Cargando…

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

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 dynam...

Descripción completa

Detalles Bibliográficos
Autores principales: Meng, Qian, Song, Yuan-Li, Zhou, Chen, He, Han, Zhang, Naixia, Zhou, Hu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Biophysics Reports Editorial Office 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10518522/
https://www.ncbi.nlm.nih.gov/pubmed/37753061
http://dx.doi.org/10.52601/bpr.2023.230006
_version_ 1785109532739895296
author Meng, Qian
Song, Yuan-Li
Zhou, Chen
He, Han
Zhang, Naixia
Zhou, Hu
author_facet Meng, Qian
Song, Yuan-Li
Zhou, Chen
He, Han
Zhang, Naixia
Zhou, Hu
author_sort Meng, Qian
collection PubMed
description 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.
format Online
Article
Text
id pubmed-10518522
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher Biophysics Reports Editorial Office
record_format MEDLINE/PubMed
spelling pubmed-105185222023-09-26 A hydrogen–deuterium exchange mass spectrometry-based protocol for protein–small molecule interaction analysis Meng, Qian Song, Yuan-Li Zhou, Chen He, Han Zhang, Naixia Zhou, Hu Biophys Rep Protocol 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. Biophysics Reports Editorial Office 2023-04-30 /pmc/articles/PMC10518522/ /pubmed/37753061 http://dx.doi.org/10.52601/bpr.2023.230006 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Protocol
Meng, Qian
Song, Yuan-Li
Zhou, Chen
He, Han
Zhang, Naixia
Zhou, Hu
A hydrogen–deuterium exchange mass spectrometry-based protocol for protein–small molecule interaction analysis
title A hydrogen–deuterium exchange mass spectrometry-based protocol for protein–small molecule interaction analysis
title_full A hydrogen–deuterium exchange mass spectrometry-based protocol for protein–small molecule interaction analysis
title_fullStr A hydrogen–deuterium exchange mass spectrometry-based protocol for protein–small molecule interaction analysis
title_full_unstemmed A hydrogen–deuterium exchange mass spectrometry-based protocol for protein–small molecule interaction analysis
title_short A hydrogen–deuterium exchange mass spectrometry-based protocol for protein–small molecule interaction analysis
title_sort hydrogen–deuterium exchange mass spectrometry-based protocol for protein–small molecule interaction analysis
topic Protocol
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10518522/
https://www.ncbi.nlm.nih.gov/pubmed/37753061
http://dx.doi.org/10.52601/bpr.2023.230006
work_keys_str_mv AT mengqian ahydrogendeuteriumexchangemassspectrometrybasedprotocolforproteinsmallmoleculeinteractionanalysis
AT songyuanli ahydrogendeuteriumexchangemassspectrometrybasedprotocolforproteinsmallmoleculeinteractionanalysis
AT zhouchen ahydrogendeuteriumexchangemassspectrometrybasedprotocolforproteinsmallmoleculeinteractionanalysis
AT hehan ahydrogendeuteriumexchangemassspectrometrybasedprotocolforproteinsmallmoleculeinteractionanalysis
AT zhangnaixia ahydrogendeuteriumexchangemassspectrometrybasedprotocolforproteinsmallmoleculeinteractionanalysis
AT zhouhu ahydrogendeuteriumexchangemassspectrometrybasedprotocolforproteinsmallmoleculeinteractionanalysis
AT mengqian hydrogendeuteriumexchangemassspectrometrybasedprotocolforproteinsmallmoleculeinteractionanalysis
AT songyuanli hydrogendeuteriumexchangemassspectrometrybasedprotocolforproteinsmallmoleculeinteractionanalysis
AT zhouchen hydrogendeuteriumexchangemassspectrometrybasedprotocolforproteinsmallmoleculeinteractionanalysis
AT hehan hydrogendeuteriumexchangemassspectrometrybasedprotocolforproteinsmallmoleculeinteractionanalysis
AT zhangnaixia hydrogendeuteriumexchangemassspectrometrybasedprotocolforproteinsmallmoleculeinteractionanalysis
AT zhouhu hydrogendeuteriumexchangemassspectrometrybasedprotocolforproteinsmallmoleculeinteractionanalysis