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Acta Crystallographica. Section F, Structural Biology Communications

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https://www.readbyqxmd.com/read/30198893/investigation-into-the-binding-of-dyes-within-protein-crystals
#1
Alexander McPherson, Steven B Larson
It was found that the crystals of at least a dozen different proteins could be thoroughly stained to an intense color with a panel of dyes. Many, if not most, of the stained protein crystals retained the dyes almost indefinitely when placed in large volumes of dye-free mother liquor. Dialysis experiments showed that most of the dyes that were retained in crystals also bound to the protein when free in solution; less frequently, some dyes bound only in the crystal. The experiments indicated a strong association of the dyes with the proteins...
September 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30198892/x-ray-structure-of-alisporivir-in-complex-with-cyclophilin-a-at-1-5-%C3%A3-resolution
#2
Marie Dujardin, Julie Bouckaert, Prakash Rucktooa, Xavier Hanoulle
Alisporivir (ALV) is an 11-amino-acid hydrophobic cyclic peptide with N-methyl-D-alanine and N-ethyl-L-valine (NEV) residues at positions 3 and 4, respectively. ALV is a non-immunosuppressive cyclosporin A (CsA) derivative. This inhibitor targets cyclophilins (Cyps), a family of proteins with peptidyl-prolyl cis/trans isomerase enzymatic activity. Cyps act as protein chaperones and are involved in numerous cellular functions. Moreover, Cyps have been shown to be an essential cofactor for the replication of many viruses, including Hepatitis C virus and Human immunodeficiency virus, and have also been shown to be involved in mitochondrial diseases...
September 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30198891/tssa-from-aeromonas-hydrophila-expression-purification-and-crystallographic-studies
#3
Samuel R Dix, Ruyue Sun, Matthew J Harris, Sarah L Batters, Svetlana E Sedelnikova, Patrick J Baker, Mark S Thomas, David W Rice
TssA is a core subunit of the type VI secretion system, which is a major player in interspecies competition in Gram-negative bacteria. Previous studies on enteroaggregative Escherichia coli TssA suggested that it is comprised of three putative domains: a conserved N-terminal domain, a middle domain and a ring-forming C-terminal domain. X-ray studies of the latter two domains have identified their respective structures. Here, the results of the expression and purification of full-length and domain constructs of TssA from Aeromonas hydrophila are reported, resulting in diffraction-quality crystals for the middle domain (Nt2) and a construct including the middle and C-terminal domains (Nt2-CTD)...
September 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30198890/mosquito-larvicidal-binary-toxin-receptor-protein-cqm1-crystallization-and-x-ray-crystallographic-analysis
#4
Mahima Sharma, Ashwitha Lakshmi, Gagan D Gupta, Vinay Kumar
Cqm1 from Culex quinquefasciatus has been identified as the receptor for Lysinibacillus sphaericus binary toxin (BinAB). It is an amylomaltase that is presented on the epithelial membrane in the larval midgut through a glycosyl-phosphatidylinositol anchor. The active core of this protein (residues 23-560) was overexpressed in Escherichia coli, purified and successfully crystallized by the sitting-drop vapor-diffusion method using D-arabinose and CaCl2 as additives, as identified using high-throughput differential scanning fluorimetry analysis...
September 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30198889/staphylococcus-aureus-lipase-purification-kinetic-characterization-crystallization-and-crystallographic-study
#5
Mutsumi Tanaka, Shigeki Kamitani, Kengo Kitadokoro
Staphylococcus aureus lipase (SAL), a triacylglycerol esterase, is an important virulence factor in S. aureus and may be a therapeutic target for infectious diseases caused by S. aureus. For the purposes of anti-SAL drug development using structure-based drug design, X-ray crystallographic analysis of SAL overexpressed in Escherichia coli was performed. The recombinant protein was purified using a three-step protocol involving immobilized metal-affinity chromatography, cation-exchange chromatography and anion-exchange chromatography flowthrough methods, yielding 40 mg of protein per litre of bacterial culture...
September 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30198888/serendipitous-crystallization-and-structure-determination-of-bacterioferritin-from-achromobacter
#6
Abhisek Dwivedy, Bhavya Jha, Khundrakpam Herojit Singh, Mohammed Ahmad, Anam Ashraf, Deepak Kumar, Bichitra Kumar Biswal
Bacterioferritins (Bfrs) are ferritin-like molecules with a hollow spherical 24-mer complex design that are unique to bacterial and archaeal species. They play a critical role in storing iron(III) within the complex at concentrations much higher than the feasible solubility limits of iron(III), thus maintaining iron homeostasis within cells. Here, the crystal structure of bacterioferritin from Achromobacter (Ach Bfr) that crystallized serendipitously during a crystallization attempt of an unrelated mycobacterial protein is reported at 1...
September 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30198887/mbp-binding-darpins-facilitate-the-crystallization-of-an-mbp-fusion-protein
#7
Rajesh Gumpena, George T Lountos, David S Waugh
The production of high-quality crystals is the main bottleneck in determining the structures of proteins using X-ray crystallography. In addition to being recognized as a very effective solubility-enhancing fusion partner, Escherichia coli maltose-binding protein (MBP) has also been successfully employed as a `fixed-arm' crystallization chaperone in more than 100 cases. Here, it is reported that designed ankyrin-repeat proteins (DARPins) that bind with high affinity to MBP can promote the crystallization of an MBP fusion protein when the fusion protein alone fails to produce diffraction-quality crystals...
September 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30198886/msmeg_6292-a-mycobacterium-smegmatis-rna-polymerase-secondary-channel-binding-protein-purification-crystallization-and-x-ray-diffraction-analysis
#8
Abyson Joseph, Valakunja Nagaraja, Ramanathan Natesh
The transcriptional activity of RNA polymerase (RNAP) is controlled by a diverse set of regulatory factors. A subset of these regulators modulate the activity of RNAP through its secondary channel. Gre factors reactivate stalled elongation complexes by enhancing the intrinsic cleavage activity of RNAP. In the present study, the protein MSMEG_6292, a Gre-factor homologue from Mycobacterium smegmatis, was expressed heterologously in Escherichia coli and purified using standard chromatographic techniques. The hanging-drop vapour-diffusion crystallization method yielded diffraction-quality crystals...
September 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30198885/tssa-from-burkholderia-cenocepacia-expression-purification-crystallization-and-crystallographic-analysis
#9
Hayley J Owen, Ruyue Sun, Asma Ahmad, Svetlana E Sedelnikova, Patrick J Baker, Mark S Thomas, David W Rice
TssA is a core component of the type VI secretion system, and phylogenetic analysis of TssA subunits from different species has suggested that these proteins fall into three distinct clades. Whilst representatives of two clades, TssA1 and TssA2, have been the subjects of investigation, no members of the third clade (TssA3) have been studied. Constructs of TssA from Burkholderia cenocepacia, a representative of clade 3, were expressed, purified and subjected to crystallization trials. Data were collected from crystals of constructs of the N-terminal and C-terminal domains...
September 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30198884/ab-initio-structure-solution-of-a-proteolytic-fragment-using-arcimboldo
#10
Jan Abendroth, Banumathi Sankaran, Peter J Myler, Donald D Lorimer, Thomas E Edwards
Crystal structure determination requires solving the phase problem. This can be accomplished using ab initio direct methods for small molecules and macromolecules at resolutions higher than 1.2 Å, whereas macromolecular structure determination at lower resolution requires either molecular replacement using a homologous structure or experimental phases using a derivative such as covalent labeling (for example selenomethionine or mercury derivatization) or heavy-atom soaking (for example iodide ions). Here, a case is presented in which crystals were obtained from a 30...
September 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30198883/structure-of-the-fc-fragment-of-the-nist-reference-antibody-rm8671
#11
D Travis Gallagher, Connor V Galvin, Ioannis Karageorgos
As the link between antigen binding and immune activation, the antibody Fc region has received extensive structural study. In this report, the structure of the Fc fragment of the NIST IgG1 mAb (reference material 8671) is described at 2.1 Å resolution in space group P21 21 21 , with approximate unit-cell parameters a = 50, b = 80, c = 138 Å. Prior Fc structures with a wide variety of modifications are also surveyed, focusing on those in the same crystal form. To facilitate the analysis of conformations, a reference frame and a two-parameter metric are proposed, considering the CH2 domains as mobile with respect to a fixed dimeric CH3 core...
September 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30084401/structure-of-the-gh9-glucosidase-glucosaminidase-from-vibrio-cholerae
#12
Liang Wu, Gideon J Davies
Glycoside hydrolase family 9 (GH9) of carbohydrate-processing enzymes primarily consists of inverting endoglucanases. A subgroup of GH9 enzymes are believed to act as exo-glucosidases or exo-glucosaminidases, with many being found in organisms of the family Vibrionaceae, where they are proposed to function within the chitin-catabolism pathway. Here, it is shown that the GH9 enzyme from the pathogen Vibrio cholerae (hereafter referred to as VC0615) is active on both chitosan-derived and β-glucoside substrates...
August 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30084400/crystal-structure-of-the-effector-binding-domain-of-synechococcus-elongatus-cmpr-in-complex-with-ribulose-1-5-bisphosphate
#13
Didel M Mahounga, Hui Sun, Yong Liang Jiang
The CO2 -concentrating mechanism (CCM) has evolved to improve the efficiency of photosynthesis in autotrophic cyanobacteria. CmpR, a LysR-type transcriptional regulator (LTTR) from Synechococcus elongatus PCC 7942, was found to regulate CCM-related genes under low-CO2 conditions. Here, the dimeric structure of the effector-binding domain of CmpR (CmpR-EBD) in complex with the co-activator ribulose 1,5-bisphosphate (RuBP) is reported at 2.15 Å resolution. One RuBP molecule binds to the inter-domain cleft between the two subunits of the CmpR-EBD dimer...
August 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30084399/structural-studies-of-the-unusual-metal-ion-site-of-the-gh124-endoglucanase-from-ruminiclostridium-thermocellum
#14
Saioa Urresti, Alan Cartmell, Feng Liu, Paul H Walton, Gideon J Davies
The recent discovery of `lytic' polysaccharide monooxygenases, copper-dependent enzymes for biomass degradation, has provided new impetus for the analysis of unusual metal-ion sites in carbohydrate-active enzymes. In this context, the CAZY family GH124 endoglucanase from Ruminiclostridium thermocellum contains an unusual metal-ion site, which was originally modelled as a Ca2+ site but features aspartic acid, asparagine and two histidine imidazoles as coordinating residues, which are more consistent with a transition-metal binding environment...
August 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30084398/structure-of-a-talaromyces-pinophilus-gh62-arabinofuranosidase-in-complex-with-aradnj-at-1-25-%C3%A3-resolution
#15
Olga V Moroz, Lukasz F Sobala, Elena Blagova, Travis Coyle, Wei Peng, Kristian B R Mørkeberg Krogh, Keith A Stubbs, Keith S Wilson, Gideon J Davies
The enzymatic hydrolysis of complex plant biomass is a major societal goal of the 21st century in order to deliver renewable energy from nonpetroleum and nonfood sources. One of the major problems in many industrial processes, including the production of second-generation biofuels from lignocellulose, is the presence of `hemicelluloses' such as xylans which block access to the cellulosic biomass. Xylans, with a polymeric β-1,4-xylose backbone, are frequently decorated with acetyl, glucuronyl and arabinofuranosyl `side-chain' substituents, all of which need to be removed for complete degradation of the xylan...
August 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30084397/crystal-structure-of-highly-glycosylated-human-leukocyte-elastase-in-complex-with-an-s2-site-binding-inhibitor
#16
Jennifer Hochscherf, Markus Pietsch, William Tieu, Kevin Kuan, Andrew D Abell, Michael Gütschow, Karsten Niefind
Glycosylated human leukocyte elastase (HLE) was crystallized and structurally analysed in complex with a 1,3-thiazolidine-2,4-dione derivative that had been identified as an HLE inhibitor in preliminary studies. In contrast to previously described HLE structures with small-molecule inhibitors, in this structure the inhibitor does not bind to the S1 and S2 substrate-recognition sites; rather, this is the first HLE structure with a synthetic inhibitor in which the S2' site is blocked that normally binds the second side chain at the C-terminal side of the scissile peptide bond in a substrate protein...
August 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30084396/conformations-of-the-type-1-lacto-n-biose-i-unit-in-protein-complex-structures
#17
Shinya Fushinobu
The lacto-N-biose I (Galβ1-3GlcNAc; LNB) disaccharide is present as a core unit of type-1 blood group antigens of animal glycoconjugates and milk oligosaccharides. Type-1 antigens often serve as cell-surface receptors for infection by pathogens. LNB in human milk oligosaccharides functions as a prebiotic for bifidobacteria and plays a key role in the symbiotic relationship of commensal gut microbes in infants. Protein Data Bank (PDB) entries exhibiting the LNB unit were investigated using the GlycoMapsDB web tool...
August 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30084395/making-glycoproteins-a-little-bit-sweeter-with-pdb-redo
#18
Bart van Beusekom, Thomas Lütteke, Robbie P Joosten
Glycosylation is one of the most common forms of protein post-translational modification, but is also the most complex. Dealing with glycoproteins in structure model building, refinement, validation and PDB deposition is more error-prone than dealing with nonglycosylated proteins owing to limitations of the experimental data and available software tools. Also, experimentalists are typically less experienced in dealing with carbohydrate residues than with amino-acid residues. The results of the reannotation and re-refinement by PDB-REDO of 8114 glycoprotein structure models from the Protein Data Bank are analyzed...
August 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30084394/spin-ballet-for-sweet-encounters-saturation-transfer-difference-nmr-and-x-ray-crystallography-complement-each-other-in-the-elucidation-of-protein-glycan-interactions
#19
Bärbel S Blaum, Ursula Neu, Thomas Peters, Thilo Stehle
Biomolecular NMR spectroscopy has limitations in the determination of protein structures: an inherent size limit and the requirement for expensive and potentially difficult isotope labelling pose considerable hurdles. Therefore, structural analysis of larger proteins is almost exclusively performed by crystallography. However, the diversity of biological NMR applications outperforms that of any other structural biology technique. For the characterization of transient complexes formed by proteins and small ligands, notably oligosaccharides, one NMR technique has recently proven to be particularly powerful: saturation-transfer difference NMR (STD-NMR) spectroscopy...
August 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30084393/a-perspective-on-structural-and-mechanistic-aspects-of-protein-o-fucosylation
#20
Erandi Lira-Navarrete, Ramon Hurtado-Guerrero
Protein O-fucosylation is an important post-translational modification (PTM) found in cysteine-rich repeats in proteins. Protein O-fucosyltransferases 1 and 2 (PoFUT1 and PoFUT2) are the enzymes responsible for this PTM and selectively glycosylate specific residues in epidermal growth factor-like (EGF) repeats and thrombospondin type I repeats (TSRs), respectively. Within the past six years, crystal structures of both enzymes have been reported, revealing important information on how they recognize protein substrates and achieve catalysis...
August 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
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