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Membrane protein crystal structure

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https://www.readbyqxmd.com/read/29159828/crystal-structure-of-the-legionella-effector-lem22
#1
Guennadi Kozlov, Kathy Wong, Kalle Gehring
Legionella pneumophila is a pathogen causing severe pneumonia in humans called Legionnaires' disease. Lem22 is a previously uncharacterized effector protein conserved in multiple Legionella strains. Here, we report the crystal structure of Lem22 from the Philadelphia strain, also known as lpg2328, at 1.40 Å resolution. The structure shows an up-and-down three-helical bundle with a significant structural similarity to a number of protein-binding domains involved in apoptosis and membrane trafficking. Sequence conservation identifies a putative functional site on the interface of helices 2 and 3...
November 21, 2017: Proteins
https://www.readbyqxmd.com/read/29158492/structural-basis-for-the-assembly-of-the-ragulator-rag-gtpase-complex
#2
Ryo Yonehara, Shigeyuki Nada, Tomokazu Nakai, Masahiro Nakai, Ayaka Kitamura, Akira Ogawa, Hirokazu Nakatsumi, Keiichi I Nakayama, Songling Li, Daron M Standley, Eiki Yamashita, Atsushi Nakagawa, Masato Okada
The mechanistic target of rapamycin complex 1 (mTORC1) plays a central role in regulating cell growth and metabolism by responding to cellular nutrient conditions. The activity of mTORC1 is controlled by Rag GTPases, which are anchored to lysosomes via Ragulator, a pentameric protein complex consisting of membrane-anchored p18/LAMTOR1 and two roadblock heterodimers. Here we report the crystal structure of Ragulator in complex with the roadblock domains of RagA-C, which helps to elucidate the molecular basis for the regulation of Rag GTPases...
November 20, 2017: Nature Communications
https://www.readbyqxmd.com/read/29158068/new-crystal-forms-of-the-integral-membrane-escherichia-coli-quinol-fumarate-reductase-suggest-that-ligands-control-domain-movement
#3
C A Starbird, Thomas M Tomasiak, Prashant K Singh, Victoria Yankovskaya, Elena Maklashina, Michael Eisenbach, Gary Cecchini, T M Iverson
Quinol:fumarate reductase (QFR) is an integral membrane protein and a member of the respiratory Complex II superfamily. Although the structure of Escherichia coli QFR was first reported almost twenty years ago, many open questions of catalysis remain. Here we report two new crystal forms of QFR, one grown from the lipidic cubic phase and one grown from dodecyl maltoside micelles. QFR crystals grown from the lipid cubic phase processed as P1, merged to 7.5 Å resolution, and exhibited crystal packing similar to previous crystal forms...
November 17, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/29149594/conversion-of-bim-bh3-from-activator-to-inhibitor-of-bak-through-structure-based-design
#4
Jason M Brouwer, Ping Lan, Angus D Cowan, Jonathan P Bernardini, Richard W Birkinshaw, Mark F van Delft, Brad E Sleebs, Adeline Y Robin, Ahmad Wardak, Iris K Tan, Boris Reljic, Erinna F Lee, W Douglas Fairlie, Melissa J Call, Brian J Smith, Grant Dewson, Guillaume Lessene, Peter M Colman, Peter E Czabotar
Certain BH3-only proteins transiently bind and activate Bak and Bax, initiating their oligomerization and the permeabilization of the mitochondrial outer membrane, a pivotal step in the mitochondrial pathway to apoptosis. Here we describe the first crystal structures of an activator BH3 peptide bound to Bak and illustrate their use in the design of BH3 derivatives capable of inhibiting human Bak on mitochondria. These BH3 derivatives compete for the activation site at the canonical groove, are the first engineered inhibitors of Bak activation, and support the role of key conformational transitions associated with Bak activation...
November 16, 2017: Molecular Cell
https://www.readbyqxmd.com/read/29144454/dynamics-of-p-type-atpase-transport-revealed-by-single-molecule-fret
#5
Mateusz Dyla, Daniel S Terry, Magnus Kjaergaard, Thomas L-M Sørensen, Jacob Lauwring Andersen, Jens Peter Andersen, Charlotte Rohde Knudsen, Roger B Altman, Poul Nissen, Scott C Blanchard
Phosphorylation-type (P-type) ATPases are ubiquitous primary transporters that pump cations across cell membranes through the formation and breakdown of a phosphoenzyme intermediate. Structural investigations suggest that the transport mechanism is defined by conformational changes in the cytoplasmic domains of the protein that are allosterically coupled to transmembrane helices so as to expose ion binding sites to alternate sides of the membrane. Here, we have used single-molecule fluorescence resonance energy transfer to directly observe conformational changes associated with the functional transitions in the Listeria monocytogenes Ca(2+)-ATPase (LMCA1), an orthologue of eukaryotic Ca(2+)-ATPases...
November 16, 2017: Nature
https://www.readbyqxmd.com/read/29133212/quantitative-and-systems-pharmacology-2-in-silico-polypharmacology-of-g-protein-coupled-receptor-ligands-via-network-based-approaches
#6
Zengrui Wu, Weiqiang Lu, Weiwei Yu, Tianduanyi Wang, Weihua Li, Guixia Liu, Hankun Zhang, Xiufeng Pang, Jin Huang, Mingyao Liu, Feixiong Cheng, Yun Tang
G protein-coupled receptors (GPCRs) are the largest super family with more than 800 membrane receptors. Currently, over 30% of the approved drugs target human GPCRs. However, only approximately 30 human GPCRs have been resolved three-dimensional crystal structures, which limits traditional structure-based drug discovery. Recent advances in network-based systems pharmacology approaches have demonstrated powerful strategies for identifying new targets of GPCR ligands. In this study, we proposed a network-based systems pharmacology framework for comprehensive identification of new drug-target interactions on GPCRs...
November 10, 2017: Pharmacological Research: the Official Journal of the Italian Pharmacological Society
https://www.readbyqxmd.com/read/29129383/the-structure-of-a-conserved-domain-of-tamb-reveals-a-hydrophobic-%C3%AE-taco-fold
#7
Inokentijs Josts, Christopher James Stubenrauch, Grishma Vadlamani, Khedidja Mosbahi, Daniel Walker, Trevor Lithgow, Rhys Grinter
The translocation and assembly module (TAM) plays a role in the transport and insertion of proteins into the bacterial outer membrane. TamB, a component of this system spans the periplasmic space to engage with its partner protein TamA. Despite efforts to characterize the TAM, the structure and mechanism of action of TamB remained enigmatic. Here we present the crystal structure of TamB amino acids 963-1,138. This region represents half of the conserved DUF490 domain, the defining feature of TamB. TamB963-1138 consists of a concave, taco-shaped β sheet with a hydrophobic interior...
November 3, 2017: Structure
https://www.readbyqxmd.com/read/29123501/gonadotropin-releasing-hormone-gnrh-receptor-structure-and-gnrh-binding
#8
REVIEW
Colleen A Flanagan, Ashmeetha Manilall
Gonadotropin-releasing hormone (GnRH) regulates reproduction. The human GnRH receptor lacks a cytoplasmic carboxy-terminal tail but has amino acid sequence motifs characteristic of rhodopsin-like, class A, G protein-coupled receptors (GPCRs). This review will consider how recent descriptions of X-ray crystallographic structures of GPCRs in inactive and active conformations may contribute to understanding GnRH receptor structure, mechanism of activation and ligand binding. The structures confirmed that ligands bind to variable extracellular surfaces, whereas the seven membrane-spanning α-helices convey the activation signal to the cytoplasmic receptor surface, which binds and activates heterotrimeric G proteins...
2017: Frontiers in Endocrinology
https://www.readbyqxmd.com/read/29117682/constant-ph-molecular-dynamics-reveals-how-proton-release-drives-the-conformational-transition-of-a-transmembrane-efflux-pump
#9
Zhi Yue, Wei Chen, Helen I Zgurskaya, Jana Shen
AcrB is the inner-membrane transporter of E. coli AcrAB-TolC tripartite efflux complex, which plays a major role in the intrinsic resistance to clinically important antibiotics. AcrB pumps a wide range of toxic substrates by utilizing the proton gradient between periplasm and cytoplasm. Crystal structures of AcrB revealed three distinct conformational states of the transport cycle, substrate access, binding and extrusion, or loose (L), tight (T) and open (O) states. However, the specific residue(s) responsible for proton binding/release and the mechanism of proton-coupled conformational cycling remain controversial...
November 9, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29117521/sparse-labeling-peldor-spectroscopy-on-multimeric-mechanosensitive-membrane-channels
#10
Katrin Ackermann, Christos Pliotas, Silvia Valera, James H Naismith, Bela E Bode
Pulse electron paramagnetic resonance (EPR) is being applied to ever more complex biological systems comprising multiple subunits. Membrane channel proteins are of great interest as pulse EPR reports on functionally significant but distinct conformational states in a native environment without the need for crystallization. Pulse EPR, in the form of pulsed electron-electron double resonance (PELDOR), using site-directed spin labeling, is most commonly employed to accurately determine distances (in the nanometer range) between different regions of the structure...
November 7, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/29113783/multiple-legumain-isoenzymes-in-ticks
#11
David Hartmann, Radek Šíma, Jitka Konvičková, Jan Perner, Petr Kopáček, Daniel Sojka
By searching nucleotide databases for the North American Lyme disease vector, Ixodes scapularis, we have complemented the previously characterized European Ixodes ricinus legumain IrAE1 with a full set of nine analogous genes (isae1-9). Six of these were PCR confirmed as genes present in all tick genomes tested. The absolute mRNA copy number examined by quantitative (q)PCR enabled expression profiling and an absolute comparison of mRNA levels for individual I. scapularis (Is)AEs in tick tissues. Four IsAEs (1, 2, 4, 9) were expressed solely in the gut and thus are proposed to be involved in host blood digestion...
November 4, 2017: International Journal for Parasitology
https://www.readbyqxmd.com/read/29109439/crystal-structure-of-tripartite-type-abc-transporter-macb-from-acinetobacter-baumannii
#12
Ui Okada, Eiki Yamashita, Arthur Neuberger, Mayu Morimoto, Hendrik W van Veen, Satoshi Murakami
The MacA-MacB-TolC tripartite complex is a transmembrane machine that spans both plasma membrane and outer membrane and actively extrudes substrates, including macrolide antibiotics, virulence factors, peptides and cell envelope precursors. These transport activities are driven by the ATPase MacB, a member of the ATP-binding cassette (ABC) superfamily. Here, we present the crystal structure of MacB at 3.4-Å resolution. MacB forms a dimer in which each protomer contains a nucleotide-binding domain and four transmembrane helices that protrude in the periplasm into a binding domain for interaction with the membrane fusion protein MacA...
November 6, 2017: Nature Communications
https://www.readbyqxmd.com/read/29108958/novel-physical-chemistry-approaches-in-biophysical-researches-with-advanced-application-of-lasers-detection-and-manipulation
#13
REVIEW
Koichi Iwata, Masahide Terazima, Hiroshi Masuhara
Novel methodologies utilizing pulsed or intense CW irradiation obtained from lasers have a major impact on biological sciences. In this article, recent development in biophysical researches fully utilizing the laser irradiation is described for three topics, time-resolved fluorescence spectroscopy, time-resolved thermodynamics, and manipulation of the biological assemblies by intense laser irradiation. First, experimental techniques for time-resolved fluorescence spectroscopy are concisely explained in Section 2...
November 3, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29098572/crystal-structure-of-psb27-from-arabidopsis-thaliana-determined-at-a-resolution-of-1-85%C3%A2-%C3%A3
#14
Cheng Xingxing, Liu Jiuyang, Zhang Huan, Li Fudong, Zhang Shuya, Xu Min, Ruan Ke, Wang Yuhua, Fu Aigen
Proper biogenesis and maintenance of photosynthetic thylakoid membrane complexes are essential for the photosynthetic light reactions. A thylakoid lumenal protein, Psb27, plays a vital role in assembly or/and maintenance of photosystem II (PSII). In cyanobacteria, it is a small lipoprotein docked to the lumenal side of PSII, and functions in the assembly of the Mn4Ca cluster and in the PSII repair cycle. However, Psb27 from Arabidopsis thaliana is not a lipoprotein, and it is involved in PSII repair and acclimation to fluctuating light stress, suggesting a functional divergence between Arabidopsis Psb27 and cyanobacterial Psb27s...
November 2, 2017: Photosynthesis Research
https://www.readbyqxmd.com/read/29095159/nogo-receptor-crystal-structures-with-a-native-disulfide-pattern-suggest-a-novel-mode-of-self-interaction
#15
Matti F Pronker, Roderick P Tas, Hedwich C Vlieg, Bert J C Janssen
The Nogo Receptor (NgR) is a glycophosphatidylinositol-anchored cell-surface protein and is a receptor for three myelin-associated inhibitors of regeneration: myelin-associated glycoprotein, Nogo66 and oligodendrocyte myelin glycoprotein. In combination with different co-receptors, NgR mediates signalling that reduces neuronal plasticity. The available structures of the NgR ligand-binding leucine-rich repeat (LRR) domain have an artificial disulfide pattern owing to truncated C-terminal construct boundaries...
November 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/29094929/structural-basis-for-the-serratia-marcescens-lipase-secretion-system-crystal-structures-of-the-membrane-fusion-protein-and-nucleotide-binding-domain
#16
Daichi Murata, Hiroyuki Okano, Clement Angkawidjaja, Masato Akutsu, Shun-Ichi Tanaka, Kenyu Kitahara, Takuya Yoshizawa, Hiroyoshi Matsumura, Yuji Kado, Eiichi Mizohata, Tsuyoshi Inoue, Satoshi Sano, Yuichi Koga, Shigenori Kanaya, Kazufumi Takano
Serratia marcescens secretes a lipase, LipA, through a type I secretion system (T1SS). The T1SS for LipA, the Lip system, is composed of an inner membrane ABC transporter with its nucleotide-binding domains (NBD), LipB, a membrane fusion protein, LipC, and an outer membrane channel protein, LipD. Passenger protein secreted by this system has been functionally and structurally characterized well, but relatively little information about the transporter complex is available. Here, we report the crystallographic studies of LipC without the membrane anchor region, LipC-, and the NBD of LipB (LipB-NBD)...
November 10, 2017: Biochemistry
https://www.readbyqxmd.com/read/29092894/mitochondrial-reactive-oxygen-species-in-lipotoxic-hearts-induces-post-translational-modifications-of-akap121-drp1-and-opa1-that-promote-mitochondrial-fission
#17
Kensuke Tsushima, Heiko Bugger, Adam R Wende, Jamie Soto, Gregory A Jenson, Austin R Tor, Rose McGlauflin, Helena C Kenny, Yuan Zhang, Rhonda Souvenir, Xiao X Hu, Crystal L Black, Renata O Pereira, Vitor A Lira, Kenneth Spitzer, Terry L Sharp, Kooresh I Shoghi, Genevieve C Sparagna, Eva A Rog-Zielinska, Peter Kohl, Oleh Khalimonchuk, Jean E Schaffer, E Dale Abel
Rationale: Cardiac lipotoxicity, characterized by increased uptake, oxidation and accumulation of lipid intermediates, contributes to cardiac dysfunction in obesity and diabetes. However, mechanisms linking lipid overload and mitochondrial dysfunction are incompletely understood. Objective: To elucidate the mechanisms for mitochondrial adaptations to lipid overload in postnatal hearts in vivo. Methods and Results: Using a transgenic mouse model of cardiac lipotoxicity overexpressing long-chain acyl-CoA synthetase 1 in cardiomyocytes, we show that modestly increased myocardial fatty acid uptake leads to mitochondrial structural remodeling with significant reduction in minimum diameter...
November 1, 2017: Circulation Research
https://www.readbyqxmd.com/read/29089903/intravesicular-phosphatase-phospho1-function-in-enamel-mineralization-and-prism-formation
#18
Mirali Pandya, Lauren Rosene, Colin Farquharson, José L Millán, Thomas G H Diekwisch
The transport of mineral ions from the enamel organ-associated blood vessels to the developing enamel crystals involves complex cargo packaging and carriage mechanisms across several cell layers, including the ameloblast layer and the stratum intermedium. Previous studies have established PHOSPHO1 as a matrix vesicle membrane-associated phosphatase that interacts with matrix vesicles molecules phosphoethanolamine and phosphocholine to initiate apatite crystal formation inside of matrix vesicles in bone. In the present study, we sought to determine the function of Phospho1 during amelogenesis...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/29083419/patb1-is-an-o-acetyltransferase-that-decorates-secondary-cell-wall-polysaccharides
#19
David Sychantha, Dustin J Little, Robert N Chapman, Geert-Jan Boons, Howard Robinson, P Lynne Howell, Anthony J Clarke
O-Acetylation of the secondary cell wall polysaccharides (SCWP) of the Bacillus cereus group of pathogens, which includes Bacillus anthracis, is essential for the proper attachment of surface-layer (S-layer) proteins to their cell walls. Using a variety of pseudosubstrates and a chemically synthesized analog of SCWP, we report here the identification of PatB1 as a SCWP O-acetyltransferase in Bacillus cereus. Additionally, we report the crystal structure of PatB1, which provides detailed insights into the mechanism of this enzyme and defines a novel subfamily of the SGNH family of esterases and lipases...
October 30, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/29082669/structural-basis-for-high-affinity-adipate-binding-to-adpc-rpa4515-an-orphan-periplasmic-binding-protein-from-the-tripartite-tricarboxylate-transporter-ttt-family-in-rhodopseudomonas-palustris
#20
Leonardo T Rosa, Samuel R Dix, John B Rafferty, David J Kelly
The Tripartite Tricarboxylate Transporter (TTT) family is a poorly characterised group of prokaryotic secondary solute transport systems, which employ a periplasmic substrate binding-protein (SBP) for initial ligand recognition. The substrates of only a small number of TTT systems are known and very few SBP structures have been solved, so the mechanisms of SBP-ligand interactions in this family are not well understood. The SBP RPA4515 (AdpC) from Rhodopseudomonas palustris was found by differential scanning fluorescence and isothermal titration calorimetry to bind aliphatic dicarboxylates of a chain length of six to nine carbons, with KD values in the μM range...
October 30, 2017: FEBS Journal
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