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Acta Crystallographica. Section D, Structural Biology

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https://www.readbyqxmd.com/read/28375152/metallomics-a-primer-of-integrated-biometal-sciences-by-wolfgang-maret-imperial-college-press-2016-pp-xiii-141-price-gbp-30-00-paperback-isbn-978-1-78326-828-3-gbp-56-00-hardback-isbn-978-1-78326-827-6
#1
https://www.readbyqxmd.com/read/28375151/free-radicals-in-biology-and-medicine-fifth-edition-by-barry-halliwell-and-john-m-c-gutteridge-oxford-university-press-2015-pp-xxxviii-905-price-gbp-70-00-paperback-isbn-9780198717485-gbp-125-00-hardback-isbn-9780198717478
#2
https://www.readbyqxmd.com/read/28375150/responses-to-atomic-resolution-a-badly-abused-term-in-structural-biology
#3
Wah Chiu, James Holton, Paul Langan, Nicholas K Sauter, Ilme Schlichting, Tom Terwilliger, Jennifer L Martin, Randy J Read, Soichi Wakatsuki
No abstract text is available yet for this article.
April 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28375149/-atomic-resolution-a-badly-abused-term-in-structural-biology
#4
Alexander Wlodawer, Zbigniew Dauter
No abstract text is available yet for this article.
April 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28375148/low-dose-fixed-target-serial-synchrotron-crystallography
#5
Robin L Owen, Danny Axford, Darren A Sherrell, Anling Kuo, Oliver P Ernst, Eike C Schulz, R J Dwayne Miller, Henrike M Mueller-Werkmeister
The development of serial crystallography has been driven by the sample requirements imposed by X-ray free-electron lasers. Serial techniques are now being exploited at synchrotrons. Using a fixed-target approach to high-throughput serial sampling, it is demonstrated that high-quality data can be collected from myoglobin crystals, allowing room-temperature, low-dose structure determination. The combination of fixed-target arrays and a fast, accurate translation system allows high-throughput serial data collection at high hit rates and with low sample consumption...
April 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28375147/crystal-structures-of-hsp104-n-terminal-domains-from-saccharomyces-cerevisiae-and-candida-albicans-suggest-the-mechanism-for-the-function-of-hsp104-in-dissolving-prions
#6
Peng Wang, Jingzhi Li, Clarissa Weaver, Aaron Lucius, Bingdong Sha
Hsp104 is a yeast member of the Hsp100 family which functions as a molecular chaperone to disaggregate misfolded polypeptides. To understand the mechanism by which the Hsp104 N-terminal domain (NTD) interacts with its peptide substrates, crystal structures of the Hsp104 NTDs from Saccharomyces cerevisiae (ScHsp104NTD) and Candida albicans (CaHsp104NTD) have been determined at high resolution. The structures of ScHsp104NTD and CaHsp104NTD reveal that the yeast Hsp104 NTD may utilize a conserved putative peptide-binding groove to interact with misfolded polypeptides...
April 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28375146/biochemical-and-structural-studies-of-mycobacterium-smegmatis-mutt1-a-sanitization-enzyme-with-unusual-modes-of-association
#7
S M Arif, A G Patil, U Varshney, M Vijayan
Mycobacterium smegmatis MutT1, which is made up of a Nudix domain (domain 1) and a histidine phosphatase domain (domain 2), efficiently hydrolyses 8-oxo-GTP and 8-oxo-dGTP to the corresponding nucleoside diphosphates and phosphate in the presence of magnesium ions. Domain 1 alone hydrolyses nucleoside triphosphates less efficiently. Under high concentrations and over long periods, the full-length enzyme as well as domain 1 catalyses the hydrolysis of the nucleoside triphosphates to the respective nucleoside monophosphates and pyrophosphate...
April 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28375145/crystal-structures-of-human-3-hydroxyanthranilate-3-4-dioxygenase-with-native-and-non-native-metals-bound-in-the-active-site
#8
Lakshmi Swarna Mukhi Pidugu, Heather Neu, Tin Lok Wong, Edwin Pozharski, John L Molloy, Sarah L J Michel, Eric A Toth
3-Hydroxyanthranilate 3,4-dioxygenase (3HAO) is an enzyme in the microglial branch of the kynurenine pathway of tryptophan degradation. 3HAO is a non-heme iron-containing, ring-cleaving extradiol dioxygenase that catalyzes the addition of both atoms of O2 to the kynurenine pathway metabolite 3-hydroxyanthranilic acid (3-HANA) to form quinolinic acid (QUIN). QUIN is a highly potent excitotoxin that has been implicated in a number of neurodegenerative conditions, making 3HAO a target for pharmacological downregulation...
April 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28375144/is-dimerization-a-common-feature-in-thioredoxins-the-case-of-thioredoxin-from-litopenaeus-vannamei
#9
Adam A Campos-Acevedo, Rogerio R Sotelo-Mundo, Javier Pérez, Enrique Rudiño-Piñera
The quaternary structure of the redox protein thioredoxin (Trx) has been debated. For bacterial Trx, there is no question regarding its monomeric state. In humans and other eukaryotes, the presence of a cysteine residue at the crystallographic symmetry axis points to the relevance of dimer formation in solution and in vivo. Crystallographic data for shrimp thioredoxin (LvTrx) obtained under different redox conditions reveal a dimeric arrangement mediated by a disulfide bond through residue Cys73 and other hydrophobic interactions located in the crystallographic interface, as reported for human Trx...
April 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28375143/data-mining-of-iron-ii-and-iron-iii-bond-valence-parameters-and-their-relevance-for-macromolecular-crystallography
#10
Heping Zheng, Karol M Langner, Gregory P Shields, Jing Hou, Marcin Kowiel, Frank H Allen, Garib Murshudov, Wladek Minor
The bond-valence model is a reliable way to validate assumed oxidation states based on structural data. It has successfully been employed for analyzing metal-binding sites in macromolecule structures. However, inconsistent results for heme-based structures suggest that some widely used bond-valence R0 parameters may need to be adjusted in certain cases. Given the large number of experimental crystal structures gathered since these initial parameters were determined and the similarity of binding sites in organic compounds and macromolecules, the Cambridge Structural Database (CSD) is a valuable resource for refining metal-organic bond-valence parameters...
April 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28375142/crystal-structure-and-rna-binding-properties-of-an-hfq-homolog-from-the-deep-branching-aquificae-conservation-of-the-lateral-rna-binding-mode
#11
Kimberly A Stanek, Jennifer Patterson-West, Peter S Randolph, Cameron Mura
The host factor Hfq, as the bacterial branch of the Sm family, is an RNA-binding protein involved in the post-transcriptional regulation of mRNA expression and turnover. Hfq facilitates pairing between small regulatory RNAs (sRNAs) and their corresponding mRNA targets by binding both RNAs and bringing them into close proximity. Hfq homologs self-assemble into homo-hexameric rings with at least two distinct surfaces that bind RNA. Recently, another binding site, dubbed the `lateral rim', has been implicated in sRNA·mRNA annealing; the RNA-binding properties of this site appear to be rather subtle, and its degree of evolutionary conservation is unknown...
April 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28375141/dissecting-random-and-systematic-differences-between-noisy-composite-data-sets
#12
Kay Diederichs
Composite data sets measured on different objects are usually affected by random errors, but may also be influenced by systematic (genuine) differences in the objects themselves, or the experimental conditions. If the individual measurements forming each data set are quantitative and approximately normally distributed, a correlation coefficient is often used to compare data sets. However, the relations between data sets are not obvious from the matrix of pairwise correlations since the numerical value of the correlation coefficient is lowered by both random and systematic differences between the data sets...
April 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28291763/wonka-and-oommppaa-analysis-of-protein-ligand-interaction-data-to-direct-structure-based-drug-design
#13
Charlotte M Deane, Ian D Wall, Darren V S Green, Brian D Marsden, Anthony R Bradley
In this work, two freely available web-based interactive computational tools that facilitate the analysis and interpretation of protein-ligand interaction data are described. Firstly, WONKA, which assists in uncovering interesting and unusual features (for example residue motions) within ensembles of protein-ligand structures and enables the facile sharing of observations between scientists. Secondly, OOMMPPAA, which incorporates protein-ligand activity data with protein-ligand structural data using three-dimensional matched molecular pairs...
March 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28291762/the-xchemexplorer-graphical-workflow-tool-for-routine-or-large-scale-protein-ligand-structure-determination
#14
Tobias Krojer, Romain Talon, Nicholas Pearce, Patrick Collins, Alice Douangamath, Jose Brandao-Neto, Alexandre Dias, Brian Marsden, Frank von Delft
XChemExplorer (XCE) is a data-management and workflow tool to support large-scale simultaneous analysis of protein-ligand complexes during structure-based ligand discovery (SBLD). The user interfaces of established crystallographic software packages such as CCP4 [Winn et al. (2011), Acta Cryst. D67, 235-242] or PHENIX [Adams et al. (2010), Acta Cryst. D66, 213-221] have entrenched the paradigm that a `project' is concerned with solving one structure. This does not hold for SBLD, where many almost identical structures need to be solved and analysed quickly in one batch of work...
March 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28291761/proper-modelling-of-ligand-binding-requires-an-ensemble-of-bound-and-unbound-states
#15
Nicholas M Pearce, Tobias Krojer, Frank von Delft
Although noncovalent binding by small molecules cannot be assumed a priori to be stoichiometric in the crystal lattice, occupancy refinement of ligands is often avoided by convention. Occupancies tend to be set to unity, requiring the occupancy error to be modelled by the B factors, and residual weak density around the ligand is necessarily attributed to `disorder'. Where occupancy refinement is performed, the complementary, superposed unbound state is rarely modelled. Here, it is shown that superior accuracy is achieved by modelling the ligand as partially occupied and superposed on a ligand-free `ground-state' model...
March 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28291760/gentle-fast-and-effective-crystal-soaking-by-acoustic-dispensing
#16
Patrick M Collins, Jia Tsing Ng, Romain Talon, Karolina Nekrosiute, Tobias Krojer, Alice Douangamath, Jose Brandao-Neto, Nathan Wright, Nicholas M Pearce, Frank von Delft
The steady expansion in the capacity of modern beamlines for high-throughput data collection, enabled by increasing X-ray brightness, capacity of robotics and detector speeds, has pushed the bottleneck upstream towards sample preparation. Even in ligand-binding studies using crystal soaking, the experiment best able to exploit beamline capacity, a primary limitation is the need for gentle and nontrivial soaking regimens such as stepwise concentration increases, even for robust and well characterized crystals...
March 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28291759/the-use-of-small-molecule-structures-to-complement-protein-ligand-crystal-structures-in-drug-discovery
#17
Colin R Groom, Jason C Cole
Many ligand-discovery stories tell of the use of structures of protein-ligand complexes, but the contribution of structural chemistry is such a core part of finding and improving ligands that it is often overlooked. More than 800 000 crystal structures are available to the community through the Cambridge Structural Database (CSD). Individually, these structures can be of tremendous value and the collection of crystal structures is even more helpful. This article provides examples of how small-molecule crystal structures have been used to complement those of protein-ligand complexes to address challenges ranging from affinity, selectivity and bioavailability though to solubility...
March 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28291758/using-more-than-801%C3%A2-296-small-molecule-crystal-structures-to-aid-in-protein-structure-refinement-and-analysis
#18
Jason C Cole, Ilenia Giangreco, Colin R Groom
The Cambridge Structural Database (CSD) is the worldwide resource for the dissemination of all published three-dimensional structures of small-molecule organic and metal-organic compounds. This paper briefly describes how this collection of crystal structures can be used en masse in the context of macromolecular crystallography. Examples highlight how the CSD and associated software aid protein-ligand complex validation, and show how the CSD could be further used in the generation of geometrical restraints for protein structure refinement...
March 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28291757/checkmymetal-a-macromolecular-metal-binding-validation-tool
#19
Heping Zheng, David R Cooper, Przemyslaw J Porebski, Ivan G Shabalin, Katarzyna B Handing, Wladek Minor
Metals are essential in many biological processes, and metal ions are modeled in roughly 40% of the macromolecular structures in the Protein Data Bank (PDB). However, a significant fraction of these structures contain poorly modeled metal-binding sites. CheckMyMetal (CMM) is an easy-to-use metal-binding site validation server for macromolecules that is freely available at http://csgid.org/csgid/metal_sites. The CMM server can detect incorrect metal assignments as well as geometrical and other irregularities in the metal-binding sites...
March 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28291756/twilight-reloaded-the-peptide-experience
#20
Christian X Weichenberger, Edwin Pozharski, Bernhard Rupp
The de facto commoditization of biomolecular crystallography as a result of almost disruptive instrumentation automation and continuing improvement of software allows any sensibly trained structural biologist to conduct crystallographic studies of biomolecules with reasonably valid outcomes: that is, models based on properly interpreted electron density. Robust validation has led to major mistakes in the protein part of structure models becoming rare, but some depositions of protein-peptide complex structure models, which generally carry significant interest to the scientific community, still contain erroneous models of the bound peptide ligand...
March 1, 2017: Acta Crystallographica. Section D, Structural Biology
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