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Crystallization of membrane protein

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https://www.readbyqxmd.com/read/28817634/cross-reactivity-between-apical-membrane-antgen-1-and-rhoptry-neck-protein-2-in-p-vivax-and-p-falciparum-a-structural-and-binding-study
#1
Brigitte Vulliez-Le Normand, Frederick A Saul, Sylviane Hoos, Bart W Faber, Graham A Bentley
Malaria, a disease endemic in many tropical and subtropical regions, is caused by infection of the erythrocyte by the apicomplexan parasite Plasmodium. Host-cell invasion is a complex process but two Plasmodium proteins, Apical Membrane Antigen 1 (AMA1) and the Rhoptry Neck protein complex (RON), play a key role. AMA1, present on the surface of the parasite, binds tightly to the RON2 component of the RON protein complex, which is inserted into the erythrocyte membrane during invasion. Blocking the AMA1-RON2 interaction with antibodies or peptides inhibits invasion, underlining its importance in the Plasmodium life cycle and as a target for therapeutic strategies...
2017: PloS One
https://www.readbyqxmd.com/read/28813412/the-primed-snare-complexin-synaptotagmin-complex-for-neuronal-exocytosis
#2
Qiangjun Zhou, Peng Zhou, Austin L Wang, Dick Wu, Minglei Zhao, Thomas C Südhof, Axel T Brunger
Synaptotagmin, complexin, and neuronal SNARE (soluble N-ethylmaleimide sensitive factor attachment protein receptor) proteins mediate evoked synchronous neurotransmitter release, but the molecular mechanisms mediating the cooperation between these molecules remain unclear. Here we determine crystal structures of the primed pre-fusion SNARE-complexin-synaptotagmin-1 complex. These structures reveal an unexpected tripartite interface between synaptotagmin-1 and both the SNARE complex and complexin. Simultaneously, a second synaptotagmin-1 molecule interacts with the other side of the SNARE complex via the previously identified primary interface...
August 16, 2017: Nature
https://www.readbyqxmd.com/read/28811607/localized-iron-accumulation-precedes-nucleation-and-growth-of-magnetite-crystals-in-magnetotactic-bacteria
#3
Jacques Werckmann, Jefferson Cypriano, Christopher T Lefèvre, Kassiogé Dembelé, Ovidiu Ersen, Dennis A Bazylinski, Ulysses Lins, Marcos Farina
Many magnetotactic bacteria (MTB) biomineralize magnetite crystals that nucleate and grow inside intracellular membranous vesicles that originate from invaginations of the cytoplasmic membrane. The crystals together with their surrounding membranes are referred to magnetosomes. Magnetosome magnetite crystals nucleate and grow using iron transported inside the vesicle by specific proteins. Here we address the question: can iron transported inside MTB for the production of magnetite crystals be spatially mapped using electron microscopy? Cultured and uncultured MTB from brackish and freshwater lagoons were studied using analytical transmission electron microscopy in an attempt to answer this question...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28807152/structure-of-thrombospondin-type-3-repeats-in-bacterial-outer-membrane-protein-a-reveals-its-intra-repeat-disulfide-bond-dependent-calcium-binding-capability
#4
Shuyan Dai, Cancan Sun, Kemin Tan, Sheng Ye, Rongguang Zhang
Eukaryotic thrombospondin type 3 repeat (TT3R) is an efficient calcium ion (Ca(2+)) binding motif only found in mammalian thrombospondin family. TT3R has also been found in prokaryotic cellulase Cel5G, which was thought to forfeit the Ca(2+)-binding capability due to the formation of intra-repeat disulfide bonds, instead of the inter-repeat ones possessed by eukaryotic TT3Rs. In this study, we have identified an enormous number of prokaryotic TT3R-containing proteins belonging to several different protein families, including outer membrane protein A (OmpA), an important structural protein connecting the outer membrane and the periplasmic peptidoglycan layer in gram-negative bacteria...
September 2017: Cell Calcium
https://www.readbyqxmd.com/read/28801553/dead-end-complex-lipid-interactions-and-catalytic-mechanism-of-microsomal-glutathione-transferase-1-an-electron-crystallography-and-mutagenesis-investigation
#5
Qie Kuang, Pasi Purhonen, Johan Ålander, Richard Svensson, Veronika Hoogland, Jens Winerdal, Linda Spahiu, Astrid Ottosson-Wadlund, Caroline Jegerschöld, Ralf Morgenstern, Hans Hebert
Microsomal glutathione transferase 1 (MGST1) is a detoxification enzyme belonging to the Membrane Associated Proteins in Eicosanoid and Glutathione Metabolism (MAPEG) superfamily. Here we have used electron crystallography of two-dimensional crystals in order to determine an atomic model of rat MGST1 in a lipid environment. The model comprises 123 of the 155 amino acid residues, two structured phospholipid molecules, two aliphatic chains and one glutathione (GSH) molecule. The functional unit is a homotrimer centered on the crystallographic three-fold axes of the unit cell...
August 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28801111/luminescence-resonance-energy-transfer-spectroscopy-of-atp-binding-cassette-proteins
#6
REVIEW
Maria E Zoghbi, Guillermo A Altenberg
The ATP-binding cassette (ABC) superfamily includes regulatory and transport proteins. Most human ABC exporters pump substrates out of cells using energy from ATP hydrolysis. Although major advances have been made toward understanding the molecular mechanism of ABC exporters, there are still many issues unresolved. During the last few years, luminescence resonance energy transfer has been used to detect conformational changes in real time, with atomic resolution, in isolated ABC nucleotide binding domains (NBDs) and full-length ABC exporters...
August 8, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28799584/molecular-determinants-involved-in-differential-behaviour-between-soluble-tissue-factor-and-full-length-tissue-factor-towards-factor-viia
#7
Ramesh Prasad, Prosenjit Sen
During blood-coagulation, the transmembrane protein tissue factor (TF) binds to its ligand, factor (F)VII, activating and allosterically modifying it to form a mature active binary complex (TF-FVIIa). Although the extracellular domain of TF (sTF) can bind to FVII, it fails to activate it. Binding of TF with FVIIa only partially enhances FVIIa proteolytic activity. Our previous kinetic study revealed that sTF has a lower binding capacity with FVIIa compared to membrane bound full-length (fl)TF. The reason behind this incapability of FVII activation and reduced catalytic activity remains unexplored due to the lack of an flTF crystal structure...
August 11, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28798393/role-of-water-and-protein-dynamics-in-proton-pumping-by-respiratory-complex-i
#8
Outi Haapanen, Vivek Sharma
Membrane bound respiratory complex I is the key enzyme in the respiratory chains of bacteria and mitochondria, and couples the reduction of quinone to the pumping of protons across the membrane. Recently solved crystal or electron microscopy structures of bacterial and mitochondrial complexes have provided significant insights into the electron and proton transfer pathways. However, due to large spatial separation between the electron and proton transfer routes, the molecular mechanism of coupling remains unclear...
August 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28796264/lytic-cell-death-induced-by-melittin-bypasses-pyroptosis-but-induces-nlrp3-inflammasome-activation-and-il-1%C3%AE-release
#9
Fátima Martín-Sánchez, Juan José Martínez-García, María Muñoz-García, Miriam Martínez-Villanueva, José A Noguera-Velasco, David Andreu, Luís Rivas, Pablo Pelegrín
The nucleotide-binding domain and leucine-rich repeat-containing receptor with a pyrin domain 3 (NLRP3) inflammasome is a sensor for different types of infections and alterations of homeostatic parameters, including abnormally high levels of the extracellular nucleotide ATP or crystallization of different metabolites. All NLRP3 activators trigger a similar intracellular pathway, where a decrease in intracellular K(+) concentration and permeabilization of plasma membrane are key steps. Cationic amphipathic antimicrobial peptides and peptide toxins permeabilize the plasma membrane...
August 10, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28792932/structural-insights-into-ligand-recognition-by-the-lysophosphatidic-acid-receptor-lpa6
#10
Reiya Taniguchi, Asuka Inoue, Misa Sayama, Akiharu Uwamizu, Keitaro Yamashita, Kunio Hirata, Masahito Yoshida, Yoshiki Tanaka, Hideaki E Kato, Yoshiko Nakada-Nakura, Yuko Otani, Tomohiro Nishizawa, Takayuki Doi, Tomohiko Ohwada, Ryuichiro Ishitani, Junken Aoki, Osamu Nureki
Lysophosphatidic acid (LPA) is a bioactive lipid composed of a phosphate group, a glycerol backbone, and a single acyl chain that varies in length and saturation. LPA activates six class A G-protein-coupled receptors to provoke various cellular reactions. Because LPA signalling has been implicated in cancer and fibrosis, the LPA receptors are regarded as promising drug targets. The six LPA receptors are subdivided into the endothelial differentiation gene (EDG) family (LPA1-LPA3) and the phylogenetically distant non-EDG family (LPA4-LPA6)...
August 9, 2017: Nature
https://www.readbyqxmd.com/read/28790314/structural-and-functional-insights-into-the-lipopolysaccharide-abc-transporter-lptb2fg
#11
Haohao Dong, Zhengyu Zhang, Xiaodi Tang, Neil G Paterson, Changjiang Dong
The cell surface of most Gram-negative bacteria contains lipopolysaccharide that is essential for their viability and drug resistance. A 134-kDa protein complex LptB2FG is unique among ATP-binding cassette transporters because it extracts lipopolysaccharide from the external leaflet of the inner membrane and propels it along a filament that extends across the periplasm to directly deliver lipopolysaccharide into the external leaflet of the outer membrane. Here we report the crystal structure of the lipopolysaccharide transporter LptB2FG from Klebsiella pneumoniae, in which both LptF and LptG are composed of a β-jellyroll-like periplasmic domain and six α-helical segments in the transmembrane domain...
August 9, 2017: Nature Communications
https://www.readbyqxmd.com/read/28782586/breaking-the-mirror-l-amino-acid-deaminase-a-novel-stereoselective-biocatalyst
#12
REVIEW
Gianluca Molla, Roberta Melis, Loredano Pollegioni
Enantiomerically pure amino acids are of increasing interest for the fine chemical, agrochemicals and pharmaceutical industries. During past years l-amino acids have been produced from deracemization of dl-solution employing the stereoselective flavoenzyme d-amino acid oxidase. On the other hand, the isolation of corresponding d-isomer was hampered by the scarce availability of a suitable l-amino acid oxidase activity. On this side, l-amino acid deaminase (LAAD), only present in the Proteus bacteria, represents a suitable alternative...
August 3, 2017: Biotechnology Advances
https://www.readbyqxmd.com/read/28781959/structure-based-design-of-ferritin-nanoparticle-immunogens-displaying-antigenic-loops-of-neisseria-gonorrhoeae
#13
Liqin Wang, Daniel Xing, Adriana Le Van, Ann E Jerse, Shuishu Wang
Effective vaccines are urgently needed to combat gonorrhea, a common sexually transmitted bacterial infection, for which treatment options are diminishing due to rapid emergence of antibiotic resistance. We have used a rational approach to the development of gonorrhea vaccines, and genetically engineered nanoparticles to present antigenic peptides of Neisseria gonorrhoeae, the causative agent of gonorrhea. We hypothesized that the ferritin nanocage could be used as a platform to display an ordered array of N...
August 2017: FEBS Open Bio
https://www.readbyqxmd.com/read/28781082/from-macrocrystals-to-microcrystals-a-strategy-for-membrane-protein-serial-crystallography
#14
Robert Dods, Petra Båth, David Arnlund, Kenneth R Beyerlein, Garrett Nelson, Mengling Liang, Rajiv Harimoorthy, Peter Berntsen, Erik Malmerberg, Linda Johansson, Rebecka Andersson, Robert Bosman, Sergio Carbajo, Elin Claesson, Chelsie E Conrad, Peter Dahl, Greger Hammarin, Mark S Hunter, Chufeng Li, Stella Lisova, Despina Milathianaki, Joseph Robinson, Cecilia Safari, Amit Sharma, Garth Williams, Cecilia Wickstrand, Oleksandr Yefanov, Jan Davidsson, Daniel P DePonte, Anton Barty, Gisela Brändén, Richard Neutze
Serial protein crystallography was developed at X-ray free-electron lasers (XFELs) and is now also being applied at storage ring facilities. Robust strategies for the growth and optimization of microcrystals are needed to advance the field. Here we illustrate a generic strategy for recovering high-density homogeneous samples of microcrystals starting from conditions known to yield large (macro) crystals of the photosynthetic reaction center of Blastochloris viridis (RCvir). We first crushed these crystals prior to multiple rounds of microseeding...
July 27, 2017: Structure
https://www.readbyqxmd.com/read/28779836/lipid-nanodiscs-as-a-tool-for-high-resolution-structure-determination-of-membrane-proteins-by-single-particle-cryo-em
#15
Rouslan G Efremov, Christos Gatsogiannis, Stefan Raunser
The "resolution revolution" in electron cryomicroscopy (cryo-EM) profoundly changed structural biology of membrane proteins. Near-atomic structures of medium size to large membrane protein complexes can now be determined without crystallization. This significantly accelerates structure determination and also the visualization of small bound ligands. There is an additional advantage: the structure of membrane proteins can now be studied in their native or nearly native lipid bilayer environment. A popular lipid bilayer mimetic are lipid nanodiscs, which have been thoroughly characterized and successfully utilized in multiple applications...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28777093/expression-and-crystallographic-studies-of-the-d1d2-domains-of-c4-4a-a-homologous-protein-to-the-urokinase-receptor
#16
Shanli Chen, Lin Lin, Cai Yuan, Henrik Gårdsvoll, Mette C Kriegbaum, Michael Ploug, Mingdong Huang
C4.4A is a glycosylphosphatidylinositol-anchored membrane protein comprised of two LU domains (Ly6/uPAR-like domains) and an extensively O-glycosylated C-terminal Ser/Thr/Pro-rich region. C4.4A is a novel biomarker for squamous epithelial differentiation. Its expression is dysregulated under various pathological conditions and it is a robust biomarker for poor prognosis in various malignant conditions such as pulmonary adenocarcinoma. To facilitate crystallization, the two LU domains were excised from intact C4...
August 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28774292/rosetta-broker-for-membrane-protein-structure-prediction-concentrative-nucleoside-transporter-3-and-corticotropin-releasing-factor-receptor-1-test-cases
#17
Dorota Latek
BACKGROUND: Membrane proteins are difficult targets for structure prediction due to the limited structural data deposited in Protein Data Bank. Most computational methods for membrane protein structure prediction are based on the comparative modeling. There are only few de novo methods targeting that distinct protein family. In this work an example of such de novo method was used to structurally and functionally characterize two representatives of distinct membrane proteins families of solute carrier transporters and G protein-coupled receptors...
August 3, 2017: BMC Structural Biology
https://www.readbyqxmd.com/read/28771501/obliteration-of-bacterial-growth-and-biofilm-through-ros-generation-by-facilely-synthesized-green-silver-nanoparticles
#18
Shariq Qayyum, Mohammad Oves, Asad U Khan
Mangifera indica inflorescence aqueous extract was utilized for production of green AgNPs. Synthesized AgNPs were characterized by UV-vis spectrophotometry, XRD, TEM, FESEM and particles size analyzer. AgNPs showed minimum inhibitory concentrations (MICs) of 8 μg ml-1 and 16 μg ml-1 for Gram negative (K. pneumoniae, P. aeruginosa and E. coli) and Gram positive (S. mutans and S. aureus) strains, respectively which was relatively quite low compared to chemically synthesized silver nanoparticles. AgNPs inhibited 80% and 75% biofilms of E...
2017: PloS One
https://www.readbyqxmd.com/read/28771466/assembly-and-stoichiometry-of-the-core-structure-of-the-bacterial-flagellar-type-iii-export-gate-complex
#19
Takuma Fukumura, Fumiaki Makino, Tobias Dietsche, Miki Kinoshita, Takayuki Kato, Samuel Wagner, Keiichi Namba, Katsumi Imada, Tohru Minamino
The bacterial flagellar type III export apparatus, which is required for flagellar assembly beyond the cell membranes, consists of a transmembrane export gate complex and a cytoplasmic ATPase complex. FlhA, FlhB, FliP, FliQ, and FliR form the gate complex inside the basal body MS ring, although FliO is required for efficient export gate formation in Salmonella enterica. However, it remains unknown how they form the gate complex. Here we report that FliP forms a homohexameric ring with a diameter of 10 nm. Alanine substitutions of conserved Phe-137, Phe-150, and Glu-178 residues in the periplasmic domain of FliP (FliPP) inhibited FliP6 ring formation, suppressing flagellar protein export...
August 2017: PLoS Biology
https://www.readbyqxmd.com/read/28771236/the-cubicon-method-for-concentrating-membrane-proteins-in-the-cubic-mesophase
#20
Pikyee Ma, Dietmar Weichert, Luba A Aleksandrov, Timothy J Jensen, John R Riordan, Xiangyu Liu, Brian K Kobilka, Martin Caffrey
The lipid cubic phase (in meso) method is an important approach for generating crystals and high-resolution X-ray structures of integral membrane proteins. However, as a consequence of instability, it can be impossible-using traditional methods-to concentrate certain membrane proteins and complexes to values suitable for in meso crystallization and structure determination. The cubicon method described here exploits the amphiphilic nature of membrane proteins and their natural tendency to partition preferentially into lipid bilayers from aqueous solution...
September 2017: Nature Protocols
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