Dynamic nuclear polarization enhanced neutron crystallography: Amplifying hydrogen in biological crystals

Pierce, J.; Cuneo, M.J.; Jennings, Anna; Li, Le; Meilleur, Flora; Zhao, Jinkui; Myles, Dean A. A.

doi:10.1016/bs.mie.2019.11.018

Cited by 10 publications

(5 citation statements)

References 51 publications

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“…These results were consistent across all of the samples, and are also consistent with the assumed 50% initial polarization. A more thorough discussion of the results of these tests (including diffraction plots) can be found in references [4] and [10]…”

Section: First Resultsmentioning

confidence: 99%

Status and Outlook for the Dynamic Nuclear Polarization Program at ORNL

Pierce¹

2020

Proceedings of the 18th International Workshop on Polarized Sources, Targets, and Polarimetry — PoS(PSTP2019)

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The spin dependence of the neutron scattering cross section, especially for hydrogen, makes Dynamic Nuclear Polarization a powerful technique for improving neutron diffraction measurements, especially for biological and soft matter systems. Oak Ridge National Laboratory has demonstrated the application of this technique to Neutron Macromolecular Crystallography, with an eye towards DNP become a normal part of the user program for the Second Target Station that is being built at the SNS. The status of the current system will be discussed.

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Section: First Resultsmentioning

confidence: 99%

Status and Outlook for the Dynamic Nuclear Polarization Program at ORNL

Pierce¹

2020

Proceedings of the 18th International Workshop on Polarized Sources, Targets, and Polarimetry — PoS(PSTP2019)

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“…To overcome this problem, we developed a closed-cycle DNP apparatus with a magnetic field of 3.4 T in 2018 (Kumada et al, 2018a;Kumada et al, 2018b), but the proton polarization obtained from this apparatus was not sufficient for the SCV-SANS measurements. In contrast, a large enhancement of proton polarization has been reported using a closed-cycle DNP apparatus at higher magnetic fields (Pierce et al, 2020;Kiswandhi et al, 2017). We plan to restart the SCV-SANS measurements at SANS-J using the high-field closed-cycle DNP system in the near future.…”

Section: Discussionmentioning

confidence: 97%

Upgrade of the small-angle neutron scattering diffractometer SANS-J at JRR-3

Kumada,

Motokawa,

Oba

et al. 2023

J Appl Cryst

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The small-angle neutron scattering diffractometer SANS-J at the research reactor JRR-3, Tokai, Japan has been upgraded. A 3He front detector was installed adjacent to the direct beam just behind the sample position to cover scattering in the range 1.3–6 nm−1 for the magnitude of the scattering vector Q. Additionally, the maximum Q covered by the existing main 3He detector was extended to 1.8 nm−1 by decreasing the minimum sample-to-detector distance. These modifications enabled gapless measurements of the scattering curve in the Q range 0.002–6 nm−1 with three standard device layouts that can be changed within 10 min. A new graphical user interface simplifies the operation of the device layouts and data acquisition.

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“…Currently, most neutron entries in the PDB (157 out of 213) reflect experiments carried out on partially deuterated samples, as 1 H/ 2 H exchange is simpler and less expensive than perdeuteration. However, the establishment of dedicated deuteration facilities and advanced experimental protocols have made perdeuteration more accessible to users (Meilleur et al, 2009;Budayova-Spano et al, 2020;Pierce et al, 2020).…”

Section: 'Deuterium Fraction' Parametrizationmentioning

confidence: 99%

Neutron crystallographic refinement with REFMAC5 from the CCP4 suite

Catapano,

Long,

Yamashita

et al. 2023

Acta Cryst Sect D Struct Biol

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Hydrogen (H) atoms are abundant in macromolecules and often play critical roles in enzyme catalysis, ligand-recognition processes and protein–protein interactions. However, their direct visualization by diffraction techniques is challenging. Macromolecular X-ray crystallography affords the localization of only the most ordered H atoms at (sub-)atomic resolution (around 1.2 Å or higher). However, many H atoms of biochemical significance remain undetectable by this method. In contrast, neutron diffraction methods enable the visualization of most H atoms, typically in the form of deuterium (2H) atoms, at much more common resolution values (better than 2.5 Å). Thus, neutron crystallography, although technically demanding, is often the method of choice when direct information on protonation states is sought. REFMAC5 from the Collaborative Computational Project No. 4 (CCP4) is a program for the refinement of macromolecular models against X-ray crystallographic and cryo-EM data. This contribution describes its extension to include the refinement of structural models obtained from neutron crystallographic data. Stereochemical restraints with accurate bond distances between H atoms and their parent atom nuclei are now part of the CCP4 Monomer Library, the source of prior chemical information used in the refinement. One new feature for neutron data analysis in REFMAC5 is refinement of the protium/deuterium (1H/2H) fraction. This parameter describes the relative 1H/2H contribution to neutron scattering for hydrogen isotopes. The newly developed REFMAC5 algorithms were tested by performing the (re-)refinement of several entries available in the PDB and of one novel structure (FutA) using either (i) neutron data only or (ii) neutron data supplemented by external restraints to a reference X-ray crystallographic structure. Re-refinement with REFMAC5 afforded models characterized by R-factor values that are consistent with, and in some cases better than, the originally deposited values. The use of external reference structure restraints during refinement has been observed to be a valuable strategy, especially for structures at medium–low resolution.

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Dynamic nuclear polarization enhanced neutron crystallography: Amplifying hydrogen in biological crystals

Cited by 10 publications

References 51 publications

Status and Outlook for the Dynamic Nuclear Polarization Program at ORNL

Status and Outlook for the Dynamic Nuclear Polarization Program at ORNL

Upgrade of the small-angle neutron scattering diffractometer SANS-J at JRR-3

Neutron crystallographic refinement with REFMAC5 from the CCP4 suite

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