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Acta Crystallographica. Section D, Structural Biology

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https://www.readbyqxmd.com/read/28777085/protein-ligand-complex-structure-from-serial-femtosecond-crystallography-using-soaked-thermolysin-microcrystals-and-comparison-with-structures-from-synchrotron-radiation
#1
Hisashi Naitow, Yoshinori Matsuura, Kensuke Tono, Yasumasa Joti, Takashi Kameshima, Takaki Hatsui, Makina Yabashi, Rie Tanaka, Tomoyuki Tanaka, Michihiro Sugahara, Jun Kobayashi, Eriko Nango, So Iwata, Naoki Kunishima
Serial femtosecond crystallography (SFX) with an X-ray free-electron laser is used for the structural determination of proteins from a large number of microcrystals at room temperature. To examine the feasibility of pharmaceutical applications of SFX, a ligand-soaking experiment using thermolysin microcrystals has been performed using SFX. The results were compared with those from a conventional experiment with synchrotron radiation (SR) at 100 K. A protein-ligand complex structure was successfully obtained from an SFX experiment using microcrystals soaked with a small-molecule ligand; both oil-based and water-based crystal carriers gave essentially the same results...
August 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28777084/the-role-of-conserved-surface-hydrophobic-residues-in-the-carbapenemase-activity-of-the-class-d-%C3%AE-lactamases
#2
Marta Toth, Clyde A Smith, Nuno T Antunes, Nichole K Stewart, Lauren Maltz, Sergei B Vakulenko
Carbapenem-hydrolyzing class D β-lactamases (CHDLs) produce resistance to the last-resort carbapenem antibiotics and render these drugs ineffective for the treatment of life-threatening infections. Here, it is shown that among the clinically important CHDLs, OXA-143 produces the highest levels of resistance to carbapenems and has the highest catalytic efficiency against these substrates. Structural data demonstrate that acylated carbapenems entirely fill the active site of CHDLs, leaving no space for water molecules, including the deacylating water...
August 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28777083/structural-basis-for-the-regulation-of-chemotaxis-by-mapz-in-the-presence-of-c-di-gmp
#3
Yingxiao Zhu, Zenglin Yuan, Lichuan Gu
The bacterial second messenger cyclic diguanylate monophosphate (c-di-GMP) mediates multiple aspects of bacterial physiology through binding to various effectors. In some cases, these effectors are single-domain proteins which only contain a PilZ domain. It remains largely unknown how single-domain PilZ proteins function and regulate their downstream targets. Recently, a single-domain PilZ protein, MapZ (PA4608), was identified to inhibit the activity of the methyltransferase CheR1. Here, crystal structures of the C-terminal domain of CheR1 containing SAH and of CheR1 in complex with c-di-GMP-bound MapZ are reported...
August 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28777082/crystal-structure-of-the-peg-bound-sh3-domain-of-myosin-ib-from-entamoeba-histolytica-reveals-its-mode-of-ligand-recognition
#4
Gunjan Gautam, Syed Arif Abdul Rehman, Preeti Pandey, Samudrala Gourinath
The versatility in the recognition of various interacting proteins by the SH3 domain drives a variety of cellular functions. Here, the crystal structure of the C-terminal SH3 domain of myosin IB from Entamoeba histolytica (EhMySH3) is reported at a resolution of 1.7 Å in native and PEG-bound states. Comparisons with other structures indicated that the PEG molecules occupy protein-protein interaction pockets similar to those occupied by the peptides in other peptide-bound SH3-domain structures. Also, analysis of the PEG-bound EhMySH3 structure led to the recognition of two additional pockets, apart from the conventional polyproline and specificity pockets, that are important for ligand interaction...
August 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28777081/binding-of-hydroxycitrate-to-human-atp-citrate-lyase
#5
Jinhong Hu, Aruna Komakula, Marie E Fraser
Hydroxycitrate from the fruit of Garcinia cambogia [i.e. (2S,3S)-2-hydroxycitrate] is the best-known inhibitor of ATP-citrate lyase. Well diffracting crystals showing how the inhibitor binds to human ATP-citrate lyase were grown by modifying the protein. The protein was modified by introducing cleavage sites for Tobacco etch virus protease on either side of a disordered linker. The protein crystallized consisted of residues 2-425-ENLYFQ and S-488-810 of human ATP-citrate lyase. (2S,3S)-2-Hydroxycitrate binds in the same orientation as citrate, but the citrate-binding domain (residues 248-421) adopts a different orientation with respect to the rest of the protein (residues 4-247, 490-746 and 748-809) from that previously seen...
August 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28777080/toscana-virus-nucleoprotein-oligomer-organization-observed-in-solution
#6
Amal Baklouti, Adeline Goulet, Julie Lichière, Bruno Canard, Rémi N Charrel, François Ferron, Bruno Coutard, Nicolas Papageorgiou
Toscana virus (TOSV) is an arthropod-borne virus belonging to the Phlebovirus genus within the Bunyaviridae family. As in other bunyaviruses, the genome of TOSV is made up of three RNA segments. They are encapsidated by the nucleoprotein (N), which also plays an essential role in virus replication. To date, crystallographic structures of phlebovirus N have systematically revealed closed-ring organizations which do not fully match the filamentous organization of the ribonucleoprotein (RNP) complex observed by electron microscopy...
August 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28777079/activity-inhibition-and-crystal-polymorphism-induced-by-active-site-metal-swapping
#7
Elsie Yekwa, Joelle Khourieh, Bruno Canard, Nicolas Papageorgiou, François Ferron
The Arenaviridae family is one of the two RNA viral families that encode a 3'-5' exonuclease in their genome. An exonuclease domain is found in the Arenaviridae nucleoprotein and targets dsRNA specifically. This domain is directly involved in suppression of innate immunity in the host cell. Like most phosphate-processing enzymes, it requires a divalent metal ion such as Mg(2+) (or Mn(2+)) as a cofactor to catalyse nucleotide-cleavage and nucleotide-transfer reactions. On the other hand, calcium (Ca(2+)) inhibits this enzymatic activity, in spite of the fact that Mg(2+) and Ca(2+) present comparable binding affinities and biological availabilities...
August 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28777078/an-overview-of-comparative-modelling-and-resources-dedicated-to-large-scale-modelling-of-genome-sequences
#8
Su Datt Lam, Sayoni Das, Ian Sillitoe, Christine Orengo
Computational modelling of proteins has been a major catalyst in structural biology. Bioinformatics groups have exploited the repositories of known structures to predict high-quality structural models with high efficiency at low cost. This article provides an overview of comparative modelling, reviews recent developments and describes resources dedicated to large-scale comparative modelling of genome sequences. The value of subclustering protein domain superfamilies to guide the template-selection process is investigated...
August 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28695863/nanomaterials-for-tumor-targeting-theranostics-a-proactive-clinical-perspective-edited-by-mingqian-tan-and-aiguo-wu-world-scientific-2016-pp-432-price-gbp-120-00-hardcover-isbn-978-981-4635-41-7
#9
https://www.readbyqxmd.com/read/28695862/factors-affecting-the-amplitude-of-the-%C3%AF-angle-in-proteins-a-revisitation
#10
Nicole Balasco, Luciana Esposito, Luigi Vitagliano
The protein folded state is the result of the fine balance of a variety of different forces. Even minor structural perturbations may have a significant impact on the stability of these macromolecules. Studies carried out in recent decades have led to the convergent view that proteins are endowed with a flexible spine. One of the open issues related to protein local backbone geometry is the identification of the factors that influence the amplitude of the τ (N-C(α)-C) angle. Here, statistical analyses performed on an updated ensemble of X-ray protein structures by dissecting the contribution of the major factors that can potentially influence the local backbone geometry of proteins are reported...
July 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28695861/seeing-but-not-believing-the-structure-of-glycerol-dehydrogenase-initially-assumed-to-be-the-structure-of-a-survival-protein-from-salmonella-typhimurium
#11
Kaushik Hatti, Yamuna Kalyani Mathiharan, Narayanaswamy Srinivasan, Mathur R N Murthy
The determination of the crystal structure of a mutant protein using phases based on a previously determined crystal structure of the wild-type protein is often a straightforward molecular-replacement protocol. Such a structure determination may be difficult if there are large-scale structural differences between the wild-type and mutant proteins. In this manuscript, an interesting case is presented of the unintentional crystallization of a contaminant protein which shared some structural features with the presumed target protein, leading to difficulties in obtaining a completely satisfactory molecular-replacement structure solution...
July 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28695860/dna-conformational-transitions-inferred-from-re-evaluation-of-m-fo-d-fc-electron-density-maps
#12
Tomoko Sunami, Toshiyuki Chatake, Hidetoshi Kono
Conformational flexibility of DNA plays important roles in biological processes such as transcriptional regulation and DNA packaging etc. To understand the mechanisms of these processes, it is important to analyse when, where and how DNA shows conformational variations. Recent analyses have indicated that conventional refinement methods do not always provide accurate models of crystallographic heterogeneities and that some information on polymorphism has been overlooked in previous crystallographic studies...
July 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28695859/octamer-formation-in-lysozyme-solutions-at-the-initial-crystallization-stage-detected-by-small-angle-neutron-scattering
#13
Anastasiia S Boikova, Yulia A Dyakova, Kseniia B Ilina, Petr V Konarev, Alyona E Kryukova, Alexandr I Kuklin, Margarita A Marchenkova, Boris V Nabatov, Alexandr E Blagov, Yurii V Pisarevsky, Mikhail V Kovalchuk
Solutions of lysozyme in heavy water were studied by small-angle neutron scattering (SANS) at concentrations of 40, 20 and 10 mg ml(-1) with and without the addition of precipitant, and at temperatures of 10, 20 and 30°C. In addition to the expected protein monomers, dimeric and octameric species were identified in solutions at the maximum concentration and close to the optimal conditions for crystallization. An optimal temperature for octamer formation was identified and both deviation from this temperature and a reduction in protein concentration led to a significant decrease in the volume fractions of octamers detected...
July 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28695858/rapid-cadmium-sad-phasing-at-the-standard-wavelength-1%C3%A2-%C3%A3
#14
Saravanan Panneerselvam, Esa Pekka Kumpula, Inari Kursula, Anja Burkhardt, Alke Meents
Cadmium ions can be effectively used to promote crystal growth and for experimental phasing. Here, the use of cadmium ions as a suitable anomalous scatterer at the standard wavelength of 1 Å is demonstrated. The structures of three different proteins were determined using cadmium single-wavelength anomalous dispersion (SAD) phasing. Owing to the strong anomalous signal, the structure of lysozyme could be automatically phased and built using a very low anomalous multiplicity (1.1) and low-completeness (77%) data set...
July 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28695857/probing-the-structural-basis-of-oxygen-binding-in-a-cofactor-independent-dioxygenase
#15
Kunhua Li, Elisha N Fielding, Heather L Condurso, Steven D Bruner
The enzyme DpgC is included in the small family of cofactor-independent dioxygenases. The chemistry of DpgC is uncommon as the protein binds and utilizes dioxygen without the aid of a metal or organic cofactor. Previous structural and biochemical studies identified the substrate-binding mode and the components of the active site that are important in the catalytic mechanism. In addition, the results delineated a putative binding pocket and migration pathway for the co-substrate dioxygen. Here, structural biology is utilized, along with site-directed mutagenesis, to probe the assigned dioxygen-binding pocket...
July 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28695856/crystal-structure-of-yersinia-pestis-virulence-factor-yfea-reveals-two-polyspecific-metal-binding-sites
#16
Christopher D Radka, Lawrence J DeLucas, Landon S Wilson, Matthew B Lawrenz, Robert D Perry, Stephen G Aller
Gram-negative bacteria use siderophores, outer membrane receptors, inner membrane transporters and substrate-binding proteins (SBPs) to transport transition metals through the periplasm. The SBPs share a similar protein fold that has undergone significant structural evolution to communicate with a variety of differentially regulated transporters in the cell. In Yersinia pestis, the causative agent of plague, YfeA (YPO2439, y1897), an SBP, is important for full virulence during mammalian infection. To better understand the role of YfeA in infection, crystal structures were determined under several environmental conditions with respect to transition-metal levels...
July 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28695855/1-8%C3%A2-%C3%A3-resolution-crystal-structure-of-the-carbapenem-intrinsic-resistance-protein-carf
#17
Evelyn M Tichy, Steven W Hardwick, Ben F Luisi, George P C Salmond
The natural production of the β-lactam antibiotic carbapenem in bacteria involves a group of enzymes that form a synthetic pathway as well as proteins that protect the cell from self-intoxification by the products. Here, the crystal structure of CarF, one of the two proteins that confer resistance to synthesis of the antibiotic in the host organism, is reported. The CarF fold places it within a widely occurring structural family, indicating an ancient structural origin from which the resistance function has been derived...
July 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28580916/cryo-electron-microscopy-of-chromatin-biology
#18
REVIEW
Marcus D Wilson, Alessandro Costa
The basic unit of chromatin, the nucleosome core particle (NCP), controls how DNA in eukaryotic cells is compacted, replicated and read. Since its discovery, biochemists have sought to understand how this protein-DNA complex can help to control so many diverse tasks. Recent electron-microscopy (EM) studies on NCP-containing assemblies have helped to describe important chromatin transactions at a molecular level. With the implementation of recent technical advances in single-particle EM, our understanding of how nucleosomes are recognized and read looks to take a leap forward...
June 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28580915/the-potential-use-of-single-particle-electron-microscopy-as-a-tool-for-structure-based-inhibitor-design
#19
S Rawson, M J McPhillie, R M Johnson, C W G Fishwick, S P Muench
Recent developments in electron microscopy (EM) have led to a step change in our ability to solve the structures of previously intractable systems, especially membrane proteins and large protein complexes. This has provided new opportunities in the field of structure-based drug design, with a number of high-profile publications resolving the binding sites of small molecules and peptide inhibitors. There are a number of advantages of EM over the more traditional X-ray crystallographic approach, such as resolving different conformational states and permitting the dynamics of a system to be better resolved when not constrained by a crystal lattice...
June 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28580914/high-resolution-cryo-em-proteasome-structures-in-drug-development
#20
Edward P Morris, Paula C A da Fonseca
With the recent advances in biological structural electron microscopy (EM), protein structures can now be obtained by cryo-EM and single-particle analysis at resolutions that used to be achievable only by crystallographic or NMR methods. We have explored their application to study protein-ligand interactions using the human 20S proteasome, a well established target for cancer therapy that is also being investigated as a target for an increasing range of other medical conditions. The map of a ligand-bound human 20S proteasome served as a proof of principle that cryo-EM is emerging as a realistic approach for more general structural studies of protein-ligand interactions, with the potential benefits of extending such studies to complexes that are unfavourable to other methods and allowing structure determination under conditions that are closer to physiological, preserving ligand specificity towards closely related binding sites...
June 1, 2017: Acta Crystallographica. Section D, Structural Biology
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