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Microcrystal electron diffraction

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Microcrystal electron diffraction, or MicroED,[1][2] is a CryoEM method that was developed by the Gonen laboratory in late 2013 at the Janelia Research Campus of the Howard Hughes Medical Institute. MicroED is a form of electron crystallography where thin 3D crystals are used for structure determination by electron diffraction. Prior to this demonstration, macromolecular (protein) electron crystallography was mainly used on 2D crystals, for example.[3][4] The method is one of several modern versions of approaches to determine atomic structures using electron diffraction first demonstrated for the positions of hydrogen atoms in NH4Cl crystals by W. E. Laschkarew and I. D. Usykin in 1933,[5] which has since been used for surfaces,[6] via precession electron diffraction,[7] with much of the early work described in the work of Boris Vainshtein[8] and Douglas L. Dorset.[9]

The method was developed for structure determination of proteins from nanocrystals that are typically not suitable for X-ray diffraction because of their size.[10] Crystals that are one billionth the size needed for X-ray crystallography can yield high quality data.[11] The samples are frozen hydrated as for all other CryoEM modalities but instead of using the transmission electron microscope (TEM) in imaging mode one uses it in diffraction mode with a low electron exposure (typically < 0.01 e−/Å2/s). The nano crystal is exposed to the diffracting beam and continuously rotated[2] while diffraction is collected on a fast camera as a movie.[2] MicroED data is then processed using software for X-ray crystallography for structure analysis and refinement.[12] The hardware and software used in a MicroED experiment are standard and broadly available.[13][14]

Development

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See also: Electron crystallography § History

Electron diffraction to solve crystal structures date back to the earliest days of electron diffraction. The first successful demonstration of MicroED was reported in 2013 by the Gonen laboratory[1] for the structure of lysozyme, a classic test protein in X-ray crystallography.

Experimental setup

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Detailed protocols for setting up the electron microscope and for data collections have been published.[15]

Instrumentation

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Microscope

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MicroED data is collected using transmission electron (cryogenic) microscopy. The microscope can be equipped with a selected area aperture but MicroED can also be done without a selected area aperture. While some structures have been reported without freezing, radiation damage is sometimes minimized and higher resolution obtained by using cryo cooling even for small molecules.[16]

Detectors

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A variety of detectors have been used to collected electron diffraction data in MicroED experiments. Detectors utilizing charge-coupled device (CCD) and complementary metal–oxide–semiconductor (CMOS) technology have been used. With CMOS detectors, individual electron counts can be interpreted.[17] More recently, direct electron detectors have been successfully used in both linear and counting modes.[18][19] In these examples electron counting allowed ab initio phasing and visualization of hydrogens in proteins.

Data collection

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Still diffraction

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The initial proof of concept publication on MicroED used lysozyme crystals.[1] Up to 90 degrees of data were collected from a single nano crystal, with discrete 1 degree steps between frames. Each diffraction pattern was collected with an ultra-low dose rate of ~0.01 e−/Å2/s. Data from 3 crystals was merged[20] to yield a 2.9Å resolution structure with good refinement statistics, enabling determination of the structure of a dose-sensitive protein from 3D microcrystals in cryogenic conditions.

Continuous rotation

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MicroED uses continuous rotation during the data collection scheme.[2] Here the crystal is slowly rotated in a single direction while diffraction is recorded on a fast camera as a movie. This led to several improvements in data quality and allowed data processing using standard X-ray crystallographic software.[2] Continuous rotation MicroED improves sampling of reciprocal space.[21]

Data processing

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Detailed protocols for MicroED data processing have been published.[12] When MicroED data is collected using continuous stage rotation, standard crystallography software[14] can be used.

Differences between MicroED and other electron diffraction methods

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Other electron diffraction methods that have been developed and demonstrated to work include Automated Diffraction Tomography (ADT)[22] and Rotation Electron Diffraction (RED[23]). These methods differ slightly from MicroED: In ADT discrete steps of goniometer tilt are used to cover reciprocal space in combination with beam precession to reduce dynamical diffraction effects.[22] ADT uses hardware and software for precession and scanning transmission electron microscopy for crystal tracking.[22] RED is done in TEM but the goniometer is tilted in discrete steps and beam tilting is used to fill in the gaps.[23] Software is used to process ADT and RED data.[23]

Milestones

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Method scope

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MicroED has been used to determine the structures of large globular proteins,[24] small proteins,[2] peptides,[25] membrane proteins,[26] organic molecules,[27][28] and inorganic compounds.[29] In many of these examples hydrogens and charged ions were observed.[25][26]

Novel structures of α-synuclein of Parkinson's disease

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The first structures solved by MicroED were published in late 2015.[25] These structures were of peptide fragments that form the toxic core of α-synculein, the protein responsible for Parkinson's disease and lead to insight into the aggregation mechanism toxic aggregates. The structures were solved at 1.4 Å resolution.

Novel protein structure of R2lox

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The first novel structure of a protein solved by MicroED was published in 2019.[30] The protein is the metalloenzyme R2-like ligand-binding oxidase (R2lox) from Sulfolobus acidocaldarius. The structure was solved at 3.0 Å resolution by molecular replacement using a model of 35% sequence identity built from the closest homolog with a known structure.

References

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  1. ^ a b c Shi, Dan; Nannenga, Brent L; Iadanza, Matthew G; Gonen, Tamir (2013-11-19). "Three-dimensional electron crystallography of protein microcrystals". eLife. 2: e01345. doi:10.7554/elife.01345. ISSN 2050-084X. PMC 3831942. PMID 24252878.
  2. ^ a b c d e f Nannenga, Brent L; Shi, Dan; Leslie, Andrew G W; Gonen, Tamir (2014-08-03). "High-resolution structure determination by continuous-rotation data collection in MicroED". Nature Methods. 11 (9): 927–930. doi:10.1038/nmeth.3043. ISSN 1548-7091. PMC 4149488. PMID 25086503.
  3. ^ Gonen, Tamir; Sliz, Piotr; Kistler, Joerg; Cheng, Yifan; Walz, Thomas (May 2004). "Aquaporin-0 membrane junctions reveal the structure of a closed water pore". Nature. 429 (6988): 193–197. doi:10.1038/nature02503. ISSN 1476-4687.
  4. ^ Walz, Thomas; Hirai, Teruhisa; Murata, Kazuyoshi; Heymann, J. Bernard; Mitsuoka, Kaoru; Fujiyoshi, Yoshinori; Smith, Barbara L.; Agre, Peter; Engel, Andreas (June 1997). "The three-dimensional structure of aquaporin-1". Nature. 387 (6633): 624–627. doi:10.1038/42512. ISSN 0028-0836.
  5. ^ Laschkarew, W. E.; Usyskin, I. D. (1933). "Die Bestimmung der Lage der Wasserstoffionen im NH4Cl-Kristallgitter durch Elektronenbeugung". Zeitschrift für Physik (in German). 85 (9–10): 618–630. doi:10.1007/BF01331003. ISSN 1434-6001.
  6. ^ Takayanagi, K.; Tanishiro, Y.; Takahashi, M.; Takahashi, S. (1985-05-01). "Structural analysis of Si(111)-7×7 by UHV-transmission electron diffraction and microscopy". Journal of Vacuum Science & Technology A: Vacuum, Surfaces, and Films. 3 (3): 1502–1506. doi:10.1116/1.573160. ISSN 0734-2101.
  7. ^ Vincent, R.; Midgley, P.A. (1994). "Double conical beam-rocking system for measurement of integrated electron diffraction intensities". Ultramicroscopy. 53 (3): 271–282. doi:10.1016/0304-3991(94)90039-6.
  8. ^ VAINSHTEIN, B.K. (1964), "Experimental Electron Diffraction Structure Investigations", Structure Analysis by Electron Diffraction, Elsevier, pp. 295–390, retrieved 2024-05-01
  9. ^ Dorset, D. L. (1995-08-31). Structural Electron Crystallography. Springer Science & Business Media. ISBN 978-0-306-45049-5.
  10. ^ Shi, Dan; Nannenga, Brent L; de la Cruz, M Jason; Liu, Jinyang; Sawtelle, Steven; Calero, Guillermo; Reyes, Francis E; Hattne, Johan; Gonen, Tamir (May 2016). "The collection of MicroED data for macromolecular crystallography". Nature Protocols. 11 (5): 895–904. doi:10.1038/nprot.2016.046. ISSN 1754-2189. PMC 5357465. PMID 27077331.
  11. ^ de la Cruz, M Jason; Hattne, Johan; Shi, Dan; Seidler, Paul; Rodriguez, Jose; Reyes, Francis E; Sawaya, Michael R; Cascio, Duilio; Weiss, Simon C (2017). "Atomic-resolution structures from fragmented protein crystals with the cryoEM method MicroED". Nature Methods. 14 (4): 399–402. doi:10.1038/nmeth.4178. ISSN 1548-7091. PMC 5376236. PMID 28192420.
  12. ^ a b Hattne, Johan; Reyes, Francis E.; Nannenga, Brent L.; Shi, Dan; de la Cruz, M. Jason; Leslie, Andrew G. W.; Gonen, Tamir (2015-07-01). "MicroED data collection and processing". Acta Crystallographica Section A. 71 (4): 353–360. doi:10.1107/s2053273315010669. ISSN 2053-2733. PMC 4487423. PMID 26131894.
  13. ^ Zatsepin, Nadia A; Li, Chufeng; Colasurd, Paige; Nannenga, Brent L (October 2019). "The complementarity of serial femtosecond crystallography and MicroED for structure determination from microcrystals". Current Opinion in Structural Biology. 58: 286–293. doi:10.1016/j.sbi.2019.06.004. PMC 6778504. PMID 31345629.
  14. ^ a b Nannenga, Brent L.; Gonen, Tamir (May 2019). "The cryo-EM method microcrystal electron diffraction (MicroED)". Nature Methods. 16 (5): 369–379. doi:10.1038/s41592-019-0395-x. ISSN 1548-7091. PMC 6568260. PMID 31040436.
  15. ^ Shi, Dan; Nannenga, Brent L; de la Cruz, M Jason; Liu, Jinyang; Sawtelle, Steven; Calero, Guillermo; Reyes, Francis E; Hattne, Johan; Gonen, Tamir (2016-04-14). "The collection of MicroED data for macromolecular crystallography". Nature Protocols. 11 (5): 895–904. doi:10.1038/nprot.2016.046. ISSN 1754-2189. PMC 5357465. PMID 27077331.
  16. ^ Christensen, Jeppe; Horton, Peter N.; Bury, Charles S.; Dickerson, Joshua L.; Taberman, Helena; Garman, Elspeth F.; Coles, Simon J. (2019-07-01). "Radiation damage in small-molecule crystallography: fact not fiction". IUCrJ. 6 (4): 703–713. doi:10.1107/S2052252519006948. ISSN 2052-2525. PMC 6608633. PMID 31316814.
  17. ^ See also https://www.gatan.com/ccd-vs-cmos and https://www.gatan.com/techniques/imaging.
  18. ^ Martynowycz, Michael W.; Clabbers, Max T. B.; Hattne, Johan; Gonen, Tamir (June 2022). "Ab initio phasing macromolecular structures using electron-counted MicroED data". Nature Methods. 19 (6): 724–729. doi:10.1038/s41592-022-01485-4. ISSN 1548-7091. PMC 9184278. PMID 35637302.
  19. ^ Clabbers, Max T.B.; Martynowycz, Michael W.; Hattne, Johan; Gonen, Tamir (2022). "Hydrogens and hydrogen-bond networks in macromolecular MicroED data". Journal of Structural Biology: X. 6: 100078. doi:10.1016/j.yjsbx.2022.100078. PMC 9731847. PMID 36507068.
  20. ^ Shi, Dan; Nannenga, Brent L; Iadanza, Matthew G; Gonen, Tamir (2013-11-19). "Three-dimensional electron crystallography of protein microcrystals". eLife. 2: e01345. doi:10.7554/eLife.01345. ISSN 2050-084X. PMC 3831942. PMID 24252878.
  21. ^ Nannenga, Brent L; Shi, Dan; Leslie, Andrew G W; Gonen, Tamir (September 2014). "High-resolution structure determination by continuous-rotation data collection in MicroED". Nature Methods. 11 (9): 927–930. doi:10.1038/nmeth.3043. ISSN 1548-7091. PMC 4149488. PMID 25086503.
  22. ^ a b c Mugnaioli, E.; Gorelik, T.; Kolb, U. (2009). ""Ab initio" structure solution from electron diffraction data obtained by a combination of automated diffraction tomography and precession technique". Ultramicroscopy. 109 (6): 758–765. doi:10.1016/j.ultramic.2009.01.011. ISSN 0304-3991. PMID 19269095.
  23. ^ a b c Wan, Wei; Sun, Junliang; Su, Jie; Hovmöller, Sven; Zou, Xiaodong (2013-11-15). "Three-dimensional rotation electron diffraction: softwareREDfor automated data collection and data processing". Journal of Applied Crystallography. 46 (6): 1863–1873. doi:10.1107/s0021889813027714. ISSN 0021-8898. PMC 3831301. PMID 24282334.
  24. ^ Nannenga, Brent L; Shi, Dan; Hattne, Johan; Reyes, Francis E; Gonen, Tamir (2014-10-10). "Structure of catalase determined by MicroED". eLife. 3: e03600. doi:10.7554/elife.03600. ISSN 2050-084X. PMC 4359365. PMID 25303172.
  25. ^ a b c Rodriguez, J.A.; Ivanova, M.; Sawaya, M.R.; Cascio, D.; Reyes, F.; Shi, D.; Johnson, L.; Guenther, E.; Sangwan, S. (2015-09-09). "MicroED structure of the segment, GVVHGVTTVA, from the A53T familial mutant of Parkinson's disease protein, alpha-synuclein residues 47-56". doi:10.2210/pdb4znn/pdb. {{cite journal}}: Cite journal requires |journal= (help)
  26. ^ a b Liu, S.; Gonen, T. (2018-09-12). "MicroED structure of NaK ion channel reveals a process of Na+ partition into the selectivity filter". doi:10.2210/pdb6cpv/pdb. S2CID 240183721. {{cite journal}}: Cite journal requires |journal= (help)
  27. ^ Gallagher-Jones, Marcus; Glynn, Calina; Boyer, David R.; Martynowycz, Michael W.; Hernandez, Evelyn; Miao, Jennifer; Zee, Chih-Te; Novikova, Irina V.; Goldschmidt, Lukasz (2018-01-15). "Sub-ångström cryo-EM structure of a prion protofibril reveals a polar clasp". Nature Structural & Molecular Biology. 25 (2): 131–134. doi:10.1038/s41594-017-0018-0. ISSN 1545-9993. PMC 6170007. PMID 29335561.
  28. ^ Jones, Christopher; Martynowycz, M; Hattne, Johan; Fulton, Tyler J.; Stoltz, Brian M.; Rodriguez, Jose A.; Nelson, Hosea; Gonen, Tamir (2018). "The CryoEM Method MicroED as a Powerful Tool for Small Molecule Structure Determination" (PDF). ACS Central Science. 4 (11): 1587–1592. doi:10.26434/chemrxiv.7215332.v1. PMC 6276044. PMID 30555912.
  29. ^ Vergara, Sandra; Lukes, Dylan A.; Martynowycz, Michael W.; Santiago, Ulises; Plascencia-Villa, Germán; Weiss, Simon C.; de la Cruz, M. Jason; Black, David M.; Alvarez, Marcos M. (2017-10-31). "MicroED Structure of Au146(p-MBA)57 at Subatomic Resolution Reveals a Twinned FCC Cluster". The Journal of Physical Chemistry Letters. 8 (22): 5523–5530. doi:10.1021/acs.jpclett.7b02621. ISSN 1948-7185. PMC 5769702. PMID 29072840.
  30. ^ Xu, Hongyi; Lebrette, Hugo; Clabbers, Max T. B.; Zhao, Jingjing; Griese, Julia J.; Zou, Xiaodong; Högbom, Martin (7 August 2019). "Solving a new R2lox protein structure by microcrystal electron diffraction". Science Advances. 5 (8): eaax4621. doi:10.1126/sciadv.aax4621. PMC 6685719. PMID 31457106.

Further reading

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