Cargando…

Improving mass spectrometry analysis of protein structures with arginine-selective chemical cross-linkers

Chemical cross-linking of proteins coupled with mass spectrometry analysis (CXMS) is widely used to study protein-protein interactions (PPI), protein structures, and even protein dynamics. However, structural information provided by CXMS is still limited, partly because most CXMS experiments use lys...

Descripción completa

Detalles Bibliográficos
Autores principales: Jones, Alexander X., Cao, Yong, Tang, Yu-Liang, Wang, Jian-Hua, Ding, Yue-He, Tan, Hui, Chen, Zhen-Lin, Fang, Run-Qian, Yin, Jili, Chen, Rong-Chang, Zhu, Xing, She, Yang, Huang, Niu, Shao, Feng, Ye, Keqiong, Sun, Rui-Xiang, He, Si-Min, Lei, Xiaoguang, Dong, Meng-Qiu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6718413/
https://www.ncbi.nlm.nih.gov/pubmed/31477730
http://dx.doi.org/10.1038/s41467-019-11917-z
_version_ 1783447721358655488
author Jones, Alexander X.
Cao, Yong
Tang, Yu-Liang
Wang, Jian-Hua
Ding, Yue-He
Tan, Hui
Chen, Zhen-Lin
Fang, Run-Qian
Yin, Jili
Chen, Rong-Chang
Zhu, Xing
She, Yang
Huang, Niu
Shao, Feng
Ye, Keqiong
Sun, Rui-Xiang
He, Si-Min
Lei, Xiaoguang
Dong, Meng-Qiu
author_facet Jones, Alexander X.
Cao, Yong
Tang, Yu-Liang
Wang, Jian-Hua
Ding, Yue-He
Tan, Hui
Chen, Zhen-Lin
Fang, Run-Qian
Yin, Jili
Chen, Rong-Chang
Zhu, Xing
She, Yang
Huang, Niu
Shao, Feng
Ye, Keqiong
Sun, Rui-Xiang
He, Si-Min
Lei, Xiaoguang
Dong, Meng-Qiu
author_sort Jones, Alexander X.
collection PubMed
description Chemical cross-linking of proteins coupled with mass spectrometry analysis (CXMS) is widely used to study protein-protein interactions (PPI), protein structures, and even protein dynamics. However, structural information provided by CXMS is still limited, partly because most CXMS experiments use lysine-lysine (K-K) cross-linkers. Although superb in selectivity and reactivity, they are ineffective for lysine deficient regions. Herein, we develop aromatic glyoxal cross-linkers (ArGOs) for arginine-arginine (R-R) cross-linking and the lysine-arginine (K-R) cross-linker KArGO. The R-R or K-R cross-links generated by ArGO or KArGO fit well with protein crystal structures and provide information not attainable by K-K cross-links. KArGO, in particular, is highly valuable for CXMS, with robust performance on a variety of samples including a kinase and two multi-protein complexes. In the case of the CNGP complex, KArGO cross-links covered as much of the PPI interface as R-R and K-K cross-links combined and improved the accuracy of Rosetta docking substantially.
format Online
Article
Text
id pubmed-6718413
institution National Center for Biotechnology Information
language English
publishDate 2019
publisher Nature Publishing Group UK
record_format MEDLINE/PubMed
spelling pubmed-67184132019-09-04 Improving mass spectrometry analysis of protein structures with arginine-selective chemical cross-linkers Jones, Alexander X. Cao, Yong Tang, Yu-Liang Wang, Jian-Hua Ding, Yue-He Tan, Hui Chen, Zhen-Lin Fang, Run-Qian Yin, Jili Chen, Rong-Chang Zhu, Xing She, Yang Huang, Niu Shao, Feng Ye, Keqiong Sun, Rui-Xiang He, Si-Min Lei, Xiaoguang Dong, Meng-Qiu Nat Commun Article Chemical cross-linking of proteins coupled with mass spectrometry analysis (CXMS) is widely used to study protein-protein interactions (PPI), protein structures, and even protein dynamics. However, structural information provided by CXMS is still limited, partly because most CXMS experiments use lysine-lysine (K-K) cross-linkers. Although superb in selectivity and reactivity, they are ineffective for lysine deficient regions. Herein, we develop aromatic glyoxal cross-linkers (ArGOs) for arginine-arginine (R-R) cross-linking and the lysine-arginine (K-R) cross-linker KArGO. The R-R or K-R cross-links generated by ArGO or KArGO fit well with protein crystal structures and provide information not attainable by K-K cross-links. KArGO, in particular, is highly valuable for CXMS, with robust performance on a variety of samples including a kinase and two multi-protein complexes. In the case of the CNGP complex, KArGO cross-links covered as much of the PPI interface as R-R and K-K cross-links combined and improved the accuracy of Rosetta docking substantially. Nature Publishing Group UK 2019-09-02 /pmc/articles/PMC6718413/ /pubmed/31477730 http://dx.doi.org/10.1038/s41467-019-11917-z Text en © The Author(s) 2019 Open Access 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Jones, Alexander X.
Cao, Yong
Tang, Yu-Liang
Wang, Jian-Hua
Ding, Yue-He
Tan, Hui
Chen, Zhen-Lin
Fang, Run-Qian
Yin, Jili
Chen, Rong-Chang
Zhu, Xing
She, Yang
Huang, Niu
Shao, Feng
Ye, Keqiong
Sun, Rui-Xiang
He, Si-Min
Lei, Xiaoguang
Dong, Meng-Qiu
Improving mass spectrometry analysis of protein structures with arginine-selective chemical cross-linkers
title Improving mass spectrometry analysis of protein structures with arginine-selective chemical cross-linkers
title_full Improving mass spectrometry analysis of protein structures with arginine-selective chemical cross-linkers
title_fullStr Improving mass spectrometry analysis of protein structures with arginine-selective chemical cross-linkers
title_full_unstemmed Improving mass spectrometry analysis of protein structures with arginine-selective chemical cross-linkers
title_short Improving mass spectrometry analysis of protein structures with arginine-selective chemical cross-linkers
title_sort improving mass spectrometry analysis of protein structures with arginine-selective chemical cross-linkers
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6718413/
https://www.ncbi.nlm.nih.gov/pubmed/31477730
http://dx.doi.org/10.1038/s41467-019-11917-z
work_keys_str_mv AT jonesalexanderx improvingmassspectrometryanalysisofproteinstructureswitharginineselectivechemicalcrosslinkers
AT caoyong improvingmassspectrometryanalysisofproteinstructureswitharginineselectivechemicalcrosslinkers
AT tangyuliang improvingmassspectrometryanalysisofproteinstructureswitharginineselectivechemicalcrosslinkers
AT wangjianhua improvingmassspectrometryanalysisofproteinstructureswitharginineselectivechemicalcrosslinkers
AT dingyuehe improvingmassspectrometryanalysisofproteinstructureswitharginineselectivechemicalcrosslinkers
AT tanhui improvingmassspectrometryanalysisofproteinstructureswitharginineselectivechemicalcrosslinkers
AT chenzhenlin improvingmassspectrometryanalysisofproteinstructureswitharginineselectivechemicalcrosslinkers
AT fangrunqian improvingmassspectrometryanalysisofproteinstructureswitharginineselectivechemicalcrosslinkers
AT yinjili improvingmassspectrometryanalysisofproteinstructureswitharginineselectivechemicalcrosslinkers
AT chenrongchang improvingmassspectrometryanalysisofproteinstructureswitharginineselectivechemicalcrosslinkers
AT zhuxing improvingmassspectrometryanalysisofproteinstructureswitharginineselectivechemicalcrosslinkers
AT sheyang improvingmassspectrometryanalysisofproteinstructureswitharginineselectivechemicalcrosslinkers
AT huangniu improvingmassspectrometryanalysisofproteinstructureswitharginineselectivechemicalcrosslinkers
AT shaofeng improvingmassspectrometryanalysisofproteinstructureswitharginineselectivechemicalcrosslinkers
AT yekeqiong improvingmassspectrometryanalysisofproteinstructureswitharginineselectivechemicalcrosslinkers
AT sunruixiang improvingmassspectrometryanalysisofproteinstructureswitharginineselectivechemicalcrosslinkers
AT hesimin improvingmassspectrometryanalysisofproteinstructureswitharginineselectivechemicalcrosslinkers
AT leixiaoguang improvingmassspectrometryanalysisofproteinstructureswitharginineselectivechemicalcrosslinkers
AT dongmengqiu improvingmassspectrometryanalysisofproteinstructureswitharginineselectivechemicalcrosslinkers