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https://www.readbyqxmd.com/read/29456023/alternative-mode-of-e-site-trna-binding-in-the-presence-of-a-downstream-mrna-stem-loop-at-the-entrance-channel
#1
Yan Zhang, Samuel Hong, Ajchareeya Ruangprasert, Georgios Skiniotis, Christine M Dunham
Structured mRNAs positioned downstream of the ribosomal decoding center alter gene expression by slowing protein synthesis. Here, we solved the cryo-EM structure of the bacterial ribosome bound to an mRNA containing a 3' stem loop that regulates translation. Unexpectedly, the E-site tRNA adopts two distinct orientations. In the first structure, normal interactions with the 50S and 30S E site are observed. However, in the second structure, although the E-site tRNA makes normal interactions with the 50S E site, its anticodon stem loop moves ∼54 Å away from the 30S E site to interact with the 30S head domain and 50S uL5...
February 8, 2018: Structure
https://www.readbyqxmd.com/read/29429877/the-amaryllidaceae-alkaloid-haemanthamine-binds-the-eukaryotic-ribosome-to-repress-cancer-cell-growth
#2
Simone Pellegrino, Mélanie Meyer, Christiane Zorbas, Soumaya A Bouchta, Kritika Saraf, Stephen C Pelly, Gulnara Yusupova, Antonio Evidente, Véronique Mathieu, Alexander Kornienko, Denis L J Lafontaine, Marat Yusupov
Alkaloids isolated from the Amaryllidaceae plants have potential as therapeutics for treating human diseases. Haemanthamine has been studied as a novel anticancer agent due to its ability to overcome cancer cell resistance to apoptosis. Biochemical experiments have suggested that hemanthamine targets the ribosome. However, a structural characterization of its mechanism has been missing. Here we present the 3.1 Å resolution X-ray structure of haemanthamine bound to the Saccharomyces cerevisiae 80S ribosome...
February 3, 2018: Structure
https://www.readbyqxmd.com/read/29429879/multispecific-substrate-recognition-in-a-proton-dependent-oligopeptide-transporter
#3
Maria Martinez Molledo, Esben M Quistgaard, Ali Flayhan, Joanna Pieprzyk, Christian Löw
Proton-dependent oligopeptide transporters (POTs) are important for uptake of dietary di- and tripeptides in many organisms, and in humans are also involved in drug absorption. These transporters accept a wide range of substrates, but the structural basis for how different peptide side chains are accommodated has so far remained obscure. Twenty-eight peptides were screened for binding to PepTSt from Streptococcus thermophilus, and structures were determined of PepTSt in complex with four physicochemically diverse dipeptides, which bind with millimolar affinity: Ala-Leu, Phe-Ala, Ala-Gln, and Asp-Glu...
February 1, 2018: Structure
https://www.readbyqxmd.com/read/29398527/crystal-structures-of-fungal-tectonin-in-complex-with-o-methylated-glycans-suggest-key-role-in-innate-immune-defense
#4
Roman Sommer, Olga N Makshakova, Therese Wohlschlager, Stephanie Hutin, May Marsh, Alexander Titz, Markus Künzler, Annabelle Varrot
Innate immunity is the first line of defense against pathogens and predators. To initiate a response, it relies on the detection of invaders, where lectin-carbohydrate interactions play a major role. O-Methylated glycans were previously identified as non-self epitopes and conserved targets for defense effector proteins belonging to the tectonin superfamily. Here, we present two crystal structures of Tectonin 2 from the mushroom Laccaria bicolor in complex with methylated ligands, unraveling the molecular basis for this original specificity...
February 1, 2018: Structure
https://www.readbyqxmd.com/read/29398526/structure-of-the-30%C3%A2-kda-hiv-1-rna-dimerization-signal-by-a-hybrid-cryo-em-nmr-and-molecular-dynamics-approach
#5
Kaiming Zhang, Sarah C Keane, Zhaoming Su, Rossitza N Irobalieva, Muyuan Chen, Verna Van, Carly A Sciandra, Jan Marchant, Xiao Heng, Michael F Schmid, David A Case, Steven J Ludtke, Michael F Summers, Wah Chiu
Cryoelectron microscopy (cryo-EM) and nuclear magnetic resonance (NMR) spectroscopy are routinely used to determine structures of macromolecules with molecular weights over 65 and under 25 kDa, respectively. We combined these techniques to study a 30 kDa HIV-1 dimer initiation site RNA ([DIS]2; 47 nt/strand). A 9 Å cryo-EM map clearly shows major groove features of the double helix and a right-handed superhelical twist. Simulated cryo-EM maps generated from time-averaged molecular dynamics trajectories (10 ns) exhibited levels of detail similar to those in the experimental maps, suggesting internal structural flexibility limits the cryo-EM resolution...
February 1, 2018: Structure
https://www.readbyqxmd.com/read/29429880/deciphering-the-fuzzy-interaction-of-fg-nucleoporins-and-transport-factors-using-small-angle-neutron-scattering
#6
Samuel Sparks, Deniz B Temel, Michael P Rout, David Cowburn
The largely intrinsically disordered phenylalanine-glycine-rich nucleoporins (FG Nups) underline a selectivity mechanism that enables the rapid translocation of transport factors (TFs) through the nuclear pore complexes (NPCs). Conflicting models of NPC transport have assumed that FG Nups undergo different conformational transitions upon interacting with TFs. To selectively characterize conformational changes in FG Nups induced by TFs we performed small-angle neutron scattering (SANS) with contrast matching...
January 29, 2018: Structure
https://www.readbyqxmd.com/read/29429878/raf-1-cysteine-rich-domain-increases-the-affinity-of-k-ras-raf-at-the-membrane-promoting-mapk-signaling
#7
Shuai Li, Hyunbum Jang, Jian Zhang, Ruth Nussinov
K-Ras4B preferentially activates Raf-1. The high-affinity interaction of Ras-binding domain (RBD) of Raf with Ras was solved, but the relative position of Raf's cysteine-rich domain (CRD) in the Ras/Raf complex at the membrane and key question of exactly how it affects Raf signaling are daunting. We show that CRD stably binds anionic membranes inserting a positively charged loop into the amphipathic interface. Importantly, when in complex with Ras/RBD, covalently connected CRD presents the same membrane interaction mechanism, with CRD locating at the space between the RBD and membrane...
January 29, 2018: Structure
https://www.readbyqxmd.com/read/29429876/-to-be-or-not-to-be-protonated-atomic-details-of-human-carbonic-anhydrase-clinical-drug-complexes-by-neutron-crystallography-and-simulation
#8
Andrey Kovalevsky, Mayank Aggarwal, Hector Velazquez, Matthew J Cuneo, Matthew P Blakeley, Kevin L Weiss, Jeremy C Smith, S Zoë Fisher, Robert McKenna
Human carbonic anhydrases (hCAs) play various roles in cells, and have been drug targets for decades. Sequence similarities of hCA isoforms necessitate designing specific inhibitors, which requires detailed structural information for hCA-inhibitor complexes. We present room temperature neutron structures of hCA II in complex with three clinical drugs that provide in-depth analysis of drug binding, including protonation states of the inhibitors, hydration water structure, and direct visualization of hydrogen-bonding networks in the enzyme's active site...
January 29, 2018: Structure
https://www.readbyqxmd.com/read/29429875/molecular-mechanistic-insights-into-drosophila-dhx36-mediated-g-quadruplex-unfolding-a-structure-based-model
#9
Wei-Fei Chen, Stephane Rety, Hai-Lei Guo, Yang-Xue Dai, Wen-Qiang Wu, Na-Nv Liu, Daniel Auguin, Qian-Wen Liu, Xi-Miao Hou, Shuo-Xing Dou, Xu-Guang Xi
Helicase DHX36 plays essential roles in cell development and differentiation at least partially by resolving G-quadruplex (G4) structures. Here we report crystal structures of the Drosophila homolog of DHX36 (DmDHX36) in complex with RNA and a series of DNAs. By combining structural, small-angle X-ray scattering, molecular dynamics simulation, and single-molecule fluorescence studies, we revealed that positively charged amino acids in RecA2 and OB-like domains constitute an elaborate structural pocket at the nucleic acid entrance, in which negatively charged G4 DNA is tightly bound and partially destabilized...
January 29, 2018: Structure
https://www.readbyqxmd.com/read/29398525/remote-coupled-drastic-%C3%AE-barrel-to-%C3%AE-sheet-transition-of-the-protein-translocation-motor
#10
Arata Furukawa, Shintaro Nakayama, Kunihito Yoshikaie, Yoshiki Tanaka, Tomoya Tsukazaki
The membrane protein SecDF, belonging to the RND superfamily, enhances protein translocation at the extracytoplasmic side using a proton gradient. Here, we report the crystal structure of SecDF in a form we named Super-membrane-facing (Super F) form, demonstrating a β-barrel architecture instead of the previously reported β-sheet structure. Through this structural insight and supporting results of an in vivo crosslinking experiment, we propose a remote coupling model in which a structural change of the transmembrane region drives a functional, extracytoplasmic conformational transition...
January 26, 2018: Structure
https://www.readbyqxmd.com/read/29395788/monores-automatic-and-accurate-estimation-of-local-resolution-for-electron-microscopy-maps
#11
Jose Luis Vilas, Josué Gómez-Blanco, Pablo Conesa, Roberto Melero, José Miguel de la Rosa-Trevín, Joaquin Otón, Jesús Cuenca, Roberto Marabini, José María Carazo, Javier Vargas, Carlos Oscar S Sorzano
Since the beginning of electron microscopy, resolution has been a critical parameter. In this article, we propose a fully automatic, accurate method for determining the local resolution of a 3D map (MonoRes). The foundation of this algorithm is an extension of the concept of analytic signal, termed monogenic signal. The map is filtered at different frequencies and the amplitude of the monogenic signal is calculated, after which a criterion is applied to determine the resolution at each voxel. MonoRes is fully automatic without compulsory user parameters, with great accuracy in all tests, and is computationally more rapid than existing methods in the field...
January 26, 2018: Structure
https://www.readbyqxmd.com/read/29395784/structural-connection-between-activation-microswitch-and-allosteric-sodium-site-in-gpcr-signaling
#12
Kate L White, Matthew T Eddy, Zhan-Guo Gao, Gye Won Han, Tiffany Lian, Alexander Deary, Nilkanth Patel, Kenneth A Jacobson, Vsevolod Katritch, Raymond C Stevens
Sodium ions are endogenous allosteric modulators of many G-protein-coupled receptors (GPCRs). Mutation of key residues in the sodium binding motif causes a striking effect on G-protein signaling. We report the crystal structures of agonist complexes for two variants in the first sodium coordination shell of the human A2A adenosine receptor, D522.50N and S913.39A. Both structures present an overall active-like conformation; however, the variants show key changes in the activation motif NPxxY. Changes in the hydrogen bonding network in this microswitch suggest a possible mechanism for modified G-protein signaling and enhanced thermal stability...
January 26, 2018: Structure
https://www.readbyqxmd.com/read/29395789/structural-basis-of-formation-of-the-microtubule-minus-end-regulating-camsap-katanin-complex
#13
Kai Jiang, Lenka Faltova, Shasha Hua, Guido Capitani, Andrea E Prota, Christiane Landgraf, Rudolf Volkmer, Richard A Kammerer, Michel O Steinmetz, Anna Akhmanova
CAMSAP/Patronin family members regulate the organization and stability of microtubule minus ends in various systems ranging from mitotic spindles to differentiated epithelial cells and neurons. Mammalian CAMSAP2 and CAMSAP3 bind to growing microtubule minus ends, where they form stretches of stabilized microtubule lattice. The microtubule-severing ATPase katanin interacts with CAMSAPs and limits the length of CAMSAP-decorated microtubule stretches. Here, by using biochemical, biophysical, and structural approaches, we reveal that a short helical motif conserved in CAMSAP2 and CAMSAP3 binds to the heterodimer formed by the N- and C-terminal domains of katanin subunits p60 and p80, respectively...
January 21, 2018: Structure
https://www.readbyqxmd.com/read/29395787/structure-of-the-deactive-state-of-mammalian-respiratory-complex-i
#14
James N Blaza, Kutti R Vinothkumar, Judy Hirst
Complex I (NADH:ubiquinone oxidoreductase) is central to energy metabolism in mammalian mitochondria. It couples NADH oxidation by ubiquinone to proton transport across the energy-conserving inner membrane, catalyzing respiration and driving ATP synthesis. In the absence of substrates, active complex I gradually enters a pronounced resting or deactive state. The active-deactive transition occurs during ischemia and is crucial for controlling how respiration recovers upon reperfusion. Here, we set a highly active preparation of Bos taurus complex I into the biochemically defined deactive state, and used single-particle electron cryomicroscopy to determine its structure to 4...
January 21, 2018: Structure
https://www.readbyqxmd.com/read/29395786/an-intramolecular-interaction-of-uhrf1-reveals-dual-control-for-its-histone-association
#15
Linfeng Gao, Xiao-Feng Tan, Shen Zhang, Tianchen Wu, Zhi-Min Zhang, Hui-Wang Ai, Jikui Song
UHRF1 (ubiquitin-like, containing PHD and RING finger domains, 1) is one of the essential components of mammalian DNA methylation machinery. Chromatin association of UHRF1 is controlled via an interplay between its intramolecular interaction and dual recognition of histone H3 trimethylated at lysine 9 (H3K9me3) and hemimethylated DNA. Here, we report the crystal structure of the N-terminal tandem Tudor domain (TTD) of UHRF1 in complex with the C-terminal polybasic region (PBR). Structural analysis reveals that PBR binding leads to displacement of the TTD-plant homeodomain (PHD) linker, as well as blockage of the H3K9me3-engaging cage, both of which contribute to a chromatin-occluded UHRF1 conformation...
January 18, 2018: Structure
https://www.readbyqxmd.com/read/29358026/regulation-of-kinase-activity-in-the-caenorhabditis-elegans-egf-receptor-let-23
#16
Lijun Liu, Tarjani M Thaker, Daniel M Freed, Nicole Frazier, Ketan Malhotra, Mark A Lemmon, Natalia Jura
In the active HER receptor dimers, kinases play distinct roles; one is the catalytically active kinase and the other is its allosteric activator. This specialization enables signaling by the catalytically inactive HER3, which functions exclusively as an allosteric activator upon heterodimerization with other HER receptors. It is unclear whether the allosteric activation mechanism evolved before HER receptors functionally specialized. We determined the crystal structure of the kinase domain of the only EGF receptor in Caenorhabditis elegans, LET-23...
January 17, 2018: Structure
https://www.readbyqxmd.com/read/29358025/chain-assembly-and-disassembly-processes-differently-affect-the-conformational-space-of-ubiquitin-chains
#17
Andreas Kniss, Denise Schuetz, Sina Kazemi, Lukas Pluska, Philipp E Spindler, Vladimir V Rogov, Koraljka Husnjak, Ivan Dikic, Peter Güntert, Thomas Sommer, Thomas F Prisner, Volker Dötsch
Ubiquitination is the most versatile posttranslational modification. The information is encoded by linkage type as well as chain length, which are translated by ubiquitin binding domains into specific signaling events. Chain topology determines the conformational space of a ubiquitin chain and adds an additional regulatory layer to this ubiquitin code. In particular, processes that modify chain length will be affected by chain conformations as they require access to the elongation or cleavage sites. We investigated conformational distributions in the context of chain elongation and disassembly using pulsed electron-electron double resonance spectroscopy in combination with molecular modeling...
January 17, 2018: Structure
https://www.readbyqxmd.com/read/29336885/structural-basis-for-activity-and-specificity-of-an-anticoagulant-anti-fxia-monoclonal-antibody-and-a-reversal-agent
#18
Lauren K Ely, Marco Lolicato, Tovo David, Kate Lowe, Yun Cheol Kim, Dharmaraj Samuel, Paul Bessette, Jorge L Garcia, Thomas Mikita, Daniel L Minor, Shaun R Coughlin
Coagulation factor XIa is a candidate target for anticoagulants that better separate antithrombotic efficacy from bleeding risk. We report a co-crystal structure of the FXIa protease domain with DEF, a human monoclonal antibody that blocks FXIa function and prevents thrombosis in animal models without detectable increased bleeding. The light chain of DEF occludes the FXIa S1 subsite and active site, while the heavy chain provides electrostatic interactions with the surface of FXIa. The structure accounts for the specificity of DEF for FXIa over its zymogen and related proteases, its active-site-dependent binding, and its ability to inhibit substrate cleavage...
January 2, 2018: Structure
https://www.readbyqxmd.com/read/29307486/structural-mechanism-for-the-temperature-dependent-activation-of-the-hyperthermophilic-pf2001-esterase
#19
Nathalia Varejão, Rafael A De-Andrade, Rodrigo V Almeida, Cristiane D Anobom, Debora Foguel, David Reverter
Lipases and esterases constitute a group of enzymes that catalyze the hydrolysis or synthesis of ester bonds. A major biotechnological interest corresponds to thermophilic esterases, due to their intrinsic stability at high temperatures. The Pf2001 esterase from Pyrococcus furiosus reaches its optimal activity between 70°C and 80°C. The crystal structure of the Pf2001 esterase shows two different conformations: monomer and dimer. The structures reveal important rearrangements in the "cap" subdomain between monomer and dimer, by the formation of an extensive intertwined helical interface...
December 28, 2017: Structure
https://www.readbyqxmd.com/read/29307485/robo1-forms-a-compact-dimer-of-dimers-assembly
#20
Nataliia Aleksandrova, Irina Gutsche, Eaazhisai Kandiah, Sergiy V Avilov, Maxim V Petoukhov, Elena Seiradake, Andrew A McCarthy
Roundabout (Robo) receptors provide an essential repulsive cue in neuronal development following Slit ligand binding. This important signaling pathway can also be hijacked in numerous cancers, making Slit-Robo an attractive therapeutic target. However, little is known about how Slit binding mediates Robo activation. Here we present the crystal structure of Robo1 Ig1-4 and Robo1 Ig5, together with a negative stain electron microscopy reconstruction of the Robo1 ectodomain. These results show how the Robo1 ectodomain is arranged as compact dimers, mainly mediated by the central Ig domains, which can further interact in a "back-to-back" fashion to generate a tetrameric assembly...
December 28, 2017: Structure
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