scholarly journals Preliminary neutron diffraction analysis of challenging human manganese superoxide dismutase crystals

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.

2014 ◽  
Vol 47 (4) ◽  
pp. 1431-1434 ◽  
Author(s):  
Leighton Coates ◽  
Stephen Tomanicek ◽  
Tobias E. Schrader ◽  
Kevin L. Weiss ◽  
Joseph D. Ng ◽  
...  

The use of cryocooling in neutron diffraction has been hampered by several technical challenges, such as the need for specialized equipment and techniques. This article reports the recent development and deployment of equipment and strategies that allow routine neutron data collection on cryocooled crystals using off-the-shelf components. This system has several advantages compared to a closed displex cooling system, such as fast cooling coupled with easier crystal mounting and centering. The ability to routinely collect cryogenic neutron data for analysis will significantly broaden the range of scientific questions that can be examined by neutron protein crystallography. Cryogenic neutron data collection for macromolecules has recently become available at the new Biological Diffractometer BIODIFF at the FRM II and the Macromolecular Diffractometer (MaNDi) at the Spallation Neutron Source, Oak Ridge National Laboratory. To evaluate the benefits of a cryocooled neutron structure, a full neutron data set was collected on the BIODIFF instrument on a Toho-1 β-lactamase structure at 100 K.


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

2017 ◽  
Vol 73 (a1) ◽  
pp. a110-a110
Author(s):  
Jahaun Azadmanesh ◽  
Scott R. Trickel ◽  
Kevin L. Weiss ◽  
Leighton Coates ◽  
Gloria E. O. Borgstahl

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.


Author(s):  
Alexandra T. Marques ◽  
Sandra P. Santos ◽  
Margarida G. Rosa ◽  
Mafalda A. A. Rodrigues ◽  
Isabel A. Abreu ◽  
...  

Manganese superoxide dismutase (MnSOD) is an essential primary antioxidant enzyme. MnSOD plays an important role in plant tolerance to abiotic stress and is a target candidate for increasing stress tolerance in crop plants. Although the structure and kinetic parameters of MnSODs from several organisms have been determined, this information is still lacking for plant MnSODs. Here, recombinant MnSOD fromArabidopsis thaliana(AtMnSOD) was expressed, purified and crystallized. A nearly complete data set could only be obtained when a total rotation range of 180° was imposed during data collection, despite the seemingly tetragonal metric of the AtMnSOD crystal diffraction. The data set extended to 1.95 Å resolution and the crystal belonged to space groupP1. Molecular-replacement calculations using an ensemble of homologous SOD structures as a search model gave a unique and unambiguous solution corresponding to eight molecules in the asymmetric unit. Structural and kinetic analysis of AtMnSOD is currently being undertaken.


Author(s):  
Jahaun Azadmanesh ◽  
William E. Lutz ◽  
Kevin L. Weiss ◽  
Leighton Coates ◽  
Gloria E. O. Borgstahl

Human manganese superoxide dismutase (MnSOD) is one of the most significant enzymes in preventing mitochondrial dysfunction and related diseases by combating reactive oxygen species (ROS) in the mitochondrial matrix. Mitochondria are the source of up to 90% of cellular ROS generation, and MnSOD performs its necessary bioprotective role by converting superoxide into oxygen and hydrogen peroxide. This vital catalytic function is conducted via cyclic redox reactions between the substrate and the active-site manganese using proton-coupled electron transfers. Owing to protons being difficult to detect experimentally, the series of proton transfers that compose the catalytic mechanism of MnSOD are unknown. Here, methods are described to discern the proton-based mechanism using chemical treatments to control the redox state of large perdeuterated MnSOD crystals and subsequent neutron diffraction. These methods could be applicable to other crystal systems in which proton information on the molecule in question in specific chemical states is desired.


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