Putting on molecular weight: Enabling cryo-EM structure determination of sub-100-kDa proteins

Current Research in Structural Biology - Tập 4 - Trang 332-337 - 2022
Koen Wentinck1, Christos Gogou1, Dimphna H. Meijer1
1Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, van der Maasweg 9, 2629HZ, Delft, the Netherlands

Tài liệu tham khảo

Aissaoui, 2021, Modular imaging scaffold for single-particle electron microscopy, ACS Nano, 15, 4186, 10.1021/acsnano.0c05113 Baek, 2021, Accurate prediction of protein structures and interactions using a three-track neural network, Science, 373, 871, 10.1126/science.abj8754 Bloch, 2021, Development of a universal nanobody-binding Fab module for fiducial-assisted cryo-EM studies of membrane proteins, Proc. Natl. Acad. Sci. U. S. A, 118, 10.1073/pnas.2115435118 Brocchieri, 2005, Protein length in eukaryotic and prokaryotic proteomes, Nucleic Acids Res., 33, 3390, 10.1093/nar/gki615 Chen, 2022, 1 Chiu, 2021, Direct visualization of a 26 kDa protein by cryo-electron microscopy aided by a small scaffold protein, Biochemistry, 60, 1075, 10.1021/acs.biochem.0c00961 Coleman, 2020, Chemical and structural investigation of the paroxetine-human serotonin transporter complex, Elife, 9, 1, 10.7554/eLife.56427 Collu, 2021, 1 Coupland, 2021, Structure, mechanism, and inhibition of Hedgehog acyltransferase, Mol. Cell, 81, 5025, 10.1016/j.molcel.2021.11.018 Deng, 2021, Cryo-EM structure of a proton-activated chloride channel TMEM206, Sci. Adv., 7, 1, 10.1126/sciadv.abe5983 Duan, 2020, Cryo-EM structure of an activated VIP1 receptor-G protein complex revealed by a NanoBiT tethering strategy, Nat. Commun., 11, 1, 10.1038/s41467-020-17933-8 García-Nafría, 2020, Cryo-electron microscopy: moving beyond X-ray crystal structures for drug receptors and drug development, Annu. Rev. Pharmacol. Toxicol., 60, 51, 10.1146/annurev-pharmtox-010919-023545 Goddard, 2018, UCSF ChimeraX: meeting modern challenges in visualization and analysis, Protein Sci., 27, 14, 10.1002/pro.3235 Goutam, 2022, Structural basis of sodium-dependent bile salt uptake into the liver, Nature, 606, 1015, 10.1038/s41586-022-04723-z Helma, 2015, Nanobodies and recombinant binders in cell biology, JCB (J. Cell Biol.), 209, 633, 10.1083/jcb.201409074 Himes, 2021, Cryo-TEM simulations of amorphous radiation-sensitive samples using multislice wave propagation, IUCrJ, 8, 943, 10.1107/S2052252521008538 Jumper, 2021, Highly accurate protein structure prediction with AlphaFold, Nature, 596, 583, 10.1038/s41586-021-03819-2 Lander, 2021, Conquer by cryo-EM without physically dividing, Biochem. Soc. Trans., 49, 2287, 10.1042/BST20210360 Liu, 2018, Near-atomic cryo-EM imaging of a small protein displayed on a designed scaffolding system, Proc. Natl. Acad. Sci. U. S. A, 115, 3362, 10.1073/pnas.1718825115 Liu, 2019, A 3.8 Å resolution cryo-EM structure of a small protein bound to an imaging scaffold, Nat. Commun., 10, 1 McIlwain, 2021, N-Terminal transmembrane-helix epitope tag for X-ray crystallography and electron microscopy of small membrane proteins, J. Mol. Biol., 433, 10.1016/j.jmb.2021.166909 Mukherjee, 2020, Synthetic antibodies against BRIL as universal fiducial marks for single−particle cryoEM structure determination of membrane proteins, Nat. Commun., 11, 1 Niu, 2022, Structural basis of inhibition of the human SGLT2–MAP17 glucose transporter, Nature, 601, 280, 10.1038/s41586-021-04212-9 Nygaard, 2020, Cryo-electron microscopy analysis of small membrane proteins, Curr. Opin. Struct. Biol., 64, 26, 10.1016/j.sbi.2020.05.009 Overington, 2006, How many drug targets are there?, Nat. Rev. Drug Discov., 5, 993, 10.1038/nrd2199 Renaud, 2018, Cryo-EM in drug discovery: achievements, limitations and prospects, Nat. Rev. Drug Discov., 17, 471, 10.1038/nrd.2018.77 Robertson, 2021, 1 Sun, 2020, A unique hormonal recognition feature of the human glucagon-like peptide-2 receptor, Cell Res., 30, 1098, 10.1038/s41422-020-00442-0 Tamura-Sakaguchi, 2021, Moving toward generalizable NZ-1 labeling for 3D structure determination with optimized epitope-Tag insertion, Acta Crystallogr. D: Struct. Biol., 77, 645, 10.1107/S2059798321002527 Tsutsumi, 2020, Structure of human frizzled5 by fiducial-assisted cryo-em supports a heterodimeric mechanism of canonical wnt signaling, Elife, 9, 1, 10.7554/eLife.58464 Uchański, 2021, Megabodies expand the nanobody toolkit for protein structure determination by single-particle cryo-EM, Nat. Methods, 18, 60, 10.1038/s41592-020-01001-6 Uchański, 2020, Nanobodies to study protein conformational states, Curr. Opin. Struct. Biol., 60, 117, 10.1016/j.sbi.2020.01.003 Vulovic, 2021, Generation of ordered protein assemblies using rigid three-body fusion, Proc. Natl. Acad. Sci. U. S. A, 118, 1, 10.1073/pnas.2015037118 Wigge, 2020, The rapidly evolving role of cryo-EM in drug design, Drug Discov. Today Technol., 38, 91, 10.1016/j.ddtec.2020.12.003 Wu, 2012, Fabs enable single particle cryoEM studies of small proteins, Structure, 20, 582, 10.1016/j.str.2012.02.017 Wu, 2021, Cryo-EM structure determination of small proteins by nanobody-binding scaffolds (Legobodies), Proc. Natl. Acad. Sci. U. S. A, 118, 1, 10.1073/pnas.2115001118 Xia, 2021, Cryo-EM structure of the human histamine H1 receptor/Gq complex, Nat. Commun., 12, 1 Xu, 2022, 1 Yao, 2019, Fusion of DARPin to aldolase enables visualization of small protein by cryo-EM, Structure, 27, 1148, 10.1016/j.str.2019.04.003 Yeates, 2020, Development of imaging scaffolds for cryo-electron microscopy, Curr. Opin. Struct. Biol., 60, 142, 10.1016/j.sbi.2020.01.012 Yonekura, 2006, Electron energy filtering significantly improves amplitude contrast of frozen-hydrated protein at 300 kV, J. Struct. Biol., 156, 524, 10.1016/j.jsb.2006.07.016 Zhang, 2022, Cryo-EM, protein engineering, and simulation enable the development of peptide therapeutics against acute myeloid leukemia, ACS Cent. Sci., 8, 214, 10.1021/acscentsci.1c01090 Zhang, 2022, Fusion protein strategies for cryo-EM study of G protein-coupled receptors, Nat. Commun., 13, 1 Zimmermann, 2018, Synthetic single domain antibodies for the conformational trapping of membrane proteins, Elife, 7, 1, 10.7554/eLife.34317