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Nicolas WJ, Gillman C, Weaver SJ, Clabbers MTB, Shiriaeva A, Her AS, Martynowycz MW, Gonen T. Comprehensive microcrystal electron diffraction sample preparation for cryo-EM. Nat Protoc 2025; 20:1275-1309. [PMID: 39706914 DOI: 10.1038/s41596-024-01088-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 10/09/2024] [Indexed: 12/23/2024]
Abstract
Microcrystal electron diffraction (MicroED) has advanced structural methods across a range of sample types, from small molecules to proteins. This cryogenic electron microscopy (cryo-EM) technique involves the continuous rotation of small 3D crystals in the electron beam, while a high-speed camera captures diffraction data in the form of a movie. The crystal structure is subsequently determined by using established X-ray crystallographic software. MicroED is a technique still under development, and hands-on expertise in sample preparation, data acquisition and processing is not always readily accessible. This comprehensive guide on MicroED sample preparation addresses commonly used methods for various sample categories, including room temperature solid-state small molecules and soluble and membrane protein crystals. Beyond detailing the steps of sample preparation for new users, and because every crystal requires unique growth and sample-preparation conditions, this resource provides instructions and optimization strategies for MicroED sample preparation. The protocol is suitable for users with expertise in biochemistry, crystallography, general cryo-EM and crystallography data processing. MicroED experiments, from sample vitrification to final structure, can take anywhere from one workday to multiple weeks, especially when cryogenic focused ion beam milling is involved.
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Affiliation(s)
- William J Nicolas
- Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA, USA
| | - Cody Gillman
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, USA
- Molecular Biology Institute, University of California, Los Angeles, CA, USA
| | - Sara J Weaver
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Max T B Clabbers
- Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Anna Shiriaeva
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Ampon Sae Her
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Michael W Martynowycz
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Tamir Gonen
- Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA, USA.
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, USA.
- Molecular Biology Institute, University of California, Los Angeles, CA, USA.
- Department of Physiology, University of California Los Angeles, Los Angeles, CA, USA.
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Dmitrieva DA, Kotova TV, Safronova NA, Sadova AA, Dashevskii DE, Mishin AV. Protein Design Strategies for the Structural–Functional Studies of G Protein-Coupled Receptors. BIOCHEMISTRY (MOSCOW) 2023; 88:S192-S226. [PMID: 37069121 DOI: 10.1134/s0006297923140110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
G protein-coupled receptors (GPCRs) are an important family of membrane proteins responsible for many physiological functions in human body. High resolution GPCR structures are required to understand their molecular mechanisms and perform rational drug design, as GPCRs play a crucial role in a variety of diseases. That is difficult to obtain for the wild-type proteins because of their low stability. In this review, we discuss how this problem can be solved by using protein design strategies developed to obtain homogeneous stabilized GPCR samples for crystallization and cryoelectron microscopy.
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Affiliation(s)
- Daria A Dmitrieva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Tatiana V Kotova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Nadezda A Safronova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Alexandra A Sadova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Dmitrii E Dashevskii
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Alexey V Mishin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.
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