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Crystallization of membrane protein

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https://www.readbyqxmd.com/read/29168638/homology-modeling-and-molecular-dynamics-simulation-combined-with-x-ray-solution-scattering-defining-protein-structures-of-thromboxane-and-prostacyclin-synthases
#1
Hsiao-Ching Yang, Cheng-Han Yang, Ming Yi Huang, Jyh-Feng Lu, Jinn-Shyan Wang, Yi-Qi Yeh, U-Ser Jeng
A combination of molecular dynamics (MD) simulations and X-ray scattering (SAXS) has emerged as the approach of choice for studying protein structures and dynamics in solution. This approach has potential applications for membrane proteins that neither are soluble nor form crystals easily. We explore the water-coupled dynamic structures of thromboxane synthase (TXAS) and prostacyclin synthase (PGIS) from scanning HPLC-SAXS measurements combined with MD ensemble analyses. Both proteins are heme-containing enzymes in the cytochrome P450 family, known as prostaglandin H2 (PGH2) isomerase, with counter functions in regulation of platelet aggregation...
November 23, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29168553/probing-the-activity-of-a-recombinant-zn-2-transporting-p-type-atpase
#2
H Ravishankar, A Barth, M Andersson
P-type ATPase proteins maintain cellular homeostasis and uphold critical concentration gradients by ATP-driven ion transport across biological membranes. Characterization of single-cycle dynamics by time-resolved X-ray scattering techniques in solution could resolve structural intermediates not amendable to for example crystallization or cryo-electron microscopy sample preparation. To pave way for such time-resolved experiments, we used biochemical activity measurements, Attenuated Total Reflectance (ATR) and time-dependent Fourier-Transform Infra-Red (FTIR) spectroscopy to identify optimal conditions for activating a Zn(2+) -transporting Type-I ATPase from Shigella sonnei (ssZntA) at high protein concentration using caged ATP...
November 23, 2017: Biopolymers
https://www.readbyqxmd.com/read/29167753/homology-modeling-of-human-concentrative-nucleoside-transporters-hcnts-and-validation-by-virtual-screening-and-experimental-testing-to-identify-novel-hcnt1-inhibitors
#3
Hemant Kumar Deokar, Hilaire Playa Barch, John K Buolamwini
Objective: The nucleoside transporter family is an emerging target for cancer, viral and cardiovascular diseases. Due to the difficulty in the expression, isolation and crystallization of membrane proteins, there is a lack of structural information on any of the mammalian and for that matter the human proteins. Thus the objective of this study was to build homology models for the three cloned concentrative nucleoside transporters hCNT1, hCNT2 and hCNT3 and validate them for screening towards the discovery of much needed inhibitors and probes...
March 2017: Drug Des
https://www.readbyqxmd.com/read/29167507/characterization-of-the-early-molecular-changes-in-the-glomeruli-of-cd151-mice-highlights-induction-of-mindin-and-mmp-10
#4
Crystal Naudin, Brian Smith, Danielle R Bond, Matthew D Dun, Rodney J Scott, Leonie K Ashman, Judith Weidenhofer, Séverine Roselli
In humans and FVB/N mice, loss of functional tetraspanin CD151 is associated with glomerular disease characterised by early onset proteinuria and ultrastructural thickening and splitting of the glomerular basement membrane (GBM). To gain insight into the molecular mechanisms associated with disease development, we characterised the glomerular gene expression profile at an early stage of disease progression in FVB/N Cd151 (-/-) mice compared to Cd151 (+/+) controls. This study identified 72 up-regulated and 183 down-regulated genes in FVB/N Cd151 (-/-) compared to Cd151 (+/+) glomeruli (p < 0...
November 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29167463/structural-insights-into-the-committed-step-of-bacterial-phospholipid-biosynthesis
#5
Zhenjian Li, Yannan Tang, Yiran Wu, Suwen Zhao, Juan Bao, Yitian Luo, Dianfan Li
The membrane-integral glycerol 3-phosphate (G3P) acyltransferase PlsY catalyses the committed and essential step in bacterial phospholipid biosynthesis by acylation of G3P, forming lysophosphatidic acid. It contains no known acyltransferase motifs, lacks eukaryotic homologs, and uses the unusual acyl-phosphate as acyl donor, as opposed to acyl-CoA or acyl-carrier protein for other acyltransferases. Previous studies have identified several PlsY inhibitors as potential antimicrobials. Here we determine the crystal structure of PlsY at 1...
November 22, 2017: Nature Communications
https://www.readbyqxmd.com/read/29166022/dynamics-of-ompf-trimer-formation-in-the-bacterial-outer-membrane-of-escherichia-coli
#6
Huilin Ma, Aliza Khan, Shikha Nangia
The self-assembly of outer membrane protein F (OmpF) in the outer membrane of Escherichia coli Gram-negative bacteria was studied using multiscale molecular dynamics simulations. To facilitate the long timescale required for protein assembly, coarse-grained parameterization of E. coli outer membrane lipids was first developed. The OmpF monomers formed stable dimers at specific protein-protein interactions sites irrespective of the lipid membrane environment. The dimer intermediate was asymmetric but provided a template to form a symmetric trimer...
November 22, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/29159828/crystal-structure-of-the-legionella-effector-lem22
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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/29112284/morphological-and-cellular-diversity-of-magnetotactic-bacteria-a-review
#18
REVIEW
Tariqul Islam, Changsheng Peng, Imran Ali
Magnetotactic bacteria (MTB) are getting much attention in the recent years due to the biomineralization in their magnetosomes (MS). MS are unique organelles that are bio-mineralized due to MTB. MS contains nanosized crystal minerals of magnetite or greigite covered by bilayer lipid membrane, which are originated from cytoplasmic membrane (CM). MS are organized as an ordered chain into the cell which acts as a miniature compass needle. Furthermore, the biodiversity of MTB and their distribution is principally linked with the characteristics and growths of the MS...
November 7, 2017: Journal of Basic Microbiology
https://www.readbyqxmd.com/read/29109439/crystal-structure-of-tripartite-type-abc-transporter-macb-from-acinetobacter-baumannii
#19
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
#20
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
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