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Beta barrell membrane protein

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https://www.readbyqxmd.com/read/28667605/cell-surface-exposure
#1
Anna Konovalova
Surface-exposed proteins of Gram-negative bacteria are represented by integral outer membrane beta-barrel proteins and lipoproteins. No computational methods exist for predicting surface-exposed lipoproteins, and therefore lipoprotein topology must be experimentally tested. This chapter describes three distinct but complementary methods for the detection of surface-exposed proteins: cell surface protein labeling, accessibility to extracellular protease and antibodies.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28620585/identification-of-a-large-family-of-slam-dependent-surface-lipoproteins-in-gram-negative-bacteria
#2
Yogesh Hooda, Christine C L Lai, Trevor F Moraes
The surfaces of many Gram-negative bacteria are decorated with soluble proteins anchored to the outer membrane via an acylated N-terminus; these proteins are referred to as surface lipoproteins or SLPs. In Neisseria meningitidis, SLPs such as transferrin-binding protein B (TbpB) and factor-H binding protein (fHbp) are essential for host colonization and infection because of their essential roles in iron acquisition and immune evasion, respectively. Recently, we identified a family of outer membrane proteins called Slam (Surface lipoprotein assembly modulator) that are essential for surface display of neisserial SLPs...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28554318/anti-cancer-compounds-targeted-to-vdac-potential-and-perspectives
#3
Simona Reina, Vito De Pinto
VDAC (Voltage-Dependent Anion selective Channel) is a small family of abundant pore-forming proteins located in the outer mitochondrial membrane. Their role range from the most intuitive, the formation of a hydrophilic conduit through the membrane thanks to its beta-barrel structure, to less understood functions that make them essential actors in the cross-talk between the bioenergetics metabolism and the cytosol components. Due to this localization, VDAC1, in particular, has been reported to be involved in apoptosis, hexokinase and tubulin binding, and in the Warburg effect...
May 29, 2017: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/28461332/a-bacteroidetes-locus-dedicated-to-fungal-1-6-%C3%AE-glucan-degradation-unique-substrate-conformation-drives-specificity-of-the-key-endo-1-6-%C3%AE-glucanase
#4
Max J Temple, Fiona Cuskin, Arnaud Baslé, Niall Hickey, Gaetano Speciale, Spencer J Williams, Harry J Gilbert, Elisabeth C Lowe
Glycans are major nutrients available to the human gut microbiota. The Bacteroides are generalist glycan degraders, and this function is mediated largely by polysaccharide utilization loci (PULs). The genomes of several Bacteroides species contain a PUL, PUL1,6-β-glucan, that was predicted to target mixed linked plant 1,3;1,4-β-glucans. To test this hypothesis we characterized the proteins encoded by this locus in Bacteroides thetaiotaomicron, a member of the human gut microbiota. We show here that PUL1,6-β-glucan does not orchestrate the degradation of a plant polysaccharide but targets a fungal cell wall glycan, 1,6-β-glucan, which is a growth substrate for the bacterium...
June 23, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28418668/computing-the-diamagnetic-susceptibility-and-diamagnetic-anisotropy-of-membrane-proteins-from-structural-subunits
#5
Mahnoush Babaei, Isaac C Jones, Kaushik Dayal, Meagan S Mauter
The behavior of large, complex molecules in the presence of magnetic fields is experimentally challenging to measure and computationally intensive to predict. This work proposes a novel, mixed-methods approach for efficiently computing the principal magnetic susceptibilities and diamagnetic anisotropy of membrane proteins. The hierarchical primary (amino acid), secondary (α helical and β sheet), and tertiary (α helix and β barrel) structure of transmembrane proteins enables analysis of a complex molecule using discrete subunits of varying size and resolution...
April 25, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28299286/the-rickettsia-conorii-adr1-interacts-with-the-c-terminus-of-human-vitronectin-in-a-salt-sensitive-manner
#6
Abigail I Fish, Sean P Riley, Birendra Singh, Kristian Riesbeck, Juan J Martinez
Spotted fever group (SFG) Rickettsia species are inoculated into the mammalian bloodstream by hematophagous arthropods. Once in the bloodstream and during dissemination, the survival of these pathogens is dependent upon the ability of these bacteria to evade serum-borne host defenses until a proper cellular host is reached. Rickettsia conorii expresses an outer membrane protein, Adr1, which binds the complement inhibitory protein vitronectin to promote resistance to the anti-bacterial effects of the terminal complement complex...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28264993/going-outside-the-tonb-box-identification-of-novel-fepa-tonb-interactions-in-vivo
#7
Michael G Gresock, Kathleen Postle
In Gram-negative bacteria, the cytoplasmic membrane protein TonB transmits energy derived from proton motive force to energize transport of important nutrients through TonB-dependent transporters in the outer membrane. Each transporter consists of a beta barrel domain and a lumen-occluding cork domain containing an essential sequence called the TonB box. To date, the only identified site of transporter-TonB interaction is between the TonB box and residues ∼158 to 162 of TonB. While the mechanism of ligand transport is a mystery, a current model based on site-directed spin labeling and molecular dynamics simulations is that, following ligand binding, the otherwise-sequestered TonB box extends into the periplasm for recognition by TonB, which mediates transport by pulling or twisting the cork...
May 15, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28224490/predicting-beta-barrel-transmembrane-proteins-using-hmms
#8
Georgios N Tsaousis, Stavros J Hamodrakas, Pantelis G Bagos
Transmembrane beta-barrels (TMBBs) constitute an important structural class of membrane proteins located in the outer membrane of gram-negative bacteria, and in the outer membrane of chloroplasts and mitochondria. They are involved in a wide variety of cellular functions and the prediction of their transmembrane topology, as well as their discrimination in newly sequenced genomes is of great importance as they are promising targets for antimicrobial drugs and vaccines. Several methods have been applied for the prediction of the transmembrane segments and the topology of beta barrel transmembrane proteins utilizing different algorithmic techniques...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28158457/efficient-computation-of-transfer-free-energies-of-amino-acids-in-beta-barrel-membrane-proteins
#9
Wei Tian, Meishan Lin, Hammad Naveed, Jie Liang
Motivation: Transmembrane beta-barrel proteins (TMBs) serve a multitude of essential cellular functions in Gram-negative bacteria, mitochondria and chloroplasts. Transfer free energies (TFEs) of residues in the transmembrane (TM) region provides fundamental quantifications of thermodynamic stabilities of TMBs, which are important for the folding and the membrane insertion processes, and may help in understanding the structure-function relationship. However, experimental measurement of TFEs of TMBs is challenging...
June 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/27935943/confined-mobility-of-tonb-and-fepa-in-escherichia-coli-membranes
#10
Yoriko Lill, Lorne D Jordan, Chuck R Smallwood, Salete M Newton, Markus A Lill, Phillip E Klebba, Ken Ritchie
The important process of nutrient uptake in Escherichia coli, in many cases, involves transit of the nutrient through a class of beta-barrel proteins in the outer membrane known as TonB-dependent transporters (TBDTs) and requires interaction with the inner membrane protein TonB. Here we have imaged the mobility of the ferric enterobactin transporter FepA and TonB by tracking them in the membranes of live E. coli with single-molecule resolution at time-scales ranging from milliseconds to seconds. We employed simple simulations to model/analyze the lateral diffusion in the membranes of E...
2016: PloS One
https://www.readbyqxmd.com/read/27587687/pred-tmbb2-improved-topology-prediction-and-detection-of-beta-barrel-outer-membrane-proteins
#11
Konstantinos D Tsirigos, Arne Elofsson, Pantelis G Bagos
MOTIVATION: The PRED-TMBB method is based on Hidden Markov Models and is capable of predicting the topology of beta-barrel outer membrane proteins and discriminate them from water-soluble ones. Here, we present an updated version of the method, PRED-TMBB2, with several newly developed features that improve its performance. The inclusion of a properly defined end state allows for better modeling of the beta-barrel domain, while different emission probabilities for the adjacent residues in strands are used to incorporate knowledge concerning the asymmetric amino acid distribution occurring there...
September 1, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27454911/crystallographic-and-computational-analysis-of-the-barrel-part-of-the-psbo-protein-of-photosystem-ii-carboxylate-water-clusters-as-putative-proton-transfer-relays-and-structural-switches
#12
Martin Bommer, Ana-Nicoleta Bondar, Athina Zouni, Holger Dobbek, Holger Dau
In all organisms that employ oxygenic photosynthesis, the membrane-extrinsic PsbO protein is a functionally important component of photosystem II. To study the previously proposed proton antenna function of carboxylate clusters at the protein-water interface, we combined crystallography and simulations of a truncated cyanobacterial (Thermosynechococcus elongatus) PsbO without peripheral loops. We expressed the PsbO β-barrel heterologously and determined crystal structures at resolutions of 1.15-1.5 Å at 100 K at various pH values and at 297 K and pH 6...
August 23, 2016: Biochemistry
https://www.readbyqxmd.com/read/27326898/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
#13
Leonie van 't Hag, Hsin-Hui Shen, Tsung-Wu Lin, Sally L Gras, Calum J Drummond, Charlotte E Conn
A fundamental understanding of the effect of amphiphilic protein encapsulation on the nanostructure of the bicontinuous cubic phase is crucial to progressing biomedical and biological applications of these hybrid protein-lipid materials, including as drug delivery vehicles, as biosensors, biofuel cells and for in meso crystallization. The relationship between the lipid nanomaterial and the encapsulated protein, however, remains poorly understood. In this study, we investigated the effect of incorporating the five transmembrane and lipo-proteins which make up the β-barrel assembly machinery from Gram-negative bacteria within a series of bicontinuous cubic phases...
November 29, 2016: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/27150630/revisiting-the-oligomerization-mechanism-of-vibrio-cholerae-cytolysin-a-beta-barrel-pore-forming-toxin
#14
Anand Kumar Rai, Kausik Chattopadhyay
Vibrio cholerae cytolysin (VCC) is a membrane-damaging beta-barrel pore-forming toxin (beta-PFT). VCC causes permeabilization of the target membranes by forming transmembrane oligomeric beta-barrel pores. Oligomerization is a key step in the mode of action of any beta-PFT, including that of VCC. Earlier studies have identified some of the key residues in VCC that are directly involved in the generation of the inter-protomer contacts, thus playing critical roles in the oligomerization of the membrane-bound toxin...
June 3, 2016: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/26947057/overexpression-of-human-sod1-in-vdac1-less-yeast-restores-mitochondrial-functionality-modulating-beta-barrel-outer-membrane-protein-genes
#15
Andrea Magrì, Maria Carmela Di Rosa, Marianna Flora Tomasello, Francesca Guarino, Simona Reina, Angela Messina, Vito De Pinto
Cu/Zn Superoxide Dismutase (SOD1), the most important antioxidant defense against ROS in eukaryotic cells, localizes in cytosol and intermembrane space of mitochondria (IMS). Several evidences show a SOD1 intersection with both fermentative and respiratory metabolism. The Voltage Dependent Anion Channel (VDAC) is the main pore-forming protein in the mitochondrial outer membrane (MOM), and is considered the gatekeeper of mitochondrial metabolism. Saccharomyces cerevisiae lacking VDAC1 (Δpor1) is a very convenient model system, since it shows an impaired growth rate on non-fermentable carbon source...
June 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/26938107/an-analysis-of-surface-proteomics-results-reveals-novel-candidates-for-intracellular-surface-moonlighting-proteins-in-bacteria
#16
REVIEW
Wangfei Wang, Constance J Jeffery
Proteins expressed on the bacterial cell surface play important roles in infection and virulence and can be targets for vaccine development or used as biomarkers. Surprisingly, an increasing number of surface proteins are being found to be identical to intracellular enzymes and chaperones, and a few dozen intracellular/surface moonlighting proteins have been found that have different functions inside the cell and on the cell surface. The results of twenty-two published bacterial surface proteomics studies were analyzed using bioinformatics tools to consider how many additional intracellular proteins are also found on the cell surface...
April 26, 2016: Molecular BioSystems
https://www.readbyqxmd.com/read/26655719/structural-and-functional-analyses-reveal-insights-into-the-molecular-properties-of-the-escherichia-coli-z-ring-stabilizing-protein-zapc
#17
Maria A Schumacher, Wenjie Zeng, Kuo-Hsiang Huang, Lukasz Tchorzewski, Anuradha Janakiraman
In Escherichia coli cell division is driven by the tubulin-like GTPase, FtsZ, which forms the cytokinetic Z-ring. The Z-ring serves as a dynamic platform for the assembly of the multiprotein divisome, which catalyzes membrane cleavage to create equal daughter cells. Several proteins effect FtsZ assembly, thereby providing spatiotemporal control over cell division. One important class of FtsZ interacting/regulatory proteins is the Z-ring-associated proteins, Zaps, which typically modulate Z-ring formation by increasing lateral interactions between FtsZ protofilaments...
January 29, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/26443900/cell-free-production-of-vdac-directly-into-liposomes-for-integration-with-biomimetic-membrane-systems
#18
Lavinia Liguori, Barry Stidder, Jean-Pierre Alcaraz, Jean-Luc Lenormand, Philippe Cinquin, Donald K Martin
The mitochondrial voltage-dependent anion channel (VDAC) is a pivotal protein since it provides the major transport pathway between the cytosol and the mitochondrial intermembrane space and it is implicated in cell apoptosis by functioning as a gatekeeper for the trafficking of mitochondrial death molecules. VDAC is a beta-barrel channel with a large conductance, and we use it as a model transport protein for the design of biomimetic systems. To overcome the limitations of classical overexpression methods for producing and purifying membrane proteins (MPs) we describe here the use of an optimized cell-free system...
August 17, 2016: Preparative Biochemistry & Biotechnology
https://www.readbyqxmd.com/read/26427673/yeast-mitochondria-as-a-model-system-to-study-the-biogenesis-of-bacterial-%C3%AE-barrel-proteins
#19
Thomas Ulrich, Philipp Oberhettinger, Ingo B Autenrieth, Doron Rapaport
Beta-barrel proteins are found in the outer membrane of Gram-negative bacteria, mitochondria, and chloroplasts. The evolutionary conservation in the biogenesis of these proteins allows mitochondria to assemble bacterial β-barrel proteins in their functional form. In this chapter, we describe exemplarily how the capacity of yeast mitochondria to process the trimeric autotransporter YadA can be used to study the role of bacterial periplasmic chaperones in this process.
2015: Methods in Molecular Biology
https://www.readbyqxmd.com/read/26370942/outer-membrane-lipoprotein-biogenesis-lol-is-not-the-end
#20
REVIEW
Anna Konovalova, Thomas J Silhavy
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...
October 5, 2015: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
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