The rise of neutron cryo-crystallography

Kwon, Hanna; Langan, Patricia S.; Coates, Leighton; Raven, Emma Lloyd; Moody, P.C.E.

doi:10.1107/s205979831800640x

Cited by 19 publications

(22 citation statements)

References 50 publications

(64 reference statements)

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“…Neutron crystallographic structures will aid in elucidating grand challenges in biology, such as specificity, cooperativity and allostery. Most diffraction instruments are now equipped with cryogenic sample environments, allowing the structures of unstable intermediates along reaction pathways to be solved (Li et al, 2017;Kwon et al, 2018). Deciphering protein chemistry will benefit from synergetic approaches combining QM/MM/MD and neutron and X-ray crystallography experiments.…”

Section: Future Applicationsmentioning

confidence: 99%

Neutron scattering in the biological sciences: progress and prospects

Ashkar

Bilheux

Bordallo³

et al. 2018

Acta Crystallogr D Struct Biol

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The scattering of neutrons can be used to provide information on the structure and dynamics of biological systems on multiple length and time scales. Pursuant to a National Science Foundation‐funded workshop in February 2018, recent developments in this field are reviewed here, as well as future prospects that can be expected given recent advances in sources, instrumentation and computational power and methods. Crystallography, solution scattering, dynamics, membranes, labeling and imaging are examined. For the extraction of maximum information, the incorporation of judicious specific deuterium labeling, the integration of several types of experiment, and interpretation using high‐performance computer simulation models are often found to be particularly powerful.

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Section: Future Applicationsmentioning

confidence: 99%

Neutron scattering in the biological sciences: progress and prospects

Ashkar

Bilheux

Bordallo³

et al. 2018

Acta Crystallogr D Struct Biol

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“…To further characterize the chemical nature of the copper-bound, activated dioxygen species and the protonation states in the LPMO copper active site, we sought to employ neutron diffraction to solve the fullatom structure of a cryogenically trapped intermediate following LPMO9D reduction. Neutron cryo-crystallography has seen a rise in implementation since, similar to X-ray cryocrystallography, it allows short-lived reaction intermediates to be captured, providing information on their chemical identity (Kwon et al, 2018). Since LPMOs oxidatively degrade ligno- cellulose alongside cellulases, which display optimum activity under acidic conditions (pH 3.5-5.5), we additionally measured neutron diffraction from LPMO9D under relevant acidic conditions (Schü lein, 1997;Boer & Koivula, 2003;Cragg et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

Preliminary results of neutron and X-ray diffraction data collection on a lytic polysaccharide monooxygenase under reduced and acidic conditions

et al. 2021

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Lytic polysaccharide monooxygenases (LPMOs) are copper-center enzymes that are involved in the oxidative cleavage of the glycosidic bond in crystalline cellulose and other polysaccharides. The LPMO reaction is initiated by the addition of a reductant and oxygen to ultimately form an unknown activated copper–oxygen species that is responsible for polysaccharide-substrate H-atom abstraction. Given the sensitivity of metalloproteins to radiation damage, neutron protein crystallography provides a nondestructive technique for structural characterization while also informing on the positions of H atoms. Neutron cryo-crystallography permits the trapping of catalytic intermediates, thereby providing insight into the protonation states and chemical nature of otherwise short-lived species in the reaction mechanism. To characterize the reaction-mechanism intermediates of LPMO9D from Neurospora crassa, a cryo-neutron diffraction data set was collected from an ascorbate-reduced crystal. A second neutron diffraction data set was collected at room temperature from an LPMO9D crystal exposed to low-pH conditions to probe the protonation states of ionizable groups involved in catalysis under acidic conditions.

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“…Alternatively, the use of cryocooling in neutron diffraction has recently become available at most neutron facilities. Cryogenic crystallography has particular advantages, such as trapping short-lived intermediates in catalysis (Blakeley et al, 2004) and reducing the atomic displacement parameters, which can lead to improvement of the resolution limit (Coates et al, 2014;Kwon et al, 2018). Structural models derived from diffraction data measured at cryogenic temperatures, however, do not always correspond to their room-temperature structures owing to cryo-artefacts, which can give rise to subtle changes in sidechain conformations, hydration structures, ligand association and protein dissociation equilibria (Deacon et al, 1997;Halle, 2004).…”

Section: Introductionmentioning

confidence: 99%

Towards cryogenic neutron crystallography on the reduced form of [NiFe]-hydrogenase

Hiromoto

Nishikawa

Inoue

et al. 2020

Acta Cryst Sect D Struct Biol

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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.

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The rise of neutron cryo-crystallography

Abstract: The application of the cryogenic data-collection environments used in protein X-ray crystallography to neutron protein crystallography is discussed.

Cited by 19 publications

References 50 publications

Neutron scattering in the biological sciences: progress and prospects

Neutron scattering in the biological sciences: progress and prospects

Preliminary results of neutron and X-ray diffraction data collection on a lytic polysaccharide monooxygenase under reduced and acidic conditions

Towards cryogenic neutron crystallography on the reduced form of [NiFe]-hydrogenase

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