Preliminary neutron diffraction analysis of challenging human manganese superoxide dismutase crystals

Azadmanesh, Jahaun; Trickel, Scott R.; Weiss, Kevin L.; Coates, Leighton; Borgstahl, Gloria E. O.

doi:10.1107/s2053230x17003508

Cited by 25 publications

(17 citation statements)

References 27 publications

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“…NMR and X-ray crystallography are not very sensitive to revealing the positions of hydrogen, especially on solvent molecules. Recently, neutron diffraction experiments, which can reveal hydrogen positions, have been employed to investigate human MnSOD [ 84 ]. The experiments use a neutron diffractometer tailored to biological samples called the Macromolecular Neutron Diffractometer (MaNDi), which opened for academic use at Oak Ridge National Laboratory in 2014 [ 93 ].…”

Section: Resultsmentioning

confidence: 99%

“…While protonation to a positive charge is unfavorable at the manganese-containing active site, the net sum of proton transfers is energetically favorable. Borgstahl and collaborators have recently employed the use of neutron diffraction to directly detect hydrogen positions and observed protonation of His30 ( Figure 4 ) [ 84 ]. This also suggests that WAT2 can be protonated as it is the nearest hydrogen-bond acceptor/donor to His30 in the crystal structure.…”

Section: Proton Transfers and The Hydrogen Bond Networkmentioning

confidence: 99%

“…( b ) Chain B shows a protonated His30. Methods and statistics for crystal growth, deuterium exchange, data collection, and data reduction are found in Azadmanesh et al, 2017 [ 84 ]. Data was refined to 2.30 Å using PHENIX.REFINE with R work and R free values of 0.28, and 0.31, respectively (unpublished) [ 85 , 86 ].…”

Section: Figurementioning

confidence: 99%

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A Review of the Catalytic Mechanism of Human Manganese Superoxide Dismutase

2018

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Superoxide dismutases (SODs) are necessary antioxidant enzymes that protect cells from reactive oxygen species (ROS). Decreased levels of SODs or mutations that affect their catalytic activity have serious phenotypic consequences. SODs perform their bio-protective role by converting superoxide into oxygen and hydrogen peroxide by cyclic oxidation and reduction reactions with the active site metal. Mutations of SODs can cause cancer of the lung, colon, and lymphatic system, as well as neurodegenerative diseases such as Parkinson’s disease and amyotrophic lateral sclerosis. While SODs have proven to be of significant biological importance since their discovery in 1968, the mechanistic nature of their catalytic function remains elusive. Extensive investigations with a multitude of approaches have tried to unveil the catalytic workings of SODs, but experimental limitations have impeded direct observations of the mechanism. Here, we focus on human MnSOD, the most significant enzyme in protecting against ROS in the human body. Human MnSOD resides in the mitochondrial matrix, the location of up to 90% of cellular ROS generation. We review the current knowledge of the MnSOD enzymatic mechanism and ongoing studies into solving the remaining mysteries.

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Section: Resultsmentioning

confidence: 99%

Section: Proton Transfers and The Hydrogen Bond Networkmentioning

confidence: 99%

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A Review of the Catalytic Mechanism of Human Manganese Superoxide Dismutase

2018

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“…Therefore, due to the superior pulse resolution of the DM, despite the minimal advantage in the overall counting statistics of the CM, we have concluded that the DM is the best choice for the new diffractometer at JSNS to target proteins with large unit cells over 250 Å [5,6]. Recently, data collection on MaNDi [7] installed at DM in Spallation Neutron Source (SNS) at Oak Ridge National Laboratory (ORNL) has been reported for a crystal with largest unit cell edge (240 Å) [8].…”

Section: Introductionmentioning

confidence: 99%

The Design of a Versatile TOF Neutron Diffractometer Providing the Complementary Use of Neutron and X-ray Scattering from a Biomacromolecular Single-Crystal with Large Unit Cells

Tomoyori

Kurihara

Tamada

2018

Proceedings of the International Conference on Neutron Optics (NOP2017)

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Membrane proteins are major players in important cell processes and, therefore, are key targets for research on human health and drug development. The crystals of these membrane proteins typically have large unit cells with repeat of a few hundred angstroms. The average intensity of a Bragg peak decreases as the number of peaks increases with large unit cells. It is proposed to develop a dedicated best-in-class high-throughput and high-resolution time-of-flight biomacromolecular single-crystal neutron diffractometer at Japan Spallation Neutron Source (JSNS). A new diffractometer is being designed to collect a full hemisphere of Bragg data with a resolution of 1.5-2 Å on a crystal over a lattice constant of 250 Å. This diffractometer will have a spherical array of over 40 detectors, all pointing inward to enclose a basketball-sized chamber where the pulsed neutron beam will collide with the crystal sample. The neutron detectors will be inserted through openings in two aluminum hemispheres, which can be pulled apart to access the interior; the hemispheres themselves will be on sturdy support structures, ensuring open accessibility to the sample area and wide coverage of the solid angle to measure a large number of reflections derived from a biomacromolecular single-crystal with large unit cells. The sample chamber implemented in the spectrometer of this diffractometer could be operated under vacuum or helium gas to provide a clean environment for the neutron detector. The neutron diffractometer will be combined with an X-ray diffractometer for consecutive data collection with two different quantum beams at a measuring station.

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“…However, by using protein perdeuteration we can reduce the incoherent scattering by a factor of 40, enhancing the signal to noise ratio and enabling data collection from small crystals with large unit cell axes. The combination of perdeuteration with high resolution TOF crystallography has enabled data collection on one of the most challenging systems to be studied with neutrons to date [5][6][7][8] .…”

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Protein Crystallography at the Spallation Neutron Source

Coates

2019

Proceedings of the 3rd International Symposium of Quantum Beam Science at Ibaraki University "Quantum Beam Science in Biology A

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The macromolecular Diffractometer (MaNDi) at the spallation neutron source (SNS) is a powerful tool for determining the position of hydrogen atoms, water molecule orientations, and for identifying different chemical species in protein structures. The wavelength bandwidth is Δλ = 2.16 or 4.3 Å, which can be selected anywhere between 1-10 Å. Data can be collected on samples of 0.1 mm 3 or larger with unit cells in the range of 5-300 Å on edge. An experimental temperature range of 80 to 400K is provided by an inbuilt Oxford diffraction cryostream. The MaNDi instrument is highly oversubscribed and efforts has focused on improving the speed at which the instrument can collect full and complete datasets. Completing the detectors in the MaNDi data array frame which surround the sample position has been a major step forward in meeting this demand. The switch from H 2 O to D 2 O in the moderator cooling system which occurred in early 2018 at the SNS has increased the incident flux on sample at MaNDi by 30% lowering the exposure time needed for each orientation. These upgrades coupled with the SNS now running at 1.4 MW will potentially double the number of experiments that MaNDi can do each year. It will also allow MaNDi to collect data from smaller more complex samples such as membrane proteins and large enzyme complexes. MaNDi Current Status The macromolecular neutron diffractometer (MaNDi) 1, 2 is situated at the first target station of the SNS. It entered the general user program in FY 2014. The instrument is designed to collect neutron diffraction data from small single crystals (0.1-1 mm 3) with large lattice constants between 10 and 300 Å. A focusing neutron guide has been designed to filter the high-energy neutron component of the spectrum and to provide a narrow beam with a wide spectral window and angular divergence almost insensitive to neutron wavelength. The system includes a final

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Preliminary neutron diffraction analysis of challenging human manganese superoxide dismutase crystals

Cited by 25 publications

References 27 publications

A Review of the Catalytic Mechanism of Human Manganese Superoxide Dismutase

A Review of the Catalytic Mechanism of Human Manganese Superoxide Dismutase

The Design of a Versatile TOF Neutron Diffractometer Providing the Complementary Use of Neutron and X-ray Scattering from a Biomacromolecular Single-Crystal with Large Unit Cells

Protein Crystallography at the Spallation Neutron Source

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