2020

Towards an Optimal Sample Delivery Method for Serial Crystallography at XFEL

Preventing Bio-Bloopers and XFEL Follies: Best Practices from your Friendly Instrument Staff

Christopher Kupitz and Raymond G. Sierra. Crystals 2020, 10(4), 251; https://doi.org/10.3390/cryst10040251
Received: 5 March 2020 / Revised: 24 March 2020 / Accepted: 24 March 2020 / Published: 27 March 2020

Membrane Protein Preparation for Serial Crystallography Using High-Viscosity Injectors: Rhodopsin as an Example

Part of the Methods in Molecular Biology book series (MIMB, volume 2127)

 

2019

Strategies for sample delivery for femtosecond crystallography

I. Martiel, H. M. Müller-Werkmeister and A. E. Cohen. Acta Cryst. (2019). D75, 160-177 https://doi.org/10.1107/S2059798318017953

Sample Delivery Media for Serial Crystallography

Ki Hyun Nam. Int. J. Mol. Sci. 2019, 20(5), 1094;  https://doi.org/10.3390/ijms20051094. Received: 15 February 2019 / Revised: 27 February 2019 / Accepted: 27 February 2019 / Published: 4 March 2019

Successful sample preparation for serial crystallography experiments

John H. Beale, Rachel Bolton, Stephen A. Marshall, Emma V. Beale, Stephen B. Carr, Ali Ebrahim, Tadeo Moreno-Chicano, Michael A. Hough, Jonathan A. R. Worrall, Ivo Tews and Robin L. Owen. 

Sample delivery for serial crystallography at free-electron lasers and synchrotrons

M. L. Grünbein and G. Nass Kovacs. Acta Cryst. (2019). D75, 178-191
https://doi.org/10.1107/S205979831801567X

Visualization of protein crystals by high-energy phase-contrast X-ray imaging

M. Polikarpov, G. Bourenkov, I. Snigireva, A. Snigirev, S. Zimmermann, K. Csanko, S. Brockhauser and T. R. Schneider. Acta Cryst. (2019). D75, 947-958
https://doi.org/10.1107/S2059798319011379

Membrane protein megahertz crystallography at the European XFEL

Gisriel, C., Coe, J., Letrun, R. et al. Membrane protein megahertz crystallography at the European XFEL. Nat Commun 10, 5021 (2019) doi:10.1038/s41467-019-12955-3

Pembrolizumab microgravity crystallization experimentation

Reichert, P., Prosise, W., Fischmann, T.O. et al. Pembrolizumab microgravity crystallization experimentation. npj Microgravity 5, 28 (2019) doi:10.1038/s41526-019-0090-3

 

2018

Supersaturation-controlled microcrystallization and visualization analysis for serial femtosecond crystallography

Lee, D.B., Kim, J., Seok, J.H. et al. Supersaturation-controlled microcrystallization and visualization analysis for serial femtosecond crystallography. Sci Rep 8, 2541 (2018) doi:10.1038/s41598-018-20899-9

 

2017

Serial millisecond crystallography of membrane and soluble protein microcrystals using synchrotron radiation

Martin-Garcia, J. M., Conrad, C. E., Nelson, G., Stander, N., Zatsepin, N. A., Zook, J., Zhu, L., Geiger, J., Chun, E., Kissick, D., Hilgart, M. C., Ogata, C., Ishchenko, A., Nagaratnam, N., Roy-Chowdhury, S., Coe, J., Subramanian, G., Schaffer, A., James, D., Ketwala, G., Venugopalan, N., Xu, S., Corcoran, S., Ferguson, D., Weierstall, U., Spence, J. C. H., Cherezov, V., Fromme, P., Fischetti, R. F. & Liu, W. (2017). IUCrJ 4, 439-454.

XFELs for structure and dynamics in biology

Spence, J. C. H. (2017). IUCrJ 4, 322-339.

Locating and Visualizing Crystals for X-Ray Diffraction Experiments

Becker M., Kissick D.J., Ogata C.M. (2017) Locating and Visualizing Crystals for X-Ray Diffraction Experiments. In: Wlodawer A., Dauter Z., Jaskolski M. (eds) Protein Crystallography. Methods in Molecular Biology, vol 1607. Humana Press, New York, NY

Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography

Nature 541, 242–246 (12 January 2017)
doi:10.1038/nature20599

 

2016

Preparation and Delivery of Protein Microcrystals in Lipidic Cubic Phase for Serial Femtosecond Crystallography

Ishchenko A, Cherezov V, Liu W. Preparation and Delivery of Protein Microcrystals in Lipidic Cubic Phase for Serial Femtosecond Crystallography. Journal of Visualized Experiments : JoVE. 2016;(115):54463. doi:10.3791/54463.

Nonlinear Optical Characterization of Membrane Protein Microcrystals and Nanocrystals

Newman J.A., Simpson G.J. (2016) Nonlinear Optical Characterization of Membrane Protein Microcrystals and Nanocrystals. In: Moraes I. (eds) The Next Generation in Membrane Protein Structure Determination. Advances in Experimental Medicine and Biology, vol 922. Springer, Cham

Second harmonic generation correlation spectroscopy for characterizing translationally diffusing protein nanocrystals

Dow XY, Dettmar CM, DeWalt EL, et al. Second harmonic generation correlation spectroscopy for characterizing translationally diffusing protein nanocrystals. Acta Crystallographica Section D, Structural Biology. 2016;72(Pt 7):849-859. doi:10.1107/S205979831600841X.

Serial femtosecond crystallography datasets from G protein-coupled receptors

Scientific Data 3, Article number: 160057 (2016)
doi:10.1038/sdata.2016.57

Guiding synchrotron X-ray diffraction by multimodal video-rate protein crystal imaging

Newman JA, Zhang S, Sullivan SZ, et al. Guiding synchrotron X-ray diffraction by multimodal video-rate protein crystal imaging. Journal of Synchrotron Radiation. 2016;23(Pt 4):959-965. doi:10.1107/S1600577516005919.

Transmission electron microscopy for the evaluation and optimization of crystal growth

Stevenson HP, Lin G, Barnes CO, et al. Transmission electron microscopy for the evaluation and optimization of crystal growth. Acta Crystallographica Section D, Structural Biology. 2016;72(Pt 5):603-615. doi:10.1107/S2059798316001546.

A pipeline for structure determination of in vivo-grown crystals using in cellulo diffraction

Boudes M, Garriga D, Fryga A, Caradoc-Davies T, Coulibaly F. A pipeline for structure determination of in vivo-grown crystals using in cellulo diffraction. Acta Crystallographica Section D, Structural Biology. 2016;72(Pt 4):576-585. doi:10.1107/S2059798316002369.

 

2015

Microfluidic sorting of protein nanocrystals by size for X-ray free-electron laser diffraction

Structural Dynamics 2, 041719 (2015); https://doi.org/10.1063/1.4928688

Serial femtosecond X-ray diffraction of enveloped virus microcrystals

Structural Dynamics 2, 041720 (2015); https://doi.org/10.1063/1.4929410

Batch crystallization of rhodopsin for structural dynamics using an X-ray free-electron laser

Wu W, Nogly P, Rheinberger J, et al. Batch crystallization of rhodopsin for structural dynamics using an X-ray free-electron laser. Acta Crystallographica Section F, Structural Biology Communications. 2015;71(Pt 7):856-860. doi:10.1107/S2053230X15009966.

Serial femtosecond crystallography: the first five years

Schlichting, I. (2015). IUCrJ 2, 246-255.

The detection and subsequent volume optimization of biological nanocrystals

Structural Dynamics 2, 041710 (2015); https://doi.org/10.1063/1.4921199

A comprehensive review of the lipid cubic phase or in meso method for crystallizing membrane and soluble proteins and complexes

Caffrey M. A comprehensive review of the lipid cubic phase or in meso method for crystallizing membrane and soluble proteins and complexes. Acta Crystallographica Section F, Structural Biology Communications. 2015;71(Pt 1):3-18. doi:10.1107/S2053230X14026843.

Reliably distinguishing protein nanocrystals from amorphous precipitate by means of depolarized dynamic light scattering

Schubert, R., Meyer, A., Dierks, K., Kapis, S., Reimer, R., Einspahr, H., Perbandt, M. & Betzel, C. (2015). J. Appl. Cryst. 48, 1476-1484.

 

2014

Crystallization of the large membrane protein complex photosystem I in a microfluidic channel

Abdallah BG, Kupitz C, Fromme P, Ros A. Crystallization of the Large Membrane Protein Complex Photosystem I in a Microfluidic Channel. ACS nano. 2013;7(12):10534-10543. doi:10.1021/nn402515q.

Preparation of microcrystals in lipidic cubic phase for serial femtosecond crystallography

Liu W, Ishchenko A, Cherezov V. Preparation of Microcrystals in Lipidic Cubic Phase for Serial Femtosecond Crystallography. Nature protocols. 2014;9(9):2123-2134. doi:10.1038/nprot.2014.141.

Expression, purification and crystallization of CTB-MPR, a candidate mucosal vaccine component against HIV-1

Lee, H.-H., Cherni, I., Yu, H., Fromme, R., Doran, J. D., Grotjohann, I., Mittman, M., Basu, S., Deb, A., Dorner, K., Aquila, A., Barty, A., Boutet, S., Chapman, H. N., Doak, R. B., Hunter, M. S., James, D., Kirian, R. A., Kupitz, C., Lawrence, R. M., Liu, H., Nass, K., Schlichting, I., Schmidt, K. E., Seibert, M. M., Shoeman, R. L., Spence, J. C. H., Stellato, F., Weierstall, U., Williams, G. J., Yoon, C., Wang, D., Zatsepin, N. A., Hogue, B. G., Matoba, N., Fromme, P. & Mor, T. S. (2014). IUCrJ 1, 305-317.

Microseed matrix screening for optimization in protein crystallization: what have we learned?

D’Arcy A, Bergfors T, Cowan-Jacob SW, Marsh M. Microseed matrix screening for optimization in protein crystallization: what have we learned? Acta Crystallographica Section F, Structural Biology Communications. 2014;70(Pt 9):1117-1126. doi:10.1107/S2053230X14015507.

Identifying, studying and making good use of macromolecular crystals

Calero G, Cohen AE, Luft JR, Newman J, Snell EH. Identifying, studying and making good use of macromolecular crystals. Acta Crystallographica Section F, Structural Biology Communications. 2014;70(Pt 8):993-1008. doi:10.1107/S2053230X14016574.

Femtosecond crystallography of membrane proteins in the lipidic cubic phase

Liu W, Wacker D, Wang C, Abola E, Cherezov V. Femtosecond crystallography of membrane proteins in the lipidic cubic phase. Philosophical Transactions of the Royal Society B: Biological Sciences. 2014;369(1647):20130314. doi:10.1098/rstb.2013.0314.

Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser

Nature 513, 261–265 (11 September 2014)
doi:10.1038/nature13453

 

2013

Characterization of salt interferences in second-harmonic generation detection of protein crystals

Closser RG, Gualtieri EJ, Newman JA, Simpson GJ. Characterization of salt interferences in second-harmonic generation detection of protein crystals. Journal of Applied Crystallography. 2013;46(Pt 6):1903-1906. doi:10.1107/S0021889813027581.

Integrated nonlinear optical imaging microscope for on-axis crystal detection and centering at a synchrotron beamline

Madden JT, Toth SJ, Dettmar CM, et al. Integrated nonlinear optical imaging microscope for on-axis crystal detection and centering at a synchrotron beamline. Journal of Synchrotron Radiation. 2013;20(Pt 4):531-540. doi:10.1107/S0909049513007942.

Visualization of membrane protein crystals in lipid cubic phase using X-ray imaging

Warren AJ, Armour W, Axford D, et al. Visualization of membrane protein crystals in lipid cubic phase using X-ray imaging. Acta Crystallographica Section D: Biological Crystallography. 2013;69(Pt 7):1252-1259. doi:10.1107/S0907444913011359.

Imaging of protein crystals with two-photon microscopy

Zhu Q, Toth SJ, Simpson GJ, Hsu H-Y, Taylor LS, Harris MT. Crystallization and Dissolution Behavior of Naproxen/Polyethylene Glycol Solid Dispersions. The journal of physical chemistry B. 2013;117(5):1494-1500. doi:10.1021/jp3106716.

Crystallization and Dissolution Behavior of Naproxen/Polyethylene Glycol Solid Dispersions

Zhu Q, Toth SJ, Simpson GJ, Hsu H-Y, Taylor LS, Harris MT. Crystallization and Dissolution Behavior of Naproxen/Polyethylene Glycol Solid Dispersions. The journal of physical chemistry B. 2013;117(5):1494-1500. doi:10.1021/jp3106716.

 

2012

Polarization-resolved second-harmonic generation microscopy as a method to visualize protein-crystal domains

DeWalt EL, Begue VJ, Ronau JA, Sullivan SZ, Das C, Simpson GJ. Polarization-resolved second-harmonic generation microscopy as a method to visualize protein-crystal domains. Acta Crystallographica Section D: Biological Crystallography. 2013;69(Pt 1):74-81. doi:10.1107/S0907444912042503.

Modeling the SHG activities of diverse protein crystals

Haupert LM, DeWalt EL, Simpson GJ. Modeling the SHG activities of diverse protein crystals. Acta Crystallographica Section D: Biological Crystallography. 2012;68(Pt 11):1513-1521. doi:10.1107/S0907444912037638.

Femtosecond nanocrystallography using X-Ray Lasers for membrane protein structure determination

Fromme P, Spence JC. Femtosecond nanocrystallography using X-Ray Lasers for membrane protein structure determination. Current opinion in structural biology. 2011;21(4):509-516. doi:10.1016/j.sbi.2011.06.001.

Selective imaging of active pharmaceutical ingredients in powdered blends with common excipients utilizing two-photon excited ultraviolet-fluorescence and ultraviolet-second order nonlinear optical imaging of chiral crystals

Toth SJ, Madden JT, Taylor LS, Marsac P, Simpson GJ. Selective Imaging of APIs in Powdered Blends with Common Excipients Utilizing TPE-UVF and UV-SONICC. Analytical chemistry. 2012;84(14):5869-5875. doi:10.1021/ac300917t.

 

2011

Screening of Protein Crystallization Trials by Second Order Nonlinear Optical Imaging of Chiral Crystals (SONICC)

Haupert L, Simpson G. Screening of Protein Crystallization Trials by Second Order Nonlinear Optical Imaging of Chiral Crystals (SONICC). Methods (San Diego, Calif). 2011;55(4):379-386. doi:10.1016/j.ymeth.2011.11.003.

Two-photon excited UV fluorescence for protein crystal detection

Madden JT, DeWalt EL, Simpson GJ. Two-photon excited UV fluorescence for protein crystal detection. Acta Crystallographica Section D: Biological Crystallography. 2011;67(Pt 10):839-846. doi:10.1107/S0907444911028253.

Lipidic cubic phase technologies for membrane protein structural studies

Vadim Cherezov, Lipidic cubic phase technologies for membrane protein structural studies, In Current Opinion in Structural Biology, Volume 21, Issue 4, 2011, Pages 559-566, ISSN 0959-440X, https://doi.org/10.1016/j.sbi.2011.06.007.

Detection of Membrane Protein Two-Dimensional Crystals in Living Cells

Gualtieri EJ, Guo F, Kissick DJ, et al. Detection of Membrane Protein Two-Dimensional Crystals in Living Cells. Biophysical Journal. 2011;100(1):207-214. doi:10.1016/j.bpj.2010.10.051.

 

2010

Nonlinear optical imaging of integral membrane protein crystals in lipidic mesophases.

Kissick DJ, Gualtieri EJ, Simpson GJ, Cherezov V. Nonlinear Optical Imaging of Integral Membrane Protein Crystals in Lipidic Mesophases. Analytical chemistry. 2010;82(2):491-497. doi:10.1021/ac902139w.

 

2008

Selective Detection of Protein Crystals by Second Harmonic Microscopy

J. Am. Chem. Soc., 2008, 130 (43), pp 14076–14077
DOI: 10.1021/ja805983b

Background Questions

Are all protein crystals detectable?

Almost all molecules that have a chiral center form a chiral crystal. Therefore, most proteins will form chiral crystals that are detectable via SONICC® (Second Order Non-linear Imaging of Chiral Crystals). Over 99% of the proteins in the Protein Data Bank have a space group that is detectable with SONICC. Crystals with extremely high symmetry classes will generate less SHG signal. Although theoretically all protein crystals should be detected with SHG, that is not always experimentally the case. The higher the space group, the less SHG is generated. Also, the hyperpolarizability (ie the SHG efficiency) of the protein significantly impacts the amount of light generated. Some proteins interact more favorably with light and therefore produce higher SHG signal, where other proteins hold their electrons closely, have a low hyperpolarizability and not give a strong, detectable SHG response.

 

What is SHG?

SHG stands for Second Harmonic Generation and is a nonlinear optical process. In intense electric fields (i.e. in the presence of a femtosecond laser) the distance between the electrons and the nucleus are distorted (anharmonicity) resulting in non-linear optical effects such as SHG where the frequency of the outgoing light is twice that of the incident (i.e. 1064 nm incident results in 532 nm exiting).

 

What does “chiral” mean?

A chiral molecule, or in this case a chiral crystal, is a crystal that lacks an internal plane of symmetry, and thus its mirror image is nonsuperimposable. Achiral crystals are symmetric and therefore produce SHG in equal and opposite directions that sum to a net zero signal.

 

Will salts produce signal?

They can if they are chiral, but the majority of salts are achiral and therefore do not generate SHG signal.

 

How is SONICC different than fluorescent imaging?

Fluorescent imaging takes advantage of either the endogenous fluorescence of the protein or the use of fluorescent tags. Although fluorescence is bright and easily detectable, it is generated from solubilized and aggregated proteins as well as crystallized proteins. The background from the solubilized protein decreases the signal to noise ratio significantly, resulting in false positives. SONICC, on the other hand, is only sensitive to crystallized proteins.

 

How does UV-TPEF compare to traditional UV imaging?

Both imaging methods probe the amino acids present in proteins that are excited by UV light (~280 nm). However, with UV-TPEF, the incident wavelength is 532 nm instead of UV and has less energy. UV imaging can cause the breakage of disulfide bonds but by using green light instead to excite, damage does not occur.

 

With which platforms are SONICC compatible?

SONICC is compatible with all optically-accessible plates and seals.

 

Will the laser damage my crystals?

Experiments show no detectable damage to protein crystals. In one experiment, a protein crystal was imaged on one half with excessive laser input. X-ray diffraction was obtained from both the exposed and un-exposed halves of the crystal. Both sides diffracted to within expected resolution (~2 Ã) and within statistical variation (i.e. there was no statistical difference between the diffraction of either side). SONICC has also imaged live cells with no observed impact (they remained adhered to a polylysine-coated slide).

 

Can I use SONICC if my sample is fluorescent?

Yes. As long as fluorescence is Stokes-shifted by 10 nm, the fluorescence will not be detected nor interfere with the SHG signal.

 

Specification Questions

*Please note that each crystal will generate different intensities of SHG signal depending on size, orientation, space group and quality, as well as the acquisition time and incident intensity.

 

How small of a crystal can SONICC detect?

Theoretically, the lower limit of detection can be estimated by the forward-to-backward ratio of the SHG signal. Based on the coherence length of the generated SHG signal and the refractive index of the material, this lower limit ranges from 90 nm – 300 nm in thickness. In practice, 1 μm^3 crystals can be routinely detected. 2D crystals have also been routinely imaged with a signal to noise ratio >30.

 

What is the spatial resolution?

Crystals can be resolved to 2 μm (detection limit is much lower).

 

What is the laser´s Z-resolution and how deeply can it penetrate?

The laser focuses to a width of ∼50 μm and can image drops >3 mm tall with multiple Z-steps, called “slices”.

 

How fast is SONICC?

The current electronic package allows 512 x 512 image acquisition for one Z-slice in 500 ms. This corresponds to eight traces of the fast-scanning mirror per line. A one-drop 96-well plate can be imaged with visible light in 3 minutes and with SHG in 15 minutes with eight Z-slices per drop.