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Acta Crystallographica. Section D, Structural Biology

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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
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
Claude Didierjean, Frédérique Tête-Favier
No abstract text is available yet for this article.
December 1, 2016: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/27917830/structural-analysis-of-the-bright-monomeric-yellow-green-fluorescent-protein-mneongreen-obtained-by-directed-evolution
#9
Damien Clavel, Guillaume Gotthard, David von Stetten, Daniele De Sanctis, Hélène Pasquier, Gerard G Lambert, Nathan C Shaner, Antoine Royant
Until recently, genes coding for homologues of the autofluorescent protein GFP had only been identified in marine organisms from the phyla Cnidaria and Arthropoda. New fluorescent-protein genes have now been found in the phylum Chordata, coding for particularly bright oligomeric fluorescent proteins such as the tetrameric yellow fluorescent protein lanYFP from Branchiostoma lanceolatum. A successful monomerization attempt led to the development of the bright yellow-green fluorescent protein mNeonGreen. The structures of lanYFP and mNeonGreen have been determined and compared in order to rationalize the directed evolution process leading from a bright, tetrameric to a still bright, monomeric fluorescent protein...
December 1, 2016: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/27917829/the-er-stress-sensor-perk-luminal-domain-functions-as-a-molecular-chaperone-to-interact-with-misfolded-proteins
#10
Peng Wang, Jingzhi Li, Bingdong Sha
PERK is one of the major sensor proteins which can detect the protein-folding imbalance generated by endoplasmic reticulum (ER) stress. It remains unclear how the sensor protein PERK is activated by ER stress. It has been demonstrated that the PERK luminal domain can recognize and selectively interact with misfolded proteins but not native proteins. Moreover, the PERK luminal domain may function as a molecular chaperone to directly bind to and suppress the aggregation of a number of misfolded model proteins...
December 1, 2016: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/27917828/molecular-determinants-of-substrate-specificity-revealed-by-the-structure-of-clostridium-thermocellum-arabinofuranosidase-43a-from-glycosyl-hydrolase-family-43-subfamily-16
#11
Arun Goyal, Shadab Ahmed, Kedar Sharma, Vikas Gupta, Pedro Bule, Victor D Alves, Carlos M G A Fontes, Shabir Najmudin
The recent division of the large glycoside hydrolase family 43 (GH43) into subfamilies offers a renewed opportunity to develop structure-function studies aimed at clarifying the molecular determinants of substrate specificity in carbohydrate-degrading enzymes. α-L-Arabinofuranosidases (EC 3.2.1.55) remove arabinose side chains from heteropolysaccharides such as xylan and arabinan. However, there is some evidence suggesting that arabinofuranosidases are substrate-specific, being unable to display a debranching activity on different polysaccharides...
December 1, 2016: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/27917827/the-n14-anti-afamin-antibody-fab-a-rare-vl1-cdr-glycosylation-crystallographic-re-sequencing-molecular-plasticity-and-conservative-versus-enthusiastic-modelling
#12
Andreas Naschberger, Barbara G Fürnrohr, Tihana Lenac Rovis, Suzana Malic, Klaus Scheffzek, Hans Dieplinger, Bernhard Rupp
The monoclonal antibody N14 is used as a detection antibody in ELISA kits for the human glycoprotein afamin, a member of the albumin family, which has recently gained interest in the capture and stabilization of Wnt signalling proteins, and for its role in metabolic syndrome and papillary thyroid carcinoma. As a rare occurrence, the N14 Fab is N-glycosylated at Asn26L at the onset of the VL1 antigen-binding loop, with the α-1-6 core fucosylated complex glycan facing out of the L1 complementarity-determining region...
December 1, 2016: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/27917826/improved-radiation-dose-efficiency-in-solution-saxs-using-a-sheath-flow-sample-environment
#13
Nigel Kirby, Nathan Cowieson, Adrian M Hawley, Stephen T Mudie, Duncan J McGillivray, Michael Kusel, Vesna Samardzic-Boban, Timothy M Ryan
Radiation damage is a major limitation to synchrotron small-angle X-ray scattering analysis of biomacromolecules. Flowing the sample during exposure helps to reduce the problem, but its effectiveness in the laminar-flow regime is limited by slow flow velocity at the walls of sample cells. To overcome this limitation, the coflow method was developed, where the sample flows through the centre of its cell surrounded by a flow of matched buffer. The method permits an order-of-magnitude increase of X-ray incident flux before sample damage, improves measurement statistics and maintains low sample concentration limits...
December 1, 2016: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/27917825/molecular-symmetry-constrained-systematic-search-approach-to-structure-solution-of-the-coiled-coil-srgap2-f-barx-domain
#14
Michael Sporny, Julia Guez-Haddad, David G Waterman, Michail N Isupov, Yarden Opatowsky
SRGAP2 (Slit-Robo GTPase-activating protein 2) is a cytoplasmic protein found to be involved in neuronal branching, restriction of neuronal migration and restriction of the length and density of dendritic postsynaptic spines. The extended F-BAR (F-BARx) domain of SRGAP2 generates membrane protrusions when expressed in COS-7 cells, while most F-BARs induce the opposite effect: membrane invaginations. As a first step to understand this discrepancy, the F-BARx domain of SRGAP2 was isolated and crystallized after co-expression with the carboxy domains of the protein...
December 1, 2016: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/27917824/on-the-interpretation-of-reflectivity-data-from-lipid-bilayers-in-terms-of-molecular-dynamics-models
#15
Arwel V Hughes, Fillip Ciesielski, Antreas C Kalli, Luke A Clifton, Timothy R Charlton, Mark S P Sansom, John R P Webster
Neutron and X-ray reflectivity of model membranes is increasingly used as a tool for the study of membrane structures and dynamics. As the systems under study become more complex, and as long, all-atom molecular-dynamics (MD) simulations of membranes become more available, there is increasing interest in the use of MD simulations in the analysis of reflectometry data from membranes. In order to perform this, it is necessary to produce a model of the complete interface, including not only the MD-derived structure of the membrane, but also the supporting substrate and any other interfacial layers that may be present...
December 1, 2016: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/27841755/cures-vs-profits-successes-in-translational-research-by-james-lyons-weiler-world-scientific-2016-softback-pp-360-price-gbp-18-00-isbn-978-981-4730-14-3
#16
Massimiliano Veroux
No abstract text is available yet for this article.
November 1, 2016: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/27841754/quadruple-space-group-ambiguity-owing-to-rotational-and-translational-noncrystallographic-symmetry-in-human-liver-fructose-1-6-bisphosphatase
#17
Armin Ruf, Tim Tetaz, Brigitte Schott, Catherine Joseph, Markus G Rudolph
Fructose-1,6-bisphosphatase (FBPase) is a key regulator of gluconeogenesis and a potential drug target for type 2 diabetes. FBPase is a homotetramer of 222 symmetry with a major and a minor dimer interface. The dimers connected via the minor interface can rotate with respect to each other, leading to the inactive T-state and active R-state conformations of FBPase. Here, the first crystal structure of human liver FBPase in the R-state conformation is presented, determined at a resolution of 2.2 Å in a tetragonal setting that exhibits an unusual arrangement of noncrystallographic symmetry (NCS) elements...
November 1, 2016: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/27841753/ultrahigh-resolution-centrosymmetric-crystal-structure-of-z-dna-reveals-the-massive-presence-of-alternate-conformations
#18
Pawel Drozdzal, Miroslaw Gilski, Mariusz Jaskolski
The self-complementary d(CGCGCG) hexanucleotide was synthesized with both D-2'-deoxyribose (the natural enantiomer) and L-2'-deoxyribose, and the two enantiomers were mixed in racemic (1:1) proportions and crystallized, producing a new crystal form with C2/c symmetry that diffracted X-rays to 0.78 Å resolution. The structure was solved by direct, dual-space and molecular-replacement methods and was refined to an R factor of 13.86%. The asymmetric unit of the crystal contains one Z-DNA duplex and three Mg(2+) sites...
November 1, 2016: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/27841752/perdeuteration-crystallization-data-collection-and-comparison-of-five-neutron-diffraction-data-sets-of-complexes-of-human-galectin-3c
#19
Francesco Manzoni, Kadhirvel Saraboji, Janina Sprenger, Rohit Kumar, Ann Louise Noresson, Ulf J Nilsson, Hakon Leffler, S Zoë Fisher, Tobias E Schrader, Andreas Ostermann, Leighton Coates, Matthew P Blakeley, Esko Oksanen, Derek T Logan
Galectin-3 is an important protein in molecular signalling events involving carbohydrate recognition, and an understanding of the hydrogen-bonding patterns in the carbohydrate-binding site of its C-terminal domain (galectin-3C) is important for the development of new potent inhibitors. The authors are studying these patterns using neutron crystallography. Here, the production of perdeuterated human galectin-3C and successive improvement in crystal size by the development of a crystal-growth protocol involving feeding of the crystallization drops are described...
November 1, 2016: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/27841751/a-public-database-of-macromolecular-diffraction-experiments
#20
Marek Grabowski, Karol M Langner, Marcin Cymborowski, Przemyslaw J Porebski, Piotr Sroka, Heping Zheng, David R Cooper, Matthew D Zimmerman, Marc André Elsliger, Stephen K Burley, Wladek Minor
The low reproducibility of published experimental results in many scientific disciplines has recently garnered negative attention in scientific journals and the general media. Public transparency, including the availability of `raw' experimental data, will help to address growing concerns regarding scientific integrity. Macromolecular X-ray crystallography has led the way in requiring the public dissemination of atomic coordinates and a wealth of experimental data, making the field one of the most reproducible in the biological sciences...
November 1, 2016: Acta Crystallographica. Section D, Structural Biology
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