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https://www.readbyqxmd.com/read/28437792/phase-plate-cryo-em-structure-of-a-class-b-gpcr-g-protein-complex
#1
Yi-Lynn Liang, Maryam Khoshouei, Mazdak Radjainia, Yan Zhang, Alisa Glukhova, Jeffrey Tarrasch, David M Thal, Sebastian G B Furness, George Christopoulos, Thomas Coudrat, Radostin Danev, Wolfgang Baumeister, Laurence J Miller, Arthur Christopoulos, Brian K Kobilka, Denise Wootten, Georgios Skiniotis, Patrick M Sexton
Class B G-protein-coupled receptors are major targets for the treatment of chronic diseases, such as osteoporosis, diabetes and obesity. Here we report the structure of a full-length class B receptor, the calcitonin receptor, in complex with peptide ligand and heterotrimeric Gαsβγ protein determined by Volta phase-plate single-particle cryo-electron microscopy. The peptide agonist engages the receptor by binding to an extended hydrophobic pocket facilitated by the large outward movement of the extracellular ends of transmembrane helices 6 and 7...
April 24, 2017: Nature
https://www.readbyqxmd.com/read/28434970/transfer-of-c-terminal-residues-of-human-apolipoprotein-a-i-to-insect-apolipophorin-iii-creates-a-two-domain-chimeric-protein-with-enhanced-lipid-binding-activity
#2
James V C Horn, Rachel A Ellena, Jesse J Tran, Wendy H J Beck, Vasanthy Narayanaswami, Paul M M Weers
Apolipophorin III (apoLp-III) is an insect apolipoprotein (18kDa) that comprises a single five-helix bundle domain. In contrast, human apolipoprotein A-I (apoA-I) is a 28kDa two-domain protein: an α-helical N-terminal domain (residues 1-189) and a less structured C-terminal domain (residues 190-243). To better understand the apolipoprotein domain organization, a novel chimeric protein was engineered by attaching residues 179 to 243 of apoA-I to the C-terminal end of apoLp-III. The apoLp-III/apoA-I chimera was successfully expressed and purified in E...
April 20, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28433529/antimicrobial-peptides-within-the-yellowtail-kingfish-seriola-lalandi
#3
Simon Muncaster, Kirsty Kraakman, Olivia Gibbons, Koen Mensink, Maria Forlenza, Gregory Jacobson, Steve Bird
A number of Seriola species are currently farmed or being investigated as future aquaculture species in countries around the world. However they face a number of issues and limitations which will need to be overcome to ensure future stability and growth, one of which are disease outbreaks. Despite this, very little has been done to understand the immune system of Seriola species and very few immune genes have been characterised. Antimicrobial peptides (AMP) are naturally occurring low molecular weight polypeptides that play a major role in an organism's immune system and act effectively as a first line of defence...
April 19, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/28432258/lil3-a-light-harvesting-complex-protein-links-terpenoid-and-tetrapyrrole-biosynthesis
#4
Daniel Hey, Maxi Rothbart, Josephine Herbst, Peng Wang, Jakob Müller, Daniel Wittmann, Kirsten Gruhl, Bernhard Grimm
LIL3 of Arabidopsis thaliana belongs to the light-harvesting complex (LHC) family, which also includes the light-harvesting chlorophyll-binding proteins of photosystems 1 and 2, the early-light-inducible proteins, PsbS involved in non-photochemical quenching, the one-helix-proteins and their cyanobacterial homologs designated high-light-inducible proteins. Each member of this family is characterized by one or two LHC transmembrane domains (referred to as the LHC motif) to which potential functions such as chlorophyll binding, protein interaction and integration of interacting partners into the plastid membranes have been attributed...
April 21, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28429592/peptide-retention-time-prediction-in-hydrophilic-interaction-liquid-chromatography-data-collection-methods-and-features-of-additive-and-sequence-specific-models
#5
Oleg V Krokhin, Peyman Ezzati, Vic Spicer
The development of a peptide retention prediction model for hydrophilic interaction liquid chromatography (XBridge Amide column) is described for a collection of ~40,000 tryptic peptides. Off-line 2D LC-MS/MS analysis (HILIC-RPLC) of S. cerevisiae whole cell lysate has been used to acquire retention information for a HILIC separation. The large size of the optimization dataset (more than two orders of magnitude compared to previous reports) permits the accurate assignment of hydrophilic retention coefficients of individual amino acids, establishing both, the effects of amino-acid position relative to peptide termini and the influence of peptide secondary structure in HILIC...
April 21, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28428744/mutational-analysis-at-intersubunit-interfaces-of-an-anionic-glutamate-receptor-reveals-a-key-interaction-important-for-channel-gating-by-ivermectin
#6
Nurit Degani-Katzav, Revital Gortler, Marina Weissman, Yoav Paas
The broad-spectrum anthelmintic drug ivermectin (IVM) activates and stabilizes an open-channel conformation of invertebrate chloride-selective glutamate receptors (GluClRs), thereby causing a continuous inflow of chloride ions and sustained membrane hyperpolarization. These effects suppress nervous impulses and vital physiological processes in parasitic nematodes. The GluClRs are pentamers. Homopentameric receptors assembled from the Caenorhabditis elegans (C. elegans) GluClα (GLC-1) subunit can inherently respond to IVM but not to glutamate (the neurotransmitter)...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28425679/soft-interactions-and-volume-exclusion-by-polymeric-crowders-can-stabilize-or-destabilize-transient-structure-in-disordered-proteins-depending-on-polymer-concentration
#7
Farai I Rusinga, David D Weis
The effects of macromolecular crowding on the transient structure of intrinsically disordered proteins is not well-understood. Crowding by biological molecules inside cells could modulate transient structure and alter IDP function. Volume exclusion theory and observations of structured proteins suggest that IDP transient structure would be stabilized by macromolecular crowding. Amide hydrogen exchange (HX) of IDPs in highly concentrated polymer solutions would provide valuable insights into IDP transient structure under crowded conditions...
April 20, 2017: Proteins
https://www.readbyqxmd.com/read/28425466/crystal-structures-of-the-no-sensor-nsrr-reveal-how-its-iron-sulfur-cluster-modulates-dna-binding
#8
Anne Volbeda, Erin L Dodd, Claudine Darnault, Jason C Crack, Oriane Renoux, Matthew I Hutchings, Nick E Le Brun, Juan C Fontecilla-Camps
NsrR from Streptomyces coelicolor (Sc) regulates the expression of three genes through the progressive degradation of its [4Fe-4S] cluster on nitric oxide (NO) exposure. We report the 1.95 Å resolution crystal structure of dimeric holo-ScNsrR and show that the cluster is coordinated by the three invariant Cys residues from one monomer and, unexpectedly, Asp8 from the other. A cavity map suggests that NO displaces Asp8 as a cluster ligand and, while D8A and D8C variants remain NO sensitive, DNA binding is affected...
April 20, 2017: Nature Communications
https://www.readbyqxmd.com/read/28425152/nmr-structures-and-molecular-dynamics-simulation-of-hylin-a1-peptide-analogs-interacting-with-micelles
#9
Edson Crusca, Amanda Souza Câmara, Carolina Oliveira Matos, Reinaldo Marchetto, Eduardo Maffud Cilli, Luciano Morais Lião, Aline Lima de Oliveira
Antimicrobial peptides are recognized candidates with pharmaceutical potential against epidemic emerging multi-drug resistant bacteria. In this study, we use nuclear magnetic resonance spectroscopy and molecular dynamics simulations to determine the unknown structure and evaluate the interaction with dodecylphosphatidylcholine (DPC) and sodium dodecylsulphate (SDS) micelles with three W(6) -Hylin-a1 analogs antimicrobial peptides (HyAc, HyK, and HyD). The HyAc, HyK, and HyD bound to DPC micelles are all formed by a unique α-helix structure...
April 20, 2017: Journal of Peptide Science: An Official Publication of the European Peptide Society
https://www.readbyqxmd.com/read/28419165/soaking-suggests-alternative-facts-only-co-crystallization-discloses-major-ligand-induced-interface-rearrangements-of-a-homodimeric-trna-binding-protein-indicating-a-novel-mode-of-inhibition
#10
Frederik Rainer Ehrmann, Johann Stojko, Alexander Metz, François Debaene, Luzi Jakob Barandun, Andreas Heine, François Diederich, Sarah Cianférani, Klaus Reuter, Gerhard Klebe
For the efficient pathogenesis of Shigella, the causative agent of bacillary dysentery, full functionality of tRNA-guanine transglycosylase (TGT) is mandatory. TGT performs post-transcriptional modifications of tRNAs in the anticodon loop taking impact on virulence development. This suggests TGT as a putative target for selective anti-shigellosis drug therapy. Since bacterial TGT is only functional as homodimer, its activity can be inhibited either by blocking its active site or by preventing dimerization. Recently, we discovered that in some crystal structures obtained by soaking the full conformational adaptation most likely induced in solution upon ligand binding is not displayed...
2017: PloS One
https://www.readbyqxmd.com/read/28415220/multistage-modeling-of-protein-dynamics-with-monomeric-myc-oncoprotein-as-an-example
#11
Jiaojiao Liu, Jin Dai, Jianfeng He, Antti J Niemi, Nevena Ilieva
We propose to combine a mean-field approach with all-atom molecular dynamics (MD) into a multistage algorithm that can model protein folding and dynamics over very long time periods yet with atomic-level precision. As an example, we investigate an isolated monomeric Myc oncoprotein that has been implicated in carcinomas including those in colon, breast, and lungs. Under physiological conditions a monomeric Myc is presumed to be an example of intrinsically disordered proteins that pose a serious challenge to existing modeling techniques...
March 2017: Physical Review. E
https://www.readbyqxmd.com/read/28413881/molecular-mechanism-on-stabilizing-huntingtin-n17-helical-structure-in-micelle-environment
#12
Leili Zhang, Hongsuk Kang, Francisco X Vázquez, Leticia Marisel Toledo-Sherman, Binquan Luan, Ruhong Zhou
Huntington's disease is a deadly neurodegenerative disease caused by the fibrilization of huntingtin (HTT) exon-1 protein mutants. Despite extensive efforts over the past decade, much remains unknown about the structures of (mutant) HTT exon-1 and their enigmatic roles in aggregation. Particularly, whether the first 17 residues in the N-terminal (HTT-N17) adopt a helical or a coiled structure remains unclear. Here, with the rigorous study of molecular dynamics simulations, we explored the most possible structures of HTT-N17 in both dodecylphosphocholine (DPC) micelles and aqueous solution, using three commonly applied force fields (OPLS-AA/L, CHARMM36 and AMBER99sb*-ILDNP) to examine the underlying molecular mechanism and rule out the potential artifacts...
April 17, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28402881/stability-and-conformation-of-a-chemoreceptor-hamp-domain-chimera-correlates-with-signaling-properties
#13
Nattakan Sukomon, Joanne Widom, Peter P Borbat, Jack H Freed, Brian R Crane
HAMP domains are dimeric, four-helix bundles that transduce conformational signals in bacterial receptors. Genetic studies of the Escherichia coli serine receptor (Tsr) provide an opportunity to understand HAMP conformational behavior in terms of functional output. To increase its stability, the Tsr HAMP domain was spliced into a poly-HAMP unit from the Pseudomonas aeruginosa Aer2 receptor. Within the chimera, the Tsr HAMP undergoes a thermal melting transition at a temperature much lower than that of the Aer2 HAMP domains...
April 11, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28396444/the-cryo-em-structure-of-yjeq-bound-to-the-30s-subunit-suggests-a-fidelity-checkpoint-function-for-this-protein-in-ribosome-assembly
#14
Aida Razi, Alba Guarné, Joaquin Ortega
Recent work suggests that bacterial YjeQ (RsgA) participates in the late stages of assembly of the 30S subunit and aids the assembly of the decoding center but also binds the mature 30S subunit with high affinity. To determine the function and mechanisms of YjeQ in the context of the mature subunit, we determined the cryo-EM structure of the fully assembled 30S subunit in complex with YjeQ at 5.8-Å resolution. We found that binding of YjeQ stabilizes helix 44 into a conformation similar to that adopted by the subunit during proofreading...
April 10, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28396405/structure-of-a-dna-glycosylase-that-unhooks-interstrand-cross-links
#15
Elwood A Mullins, Garrett M Warren, Noah P Bradley, Brandt F Eichman
DNA glycosylases are important editing enzymes that protect genomic stability by excising chemically modified nucleobases that alter normal DNA metabolism. These enzymes have been known only to initiate base excision repair of small adducts by extrusion from the DNA helix. However, recent reports have described both vertebrate and microbial DNA glycosylases capable of unhooking highly toxic interstrand cross-links (ICLs) and bulky minor groove adducts normally recognized by Fanconi anemia and nucleotide excision repair machinery, although the mechanisms of these activities are unknown...
April 10, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28396019/synthesis-of-oligonucleotides-containing-novel-g-clamp-analogue-with-c8-tethered-group-in-phenoxazine-ring-implication-to-qpcr-detection-of-the-low-copy-kemerovo-virus-dsrna
#16
Anna M Varizhuk, Timofei S Zatsepin, Andrey V Golovin, Evgeny S Belyaev, Yury I Kostyukevich, Vladimir G Dedkov, German A Shipulin, George V Shpakovski, Andrey V Aralov
Nowadays modified oligonucleotides are widely used in diagnostics and as novel therapeutics. Introduction of modified or unnatural residues into oligonucleotides allows fine tuning of their binding properties to complementary nucleic acids and leads to improved stability both in vitro and in vivo. Previously it was demonstrated that insertion of phenoxazine nucleotides with various groups in C9-position into oligonucleotides leads to a significant increase of duplex stability with complementary DNA and RNA...
March 31, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/28393861/capturing-rna-folding-free-energy-with-coarse-grained-molecular-dynamics-simulations
#17
David R Bell, Sara Y Cheng, Heber Salazar, Pengyu Ren
We introduce a coarse-grained RNA model for molecular dynamics simulations, RACER (RnA CoarsE-gRained). RACER achieves accurate native structure prediction for a number of RNAs (average RMSD of 2.93 Å) and the sequence-specific variation of free energy is in excellent agreement with experimentally measured stabilities (R(2) = 0.93). Using RACER, we identified hydrogen-bonding (or base pairing), base stacking, and electrostatic interactions as essential driving forces for RNA folding. Also, we found that separating pairing vs...
April 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28380438/imaging-of-hypoxia-inducible-factor-1%C3%AE-and-septin-9-interaction-by-bimolecular-fluorescence-complementation-in-live-cancer-cells
#18
Maya Golan, Nicola J Mabjeesh
Hypoxia-inducible factor 1 (HIF-1) is a major mediator of the hypoxic response involved in tumor progression. We had earlier described the interaction between septin 9 isoform 1 (SEPT9_i1) protein and the oxygen-regulated subunit, HIF-1α. SEPT9_i1 is a member of the conserved family of GTP-binding cytoskeleton septins. SEPT9_i1 stabilizes HIF-1α and facilitates its cytoplasmic-nuclear translocation. We utilized split yellow fluorescent protein (YFP) bimolecular fluorescence complementation (BiFC) methodology to monitor the interaction between HIF-1α and SEPT9_i1 in live cells...
March 23, 2017: Oncotarget
https://www.readbyqxmd.com/read/28379944/structural-basis-for-selectivity-and-diversity-in-angiotensin-ii-receptors
#19
Haitao Zhang, Gye Won Han, Alexander Batyuk, Andrii Ishchenko, Kate L White, Nilkanth Patel, Anastasiia Sadybekov, Beata Zamlynny, Michael T Rudd, Kaspar Hollenstein, Alexandra Tolstikova, Thomas A White, Mark S Hunter, Uwe Weierstall, Wei Liu, Kerim Babaoglu, Eric L Moore, Ryan D Katz, Jennifer M Shipman, Margarita Garcia-Calvo, Sujata Sharma, Payal Sheth, Stephen M Soisson, Raymond C Stevens, Vsevolod Katritch, Vadim Cherezov
The angiotensin II receptors AT1R and AT2R serve as key components of the renin-angiotensin-aldosterone system. AT1R has a central role in the regulation of blood pressure, but the function of AT2R is unclear and it has a variety of reported effects. To identify the mechanisms that underlie the differences in function and ligand selectivity between these receptors, here we report crystal structures of human AT2R bound to an AT2R-selective ligand and to an AT1R/AT2R dual ligand, capturing the receptor in an active-like conformation...
April 20, 2017: Nature
https://www.readbyqxmd.com/read/28379137/structural-basis-of-protein-translocation-by-the-vps4-vta1-aaa-atpase
#20
Nicole Monroe, Han Han, Peter S Shen, Wesley I Sundquist, Christopher P Hill
Many important cellular membrane fission reactions are driven by ESCRT pathways, which culminate in disassembly of ESCRT-III polymers by the AAA ATPase Vps4. We report a 4.3 Å resolution cryo-EM structure of the active Vps4 hexamer with its cofactor Vta1, ADP•BeFx, and an ESCRT-III substrate peptide. Four Vps4 subunits form a helix whose interfaces are consistent with ATP-binding, is stabilized by Vta1, and binds the substrate peptide. The fifth subunit approximately continues this helix but appears to be dissociating...
April 5, 2017: ELife
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