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https://www.readbyqxmd.com/read/28434916/the-tetrameric-plant-lectin-banlec-neutralizes-hiv-through-bidentate-binding-to-specific-viral-glycans
#1
Jonathan T S Hopper, Stephen Ambrose, Oliver C Grant, Stefanie A Krumm, Timothy M Allison, Matteo T Degiacomi, Mark D Tully, Laura K Pritchard, Gabriel Ozorowski, Andrew B Ward, Max Crispin, Katie J Doores, Robert J Woods, Justin L P Benesch, Carol V Robinson, Weston B Struwe
Select lectins have powerful anti-viral properties that effectively neutralize HIV-1 by targeting the dense glycan shield on the virus. Here, we reveal the mechanism by which one of the most potent lectins, BanLec, achieves its inhibition. We identify that BanLec recognizes a subset of high-mannose glycans via bidentate interactions spanning the two binding sites present on each BanLec monomer that were previously considered separate carbohydrate recognition domains. We show that both sites are required for high-affinity glycan binding and virus neutralization...
April 17, 2017: Structure
https://www.readbyqxmd.com/read/28434915/x-ray-crystallography-and-electron-microscopy-of-cross-and-multi-module-nonribosomal-peptide-synthetase-proteins-reveal-a-flexible-architecture
#2
Michael J Tarry, Asfarul S Haque, Khanh Huy Bui, T Martin Schmeing
Nonribosomal peptide synthetases (NRPS) are macromolecular machines that produce peptides with diverse activities. Structural information exists for domains, didomains, and even modules, but little is known about higher-order organization. We performed a multi-technique study on constructs from the dimodular NRPS DhbF. We determined a crystal structure of a cross-module construct including the adenylation (A) and peptidyl carrier protein (PCP) domains from module 1 and the condensation domain from module 2, complexed with an adenosine-vinylsulfonamide inhibitor and an MbtH-like protein (MLP)...
April 17, 2017: Structure
https://www.readbyqxmd.com/read/28434917/conformational-dynamics-and-allostery-in-e2-e3-interactions-drive-ubiquitination-gp78-and-ube2g2
#3
Kalyan S Chakrabarti, Jess Li, Ranabir Das, R Andrew Byrd
Conformational dynamics plays a fundamental role in molecular recognition and activity in enzymes. The ubiquitin-conjugating enzyme (E2) Ube2g2 functions with the ubiquitin ligase (E3) gp78 to assemble poly-ubiquitin chains on target substrates. Two domains in gp78, RING and G2BR, bind to two distant regions of Ube2g2, and activate it for ubiquitin (Ub) transfer. G2BR increases the affinity between the RING and Ube2g2 by 50-fold, while the RING catalyzes the transfer of Ub from the Ube2g2∼Ub conjugate. How G2BR and RING activate Ube2g2 is unclear...
April 13, 2017: Structure
https://www.readbyqxmd.com/read/28416112/flexibility-and-design-conformational-heterogeneity-along-the-evolutionary-trajectory-of-a-redesigned-ubiquitin
#4
Justin T Biel, Michael C Thompson, Christian N Cunningham, Jacob E Corn, James S Fraser
Although protein design has been used to introduce new functions, designed variants generally only function as well as natural proteins after rounds of laboratory evolution. One possibility for this pattern is that designed mutants frequently sample nonfunctional conformations. To test this idea, we exploited advances in multiconformer modeling of room-temperature X-ray data collection on redesigned ubiquitin variants selected for increasing binding affinity to the deubiquitinase USP7. Initial core mutations disrupt natural packing and lead to increased flexibility...
April 12, 2017: Structure
https://www.readbyqxmd.com/read/28416111/structural-analysis-reveals-features-of-ribosome-assembly-factor-nsa1-wdr74-important-for-localization-and-interaction-with-rix7-nvl2
#5
Yu-Hua Lo, Erin M Romes, Monica C Pillon, Mack Sobhany, Robin E Stanley
Ribosome assembly is a complex process that requires hundreds of essential assembly factors, including Rix7 (NVL2 in mammals) and Nsa1 (WDR74 in mammals). Rix7 is a type II double ring, AAA-ATPase, which is closely related to the well-known Cdc48/p97. Previous studies in Saccharomyces cerevisiae suggest that Rix7 mediates the release of Nsa1 from nucleolar pre-60S particles; however, the underlying mechanisms of this release are unknown. Through multiple structural analyses we show that S. cerevisiae Nsa1 is composed of an N-terminal seven-bladed WD40 domain followed by a lysine-rich C terminus that extends away from the WD40 domain and is required for nucleolar localization...
April 12, 2017: Structure
https://www.readbyqxmd.com/read/28434914/full-length-oligomeric-structure-of-wzz-determined-by-cryoelectron-microscopy-reveals-insights-into-membrane-bound-states
#6
Richard F Collins, Vasileios Kargas, Brad R Clarke, C Alistair Siebert, Daniel K Clare, Peter J Bond, Chris Whitfield, Robert C Ford
Wzz is an integral inner membrane protein involved in regulating the length of lipopolysaccharide O-antigen glycans and essential for the virulence of many Gram-negative pathogens. In all Wzz homologs, the large periplasmic domain is proposed to be anchored by two transmembrane helices, but no information is available for the transmembrane and cytosolic domains. Here we have studied purified oligomeric Wzz complexes using cryoelectron microscopy and resolved the transmembrane regions within a semi-continuous detergent micelle...
April 11, 2017: Structure
https://www.readbyqxmd.com/read/28416110/structural-basis-for-kinase-mediated-macrolide-antibiotic-resistance
#7
Desiree H Fong, David L Burk, Jonathan Blanchet, Amy Y Yan, Albert M Berghuis
The macrolides are a class of antibiotic, characterized by a large macrocyclic lactone ring that can be inactivated by macrolide phosphotransferase enzymes. We present structures for MPH(2')-I and MPH(2')-II in the apo state, and in complex with GTP analogs and six different macrolides. These represent the first structures from the two main classes of macrolide phosphotransferases. The structures show that the enzymes are related to the aminoglycoside phosphotransferases, but are distinguished from them by the presence of a large interdomain linker that contributes to an expanded antibiotic binding pocket...
April 1, 2017: Structure
https://www.readbyqxmd.com/read/28392259/active-site-flexibility-and-substrate-specificity-in-a-bacterial-virulence-factor-crystallographic-snapshots-of-an-epoxide-hydrolase
#8
Kelli L Hvorecny, Christopher D Bahl, Seiya Kitamura, Kin Sing Stephen Lee, Bruce D Hammock, Christophe Morisseau, Dean R Madden
Pseudomonas aeruginosa secretes an epoxide hydrolase with catalytic activity that triggers degradation of the cystic fibrosis transmembrane conductance regulator (CFTR) and perturbs other host defense networks. Targets of this CFTR inhibitory factor (Cif) are largely unknown, but include an epoxy-fatty acid. In this class of signaling molecules, chirality can be an important determinant of physiological output and potency. Here we explore the active-site chemistry of this two-step α/β-hydrolase and its implications for an emerging class of virulence enzymes...
March 31, 2017: Structure
https://www.readbyqxmd.com/read/28392260/hybrid-mass-spectrometry-approaches-to-determine-how-l-histidine-feedback-regulates-the-enzyzme-mtatp-phosphoribosyltransferase
#9
Kamila J Pacholarz, Rebecca J Burnley, Thomas A Jowitt, Victoria Ordsmith, João Pedro Pisco, Massimiliano Porrini, Gérald Larrouy-Maumus, Rachel A Garlish, Richard J Taylor, Luiz Pedro Sório de Carvalho, Perdita E Barran
MtATP-phosphoribosyltransferase (MtATP-PRT) is an enzyme catalyzing the first step of the biosynthesis of L-histidine in Mycobacterium tuberculosis, and proposed to be regulated via an allosteric mechanism. Native mass spectrometry (MS) reveals MtATP-PRT to exist as a hexamer. Conformational changes induced by L-histidine binding and the influence of buffer pH are determined with ion mobility MS, hydrogen deuterium exchange (HDX) MS, and analytical ultracentrifugation. The experimental collision cross-section ((DT)CCSHe) decreases from 76...
March 30, 2017: Structure
https://www.readbyqxmd.com/read/28392261/bound-waters-mediate-binding-of-diverse-substrates-to-a-ubiquitin-ligase
#10
Juliana Muñoz-Escobar, Edna Matta-Camacho, Cordelia Cho, Guennadi Kozlov, Kalle Gehring
The N-end rule pathway controls the half-life of proteins based on their N-terminal residue. Positively charged type 1 N-degrons are recognized by a negatively charged pocket on the Zn finger named the UBR box. Here, we show that the UBR box is rigid, but bound water molecules in the pocket provide the structural plasticity required to bind different positively charged amino acids. Ultra-high-resolution crystal structures of arginine, histidine, and methylated arginine reveal that water molecules mediate the binding of N-degron peptides...
March 27, 2017: Structure
https://www.readbyqxmd.com/read/28392258/bilayer-mediated-structural-transitions-control-mechanosensitivity-of-the-trek-2-k2p-channel
#11
Prafulla Aryal, Viwan Jarerattanachat, Michael V Clausen, Marcus Schewe, Conor McClenaghan, Liam Argent, Linus J Conrad, Yin Y Dong, Ashley C W Pike, Elisabeth P Carpenter, Thomas Baukrowitz, Mark S P Sansom, Stephen J Tucker
The mechanosensitive two-pore domain (K2P) K(+) channels (TREK-1, TREK-2, and TRAAK) are important for mechanical and thermal nociception. However, the mechanisms underlying their gating by membrane stretch remain controversial. Here we use molecular dynamics simulations to examine their behavior in a lipid bilayer. We show that TREK-2 moves from the "down" to "up" conformation in direct response to membrane stretch, and examine the role of the transmembrane pressure profile in this process. Furthermore, we show how state-dependent interactions with lipids affect the movement of TREK-2, and how stretch influences both the inner pore and selectivity filter...
March 24, 2017: Structure
https://www.readbyqxmd.com/read/28380340/a-self-assisting-protein-folding-model-for-teaching-structural-molecular-biology
#12
Jodi Davenport, Michael Pique, Elizabeth Getzoff, Jon Huntoon, Adam Gardner, Arthur Olson
Structural molecular biology is now becoming part of high school science curriculum thus posing a challenge for teachers who need to convey three-dimensional (3D) structures with conventional text and pictures. In many cases even interactive computer graphics does not go far enough to address these challenges. We have developed a flexible model of the polypeptide backbone using 3D printing technology. With this model we have produced a polypeptide assembly kit to create an idealized model of the Triosephosphate isomerase mutase enzyme (TIM), which forms a structure known as TIM barrel...
April 4, 2017: Structure
https://www.readbyqxmd.com/read/28380339/molecular-basis-of-substrate-specific-acetylation-by-n-terminal-acetyltransferase-natb
#13
Haiyan Hong, Yongfei Cai, Shijun Zhang, Hongyan Ding, Haitao Wang, Aidong Han
The NatB N-terminal acetyltransferase specifically acetylates the N-terminal group of substrate protein peptides starting with Met-Asp/Glu/Asn/Gln. How NatB recognizes and acetylates these substrates remains unknown. Here, we report crystal structures of a NatB holoenzyme from Candida albicans in the presence of its co-factor CoA and substrate peptides. The auxiliary subunit Naa25 of NatB forms a horseshoe-like deck to hold specifically its catalytic subunit Naa20. The first two amino acids Met and Asp of a substrate peptide mediate the major interactions with the active site in the Naa20 subunit...
April 4, 2017: Structure
https://www.readbyqxmd.com/read/28380338/understanding-card-tricks-in-apoptosomes
#14
Li Wang, Qi Qiao, Hao Wu
While earlier studies of Apaf-1 holo-apoptosome architecture revealed the spectacular heptameric wheel-like structure formed by Apaf-1, the central CARD disk responsible for caspase-9 recruitment remained incompletely resolved. In a recent issue of Structure, Su et al. (2017) describe a crystal structure of the complex between Apaf-1 CARD and caspase-9 CARD. Together with two recent cryo-EM structures, this work brings us closer to a full view of the holo-apoptosome.
April 4, 2017: Structure
https://www.readbyqxmd.com/read/28380337/what-s-in-an-average-an-ensemble-view-of-phosphorylation-effects
#15
Alexander F Chin, Vincent J Hilser
The number of examples of functional post-translational modulation of disordered proteins rapidly grows. In a recent issue of Structure, Jie et al. (2017) show that phosphorylation of dynein intermediate chain alters partner binding but retains its dynamic, disorder character. An ensemble model offers an organizing framework to relate function, conformation, and phosphorylation in disordered and ordered proteins alike.
April 4, 2017: Structure
https://www.readbyqxmd.com/read/28380336/expanding-the-reader-landscape-of-histone-acylation
#16
Abid Khan, Joseph B Bridgers, Brian D Strahl
In this issue of Structure,Klein et al. (2017) expand our understanding of what reader domains bind to by showing that MORF, a double PHD domain containing lysine acetyltransferase, is a preferential reader of histone lysine acylation.
April 4, 2017: Structure
https://www.readbyqxmd.com/read/28380335/open-and-closed-questions-about-open-and%C3%A2-closed-smc
#17
Hironori Niki
The tripartite ring of the bacterial condensin complex Smc-ScpAB entraps DNA to separate replicated chromosomes. The cycle of ring opening and closing is dependent on ATP hydrolysis. In this issue of Structure, Kamada et al. (2017) report on the tripartite-ring structural dynamics and their role in regulating this cycle.
April 4, 2017: Structure
https://www.readbyqxmd.com/read/28319010/exploring-protein-peptide-recognition-pathways-using-a-supervised-molecular-dynamics-approach
#18
Veronica Salmaso, Mattia Sturlese, Alberto Cuzzolin, Stefano Moro
Peptides have gained increased interest as therapeutic agents during recent years. The high specificity and relatively low toxicity of peptide drugs derive from their extremely tight binding to their targets. Indeed, understanding the molecular mechanism of protein-peptide recognition has important implications in the fields of biology, medicine, and pharmaceutical sciences. Even if crystallography and nuclear magnetic resonance are offering valuable atomic insights into the assembling of the protein-peptide complexes, the mechanism of their recognition and binding events remains largely unclear...
April 4, 2017: Structure
https://www.readbyqxmd.com/read/28319009/the-unique-domain-forms-a-fuzzy-intramolecular-complex-in-src-family-kinases
#19
Miguel Arbesú, Mariano Maffei, Tiago N Cordeiro, João M C Teixeira, Yolanda Pérez, Pau Bernadó, Serge Roche, Miquel Pons
The N-terminal regulatory region of c-Src including the SH4, Unique, and SH3 domains adopts a compact, yet highly dynamic, structure that can be described as an intramolecular fuzzy complex. Most of the long-range interactions within the Unique domain are also observed in constructs lacking the structured SH3, indicating a considerable degree of preorganization of the disordered Unique domain. Here we report that members of the Src family of kinases (SFK) share well-conserved sequence features involving aromatic residues in their Unique domains...
April 4, 2017: Structure
https://www.readbyqxmd.com/read/28319008/structure-of-yeast-osbp-related-protein-osh1-reveals-key-determinants-for-lipid-transport-and-protein-targeting-at-the-nucleus-vacuole-junction
#20
Mohammad Kawsar Manik, Huiseon Yang, Junsen Tong, Young Jun Im
Yeast Osh1 belongs to the oxysterol-binding protein (OSBP) family of proteins and contains multiple targeting modules optimized for lipid transport at the nucleus-vacuole junction (NVJ). The key determinants for NVJ targeting and the role of Osh1 at NVJs have remained elusive because of unknown lipid specificities. In this study, we determined the structures of the ankyrin repeat domain (ANK), and OSBP-related domain (ORD) of Osh1, in complex with Nvj1 and ergosterol, respectively. The Osh1 ANK forms a unique bi-lobed structure that recognizes a cytosolic helical segment of Nvj1...
April 4, 2017: Structure
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