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https://www.readbyqxmd.com/read/28803692/a-janus-faced-im30-ring-involved-in-thylakoid-membrane-fusion-is-assembled-from-im30-tetramers
#1
Michael Saur, Raoul Hennig, Phoebe Young, Kristiane Rusitzka, Nadja Hellmann, Jennifer Heidrich, Nina Morgner, Jürgen Markl, Dirk Schneider
Biogenesis and dynamics of thylakoid membranes likely involves membrane fusion events. Membrane attachment of the inner membrane-associated protein of 30 kDa (IM30) affects the structure of the lipid bilayer, finally resulting in membrane fusion. Yet, how IM30 triggers membrane fusion is largely unclear. IM30 monomers pre-assemble into stable tetrameric building blocks, which further align to form oligomeric ring structures, and differently sized IM30 rings bind to membranes. Based on a 3D reconstruction of IM30 rings, we locate the IM30 loop 2 region at the bottom of the ring and show intact membrane binding but missing fusogenic activity of loop 2 mutants...
August 2, 2017: Structure
https://www.readbyqxmd.com/read/28781082/from-macrocrystals-to-microcrystals-a-strategy-for-membrane-protein-serial-crystallography
#2
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/28781083/kras-g12c-drug-development-discrimination-between-switch-ii-pocket-configurations-using-hydrogen-deuterium-exchange-mass-spectrometry
#3
Jia Lu, Rane A Harrison, Lianbo Li, Mei Zeng, Sudershan Gondi, David Scott, Nathanael S Gray, John R Engen, Kenneth D Westover
KRAS G12C, the most common RAS mutation found in non-small-cell lung cancer, has been the subject of multiple recent covalent small-molecule inhibitor campaigns including efforts directed at the guanine nucleotide pocket and separate work focused on an inducible pocket adjacent to the switch motifs. Multiple conformations of switch II have been observed, suggesting that switch II pocket (SIIP) binders may be capable of engaging a range of KRAS conformations. Here we report the use of hydrogen/deuterium-exchange mass spectrometry (HDX MS) to discriminate between conformations of switch II induced by two chemical classes of SIIP binders...
July 25, 2017: Structure
https://www.readbyqxmd.com/read/28781084/crystal-structure-and-regulation-of-the-citrus-pol-iii-repressor-maf1-by-auxin-and-phosphorylation
#4
Adriana Santos Soprano, Priscila Oliveira de Giuseppe, Hugo Massayoshi Shimo, Tatiani Brenelli Lima, Fernanda Aparecida Heleno Batista, Germanna Lima Righetto, José Geraldo de Carvalho Pereira, Daniela Campos Granato, Andrey Fabricio Ziem Nascimento, Fabio Cesar Gozzo, Paulo Sérgio Lopes de Oliveira, Ana Carolina Migliorini Figueira, Juliana Helena Costa Smetana, Adriana Franco Paes Leme, Mario Tyago Murakami, Celso Eduardo Benedetti
MAF1 is the main RNA polymerase (Pol) III repressor that controls cell growth in eukaryotes. The Citrus ortholog, CsMAF1, was shown to restrict cell growth in citrus canker disease but its role in plant development and disease is still unclear. We solved the crystal structure of the globular core of CsMAF1, which reveals additional structural elements compared with the previously available structure of hMAF1, and explored the dynamics of its flexible regions not present in the structure. CsMAF1 accumulated in the nucleolus upon leaf excision, and this translocation was inhibited by auxin and by mutation of the PKA phosphorylation site, S45, to aspartate...
July 24, 2017: Structure
https://www.readbyqxmd.com/read/28781081/specific-interaction-of-the-human-mitochondrial-uncoupling-protein-1-with-free-long-chain-fatty-acid
#5
Linlin Zhao, Shuqing Wang, Qianli Zhu, Bin Wu, Zhijun Liu, Bo OuYang, James J Chou
The mitochondrial uncoupling protein 1 (UCP1) generates heat by causing proton leak across the mitochondrial inner membrane that requires fatty acid (FA). The mechanism by which UCP1 uses FA to conduct proton remains unsolved, and it is also unclear whether a direct physical interaction between UCP1 and FA exists. Here, we have shown using nuclear magnetic resonance that FA can directly bind UCP1 at a helix-helix interface site composed of residues from the transmembrane helices H1 and H6. According to the paramagnetic relaxation enhancement data and molecular dynamics simulation, the FA acyl chain appears to fit into the groove between H1 and H6 while the FA carboxylate group interacts with the basic residues near the matrix side of UCP1...
July 19, 2017: Structure
https://www.readbyqxmd.com/read/28757145/structural-basis-for-substrate-recognition-by-the-ankyrin-repeat-domain-of-human-dhhc17-palmitoyltransferase
#6
Raffaello Verardi, Jin-Sik Kim, Rodolfo Ghirlando, Anirban Banerjee
DHHC enzymes catalyze palmitoylation, a major post-translational modification that regulates a number of key cellular processes. There are up to 24 DHHCs in mammals and hundreds of substrate proteins that get palmitoylated. However, how DHHC enzymes engage with their substrates is still poorly understood. There is currently no structural information about the interaction between any DHHC enzyme and protein substrates. In this study we have investigated the structural and thermodynamic bases of interaction between the ankyrin repeat domain of human DHHC17 (ANK17) and Snap25b...
July 18, 2017: Structure
https://www.readbyqxmd.com/read/28781080/structural-analysis-of-a-family-81-glycoside-hydrolase-implicates-its-recognition-of-%C3%AE-1-3-glucan-quaternary-structure
#7
Benjamin Pluvinage, Alexander Fillo, Patricia Massel, Alisdair B Boraston
Family 81 glycoside hydrolases (GHs), which are known to cleave β-1,3-glucans, are found in archaea, bacteria, eukaryotes, and viruses. Here we examine the structural and functional features of the GH81 catalytic module, BhGH81, from the Bacillus halodurans protein BH0236 to probe the molecular basis of β-1,3-glucan recognition and cleavage. BhGH81 displayed activity on laminarin, curdlan, and pachyman, but not scleroglucan; the enzyme also cleaved β-1,3-glucooligosaccharides as small as β-1,3-glucotriose...
July 17, 2017: Structure
https://www.readbyqxmd.com/read/28757146/regulation-of-receptor-binding-specificity-of-fgf9-by-an-autoinhibitory-homodimerization
#8
Yang Liu, Jinghong Ma, Andrew Beenken, Lakshmi Srinivasan, Anna V Eliseenkova, Moosa Mohammadi
The epithelial fibroblast growth factor 9 (FGF9) subfamily specifically binds and activates the mesenchymal "c" splice isoform of FGF receptors 1-3 (FGFR1-3) to regulate organogenesis and tissue homeostasis. The unique N and C termini of FGF9 subfamily ligands mediate a reversible homodimerization that occludes major receptor binding sites within the ligand core region. Here we provide compelling X-ray crystallographic, biophysical, and biochemical data showing that homodimerization controls receptor binding specificity of the FGF9 subfamily by keeping the concentration of active FGF9 monomers at a level, which is sufficient for a normal FGFR "c" isoform binding/signaling, but is insufficient for an illegitimate FGFR "b" isoform binding/signaling...
July 11, 2017: Structure
https://www.readbyqxmd.com/read/28757144/refined-cryo-em-structure-of-the-t4-tail-tube-exploring-the-lowest-dose-limit
#9
Weili Zheng, Fengbin Wang, Nicholas M I Taylor, Ricardo C Guerrero-Ferreira, Petr G Leiman, Edward H Egelman
The bacteriophage T4 contractile tail (containing a tube and sheath) was the first biological assembly reconstructed in three dimensions by electron microscopy at a resolution of ∼35 Å in 1968. A single-particle reconstruction of the T4 baseplate was able to generate a 4.1 Å resolution map for the first two rings of the tube using the overall baseplate for alignment. We have now reconstructed the T4 tail tube at a resolution of 3.4 Å, more than a 1,000-fold increase in information content for the tube from 1968...
July 10, 2017: Structure
https://www.readbyqxmd.com/read/28768162/structural-biology-of-the-immune-checkpoint-receptor-pd-1-and-its-ligands-pd-l1-pd-l2
#10
REVIEW
Krzysztof M Zak, Przemyslaw Grudnik, Katarzyna Magiera, Alexander Dömling, Grzegorz Dubin, Tad A Holak
Cancer cells can avoid and suppress immune responses through activation of inhibitory immune checkpoint proteins, such as PD-1, PD-L1, and CTLA-4. Blocking the activities of these proteins with monoclonal antibodies, and thus restoring T cell function, has delivered breakthrough therapies against cancer. In this review, we describe the latest work on structural characterization of the checkpoint proteins, their interactions with cognate ligands and with therapeutic antibodies. Structures of the extracellular portions of these proteins reveal that they all have a similar modular structure, composed of small domains similar in topology to the domains found in antibodies...
August 1, 2017: Structure
https://www.readbyqxmd.com/read/28712810/conformational-heterogeneity-in-the-activation-mechanism-of-bax
#11
C Ashley Barnes, Pushpa Mishra, James L Baber, Marie-Paule Strub, Nico Tjandra
Bax is known for its pro-apoptotic role within the mitochondrial pathway of apoptosis. However, the mechanism for transitioning Bax from cytosolic to membrane-bound oligomer remains elusive. Previous nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) studies defined monomeric Bax as conformationally homogeneous. Yet it has recently been proposed that monomeric Bax exists in equilibrium with a minor state that is distinctly different from its NMR structure. Here, we revisited the structural analysis of Bax using methods uniquely suited for unveiling "invisible" states of proteins, namely, NMR paramagnetic relaxation enhancements and EPR double electron-electron resonance (DEER)...
August 1, 2017: Structure
https://www.readbyqxmd.com/read/28712809/near-atomic-resolution-structure-of-a-plant-geminivirus-determined-by-electron-cryomicroscopy
#12
Katharina Hipp, Clemens Grimm, Holger Jeske, Bettina Böttcher
African cassava mosaic virus is a whitefly-transmitted geminivirus which forms unique twin particles of incomplete icosahedra that are joined at five-fold vertices, building an unusual waist. How its 22 capsomers interact within a half-capsid or across the waist is unknown thus far. Using electron cryo-microscopy and image processing, we determined the virion structure with a resolution of 4.2 Å and built an atomic model for its capsid protein. The inter-capsomer contacts mediated by the flexible N termini and loop regions differed within the half-capsids and at the waist, explaining partly the unusual twin structure...
August 1, 2017: Structure
https://www.readbyqxmd.com/read/28712808/structural-insight-into-the-activation-of-pkni-kinase-from-m-%C3%A2-tuberculosis-via-dimerization-of-the-extracellular-sensor-domain
#13
Qiaoling Yan, Dunquan Jiang, Lanfang Qian, Qingqing Zhang, Wei Zhang, Weihong Zhou, Kaixia Mi, Luke Guddat, Haitao Yang, Zihe Rao
Protein kinases play central roles in the survival of Mycobacterium tuberculosis within host. Here we report the individual high-resolution crystal structures of the sensor domain (in both monomer and dimer forms) and the kinase domain of PknI, a transmembrane protein member of the serine/threonine protein kinases (STPKs) family. PknI is the first STPK identified whose sensor domain exists in a monomer-dimer equilibrium. Inspection of the two structures of the sensor domain (PknI_SD) revealed conformational changes upon dimerization, with an arm region of critical importance for dimer formation identified...
August 1, 2017: Structure
https://www.readbyqxmd.com/read/28712807/snx16-regulates-the-recycling-of-e-cadherin-through-a-unique-mechanism-of-coordinated-membrane-and-cargo-binding
#14
Jinxin Xu, Leilei Zhang, Yinghua Ye, Yongli Shan, Chanjuan Wan, Junfeng Wang, Duanqing Pei, Xiaodong Shu, Jinsong Liu
E-Cadherin is a major component of adherens junctions on cell surfaces. SNX16 is a unique member of sorting nexins that contains a coiled-coil (CC) domain downstream of the PX domain. We report here that SNX16 regulates the recycling trafficking of E-cadherin. We solved the crystal structure of PX-CC unit of SNX16 and revealed a unique shear shaped homodimer. We identified a novel PI3P binding pocket in SNX16 that consists of both the PX and the CC domains. Surprisingly, we showed that the PPII/α2 loop, which is generally regarded as a membrane insertion loop in PX family proteins, is involved in the E-cadherin binding with SNX16...
August 1, 2017: Structure
https://www.readbyqxmd.com/read/28712806/structures-of-human-a1-and-a2a-adenosine-receptors-with-xanthines-reveal-determinants-of-selectivity
#15
Robert K Y Cheng, Elena Segala, Nathan Robertson, Francesca Deflorian, Andrew S Doré, James C Errey, Cédric Fiez-Vandal, Fiona H Marshall, Robert M Cooke
The adenosine A1 and A2A receptors belong to the purinergic family of G protein-coupled receptors, and regulate diverse functions of the cardiovascular, respiratory, renal, inflammation, and CNS. Xanthines such as caffeine and theophylline are weak, non-selective antagonists of adenosine receptors. Here we report the structure of a thermostabilized human A1 receptor at 3.3 Å resolution with PSB36, an A1-selective xanthine-based antagonist. This is compared with structures of the A2A receptor with PSB36 (2...
August 1, 2017: Structure
https://www.readbyqxmd.com/read/28712805/direct-spectroscopic-detection-of-atp-turnover-reveals-mechanistic-divergence-of-abc-exporters
#16
Alberto Collauto, Smriti Mishra, Aleksei Litvinov, Hassane S Mchaourab, Daniella Goldfarb
We have applied high-field (W-band) pulse electron-nuclear double resonance (ENDOR) and electron-electron double resonance (ELDOR)-detected nuclear magnetic resonance (EDNMR) to characterize the coordination sphere of the Mn(2+) co-factor in the nucleotide binding sites (NBSs) of ABC transporters. MsbA and BmrCD are two efflux transporters hypothesized to represent divergent catalytic mechanisms. Our results reveal distinct coordination of Mn(2+) to ATP and transporter residues in the consensus and degenerate NBSs of BmrCD...
August 1, 2017: Structure
https://www.readbyqxmd.com/read/28689970/structural-dynamics-of-zika-virus-ns2b-ns3-protease-binding-to-dipeptide-inhibitors
#17
Yan Li, Zhenzhen Zhang, Wint Wint Phoo, Ying Ru Loh, Weiling Wang, Shuang Liu, Ming Wei Chen, Alvin W Hung, Thomas H Keller, Dahai Luo, CongBao Kang
The NS2B-NS3 viral protease is an attractive drug target against Zika virus (ZIKV) due to its importance in viral replication and maturation. Here we report the crystal structure of protease in complex with a dipeptide inhibitor, Acyl-KR-aldehyde (compound 1). The aldehyde moiety forms a covalent bond with the catalytic Ser(135) of NS3. The Arg and Lys residues in the inhibitor occupy the S1 and S2 sites of the protease, respectively. Nuclear magnetic resonance studies demonstrate that the complex is in the closed conformation in solution...
August 1, 2017: Structure
https://www.readbyqxmd.com/read/28689969/ancestral-reconstruction-approach-to-acetylcholine-receptor-structure-and-function
#18
Jethro E Prinston, Johnathon R Emlaw, Mathieu F Dextraze, Christian J G Tessier, F Javier Pérez-Areales, Melissa S McNulty, Corrie J B daCosta
Acetylcholine receptors (AChRs) are members of a superfamily of proteins called pentameric ligand-gated ion channels, which are found in almost all forms of life and thus have a rich evolutionary history. Muscle-type AChRs are heteropentameric complexes assembled from four related subunits (α, β, δ, and ɛ). Here we reconstruct the amino acid sequence of a β subunit ancestor shared by humans and cartilaginous fishes (i.e., Torpedo). Then, by resurrecting this ancestral β subunit and co-expressing it with human α, δ, and ɛ subunits, we show that despite 132 substitutions, the ancestral subunit is capable of forming human/ancestral hybrid AChRs...
August 1, 2017: Structure
https://www.readbyqxmd.com/read/28689968/the-ribosomal-protein-ul22-modulates-the-shape-of-the-protein-exit-tunnel
#19
Itai Wekselman, Ella Zimmerman, Chen Davidovich, Matthew Belousoff, Donna Matzov, Miri Krupkin, Haim Rozenberg, Anat Bashan, Gilgi Friedlander, Jette Kjeldgaard, Hanne Ingmer, Lasse Lindahl, Janice M Zengel, Ada Yonath
Erythromycin is a clinically useful antibiotic that binds to an rRNA pocket in the ribosomal exit tunnel. Commonly, resistance to erythromycin is acquired by alterations of rRNA nucleotides that interact with the drug. Mutations in the β hairpin of ribosomal protein uL22, which is rather distal to the erythromycin binding site, also generate resistance to the antibiotic. We have determined the crystal structure of the large ribosomal subunit from Deinococcus radiodurans with a three amino acid insertion within the β hairpin of uL22 that renders resistance to erythromycin...
August 1, 2017: Structure
https://www.readbyqxmd.com/read/28669634/structure-of-phytoene-desaturase-provides-insights-into-herbicide-binding-and-reaction-mechanisms-involved-in-carotene-desaturation
#20
Anton Brausemann, Sandra Gemmecker, Julian Koschmieder, Sandro Ghisla, Peter Beyer, Oliver Einsle
Cyanobacteria and plants synthesize carotenoids via a poly-cis pathway starting with phytoene, a membrane-bound C40 hydrocarbon. Phytoene desaturase (PDS) introduces two double bonds and concomitantly isomerizes two neighboring double bonds from trans to cis. PDS assembles into homo-tetramers that interact monotopically with membranes. A long hydrophobic tunnel is proposed to function in the sequential binding of phytoene and the electron acceptor plastoquinone. The herbicidal inhibitor norflurazon binds at a plastoquinone site thereby blocking reoxidation of FADred...
August 1, 2017: Structure
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