Name: preparation of high-temperature sample grids for cryo-em
Uploaded: 2021-07-26T15:00:00
Description: Watch this Scientific Journal Video about Preparation of High-Temperature Sample Grids for Cryo-EM at JoVE.com

The authors thank Dr. Herv&#233; Remigy of Thermo Fisher Scientific for useful advice. The cryo-EM experiments were performed at the Academia Sinica Cryo-EM Facility (ASCEM). ASCEM is supported by Academia Sinica (Grant No. AS-CFII-108-110) and Taiwan Protein Project (Grant No. AS-KPQ-109-TPP2). The authors also thank Ms. Hui-Ju Huang for the assistance with the sample preparation.

NOTE: This protocol aims to use a modified commercial vitrification apparatus to prepare the cryo-electron microscopy (cryo-EM) samples at specific temperatures, especially higher than 37 &#176;C. The overall experimental setup is shown in Figure 1. The protocol uses 55 &#176;C as an example. For the specific conditions at other temperatures, please refer to Supplementary Table 2 in reference12.
1. Preparation of the vitrification apparatus</...

<ol>
	<li>Yip, K. M., Fischer, N., Paknia, E., Chari, A., Stark, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Atomic-resolution+protein+structure+determination+by+cryo-EM.">Atomic-resolution protein structure determination by cryo-EM.</a> Nature. 587, 157-161 (2020).</li><li>Nakane, T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Single-particle+cryo-EM+at+atomic+resolution.">Single-particle cryo-EM at atomic resolution.</a> Nature. 587, 152-156 (2020).</li><li>Chen, C. Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Use+of+Cryo-EM+to+uncover+structural+bases+of+pH+effect+and+cofactor+bi-specificity+of+ketol-acid+reductoisomerase.">Use of Cryo-EM to uncover structural bases of pH effect and cofactor bi-specificity of ketol-acid reductoisomerase.</a> Journal of the American Chemical Society. 141, 6136-6140 (2019).</li><li>Cabra, V., Sams&#243;, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Do's+and+don'ts+of+cryo-electron+microscopy:+A+primer+on+sample+preparation+and+high+quality+data+collection+for+macromolecular+3D+reconstruction.">Do's and don'ts of cryo-electron microscopy: A primer on sample preparation and high quality data collection for macromolecular 3D reconstruction.</a> Journal of Visualized Experiments. (95), e52311 (2015).</li><li>Klebl, D. P., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Need+for+speed:+Examining+protein+behavior+during+CryoEM+grid+preparation+at+different+timescales.">Need for speed: Examining protein behavior during CryoEM grid preparation at different timescales.</a> Structure. 28 (11), 1238-1248 (2020).</li><li>Passmore, L. A., Russo, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Specimen+preparation+for+high+resolution+cryo-EM.">Specimen preparation for high resolution cryo-EM.</a> J. Methods in Enzymology. 579, 51-86 (2016).</li><li>Laughlin, T. G., Bayne, A. N., Trempe, J. -. F., Savage, D. F., Davies, K. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Structure+of+the+complex+I-like+molecule+NDH+of+oxygenic+photosynthesis.">Structure of the complex I-like molecule NDH of oxygenic photosynthesis.</a> Nature. 566, 411-414 (2019).</li><li>Gao, Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Structures+and+operating+principles+of+the+replisome.">Structures and operating principles of the replisome.</a> Science. 363, (2019).</li><li>Zhao, Y., Chen, S., Swensen, A. C., Qian, W. -. J., Gouaux, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Architecture+and+subunit+arrangement+of+native+AMPA+receptors+elucidated+by+cryo-EM.">Architecture and subunit arrangement of native AMPA receptors elucidated by cryo-EM.</a> Science. 364, 355-362 (2019).</li><li>Chen, B., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Structural+dynamics+of+ribosome+subunit+association+studied+by+mixing-spraying+time-resolved+cryogenic+electron+microscopy.">Structural dynamics of ribosome subunit association studied by mixing-spraying time-resolved cryogenic electron microscopy.</a> Structure. 23, 1097-1105 (2015).</li><li>Singh, A. K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Structural+basis+of+temperature+sensation+by+the+TRP+channel+TRPV3.">Structural basis of temperature sensation by the TRP channel TRPV3.</a> Nature Structure and Molecular Biology. 26, 994-998 (2019).</li><li>Chen, C. Y., Chang, Y. C., Lin, B. L., Huang, C. H., Tsai, M. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Temperature-resolved+cryo-EM+uncovers+structural+bases+of+temperature-dependent+enzyme+functions.">Temperature-resolved cryo-EM uncovers structural bases of temperature-dependent enzyme functions.</a> Journal of the American Chemical Society. 141, 19983-19987 (2019).</li></ol>

In step 1 of the protocol, make sure that the centrifuge tube has been installed well and does not fall when the experiment is in progress. Due to the accumulation of a large number of water droplets in the chamber, which could change the adsorption capacity of the filter paper, it is recommended that the overall time of the experiment should not exceed 30 min after the vitrification apparatus chamber reached the equilibration temperature. If the operation time exceeds 30 min, the operator needs to replace the filter pap...

The cryo-EM technology for solving the structures of protein complexes has continued to improve, particularly in the direction of obtaining high-resolution structures1,2. In the meantime, the landscape of its application has also been expanded by varying the sample conditions such as pH or ligands prior to the vitrification process3, which involves the preparation of sample grids followed by plunge freezing4,5. Another important condition is the temperature. Although cryo-EM experiments, like X-ray crystallography, are performed at low temperatures, the structure solved by cryo-EM reflects the structure at the solution state prior to vitrification. Until recently, the majority of single particle analysis (SPA) cryo-EM studies use samples that are kept on ice (i.e., at 4 &#176;C) prior to vitrification6, though a number of studies use samples at around room temperature7,8,9,10 or as high as 42 &#176;C11. In a recent report, we performed temperature-dependent studies of the enzyme ketol-acid reductoisomerase (KARI) from the thermophilic archaeon Sulfolobus solfataricus (Sso) at six different temperatures from 4 &#176;C to 70&#176;C12. Our studies suggest that it is important to prepare sample grids at functionally relevant temperatures and that cryo-EM is the only structural method that is practically feasible for solving the structure of the same protein complex at multiple temperatures.
The major difficulty for vitrification at high temperatures is to minimize vapor condensation and achieve thin ice. Here we report the detailed protocol used for preparing sample grids at high temperatures in our previous study of the Sso-KARI12. We assume that the readers or viewers are already experienced in the overall sample preparation and data processing procedures for cryo-EM experiments and emphasize the aspects relevant to high temperature.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Falcon tube</td>
			<td>Falcon</td>
			<td>352070</td>
			<td>size: 50 mL</td>
		</tr>
		<tr>
			<td>Filter paper</td>
			<td>Ted Pella</td>
			<td>47000-100</td>
			<td>&#216;55/20mm, Grade 595</td>
		</tr>
		<tr>
			<td>HI1210</td>
			<td>Leica</td>
			<td></td>
			<td>water bath</td>
		</tr>
		<tr>
			<td>K100X</td>
			<td>Electron Microscopy Sciences</td>
			<td></td>
			<td>glow discharge</td>
		</tr>
		<tr>
			<td>Quantifoil, 1.2/1.3 200Mesh Cu grid</td>
			<td>Ted Pella</td>
			<td>658-200-CU-100</td>
			<td></td>
		</tr>
		<tr>
			<td>Titan Krios G3</td>
			<td>Thermo Fisher Scientific</td>
			<td>1063996</td>
			<td>low dose imaging</td>
		</tr>
		<tr>
			<td>Vitrobot Mark IV</td>
			<td>Thermo Fisher Scientific</td>
			<td>1086439</td>
			<td></td>
		</tr>
		<tr>
			<td>Vitrobot Tweezer</td>
			<td>Ted Pella</td>
			<td>47000-500</td>
			<td></td>
		</tr>
	</tbody>
</table>

preparation of high-temperature sample grids for cryo-em

The sample grids for cryo-electron microscopy (cryo-EM) experiments are usually prepared at a temperature optimal for the storage of biological samples, mostly at 4 &#176;C and occasionally at room temperature. Recently, we discovered that the protein structure solved at low temperature may not be functionally relevant, particularly for proteins from thermophilic archaea. A procedure was developed to prepare protein samples at higher temperatures (up to 70 &#176;C) for cryo-EM analysis. We showed that the structures from samples prepared at higher temperatures are functionally relevant and temperature dependent. Here we describe a detailed protocol for preparing sample grids at high temperature, using 55 &#176;C as an example. The experiment made use of a vitrification apparatus modified using an additional centrifuge tube, and samples were incubated at 55 &#176;C. The detailed procedures were fine-tuned to minimize vapor condensation and obtain a thin layer of ice on the grid. Examples of successful and unsuccessful experiments are provided.

The low magnification overview is shown in Figure 5A,B. Panel A is an example of a successful grid. There is an ice gradient from top left (thicker) to bottom right (thinner or empty). Such a grid makes it easier to find an appropriate thickness of the ice layer in the middle area suitable for data collection, such as the blue and green boxes. The grid B is too dry. The squares in the grid have bright contrast, which means that the ice layer is too thin or there is no ice la...

Watch this Scientific Journal Video about Preparation of High-Temperature Sample Grids for Cryo-EM at JoVE.com

Preparation of High-Temperature Sample Grids for Cryo-EM

This paper provides a detailed protocol for preparing sample grids at temperatures as high as 70 &#176;C, prior to plunge freezing for cryo-EM experiments.

The sample grids for cryo-electron microscopy (cryo-EM) experiments are usually prepared at a temperature optimal for the storage of biological samples, ...

The functions of proteins are temperature dependent and are optimal at the temperature. This protocol provides a way to solve protein structures at higher temperatures. This approach can provide functionally relevant structures and enhance the understanding of the temperature dependence of protein structures.Demonstrating the procedure will be Yuan-Chih Chang, Manager of the Academia Sinica Cryo EM facility. Begin by making a one centimeter hole in a 50 millimeter centrifuge tube on its closed end. Place the tube in the vitrification apparatus chamber at the ultrasonic water outlet.Set up the vitrification apparatus temperature to the specified temperature, and allow the vitrification apparatus chamber to reach 55 degrees Celsius and 100%relative humidity. Let it stand for at least half an hour to stabilize the conditions before starting the experiment. Place the water bath on a hot plate and set the hot plate to the desired temperature.Check with a thermometer to ensure that the water reaches 55 degrees Celsius. Incubate the sample in the water bath, and preheat the pipette tip on the edge of the hot plate for two minutes or longer before the blotting experiment. Glow discharge a holey carbon supported grid at 25 milliampere for 30 seconds.Place the vitrification filter paper into the vitrification apparatus chamber no sooner than five minutes before the blotting experiment. Incubate the tweezers with the grid in the vitrification apparatus for two minutes or longer. Build the ethane container with ethane according to standard procedures, ensuring that the ethane does not overflow.Use a pipette to apply seven to nine microliters of the sample to the grid. Then wait for one to two seconds, blot for one to one and a half seconds, and quickly plunge the sample into liquid ethane. Transfer the grid from liquid ethane to the cryo box stored in liquid nitrogen.Clip the grids and unload them to acquire electron microscope or Cryo EM instrument. Use the display screen of the Cryo EM instrument and the low dose function of the software, to screen the ice condition on the grid and the distribution of the sample on the grid. If the quality of the resulting grid is not good, repeat the process of grid preparation with varied conditions such as waiting time, blotting time, et cetera.If the quality of the resulting grid is good, repeat the same steps to make grids at a different temperature. Transfer the good quality grids to a high resolution Cryo EM instrument. Perform data collection and data analyses according to established procedures.In the case of the successful grid, an ice gradient formed with thicker ice at the top left of the grid and thinner ice at the bottom right. Blue and green boxes suitable for data collection were observed in the successful grid. A bright contrast was observed in the other grid.Indicating a thin layer, of ice or an absence of ice. Only two squares were found to be suitable for data collection in the second grid. One of the grids consisted of ice mostly in the crystalin form, which was unsuitable for data collection.On the other hand, the other grid showed that the ice layer was mostly in an amorphous state suitable for data collection. The preparation of the as a container and others need to be complete according to a time point. Time control and and finishing the experiment quickly and accurately are most important.Depending on the results obtained using this protocol, the researcher may have to be more careful in setting up the simple conditions.

Research

JoVE Journal

Biochemistry

Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions

Noncoding RNAs play important roles in several nuclear processes, including regulating gene expression, chromatin structure, and DNA repair. In most ...

An All-in-one Sample Holder for Macromolecular X-ray Crystallography with Minimal Background Scattering

Macromolecular X-ray crystallography (MX) is the most prominent method to obtain high-resolution three-dimensional knowledge of biological macromolecules. ...

Sample Preparation for Probe Electrospray Ionization Mass Spectrometry

Mass spectrometry (MS) is a powerful tool in analytical chemistry because it provides very accurate information about molecules, such as mass-to-charge ...

TMT Sample Preparation for Proteomics Facility Submission and Subsequent Data Analysis

Proteomic technologies are powerful methodologies that can aid our understanding of mechanisms of action in biological systems by providing a global view ...

Cryo-EM and Single-Particle Analysis with Scipion

Cryo-electron microscopy has become one of the most important tools in biological research to reveal the structural information of macromolecules at ...

A Robust Single-Particle Cryo-Electron Microscopy (cryo-EM) Processing Workflow with cryoSPARC, RELION, and Scipion

A Robust Single-Particle Cryo-Electron Microscopy cryo-EM Processing Workflow with cryoSPARC, RELION, and Scipion

Recent advances in both instrumentation and image processing software have made single-particle cryo-electron microscopy (cryo-EM) the preferred method ...

Routine Collection of High-Resolution cryo-EM Datasets Using 200 KV Transmission Electron Microscope

Cryo-electron microscopy (cryo-EM) has been established as a routine method for protein structure determination during the past decade, taking an ...

The Peel-Blot Technique: A Cryo-EM Sample Preparation Method to Separate Single Layers From Multi-Layered or Concentrated Biological Samples

The peel-blot cryo-EM grid preparation technique is a significantly modified back-injection method with the objective of achieving a reduction in layers ...

Single-Particle Cryo-EM Data Collection with Stage Tilt using Leginon

Single-particle analysis (SPA) by cryo-electron microscopy (cryo-EM) is now a mainstream technique for high-resolution structural biology. Structure ...

Coating CryoEM Grids with Monolayer Graphene to Improve Cryo-Sample Preparation

Application of Monolayer Graphene to Cryo-Electron Microscopy Grids for High-resolution Structure Determination

Author Spotlight: Enhancing CryoEM Sample Preparation Using Graphene Monolayer on Microscopy Grids 

In cryogenic electron microscopy (cryoEM), purified macromolecules are applied to a grid bearing a holey carbon foil; the molecules are then blotted to ...