A hydrogen–deuterium exchange mass spectrometry-based protocol for protein–small molecule interaction analysis

Qian Meng; Yuan-Li Song; Chen Zhou; Han He; Naixia Zhang; Hu Zhou

doi:10.52601/bpr.2023.230006

Volume 9 Issue 2

Apr. 2023

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Qian Meng, Yuan-Li Song, Chen Zhou, Han He, Naixia Zhang, Hu Zhou. A hydrogen–deuterium exchange mass spectrometry-based protocol for protein–small molecule interaction analysis. Biophysics Reports, 2023, 9(2): 99-111. doi: 10.52601/bpr.2023.230006

Citation:

Qian Meng, Yuan-Li Song, Chen Zhou, Han He, Naixia Zhang, Hu Zhou. A hydrogen–deuterium exchange mass spectrometry-based protocol for protein–small molecule interaction analysis. Biophysics Reports, 2023, 9(2): 99-111. doi: 10.52601/bpr.2023.230006

Citation:

Qian Meng, Yuan-Li Song, Chen Zhou, Han He, Naixia Zhang, Hu Zhou. A hydrogen–deuterium exchange mass spectrometry-based protocol for protein–small molecule interaction analysis. Biophysics Reports, 2023, 9(2): 99-111. doi: 10.52601/bpr.2023.230006

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A hydrogen–deuterium exchange mass spectrometry-based protocol for protein–small molecule interaction analysis

doi: 10.52601/bpr.2023.230006

Qian Meng^{1, 3, Q},
Yuan-Li Song^{1, 2, Y},
Chen Zhou¹,
Han He¹,
Naixia Zhang^{1, 2
,
,},
Hu Zhou^{1, 2, 4
,
,}

1.
Analytical Research Center for Organic and Biological Molecules, State Key Laboratory of Drug Research, State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
2.
University of Chinese Academy of Sciences, Beijing 100049, China
3.
Department of Pharmacology, School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
4.
School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China

More Information

Corresponding author: nxzhang@simm.ac.cn (N. Zhang); zhouhu@simm.ac.cn (H. Zhou)
Received Date: 28 March 2023
Accepted Date: 17 April 2023

Available Online: 08 September 2023

Publish Date: 01 April 2023

Abstract

Abstract

Protein–small molecule interaction is vital in regulating protein functions and controlling various cellular processes. Hydrogen deuterium exchange mass spectrometry (HDX-MS) is a powerful methodology to study protein–small molecule interactions, however, to accurately probe the conformational dynamics of the protein upon small molecule binding, the HDX-MS experimental conditions should be carefully controlled and optimized. Here, we present the detailed continuous-labeling, bottom-up HDX-MS protocol for studying protein–small molecule interactions. We took a side-by-side HDX kinetics comparison of the Hsp90N protein with or without the treatment of small molecules (i.e., Radicicol, Geldanamycin) for displaying conformational changes induced by molecular interactions between Hsp90N and small molecules. Our sensitive and robust experimental protocol can facilitate the novice to quickly carry out the structural characterization of protein–small molecule interactions.
- Hydrogen–deuterium exchange mass spectrometry (HDX-MS),
- Protein dynamics,
- Protein–small molecule interactions,
- Hsp90N

Qian Meng, Yuanli Song, Chen Zhou, Han He, Naixia Zhang and Hu Zhou declare that they have no conflict of interest.
This article does not contain any studies with human or animal subjects performed by any of the authors.
Yuan-Li Song contributed equally to this work

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References(57)

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