A peptide-centric local stability assay enables proteome-scale identification of the protein targets and binding regions of diverse ligands

Kejia Li; Shijie Chen; Keyun Wang; Yan Wang; Lianji Xue; Yuying Ye; Zheng Fang; Jiawen Lyu; Haiyang Zhu; Yanan Li; Ting Yu; Feng Yang; Xiaolei Zhang; Siqi Guo; Chengfei Ruan; Jiahua Zhou; Qi Wang; Mingming Dong; Cheng Luo; Mingliang Ye

doi:10.1038/s41592-024-02553-7

A peptide-centric local stability assay enables proteome-scale identification of the protein targets and binding regions of diverse ligands

Nat Methods. 2024 Dec 10. doi: 10.1038/s41592-024-02553-7. Online ahead of print.

Authors

Kejia Li^{1

2

3}, Shijie Chen⁴, Keyun Wang¹, Yan Wang¹, Lianji Xue^{1

2}, Yuying Ye^{1

2}, Zheng Fang^{1

2}, Jiawen Lyu^{1

2

5}, Haiyang Zhu^{1

2}, Yanan Li¹, Ting Yu^{1

2}, Feng Yang⁴, Xiaolei Zhang¹, Siqi Guo⁴, Chengfei Ruan^{1

2}, Jiahua Zhou^{1

2}, Qi Wang^{1

2}, Mingming Dong⁶, Cheng Luo^{7

8}, Mingliang Ye^{9

10}

Affiliations

¹ State Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, China.
² University of Chinese Academy of Sciences, Beijing, China.
³ Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
⁴ Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
⁵ Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden.
⁶ MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian, China.
⁷ Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China. cluo@simm.ac.cn.
⁸ School of Pharmacy, Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, China. cluo@simm.ac.cn.
⁹ State Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, China. mingliang@dicp.ac.cn.
¹⁰ University of Chinese Academy of Sciences, Beijing, China. mingliang@dicp.ac.cn.

PMID: 39658593
DOI: 10.1038/s41592-024-02553-7

Abstract

By using a limited-proteolysis strategy that employs a large amount of trypsin to generate peptides directly from native proteins, we found that ligand-induced protein local stability shifts can be sensitively detected on a proteome-wide scale. This enabled us to develop the peptide-centric local stability assay, a modification-free approach that achieves unprecedented sensitivity in proteome-wide target identification and binding-region determination. We demonstrate the broad applications of the peptide-centric local stability assay by investigating interactions across various biological contexts.

Abstract

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