scholarly journals Neutron diffraction analysis ofPseudomonas aeruginosapeptidyl-tRNA hydrolase 1

Author(s):  
Hana McFeeters ◽  
Venu Gopal Vandavasi ◽  
Kevin L. Weiss ◽  
Leighton Coates ◽  
Robert L. McFeeters

Perdeuterated peptidyl-tRNA hydrolase 1 fromPseudomonas aeruginosawas crystallized for structural analysis using neutron diffraction. Crystals of perdeuterated protein were grown to 0.15 mm3in size using batch crystallization in 22.5% polyethylene glycol 4000, 100 mMTris pH 7.5, 10%(v/v) isopropyl alcohol with a 20-molar excess of trilysine as an additive. Neutron diffraction data were collected from a crystal at room temperature using the MaNDi single-crystal diffractometer at Oak Ridge National Laboratory.

Author(s):  
Martin Bommer ◽  
Leighton Coates ◽  
Holger Dau ◽  
Athina Zouni ◽  
Holger Dobbek

The PsbO protein of photosystem II stabilizes the active-site manganese cluster and is thought to act as a proton antenna. To enable neutron diffraction studies, crystals of the β-barrel core of PsbO were grown in capillaries. The crystals were optimized by screening additives in a counter-diffusion setup in which the protein and reservoir solutions were separated by a 1% agarose plug. Crystals were cross-linked with glutaraldehyde. Initial neutron diffraction data were collected from a 0.25 mm3crystal at room temperature using the MaNDi single-crystal diffractometer at the Spallation Neutron Source, Oak Ridge National Laboratory.


2017 ◽  
Vol 905 ◽  
pp. 123-130
Author(s):  
Adrian Brügger ◽  
Seung Yub Lee ◽  
İsmail Cevdet Noyan ◽  
Raimondo Betti

Suspension-bridge cables are constructed from strands of galvanized steel wire. They are failure-critical structural members, so a fundamental understanding of their mechanics is imminently important in quantifying suspension bridge safety. The load-carrying capabilities of such strands after local wire failures have been the subject of many theoretical studies utilizing analytical equations and finite-element analysis. Little experimental data, however, exists to validate these models.Over the past five years we have developed a methodology for measuring stress/strain transfer within parallel wire strands of suspension bridge cables using neutron diffraction [1,2]. In this paper we describe the design and verification of parallel cable strands used in our studies. We describe the neutron diffraction strain measurements performed on standard 7-wire and expanded 19-wire models in various configurations at both the Los Alamos National Laboratory Spectrometer for Materials Research at Temperature and Stress (LANL SMARTS) and at the Oak Ridge National Laboratory VULCAN Engineering Materials Diffractometer (ORNL VULCAN). Particular attention is placed on the challenges of aligning and measuring multibody systems with high strain gradients at body-to-body contact points.


2018 ◽  
Vol 89 (9) ◽  
pp. 092601
Author(s):  
Katharine Page ◽  
Bianca Haberl ◽  
Leighton Coates ◽  
Matthew Tucker

Author(s):  
Qun Wan ◽  
Andrey Y. Kovalevsky ◽  
Mark A. Wilson ◽  
Brad C. Bennett ◽  
Paul Langan ◽  
...  

A crystal ofEscherichia colidihydrofolate reductase (ecDHFR) complexed with folate and NADP+of 4 × 1.3 × 0.7 mm (3.6 mm3) in size was obtained by sequential application of microseeding and macroseeding. A neutron diffraction data set was collected to 2.0 Å resolution using the IMAGINE diffractometer at the High Flux Isotope Reactor within Oak Ridge National Laboratory. A 1.6 Å resolution X-ray data set was also collected from a smaller crystal at room temperature. The neutron and X-ray data were used together for joint refinement of the ecDHFR–folate–NADP+ternary-complex structure in order to examine the protonation state, protein dynamics and solvent structure of the complex, furthering understanding of the catalytic mechanism.


2018 ◽  
Vol 2 (1) ◽  
pp. 39-55 ◽  
Author(s):  
Matthew P. Blakeley ◽  
Alberto D. Podjarny

Neutron diffraction techniques permit direct determination of the hydrogen (H) and deuterium (D) positions in crystal structures of biological macromolecules at resolutions of ∼1.5 and 2.5 Å, respectively. In addition, neutron diffraction data can be collected from a single crystal at room temperature without radiation damage issues. By locating the positions of H/D-atoms, protonation states and water molecule orientations can be determined, leading to a more complete understanding of many biological processes and drug-binding. In the last ca. 5 years, new beamlines have come online at reactor neutron sources, such as BIODIFF at Heinz Maier-Leibnitz Zentrum and IMAGINE at Oak Ridge National Laboratory (ORNL), and at spallation neutron sources, such as MaNDi at ORNL and iBIX at the Japan Proton Accelerator Research Complex. In addition, significant improvements have been made to existing beamlines, such as LADI-III at the Institut Laue-Langevin. The new and improved instrumentations are allowing sub-mm3 crystals to be regularly used for data collection and permitting the study of larger systems (unit-cell edges >100 Å). Owing to this increase in capacity and capability, many more studies have been performed and for a wider range of macromolecules, including enzymes, signalling proteins, transport proteins, sugar-binding proteins, fluorescent proteins, hormones and oligonucleotides; of the 126 structures deposited in the Protein Data Bank, more than half have been released since 2013 (65/126, 52%). Although the overall number is still relatively small, there are a growing number of examples for which neutron macromolecular crystallography has provided the answers to questions that otherwise remained elusive.


2020 ◽  
Vol 76 (10) ◽  
pp. 946-953
Author(s):  
Takeshi Hiromoto ◽  
Koji Nishikawa ◽  
Seiya Inoue ◽  
Hiroaki Matsuura ◽  
Yu Hirano ◽  
...  

A membrane-bound hydrogenase from Desulfovibrio vulgaris Miyazaki F is a metalloenzyme that contains a binuclear Ni–Fe complex in its active site and mainly catalyzes the oxidation of molecular hydrogen to generate a proton gradient in the bacterium. The active-site Ni–Fe complex of the aerobically purified enzyme shows its inactive oxidized form, which can be reactivated through reduction by hydrogen. Here, in order to understand how the oxidized form is reactivated by hydrogen and further to directly evaluate the bridging of a hydride ligand in the reduced form of the Ni–Fe complex, a neutron structure determination was undertaken on single crystals grown in a hydrogen atmosphere. Cryogenic crystallography is being introduced into the neutron diffraction research field as it enables the trapping of short-lived intermediates and the collection of diffraction data to higher resolution. To optimize the cooling of large crystals under anaerobic conditions, the effects on crystal quality were evaluated by X-rays using two typical methods, the use of a cold nitrogen-gas stream and plunge-cooling into liquid nitrogen, and the former was found to be more effective in cooling the crystals uniformly than the latter. Neutron diffraction data for the reactivated enzyme were collected at the Japan Photon Accelerator Research Complex under cryogenic conditions, where the crystal diffracted to a resolution of 2.0 Å. A neutron diffraction experiment on the reduced form was carried out at Oak Ridge National Laboratory under cryogenic conditions and showed diffraction peaks to a resolution of 2.4 Å.


2006 ◽  
Vol 39 (2) ◽  
pp. 222-229 ◽  
Author(s):  
Stephen J. Covey-Crump ◽  
Robert F. Holloway ◽  
Paul F. Schofield ◽  
Mark R. Daymond

A simple pressure vessel suitable for use at room temperature has been developed which allows neutron diffraction data to be collected from cylindrical samples of up to 10 mm diameter, at confining pressures of up to 160 MPa, whilst they are also being deformed in compression by the application of a uniaxially symmetric load. The vessel has been commissioned on the ENGIN-X beamline at the ISIS neutron facility (Rutherford Appleton Laboratory, Chilton, UK). The commissioning results show that neutron diffraction data of quality equivalent to that obtained using an identical experiment geometry at room pressure can be acquired using the pressure vessel with only about a factor of two increase in count times.


Author(s):  
Jahaun Azadmanesh ◽  
Scott R. Trickel ◽  
Kevin L. Weiss ◽  
Leighton Coates ◽  
Gloria E. O. Borgstahl

Superoxide dismutases (SODs) are enzymes that protect against oxidative stress by dismutation of superoxide into oxygen and hydrogen peroxide through cyclic reduction and oxidation of the active-site metal. The complete enzymatic mechanisms of SODs are unknown since data on the positions of hydrogen are limited. Here, methods are presented for large crystal growth and neutron data collection of human manganese SOD (MnSOD) using perdeuteration and the MaNDi beamline at Oak Ridge National Laboratory. The crystal from which the human MnSOD data set was obtained is the crystal with the largest unit-cell edge (240 Å) from which data have been collectedvianeutron diffraction to sufficient resolution (2.30 Å) where hydrogen positions can be observed.


2005 ◽  
Vol 480-481 ◽  
pp. 565-572 ◽  
Author(s):  
G. Aurelio ◽  
A. Fernández Guillermet ◽  
G.J. Cuello ◽  
P.B. Bozzano

The lattice parameters of the bcc (b) and omega (W) phases occurring metastably in a series of Zr-rich Zr-Nb alloys have been determined at and above room temperature (TR) using neutron diffraction techniques. In the first place, the effect of temperature changes upon the lattice parameters of the b and W phases in alloys with 10 and 18 at.% Nb was monitored using neutron thermodiffraction. A method of analysis is applied to the data which involves a confrontation between the observed structural properties and an idealised -or ``reference'- behaviour (RB) which admits a simple mathematical description. A generalised form of Vegard's law is adopted as RB for the b phase, whereas a specific RB is proposed for the W structure. The experimental data are well accounted for by this interpretation scheme, leading to a picture of the isothermal reactions occurring at high temperature which involves the transfer of Nb from the W to the b phase. Finally, the neutron diffraction data on the W phase are combined with an electron microscopy study for the alloy with 10 at.% Nb aged at 773 K, which provides information on the composition of this phase and its evolution towards thermodynamic equilibrium.


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