porins OmpF and OmpC, our results show that the Cpx envelope stress response system plays a role in regulating their expression.

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32

Jiao, Yongqin, and Dianne K. Newman. "The pio Operon Is Essential for Phototrophic Fe(II) Oxidation in Rhodopseudomonas palustris TIE-1." Journal of Bacteriology 189, no. 5 (December 22, 2006): 1765–73. http://dx.doi.org/10.1128/jb.00776-06.

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ABSTRACT Phototrophic Fe(II)-oxidizing bacteria couple the oxidation of ferrous iron [Fe(II)] to reductive CO2 fixation by using light energy, but until recently, little has been understood about the molecular basis for this process. Here we report the discovery, with Rhodopseudomonas palustris TIE-1 as a model organism, of a three-gene operon, designated the pio operon (for phototrophic iron oxidation), that is necessary for phototrophic Fe(II) oxidation. The first gene in the operon, pioA, encodes a c-type cytochrome that is upregulated under Fe(II)-grown conditions. PioA contains a signal sequence and shares homology with MtrA, a decaheme c-type cytochrome from Shewanella oneidensis MR-1. The second gene, pioB, encodes a putative outer membrane beta-barrel protein. PioB is a homologue of MtrB from S. oneidensis MR-1. The third gene, pioC, encodes a putative high potential iron sulfur protein (HiPIP) with a twin-arginine translocation (Tat) signal sequence and is similar to the putative Fe(II) oxidoreductase (Iro) from Acidithiobacillus ferrooxidans. Like PioA, PioB and PioC appear to be secreted proteins. Deletion of the pio operon results in loss of Fe(II) oxidation activity and growth on Fe(II). Complementation studies confirm that the phenotype of this mutant is due to loss of the pio genes. Deletion of pioA alone results in loss of almost all Fe(II) oxidation activity; however, deletion of either pioB or pioC alone results in only partial loss of Fe(II) oxidation activity. Together, these results suggest that proteins encoded by the pio operon are essential and specific for phototrophic Fe(II) oxidation in R. palustris TIE-1.

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33

Tamposis, Ioannis A., Konstantinos D. Tsirigos, Margarita C. Theodoropoulou, Panagiota I. Kontou, and Pantelis G. Bagos. "Semi-supervised learning of Hidden Markov Models for biological sequence analysis." Bioinformatics 35, no. 13 (November 16, 2018): 2208–15. http://dx.doi.org/10.1093/bioinformatics/bty910.

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Abstract Motivation Hidden Markov Models (HMMs) are probabilistic models widely used in applications in computational sequence analysis. HMMs are basically unsupervised models. However, in the most important applications, they are trained in a supervised manner. Training examples accompanied by labels corresponding to different classes are given as input and the set of parameters that maximize the joint probability of sequences and labels is estimated. A main problem with this approach is that, in the majority of the cases, labels are hard to find and thus the amount of training data is limited. On the other hand, there are plenty of unclassified (unlabeled) sequences deposited in the public databases that could potentially contribute to the training procedure. This approach is called semi-supervised learning and could be very helpful in many applications. Results We propose here, a method for semi-supervised learning of HMMs that can incorporate labeled, unlabeled and partially labeled data in a straightforward manner. The algorithm is based on a variant of the Expectation-Maximization (EM) algorithm, where the missing labels of the unlabeled or partially labeled data are considered as the missing data. We apply the algorithm to several biological problems, namely, for the prediction of transmembrane protein topology for alpha-helical and beta-barrel membrane proteins and for the prediction of archaeal signal peptides. The results are very promising, since the algorithms presented here can significantly improve the prediction performance of even the top-scoring classifiers. Supplementary information Supplementary data are available at Bioinformatics online.

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34

Schulz, Georg E. "β-Barrel membrane proteins." Current Opinion in Structural Biology 10, no. 4 (August 2000): 443–47. http://dx.doi.org/10.1016/s0959-440x(00)00120-2.

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35

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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36

Asamoto, DeeAnn. "Beta-Barrel Membrane Protein Folding into Nanodiscs." Biophysical Journal 118, no. 3 (February 2020): 366a—367a. http://dx.doi.org/10.1016/j.bpj.2019.11.2103.

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Ishikawa, Daigo, Hayashi Yamamoto, Yasushi Tamura, Kaori Moritoh, and Toshiya Endo. "Two novel proteins in the mitochondrial outer membrane mediate β-barrel protein assembly." Journal of Cell Biology 166, no. 5 (August 23, 2004): 621–27. http://dx.doi.org/10.1083/jcb.200405138.

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Mitochondrial outer and inner membranes contain translocators that achieve protein translocation across and/or insertion into the membranes. Recent evidence has shown that mitochondrial β-barrel protein assembly in the outer membrane requires specific translocator proteins in addition to the components of the general translocator complex in the outer membrane, the TOM40 complex. Here we report two novel mitochondrial outer membrane proteins in yeast, Tom13 and Tom38/Sam35, that mediate assembly of mitochondrial β-barrel proteins, Tom40, and/or porin in the outer membrane. Depletion of Tom13 or Tom38/Sam35 affects assembly pathways of the β-barrel proteins differently, suggesting that they mediate different steps of the complex assembly processes of β-barrel proteins in the outer membrane.

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Ulrich, Thomas, and Doron Rapaport. "Biogenesis of beta-barrel proteins in evolutionary context." International Journal of Medical Microbiology 305, no. 2 (February 2015): 259–64. http://dx.doi.org/10.1016/j.ijmm.2014.12.009.

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Miyoshi, Taro, Yuhei Nagai, Tomoyasu Aizawa, Katsuki Kimura, and Yoshimasa Watanabe. "Proteins causing membrane fouling in membrane bioreactors." Water Science and Technology 72, no. 6 (June 2, 2015): 844–49. http://dx.doi.org/10.2166/wst.2015.282.

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In this study, the details of proteins causing membrane fouling in membrane bioreactors (MBRs) treating real municipal wastewater were investigated. Two separate pilot-scale MBRs were continuously operated under significantly different operating conditions; one MBR was a submerged type whereas the other was a side-stream type. The submerged and side-stream MBRs were operated for 20 and 10 days, respectively. At the end of continuous operation, the foulants were extracted from the fouled membranes. The proteins contained in the extracted foulants were enriched by using the combination of crude concentration with an ultrafiltration membrane and trichloroacetic acid precipitation, and then separated by two-dimensional polyacrylamide gel electrophoresis (2D-PAGE). The N-terminal amino acid sequencing analysis of the proteins which formed intensive spots on the 2D-PAGE gels allowed us to partially identify one protein (OmpA family protein originated from genus Brevundimonas or Riemerella anatipestifer) from the foulant obtained from the submerged MBR, and two proteins (OprD and OprF originated from genus Pseudomonas) from that obtained from the side-stream MBR. Despite the significant difference in operating conditions of the two MBRs, all proteins identified in this study belong to β-barrel protein. These findings strongly suggest the importance of β-barrel proteins in developing membrane fouling in MBRs.

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Rapaport, Doron. "How does the TOM complex mediate insertion of precursor proteins into the mitochondrial outer membrane?" Journal of Cell Biology 171, no. 3 (October 31, 2005): 419–23. http://dx.doi.org/10.1083/jcb.200507147.

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A multisubunit translocase of the outer mitochondrial membrane (TOM complex) mediates both the import of mitochondrial precursor proteins into the internal compartments of the organelle and the insertion of proteins residing in the mitochondrial outer membrane. The proposed β-barrel structure of Tom40, the pore-forming component of the translocase, raises the question of how the apparent uninterrupted β-barrel topology can be compatible with a role of Tom40 in releasing membrane proteins into the lipid core of the bilayer. In this review, I discuss insertion mechanisms of proteins into the outer membrane and present alternative models based on the opening of a multisubunit β-barrel TOM structure or on the interaction of outer membrane precursors with the outer face of the Tom40 β-barrel structure.

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Mohammad, Mohammad M., Khalil R. Howard, and Liviu Movileanu. "Rationale Membrane Protein Design of a Beta-Barrel." Biophysical Journal 102, no. 3 (January 2012): 624a. http://dx.doi.org/10.1016/j.bpj.2011.11.3401.

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42

Gruss, Fabian, Franziska Zaehringer, Roman Jakob, Björn Burmann, Sebastian Hiller, and Timm Maier. "A lateral gate for autotransporter and outer membrane protein assembly." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C1492. http://dx.doi.org/10.1107/s2053273314085076.

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β-barrel proteins are key functional components of the outer membranes of gram-negative bacteria, mitochondria and plastids. They mediate transport across the membrane, act as receptors and are involved in bacterial pathogenicity. Despite their crucial roles, assembly and membrane insertion of β-barrel outer membrane proteins, which are mediated by β-barrel membrane proteins of the OMP85 family, have remained elusive. The crystal structure of the Escherichia coli OMP85 protein TamA [1], which is involved in autotransporter biogenesis, now provides a novel perspective on β-barrel membrane protein assembly. The protein was crystallized in lipidic phase and microseeding was employed to obtain high-quality 2.3 Å diffraction data. TamA comprises a 16-stranded transmembrane β-barrel and three N-terminal POTRA domains. The barrel is closed at the extracellular face by a conserved lid loop tightly interacting with a conserved lock region on the inner barrel wall. The C-terminal β-strand of the barrel forms an unusual inward kink, which creates a gate for substrate access to the lipid bilayer and weakens lateral inter-strand connection. These structural features immediately suggest a mechanism of autotransporter insertion based on barrel expansion and lateral release. Based on structural conservation of all core elements [2], this mechanism might well be relevant for the entire OMP85 family.

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Bohnert, Maria, Lena-Sophie Wenz, Ralf M. Zerbes, Susanne E. Horvath, David A. Stroud, Karina von der Malsburg, Judith M. Müller, et al. "Role of mitochondrial inner membrane organizing system in protein biogenesis of the mitochondrial outer membrane." Molecular Biology of the Cell 23, no. 20 (October 15, 2012): 3948–56. http://dx.doi.org/10.1091/mbc.e12-04-0295.

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Mitochondria contain two membranes, the outer membrane and the inner membrane with folded cristae. The mitochondrial inner membrane organizing system (MINOS) is a large protein complex required for maintaining inner membrane architecture. MINOS interacts with both preprotein transport machineries of the outer membrane, the translocase of the outer membrane (TOM) and the sorting and assembly machinery (SAM). It is unknown, however, whether MINOS plays a role in the biogenesis of outer membrane proteins. We have dissected the interaction of MINOS with TOM and SAM and report that MINOS binds to both translocases independently. MINOS binds to the SAM complex via the conserved polypeptide transport–associated domain of Sam50. Mitochondria lacking mitofilin, the large core subunit of MINOS, are impaired in the biogenesis of β-barrel proteins of the outer membrane, whereas mutant mitochondria lacking any of the other five MINOS subunits import β-barrel proteins in a manner similar to wild-type mitochondria. We show that mitofilin is required at an early stage of β-barrel biogenesis that includes the initial translocation through the TOM complex. We conclude that MINOS interacts with TOM and SAM independently and that the core subunit mitofilin is involved in biogenesis of outer membrane β-barrel proteins.

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Urfer, Matthias, Jasmina Bogdanovic, Fabio Lo Monte, Kerstin Moehle, Katja Zerbe, Ulrich Omasits, Christian H. Ahrens, Gabriella Pessi, Leo Eberl, and John A. Robinson. "A Peptidomimetic Antibiotic Targets Outer Membrane Proteins and Disrupts Selectively the Outer Membrane in Escherichia coli." Journal of Biological Chemistry 291, no. 4 (December 1, 2015): 1921–32. http://dx.doi.org/10.1074/jbc.m115.691725.

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Increasing antibacterial resistance presents a major challenge in antibiotic discovery. One attractive target in Gram-negative bacteria is the unique asymmetric outer membrane (OM), which acts as a permeability barrier that protects the cell from external stresses, such as the presence of antibiotics. We describe a novel β-hairpin macrocyclic peptide JB-95 with potent antimicrobial activity against Escherichia coli. This peptide exhibits no cellular lytic activity, but electron microscopy and fluorescence studies reveal an ability to selectively disrupt the OM but not the inner membrane of E. coli. The selective targeting of the OM probably occurs through interactions of JB-95 with selected β-barrel OM proteins, including BamA and LptD as shown by photolabeling experiments. Membrane proteomic studies reveal rapid depletion of many β-barrel OM proteins from JB-95-treated E. coli, consistent with induction of a membrane stress response and/or direct inhibition of the Bam folding machine. The results suggest that lethal disruption of the OM by JB-95 occurs through a novel mechanism of action at key interaction sites within clusters of β-barrel proteins in the OM. These findings open new avenues for developing antibiotics that specifically target β-barrel proteins and the integrity of the Gram-negative OM.

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Tomasek, David, and Daniel Kahne. "The assembly of β-barrel outer membrane proteins." Current Opinion in Microbiology 60 (April 2021): 16–23. http://dx.doi.org/10.1016/j.mib.2021.01.009.

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Wenz, Lena-Sophie, Jian Qiu, Thomas Becker, and Nils Wiedemann. "Biogenesis and folding of β-barrel membrane proteins." Cell Cycle 13, no. 2 (November 15, 2013): 169–70. http://dx.doi.org/10.4161/cc.27035.

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Tian, Wei, Meishan Lin, Ke Tang, Jie Liang, and Hammad Naveed. "High-resolution structure prediction ofβ-barrel membrane proteins." Proceedings of the National Academy of Sciences 115, no. 7 (January 29, 2018): 1511–16. http://dx.doi.org/10.1073/pnas.1716817115.

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β-Barrel membrane proteins (βMPs) play important roles, but knowledge of their structures is limited. We have developed a method to predict their 3D structures. We predict strand registers and construct transmembrane (TM) domains of βMPs accurately, including proteins for which no prediction has been attempted before. Our method also accurately predicts structures from protein families with a limited number of sequences and proteins with novel folds. An average main-chain rmsd of 3.48 Å is achieved between predicted and experimentally resolved structures of TM domains, which is a significant improvement (>3 Å) over a recent study. For βMPs with NMR structures, the deviation between predictions and experimentally solved structures is similar to the difference among the NMR structures, indicating excellent prediction accuracy. Moreover, we can now accurately model the extended β-barrels and loops in non-TM domains, increasing the overall coverage of structure prediction by>30%. Our method is general and can be applied to genome-wide structural prediction of βMPs.

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Paschen, Stefan A., Walter Neupert, and Doron Rapaport. "Biogenesis of β-barrel membrane proteins of mitochondria." Trends in Biochemical Sciences 30, no. 10 (October 2005): 575–82. http://dx.doi.org/10.1016/j.tibs.2005.08.009.

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Tamm, Lukas K., Heedeok Hong, and Binyong Liang. "Folding and assembly of β-barrel membrane proteins." Biochimica et Biophysica Acta (BBA) - Biomembranes 1666, no. 1-2 (November 2004): 250–63. http://dx.doi.org/10.1016/j.bbamem.2004.06.011.

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Tamm, Lukas K., Ashish Arora, and Jörg H. Kleinschmidt. "Structure and Assembly of β-Barrel Membrane Proteins." Journal of Biological Chemistry 276, no. 35 (June 29, 2001): 32399–402. http://dx.doi.org/10.1074/jbc.r100021200.

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