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journal article·2024-05

Capturing Protein–Protein Interactions with Acidic Amino Acids Reactive Cross‐Linkers

Qing‐Qing Liao, Xin Shu, Wei Sun, Hyma Mandapaka, Feng Xie, Zhengkui Zhang, Tong Dai, Shuai Wang, Jinghua Zhao, Hong Jiang, Long Zhang, Jinzhong Lin, Shu‐Wei Li, Irene Coin, Fan Yang, Jinrong Peng, Kui Li, Haifan Wu, Fangfang Zhou, Bing Yang

Small· Volume 20· Issue 20
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Source abstract

Abstract

Abstract Acidic residues (Asp and Glu) have a high prevalence on protein surfaces, but cross‐linking reactions targeting these residues are limited. Existing methods either require high‐concentration coupling reagents or have low structural compatibility. Here a previously reported “plant‐and‐cast” strategy is extended to develop heterobifunctional cross‐linkers. These cross‐linkers first react rapidly with Lys sidechains and then react with Asp and Glu sidechains, in a proximity‐enhanced fashion. The cross‐linking reaction proceeds at neutral pH and room temperature without coupling reagents. The efficiency and robustness of cross‐linking using model proteins, ranging from small monomeric proteins to large protein complexes are demonstrated. Importantly, it is shown that this type of cross‐linkers are efficient at identifying protein–protein interactions involving acidic domains. The Cross‐linking mass spectrometry (XL‐MS) study with p53 identified 87 putative binders of the C‐terminal domain of p53. Among them, SARNP, ZRAB2, and WBP11 are shown to regulate the expression and alternative splicing of p53 target genes. Thus, these carboxylate‐reactive cross‐linkers will further expand the power of XL‐MS in the analysis of protein structures and protein–protein interactions.
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Research context

OpenAlex topics: Microbial Natural Products and Biosynthesis · Viral Infectious Diseases and Gene Expression in Insects · Click Chemistry and Applications

SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.

Affiliations

Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology Life Sciences Institute Cancer Center Zhejiang University Hangzhou Zhejiang 310058 China

Institute of Biology and Medical Science Soochow University Suzhou Jiangsu 215123 China

Department of Chemistry and Biochemistry Wichita State University Wichita KS 67260 USA

State Key Laboratory of Genetic Engineering School of Life Sciences Zhongshan Hospital Fudan University Shanghai 200438 China

Kidney Disease Center The First Affiliated Hospital College of Medicine Zhejiang University Hangzhou Zhejiang 310003 China

Nanjing Apollomics Biotech, Inc Nanjing Jiangsu 210033 China

Institute of Biochemistry Faculty of Life Sciences University of Leipzig 04103 Leipzig Germany

Department of Biophysics Kidney Disease Center of the First Affiliated Hospital Zhejiang University School of Medicine Hangzhou 310058 China

MOE Key Laboratory of Biosystems Homeostasis & Protection College of Animal Sciences Zhejiang University Hangzhou Zhejiang 310058 China

Institute of Animal Sciences Chinese Academy of Agricultural Sciences Beijing 100193 China

Funding

National Basic Research Program of China · National Natural Science Foundation of China · Zhejiang Provincial Outstanding Youth Science Foundation

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