氢/氘交换质谱与冷冻电子显微镜的互补性。
Complementarity of Hydrogen/Deuterium Exchange Mass Spectrometry and Cryo-Electron Microscopy.
机构信息
Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA.
Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA.
出版信息
Trends Biochem Sci. 2020 Oct;45(10):906-918. doi: 10.1016/j.tibs.2020.05.005. Epub 2020 May 30.
Abstract
Methodological improvements in both single particle cryo-electron microscopy (cryo-EM) and hydrogen/deuterium exchange mass spectrometry (HDX-MS) mean that the two methods are being more frequently used together to tackle complex problems in structural biology. There are many benefits to this combination, including for the analysis of low-resolution density, for structural validation, in the analysis of individual proteins versus the same proteins in large complexes, studies of allostery, protein quality control during cryo-EM construct optimization, and in the study of protein movements/dynamics during function. As will be highlighted in this review, through careful considerations of potential sample and conformational heterogeneity, many joint studies have recently been demonstrated, and many future studies using this combination are anticipated.
摘要
方法学的改进，无论是在单颗粒冷冻电子显微镜（cryo-EM）还是氢/氘交换质谱（HDX-MS）方面，都意味着这两种方法越来越频繁地被一起用于解决结构生物学中的复杂问题。这种组合有很多好处，包括对低分辨率密度的分析、结构验证、对单个蛋白质与大复合物中相同蛋白质的分析、变构研究、在冷冻电子显微镜构建优化过程中的蛋白质质量控制，以及在功能过程中研究蛋白质的运动/动力学。正如本文综述所强调的，通过对潜在的样品和构象异质性的仔细考虑，最近已经证明了许多联合研究，并且预计未来将有许多使用这种组合的研究。
相似文献
1
Complementarity of Hydrogen/Deuterium Exchange Mass Spectrometry and Cryo-Electron Microscopy.氢/氘交换质谱与冷冻电子显微镜的互补性。
Trends Biochem Sci. 2020 Oct;45(10):906-918. doi: 10.1016/j.tibs.2020.05.005. Epub 2020 May 30.
2
Dynamics, allostery, and stabilities of whole virus particles by amide hydrogen/deuterium exchange mass spectrometry (HDXMS).酰胺氢/氘交换质谱（HDXMS）研究完整病毒颗粒的动力学、别构和稳定性。
Curr Opin Struct Biol. 2024 Jun;86:102787. doi: 10.1016/j.sbi.2024.102787. Epub 2024 Mar 7.
3
A Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS) Platform for Investigating Peptide Biosynthetic Enzymes.一种用于研究肽生物合成酶的氢-氘交换质谱（HDX-MS）平台。
J Vis Exp. 2020 May 4(159). doi: 10.3791/61053.
4
Equilibrium Dynamics of a Biomolecular Complex Analyzed at Single-amino Acid Resolution by Cryo-electron Microscopy.冷冻电镜单氨基酸分辨率分析的生物分子复合物的平衡动力学。
J Mol Biol. 2023 Apr 15;435(8):168024. doi: 10.1016/j.jmb.2023.168024. Epub 2023 Feb 23.
5
Hydrogen-Deuterium Exchange Mass Spectrometry: A Novel Structural Biology Approach to Structure, Dynamics and Interactions of Proteins and Their Complexes.氢-氘交换质谱法：一种研究蛋白质及其复合物的结构、动力学和相互作用的新型结构生物学方法。
Life (Basel). 2020 Nov 15;10(11):286. doi: 10.3390/life10110286.
6
Hydrogen-Deuterium Exchange Mass Spectrometry for Probing Changes in Conformation and Dynamics of Proteins.氢氘交换质谱法用于探测蛋白质构象和动力学的变化。
Methods Mol Biol. 2021;2199:159-173. doi: 10.1007/978-1-0716-0892-0_10.
7
Strategies for Top-Down Hydrogen Deuterium Exchange-Mass Spectrometry: A Mini Review and Perspective.自上而下的氢氘交换-质谱策略：综述与展望
J Mass Spectrom. 2024 Nov;59(11):e5097. doi: 10.1002/jms.5097.
8
Higher-Order Structure of Adeno-Associated Virus Serotype 8 by Hydrogen/Deuterium Exchange Mass Spectrometry.利用氢/氘交换质谱法分析腺相关病毒8型的高级结构
Viruses. 2024 Apr 10;16(4):585. doi: 10.3390/v16040585.
9
Fundamentals of HDX-MS.HDX-MS 基础。
Essays Biochem. 2023 Mar 29;67(2):301-314. doi: 10.1042/EBC20220111.
10
Combining Small-Molecule Bioconjugation and Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS) to Expose Allostery: the Case of Human Cytochrome P450 3A4.结合小分子生物缀合和氢氘交换质谱（HDX-MS）揭示变构：以人细胞色素 P450 3A4 为例。
ACS Chem Biol. 2021 May 21;16(5):882-890. doi: 10.1021/acschembio.1c00084. Epub 2021 Apr 29.
引用本文的文献
1
The main protease (M) from SARS-CoV-2 triggers plasma clotting in vitro by activating coagulation factors VII and FXII.新型冠状病毒（SARS-CoV-2）的主要蛋白酶（M）通过激活凝血因子VII和FXII在体外引发血浆凝固。
Commun Biol. 2025 Aug 1;8(1):1145. doi: 10.1038/s42003-025-08570-2.
2
Driving Therapeutic Innovation in Neurodegenerative Disease With Hydrogen Deuterium eXchange Mass Spectrometry.利用氢氘交换质谱法推动神经退行性疾病的治疗创新
Mol Cell Proteomics. 2025 Jun 20;24(8):101017. doi: 10.1016/j.mcpro.2025.101017.
3
MultiPassMerger: Automated data processing for multipass cyclic ion mobility HDX-MS.多通道合并器：用于多通道循环离子迁移率氢/氘交换质谱法的自动化数据处理
Protein Sci. 2025 Jun;34(6):e70168. doi: 10.1002/pro.70168.
4
CRISPR RNA binding drives structural ordering that primes Cas7-11 for target cleavage.CRISPR RNA结合驱动结构排序，为Cas7-11进行靶标切割做好准备。
Nucleic Acids Res. 2025 Apr 10;53(7). doi: 10.1093/nar/gkaf271.
5
Structural basis for allosteric modulation of M. tuberculosis proteasome core particle.结核分枝杆菌蛋白酶体核心颗粒变构调节的结构基础
Nat Commun. 2025 Apr 1;16(1):3138. doi: 10.1038/s41467-025-58430-0.
6
Advancing Structural Biology and Protein-Ligand Interactions through Hydrogen/Deuterium Exchange Mass Spectrometry (HDX-MS).通过氢/氘交换质谱法（HDX-MS）推动结构生物学和蛋白质-配体相互作用的发展。
Methods Mol Biol. 2025;2905:181-192. doi: 10.1007/978-1-0716-4418-8_12.
7
Exploring the CNOT1(800-999) HEAT Domain and Its Interactions with Tristetraprolin (TTP) as Revealed by Hydrogen/Deuterium Exchange Mass Spectrometry.通过氢/氘交换质谱法揭示的CNOT1(800 - 999) HEAT结构域及其与锌指蛋白（TTP）的相互作用
Biomolecules. 2025 Mar 11;15(3):403. doi: 10.3390/biom15030403.
8
The Evolving Landscape of Protein Allostery: From Computational and Experimental Perspectives.蛋白质变构的演变态势：从计算和实验视角看
J Mol Biol. 2025 Mar 4:169060. doi: 10.1016/j.jmb.2025.169060.
9
Chemical Synthesis and Structure-Activity Relationship Studies of the Coagulation Factor Xa Inhibitor Tick Anticoagulant Peptide from the Hematophagous Parasite .吸血寄生虫凝血因子Xa抑制剂蜱抗凝肽的化学合成及构效关系研究
Biomimetics (Basel). 2024 Aug 12;9(8):485. doi: 10.3390/biomimetics9080485.
10
Higher-Order Structure of Adeno-Associated Virus Serotype 8 by Hydrogen/Deuterium Exchange Mass Spectrometry.利用氢/氘交换质谱法分析腺相关病毒8型的高级结构
Viruses. 2024 Apr 10;16(4):585. doi: 10.3390/v16040585.
本文引用的文献
1
Structure and dynamics of the ASB9 CUL-RING E3 Ligase.ASB9 CUL-RING E3 连接酶的结构与动态
Nat Commun. 2020 Jun 8;11(1):2866. doi: 10.1038/s41467-020-16499-9.
2
Structural analysis of lecithin:cholesterol acyltransferase bound to high density lipoprotein particles.结合态高密度脂蛋白中卵磷脂胆固醇脂酰转移酶的结构分析。
Commun Biol. 2020 Jan 15;3(1):28. doi: 10.1038/s42003-019-0749-z.
3
Crl activates transcription by stabilizing active conformation of the master stress transcription initiation factor.Crl 通过稳定主应激转录起始因子的活性构象来激活转录。
Elife. 2019 Dec 17;8:e50928. doi: 10.7554/eLife.50928.
4
Molybdate pumping into the molybdenum storage protein via an ATP-powered piercing mechanism.通过一种由ATP驱动的穿透机制将钼酸盐泵入钼储存蛋白。
Proc Natl Acad Sci U S A. 2019 Dec 26;116(52):26497-26504. doi: 10.1073/pnas.1913031116. Epub 2019 Dec 6.
5
FACT caught in the act of manipulating the nucleosome.FACT 正在被抓现行，它在操纵核小体。
Nature. 2020 Jan;577(7790):426-431. doi: 10.1038/s41586-019-1820-0. Epub 2019 Nov 27.
6
Cryo-electron microscopy structure and analysis of the P-Rex1-Gβγ signaling scaffold.冷冻电子显微镜结构分析 P-Rex1-Gβγ 信号支架。
Sci Adv. 2019 Oct 16;5(10):eaax8855. doi: 10.1126/sciadv.aax8855. eCollection 2019 Oct.
7
Dynamics of ABC Transporter P-glycoprotein in Three Conformational States.ABC 转运蛋白 P-糖蛋白三种构象态的动力学。
Sci Rep. 2019 Oct 22;9(1):15092. doi: 10.1038/s41598-019-50578-2.
8
Structural Basis for Tetherin Antagonism as a Barrier to Zoonotic Lentiviral Transmission.作为一种阻止人畜共患慢病毒传播的屏障， tetherin 拮抗作用的结构基础。
Cell Host Microbe. 2019 Sep 11;26(3):359-368.e8. doi: 10.1016/j.chom.2019.08.002. Epub 2019 Aug 22.
9
Structural basis of Cullin 2 RING E3 ligase regulation by the COP9 signalosome.COP9 信号osome 调控 Cullin 2 RING E3 连接酶的结构基础。
Nat Commun. 2019 Aug 23;10(1):3814. doi: 10.1038/s41467-019-11772-y.
10
Protein dynamics and conformational changes explored by hydrogen/deuterium exchange mass spectrometry.通过氢/氘交换质谱法探索蛋白质的动态和构象变化。
Curr Opin Struct Biol. 2019 Oct;58:305-313. doi: 10.1016/j.sbi.2019.06.007. Epub 2019 Jul 25.
Zotero 插件