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Wang J, Wang X, Li M, Wang H, Gao H, Zheng X, Liu G, Niu C, Liu Q, Hu Z, Zhou Y, Zhao Z, Yang J, Liu L. Stimuli-responsive AIEgens with an ultra acidochromic scope for self-reporting soft actuators. Biosens Bioelectron 2024; 263:116582. [PMID: 39038401 DOI: 10.1016/j.bios.2024.116582] [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: 04/29/2024] [Revised: 06/23/2024] [Accepted: 07/16/2024] [Indexed: 07/24/2024]
Abstract
This study develops a series of NBI-based acidochromic AIEgens engineered for ultra-wide acidochromic scope in self-reporting soft actuators, establishing the relationship between the photophysical properties and structural configurations of the AIEgens, further investigating their acidochromic behavior and fabricating acidity monitoring chips. The acidochromic behaviors were thoroughly investigated, and high-precision acidity monitoring chips were fabricated. We confirmed the protonation order of nitrogen atoms within the molecules and elucidated the acidochromic mechanisms through DFT and 1H NMR analyses. Utilizing these findings, we designed acid-driven hydrogel-based biomimetic actuators that can self-report and control the release of heavy loads under acidic conditions. These actuators hold significant potential for applications in targeted drug delivery within acidic biological environments, controlled release systems, and specialized transportation of heavy loads under acidic conditions.
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Affiliation(s)
- Jinjin Wang
- College of Science, Henan Agricultural University, 63 Agricultural Road, Zhengzhou, Henan, 450002, China
| | - Xingxiao Wang
- College of Science, Henan Agricultural University, 63 Agricultural Road, Zhengzhou, Henan, 450002, China
| | - Mengzhen Li
- College of Science, Henan Agricultural University, 63 Agricultural Road, Zhengzhou, Henan, 450002, China
| | - Haoran Wang
- Faculty of Materials Science, Shenzhen MSU-BIT University, Shenzhen, 518115, China
| | - Haoyu Gao
- College of Science, Henan Agricultural University, 63 Agricultural Road, Zhengzhou, Henan, 450002, China
| | - Xin Zheng
- College of Science, Henan Agricultural University, 63 Agricultural Road, Zhengzhou, Henan, 450002, China
| | - Guoxing Liu
- College of Science, Henan Agricultural University, 63 Agricultural Road, Zhengzhou, Henan, 450002, China
| | - Caoyuan Niu
- College of Science, Henan Agricultural University, 63 Agricultural Road, Zhengzhou, Henan, 450002, China
| | - Qian Liu
- Department of Urology, Tianjin First Central Hospital, Tianjin 300192, China
| | - Zhiyuan Hu
- Henan Engineering Research Center of Green Synthesis for Pharmaceuticals, School of Chemistry and Chemical Engineering, Shangqiu Normal University, Shangqiu 476000, China
| | - Yuanyuan Zhou
- School of Materials Science and Engineering, Henan Engineering Research Center of Design and Recycle for Advanced Electrochemical Energy Storage Materials, Henan Normal University, Xinxiang, 453007, China
| | - Zheng Zhao
- School of Science and Engineering, Shenzhen Institute of Aggregate Science and Technology, The Chinese University of Hong Kong Shenzhen (CUHK-Shenzhen), Guangdong, 518172, China.
| | - Jinglei Yang
- Department of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, China.
| | - Lijie Liu
- College of Science, Henan Agricultural University, 63 Agricultural Road, Zhengzhou, Henan, 450002, China; Department of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, China.
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2
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Gao Z, Jing B, Wang Y, Wan W, Dong X, Liu Y. Exploring the impact of lipid nanoparticles on protein stability and cellular proteostasis. J Colloid Interface Sci 2024; 678:656-665. [PMID: 39216393 DOI: 10.1016/j.jcis.2024.08.146] [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: 05/14/2024] [Revised: 07/29/2024] [Accepted: 08/19/2024] [Indexed: 09/04/2024]
Abstract
Lipid nanoparticles (LNPs) have become pivotal in advancing modern medicine, from mRNA-based vaccines to gene editing with CRISPR-Cas9 systems. Though LNPs based therapeutics offer promising drug delivery with satisfactory clinical safety profiles, concerns are raised regarding their potential nanotoxicity. Here, we explore the impacts of LNPs on protein stability in buffer and cellular protein homeostasis (proteostasis) in HepG2 cells. First, we show that LNPs of different polyethylene glycol (PEG) molar ratios to total lipid ratio boost protein aggregation propensity by reducing protein stability in cell lysate and blood plasma. Second, in HepG2 liver cells, these LNPs induce global proteome aggregation, as imaged by a cellular protein aggregation fluorescent dye (AggStain). Such LNPs induced proteome aggregation is accompanied by decrease in cellular micro-environmental polarity as quantified by a solvatochromic protein aggregation sensor (AggRetina). The observed local polarity fluctuations may be caused by the hydrophobic contents of LNPs that promote cellular proteome aggregation. Finally, we exploit RNA sequencing analysis (RNA-Seq) to reveal activation of unfolded protein response (UPR) pathway and other proteostasis genes upon LNPs treatment. Together, these findings highlight that LNPs may induce subtle proteome stress by compromising protein stability and proteostasis even without obvious damage to cell viability.
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Affiliation(s)
- Zifan Gao
- Dalian Medical University, Dalian 116044, China
| | - Biao Jing
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yuhui Wang
- The Second Hospital of Dalian Medical University, Dalian 116023, China
| | - Wang Wan
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - Xuepeng Dong
- The Second Hospital of Dalian Medical University, Dalian 116023, China.
| | - Yu Liu
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
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3
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Jia X, Shen D, Deng J, Wang K, Wang X, Guo Y, Sun L, Jin H, Xia Q, Feng H, Jing B, Sun J, Wan W, Liu Y, Li M. Isophorone-based crystallization-induced-emission sensors detect proteome aggregation in live cells and tissues with breast cancer. Anal Chim Acta 2024; 1317:342916. [PMID: 39030013 DOI: 10.1016/j.aca.2024.342916] [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: 04/16/2024] [Revised: 06/14/2024] [Accepted: 06/25/2024] [Indexed: 07/21/2024]
Abstract
BACKGROUND Protein misfolding and aggregation can lead to various diseases. Recent studies have shed light on the aggregated protein in breast cancer pathology, which suggests that it is crucial to design chemical sensors that visualize protein aggregates in breast cancer, especially in clinical patient-derived samples. However, most reported sensors are constrained in cultured cell lines. RESULTS In this work, we present the development of two isophorone-based crystallization-induced-emission fluorophores for detecting proteome aggregation in breast cancer cell line and tissues biopsied from diseased patients, designated as A1 and A2. These probes exhibited viscosity sensitivity and recovered their fluorescence strongly at crystalline state. Moreover, A1 and A2 exhibit selective binding capacity and strong fluorescence for various aggregated proteins. Utilizing these probes, we detect protein aggregation in stressed breast cancer cells, xenograft mouse model of human breast cancer and clinical patient-derived samples. Notably, the fluorescence intensity of both probes light up in tumor tissues. SIGNIFICANCE The synthesized isophorone-based crystallization-induced-emission fluorophores, A1 and A2, enable sensitive detection of protein aggregation in breast cancer cells and tissues. In the future, aggregated proteins are expected to become indicators for early diagnosis and clinical disease monitoring of breast cancer.
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Affiliation(s)
- Xiaomeng Jia
- The Second Hospital of Dalian Medical University, Dalian, 116023, PR China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
| | - Di Shen
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
| | - Jintai Deng
- The Second Hospital of Dalian Medical University, Dalian, 116023, PR China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
| | - Kainan Wang
- The Second Hospital of Dalian Medical University, Dalian, 116023, PR China
| | - Xueqing Wang
- The Second Hospital of Dalian Medical University, Dalian, 116023, PR China
| | - Yijin Guo
- The Second Hospital of Dalian Medical University, Dalian, 116023, PR China
| | - Lu Sun
- The Second Hospital of Dalian Medical University, Dalian, 116023, PR China
| | - Hao Jin
- The Second Hospital of Dalian Medical University, Dalian, 116023, PR China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
| | - Qiuxuan Xia
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Huan Feng
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Biao Jing
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
| | - Jialu Sun
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
| | - Wang Wan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China.
| | - Man Li
- The Second Hospital of Dalian Medical University, Dalian, 116023, PR China.
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4
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Wang Z, Xia Q, Wan W, Wang M, Zhang Z, Deng J, Jing B, Sun J, Lyu H, Jin H, Yan J, Shen D, Ge Y. Chemical sensors detect and resolve proteome aggregation in peripheral neuropathy cell model induced by chemotherapeutic agents. Bioorg Chem 2024; 148:107491. [PMID: 38788365 DOI: 10.1016/j.bioorg.2024.107491] [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: 01/02/2024] [Revised: 05/10/2024] [Accepted: 05/21/2024] [Indexed: 05/26/2024]
Abstract
As a consequence of somatosensory nervous system injury or disease, neuropathic pain is commonly associated with chemotherapies, known as chemotherapy-induced peripheral neuropathy (CIPN). However, the mechanisms underlying CIPN-induced proteome aggregation in neuronal cells remain elusive due to limited detection tools. Herein, we present series sensors for fluorescence imaging (AggStain) and proteomics analysis (AggLink) to visualize and capture aggregated proteome in CIPN neuronal cell model. The environment-sensitive AggStain imaging sensor selectively binds and detects protein aggregation with 12.3 fold fluorescence enhancement. Further, the covalent AggLink proteomic sensor captures cellular aggregated proteins and profiles their composition via LC-MS/MS analysis. This integrative sensor platform reveals the presence of proteome aggregation in CIPN cell model and highlights its potential for broader applications in assessing proteome stability under various cellular stress conditions.
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Affiliation(s)
- Zhiming Wang
- The Second Hospital of Dalian Medical University, Dalian 116023, China; State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Qiuxuan Xia
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wang Wan
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Mengdie Wang
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhenduo Zhang
- The Second Hospital of Dalian Medical University, Dalian 116023, China; State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Jintai Deng
- The Second Hospital of Dalian Medical University, Dalian 116023, China; State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Biao Jing
- The Second Hospital of Dalian Medical University, Dalian 116023, China; State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Jialu Sun
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Haochen Lyu
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Hao Jin
- The Second Hospital of Dalian Medical University, Dalian 116023, China; State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Jing Yan
- The Second Hospital of Dalian Medical University, Dalian 116023, China; State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Di Shen
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - Yusong Ge
- The Second Hospital of Dalian Medical University, Dalian 116023, China.
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5
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Feng H, Zhao Q, Zhao N, Liang Z, Huang Y, Zhang X, Zhang L, Liu Y. A Cell-Permeable Photosensitizer for Selective Proximity Labeling and Crosslinking of Aggregated Proteome. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306950. [PMID: 38441365 PMCID: PMC11095223 DOI: 10.1002/advs.202306950] [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: 09/22/2023] [Revised: 02/08/2024] [Indexed: 05/16/2024]
Abstract
Intracellular proteome aggregation is a ubiquitous disease hallmark with its composition associated with pathogenicity. Herein, this work reports on a cell-permeable photosensitizer (P8, Rose Bengal derivative) for selective photo induced proximity labeling and crosslinking of cellular aggregated proteome. Rose Bengal is identified out of common photosensitizer scaffolds for its unique intrinsic binding affinity to various protein aggregates driven by the hydrophobic effect. Further acetylation permeabilizes Rose Bengal to selectively image, label, and crosslink aggregated proteome in live stressed cells. A combination of photo-chemical, tandem mass spectrometry, and protein biochemistry characterizations reveals the complexity in photosensitizing pathways (both Type I & II), modification sites and labeling mechanisms. The diverse labeling sites and reaction types result in highly effective enrichment and identification of aggregated proteome. Finally, aggregated proteomics and interaction analyses thereby reveal extensive entangling of proteostasis network components mediated by HSP70 chaperone (HSPA1B) and active participation of autophagy pathway in combating proteasome inhibition. Overall, this work exemplifies the first photo induced proximity labeling and crosslinking method (namely AggID) to profile intracellular aggregated proteome and analyze its interactions.
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Affiliation(s)
- Huan Feng
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qun Zhao
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Nan Zhao
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Zhen Liang
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Yanan Huang
- Department of Chemistry and Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, 18 Shilongshan Road, Hangzhou, 310024, China
| | - Xin Zhang
- Department of Chemistry and Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, 18 Shilongshan Road, Hangzhou, 310024, China
| | - Lihua Zhang
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Yu Liu
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
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6
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Zhang Z, Dong X, Wan W, Guo H, Sun R, Feng H, Wang M, Wang Z, Jin H, Sun J, Xia Q, Zhao Q, Shen D, Gao Z, Liu Y. Unraveling Intracellular Protein Corona Components of Nanoplastics via Photocatalytic Protein Proximity Labeling. Anal Chem 2024; 96:4978-4986. [PMID: 38471057 DOI: 10.1021/acs.analchem.4c00050] [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: 03/14/2024]
Abstract
Bioaccumulation of nanoplastic particles has drawn increasing attention regarding environmental sustainability and biosafety. How nanoplastic particles interact with the cellular milieu still remains elusive. Herein, we exemplify a general approach to profile the composition of a "protein corona" interacting with nanoparticles via the photocatalytic protein proximity labeling method. To enable photocatalytic proximity labeling of the proteome interacting with particles, iodine-substituted BODIPY (I-BODIPY) is selected as the photosensitizer and covalently conjugated onto amino-polystyrene nanoparticles as a model system. Next, selective proximity labeling of interacting proteins is demonstrated using I-BODIPY-labeled nanoplastic particles in both Escherichia coli lysate and live alpha mouse liver 12 cells. Mechanistic studies reveal that the covalent modifications of proteins by an aminoalkyne substrate are conducted via a reactive oxygen species photosensitization pathway. Further proteomic analysis uncovers that mitochondria-related proteins are intensively involved in the protein corona, indicating substantial interactions between nanoplastic particles and mitochondria. In addition, proteostasis network components are also identified, accompanied by consequent cellular proteome aggregation confirmed by fluorescence imaging. Together, this work exemplifies a general strategy to interrogate the composition of the protein corona of nanomaterials by endowing them with photooxidation properties to enable photocatalytic protein proximity labeling function.
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Affiliation(s)
- Zhenduo Zhang
- The Second Hospital of Dalian Medical University, Dalian 116023, China
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Xuepeng Dong
- The Second Hospital of Dalian Medical University, Dalian 116023, China
| | - Wang Wan
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Hengke Guo
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Rui Sun
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Huan Feng
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Mengdie Wang
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zhiming Wang
- The Second Hospital of Dalian Medical University, Dalian 116023, China
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Hao Jin
- The Second Hospital of Dalian Medical University, Dalian 116023, China
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Jialu Sun
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Qiuxuan Xia
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Qi Zhao
- The Second Hospital of Dalian Medical University, Dalian 116023, China
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Di Shen
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zhenming Gao
- The Second Hospital of Dalian Medical University, Dalian 116023, China
| | - Yu Liu
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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7
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Jing B, Bi Y, Kong H, Wan W, Wang J, Yu B. Dual-environment-sensitive probe to detect protein aggregation in stressed laryngeal carcinoma cells and tissues. J Mater Chem B 2024; 12:2505-2510. [PMID: 38334693 DOI: 10.1039/d3tb02627b] [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: 02/10/2024]
Abstract
The interplay between protein folding and biological activity is crucial, with the integrity of the proteome being paramount to ensuring effective biological function execution. In this study, we report a dual-environment-sensitive probe A1, capable of selectively binding to protein aggregates and dynamically monitoring their formation and degradation. Through in vitro, cellular, and tissue assays, A1 demonstrated specificity in distinguishing aggregated from folded protein states, selectively partitioning into aggregated proteins. Thermal shift assays revealed A1 could monitor the process of protein aggregation upon binding to misfolded proteins and preceding to insoluble aggregate formation. In cellular models, A1 detected stress-induced proteome aggregation in TU212 cells (laryngeal carcinoma cells), revealing a less polar microenvironment within the aggregated proteome. Similarly, tissue samples showed more severe proteome aggregation in cancerous tissues compared to paracancerous tissues. Overall, A1 represents a versatile tool for probing protein aggregation with significant implications for both fundamental research and clinical diagnostics.
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Affiliation(s)
- Biao Jing
- Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Yanjie Bi
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, China.
| | - Hui Kong
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, China.
| | - Wang Wan
- Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Jizhe Wang
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, China.
| | - Bo Yu
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, China.
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8
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Paez‐Perez M, Kuimova MK. Molecular Rotors: Fluorescent Sensors for Microviscosity and Conformation of Biomolecules. Angew Chem Int Ed Engl 2024; 63:e202311233. [PMID: 37856157 PMCID: PMC10952837 DOI: 10.1002/anie.202311233] [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: 08/03/2023] [Revised: 10/17/2023] [Accepted: 10/17/2023] [Indexed: 10/20/2023]
Abstract
The viscosity and crowding of biological environment are considered vital for the correct cellular function, and alterations in these parameters are known to underly a number of pathologies including diabetes, malaria, cancer and neurodegenerative diseases, to name a few. Over the last decades, fluorescent molecular probes termed molecular rotors proved extremely useful for exploring viscosity, crowding, and underlying molecular interactions in biologically relevant settings. In this review, we will discuss the basic principles underpinning the functionality of these probes and will review advances in their use as sensors for lipid order, protein crowding and conformation, temperature and non-canonical nucleic acid structures in live cells and other relevant biological settings.
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Affiliation(s)
- Miguel Paez‐Perez
- Department of Chemistry, Imperial College London, MSRHImperial College LondonWood LaneLondonW12 0BZUK
| | - Marina K. Kuimova
- Department of Chemistry, Imperial College London, MSRHImperial College LondonWood LaneLondonW12 0BZUK
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9
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Bai Y, Zhang S, Dong H, Liu Y, Liu C, Zhang X. Advanced Techniques for Detecting Protein Misfolding and Aggregation in Cellular Environments. Chem Rev 2023; 123:12254-12311. [PMID: 37874548 DOI: 10.1021/acs.chemrev.3c00494] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Protein misfolding and aggregation, a key contributor to the progression of numerous neurodegenerative diseases, results in functional deficiencies and the creation of harmful intermediates. Detailed visualization of this misfolding process is of paramount importance for improving our understanding of disease mechanisms and for the development of potential therapeutic strategies. While in vitro studies using purified proteins have been instrumental in delivering significant insights into protein misfolding, the behavior of these proteins in the complex milieu of living cells often diverges significantly from such simplified environments. Biomedical imaging performed in cell provides cellular-level information with high physiological and pathological relevance, often surpassing the depth of information attainable through in vitro methods. This review highlights a variety of methodologies used to scrutinize protein misfolding within biological systems. This includes optical-based methods, strategies leaning on mass spectrometry, in-cell nuclear magnetic resonance, and cryo-electron microscopy. Recent advancements in these techniques have notably deepened our understanding of protein misfolding processes and the features of the resulting misfolded species within living cells. The progression in these fields promises to catalyze further breakthroughs in our comprehension of neurodegenerative disease mechanisms and potential therapeutic interventions.
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Affiliation(s)
- Yulong Bai
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang Province, China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Shengnan Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
| | - Hui Dong
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
- University of the Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Xin Zhang
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
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10
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Jin H, Shen D, Jing B, Zhang Z, Wang Z, Sun R, Zhang H, Sun J, Lyu H, Liu Y, Wang L. An epoxide-based covalent sensor to detect cardiac proteome aggregation in a cardio-oncology model. Anal Chim Acta 2023; 1278:341704. [PMID: 37709448 DOI: 10.1016/j.aca.2023.341704] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 07/25/2023] [Accepted: 08/08/2023] [Indexed: 09/16/2023]
Abstract
Covalent sensors to detect and capture aggregated proteome in stressed cells are rare. Herein, we construct a series of covalent fluorogenic sensors for aggregated proteins by structurally modulating GFP chromophore and arming it with an epoxide warhead. Among them, P2 probe selectively modifies aggregated proteins over folded ones and turns on fluorescence as evidenced by biochemical and mass spectrometry results. The coverage of this epoxide-based covalent chemistry is demonstrated using different types of aggregated proteins. Finally, the covalent fluorescent sensor P2 allows for direct visualization and capture of aggregated proteome in stressed cardiomyocytes and cardiac tissue samples from a cardio-oncology mouse model. The epoxide-based covalent sensor developed herein may become useful for future chemical proteomics analysis of aggregated proteins to dissect the mechanism underlying cardio-oncology.
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Affiliation(s)
- Hao Jin
- The Second Hospital of Dalian Medical University, Dalian, 116023, PR China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
| | - Di Shen
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
| | - Biao Jing
- The Second Hospital of Dalian Medical University, Dalian, 116023, PR China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
| | - Zhenduo Zhang
- The Second Hospital of Dalian Medical University, Dalian, 116023, PR China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
| | - Zhiming Wang
- The Second Hospital of Dalian Medical University, Dalian, 116023, PR China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
| | - Rui Sun
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Huaiyue Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Jialu Sun
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
| | - Haochen Lyu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
| | - Yu Liu
- The Second Hospital of Dalian Medical University, Dalian, 116023, PR China.
| | - Lili Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China.
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11
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Zang T, Wang Y, Zhang F, Zhang X, Cao Y, Jing J, Zhang R, Zhang X. Molecular Design Strategy of Protein Isoform-Specific Fluorescent Probes by Considering Molecule in Its Entirety. Anal Chem 2023; 95:13438-13445. [PMID: 37649365 DOI: 10.1021/acs.analchem.3c00707] [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: 09/01/2023]
Abstract
Generally, different isoforms of proteins exert separate biological functions. However, due to similar structures and identical catalysis functions, distinguishing isoforms is challenging. Summarizing a molecular design strategy has great significance in developing a protein-specific fluorescent probe. Usually, recognition of a group was deemed to be the key to a protein isoform-specific response. However, some novel literature reported that fluorophore could play a vital role in the protein isoform-specific response. It means that any part of the fluorescent probe could affect the detected properties. In this work, we report the generation of the first probe to specifically recognize HexA(β-N-acetylhexosaminidase A), Hex-C4, by adjusting the length of the linker. Hex-C4 exhibits specific recognition of HexA both in vitro and in living cells. The integration of the fluorescent spectrum and the MD (molecular dynamics) results provide two factors for the molecular design of isoform-specific fluorescent probes. One is the interaction between tetraphenyl ethylene (AIE fluorogen) and amino acid residues, and the other is the interaction between amino acid residues and the binding group. In this work, a powerful tool to detect HexA in living cells is reported for the first time. Further, a workable molecular design strategy for protein isoform-specific fluorescent probes is summarized.
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Affiliation(s)
- Tienan Zang
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photo-electronic/Electro-photonic Conversion Materials, Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Analytical and Testing Center, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, People's Republic of China
| | - Yunpeng Wang
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photo-electronic/Electro-photonic Conversion Materials, Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Analytical and Testing Center, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, People's Republic of China
| | - Feng Zhang
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photo-electronic/Electro-photonic Conversion Materials, Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Analytical and Testing Center, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, People's Republic of China
| | - Xiaoli Zhang
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photo-electronic/Electro-photonic Conversion Materials, Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Analytical and Testing Center, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, People's Republic of China
| | - Yuan Cao
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photo-electronic/Electro-photonic Conversion Materials, Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Analytical and Testing Center, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, People's Republic of China
| | - Jing Jing
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photo-electronic/Electro-photonic Conversion Materials, Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Analytical and Testing Center, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, People's Republic of China
| | - Rubo Zhang
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photo-electronic/Electro-photonic Conversion Materials, Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Analytical and Testing Center, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, People's Republic of China
| | - Xiaoling Zhang
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photo-electronic/Electro-photonic Conversion Materials, Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Analytical and Testing Center, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, People's Republic of China
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12
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Jing B, Li J, Guo K, Zeng L, Sui J, Zhang Z, Wang Z, Jin H, Sun J, Xue Z, Zhao Q, Wan W, Dong X. Solvatochromic sensors detect proteome aggregation in stressed liver tissues with hepatic cancer and cirrhosis. J Mater Chem B 2023; 11:7654-7662. [PMID: 37464917 DOI: 10.1039/d3tb00984j] [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: 07/20/2023]
Abstract
Protein misfolding and aggregation involve complex cellular processes with clinical implications in various diseases. However, the detection of aggregated proteomes without defined 3-D structures in a complex biological milieu is challenging. This study utilizes chromone scaffold-based environment-sensitive fluorophores P1 and P2 to detect misfolded and aggregated proteome in stressed liver cells and the liver tissues diseased patients. The reported crystallization induced emission probes (P1 and P2) exhibit both polarity and viscosity sensitivity, with emission intensity and wavelength linearly correlated to viscosity and polarity. Meanwhile, P1 and P2 selectively and generally fluoresce upon binding to various aggregated proteins. In hepatic cells, P2 outperforms P1 in detecting stress-induced global proteome aggregation. In mouse liver tissue upon drug-induced injury, the fluorescence intensity of P2 correlated with the severity of liver injury, serving as an earlier indicator for liver stress prior to ALT/AST increase. The quantification of emission wavelength reveals lower micro-environmental polarity in liver-injury tissue. In patient-derived tissues with hepatic cancer and cirrhosis, P1 and P2 also report on the presence of aggregated proteome. Together, the reported solvatochromic proteome aggregation sensors can detect hepatic proteome aggregation and analyze its local polarity in cultured cell lines, animal model tissues, and human clinical samples.
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Affiliation(s)
- Biao Jing
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, China.
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.
| | - Junpeng Li
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, China.
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.
| | - Kun Guo
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, China.
| | - Lianggang Zeng
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.
| | - Jidong Sui
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, China.
| | - Zhenduo Zhang
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, China.
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.
| | - Zhiming Wang
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, China.
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.
| | - Hao Jin
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, China.
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.
| | - Jialu Sun
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.
| | - Zhao Xue
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, China.
| | - Qi Zhao
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, China.
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.
| | - Wang Wan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.
| | - Xuepeng Dong
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, China.
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13
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Chen B, Hu JJ, Ouyang H, Zhang W, Dai J, Xu L, Xia F, Lou X. Peptide-Conjugated Probe Inducing Mitochondrial Dysfunction and Self-Reporting Cell Apoptosis by Aggregated Proteins. Anal Chem 2023; 95:12903-12912. [PMID: 37594437 DOI: 10.1021/acs.analchem.3c02275] [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: 08/19/2023]
Abstract
Inducing and monitoring cell apoptosis in a real-time manner are crucial for evaluating the therapeutic effect of drugs and avoiding excessive treatment. Although promising advancements have been made to monitor cell apoptosis by assessing cell membrane integrity, the chronic compromise of cellular fitness caused by imbalance proteostasis is not visible and hard to be detected. As an indicator for cell apoptosis, imaging of aggregated proteins provides a new direction. Herein, we design a peptide-conjugated probe (QRKN) that can induce mitochondrial dysfunction for self-reporting cell apoptosis by imaging aggregated proteins. Specifically, QRKN can be cleaved into the α-helix-forming part (QRK) and azide-modified small-molecule part (N) by overexpressed cathepsin B (CB) in tumor cells. The QRK part can destroy the mitochondrial membrane and promote cytochrome c (Cyt c) efflux and caspase 3 expression. The other N part can inhibit the activity of mitochondrial complex IV (Mito-IV) and decrease the expression level of adenosine triphosphate (ATP). Two signaling pathways cooperatively induce mitochondrial dysfunction, resulting in protein aggregation and cell apoptosis ultimately. Meanwhile, the cell apoptosis process can be monitored based on QRKN, which is highly sensitive to the aggregated protein-triggered viscosity change. The self-reporting probe can monitor therapeutic responses and provide valuable diagnosis information.
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Affiliation(s)
- Bochao Chen
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Jing-Jing Hu
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Hanzhi Ouyang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Wei Zhang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Jun Dai
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Liang Xu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Fan Xia
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Xiaoding Lou
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
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14
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Jing B, Wan W, Hu B, Jin W, Zhang Z, Peng C, Wang M, Deng J, Dong X, Liu Y, Gao Z. Plastic nanoparticles cause proteome stress and aggregation by compromising cellular protein homeostasis ex vivo and in vivo. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 262:115347. [PMID: 37572624 DOI: 10.1016/j.ecoenv.2023.115347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 08/14/2023]
Abstract
Decomposition of plastic materials into minuscule particles and their long-term uptake pose increasing concerns on environmental sustainability and biosafety. Besides common cell viability and cytotoxicity evaluations, how plastic nanoparticles interfere with different stress response pathways and affect cellular fitness has been less explored. Here, we provided the first piece of evidence to demonstrate plastic nanoparticles potentially can deteriorate proteome stability, compromise cellular protein homeostasis, and consequently cause global proteome misfolding and aggregation. Polystyrene (PS) nanoparticles of different sizes and surface charges were exploited as model plastic materials. In cell lysate and human blood plasma, naked PS nanoparticles with hydrophobic surface deteriorated proteome thermodynamic stability and exaggerated its aggregation propensity. While no cell viability ablation was observed in cells treated with PS nanoparticles up to 200 μg·mL-1, global proteome aggregation and stress was detected by a selective proteome aggregation sensor. Further proteomics analysis revealed how protein homeostasis network was remodeled by positively charged PS nanoparticles via differential expression of key proteins to counteract proteome stress. In mice model, size-dependent liver accumulation of positively charged PS nanoparticles induced hepatocellular proteome aggregation and compromised protein homeostasis network capacity that were invisible to standard alanine transaminase and aspartate transaminase (ALT/AST) liver function as-say and histology. Meanwhile, long-term liver accumulation of plastic nanoparticles deteriorated liver metabolism and saturated liver detoxification capacity of overdosed acetaminophen. This work highlighted the impact of nanoplastics on cellular proteome integrity and cellular fitness that are invisible to current biochemical assays and clinical tests.
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Affiliation(s)
- Biao Jing
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian 116023, PR China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, PR China
| | - Wang Wan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, PR China
| | - Bo Hu
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian 116023, PR China
| | - Wenhan Jin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, PR China
| | - Zhenduo Zhang
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian 116023, PR China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, PR China
| | - Congcong Peng
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian 116023, PR China
| | - Mengdie Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, PR China
| | - Jintai Deng
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian 116023, PR China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, PR China
| | - Xuepeng Dong
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian 116023, PR China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, PR China.
| | - Zhenming Gao
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian 116023, PR China.
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15
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Wang M, Zhang Z, Jing B, Dong X, Guo K, Deng J, Wang Z, Wan W, Jin W, Gao Z, Liu Y. Tailoring the Amphiphilicity of Fluorescent Protein Chromophores to Detect Intracellular Proteome Aggregation in Diverse Biological Samples. Anal Chem 2023; 95:11751-11760. [PMID: 37506028 DOI: 10.1021/acs.analchem.3c01903] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
The formation of amorphous misfolded and aggregated proteins is a hallmark of proteome stress in diseased cells. Given its lack of defined targeting sites, the rational design of intracellular proteome aggregation sensors has been challenging. Herein, we modulate the amphiphilicity of fluorescent protein chromophores to enable selective detection of aggregated proteins in different biological samples, including recombinant proteins, stressed live cells, intoxicated mouse liver tissue, and human hepatocellular carcinoma tissue. By tuning the number of hydroxyl groups, we optimize the selectivity of fluorescent protein chromophores toward aggregated proteins in these biological samples. In recombinant protein applications, the most hydrophobic P0 (cLogP = 5.28) offers the highest fold change (FC = 31.6), sensitivity (LLOD = 0.1 μM), and brightness (Φ = 0.20) upon binding to aggregated proteins. In contrast, P4 of balanced amphiphilicity (cLogP = 2.32) is required for selective detection of proteome stresses in live cells. In mouse and human liver histology tissues, hydrophobic P1 exhibits the best performance in staining the aggregated proteome. Overall, the amphiphilicity of fluorescent chromophores governs the sensor's performance by matching the diverse nature of different biological samples. Together with common extracellular amyloid sensors (e.g., Thioflavin T), these sensors developed herein for intracellular amorphous aggregation complement the toolbox to study protein aggregation.
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Affiliation(s)
- Mengdie Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhenduo Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
- The Second Hospital of Dalian Medical University, Dalian 116023, China
| | - Biao Jing
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
- The Second Hospital of Dalian Medical University, Dalian 116023, China
| | - Xuepeng Dong
- The Second Hospital of Dalian Medical University, Dalian 116023, China
| | - Kun Guo
- The Second Hospital of Dalian Medical University, Dalian 116023, China
| | - Jintai Deng
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
- The Second Hospital of Dalian Medical University, Dalian 116023, China
| | - Zhiming Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
- The Second Hospital of Dalian Medical University, Dalian 116023, China
| | - Wang Wan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Wenhan Jin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Zhenming Gao
- The Second Hospital of Dalian Medical University, Dalian 116023, China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
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16
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Dong X, Zhang Z, Wan W, Jing B, Deng J, Jin W, Shen D, Gao Z, Liu Y. Integrated Imaging and Proteomic Sensors Resolve Proteome Aggregation in Liver Caused by Non-steroidal Anti-inflammatory Drug Overdose. ACS Sens 2023; 8:2247-2254. [PMID: 37248847 DOI: 10.1021/acssensors.3c00216] [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: 05/31/2023]
Abstract
Given the extreme heterogeneity and the loss of defined protein structures, misfolded and aggregated proteins are technically challenging to visualize and analyze. Herein, we assembled an integrated sensor system to resolve aggregated proteome in live cells and animal liver tissues that are overdosed by non-steroidal anti-inflammatory drugs (NSAIDs). A fluorogenic protein aggregation sensor (AggStain) first discovered the presence of aggregated proteome upon overdosing liver cells with NSAIDs. A solvatochromic protein aggregation sensor (AggRetina) further quantified the compactness (polarity) inside these cellular aggregates. Importantly, we exploited a proteomic sensor (AggLink) to selectively capture aggregated proteins upon NSAID overdose and profile their composition, revealing global collapse of cellular protein homeostasis. Finally, we detected subtle proteome aggregation in mouse liver tissue without obvious acute injury at a low NSAID dosage. Overall, we demonstrated an integrated sensor toolset for proteome aggregation studies and unveiled for the first time that NSAID overdose can cause proteome aggregation in liver cells and tissues.
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Affiliation(s)
- Xuepeng Dong
- The Second Hospital of Dalian Medical University, Dalian, Liaoning 116023, China
| | - Zhenduo Zhang
- The Second Hospital of Dalian Medical University, Dalian, Liaoning 116023, China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Wang Wan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Biao Jing
- The Second Hospital of Dalian Medical University, Dalian, Liaoning 116023, China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Jintai Deng
- The Second Hospital of Dalian Medical University, Dalian, Liaoning 116023, China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Wenhan Jin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Di Shen
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Zhenming Gao
- The Second Hospital of Dalian Medical University, Dalian, Liaoning 116023, China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
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17
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Sun R, Zhang S, Liu Y, Li D. Chemical probes for investigating protein liquid-liquid phase separation and aggregation. Curr Opin Chem Biol 2023; 74:102291. [PMID: 37004350 DOI: 10.1016/j.cbpa.2023.102291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/22/2023] [Accepted: 02/26/2023] [Indexed: 04/03/2023]
Abstract
Protein liquid-liquid phase separation drives the dynamic assembly of membraneless organelles for fulfilling different physiological functions. Under diseased condition, protein may undergo liquid-to-solid condensation to form pathological amyloid aggregates closely associated with neurodegenerative diseases. Chemical probe serves as an important chemical tool not only for exploring the basic principle of the dynamic assembly of different protein condensates in vitro and in cell but also for clinical diagnosis and therapeutics of the related diseases. In this review, we first introduce chemical probes to image and regulate protein condensates. Then, we summarized three different categories of chemical probes including general amyloid dye, selective positron emission tomography tracer, and disaggregating binder, which feature distinct interaction pattern and activity upon binding to different pathological amyloid fibrillar aggregates. Next, we discuss the development of chemical probes for tracking protein amorphous aggregates in cells. Finally, we point out future direction in expanding the probes' chemical space and applications.
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Affiliation(s)
- Rui Sun
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Shenqing Zhang
- Bio-X-Renji Hospital Research Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200030, China; Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China.
| | - Dan Li
- Bio-X-Renji Hospital Research Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200030, China; Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China; WLA Laboratories, World Laureates Association, Shanghai 201203, China.
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18
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Leng H, Yang J, Long L, Yan Y, Shi WJ, Zhang L, Yan JW. GFP-based red-emissive fluorescent probes for dual imaging of β-amyloid plaques and mitochondrial viscosity. Bioorg Chem 2023; 136:106540. [PMID: 37084586 DOI: 10.1016/j.bioorg.2023.106540] [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: 10/06/2022] [Revised: 11/26/2022] [Accepted: 04/09/2023] [Indexed: 04/23/2023]
Abstract
Alzheimer's disease (AD), with incurable neurodegenerative damage, has attracted growing interest in exploration of better AD biomarkers in its early diagnosis. Among various biomarkers, amyloid-β (Aβ) aggregates and mitochondrial viscosity are closely related to AD and their dual imaging might provide a potential and feasible strategy. In this work, five GFP-based red-emissive fluorescent probes were rationally designed and synthesized for selective detection of β-amyloid plaques and viscosity, among which C25e exhibited superior properties and could successfully image β-amyloid plaques and mitochondrial viscosity with different fluorescence wavelength signals "turn-on" at around 624 and 640 nm, respectively. Moreover, the staining of brain sections from a transgenic AD mouse showed that probe C25e showed higher selectivity and signal-to-noise ratio towards Aβ plaques than commercially-available Thio-S. In addition, the probe C25e was, for the first time, employed for monitoring amyloid-β induced mitochondrial viscosity changes. Therefore, this GFP-based red-emissive fluorescent probe C25e could serve as a dual-functional tool for imaging β-amyloid plaques and mitochondrial viscosity, which might provide a unique strategy for the early diagnosis of Alzheimer's disease.
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Affiliation(s)
- Huaxiang Leng
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Jinrong Yang
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Liansheng Long
- Department of General Surgery, General Hospital of Southern Theater Command, Guangzhou, 510010, P.R. China
| | - Yiyong Yan
- Shenzhen Bioeasy Biotechnology Co., Ltd, Shenzhen, Guangdong 510010, PR China
| | - Wen-Jing Shi
- School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, PR China
| | - Lei Zhang
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China.
| | - Jin-Wu Yan
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China.
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19
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Zhou Y, Dai J, Qi J, Wu J, Huang Y, Shen B, Zhi X, Fu Y. Construction of a red emission fluorescent probe for selectively detection of cysteine in living cells. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 286:121946. [PMID: 36242837 DOI: 10.1016/j.saa.2022.121946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 09/08/2022] [Accepted: 10/01/2022] [Indexed: 06/16/2023]
Abstract
Cysteine (Cys) is a vital amino acid in the body, and its abnormal expression level is associated with many diseases. In this study, a novel fluorescent probe ACHB was synthesized, showing high selectivity, anti-interference ability and achieving accurate detection of cysteine. Different from most previous off-on probes, ACHB showed an on-off fluorescence response to Cys. Acrylic ester was used as a recognizer while green fluorescence protein (GFP) chromophore derivative 4-hydroxybenzylidene-imidazolinone (HBI) was used as the fluorophore. The addition of Cys leads to the hydrolysis of the red-emitting probe (613 nm), releasing a precursor with a lower fluorescent signal and showing an on-off spectral signal, which was ideal for obtaining sensitive detection with high specificity. Furthermore, the probe was successfully applied for simultaneous determination of cysteine (Cys) in living cells and biological sample (mouse serum). In conclusion, probe ACHB is a promising tool to display the intracellular cysteine concentration level, providing a good visualization method for clinical diagnosis and scientific basic research.
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Affiliation(s)
- Yufeng Zhou
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Jianan Dai
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Jinzhi Qi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Jichun Wu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Yubo Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Baoxing Shen
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, China.
| | - Xu Zhi
- State Key Laboratory of Coordination Chemistry, Collaborative Innovation Center of Advanced Microstructures, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.
| | - Yongqian Fu
- School of Life Science, Taizhou University, Taizhou, Zhejiang 318000, China.
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20
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Feng H, Zhao Q, Zhang B, Hu H, Liu M, Wu K, Li X, Zhang X, Zhang L, Liu Y. Enabling Photo-Crosslinking and Photo-Sensitizing Properties for Synthetic Fluorescent Protein Chromophores. Angew Chem Int Ed Engl 2023; 62:e202215215. [PMID: 36370037 DOI: 10.1002/anie.202215215] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Indexed: 11/13/2022]
Abstract
Synthetic fluorescent protein chromophores have been reported for their singlet state fluorescence properties and applications in bioimaging, but rarely for the triplet state chemistries. Herein, we enabled their photo-sensitizing and photo-crosslinking properties through rational modulations. Extension of molecular conjugation and introduction of heavy atoms promoted the generation of reactive oxygen species. Unlike other photosensitizers, these chromophores selectively photo-crosslinked aggregated proteins and uncovered the interactome profiles. We also exemplified their general applications in chromophore-assisted light inactivation, photodynamic therapy and photo induced polymerization. Theoretical calculation, pathway analysis and transient absorption spectroscopy provided mechanistic insights for this triplet state chemistry. Overall, this work expands the function and application of synthetic fluorescent protein chromophores by enabling their triplet excited state properties.
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Affiliation(s)
- Huan Feng
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qun Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Beirong Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hang Hu
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Meng Liu
- University of Chinese Academy of Sciences, Beijing, 100049, China.,State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Kaifeng Wu
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Xiaosong Li
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Xin Zhang
- Department of Chemistry and Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, 18 Shilongshan Road, Hangzhou, 310024, China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
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21
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Shen D, Jin W, Zhao Q, Wang M, Zhang B, Feng H, Wan W, Bai Y, Lyu H, Sun J, Zhang L, Liu Y. Covalent Solvatochromic Proteome Stress Sensor Based on the Schiff Base Reaction. Anal Chem 2022; 94:14143-14150. [PMID: 36194526 DOI: 10.1021/acs.analchem.2c01281] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Covalent-type probes or sensors have been seldom reported for aggregated proteins. Herein, we reported a series of covalent solvatochromic probes to selectively modify and detect aggregated proteomes through the Schiff base reaction. Such covalent modification was discovered by serendipity using the P1 probe with an aldehyde functional group, exhibiting enhanced fluorescence intensity and unusually large blue shift upon protein aggregation. Supported by the biochemical and mass spectrometry results, we identified that this probe can modify the lysine residue of aggregated proteins selectively over folded ones via the Schiff base reaction. The generality of designing such a covalent-type probe was demonstrated in multiple probe scaffolds using different model proteins. Finally, we exploited the distinct solvatochromism of P1 after Schiff base linkage with aggregated proteins to visualize the distinct morphology of aggregated proteomes, as well as to quantify the polarity heterogeneity inside it. This work may intrigue the exploration of other chemical reaction types to covalently functionalize aggregated proteins that were difficult to analyze.
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Affiliation(s)
- Di Shen
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Wenhan Jin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Qun Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Mengdie Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Beirong Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Huan Feng
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Wang Wan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Yulong Bai
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Haochen Lyu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Jialu Sun
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
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22
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Xia Q, Wan W, Jin W, Huang Y, Sun R, Wang M, Jing B, Peng C, Dong X, Zhang R, Gao Z, Liu Y. Solvatochromic Cellular Stress Sensors Reveal the Compactness Heterogeneity and Dynamics of Aggregated Proteome. ACS Sens 2022; 7:1919-1925. [PMID: 35776067 DOI: 10.1021/acssensors.2c00566] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Deterioration of protein homeostasis (proteostasis) often induces aberrant proteome aggregation. Visualization and dissection of the stressed proteome are of particular interest given their association with numerous degenerative diseases. Recent progress in chemical cellular stress sensors allows for direct visualization of aggregated proteome. Beyond its localization and morphology, the physicochemical nature and the dynamics of the aggregated proteome have been challenging to explore. Herein, we developed a series of solvatochromic fluorene-based D-π-A probes that can selectively and noncovalently bind to a misfolded and aggregated proteome and report on their compactness heterogeneity upon cellular stresses. We achieved this goal by variation of the heterocyclic acceptors to modulate their solvatochromism and binding affinity to amorphous aggregated proteins. The optimized sensor P6 was capable of sensing the polarity differences among different aggregated proteins via its fluorescence emission wavelength. In live cells, P6 revealed the cellular compactness heterogeneity in the aggregated proteome upon cellular stresses. Given the combinative solvatochromic and noncovalent properties, our probe can reversibly monitor the dynamic changes in the aggregated proteome compactness upon stress and after stress recovery, suggesting its potential applications in search of therapeutics to counteract disease-causing proteome stresses.
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Affiliation(s)
- Qiuxuan Xia
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Wang Wan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Wenhan Jin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Yanan Huang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Rui Sun
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Mengdie Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Biao Jing
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.,The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, China
| | - Congcong Peng
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.,The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, China
| | - Xuepeng Dong
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, China
| | - Rixin Zhang
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, China
| | - Zhenming Gao
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
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23
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Peng MZ, Shao YX, Li XZ, Zhang KD, Cai YN, Lin YT, Jiang MY, Liu ZC, Su XY, Zhang W, Jiang XL, Liu L. Mitochondrial FAD shortage in SLC25A32 deficiency affects folate-mediated one-carbon metabolism. Cell Mol Life Sci 2022; 79:375. [PMID: 35727412 PMCID: PMC11072207 DOI: 10.1007/s00018-022-04404-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/06/2022] [Accepted: 05/27/2022] [Indexed: 11/03/2022]
Abstract
The SLC25A32 dysfunction is associated with neural tube defects (NTDs) and exercise intolerance, but very little is known about disease-specific mechanisms due to a paucity of animal models. Here, we generated homozygous (Slc25a32Y174C/Y174C and Slc25a32K235R/K235R) and compound heterozygous (Slc25a32Y174C/K235R) knock-in mice by mimicking the missense mutations identified from our patient. A homozygous knock-out (Slc25a32-/-) mouse was also generated. The Slc25a32K235R/K235R and Slc25a32Y174C/K235R mice presented with mild motor impairment and recapitulated the biochemical disturbances of the patient. While Slc25a32-/- mice die in utero with NTDs. None of the Slc25a32 mutations hindered the mitochondrial uptake of folate. Instead, the mitochondrial uptake of flavin adenine dinucleotide (FAD) was specifically blocked by Slc25a32Y174C/K235R, Slc25a32K235R/K235R, and Slc25a32-/- mutations. A positive correlation between SLC25A32 dysfunction and flavoenzyme deficiency was observed. Besides the flavoenzymes involved in fatty acid β-oxidation and amino acid metabolism being impaired, Slc25a32-/- embryos also had a subunit of glycine cleavage system-dihydrolipoamide dehydrogenase damaged, resulting in glycine accumulation and glycine derived-formate reduction, which further disturbed folate-mediated one-carbon metabolism, leading to 5-methyltetrahydrofolate shortage and other folate intermediates accumulation. Maternal formate supplementation increased the 5-methyltetrahydrofolate levels and ameliorated the NTDs in Slc25a32-/- embryos. The Slc25a32K235R/K235R and Slc25a32Y174C/K235R mice had no glycine accumulation, but had another formate donor-dimethylglycine accumulated and formate deficiency. Meanwhile, they suffered from the absence of all folate intermediates in mitochondria. Formate supplementation increased the folate amounts, but this effect was not restricted to the Slc25a32 mutant mice only. In summary, we established novel animal models, which enabled us to understand the function of SLC25A32 better and to elucidate the role of SLC25A32 dysfunction in human disease development and progression.
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Affiliation(s)
- Min-Zhi Peng
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, the Affiliated Hospital of Guangzhou Medical University, 9 Jinsui Road, Guangzhou, China
| | - Yong-Xian Shao
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, the Affiliated Hospital of Guangzhou Medical University, 9 Jinsui Road, Guangzhou, China
| | - Xiu-Zhen Li
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, the Affiliated Hospital of Guangzhou Medical University, 9 Jinsui Road, Guangzhou, China
| | - Kang-Di Zhang
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, the Affiliated Hospital of Guangzhou Medical University, 9 Jinsui Road, Guangzhou, China
| | - Yan-Na Cai
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, the Affiliated Hospital of Guangzhou Medical University, 9 Jinsui Road, Guangzhou, China
| | - Yun-Ting Lin
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, the Affiliated Hospital of Guangzhou Medical University, 9 Jinsui Road, Guangzhou, China
| | - Min-Yan Jiang
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, the Affiliated Hospital of Guangzhou Medical University, 9 Jinsui Road, Guangzhou, China
| | - Zong-Cai Liu
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, the Affiliated Hospital of Guangzhou Medical University, 9 Jinsui Road, Guangzhou, China
| | - Xue-Ying Su
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, the Affiliated Hospital of Guangzhou Medical University, 9 Jinsui Road, Guangzhou, China
| | - Wen Zhang
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, the Affiliated Hospital of Guangzhou Medical University, 9 Jinsui Road, Guangzhou, China.
| | - Xiao-Ling Jiang
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, the Affiliated Hospital of Guangzhou Medical University, 9 Jinsui Road, Guangzhou, China.
| | - Li Liu
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, the Affiliated Hospital of Guangzhou Medical University, 9 Jinsui Road, Guangzhou, China.
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24
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Leng H, Wang Y, Wang J, Sun H, Sun A, Pistolozzi M, Zhang L, Yan J. Dual-Emission GFP Chromophore-Based Derivative for Imaging and Discriminating Aβ Oligomers and Aggregates. Anal Chem 2022; 94:1999-2006. [PMID: 35041386 DOI: 10.1021/acs.analchem.1c03452] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
β-Amyloid deposition is one of the main pathological features of Alzheimer's disease (AD). The development of fluorescent probes targeting specific β-amyloid species has recently become an attractive strategy to achieve the early diagnosis of AD. In this work, a dual-channel fluorescent protein chromophore derivative C17 was rationally designed and synthesized for the detection and discrimination of Aβ42 aggregates and oligomers. C17 exhibits a specific turn-on emission peak for Aβ42 oligomers at ∼470 nm (peak A) and a peak at ∼600 nm (peak B) for both Aβ42 oligomers and Aβ42 aggregates. Taking advantage of the dual emission of the probe, the dynamic aggregation process of the Aβ42 peptide was monitored in solution. Moreover, double staining of brain sections from transgenic AD mice revealed that peak A of C17 preferentially detected Aβ42 oligomers, whereas peak B was more sensitive to Aβ42 aggregates. The fact that probe C17 can be used for dissecting these two Aβ42 species makes C17 a comprehensive tool for β-amyloid aggregation studies in AD research.
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Affiliation(s)
- Huaxiang Leng
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Yuxuan Wang
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Juan Wang
- Laboratory of Neurogenerative Diseases & Molecular Imaging, Shanghai University of Medicine & Health Sciences, Shanghai 201318, P. R. China
| | - Han Sun
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Anyang Sun
- Laboratory of Neurogenerative Diseases & Molecular Imaging, Shanghai University of Medicine & Health Sciences, Shanghai 201318, P. R. China
| | - Marco Pistolozzi
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China.,International School, Jinan University, 601 Huangpu Avenue West, 510632 Guangzhou, P. R. China
| | - Lei Zhang
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Jinwu Yan
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
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25
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Sun R, Wan W, Jin W, Bai Y, Xia Q, Wang M, Huang Y, Zeng L, Sun J, Peng C, Jing B, Liu Y. Derivatizing Nile Red Fluorophores to Quantify the Heterogeneous Polarity upon Protein Aggregation in the Cell. Chem Commun (Camb) 2022; 58:5407-5410. [DOI: 10.1039/d2cc00629d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Protein aggregation in the cell is often manifested by the formation of subcellular punctate structures. Herein, we modulated the solvatochromism and solubity of Nile Red fluorophore derivatives to quantitatively study...
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26
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Zheng X, Sun W, Ju M, Wu J, Huang H, Shen B. Chemical Biology Toolbox to Overcome Hypoxic Tumor Microenvironment of Photodynamic Therapy: A Review. Biomater Sci 2022; 10:4681-4693. [DOI: 10.1039/d2bm00776b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cancer is currently a disease that seriously threatens human health. Over the past few decades, researchers have continued to find ways to cure cancer. Currently, the most commonly used clinical...
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27
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Dong X, Wan W, Zeng L, Jin W, Huang Y, Shen D, Bai Y, Zhao Q, Zhang L, Liu Y, Gao Z. Regulation of Fluorescence Solvatochromism To Resolve Cellular Polarity upon Protein Aggregation. Anal Chem 2021; 93:16447-16455. [PMID: 34859995 DOI: 10.1021/acs.analchem.1c03401] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Common solvatochromic fluorophores exhibit a bathochromic fluorescence emission wavelength shift accompanied by intensity attenuation due to the presence of nonradiative decay pathways at the excited state. Such intrinsic but inevitable fluorescence quenching of solvatochromism impedes its applications to faithfully quantify local polarity, especially in a polar environment. Herein, we report a new donor-π-acceptor (D-π-A) type solvatochromic fluorophore scaffold containing a perfluorophenyl group that exhibits both a solvatochromic emission wavelength shift and a controllable emission intensity upon polarity fluctuation. The regulation of fluorescence solvatochromism and colors was achieved by tuning the aryl donors. We exploited such desired solvatochromism of these probes to monitor protein misfolding and aggregation via wavelength shift. Finally, the polarity of pathogenic aggregated proteins was quantified by HaloTag bioorthogonal labeling technology in live cells. While much effort has been devoted to resolving the morphology of pathogenic aggregated proteins, this work provides quantitative hints regarding the chemical information at this disease-related protein interphase.
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Affiliation(s)
- Xuepeng Dong
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, P. R. China
| | - Wang Wan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Lianggang Zeng
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Wenhan Jin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Yanan Huang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Di Shen
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Yulong Bai
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China.,University of the Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Qun Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Zhenming Gao
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, P. R. China
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Bai Y, Huang Y, Wan W, Jin W, Shen D, Lyu H, Zeng L, Liu Y. Derivatizing merocyanine dyes to balance their polarity and viscosity sensitivities for protein aggregation detection. Chem Commun (Camb) 2021; 57:13313-13316. [PMID: 34812440 DOI: 10.1039/d1cc05200d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Protein misfolding and aggregation processes involve local polarity and viscosity fluctuation. Herein we modulated the polarity and viscosity sensitivities of merocyanine dyes to detect protein aggregation. We demonstrated how structural modulation balanced these two fluorescence sensitivities and affected the detection of misfolded and aggregated proteins.
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Affiliation(s)
- Yulong Bai
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China. .,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanan Huang
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - Wang Wan
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - Wenhan Jin
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - Di Shen
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - Haochen Lyu
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - Lianggang Zeng
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
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29
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Wan W, Zeng L, Jin W, Chen X, Shen D, Huang Y, Wang M, Bai Y, Lyu H, Dong X, Gao Z, Wang L, Liu X, Liu Y. A Solvatochromic Fluorescent Probe Reveals Polarity Heterogeneity upon Protein Aggregation in Cells. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202107943] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Wang Wan
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Lianggang Zeng
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Wenhan Jin
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Xinxin Chen
- National Laboratory of Biomacromolecules CAS Center for Excellence in Biomacromolecules Institute of Biophysics Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
| | - Di Shen
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Yanan Huang
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Mengdie Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Yulong Bai
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Haochen Lyu
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Xuepeng Dong
- The Second Hospital of Dalian Medical University 467 Zhongshan Road 116023 China Dalian
| | - Zhenming Gao
- The Second Hospital of Dalian Medical University 467 Zhongshan Road 116023 China Dalian
| | - Lei Wang
- National Laboratory of Biomacromolecules CAS Center for Excellence in Biomacromolecules Institute of Biophysics Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
| | - Xiaojing Liu
- Institute of Molecular Sciences and Engineering Shan Dong University 72 Binhai Road Qingdao 266237 China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
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30
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Shen D, Bai Y, Liu Y. Chemical Biology Toolbox to Visualize Protein Aggregation in Live Cells. Chembiochem 2021; 23:e202100443. [PMID: 34613660 DOI: 10.1002/cbic.202100443] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/05/2021] [Indexed: 11/09/2022]
Abstract
Protein misfolding and aggregation is a complex biochemical process and has been associated with numerous human degenerative diseases. Developing novel chemical and biological tools and approaches to visualize aggregated proteins in live cells is in high demand for mechanistic studies, diagnostics, and therapeutics. In this review, we summarize the recent developments in the chemical biology toolbox applied to protein aggregation studies in live cells. These methods exploited fluorescent protein tags, fluorescent chemical tags, and small-molecule probes to visualize the protein-aggregation process, detect proteome stresses, and quantify the protein homeostasis network capacity. Inspired by these seminal works, we have generalized design principles for the development of new detection methods and probes in the future that will illuminate this important biological process.
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Affiliation(s)
- Di Shen
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, P. R. China
| | - Yulong Bai
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, P. R. China
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31
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Wan W, Zeng L, Jin W, Chen X, Shen D, Huang Y, Wang M, Bai Y, Lyu H, Dong X, Gao Z, Wang L, Liu X, Liu Y. A Solvatochromic Fluorescent Probe Reveals Polarity Heterogeneity upon Protein Aggregation in Cells. Angew Chem Int Ed Engl 2021; 60:25865-25871. [PMID: 34562048 DOI: 10.1002/anie.202107943] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/27/2021] [Indexed: 02/02/2023]
Abstract
We report a crystallization-induced emission fluorophore to quantitatively interrogate the polarity of aggregated proteins. This solvatochromic probe, namely "AggRetina" probe, inherently binds to aggregated proteins and exhibits both a polarity-dependent fluorescence emission wavelength shift and a viscosity-dependent fluorescence intensity increase. Regulation of its polarity sensitivity was achieved by extending the conjugation length. Different proteins bear diverse polarity upon aggregation, leading to different resistance to proteolysis. Polarity primarily decreases during protein misfolding but viscosity mainly increases upon the formation of insoluble aggregates. We quantified the polarity of aggregated protein-of-interest in live cells via HaloTag bioorthogonal labeling, revealing polarity heterogeneity within cellular aggregates. The enriched micro-environment details inside misfolded and aggregated proteins may correlate to their bio-chemical properties and pathogenicity.
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Affiliation(s)
- Wang Wan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Lianggang Zeng
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Wenhan Jin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Xinxin Chen
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Di Shen
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Yanan Huang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Mengdie Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Yulong Bai
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Haochen Lyu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Xuepeng Dong
- The Second Hospital of, Dalian Medical University, 467 Zhongshan Road, 116023, China, Dalian
| | - Zhenming Gao
- The Second Hospital of, Dalian Medical University, 467 Zhongshan Road, 116023, China, Dalian
| | - Lei Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Xiaojing Liu
- Institute of Molecular Sciences and Engineering, Shan Dong University, 72 Binhai Road, Qingdao, 266237, China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
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32
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Huang Y, Bai Y, Jin W, Shen D, Lyu H, Zeng L, Wang M, Liu Y. Common Pitfalls and Recommendations for Using a Turbidity Assay to Study Protein Phase Separation. Biochemistry 2021; 60:2447-2456. [PMID: 34369156 DOI: 10.1021/acs.biochem.1c00386] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The turbidity assay is commonly exploited to study protein liquid-to-liquid phase separation (LLPS) or liquid-to-solid phase separation (LSPS) processes in biochemical analyses. Herein, we present common pitfalls of this assay caused by exceeding the detection linear range. We showed that aggregated proteins of high concentration and large particle size can lead to inaccurate quantification in multiple applications, including the optical density measurement, the thermal shift assay, and the dynamic light scattering experiment. Finally, we demonstrated that a simple sample dilution of insoluble aggregated protein (LSPS) samples or direct imaging of liquid droplets (LLPS) can address these issues and improve the accuracy of the turbidity assay.
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Affiliation(s)
- Yanan Huang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Yulong Bai
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenhan Jin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Di Shen
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Haochen Lyu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Lianggang Zeng
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Mengdie Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
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33
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Bai Y, Liu Y. Illuminating Protein Phase Separation: Reviewing Aggregation-Induced Emission, Fluorescent Molecular Rotor and Solvatochromic Fluorophore based Probes. Chemistry 2021; 27:14564-14576. [PMID: 34342071 DOI: 10.1002/chem.202102344] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Indexed: 11/09/2022]
Abstract
Protein phase separation process involving protein unfolding, misfolding, condensation and aggregation etc. has been associated with numerous human degenerative diseases. The complexity in protein conformational transitions results in multi-step and multi-species biochemical pathways upon protein phase separation. Recent progresses in designing novel fluorescent probes have unraveled the enriched details of phase separated proteins and provided mechanistic insights towards disease pathology. In this review, we summarized the design and characterizations of fluorescent probes that selectively illuminate proteins at different phase separated states with a focus on aggregation-induced emission probes, fluorescent molecular rotors, and solvatochromic fluorophores. Inspired by these pioneering works, a design blueprint was proposed to further develop fluorescent probes that can potentially shed light on the unresolved protein phase separated states in the future.
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Affiliation(s)
- Yulong Bai
- Dalian Institute of Chemical Physics, Chemistry, 457 Zhongshan Road, 116023, Dalian, CHINA
| | - Yu Liu
- Chinese Academy of Sciences, Dalian Institute of Chemical Physics, 457 Zhongshan Road, 116023, Dalian, CHINA
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34
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Shen D, Jin W, Bai Y, Huang Y, Lyu H, Zeng L, Wang M, Tang Y, Wan W, Dong X, Gao Z, Piao H, Liu X, Liu Y. Rational Design of Crystallization‐Induced‐Emission Probes To Detect Amorphous Protein Aggregation in Live Cells. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Di Shen
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Wenhan Jin
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Yulong Bai
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Yanan Huang
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Haochen Lyu
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Lianggang Zeng
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Mengdie Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Yuqi Tang
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Wang Wan
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Xuepeng Dong
- The Second Hospital of Dalian Medical University 467 Zhongshan Road Dalian 116044 China
| | - Zhenming Gao
- The Second Hospital of Dalian Medical University 467 Zhongshan Road Dalian 116044 China
| | - Hai‐Long Piao
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Xiaojing Liu
- Institute of Molecular Sciences and Engineering Shan Dong University Jimobinhai Road Qingdao 266237 China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
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35
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Shen D, Jin W, Bai Y, Huang Y, Lyu H, Zeng L, Wang M, Tang Y, Wan W, Dong X, Gao Z, Piao HL, Liu X, Liu Y. Rational Design of Crystallization-Induced-Emission Probes To Detect Amorphous Protein Aggregation in Live Cells. Angew Chem Int Ed Engl 2021; 60:16067-16076. [PMID: 33991044 DOI: 10.1002/anie.202103674] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Indexed: 12/19/2022]
Abstract
Unlike amyloid aggregates, amorphous protein aggregates with no defined structures have been challenging to target and detect in a complex cellular milieu. In this study, we rationally designed sensors of amorphous protein aggregation from aggregation-induced-emission probes (AIEgens). Utilizing dicyanoisophorone as a model AIEgen scaffold, we first sensitized the fluorescence of AIEgens to a nonpolar and viscous environment mimicking the interior of amorphous aggregated proteins. We identified a generally applicable moiety (dimethylaminophenylene) for selective binding and fluorescence enhancement. Regulation of the electron-withdrawing groups tuned the emission wavelength while retaining selective detection. Finally, we utilized the optimized probe to systematically image aggregated proteome upon proteostasis network regulation. Overall, we present a rational approach to develop amorphous protein aggregation sensors from AIEgens with controllable sensitivity, spectral coverage, and cellular performance.
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Affiliation(s)
- Di Shen
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Wenhan Jin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Yulong Bai
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Yanan Huang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Haochen Lyu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Lianggang Zeng
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Mengdie Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Yuqi Tang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Wang Wan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Xuepeng Dong
- The Second Hospital of, Dalian Medical University, 467 Zhongshan Road, Dalian, 116044, China
| | - Zhenming Gao
- The Second Hospital of, Dalian Medical University, 467 Zhongshan Road, Dalian, 116044, China
| | - Hai-Long Piao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Xiaojing Liu
- Institute of Molecular Sciences and Engineering, Shan Dong University, Jimobinhai Road, Qingdao, 266237, China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
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36
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Tang S, Wang W, Zhang X. Direct visualization and profiling of protein misfolding and aggregation in live cells. Curr Opin Chem Biol 2021; 64:116-123. [PMID: 34246835 DOI: 10.1016/j.cbpa.2021.05.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 04/27/2021] [Accepted: 05/09/2021] [Indexed: 10/20/2022]
Abstract
Over the past few years, research tools have been developed to monitor the multistep protein aggregation process in live cells, a process that has been associated with a growing number of human diseases. Herein, we describe recent advances in methods that can either survey the distribution of aggregation at the level of the cellular proteome using mass spectroscopy or discern the multistep aggregation process of specific proteins of interest via fluorescence signals. Future development and application of such technologies are expected to provide insights on mechanisms, diagnosis, and treatment of diseases rooted in protein aggregation.
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Affiliation(s)
- Sicheng Tang
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, United States.
| | - Wenting Wang
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, United States
| | - Xin Zhang
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, United States; Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, United States.
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Abstract
BACKGROUND Precision medicine, space exploration, drug discovery to characterization of dark chemical space of habitats and organisms, metabolomics takes a centre stage in providing answers to diverse biological, biomedical, and environmental questions. With technological advances in mass-spectrometry and spectroscopy platforms that aid in generation of information rich datasets that are complex big-data, data analytics tend to co-evolve to match the pace of analytical instrumentation. Software tools, resources, databases, and solutions help in harnessing the concealed information in the generated data for eventual translational success. AIM OF THE REVIEW In this review, ~ 85 metabolomics software resources, packages, tools, databases, and other utilities that appeared in 2020 are introduced to the research community. KEY SCIENTIFIC CONCEPTS OF REVIEW In Table 1 the computational dependencies and downloadable links of the tools are provided, and the resources are categorized based on their utility. The review aims to keep the community of metabolomics researchers updated with all the resources developed in 2020 at a collated avenue, in line with efforts form 2015 onwards to help them find these at one place for further referencing and use.
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38
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Wan W, Huang Y, Xia Q, Bai Y, Chen Y, Jin W, Wang M, Shen D, Lyu H, Tang Y, Dong X, Gao Z, Zhao Q, Zhang L, Liu Y. Covalent Probes for Aggregated Protein Imaging via Michael Addition. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202015988] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Wang Wan
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Yanan Huang
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Qiuxuan Xia
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Yulong Bai
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Yuwen Chen
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Wenhan Jin
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Mengdie Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Di Shen
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Haochen Lyu
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Yuqi Tang
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Xuepeng Dong
- The Second Hospital of Dalian Medical University 467 Zhongshan Road Dalian 116044 China
| | - Zhenming Gao
- The Second Hospital of Dalian Medical University 467 Zhongshan Road Dalian 116044 China
| | - Qun Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
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39
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Wan W, Huang Y, Xia Q, Bai Y, Chen Y, Jin W, Wang M, Shen D, Lyu H, Tang Y, Dong X, Gao Z, Zhao Q, Zhang L, Liu Y. Covalent Probes for Aggregated Protein Imaging via Michael Addition. Angew Chem Int Ed Engl 2021; 60:11335-11343. [DOI: 10.1002/anie.202015988] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/04/2021] [Indexed: 12/19/2022]
Affiliation(s)
- Wang Wan
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Yanan Huang
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Qiuxuan Xia
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Yulong Bai
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Yuwen Chen
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Wenhan Jin
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Mengdie Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Di Shen
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Haochen Lyu
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Yuqi Tang
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Xuepeng Dong
- The Second Hospital of Dalian Medical University 467 Zhongshan Road Dalian 116044 China
| | - Zhenming Gao
- The Second Hospital of Dalian Medical University 467 Zhongshan Road Dalian 116044 China
| | - Qun Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
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Cingolani M, Mummolo L, Lugli F, Zaffagnini M, Genovese D. Protein aggregation detection with fluorescent macromolecular and nanostructured probes: challenges and opportunities. NEW J CHEM 2021. [DOI: 10.1039/d1nj01606g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Nanoprobes based on various nanomaterials, polymers or AIEgens are overcoming previous limitations for diagnosis and therapy of early-stage protein aggregation.
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Affiliation(s)
- Matteo Cingolani
- Dipartimento di Chimica “Giacomo Ciamician”
- Università di Bologna
- 40126 Bologna
- Italy
| | - Liviana Mummolo
- Dipartimento di Chimica “Giacomo Ciamician”
- Università di Bologna
- 40126 Bologna
- Italy
| | - Francesca Lugli
- Dipartimento di Chimica “Giacomo Ciamician”
- Università di Bologna
- 40126 Bologna
- Italy
| | - Mirko Zaffagnini
- Dipartimento di Farmacia e Biotecnologia
- Università di Bologna
- 40126 Bologna
- Italy
| | - Damiano Genovese
- Dipartimento di Chimica “Giacomo Ciamician”
- Università di Bologna
- 40126 Bologna
- Italy
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