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Acta Crystallographica. Section D, Structural Biology

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https://www.readbyqxmd.com/read/29095166/iron-metabolism-from-molecular-mechanisms-to-clinical-consequences-fourth-edition-by-robert-crichton-wiley-2016-pp-xviii-556-price-gbp%C3%A2-135-00-eur%C3%A2-162-00-hardcover-isbn-978-1-118-92561-4
#1
Massimo Nespolo
No abstract text is available yet for this article.
November 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/29095165/four-highly-pseudosymmetric-and-or-twinned-structures-of-d-cgcgcg-2-extend-the-repertoire-of-crystal-structures-of-z-dna
#2
Zhipu Luo, Zbigniew Dauter, Miroslaw Gilski
DNA oligomer duplexes containing alternating cytosines and guanines in their sequences tend to form left-handed helices of the Z-DNA type, with the sugar and phosphate backbone in a zigzag conformation and a helical repeat of two successive nucleotides. Z-DNA duplexes usually crystallize as hexagonally arranged parallel helical tubes, with various relative orientations and translation of neighboring duplexes. Four novel high-resolution crystal structures of d(CGCGCG)2 duplexes are described here. They are characterized by a high degree of pseudosymmetry and/or twinning, with three or four independent duplexes differently oriented in a monoclinic P21 lattice of hexagonal metric...
November 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/29095164/the-crystal-structure-of-the-yersinia-pestis-iron-chaperone-yiua-reveals-a-basic-triad-binding-motif-for-the-chelated-metal
#3
Christopher D Radka, Dongquan Chen, Lawrence J DeLucas, Stephen G Aller
Biological chelating molecules called siderophores are used to sequester iron and maintain its ferric state. Bacterial substrate-binding proteins (SBPs) bind iron-siderophore complexes and deliver these complexes to ATP-binding cassette (ABC) transporters for import into the cytoplasm, where the iron can be transferred from the siderophore to catalytic enzymes. In Yersinia pestis, the causative agent of plague, the Yersinia iron-uptake (Yiu) ABC transporter has been shown to improve iron acquisition under iron-chelated conditions...
November 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/29095163/structural-basis-of-antigen-recognition-crystal-structure-of-duck-egg-lysozyme
#4
David Brent Langley, Ben Crossett, Peter Schofield, Jenny Jackson, Mahdi Zeraati, David Maltby, Mary Christie, Deborah Burnett, Robert Brink, Christopher Goodnow, Daniel Christ
Duck egg lysozyme (DEL) is a widely used model antigen owing to its capacity to bind with differential affinity to anti-chicken egg lysozyme antibodies. However, no structures of DEL have so far been reported, and the situation had been complicated by the presence of multiple isoforms and conflicting reports of primary sequence. Here, the structures of two DEL isoforms from the eggs of the commonly used Pekin duck (Anas platyrhynchos) are reported. Using structural analyses in combination with mass spectrometry, non-ambiguous DEL primary sequences are reported...
November 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/29095162/crystal-structures-of-serum-albumins-from-domesticated-ruminants-and-their-complexes-with-3-5-diiodosalicylic-acid
#5
Anna Bujacz, Julita A Talaj, Kamil Zielinski, Agnieszka J Pietrzyk-Brzezinska, Piotr Neumann
Serum albumin (SA) is the most abundant protein in plasma and is the main transporter of molecules in the circulatory system of all vertebrates, with applications in medicine, the pharmaceutical industry and molecular biology. It is known that albumins from different organisms vary in sequence; thus, it is important to know the impact of the amino-acid sequence on the three-dimensional structure and ligand-binding properties. Here, crystal structures of ovine (OSA) and caprine (CSA) serum albumins, isolated from sheep and goat blood, are described, as well those of their complexes with 3,5-diiodosalicylic acid (DIS): OSA-DIS (2...
November 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/29095161/structure-and-function-of-the-thermostable-l-asparaginase-from-thermococcus-kodakarensis
#6
Jingxu Guo, Alun R Coker, Steve P Wood, Jonathan B Cooper, Shahid Mahmood Chohan, Naeem Rashid, Muhummad Akhtar
L-Asparaginases catalyse the hydrolysis of asparagine to aspartic acid and ammonia. In addition, L-asparaginase is involved in the biosynthesis of amino acids such as lysine, methionine and threonine. These enzymes have been used as chemotherapeutic agents for the treatment of acute lymphoblastic leukaemia and other haematopoietic malignancies since the tumour cells cannot synthesize sufficient L-asparagine and are thus killed by deprivation of this amino acid. L-Asparaginases are also used in the food industry and have potential in the development of biosensors, for example for asparagine levels in leukaemia...
November 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/29095160/synergy-among-phase-refinement-techniques-in-macromolecular-crystallography
#7
Maria Cristina Burla, Giovanni Luca Cascarano, Carmelo Giacovazzo, Giampiero Polidori
Ab initio and non-ab initio phasing methods are often unable to provide phases of sufficient quality to allow the molecular interpretation of the resulting electron-density maps. Phase extension and refinement is therefore a necessary step: its success or failure can make the difference between solution and nonsolution of the crystal structure. Today phase refinement is trusted to electron-density modification (EDM) techniques, and in practice to dual-space methods which try, via suitable constraints in direct and in reciprocal space, to generate higher quality electron-density maps...
November 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/29095159/nogo-receptor-crystal-structures-with-a-native-disulfide-pattern-suggest-a-novel-mode-of-self-interaction
#8
Matti F Pronker, Roderick P Tas, Hedwich C Vlieg, Bert J C Janssen
The Nogo Receptor (NgR) is a glycophosphatidylinositol-anchored cell-surface protein and is a receptor for three myelin-associated inhibitors of regeneration: myelin-associated glycoprotein, Nogo66 and oligodendrocyte myelin glycoprotein. In combination with different co-receptors, NgR mediates signalling that reduces neuronal plasticity. The available structures of the NgR ligand-binding leucine-rich repeat (LRR) domain have an artificial disulfide pattern owing to truncated C-terminal construct boundaries...
November 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28994414/mismodeled-purines-implicit-alternates-and-hidden-hoogsteens
#9
Bradley J Hintze, Jane S Richardson, David C Richardson
Hoogsteen base pairs are seen in DNA crystal structures, but only rarely. This study tests whether Hoogsteens or other syn purines are either under-modeled or over-modeled, which are known problems for rare conformations. Candidate purines needing a syn/anti 180° flip were identified by diagnostic patterns of difference electron-density peaks. Manual inspection narrowed 105 flip candidates to 20 convincing cases, all at ≤2.7 Å resolution. Rebuilding and refinement confirmed that 14 of these were authentic purine flips...
October 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28994413/flexed8-the-first-member-of-a-fast-and-flexible-sample-changer-family-for-macromolecular-crystallography
#10
Gergely Papp, Franck Felisaz, Clement Sorez, Marcos Lopez-Marrero, Robert Janocha, Babu Manjasetty, Alexandre Gobbo, Hassan Belrhali, Matthew W Bowler, Florent Cipriani
Automated sample changers are now standard equipment for modern macromolecular crystallography synchrotron beamlines. Nevertheless, most are only compatible with a single type of sample holder and puck. Recent work aimed at reducing sample-handling efforts and crystal-alignment times at beamlines has resulted in a new generation of compact and precise sample holders for cryocrystallography: miniSPINE and NewPin [see the companion paper by Papp et al. (2017, Acta Cryst., D73, 829-840)]. With full data collection now possible within seconds at most advanced beamlines, and future fourth-generation synchrotron sources promising to extract data in a few tens of milliseconds, the time taken to mount and centre a sample is rate-limiting...
October 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28994412/towards-a-compact-and-precise-sample-holder-for-macromolecular-crystallography
#11
Gergely Papp, Christopher Rossi, Robert Janocha, Clement Sorez, Marcos Lopez-Marrero, Anthony Astruc, Andrew McCarthy, Hassan Belrhali, Matthew W Bowler, Florent Cipriani
Most of the sample holders currently used in macromolecular crystallography offer limited storage density and poor initial crystal-positioning precision upon mounting on a goniometer. This has now become a limiting factor at high-throughput beamlines, where data collection can be performed in a matter of seconds. Furthermore, this lack of precision limits the potential benefits emerging from automated harvesting systems that could provide crystal-position information which would further enhance alignment at beamlines...
October 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28994411/x-ray-and-em-structures-of-a-natively-glycosylated-hiv-1-envelope-trimer
#12
Harry B Gristick, Haoqing Wang, Pamela J Bjorkman
The structural and biochemical characterization of broadly neutralizing anti-HIV-1 antibodies (bNAbs) has been essential in guiding the design of potential vaccines to prevent infection by HIV-1. While these studies have revealed critical mechanisms by which bNAbs recognize and/or accommodate N-glycans on the trimeric envelope glycoprotein (Env), they have been limited to the visualization of high-mannose glycan forms only, since heterogeneity introduced from the presence of complex glycans makes it difficult to obtain high-resolution structures...
October 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28994410/structure-of-the-conserved-francisella-virulence-protein-fvfa
#13
Subramania Kolappan, Karen Y Lo, Chiao Ling Jennifer Shen, Julian A Guttman, Lisa Craig
Francisella tularensis is a potent human pathogen that invades and survives in macrophage and epithelial cells. Two identical proteins, FTT_0924 from F. tularensis subsp. tularensis and FTL_1286 from F. tularensis subsp. holarctica LVS, have previously been identified as playing a role in protection of the bacteria from osmotic shock and its survival in macrophages. FTT_0924 has been shown to localize to the inner membrane, with its C-terminus exposed to the periplasm. Here, crystal structures of the F. novicida homologue FTN_0802, which we call FvfA, in two crystal forms are reported at 1...
October 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28994409/introducing-site-specific-cysteines-into-nanobodies-for-mercury-labelling-allows-de-novo-phasing-of-their-crystal-structures
#14
Simon Boje Hansen, Nick Stub Laursen, Gregers Rom Andersen, Kasper R Andersen
The generation of high-quality protein crystals and the loss of phase information during an X-ray crystallography diffraction experiment represent the major bottlenecks in the determination of novel protein structures. A generic method for introducing Hg atoms into any crystal independent of the presence of free cysteines in the target protein could considerably facilitate the process of obtaining unbiased experimental phases. Nanobodies (single-domain antibodies) have recently been shown to promote the crystallization and structure determination of flexible proteins and complexes...
October 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28994408/conformational-dynamics-of-the-essential-sensor-histidine-kinase-walk
#15
Yongfei Cai, Mingyang Su, Ashfaq Ahmad, Xiaojie Hu, Jiayan Sang, Lingyuan Kong, Xingqiang Chen, Chen Wang, Jianwei Shuai, Aidong Han
Two-component systems (TCSs) are key elements in bacterial signal transduction in response to environmental stresses. TCSs generally consist of sensor histidine kinases (SKs) and their cognate response regulators (RRs). Many SKs exhibit autokinase, phosphoryltransferase and phosphatase activities, which regulate RR activity through a phosphorylation and dephosphorylation cycle. However, how SKs perform different enzymatic activities is poorly understood. Here, several crystal structures of the minimal catalytic region of WalK, an essential SK from Lactobacillus plantarum that shares 60% sequence identity with its homologue VicK from Streptococcus mutans, are presented...
October 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28876241/structural-insights-into-the-interaction-of-the-conserved-mammalian-proteins-gapr-1-and-beclin-1-a-key-autophagy-protein
#16
Yue Li, Yuting Zhao, Minfei Su, Karen Glover, Srinivas Chakravarthy, Christopher L Colbert, Beth Levine, Sangita C Sinha
Mammalian Golgi-associated plant pathogenesis-related protein 1 (GAPR-1) is a negative autophagy regulator that binds Beclin 1, a key component of the autophagosome nucleation complex. Beclin 1 residues 267-284 are required for binding GAPR-1. Here, sequence analyses, structural modeling, mutagenesis combined with pull-down assays, X-ray crystal structure determination and small-angle X-ray scattering were used to investigate the Beclin 1-GAPR-1 interaction. Five conserved residues line an equatorial GAPR-1 surface groove that is large enough to bind a peptide...
September 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28876240/crystal-structures-of-the-methyltransferase-and-helicase-from-the-zika-1947-mr766-uganda-strain
#17
Malgorzata Bukrejewska, Urszula Derewenda, Malwina Radwanska, Daniel A Engel, Zygmunt S Derewenda
Two nonstructural proteins encoded by Zika virus strain MR766 RNA, a methyltransferase and a helicase, were crystallized and their structures were solved and refined at 2.10 and 2.01 Å resolution, respectively. The NS5 methyltransferase contains a bound S-adenosyl-L-methionine (SAM) co-substrate. The NS3 helicase is in the apo form. Comparison with published crystal structures of the helicase in the apo, nucleotide-bound and single-stranded RNA (ssRNA)-bound states suggests that binding of ssRNA to the helicase may occur through conformational selection rather than induced fit...
September 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28876239/designing-better-diffracting-crystals-of-biotin-carboxyl-carrier-protein-from-pyrococcus-horikoshii-by-a-mutation-based-on-the-crystal-packing-propensity-of-amino-acids
#18
Kazunori D Yamada, Naoki Kunishima, Yoshinori Matsuura, Koshiro Nakai, Hisashi Naitow, Yoshinori Fukasawa, Kentaro Tomii
An alternative rational approach to improve protein crystals by using single-site mutation of surface residues is proposed based on the results of a statistical analysis using a compiled data set of 918 independent crystal structures, thereby reflecting not only the entropic effect but also other effects upon protein crystallization. This analysis reveals a clear difference in the crystal-packing propensity of amino acids depending on the secondary-structural class. To verify this result, a systematic crystallization experiment was performed with the biotin carboxyl carrier protein from Pyrococcus horikoshii OT3 (PhBCCP)...
September 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28876238/the-structure-of-the-pfp1-protease-from-the-hyperthermophilic-archaeon-thermococcus-thioreducens-in-two-crystal-forms
#19
Steven B Larson, Alexander McPherson
The Pfp1 protease, a cysteine protease of unknown specificity from the hyperthermophilic archaeon Thermococcus thioreducens, was crystallized in two distinctive crystal forms: from concentrated citrate in one case and PEG in the other. X-ray data were collected from both crystal forms at room temperature to about 1.9 Å resolution using a laboratory source and detector, and the structures were solved by molecular replacement using the Pfp1 protease from Pyrococcus horikoshii as the search model. In the T...
September 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28876237/protein-structure-determination-by-electron-diffraction-using-a-single-three-dimensional-nanocrystal
#20
M T B Clabbers, E van Genderen, W Wan, E L Wiegers, T Gruene, J P Abrahams
Three-dimensional nanometre-sized crystals of macromolecules currently resist structure elucidation by single-crystal X-ray crystallography. Here, a single nanocrystal with a diffracting volume of only 0.14 µm(3), i.e. no more than 6 × 10(5) unit cells, provided sufficient information to determine the structure of a rare dimeric polymorph of hen egg-white lysozyme by electron crystallography. This is at least an order of magnitude smaller than was previously possible. The molecular-replacement solution, based on a monomeric polyalanine model, provided sufficient phasing power to show side-chain density, and automated model building was used to reconstruct the side chains...
September 1, 2017: Acta Crystallographica. Section D, Structural Biology
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