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Acta Crystallographica. Section D, Structural Biology

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https://www.readbyqxmd.com/read/29199983/iron-sulfur-clusters-in-chemistry-and-biology-volume-1-characterization-properties-and-applications-second-edition-edited-by-tracey-rouault-de-gruyter-2017-pp-xv-447-price-eur-99-95-gbp-90-99-usd-114-99-hardcover-isbn-978-3-11-047850-1
#1
https://www.readbyqxmd.com/read/29199982/using-more-than-801%C3%A2-296-small-molecule-crystal-structures-to-aid-in-protein-structure-refinement-and-analysis-addendum
#2
Jason C Cole, Ilenia Giangreco, Colin R Groom
An addendum to the Introduction of Cole et al. [(2017), Acta Cryst. D73, 234-239] is made to recognize the work of Bricogne, Smart and others in the development of methods to make use of Cambridge Structural Database data in protein structure solution.
December 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/29199981/solving-the-scalability-issue-in-quantum-based-refinement-q-r-1
#3
Min Zheng, Nigel W Moriarty, Yanting Xu, Jeffrey R Reimers, Pavel V Afonine, Mark P Waller
Accurately refining biomacromolecules using a quantum-chemical method is challenging because the cost of a quantum-chemical calculation scales approximately as nm, where n is the number of atoms and m (≥3) is based on the quantum method of choice. This fundamental problem means that quantum-chemical calculations become intractable when the size of the system requires more computational resources than are available. In the development of the software package called Q|R, this issue is referred to as Q|R#1. A divide-and-conquer approach has been developed that fragments the atomic model into small manageable pieces in order to solve Q|R#1...
December 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/29199980/molecular-architectures-of-benzoic-acid-specific-type-iii-polyketide-synthases
#4
Charles Stewart, Kate Woods, Greg Macias, Andrew C Allan, Roger P Hellens, Joseph P Noel
Biphenyl synthase and benzophenone synthase constitute an evolutionarily distinct clade of type III polyketide synthases (PKSs) that use benzoic acid-derived substrates to produce defense metabolites in plants. The use of benzoyl-CoA as an endogenous substrate is unusual for type III PKSs. Moreover, sequence analyses indicate that the residues responsible for the functional diversification of type III PKSs are mutated in benzoic acid-specific type III PKSs. In order to gain a better understanding of structure-function relationships within the type III PKS family, the crystal structures of biphenyl synthase from Malus × domestica and benzophenone synthase from Hypericum androsaemum were compared with the structure of an archetypal type III PKS: chalcone synthase from Malus × domestica...
December 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/29199979/a-standardized-technique-for-high-pressure-cooling-of-protein-crystals
#5
David Quirnheim Pais, Barbara Rathmann, Juergen Koepke, Cveta Tomova, Paul Wurzinger, Yvonne Thielmann
Cryogenic temperatures slow down secondary radiation damage during data collection from macromolecular crystals. In 1973, cooling at high pressure was identified as a method for cryopreserving crystals in their mother liquor [Thomanek et al. (1973). Acta Cryst. A29, 263-265]. Results from different groups studying different crystal systems indicated that the approach had merit, although difficulties in making the process work have limited its widespread use. Therefore, a simplified and reliable technique has been developed termed high-pressure cooling (HPC)...
December 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/29199978/approaches-to-ab-initio-molecular-replacement-of-%C3%AE-helical-transmembrane-proteins
#6
Jens M H Thomas, Felix Simkovic, Ronan Keegan, Olga Mayans, Chengxin Zhang, Yang Zhang, Daniel J Rigden
α-Helical transmembrane proteins are a ubiquitous and important class of proteins, but present difficulties for crystallographic structure solution. Here, the effectiveness of the AMPLE molecular replacement pipeline in solving α-helical transmembrane-protein structures is assessed using a small library of eight ideal helices, as well as search models derived from ab initio models generated both with and without evolutionary contact information. The ideal helices prove to be surprisingly effective at solving higher resolution structures, but ab initio-derived search models are able to solve structures that could not be solved with the ideal helices...
December 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/29199977/structural-insight-into-the-rearrangement-of-the-switch-i-region-in-gtp-bound-g12a-k-ras
#7
Shenyuan Xu, Brian N Long, Gabriel H Boris, Anqi Chen, Shuisong Ni, Michael A Kennedy
K-Ras, a molecular switch that regulates cell growth, apoptosis and metabolism, is activated when it undergoes a conformation change upon binding GTP and is deactivated following the hydrolysis of GTP to GDP. Hydrolysis of GTP in water is accelerated by coordination to K-Ras, where GTP adopts a high-energy conformation approaching the transition state. The G12A mutation reduces intrinsic K-Ras GTP hydrolysis by an unexplained mechanism. Here, crystal structures of G12A K-Ras in complex with GDP, GTP, GTPγS and GppNHp, and of Q61A K-Ras in complex with GDP, are reported...
December 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/29199976/hydrogen-bonds-are-a-primary-driving-force-for-de-novo-protein-folding
#8
Schuyler Lee, Chao Wang, Haolin Liu, Jian Xiong, Renee Jiji, Xia Hong, Xiaoxue Yan, Zhangguo Chen, Michal Hammel, Yang Wang, Shaodong Dai, Jing Wang, Chengyu Jiang, Gongyi Zhang
The protein-folding mechanism remains a major puzzle in life science. Purified soluble activation-induced cytidine deaminase (AID) is one of the most difficult proteins to obtain. Starting from inclusion bodies containing a C-terminally truncated version of AID (residues 1-153; AID153), an optimized in vitro folding procedure was derived to obtain large amounts of AID153, which led to crystals with good quality and to final structural determination. Interestingly, it was found that the final refolding yield of the protein is proline residue-dependent...
December 1, 2017: Acta Crystallographica. Section D, Structural Biology
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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