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Crystallization of membrane protein

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https://www.readbyqxmd.com/read/29343583/structural-study-of-the-c-terminal-domain-of-non-structural-protein-1-from-japanese-encephalitis-virus
#1
Thanalai Poonsiri, Gareth S A Wright, Michael S Diamond, Lance Turtle, Tom Solomon, Svetlana V Antonyuk
Japanese encephalitis virus (JEV) is a mosquito-transmitted Flavivirus that is closely related to other emerging viral pathogens including dengue, West Nile (WNV) and Zika viruses. JEV infection can result in meningitis and encephalitis, which in severe cases cause permanent brain damage and death. JEV occurs predominantly in rural areas throughout Southeast Asia, the Pacific islands and the Far East, causing around 68,000 cases worldwide each year. In this study, we present a 2.1 Å resolution crystal structure of the C-terminal β-ladder domain of JEV non-structural protein 1 (NS1-C)...
January 17, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29339490/structural-basis-of-sterol-recognition-and-nonvesicular-transport-by-lipid-transfer-proteins-anchored-at-membrane-contact-sites
#2
Junsen Tong, Mohammad Kawsar Manik, Young Jun Im
Membrane contact sites (MCSs) in eukaryotic cells are hotspots for lipid exchange, which is essential for many biological functions, including regulation of membrane properties and protein trafficking. Lipid transfer proteins anchored at membrane contact sites (LAMs) contain sterol-specific lipid transfer domains [StARkin domain (SD)] and multiple targeting modules to specific membrane organelles. Elucidating the structural mechanisms of targeting and ligand recognition by LAMs is important for understanding the interorganelle communication and exchange at MCSs...
January 16, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29338257/a-dynamic-protein-protein-coupling-between-the-tonb-dependent-transporter-fhua-and-tonb
#3
Jessica Sarver, Michael Zhang, Lishan Liu, David Nyenhuis, David S Cafiso
Bacterial outer membrane TonB-dependent transporters function by executing cycles of binding and unbinding to the inner membrane protein TonB. In the vitamin B12 transporter BtuB and the ferric citrate transporter FecA, substrate binding increases the periplasmic exposure of the Ton box, an energy-coupling segment. This increased exposure appears to enhance the affinity of the transporter for TonB. Here, continuous wave and pulse EPR spectroscopy were used to examine the state of the Ton box in the Escherichia coli ferrichrome transporter, FhuA...
January 17, 2018: Biochemistry
https://www.readbyqxmd.com/read/29335469/structural-basis-for-chitin-acquisition-by-marine-vibrio-species
#4
Anuwat Aunkham, Michael Zahn, Anusha Kesireddy, Karunakar Reddy Pothula, Albert Schulte, Arnaud Baslé, Ulrich Kleinekathöfer, Wipa Suginta, Bert van den Berg
Chitin, an insoluble polymer of N-acetylglucosamine, is one of the most abundant biopolymers on Earth. By degrading chitin, chitinolytic bacteria such as Vibrio harveyi are critical for chitin recycling and maintenance of carbon and nitrogen cycles in the world's oceans. A decisive step in chitin degradation is the uptake of chito-oligosaccharides by an outer membrane protein channel named chitoporin (ChiP). Here, we report X-ray crystal structures of ChiP from V. harveyi in the presence and absence of chito-oligosaccharides...
January 15, 2018: Nature Communications
https://www.readbyqxmd.com/read/29330069/conformation-and-trimer-association-of-the-transmembrane-domain-of-the-parainfluenza-virus-fusion-protein-in-lipid-bilayers-from-solid-state-nmr-insights-into-the-sequence-determinants-of-trimer-structure-and-fusion-activity
#5
Myungwoon Lee, Hongwei Yao, Byungsu Kwon, Alan J Waring, Peter Ruchala, Chandan Singh, Mei Hong
Enveloped viruses enter cells by using their fusion proteins to merge the virus lipid envelope and the cell membrane. While crystal structures of the water-soluble ectodomains of many viral fusion proteins have been determined, the structure and assembly of the C-terminal transmembrane domain (TMD) remains poorly understood. Here we use solid-state NMR to determine the backbone conformation and oligomeric structure of the TMD of the parainfluenza virus 5 (PIV5) fusion protein. 13C chemical shifts indicate that the central leucine-rich segment of the TMD is α-helical in POPC/cholesterol membranes and POPE membranes, while the Ile- and Val-rich termini shift to the β-strand conformation in the POPE membrane...
January 9, 2018: Journal of Molecular Biology
https://www.readbyqxmd.com/read/29329285/a-direct-interaction-of-cholesterol-with-the-dopamine-transporter-prevents-its-out-to-inward-transition
#6
Talia Zeppelin, Lucy Kate Ladefoged, Steffen Sinning, Xavier Periole, Birgit Schiøtt
Monoamine transporters (MATs) carry out neurotransmitter reuptake from the synaptic cleft, a key step in neurotransmission, which is targeted in the treatment of neurological disorders. Cholesterol (CHOL), a major component of the synaptic plasma membrane, has been shown to exhibit a modulatory effect on MATs. Recent crystal structures of the dopamine transporter (DAT) revealed the presence of two conserved CHOL-like molecules, suggesting a functional protein-CHOL direct interaction. Here, we present extensive atomistic molecular dynamics (MD) simulations of DAT in an outward-facing conformation...
January 12, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29326245/fatty-acyl-recognition-and-transfer-by-an-integral-membrane-s-acyltransferase
#7
Mitra S Rana, Pramod Kumar, Chul-Jin Lee, Raffaello Verardi, Kanagalaghatta R Rajashankar, Anirban Banerjee
DHHC (Asp-His-His-Cys) palmitoyltransferases are eukaryotic integral membrane enzymes that catalyze protein palmitoylation, which is important in a range of physiological processes, including small guanosine triphosphatase (GTPase) signaling, cell adhesion, and neuronal receptor scaffolding. We present crystal structures of two DHHC palmitoyltransferases and a covalent intermediate mimic. The active site resides at the membrane-cytosol interface, which allows the enzyme to catalyze thioester-exchange chemistry by using fatty acyl-coenzyme A and explains why membrane-proximal cysteines are candidates for palmitoylation...
January 12, 2018: Science
https://www.readbyqxmd.com/read/29320700/role-of-phosphorylation-in-moesin-interactions-with-pip2-containing-biomimetic-membranes
#8
Quentin Lubart, Helene Vitet, Fabien Dalonneau, Aline Le Roy, Mathieu Kowalski, Morgane Lourdin, Christine Ebel, Marianne Weidenhaupt, Catherine Picart
Moesin, a protein of the ezrin, radixin, and moesin family, which links the plasma membrane to the cytoskeleton, is involved in multiple physiological and pathological processes, including viral budding and infection. Its interaction with the plasma membrane occurs via a key phosphoinositide, the phosphatidyl(4,5)inositol-bisphosphate (PIP2), and phosphorylation of residue T558, which has been shown to contribute, in cellulo, to a conformationally open protein. We study the impact of a double phosphomimetic mutation of moesin (T235D, T558D), which mimics the phosphorylation state of the protein, on protein/PIP2/microtubule interactions...
January 9, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/29311697/mechanistic-insights-into-the-role-of-prenyl-binding-protein-prbp-%C3%AE-in-membrane-dissociation-of-phosphodiesterase-6
#9
Bilal M Qureshi, Andrea Schmidt, Elmar Behrmann, Jörg Bürger, Thorsten Mielke, Christian M T Spahn, Martin Heck, Patrick Scheerer
Isoprenylated proteins are associated with membranes and their inter-compartmental distribution is regulated by solubilization factors, which incorporate lipid moieties in hydrophobic cavities and thereby facilitate free diffusion during trafficking. Here we report the crystal structure of a solubilization factor, the prenyl-binding protein (PrBP/δ), at 1.81 Å resolution in its ligand-free apo-form. Apo-PrBP/δ harbors a preshaped, deep hydrophobic cavity, capacitating apo-PrBP/δ to readily bind its prenylated cargo...
January 8, 2018: Nature Communications
https://www.readbyqxmd.com/read/29300389/high-throughput-in-situ-x-ray-screening-of-and-data-collection-from-protein-crystals-at-room-temperature-and-under-cryogenic-conditions
#10
Jana Broecker, Takefumi Morizumi, Wei-Lin Ou, Viviane Klingel, Anling Kuo, David J Kissick, Andrii Ishchenko, Ming-Yue Lee, Shenglan Xu, Oleg Makarov, Vadim Cherezov, Craig M Ogata, Oliver P Ernst
Protein crystallography has significantly advanced in recent years, with in situ data collection, in which crystals are placed in the X-ray beam within their growth medium, being a major point of focus. In situ methods eliminate the need to harvest crystals, a previously unavoidable drawback, particularly for often small membrane-protein crystals. Here, we present a protocol for the high-throughput in situ X-ray screening of and data collection from soluble and membrane-protein crystals at room temperature (20-25°C) and under cryogenic conditions...
February 2018: Nature Protocols
https://www.readbyqxmd.com/read/29295859/structure-of-yidc-from-thermotoga-maritima-and-its-implications-for-yidc-mediated-membrane-protein-insertion
#11
Yanlong Xin, Yan Zhao, Jiangge Zheng, Haizhen Zhou, Xuejun Cai Zhang, Changlin Tian, Yihua Huang
The evolutionarily conserved YidC/Oxa1/Alb3 family of proteins represents a unique membrane protein family that facilitates the insertion, folding, and assembly of a cohort of α-helical membrane proteins in all kingdoms of life, yet its underlying mechanisms remain elusive. We report the crystal structures of the periplasmic domain (TmPD) and the full-length YidC (TmYidC) from Thermotoga maritima at a resolution of 2.5 and 3.8 Å, respectively. The crystal structure of TmPD reveals a β-supersandwich fold but with apparently shortened β strands and different connectivity, as compared to the periplasmic domain (EcPD) of Escherichia coli YidC (EcYidC)...
January 2, 2018: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/29290736/chemically-stable-lipids-for-membrane-protein-crystallization
#12
Andrii Ishchenko, Lingling Peng, Egor Zinovev, Alexey Vlasov, Sung Chang Lee, Alexander Kuklin, Alexey Mishin, Valentin Borshchevskiy, Qinghai Zhang, Vadim Cherezov
Lipidic cubic phase (LCP) has been widely recognized as a promising membrane-mimicking matrix for biophysical studies of membrane proteins and their crystallization in a lipidic environment. Application of this material to a wide variety of membrane proteins, however, is hindered due to a limited number of available host lipids, mostly monoacylglycerols (MAGs). Here, we designed, synthesized and characterized a series of chemically stable lipids resistant to hydrolysis, with properties complementary to the widely used MAGs...
June 7, 2017: Crystal Growth & Design
https://www.readbyqxmd.com/read/29290112/insight-into-the-role-of-the-hv1-c-terminal-domain-in-dimer-stabilization
#13
Panisak Boonamnaj, Pornthep Sompornpisut
The voltage-gated proton-selective channel (Hv1) conducts protons in response to changes in membrane potential. The Hv1 protein forms dimers in the membrane. Crystal structures of Hv1 channels have revealed that the primary contacts between the two monomers are in the C-terminal domain (CTD), which forms a coiled-coil structure. The role of Hv1-CTD in channel assembly and activity is not fully understood. Here, molecular dynamics (MD) simulations of full-length and truncated CTD models of human and mouse Hv1 channels reveal a strong contribution of the CTD to the packing of the transmembrane domains...
January 1, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29288668/structural-insights-into-k48-linked-ubiquitin-chain-formation-by-the-pex4p-pex22p-complex
#14
Matthew R Groves, Carsten F E Schroer, Adam J Middleton, Sergey Lunev, Natasha Danda, Ameena M Ali, Siewert J Marrink, Chris Williams
Pex4p is a peroxisomal E2 involved in ubiquitinating the conserved cysteine residue of the cycling receptor protein Pex5p. Previously, we demonstrated that Pex4p from the yeast Saccharomyces cerevisiae binds directly to the peroxisomal membrane protein Pex22p and that this interaction is vital for receptor ubiquitination. In addition, Pex22p binding allows Pex4p to specifically produce lysine 48 linked ubiquitin chains in vitro through an unknown mechanism. This activity is likely to play a role in targeting peroxisomal proteins for proteasomal degradation...
December 27, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29288126/high-resolution-crystal-structures-of-clostridium-botulinum-neurotoxin-a3-and-a4-binding-domains
#15
Jonathan Davies, Jay Rees, Sai Man Liu, K Ravi Acharya
Clostridium botulinum neurotoxins (BoNTs) cause the life-threatening condition, botulism. However, while they have the potential to cause serious harm, they are increasingly being utilised for therapeutic applications. BoNTs comprise of seven distinct serotypes termed BoNT/A through BoNT/G, with the most widely characterised being sub-serotype BoNT/A1. Each BoNT consists of three structurally distinct domains, a binding domain (HC), a translocation domain (HN), and a proteolytic domain (LC). The HC domain is responsible for the highly specific targeting of the neurotoxin to neuronal cell membranes...
December 26, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/29287778/structural-evidence-for-a-fatty-acid-independent-myotoxic-mechanism-for-a-phospholipase-a2-like-toxin
#16
Guilherme H M Salvador, Juliana I Dos Santos, Rafael J Borges, Marcos R M Fontes
The myotoxic mechanism for PLA2-like toxins has been proposed recently to be initiated by an allosteric change induced by a fatty acid binding to the protein, leading to the alignment of the membrane docking site (MDoS) and membrane disrupting site (MDiS). Previous structural studies performed by us demonstrated that MjTX-II, a PLA2-like toxin isolated from Bothrops moojeni, presents a different mode of ligand-interaction, with its hydrophobic channels caused by natural amino acid substitutions and an insertion...
December 26, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29285400/structural-insight-into-the-ragulator-complex-which-anchors-mtorc1-to-the-lysosomal-membrane
#17
Zongkai Mu, Lei Wang, Wei Deng, Jiawei Wang, Geng Wu
The mechanistic target of rapamycin (mTOR) signal-transduction pathway plays a key role in regulating many aspects of metabolic processes. The central player of the mTOR signaling pathway, mTOR complex 1 (mTORC1), is recruited by the pentameric Ragulator complex and the heterodimeric Rag GTPase complex to the lysosomal membrane and thereafter activated. Here, we determined the crystal structure of the human Ragulator complex, which shows that Lamtor1 possesses a belt-like shape and wraps the other four subunits around...
2017: Cell Discovery
https://www.readbyqxmd.com/read/29280296/lock-and-chop-a-novel-method-for-the-generation-of-a-pick1-pdz-domain-and-piperidine-based-inhibitor-co-crystal-structure
#18
Douglas J Marcotte, Jean-Christophe Hus, Charles C Banos, Craig Wildes, Robert Arduini, Chris Bergeron, Catherine A Hession, Darren P Baker, Edward Lin, Kevin M Guckian, Anthone W Dunah, Laura F Silvian
The membrane protein interacting with kinase C1 (PICK1) plays a trafficking role in the internalization of neuron receptors such as the amino-3-hydroxyl-5-methyl-4-isoxazole-propionate (AMPA) receptor. Reduction of surface AMPA type receptors on neurons reduces synaptic communication leading to cognitive impairment in progressive neurodegenerative diseases such as Alzheimer disease. The internalization of AMPA receptors is mediated by the PDZ domain of PICK1 which binds to the GluA2 subunit of AMPA receptors and targets the receptor for internalization through endocytosis, reducing synaptic communication...
December 27, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/29259089/peptide-uptake-is-essential-for-borrelia-burgdorferi-viability-and-involves-structural-and-regulatory-complexity-of-its-oligopeptide-transporter
#19
Ashley M Groshong, Abhishek Dey, Irina Bezsonova, Melissa J Caimano, Justin D Radolf
Borrelia burgdorferi is an extreme amino acid (AA) auxotroph whose genome encodes few free AA transporters and an elaborate oligopeptide transport system (B. burgdorferi Opp [BbOpp]). BbOpp consists of five oligopeptide-binding proteins (OBPs), two heterodimeric permeases, and a heterodimeric nucleotide-binding domain (NBD). Homology modeling based on the crystal structure of liganded BbOppA4 revealed that each OBP likely binds a distinct range of peptides. Transcriptional analyses demonstrated that the OBPs are differentially and independently regulated whereas the permeases and NBDs are constitutively expressed...
December 19, 2017: MBio
https://www.readbyqxmd.com/read/29243866/the-dual-role-of-mamb-in-magnetosome-membrane-assembly-and-magnetite-biomineralization
#20
René Uebe, Noa Keren-Khadmy, Natalie Zeytuni, Emanuel Katzmann, Yotam Navon, Geula Davidov, Ronit Bitton, Jürgen M Plitzko, Dirk Schüler, Raz Zarivach
Magnetospirillum gryphiswaldense MSR-1 synthesizes membrane-enclosed magnetite (Fe3 O4 ) nanoparticles, magnetosomes, for magnetotaxis. Formation of these organelles involves a complex process comprising key steps which are governed by specific magnetosome-associated proteins. MamB, a cation diffusion facilitator (CDF) family member has been implicated in magnetosome-directed iron transport. However, deletion mutagenesis studies revealed that MamB is essential for the formation of magnetosome membrane vesicles, but its precise role remains elusive...
December 15, 2017: Molecular Microbiology
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