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Acta Crystallographica. Section D, Structural Biology

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https://www.readbyqxmd.com/read/30198902/crystallographically-correct-but-confusing-presentation-of-structural-models-deposited-in-the-protein-data-bank
#1
Zbigniew Dauter, Alexander Wlodawer
The Protein Data Bank (PDB) constitutes a collection of the available atomic models of macromolecules and their complexes obtained by various methods used in structural biology, but chiefly by crystallography. It is an indispensable resource for all branches of science that deal with the structures of biologically active molecules, such as structural biology, bioinformatics, the design of novel drugs etc. Since not all users of the PDB are familiar with the methods of crystallography, it is important to present the results of crystallographic analyses in a form that is easy to interpret by nonspecialists...
September 1, 2018: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/30198901/the-impact-of-cryosolution-thermal-contraction-on-proteins-and-protein-crystals-volumes-conformation-and-order
#2
Douglas H Juers, Christopher A Farley, Christopher P Saxby, Rosemary A Cotter, Jackson K B Cahn, R Conor Holton-Burke, Kaitlin Harrison, Zhenguo Wu
Cryocooling of macromolecular crystals is commonly employed to limit radiation damage during X-ray diffraction data collection. However, cooling itself affects macromolecular conformation and often damages crystals via poorly understood processes. Here, the effects of cryosolution thermal contraction on macromolecular conformation and crystal order in crystals ranging from 32 to 67% solvent content are systematically investigated. It is found that the solution thermal contraction affects macromolecule configurations and volumes, unit-cell volumes, crystal packing and crystal order...
September 1, 2018: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/30198900/the-crystal-structure-of-an-essential-high-temperature-requirement-protein-htra1-rv1223-from-mycobacterium-tuberculosis-reveals-its-unique-features
#3
Khundrakpam Herojit Singh, Savita Yadav, Deepak Kumar, Bichitra Kumar Biswal
High-temperature requirement A (HtrA) proteins, which are members of the heat-shock-induced serine protease family, are involved in extracytoplasmic protein quality control and bacterial survival strategies under stress conditions, and are associated with the virulence of several pathogens; they are therefore major drug targets. Mycobacterium tuberculosis possesses three putative HtrAs: HtrA1 (Rv1223), HtrA2 (Rv0983) and HtrA3 (Rv0125). Each has a cytoplasmic region, a transmembrane helix and a periplasmic region...
September 1, 2018: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/30198899/high-pressure-protein-crystal-structure-analysis-of-escherichia-coli-dihydrofolate-reductase-complexed-with-folate-and-nadp
#4
Takayuki Nagae, Hiroyuki Yamada, Nobuhisa Watanabe
A high-pressure crystallographic study was conducted on Escherichia coli dihydrofolate reductase (ecDHFR) complexed with folate and NADP+ in crystal forms containing both the open and closed conformations of the M20 loop under high-pressure conditions of up to 800 MPa. At pressures between 270 and 500 MPa the crystal form containing the open conformation exhibited a phase transition from P21 to C2. Several structural changes in ecDHFR were observed at high pressure that were also accompanied by structural changes in the NADP+ cofactor and the hydration structure...
September 1, 2018: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/30198898/improving-signal-strength-in-serial-crystallography-with-dials-geometry-refinement
#5
Aaron S Brewster, David G Waterman, James M Parkhurst, Richard J Gildea, Iris D Young, Lee J O'Riordan, Junko Yano, Graeme Winter, Gwyndaf Evans, Nicholas K Sauter
The DIALS diffraction-modeling software package has been applied to serial crystallography data. Diffraction modeling is an exercise in determining the experimental parameters, such as incident beam wavelength, crystal unit cell and orientation, and detector geometry, that are most consistent with the observed positions of Bragg spots. These parameters can be refined by nonlinear least-squares fitting. In previous work, it has been challenging to refine both the positions of the sensors (metrology) on multipanel imaging detectors such as the CSPAD and the orientations of all of the crystals studied...
September 1, 2018: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/30198897/structure-and-function-of-l-threonine-3-dehydrogenase-from-the-parasitic-protozoan-trypanosoma-brucei-revealed-by-x-ray-crystallography-and-geometric-simulations
#6
Eyram Adjogatse, Peter Erskine, Stephen A Wells, John M Kelly, Jonathan D Wilden, A W Edith Chan, David Selwood, Alun Coker, Steve Wood, Jonathan B Cooper
Two of the world's most neglected tropical diseases, human African trypanosomiasis (HAT) and Chagas disease, are caused by protozoan parasites of the genus Trypanosoma. These organisms possess specialized metabolic pathways, frequently distinct from those in humans, which have potential to be exploited as novel drug targets. This study elucidates the structure and function of L-threonine-3-dehydrogenase (TDH) from T. brucei, the causative pathogen of HAT. TDH is a key enzyme in the metabolism of L-threonine, and an inhibitor of TDH has been shown to have trypanocidal activity in the procyclic form of T...
September 1, 2018: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/30198896/crystal-structure-of-the-acinetobacter-baumannii-outer-membrane-protein-omp33
#7
Javier Abellón-Ruiz, Michael Zahn, Arnaud Baslé, Bert van den Berg
Acinetobacter baumannii is becoming a major threat to human health due to its multidrug resistance. This is owing in a large part to the low permeability of its outer membrane (OM), which prevents high internal antibiotic concentrations and makes antibiotic-resistance mechanisms more effective. To exploit OM channels as potential delivery vehicles for future antibiotics, structural information is required. One abundant OM protein in A. baumannii is Omp33. This protein has been reported to be important for the in vivo fitness and virulence of A...
September 1, 2018: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/30198895/crystal-structure-of-the-post-fusion-core-of-the-human-coronavirus-229e-spike-protein-at-1-86-%C3%A3-resolution
#8
Lei Yan, Bing Meng, Jiangchao Xiang, Ian A Wilson, Bei Yang
Human coronavirus 229E (HCoV-229E) usually causes mild upper respiratory infections in heathy adults, but may lead to severe complications or mortality in individuals with weakened immune systems. Virus entry of HCoV-229E is mediated by its spike (S) protein, where the S1 domain facilitates attachment to host cells and the S2 domain is involved in subsequent fusion of the virus and host membranes. During the fusion process, two heptad repeats, HR1 and HR2, in the S2 domain assemble into a six-helix membrane-fusion structure termed the fusion core...
September 1, 2018: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/30198894/new-tools-for-the-analysis-and-validation-of-cryo-em-maps-and-atomic-models
#9
Pavel V Afonine, Bruno P Klaholz, Nigel W Moriarty, Billy K Poon, Oleg V Sobolev, Thomas C Terwilliger, Paul D Adams, Alexandre Urzhumtsev
Recent advances in the field of electron cryomicroscopy (cryo-EM) have resulted in a rapidly increasing number of atomic models of biomacromolecules that have been solved using this technique and deposited in the Protein Data Bank and the Electron Microscopy Data Bank. Similar to macromolecular crystallography, validation tools for these models and maps are required. While some of these validation tools may be borrowed from crystallography, new methods specifically designed for cryo-EM validation are required...
September 1, 2018: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/30082516/evaluation-of-models-determined-by-neutron-diffraction-and-proposed-improvements-to-their-validation-and-deposition
#10
Dorothee Liebschner, Pavel V Afonine, Nigel W Moriarty, Paul Langan, Paul D Adams
The Protein Data Bank (PDB) contains a growing number of models that have been determined using neutron diffraction or a hybrid method that combines X-ray and neutron diffraction. The advantage of neutron diffraction experiments is that the positions of all atoms can be determined, including H atoms, which are hardly detectable by X-ray diffraction. This allows the determination of protonation states and the assignment of H atoms to water molecules. Because neutrons are scattered differently by hydrogen and its isotope deuterium, neutron diffraction in combination with H/D exchange can provide information on accessibility, dynamics and chemical lability...
August 1, 2018: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/30082515/the-rise-of-neutron-cryo-crystallography
#11
Hanna Kwon, Patricia S Langan, Leighton Coates, Emma L Raven, Peter C E Moody
The use of boiled-off liquid nitrogen to maintain protein crystals at 100 K during X-ray data collection has become almost universal. Applying this to neutron protein crystallography offers the opportunity to significantly broaden the scope of biochemical problems that can be addressed, although care must be taken in assuming that direct extrapolation to room temperature is always valid. Here, the history to date of neutron protein cryo-crystallography and the particular problems and solutions associated with the mounting and cryocooling of the larger crystals needed for neutron crystallography are reviewed...
August 1, 2018: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/30082514/cryoprotectant-free-high-pressure-cooling-and-dynamic-nuclear-polarization-for-more-sensitive-detection-of-hydrogen-in-neutron-protein-crystallography
#12
Ichiro Tanaka, Naoya Komatsuzaki, Wen Xue Yue, Toshiyuki Chatake, Katsuhiro Kusaka, Nobuo Niimura, Daisuke Miura, Takahiro Iwata, Yoshiyuki Miyachi, Genki Nukazuka, Hiroki Matsuda
To improve the sensitivity of hydrogen detection using neutrons, a proton-polarization technique together with a high-pressure cooling method is necessary. The highest pressure (200 MPa) used in the experiment described here enabled relatively large protein crystals to be cooled without any cryoprotectants while retaining the protein structure, and it was confirmed that high-pressure-cooled crystals diffracted to nearly the same resolution as flash-cooled small crystals soaked with cryoprotectants. Dynamic nuclear polarization was used as a proton-polarization technique for protein crystals, and ∼300 mg polycrystalline protein doped with TEMPOL gave a maximum proton polarization of 22...
August 1, 2018: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/30082513/imagine-neutrons-reveal-enzyme-chemistry
#13
Gabriela C Schröder, William B O'Dell, Dean A A Myles, Andrey Kovalevsky, Flora Meilleur
Neutron diffraction is exquisitely sensitive to the positions of H atoms in protein crystal structures. IMAGINE is a high-intensity, quasi-Laue neutron crystallography beamline developed at the High Flux Isotope Reactor (HFIR) at Oak Ridge National Laboratory. This state-of-the-art facility for neutron diffraction has enabled detailed structural analysis of macromolecules. IMAGINE is especially suited to resolve individual H atoms in protein structures, enabling neutron protein structures to be determined at or near atomic resolutions from crystals with volumes of less than 1 mm3 and unit-cell edges of less than 150 Å...
August 1, 2018: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/30082512/crystallographic-study-of-dioxygen-chemistry-in-a-copper-containing-nitrite-reductase-from-geobacillus-thermodenitrificans
#14
Yohta Fukuda, Takuro Matsusaki, Ka Man Tse, Eiichi Mizohata, Michael E P Murphy, Tsuyoshi Inoue
Copper-containing nitrite reductases (CuNIRs) are multifunctional enzymes that catalyse the one-electron reduction of nitrite (NO2 - ) to nitric oxide (NO) and the two-electron reduction of dioxygen (O2 ) to hydrogen peroxide (H2 O2 ). In contrast to the mechanism of nitrite reduction, that of dioxygen reduction is poorly understood. Here, results from anaerobic synchrotron-radiation crystallography (SRX) and aerobic in-house radiation crystallography (iHRX) with a CuNIR from the thermophile Geobacillus thermodenitrificans (GtNIR) support the hypothesis that the dioxygen present in an aerobically manipulated crystal can bind to the catalytic type 2 copper (T2Cu) site of GtNIR during SRX experiments...
August 1, 2018: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/30082511/apurinic-apyrimidinic-ap-endonuclease-1-processing-of-ap-sites-with-5-mismatches
#15
Max S Fairlamb, Amy M Whitaker, Bret D Freudenthal
Despite the DNA duplex being central to biological functions, many intricacies of this molecule, including the dynamic nature of mismatched base pairing, are still unknown. The unique conformations adopted by DNA mismatches can provide insight into the forces at play between nucleotides. Moreover, DNA-binding proteins apply their own individualized steric and electrochemical influences on the nucleotides that they interact with, further altering base-pairing conformations. Here, seven X-ray crystallographic structures of the human nuclease apurinic/apyrimidinic (AP) endonuclease 1 (APE1) in complex with its substrate target flanked by a 5' mismatch are reported...
August 1, 2018: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/30082510/the-crystal-structure-of-proteus-vulgaris-tryptophan-indole-lyase-complexed-with-oxindolyl-l-alanine-implications-for-the-reaction-mechanism
#16
Robert S Phillips, Adriaan A Buisman, Sarah Choi, Anusha Hussaini, Zachary A Wood
Tryptophan indole-lyase (TIL) is a bacterial enzyme which catalyzes the reversible formation of indole and ammonium pyruvate from L-tryptophan. Oxindolyl-L-alanine (OIA) is an inhibitor of TIL, with a Ki value of about 5 µM. The crystal structure of the complex of Proteus vulgaris TIL with OIA has now been determined at 2.1 Å resolution. The ligand forms a closed quinonoid complex with the pyridoxal 5'-phosphate (PLP) cofactor. The small domain rotates about 10° to close the active site, bringing His458 into position to donate a hydrogen bond to Asp133, which also accepts a hydrogen bond from the heterocyclic NH of the inhibitor...
August 1, 2018: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/30082509/phosphoramidon-inhibits-the-integral-membrane-protein-zinc-metalloprotease-zmpste24
#17
Brandon R Goblirsch, Buenafe T Arachea, Daniel J Councell, Michael C Wiener
The integral membrane protein zinc metalloprotease ZMPSTE24 possesses a completely novel structure, comprising seven long kinked transmembrane helices that encircle a voluminous 14 000 Å3 cavity within the membrane. Functionally conserved soluble zinc metalloprotease residues are contained within this cavity. As part of an effort to understand the structural and functional relationships between ZMPSTE24 and soluble zinc metalloproteases, the inhibition of ZMPSTE24 by phosphoramidon [N-(α-rhamnopyranosyl-oxyhydroxyphosphinyl)-Leu-Trp], a transition-state analog and competitive inhibitor of multiple soluble zinc metalloproteases, especially gluzincins, has been characterized functionally and structurally...
August 1, 2018: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/30082508/predicting-data-quality-in-biological-x-ray-solution-scattering
#18
Chenzheng Wang, Yuexia Lin, Devin Bougie, Richard E Gillilan
Biological small-angle X-ray solution scattering (BioSAXS) is now widely used to gain information on biomolecules in the solution state. Often, however, it is not obvious in advance whether a particular sample will scatter strongly enough to give useful data to draw conclusions under practically achievable solution conditions. Conformational changes that appear to be large may not always produce scattering curves that are distinguishable from each other at realistic concentrations and exposure times. Emerging technologies such as time-resolved SAXS (TR-SAXS) pose additional challenges owing to small beams and short sample path lengths...
August 1, 2018: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/30082507/biological-small-angle-neutron-scattering-recent-results-and-development
#19
Emilie Mahieu, Frank Gabel
Small-angle neutron scattering (SANS) has increasingly been used by the structural biology community in recent years to obtain low-resolution information on solubilized biomacromolecular complexes in solution. In combination with deuterium labelling and solvent-contrast variation (H2 O/D2 O exchange), SANS provides unique information on individual components in large heterogeneous complexes that is perfectly complementary to the structural restraints provided by crystallography, nuclear magnetic resonance and electron microscopy...
August 1, 2018: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/30082506/diffraction-structural-biology-introductory-overview
#20
Volker Urban, Paul Langan
No abstract text is available yet for this article.
August 1, 2018: Acta Crystallographica. Section D, Structural Biology
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