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Acta Crystallographica. Section D, Structural Biology

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https://www.readbyqxmd.com/read/28177314/glycoblocks-a-schematic-three-dimensional-representation-for-glycans-and-their-interactions
#1
Stuart McNicholas, Jon Agirre
The close-range interactions provided by covalently linked glycans are essential for the correct folding of glycoproteins and also play a pivotal role in recognition processes. Being able to visualise protein-glycan and glycan-glycan contacts in a clear way is thus of great importance for the understanding of these biological processes. In structural terms, glycosylation sugars glue the protein together via hydrogen bonds, whereas non-covalently bound glycans frequently harness additional stacking interactions...
February 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28177313/strategies-for-carbohydrate-model-building-refinement-and-validation
#2
Jon Agirre
Sugars are the most stereochemically intricate family of biomolecules and present substantial challenges to anyone trying to understand their nomenclature, reactions or branched structures. Current crystallographic programs provide an abstraction layer allowing inexpert structural biologists to build complete protein or nucleic acid model components automatically either from scratch or with little manual intervention. This is, however, still not generally true for sugars. The need for carbohydrate-specific building and validation tools has been highlighted a number of times in the past, concomitantly with the introduction of a new generation of experimental methods that have been ramping up the production of protein-sugar complexes and glycoproteins for the past decade...
February 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28177312/ligand-fitting-with-ccp4
#3
Robert A Nicholls
Crystal structures of protein-ligand complexes are often used to infer biology and inform structure-based drug discovery. Hence, it is important to build accurate, reliable models of ligands that give confidence in the interpretation of the respective protein-ligand complex. This paper discusses key stages in the ligand-fitting process, including ligand binding-site identification, ligand description and conformer generation, ligand fitting, refinement and subsequent validation. The CCP4 suite contains a number of software tools that facilitate this task: AceDRG for the creation of ligand descriptions and conformers, Lidia and JLigand for two-dimensional and three-dimensional ligand editing and visual analysis, Coot for density interpretation, ligand fitting, analysis and validation, and REFMAC5 for macromolecular refinement...
February 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28177311/polder-maps-improving-omit-maps-by-excluding-bulk-solvent
#4
Dorothee Liebschner, Pavel V Afonine, Nigel W Moriarty, Billy K Poon, Oleg V Sobolev, Thomas C Terwilliger, Paul D Adams
The crystallographic maps that are routinely used during the structure-solution workflow are almost always model-biased because model information is used for their calculation. As these maps are also used to validate the atomic models that result from model building and refinement, this constitutes an immediate problem: anything added to the model will manifest itself in the map and thus hinder the validation. OMIT maps are a common tool to verify the presence of atoms in the model. The simplest way to compute an OMIT map is to exclude the atoms in question from the structure, update the corresponding structure factors and compute a residual map...
February 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28177310/combining-x-ray-and-neutron-crystallography-with-spectroscopy
#5
Hanna Kwon, Oliver Smith, Emma Lloyd Raven, Peter C E Moody
X-ray protein crystallography has, through the determination of the three-dimensional structures of enzymes and their complexes, been essential to the understanding of biological chemistry. However, as X-rays are scattered by electrons, the technique has difficulty locating the presence and position of H atoms (and cannot locate H(+) ions), knowledge of which is often crucially important for the understanding of enzyme mechanism. Furthermore, X-ray irradiation, through photoelectronic effects, will perturb the redox state in the crystal...
February 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28177309/getting-the-chemistry-right-protonation-tautomers-and-the-importance-of-h-atoms-in-biological-chemistry
#6
Ben Bax, Chun Wa Chung, Colin Edge
There are more H atoms than any other type of atom in an X-ray crystal structure of a protein-ligand complex, but as H atoms only have one electron they diffract X-rays weakly and are `hard to see'. The positions of many H atoms can be inferred by our chemical knowledge, and such H atoms can be added with confidence in `riding positions'. For some chemical groups, however, there is more ambiguity over the possible hydrogen placements, for example hydroxyls and groups that can exist in multiple protonation states or tautomeric forms...
February 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28177308/an-editor-for-the-generation-and-customization-of-geometry-restraints
#7
Nigel W Moriarty, Eli J Draizen, Paul D Adams
Chemical restraints for use in macromolecular structure refinement are produced by a variety of methods, including a number of programs that use chemical information to generate the required bond, angle, dihedral, chiral and planar restraints. These programs help to automate the process and therefore minimize the errors that could otherwise occur if it were performed manually. Furthermore, restraint-dictionary generation programs can incorporate chemical and other prior knowledge to provide reasonable choices of types and values...
February 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28177307/acedrg-a-stereochemical-description-generator-for-ligands
#8
Fei Long, Robert A Nicholls, Paul Emsley, Saulius Graǽulis, Andrius Merkys, Antanas Vaitkus, Garib N Murshudov
The program AceDRG is designed for the derivation of stereochemical information about small molecules. It uses local chemical and topological environment-based atom typing to derive and organize bond lengths and angles from a small-molecule database: the Crystallography Open Database (COD). Information about the hybridization states of atoms, whether they belong to small rings (up to seven-membered rings), ring aromaticity and nearest-neighbour information is encoded in the atom types. All atoms from the COD have been classified according to the generated atom types...
February 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28177306/validation-and-extraction-of-molecular-geometry-information-from-small-molecule-databases
#9
Fei Long, Robert A Nicholls, Paul Emsley, Saulius Graǽulis, Andrius Merkys, Antanas Vaitkus, Garib N Murshudov
A freely available small-molecule structure database, the Crystallography Open Database (COD), is used for the extraction of molecular-geometry information on small-molecule compounds. The results are used for the generation of new ligand descriptions, which are subsequently used by macromolecular model-building and structure-refinement software. To increase the reliability of the derived data, and therefore the new ligand descriptions, the entries from this database were subjected to very strict validation...
February 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28177305/keep-it-together-restraints-in-crystallographic-refinement-of-macromolecule-ligand-complexes
#10
Roberto A Steiner, Julie A Tucker
A short introduction is provided to the concept of restraints in macromolecular crystallographic refinement. A typical ligand restraint-generation process is then described, covering types of input, the methodology and the mechanics behind the software in general terms, how this has evolved over recent years and what to look for in the output. Finally, the currently available restraint-generation software is compared, concluding with some thoughts for the future.
February 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28177304/guidelines-for-the-successful-generation-of-protein-ligand-complex-crystals
#11
Ilka Müller
With continuous technical improvements at synchrotron facilities, data-collection rates have increased dramatically. This makes it possible to collect diffraction data for hundreds of protein-ligand complexes within a day, provided that a suitable crystal system is at hand. However, developing a suitable crystal system can prove challenging, exceeding the timescale of data collection by several orders of magnitude. Firstly, a useful crystallization construct of the protein of interest needs to be chosen and its expression and purification optimized, before screening for suitable crystallization and soaking conditions can start...
February 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28177303/ligand-complex-structures-in-protein-crystallography
#12
Judit É Debreczeni, Paul Emsley
No abstract text is available yet for this article.
February 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28045386/learning-from-oligosaccharide-soaks-of-crystals-of-an-aa13-lytic-polysaccharide-monooxygenase-crystal-packing-ligand-binding-and-active-site-disorder
#13
Kristian E H Frandsen, Jens Christian Navarro Poulsen, Morten Tovborg, Katja S Johansen, Leila Lo Leggio
Lytic polysaccharide monooxygenases (LPMOs) are a class of copper-dependent enzymes discovered within the last ten years. They oxidatively cleave polysaccharides (chitin, lignocellulose, hemicellulose and starch-derived), presumably making recalcitrant substrates accessible to glycoside hydrolases. Recently, the first crystal structure of an LPMO-substrate complex was reported, giving insights into the interaction of LPMOs with β-linked substrates (Frandsen et al., 2016). The LPMOs acting on α-linked glycosidic bonds (family AA13) display binding surfaces that are quite different from those of LPMOs that act on β-linked glycosidic bonds (families AA9-AA11), as revealed from the first determined structure (Lo Leggio et al...
January 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28045385/crystal-structure-of-human-chondroadherin-solving-a-difficult-molecular-replacement-problem-using-de-novo-models
#14
Sebastian Rämisch, Anna Pramhed, Viveka Tillgren, Anders Aspberg, Derek T Logan
Chondroadherin (CHAD) is a cartilage matrix protein that mediates the adhesion of isolated chondrocytes. Its protein core is composed of 11 leucine-rich repeats (LRR) flanked by cysteine-rich domains. CHAD makes important interactions with collagen as well as with cell-surface heparin sulfate proteoglycans and α2β1 integrins. The integrin-binding site is located in a region of hitherto unknown structure at the C-terminal end of CHAD. Peptides based on the C-terminal human CHAD (hCHAD) sequence have shown therapeutic potential for treating osteoporosis...
January 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28045384/q-r-quantum-based-refinement
#15
Min Zheng, Jeffrey R Reimers, Mark P Waller, Pavel V Afonine
Quantum-based refinement utilizes chemical restraints derived from quantum-chemical methods instead of the standard parameterized library-based restraints used in refinement packages. The motivation is twofold: firstly, the restraints have the potential to be more accurate, and secondly, the restraints can be more easily applied to new molecules such as drugs or novel cofactors. Here, a new project called Q|R aimed at developing quantum-based refinement of biomacromolecules is under active development by researchers at Shanghai University together with PHENIX developers...
January 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28045383/the-structure-of-a-calcium-dependent-phosphoinositide-specific-phospholipase-c-from-pseudomonas-sp-62186-the-first-from-a-gram-negative-bacterium
#16
Olga V Moroz, Elena Blagova, Andrey A Lebedev, Allan Nørgaard, Dorotea R Segura, Thomas H Blicher, Jesper Brask, Keith S Wilson
Bacterial phosphoinositide-specific phospholipases C (PI-PLCs) are the smallest members of the PI-PLC family, which includes much larger mammalian enzymes responsible for signal transduction as well as enzymes from protozoan parasites, yeast and plants. Eukaryotic PI-PLCs have calcium in the active site, but this is absent in the known structures of Gram-positive bacteria, where its role is instead played by arginine. In addition to their use in a number of industrial applications, the bacterial enzymes attract special interest because they can serve as convenient models of the catalytic domains of eukaryotic enzymes for in vitro activity studies...
January 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28045382/solution-of-the-structure-of-a-calmodulin-peptide-complex-in-a-novel-configuration-from-a-variably-twinned-data-set
#17
Jacob Pearson Keller
Structure determination of conformationally variable proteins can prove challenging even when many possible molecular-replacement (MR) search models of high sequence similarity are available. Calmodulin (CaM) is perhaps the best-studied archetype of these flexible proteins: while there are currently ∼450 structures of significant sequence similarity available in the Protein Data Bank (PDB), novel conformations of CaM and complexes thereof continue to be reported. Here, the details of the solution of a novel peptide-CaM complex structure by MR are presented, in which only one MR solution of marginal quality was found despite the use of 120 different search models, an exclusivity enhanced by the presence of a high degree of hemihedral twinning (overall refined twin fraction = 0...
January 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28045381/structural-studies-of-substrate-and-product-complexes-of-5-aminolaevulinic-acid-dehydratase-from-humans-escherichia-coli-and-the-hyperthermophile-pyrobaculum-calidifontis
#18
N Mills-Davies, D Butler, E Norton, D Thompson, M Sarwar, J Guo, R Gill, N Azim, A Coker, S P Wood, P T Erskine, L Coates, J B Cooper, N Rashid, M Akhtar, P M Shoolingin-Jordan
A number of X-ray analyses of an enzyme involved in a key early stage of tetrapyrrole biosynthesis are reported. Two structures of human 5-aminolaevulinate dehydratase (ALAD), native and recombinant, have been determined at 2.8 Å resolution, showing that the enzyme adopts an octameric quaternary structure in accord with previously published analyses of the enzyme from a range of other species. However, this is in contrast to the finding that a disease-related F12L mutant of the human enzyme uniquely forms hexamers [Breinig et al...
January 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28045380/structure-and-conformational-plasticity-of-the-u6-small-nuclear-ribonucleoprotein-core
#19
Eric J Montemayor, Allison L Didychuk, Honghong Liao, Panzhou Hu, David A Brow, Samuel E Butcher
U6 small nuclear RNA (snRNA) is a key component of the active site of the spliceosome, a large ribonucleoprotein complex that catalyzes the splicing of precursor messenger RNA. Prior to its incorporation into the spliceosome, U6 is bound by the protein Prp24, which facilitates unwinding of the U6 internal stem-loop (ISL) so that it can pair with U4 snRNA. A previously reported crystal structure of the `core' of the U6 small nuclear ribonucleoprotein (snRNP) contained an ISL-stabilized A62G mutant of U6 bound to all four RNA-recognition motif (RRM) domains of Prp24 [Montemayor et al...
January 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/27917831/introduction-to-protein-science-architecture-function-and-genomics-third-edition-by-arthur-m-lesk-oxford-university-press-2016-pp-466-paperback-price-gbp-39-99-isbn-9780198716846
#20
Claude Didierjean, Frédérique Tête-Favier
No abstract text is available yet for this article.
December 1, 2016: Acta Crystallographica. Section D, Structural Biology
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