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Wen Y, Shan S, Ye F, Liao W, Wu X, Chen W, Zhao C. Prospects of phycoerythrin: Structural features, antioxidation and applications in food. Food Chem 2024; 463:141425. [PMID: 39348767 DOI: 10.1016/j.foodchem.2024.141425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 09/12/2024] [Accepted: 09/23/2024] [Indexed: 10/02/2024]
Abstract
Phycoerythrin (PE) is a naturally occurring plant protein of algal origin. The colour, bioactivity and stability of PE are inextricably linked to its structure. PE has powerful antioxidant properties that effectively prevent oxidative stress and cellular damage, for which the chromophore structure plays a key role. However, the relationship between the chromophore and thermal stability is unclear in PE. The environmental factors affecting the thermal stability of PE are mainly light, high temperature and extreme pH. PE stability can be enhanced through various techniques, including the incorporation of additives, cross-linking processes, and the formation of complexes. Improving the stability of PE is of significant importance for its applications within the food industry. This paper outlines the structural characteristics of PE, discusses the relationship between its structure and antioxidant activity, and focuses on the application of PE in the food industry, as well as the factors affecting its stability and strategies for its improvement.
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Affiliation(s)
- Yuxi Wen
- State Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China; University of Vigo, Nutrition and Bromatology Group, Department of Analytical Chemistry and Food Science, Faculty of Science, E32004 Ourense, Spain
| | - Shuo Shan
- State Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China; University of Vigo, Nutrition and Bromatology Group, Department of Analytical Chemistry and Food Science, Faculty of Science, E32004 Ourense, Spain
| | - Fangting Ye
- College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wei Liao
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xue Wu
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Weichao Chen
- State Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China; College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Chao Zhao
- State Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China; College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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2
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Cheng J, Wang H, Zhang Y, Wang X, Liu G. Advances in crosslinking chemistry and proximity-enabled strategies: deciphering protein complexes and interactions. Org Biomol Chem 2024; 22:7549-7559. [PMID: 39192765 DOI: 10.1039/d4ob01058b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2024]
Abstract
Mass spectrometry, coupled with innovative crosslinking techniques to decode protein conformations and interactions through uninterrupted signal connections, has undergone remarkable progress in recent years. It is crucial to develop selective crosslinking reagents that minimally disrupt protein structure and dynamics, providing insights into protein network regulation and biological functions. Compared to traditional crosslinkers, new bifunctional chemical crosslinkers exhibit high selectivity and specificity in connecting proximal amino acid residues, resulting in stable molecular crosslinked products. The conjugation with specific amino acid residues like lysine, cysteine, arginine and tyrosine expands the XL-MS toolbox, enabling more precise modeling of target substrates and leading to improved data quality and reliability. Another emerging crosslinking method utilizes unnatural amino acids (UAAs) derived from proximity-enabled reactivity with specific amino acids or sulfur-fluoride exchange (SuFEx) reactions with nucleophilic residues. These UAAs are genetically encoded into proteins for the formation of specific covalent bonds. This technique combines the benefits of genetic encoding for live cell compatibility with chemical crosslinking, providing a valuable method for capturing transient and weak protein-protein interactions (PPIs) for mapping PPI coordinates and improving the pharmacological properties of proteins. With continued advancements in technology and applications, crosslinking mass spectrometry is poised to play an increasingly significant role in guiding our understanding of protein dynamics and function in the future.
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Affiliation(s)
- Jiongjia Cheng
- Key Laboratory of Advanced Functional Materials of Nanjing, School of Environmental Science, Nanjing Xiaozhuang University, Nanjing, 211171, China.
| | - Haiying Wang
- Key Laboratory of Advanced Functional Materials of Nanjing, School of Environmental Science, Nanjing Xiaozhuang University, Nanjing, 211171, China.
| | - Yuchi Zhang
- Key Laboratory of Advanced Functional Materials of Nanjing, School of Environmental Science, Nanjing Xiaozhuang University, Nanjing, 211171, China.
| | - Xiaofeng Wang
- Key Laboratory of Advanced Functional Materials of Nanjing, School of Environmental Science, Nanjing Xiaozhuang University, Nanjing, 211171, China.
| | - Guangxiang Liu
- Key Laboratory of Advanced Functional Materials of Nanjing, School of Environmental Science, Nanjing Xiaozhuang University, Nanjing, 211171, China.
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3
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Wang T, Liang Y, Wang G, Ma S, Zhang L, Lu H, Zhang Y. Ultrafast and Chemoselective Biotinylation of Living Cell Surfaces for Time-Resolved Surfaceome Analysis. Anal Chem 2024; 96:14448-14455. [PMID: 39192718 DOI: 10.1021/acs.analchem.4c02271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2024]
Abstract
Cell surface proteins participate in many important biological processes, such as cell-to-cell interaction, signal transduction, cell adhesion, and protein transportation. In-depth study of the cell surface protein group is of great significance. Nevertheless, detection and analysis of the surfaceome remain a significant challenge due to their low abundance and hydrophobicity. Herein, we reported an ultrafast and chemoselective labeling method using our newly developed trifunctional probe, the OPA-S-S-alkyne, which labeled cell surface lysine residues, and then established a novel cell surfaceome profiling approach. According to our experimental results, the OPA-S-S-alkyne probe can react extremely fast with living cells, labeling cells in only 1 min, while traditional NHS (labeling cell surface lysine with N-hydroxysuccinimide ester probe) and CSC (labeling cell surface glycan with hydrazide biotin probe) methods normally take longer time of more than 30 min and 1 h, respectively. Taking advantage of this ultrafast property of the method, we highlight the utility of this method by exploring the temporal dynamic changes of surfaceome upon EGF stimulation in living Hela cells and reported "early" and "late" EGF-regulated cell surface proteins, which are difficult to be distinguished by the current cell surface profiling approaches.
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Affiliation(s)
- Ting Wang
- Department of Chemistry and Liver Cancer Institute of Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yuying Liang
- Department of Chemistry and Liver Cancer Institute of Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Guoli Wang
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, China
| | - Shiyun Ma
- Department of Chemistry and Liver Cancer Institute of Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Lei Zhang
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, China
| | - Haojie Lu
- Department of Chemistry and Liver Cancer Institute of Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, China
| | - Ying Zhang
- Department of Chemistry and Liver Cancer Institute of Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, China
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4
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Botticelli L, Bakhtina AA, Kaiser NK, Keller A, McNutt S, Bruce JE, Chu F. Chemical cross-linking and mass spectrometry enabled systems-level structural biology. Curr Opin Struct Biol 2024; 87:102872. [PMID: 38936319 PMCID: PMC11283951 DOI: 10.1016/j.sbi.2024.102872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Revised: 05/22/2024] [Accepted: 06/04/2024] [Indexed: 06/29/2024]
Abstract
Structural information on protein-protein interactions (PPIs) is essential for improved understanding of regulatory interactome networks that confer various physiological and pathological responses. Additionally, maladaptive PPIs constitute desirable therapeutic targets due to inherently high disease state specificity. Recent advances in chemical cross-linking strategies coupled with mass spectrometry (XL-MS) have positioned XL-MS as a promising technology to not only elucidate the molecular architecture of individual protein assemblies, but also to characterize proteome-wide PPI networks. Moreover, quantitative in vivo XL-MS provides a new capability for the visualization of cellular interactome dynamics elicited by drug treatments, disease states, or aging effects. The emerging field of XL-MS based complexomics enables unique insights on protein moonlighting and protein complex remodeling. These techniques provide complimentary information necessary for in-depth structural interactome studies to better comprehend how PPIs mediate function in living systems.
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Affiliation(s)
- Luke Botticelli
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA
| | - Anna A Bakhtina
- Department of Genome Sciences, University of Washington, Seattle WA, USA
| | - Nathan K Kaiser
- Department of Genome Sciences, University of Washington, Seattle WA, USA
| | - Andrew Keller
- Department of Genome Sciences, University of Washington, Seattle WA, USA
| | - Seth McNutt
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA
| | - James E Bruce
- Department of Genome Sciences, University of Washington, Seattle WA, USA.
| | - Feixia Chu
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA.
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5
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Jiang Y, Zhang X, Nie H, Fan J, Di S, Fu H, Zhang X, Wang L, Tang C. Dissecting diazirine photo-reaction mechanism for protein residue-specific cross-linking and distance mapping. Nat Commun 2024; 15:6060. [PMID: 39025860 PMCID: PMC11258254 DOI: 10.1038/s41467-024-50315-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 07/08/2024] [Indexed: 07/20/2024] Open
Abstract
While photo-cross-linking (PXL) with alkyl diazirines can provide stringent distance restraints and offer insights into protein structures, unambiguous identification of cross-linked residues hinders data interpretation to the same level that has been achieved with chemical cross-linking (CXL). We address this challenge by developing an in-line system with systematic modulation of light intensity and irradiation time, which allows for a quantitative evaluation of diazirine photolysis and photo-reaction mechanism. Our results reveal a two-step pathway with mainly sequential generation of diazo and carbene intermediates. Diazo intermediate preferentially targets buried polar residues, many of which are inaccessible with known CXL probes for their limited reactivity. Moreover, we demonstrate that tuning light intensity and duration enhances selectivity towards polar residues by biasing diazo-mediated cross-linking reactions over carbene ones. This mechanistic dissection unlocks the full potential of PXL, paving the way for accurate distance mapping against protein structures and ultimately, unveiling protein dynamic behaviors.
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Affiliation(s)
- Yida Jiang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Xinghe Zhang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Honggang Nie
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Analytical Instrumentation Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Jianxiong Fan
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Shuangshuang Di
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Analytical Instrumentation Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Hui Fu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Analytical Instrumentation Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Xiu Zhang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Analytical Instrumentation Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Lijuan Wang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Analytical Instrumentation Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Chun Tang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
- Center for Quantitative Biology, PKU-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
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6
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He Y, Li Y, Zhao L, Ying G, Lu G, Zhang L, Zhang Z. An Optimized Miniaturized Filter-Aided Sample Preparation Method for Sensitive Cross-Linking Mass Spectrometry Analysis of Microscale Samples. Anal Chem 2024. [PMID: 39007547 DOI: 10.1021/acs.analchem.4c01600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Cross-linking mass spectrometry (XL-MS) is a powerful tool for elucidating protein structures and protein-protein interactions (PPIs) at the global scale. However, sensitive XL-MS analysis of mass-limited samples remains challenging, due to serious sample loss during sample preparation of the low-abundance cross-linked peptides. Herein, an optimized miniaturized filter-aided sample preparation (O-MICROFASP) method was presented for sensitive XL-MS analysis of microscale samples. By systematically investigating and optimizing crucial experimental factors, this approach dramatically improves the XL identification of low and submicrogram samples. Compared with the conventional FASP method, more than 7.4 times cross-linked peptides were identified from single-shot analysis of 1 μg DSS cross-linked HeLa cell lysates (440 vs 59). The number of cross-linked peptides identified from 0.5 μg HeLa cell lysates was increased by 58% when further reducing the surface area of the filter to 0.058 mm2 in the microreactor. To deepen the identification coverage of XL-proteome, five different types of cross-linkers were used and each μg of cross-linked HeLa cell lysates was processed by O-MICROFASP integrated with tip-based strong cation exchange (SCX) fractionation. Up to 2741 unique cross-linked peptides were identified from the 5 μg HeLa cell lysates, representing 2579 unique K-K linkages on 1092 proteins. About 96% of intraprotein cross-links were within the maximal distance restraints of 26 Å, and 75% of the identified PPIs reported by the STRING database were with high confidence (scores ≥0.9), confirming the high validity of the identified cross-links for protein structural mapping and PPI analysis. This study demonstrates that O-MICROFASP is a universal and efficient method for proteome-wide XL-MS analysis of microscale samples with high sensitivity and reliability.
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Affiliation(s)
- Yu He
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Yang Li
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Lili Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Guojin Ying
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Gang Lu
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Zhenbin Zhang
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang 315211, China
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7
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Liao QQ, Shu X, Sun W, Mandapaka H, Xie F, Zhang Z, Dai T, Wang S, Zhao J, Jiang H, Zhang L, Lin J, Li SW, Coin I, Yang F, Peng J, Li K, Wu H, Zhou F, Yang B. Capturing Protein-Protein Interactions with Acidic Amino Acids Reactive Cross-Linkers. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2308383. [PMID: 38073323 DOI: 10.1002/smll.202308383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/14/2023] [Indexed: 05/18/2024]
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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Affiliation(s)
- Qing-Qing Liao
- 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
| | - Xin Shu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Wei Sun
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Hyma Mandapaka
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, KS, 67260, USA
| | - Feng Xie
- Institute of Biology and Medical Science, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Zhengkui Zhang
- Institute of Biology and Medical Science, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Tong Dai
- Institute of Biology and Medical Science, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Shuai Wang
- Institute of Biology and Medical Science, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Jinghua Zhao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital Fudan University, Shanghai, 200438, China
| | - Hong Jiang
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China
| | - Long Zhang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Jinzhong Lin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital Fudan University, Shanghai, 200438, China
| | - Shu-Wei Li
- Nanjing Apollomics Biotech, Inc, Nanjing, Jiangsu, 210033, China
| | - Irene Coin
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, 04103, Leipzig, Germany
| | - Fan Yang
- Department of Biophysics, Kidney Disease Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Jinrong Peng
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Kui Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Haifan Wu
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, KS, 67260, USA
| | - Fangfang Zhou
- Institute of Biology and Medical Science, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Bing Yang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China
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Zhu Y, Akkaya KC, Ruta J, Yokoyama N, Wang C, Ruwolt M, Lima DB, Lehmann M, Liu F. Cross-link assisted spatial proteomics to map sub-organelle proteomes and membrane protein topologies. Nat Commun 2024; 15:3290. [PMID: 38632225 PMCID: PMC11024108 DOI: 10.1038/s41467-024-47569-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 04/05/2024] [Indexed: 04/19/2024] Open
Abstract
The functions of cellular organelles and sub-compartments depend on their protein content, which can be characterized by spatial proteomics approaches. However, many spatial proteomics methods are limited in their ability to resolve organellar sub-compartments, profile multiple sub-compartments in parallel, and/or characterize membrane-associated proteomes. Here, we develop a cross-link assisted spatial proteomics (CLASP) strategy that addresses these shortcomings. Using human mitochondria as a model system, we show that CLASP can elucidate spatial proteomes of all mitochondrial sub-compartments and provide topological insight into the mitochondrial membrane proteome. Biochemical and imaging-based follow-up studies confirm that CLASP allows discovering mitochondria-associated proteins and revising previous protein sub-compartment localization and membrane topology data. We also validate the CLASP concept in synaptic vesicles, demonstrating its applicability to different sub-cellular compartments. This study extends the scope of cross-linking mass spectrometry beyond protein structure and interaction analysis towards spatial proteomics, and establishes a method for concomitant profiling of sub-organelle and membrane proteomes.
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Affiliation(s)
- Ying Zhu
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany
| | - Kerem Can Akkaya
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany
- Department of Molecular Physiology and Cell Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany
| | - Julia Ruta
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany
| | - Nanako Yokoyama
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany
| | - Cong Wang
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany
| | - Max Ruwolt
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany
| | - Diogo Borges Lima
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany
| | - Martin Lehmann
- Department of Molecular Physiology and Cell Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany
| | - Fan Liu
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany.
- Charité - Universitätsmedizin Berlin, Charitépl. 1, 10117, Berlin, Germany.
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9
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Wang T, Ma S, Ji G, Wang G, Liu Y, Zhang L, Zhang Y, Lu H. A chemical proteomics approach for global mapping of functional lysines on cell surface of living cell. Nat Commun 2024; 15:2997. [PMID: 38589397 PMCID: PMC11001985 DOI: 10.1038/s41467-024-47033-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 03/19/2024] [Indexed: 04/10/2024] Open
Abstract
Cell surface proteins are responsible for many crucial physiological roles, and they are also the major category of drug targets as the majority of therapeutics target membrane proteins on the surface of cells to alter cellular signaling. Despite its great significance, ligand discovery against membrane proteins has posed a great challenge mainly due to the special property of their natural habitat. Here, we design a new chemical proteomic probe OPA-S-S-alkyne that can efficiently and selectively target the lysines exposed on the cell surface and develop a chemical proteomics strategy for global analysis of surface functionality (GASF) in living cells. In total, we quantified 2639 cell surface lysines in Hela cell and several hundred residues with high reactivity were discovered, which represents the largest dataset of surface functional lysine sites to date. We discovered and validated that hyper-reactive lysine residues K382 on tyrosine kinase-like orphan receptor 2 (ROR2) and K285 on Endoglin (ENG/CD105) are at the protein interaction interface in co-crystal structures of protein complexes, emphasizing the broad potential functional consequences of cell surface lysines and GASF strategy is highly desirable for discovering new active and ligandable sites that can be functionally interrogated for drug discovery.
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Affiliation(s)
- Ting Wang
- Liver Cancer Institute, Zhongshan Hospital and Department of Chemistry, Fudan University, Shanghai, China
| | - Shiyun Ma
- Liver Cancer Institute, Zhongshan Hospital and Department of Chemistry, Fudan University, Shanghai, China
| | - Guanghui Ji
- Liver Cancer Institute, Zhongshan Hospital and Department of Chemistry, Fudan University, Shanghai, China
| | - Guoli Wang
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Shanghai, China
| | - Yang Liu
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Shanghai, China
| | - Lei Zhang
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Shanghai, China
| | - Ying Zhang
- Liver Cancer Institute, Zhongshan Hospital and Department of Chemistry, Fudan University, Shanghai, China.
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Shanghai, China.
| | - Haojie Lu
- Liver Cancer Institute, Zhongshan Hospital and Department of Chemistry, Fudan University, Shanghai, China.
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Shanghai, China.
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10
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Sun M, Chen J, Zhao C, Zhang L, Liu M, Zhang Y, Zhao Q, Gong Z. Enhancing protein dynamics analysis with hydrophilic polyethylene glycol cross-linkers. Brief Bioinform 2024; 25:bbae026. [PMID: 38343324 PMCID: PMC10859660 DOI: 10.1093/bib/bbae026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/30/2023] [Accepted: 01/11/2024] [Indexed: 02/15/2024] Open
Abstract
Cross-linkers play a critical role in capturing protein dynamics in chemical cross-linking mass spectrometry techniques. Various types of cross-linkers with different backbone features are widely used in the study of proteins. However, it is still not clear how the cross-linkers' backbone affect their own structure and their interactions with proteins. In this study, we systematically characterized and compared methylene backbone and polyethylene glycol (PEG) backbone cross-linkers in terms of capturing protein structure and dynamics. The results indicate the cross-linker with PEG backbone have a better ability to capture the inter-domain dynamics of calmodulin, adenylate kinase, maltodextrin binding protein and dual-specificity protein phosphatase. We further conducted quantum chemical calculations and all-atom molecular dynamics simulations to analyze thermodynamic and kinetic properties of PEG backbone and methylene backbone cross-linkers. Solution nuclear magnetic resonance was employed to validate the interaction interface between proteins and cross-linkers. Our findings suggest that the polarity distribution of PEG backbone enhances the accessibility of the cross-linker to the protein surface, facilitating the capture of sites located in dynamic regions. By comprehensively benchmarking with disuccinimidyl suberate (DSS)/bis-sulfosuccinimidyl-suberate(BS3), bis-succinimidyl-(PEG)2 revealed superior advantages in protein dynamic conformation analysis in vitro and in vivo, enabling the capture of a greater number of cross-linking sites and better modeling of protein dynamics. Furthermore, our study provides valuable guidance for the development and application of PEG backbone cross-linkers.
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Affiliation(s)
- Min Sun
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Innovation Academy for Precision Measurement Science and Technology Chinese Academy of Sciences, Wuhan, Hubei 430071, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Jing Chen
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
- School of Chemistry and Material Science, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Chang Zhao
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Innovation Academy for Precision Measurement Science and Technology Chinese Academy of Sciences, Wuhan, Hubei 430071, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Innovation Academy for Precision Measurement Science and Technology Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Yukui Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Qun Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Zhou Gong
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Innovation Academy for Precision Measurement Science and Technology Chinese Academy of Sciences, Wuhan, Hubei 430071, China
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11
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Wang T, Wang Z, Wang R, Zhang L, Zhang Y, Lu H. Highly efficient and chemoselective blocking of free amino group by ortho-phthalaldehyde (OPA) for comprehensive analysis of protein terminome. Talanta 2024; 267:125262. [PMID: 37804787 DOI: 10.1016/j.talanta.2023.125262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 09/24/2023] [Accepted: 09/30/2023] [Indexed: 10/09/2023]
Abstract
Herein, we introduced ortho-phthalaldehyde (OPA) for blocking free amino groups and established a simple and robust method for comprehensive profiling of protein terminome based on strong cation exchange chromatography (SCX) fractionation. With the highly efficient and chemoseletive amine-group blocking, we identified 2271 canonical human protein N-termini, 1650 canonical human protein C-termini, as well as 645 protein neo-N-termini from HeLa cells.
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Affiliation(s)
- Ting Wang
- Department of Chemistry and Liver Cancer Institute of Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Zhongjie Wang
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, 200032, China
| | - Rui Wang
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, 200032, China
| | - Lei Zhang
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, 200032, China
| | - Ying Zhang
- Department of Chemistry and Liver Cancer Institute of Zhongshan Hospital, Fudan University, Shanghai, 200032, China; Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, 200032, China.
| | - Haojie Lu
- Department of Chemistry and Liver Cancer Institute of Zhongshan Hospital, Fudan University, Shanghai, 200032, China; Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, 200032, China.
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12
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Yu C, Huang L. New advances in cross-linking mass spectrometry toward structural systems biology. Curr Opin Chem Biol 2023; 76:102357. [PMID: 37406423 PMCID: PMC11091472 DOI: 10.1016/j.cbpa.2023.102357] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 06/02/2023] [Accepted: 06/04/2023] [Indexed: 07/07/2023]
Abstract
Elucidating protein-protein interaction (PPI) networks and their structural features within cells is central to understanding fundamental biology and associations of cell phenotypes with human pathologies. Owing to technological advancements during the last decade, cross-linking mass spectrometry (XL-MS) has become an enabling technology for delineating interaction landscapes of proteomes as they exist in living systems. XL-MS is unique due to its capability to simultaneously capture PPIs from native environments and uncover interaction contacts though identification of cross-linked peptides, thereby permitting the determination of both identity and connectivity of PPIs in cells. In combination with high resolution structural tools such as cryo-electron microscopy and AI-assisted prediction, XL-MS has contributed significantly to elucidating architectures of large protein assemblies. This review highlights the latest developments in XL-MS technologies and their applications in proteome-wide analysis to advance structural systems biology.
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Affiliation(s)
- Clinton Yu
- Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA 92697, USA
| | - Lan Huang
- Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA 92697, USA.
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13
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Nie M, Li H. Innovation in Cross-Linking Mass Spectrometry Workflows: Toward a Comprehensive, Flexible, and Customizable Data Analysis Platform. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:1949-1956. [PMID: 37537999 DOI: 10.1021/jasms.3c00123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Cross-linking mass spectrometry (XL-MS) is widely used in the analysis of protein structure and protein-protein interactions (PPIs). Throughout the entire workflow, the utilization of cross-linkers and the interpretation of cross-linking data are the core steps. In recent years, the development of cross-linkers and analytical software mostly follow up on the classical models of non-cleavable cross-linkers such as BS3/DSS and MS-cleavable cross-linkers such as DSSO. Although such a paradigm promotes the maturity and robustness of the XL-MS field, it confines the innovation and flexibility of new cross-linkers and analytical software. This critical insight will discuss the classification, advantages, and disadvantages of existing data analysis search engines. Take the new platinum-based metal cross-linker as an example, potential pitfalls in characterization of cross-linked peptides using existing software are discussed. Finally, ideas on developing more flexible, comprehensive, and user-friendly cross-linkers and software tools are proposed.
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Affiliation(s)
- Minhan Nie
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Huilin Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
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14
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Cao Y, Liu XT, Mao PZ, Chen ZL, Tarn C, Dong MQ. Comparative Analysis of Chemical Cross-Linking Mass Spectrometry Data Indicates That Protein STY Residues Rarely React with N-Hydroxysuccinimide Ester Cross-Linkers. J Proteome Res 2023; 22:2593-2607. [PMID: 37494005 DOI: 10.1021/acs.jproteome.3c00037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
When it comes to mass spectrometry data analysis for identification of peptide pairs linked by N-hydroxysuccinimide (NHS) ester cross-linkers, search engines bifurcate in their setting of cross-linkable sites. Some restrict NHS ester cross-linkable sites to lysine (K) and protein N-terminus, referred to as K only for short, whereas others additionally include serine (S), threonine (T), and tyrosine (Y) by default. Here, by setting amino acids with chemically inert side chains such as glycine (G), valine (V), and leucine (L) as cross-linkable sites, which serves as a negative control, we show that software-identified STY-cross-links are only as reliable as GVL-cross-links. This is true across different NHS ester cross-linkers including DSS, DSSO, and DSBU, and across different search engines including MeroX, xiSearch, and pLink. Using a published data set originated from synthetic peptides, we demonstrate that STY-cross-links indeed have a high false discovery rate. Further analysis revealed that depending on the data and the search engine used to analyze the data, up to 65% of the STY-cross-links identified are actually K-K cross-links of the same peptide pairs, up to 61% are actually K-mono-links, and the rest tend to contain short peptides at high risk of false identification.
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Affiliation(s)
- Yong Cao
- National Institute of Biological Sciences, Beijing, Beijing 102206, China
| | - Xin-Tong Liu
- National Institute of Biological Sciences, Beijing, Beijing 102206, China
| | - Peng-Zhi Mao
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen-Lin Chen
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ching Tarn
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
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15
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Zheng J, Zheng Z, Fu C, Weng Y, He A, Ye X, Gao W, Tian R. Deciphering intercellular signaling complexes by interaction-guided chemical proteomics. Nat Commun 2023; 14:4138. [PMID: 37438365 DOI: 10.1038/s41467-023-39881-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 06/27/2023] [Indexed: 07/14/2023] Open
Abstract
Indirect cell-cell interactions mediated by secreted proteins and their plasma membrane receptors play essential roles for regulating intercellular signaling. However, systematic profiling of the interactions between living cell surface receptors and secretome from neighboring cells remains challenging. Here we develop a chemical proteomics approach, termed interaction-guided crosslinking (IGC), to identify ligand-receptor interactions in situ. By introducing glycan-based ligation and click chemistry, the IGC approach via glycan-to-glycan crosslinking successfully captures receptors from as few as 0.1 million living cells using only 10 ng of secreted ligand. The unparalleled sensitivity and selectivity allow systematic crosslinking and identification of ligand-receptor complexes formed between cell secretome and surfaceome in an unbiased and all-to-all manner, leading to the discovery of a ligand-receptor interaction between pancreatic cancer cell-secreted urokinase (PLAU) and neuropilin 1 (NRP1) on pancreatic cancer-associated fibroblasts. This approach is thus useful for systematic exploring new ligand-receptor pairs and discovering critical intercellular signaling events.
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Affiliation(s)
- Jiangnan Zheng
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Zhendong Zheng
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen, 518055, China
- School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Changying Fu
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yicheng Weng
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen, 518055, China
| | - An He
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xueting Ye
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Weina Gao
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Ruijun Tian
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen, 518055, China.
- Research Center for Chemical Biology and Omics Analysis, School of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen, 518055, China.
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16
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Mathay M, Keller A, Bruce JE. Studying Protein-Ligand Interactions by Protein Denaturation and Quantitative Cross-Linking Mass Spectrometry. Anal Chem 2023; 95:9432-9436. [PMID: 37307416 PMCID: PMC10848897 DOI: 10.1021/acs.analchem.2c04501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Recently, several mass spectrometry methods have utilized protein structural stability for the quantitative study of protein-ligand engagement. These protein-denaturation approaches, which include thermal proteome profiling (TPP) and stability of proteins from rates of oxidation (SPROX), evaluate ligand-induced denaturation susceptibility changes with a MS-based readout. The different techniques of bottom-up protein-denaturation methods each have their own advantages and challenges. Here, we report the combination of protein-denaturation principles with quantitative cross-linking mass spectrometry using isobaric quantitative protein interaction reporter technologies. This method enables the evaluation of ligand-induced protein engagement through analysis of cross-link relative ratios across chemical denaturation. As a proof of concept, we found ligand-stabilized cross-linked lysine pairs in well-studied bovine serum albumin and ligand bilirubin. These links map to the known binding sites Sudlow Site I and subdomain IB. We propose that protein denaturation and qXL-MS can be combined with similar peptide-level quantification approaches, like SPROX, to increase the coverage information profiled for facilitating protein-ligand engagement efforts.
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Affiliation(s)
- Martin Mathay
- Department of Genome Sciences, University of Washington, Seattle, Washington 98109, United States
| | - Andrew Keller
- Department of Genome Sciences, University of Washington, Seattle, Washington 98109, United States
| | - James E Bruce
- Department of Genome Sciences, University of Washington, Seattle, Washington 98109, United States
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17
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Li S, Zhu C, Zhao Q, Zhang ZM, Sun P, Li Z. Ynamide Coupling Reagent for the Chemical Cross-Linking of Proteins in Live Cells. ACS Chem Biol 2023; 18:1405-1415. [PMID: 37231651 DOI: 10.1021/acschembio.3c00149] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Chemical cross-linking of proteins coupled with mass spectrometry analysis (CXMS) is a powerful method for the study of protein structure and protein-protein interactions (PPIs). However, the chemical probes used in the CXMS are limited to bidentate reactive warheads, and the available zero-length cross-linkers are restricted to 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride/N-hydroxysuccinimide (EDC/NHS) and 4-(4,6-dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium chloride (DMTMM). To alleviate this issue, an efficient coupling reagent, sulfonyl ynamide, was developed as a new zero-length cross-linker that can connect high-abundance carboxyl residues (D/E) with lysine (K) to form amide bonds in the absence of any catalyst. Significant improvement in the cross-linking efficiency and specificity in comparison with traditional EDC/NHS was achieved with model proteins, which includes inter- and intramolecular conjugations. The cross-linked structures were validated by X-ray crystallography. Importantly, this coupling reagent can be successfully used to capture interacting proteins in the whole proteome and can be a useful reagent for probing potential protein-protein interactions in situ.
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Affiliation(s)
- Shengrong Li
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Chengjun Zhu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Qian Zhao
- Department of Applied Biology and Chemical Technology, State Key Laboratory of Chemical Biology and Drug Discovery, Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Zhi-Min Zhang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Pinghua Sun
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Zhengqiu Li
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), MOE Key Laboratory of Tumor Molecular Biology, School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
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18
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Zhang B, Gao H, Gong Z, Zhao L, Zhong B, Sui Z, Liang Z, Zhang Y, Zhao Q, Zhang L. Improved Cross-Linking Coverage for Protein Complexes Containing Low Levels of Lysine by Using an Enrichable Photo-Cross-Linker. Anal Chem 2023. [PMID: 37303169 DOI: 10.1021/acs.analchem.2c05020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Chemical cross-linking coupled with mass spectrometry (XL-MS) is an important technique for the structural analysis of protein complexes where the coverage of amino acids and the identification of cross-linked sites are crucial. Photo-cross-linking has multisite reactivity and is valuable for the structural analysis of chemical cross-linking. However, a high degree of heterogeneity results from this multisite reactivity, which results in samples with higher complexity and lower abundance. Additionally, the applicability of photo-cross-linking is limited to purified protein complexes. In this work, we demonstrate a photo-cross-linker, alkynyl-succinimidyl-diazirine (ASD) with the reactive groups of N-hydroxysuccinimide ester and diazirine, as well as the click-enrichable alkyne group. Photo-cross-linkers can provide higher site reactivity for proteins that contain only a small number of lysine residues, thereby complementing the more commonly used lysine-targeting cross-linkers. By systematically analyzing proteins with differing lysine contents and differing flexibilities, we demonstrated clear enhancement in structure elucidation for proteins containing less lysine and with high flexibility. In addition, enrichment approaches of alkynyl-azide click chemistry conjugated with biotin-streptavidin purification (coinciding with parallel orthogonal digestion) improved the identification coverage of cross-links. We show that this photo-cross-linking approach can be used for membrane proteome-wide complex analysis. This method led to the identification of a total of 14066 lysine-X cross-linked site pairs from a total of 2784 proteins. Thus, this cross-linker is a valuable addition to a photo-cross-linking toolkit and improves the identification coverage of XL-MS in functional structure analysis.
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Affiliation(s)
- Beirong Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Hang Gao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Zhou Gong
- CAS Innovation Academy for Precision Measurement Science and Technology, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Chinese Academy of Sciences, Wuhan, Hubei 430071, People's Republic of China
| | - Lili Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Bowen Zhong
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, People's Republic of China
| | - Zhigang Sui
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, People's Republic of China
| | - Zhen Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, People's Republic of China
| | - Yukui Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, People's Republic of China
| | - Qun Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, People's Republic of China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, People's Republic of China
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19
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Chen ZA, Rappsilber J. Protein structure dynamics by crosslinking mass spectrometry. Curr Opin Struct Biol 2023; 80:102599. [PMID: 37104977 DOI: 10.1016/j.sbi.2023.102599] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/22/2023] [Accepted: 03/27/2023] [Indexed: 04/29/2023]
Abstract
Crosslinking mass spectrometry captures protein structures in solution. The crosslinks reveal spatial proximities as distance restraints, but do not easily reveal which of these restraints derive from the same protein conformation. This superposition can be reduced by photo-crosslinking, and adding information from protein structure models, or quantitative crosslinking reveals conformation-specific crosslinks. As a consequence, crosslinking MS has proven useful already in the context of multiple dynamic protein systems. We foresee a breakthrough in the resolution and scale of studying protein dynamics when crosslinks are used to guide deep-learning-based protein modelling. Advances in crosslinking MS, such as photoactivatable crosslinking and in-situ crosslinking, will then reveal protein conformation dynamics in the cellular context, at a pseudo-atomic resolution, and plausibly in a time-resolved manner.
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Affiliation(s)
- Zhuo Angel Chen
- Technische Universität Berlin, Chair of Bioanalytics, 10623 Berlin, Germany
| | - Juri Rappsilber
- Technische Universität Berlin, Chair of Bioanalytics, 10623 Berlin, Germany; Si-M/"Der Simulierte Mensch", a Science Framework of Technische Universität Berlin and Charité - Universitätsmedizin Berlin, 10623 Berlin, Germany; Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK.
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20
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Cheung CHP, Chong TH, Wei T, Liu H, Li X. Guanidine Additive Enabled Intermolecular ortho-Phthalaldehyde-Amine-Thiol Three-Component Reactions for Modular Constructions. Angew Chem Int Ed Engl 2023; 62:e202217150. [PMID: 36624047 DOI: 10.1002/anie.202217150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/03/2023] [Accepted: 01/09/2023] [Indexed: 01/11/2023]
Abstract
Recently, ortho-phthalaldehyde (OPA) is experiencing a renascence for the modification of proteins and peptides through OPA-amine two-component reactions for bioconjugation and intramolecular OPA-amine-thiol three-component reactions for cyclization. Historically, small thiol molecules were used in large excess to allow for the intermolecular OPA-amine-thiol reaction forming 1-thio-isoindole derivatives. In this study, we discovered that guanidine could serve as an effective additive to switch the intermolecular OPA-amine-thiol three-component reaction to a stoichiometric process and enable the modular construction of peptide-peptide, and peptide-drug conjugate structures. Thus, 12 model peptide-peptide conjugates have been synthesized from unprotected peptides featuring all proteinogenic residues. Besides, 6 peptide-drug conjugates have been prepared in one step, with excellent conversions and isolated yields. In addition, a conjugate product has been further functionalized by utilizing a premodified OPA derivative, demonstrating the versatility and flexibility of this reaction.
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Affiliation(s)
- Carina Hey Pui Cheung
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, P. R. China
| | - Tin Hang Chong
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, P. R. China
| | - Tongyao Wei
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, P. R. China
| | - Han Liu
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, P. R. China
| | - Xuechen Li
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, P. R. China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, P. R. China
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21
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Wang Z, Rabb JD, Lin Q. Orthogonal Crosslinking: A Strategy to Generate Novel Protein Topology and Function. Chemistry 2023; 29:e202202828. [PMID: 36251567 PMCID: PMC9839582 DOI: 10.1002/chem.202202828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Indexed: 11/27/2022]
Abstract
Compared to the disulfide bond, other naturally occurring intramolecular crosslinks have received little attention, presumably due to their rarity in the vast protein space. Here we presented examples of natural non-disulfide crosslinks, which we refer to as orthogonal crosslinks, emphasizing their effect on protein topology and function. We summarize recent efforts on expanding orthogonal crosslinks by using either the enzymes that catalyze protein circularization or the genetic code expansion strategy to add electrophilic amino acids site-specifically in proteins. The advantages and disadvantages of each method are discussed, along with their applications to generate novel protein topology and function. In particular, we highlight our recent work on spontaneous orthogonal crosslinking, in which a carbamate-based crosslink was generated in situ, and its applications in designing orthogonally crosslinked domain antibodies with their topology-mimicking bacterial adhesins.
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Affiliation(s)
- Zheng Wang
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY 14260-3000, USA
| | - Johnathan D Rabb
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY 14260-3000, USA
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY 14260-3000, USA
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22
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Chu X, Li B, Liu HY, Sun X, Yang X, He G, Zhou C, Xuan W, Liu SL, Chen G. Bioconjugation via Hetero-Selective Clamping of Two Different Amines with ortho-Phthalaldehyde. Angew Chem Int Ed Engl 2023; 62:e202212199. [PMID: 36398699 DOI: 10.1002/anie.202212199] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Indexed: 11/19/2022]
Abstract
Amino groups are common in both natural and synthetic compounds and offer a very attractive class of endogenous handles for bioconjugation. However, the ability to differentiate two types of amino groups and join them with high hetero-selectivity and efficiency in a complex setting remains elusive. Herein, we report a new method for bioconjugation via one-pot chemoselective clamping of two different amine nucleophiles using a simple ortho-phthalaldehyde (OPA) reagent. Various α-amino acids, aryl amines, and secondary amines can be crosslinked to the ϵ-amino side chain of lysine on peptides or proteins with high efficiency and hetero-selectivity. This method offers a simple and powerful means to crosslink small molecule drugs, imaging probes, peptides, proteins, carbohydrates, and even virus particles without any pre-functionalization.
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Affiliation(s)
- Xin Chu
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Bo Li
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Hao-Yang Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Xiaowei Sun
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Xiaochen Yang
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Gang He
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Chuanzheng Zhou
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China.,Haihe Laboratory of Sustainable Chemical Transformations, Tianjin, 300192, China
| | - Weimin Xuan
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Shu-Lin Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Chemistry, Nankai University, Tianjin, 300071, China.,Frontiers Science Center for New Organic Matter, Nankai University, Tianjin, 300071, China
| | - Gong Chen
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China.,Frontiers Science Center for New Organic Matter, Nankai University, Tianjin, 300071, China.,Haihe Laboratory of Sustainable Chemical Transformations, Tianjin, 300192, China
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