Xin Zhang

Scopus Publications

The endoplasmic reticulum displays high polarity with low protein aggregation in human cells
Xinwei Hu, Junlin Chen, Ping Liu, Huaiyue Zhang, Yu Liu, Xin Zhang, Lei Wang
Communications Biology, 2026
Many physicochemical properties in the cellular milieu are important for cell function and survival. However, the polarity of different subcellular compartments and its role in protein condensate and aggregate formation within cells are less characterized. Here, we develop a method to compare the polarity in different subcellular compartments using the same polarity-sensitive solvatochromic fluorescent probe. Unexpectedly, the endoplasmic reticulum (ER) lumen displays a higher polarity and a more crowded environment than the cytosol in human cells. Polarity-decreasing and crowding-increasing hypertonic conditions induce condensate or aggregate formation of two intrinsically disordered proteins, with-no-lysine kinase 1 and Huntingtin gene (Htt) exon1 with an expanded polyQ stretch (Htt-polyQ), in the cytosol. However, targeting Htt-polyQ to the ER prevents its aggregation, suggesting that polarity but not crowding is more relevant to protein aggregation. Our results reveal the heterogeneity in subcellular polarity and crowding, and uncover previously unrecognized high-polarity in the ER lumen, which provides a unique environment for maintaining robust proteostasis. The endoplasmic reticulum (ER) lumen displays a higher polarity and a more crowded environment than the cytosol in human cells, which provides a unique environment for maintaining robust proteostasis.
Amyloid-ID: photocatalytic profiling of amyloid deposits in Alzheimer’s disease tissue
Huan Feng, Qun Zhao, Fangliang Guo, Jing Yan, Nan Zhao, Junbao Ma, Rui Sun, Kaini Shen, Yusong Ge, Xin Zhang, Lihua Zhang, Yu Liu
Nature Communications, 2026
Deposition of amyloid proteins and their associated interactome is a hallmark of Alzheimer’s disease (AD) and other amyloidosis diseases, with their composition implying disease etiology. However, precise in-situ micro-dissection of amyloid deposits in AD brain tissue remains a challenge. In this work, we first divert the excited state energy of Thioflavin T from singlet fluorescence to triplet photocatalytic amyloid protein labeling through molecular engineering, while maintain its pan-amyloid binding affinity and selectivity. We further demonstrate that the amyloid labeling is catalyzed via type-I radical-based photosensitization with diverse residue modification sites. In female AD mouse brain tissue without homogenization, Amyloid-ID in-situ captures and profiles amyloid deposits, reliably reporting the often-lost tau biomarker. Finally, we provide comparative amyloidomics resources across 3 commonly used AD mouse models, revealing conjunct mitochondrial entangling pattern within amyloid deposits. Overall, we report a photocatalytic proteomics strategy (namely Amyloid-ID) to profile amyloid deposits directly from AD brain tissue. Alzheimer’s disease is characterized by the accumulation of amyloid plaques in the brain. Here, Liu et al. develop a new method, Amyloid-ID, which uses light to label and analyze amyloid deposits in brain tissues, revealing their protein composition and associated molecules.
Discovery of Eosin Y as a photocatalytic labeling sensor to detect, capture and profile amyloid plaques in Alzheimer's disease brain tissue
Fangliang Guo, Huan Feng, Rui Sun, Jing Yan, Yusong Ge, Xiaoqi Liu, Xiaobo Zhang, Xin Zhang, Xiaowen Zhang, Yu Liu
Sensors and Actuators B Chemical, 2026
Distinct RNA Physical Microenvironments Shape Unique Properties and Functions within Biomolecular Condensates
Huan Feng, Yuening Yang, Yulong Bai, Zhili Wu, Yanan Huang, Yifei Pan, Longchen Zhu, Yu Liu, Lu Xiao, Xin Zhang
Journal of the American Chemical Society, 2026
Most of the biomolecular condensates form through multivalent interactions between proteins and RNAs. These multicomponent condensates create specialized physical microenvironments that are critical for cellular regulation. While physical microenvironments of proteins have been recently studied in condensates, the physical microenvironments of RNA remain less understood. Here, we develop a chemical method to quantitatively measure RNA physical microenvironments by integrating RNA-labeling chemistry with environmentally sensitive fluorophores and fluorescence lifetime imaging microscopy. We show that RNAs exhibit distinct micropolarity and microviscosity from proteins while remaining miscible in condensates, in contrast to protein-protein systems that demix upon differing micropolarity. This behavior may be attributed to the formation of transient RNA-protein interactions, whose status is influenced by micropolarity compatibility. We further demonstrate that micropolarity differences between RNAs and proteins correlates to RNA partitioning and selective RNA distribution among condensates. In terms of RNA function, we show that elevated RNA micropolarity is associated with ribozyme catalytic activity. Taken together, these results reveal that RNA physical microenvironments play an active role in shaping RNA organization and function within biomolecular condensates.
Author Correction: Navigating condensate micropolarity to enhance small-molecule drug targeting (Nature Chemical Biology, (2025), 10.1038/s41589-025-02017-9)
Jian Ouyang, Junlin Chen, Zhili Wu, Kaiqiang You, Taoyu Chen, Yi Qin Gao, Pilong Li, Xin Zhang, Tingting Li
Nature Chemical Biology, 2026
Navigating condensate micropolarity to enhance small-molecule drug targeting
Jian Ouyang, Junlin Chen, Zhili Wu, Kaiqiang You, Taoyu Chen, Yi Qin Gao, Pilong Li, Xin Zhang, Tingting Li
Nature Chemical Biology, 2026
Time-Resolved Genetically Encoded Indicators toward Quantitative Imaging of Calcium Dynamics in Living Cells
Zizhu Tan, Yadan Hou, Yanan Huang, Kairan Zhang, Peilong Lu, Xin Zhang
ACS Sensors, 2026
Quantitative imaging of dynamic concentrations of cellular ions and metabolites is fundamental to understanding signaling networks. However, applications of intensity-based biosensors are fundamentally confounded by their dependence on probe concentration and excitation intensity. To address this challenge, we report a class of time-resolved genetically encoded calcium indicators (tr-GECIs)tr-CCaMP, tr-GCaMP, and tr-RCaMP. These sensors convert calcium levels into changes in fluorescence lifetime, a photophysical parameter intrinsically insensitive to variations in probe concentration or excitation light intensity. Our design maintains high brightness in both Ca 2+ -bound and Ca 2+ -free states, enabling robust detection via fluorescence lifetime imaging microscopy (FLIM). Engineering key residues near the chromophore and optimizing linkers yielded broad lifetime dynamic ranges: 2.14 ns for tr-CCaMP, 1.32 ns for tr-GCaMP, and 1.57 ns for tr-RCaMP. The sensors cover complementary Ca 2+ affinity ranges with K d values from 23.8 nM to 416 nM at 37 °C, allowing concentration determination from tens of nanomolars to micromolars. We applied tr-GECIs to map resting Ca 2+ in proximity to multiple organelles and uncovered localized microdomains near organelle membranes, suggesting sites of active Ca 2+ exchange. Unlike ratiometric or FRET sensors, tr-GECIs require only a single optical channel, simplifying multiplexed imaging. This work establishes a generalizable platform for developing lifetime-based biosensors, facilitating quantitative analysis of cellular signaling events with high spatial precision.
Photo-Catalyzed Labeling of Amyloid Deposits in Human Tissue to Proteotype Amyloidosis Diseases
Huan Feng, Fangliang Guo, Yan Wang, Meng You, Qiuxuan Xia, Wang Wan, Di Shen, Kaini Shen, Xin Zhang, Wei Li, Yu Liu
Aggregate, 2026
Over 40 amyloidogenic proteins have been identified to cause amyloidosis diseases in clinics. Tissue deposition of amyloid proteins entangled with interacting partners is a characteristic pathological hallmark of amyloidosis diseases. However, the proteomic complexity of co‐aggregated amyloid deposits poses a clinical challenge to diagnose the exact disease‐causing pathogenic proteins in patients’ biopsied tissue. Herein, we present a photocatalytic proteomic method, named Amyloid‐ID, as a promising approach to identify the composition of amyloid deposits for clinical proteotyping of amyloidosis diseases. Amyloid‐ID is enabled by a photosensitized probe analogous to a pan‐amyloid sensor, Thioflavin T. We show this probe photocatalyzes protein labeling via reactive oxygen species and demonstrate its applicability in both AD mouse models and human laryngeal samples. Next, we exemplify its utility by proteotyping the pathogenic protein underlying the rare laryngeal amyloidosis (LA). Using patients’ biopsied tissue sections, we label, enrich, and profile the amyloid deposits. Proteomics analysis top‐ranks fibrinogen as a potential pathogenic protein. Biochemical and biophysical characterizations confirm that fibrinogen can aggregate into amyloid fibrils. Intriguingly, we observe that fibrinogen's fibrillation is sensitive to mechanical forces, particularly impacted by sonication. Such observation coincides with its primary larynx deposition, where frequent vocal cord friction occurs. Overall, given the photocatalytic properties, our Amyloid‐ID serves as a promising clinical proteotyping method for amyloidosis diseases.
Dexter Energy Transfer Photocatalytic Microdissection of Amyloid Plaques in Alzheimer’s Disease
Rui Sun, Jintai Deng, Di Shen, Jing Yan, Yanan Huang, Huan Feng, Man Li, Yusong Ge, Xin Zhang, Yu Liu
Jacs Au, 2026
Amyloid plaque is a pathological hallmark in Alzheimer's disease (AD) brain with its composition associated with disease etiology. Here, we report a photocatalyst, namely, AmyCAT, that selectively binds to amyloid fibrils in AD brain tissues and undergoes Dexter energy transfer (DET) to catalyze carbene production for amyloid proximity labeling. First, we designed the AmyCAT photocatalyst to universally bind different types of amyloids. Second, we energetically match the DET effect in a 12 × 4 photocatalyst-substrate array to activate the diazo substrate into reactive carbene species by visible green light (530-545 nm). Further, we demonstrate that the optimal AmyCAT probe catalyzes pan-amyloid protein labeling with a 30-fold selectivity over folded counterparts. Mechanistic studies confirm that the photocatalytic labeling is indeed via the DET process, which tailors the proximity effect for spatially confined amyloid labeling. Finally, we employ the AmyCAT photocatalyst to label, enrich, and profile amyloid plaques in AD brain tissues, identifying key proteins and pathways associated with AD pathological deposition and etiology. The small-molecule-based strategy reported herein dispenses with the antibody, genetic modification, or microscopes to dissect and profile amyloid deposits from AD tissues.
Congo Red Derived Covalent Proteotyping Sensor for Amyloid Deposits in Alzheimer’s Disease
Huan Feng, Rui Gao, Fangliang Guo, Wang Wan, Di Shen, Jing Yan, Yusong Ge, Kaini Shen, Xin Zhang, Yu Liu
ACS Sensors, 2026
Congo Red (CR) is the histochemical staining sensor used to diagnose amyloid tissue deposition in current clinical practice. Its characteristic aryl azo linkage is generally considered to be chemically stable. Here, we discovered by serendipity that neutral borate buffer can activate the inert azo bond in CR to covalently modify amyloid proteins at ambient temperature. Such chemistry allowed us to develop a covalent amyloid sensor to image, enrich, and proteotype amyloid deposits in Alzheimer’s disease (AD) tissue. We first pinpointed the boronic acid in borate buffer triggers such amyloid bioconjugation and found that ultraviolet-light-induced azo trans -to- cis isomerization further enhanced labeling efficiency. Leveraging this boron-azo bioconjugation chemistry, we developed a covalent sensor based on CR for selective detection and microdissection of amyloid deposits from AD mouse brain tissues. By incorporating an alkyne handle into the CR scaffold, we enabled click-chemistry-assisted enrichment of amyloid aggregates, followed by proteotyping via LC-MS/MS. The covalent amyloid sensor proteotyped a complex network of protein interactors including the AD biomarkers Tau and ApoE within amyloid deposits. Overall, this work establishes a borate-activated azo-based covalent sensor for selective imaging, dissecting and proteotyping of amyloid deposits in AD tissues.
Cellular water-potential sensing through biomolecular condensation
Yunhe Wang, Longchen Zhu, Yun Yang, Xiaoshuang Li, Xin Zhang, Xiaofeng Fang
Nature, 2026
LipoID profiles lipid droplet interactions and identifies interorganelle regulators
Hengke Guo, Wang Wan, Yanan Huang, Nan Zhao, Ci Wu, Bowen Zhong, Rui Sun, Huan Feng, Jing Yan, Di Shen, Xuepeng Dong, Qun Zhao, Xin Zhang, Lihua Zhang, Yu Liu
Nature Chemical Biology, 2026
A Probe Design Strategy Based on Cholesterol-Induced Differential Cellular Uptake for Cancer Cells Specific Penetration and Imaging
Zhuoran Xia, Tianping Xia, Jie Fei, Jianjun Du, Xin Zhang, Jiangli Fan, Xiaojun Peng
Angewandte Chemie International Edition, 2025
Multiphasic condensates formed with mono-component of tetrapeptides via phase separation
Laicheng Zhou, Longchen Zhu, Cong Wang, Tengyan Xu, Jing Wang, Bin Zhang, Xin Zhang, Huaimin Wang
Nature Communications, 2025
Erratum to: Time-resolved fluorescent proteins expand fluorescent microscopy in temporal and spectral domains (Cell, (2025), (S009286742501027X), 10.1016/j.cell.2025.08.035)
Zizhu Tan, Chia-Heng Hsiung, Jiahui Feng, Yangye Zhang, Yihan Wan, Junlin Chen, Ke Sun, Peilong Lu, Jianyang Zang, Wenxing Yang, Ya Gao, Jiabin Yin, Tong Zhu, Yang Lu, Zijian Pan, Yilong Zou, Can Liao, Xiaosong Li, Yuxuan Ye, Yu Liu, Xin Zhang
Cell, 2025
Time-resolved fluorescent proteins expand fluorescent microscopy in temporal and spectral domains
Zizhu Tan, Chia-Heng Hsiung, Jiahui Feng, Yangye Zhang, Yihan Wan, Junlin Chen, Ke Sun, Peilong Lu, Jianyang Zang, Wenxing Yang, Ya Gao, Jiabin Yin, Tong Zhu, Yang Lu, Zijian Pan, Yilong Zou, Can Liao, Xiaosong Li, Yuxuan Ye, Yu Liu, Xin Zhang
Cell, 2025
Investigating the interplay between iron-mediated protein aggregation and mitochondrial damage using polarity-sensitive fluorescent lifetime probes
Jia Zhai, Man Zhang, Ziyue Chen, Jiabao Fang, Minzi Ju, Baoxing Shen, Xin Zhang
Sensors and Actuators B Chemical, 2025
Purinosomes and lysosomes interact to maintain the purine pools
Yubing Liu, Vidhi Pareek, Dipankar Bhowmik, Xin Zhang, Stephen J. Benkovic
International Journal of Biochemistry and Cell Biology, 2025
Smart fluorogenic tools: From designing principles to visualization of multistep protein aggregation
Jingyang Wan, Chenyang Huang, Ziyue Chen, Jiarui Wan, Wenjing Ding, Dandan Liu, Liang Feng, Yue Meng, Menghan Li, Minzi Ju, Xin Zhang, Baoxing Shen, He Huang
Coordination Chemistry Reviews, 2025
Small Molecules Influence the Physical Microenvironment of Biomolecular Condensates
Yifei Pan, Junlin Lei, Shiqi Mou, Zhili Wu, Longchen Zhu, Liyao Zeng, Feng Luo, Yaping Ding, Yu Liu, Xin Zhang
Journal of the American Chemical Society, 2025
Endoplasmic Reticulum Stress Induces Liquid-Liquid Phase Separation of GRP78 and Modulates Protein Aggregation Dynamics
Jiaqi Li, Xiangyu Zi, Jiabao Fang, Min Liang, Minzi Ju, Zhenglong Sun, Baoxing Shen, Xin Zhang
ACS Sensors, 2025
Exploring Endoplasmic Reticulum Dysfunction on Protein Phase Separation Using Viscosity-Sensitive Fluorescent Lifetime Probe
Yu Wei, Xiangyu Zi, Jia Zhai, Man Zhang, Jiaqi Li, Zhenglong Sun, Minzi Ju, Xin Zhang, Baoxing Shen
Analytical Chemistry, 2025
Chemical Control of Fluorescence Lifetime of Molecular Rotors Provides Insights into Subcellular Viscosities during Ferroptosis
Jianan Dai, Chia-Heng Hsiung, Lina Ding, Shiqi Mou, Yang Lu, Yuqi Wang, Baoxing Shen, Yilong Zou, Jiangli Fan, Xin Zhang
Analytical Chemistry, 2025
1000 fold Ultra-Photosensitized Fluorescent Protein Mimics Toward Photocatalytic Proximity Labeling and Proteomic Profiling Functions
Rui Sun, Yanan Huang, Huan Feng, Nan Zhao, Wang Wan, Di Shen, Bowen Zhong, Yukui Zhang, Xin Zhang, Qun Zhao, Lihua Zhang, Yu Liu
Advanced Science, 2025
A Solvatochromic and Photosensitized Lipid Droplet Probe Detects Local Polarity Heterogeneity and Labels Interacting Proteins in Human Liver Disease Tissue
Yuhui Wang, Hengke Guo, Wang Wan, Biao Jing, Yulong Bai, Jialu Sun, Xin Zhang, Zhenming Gao, Yu Liu, Xuepeng Dong
Advanced Healthcare Materials, 2025
Mimicking fluorophores from nature to generate artificial fluorescent proteins and biosensors: Fluorescent proteins
Chia-Heng Hsiung, Xin Zhang
Nature Chemistry, 2024
Live-cell visualization of tau aggregation in human neurons
Bryan Hurtle, Christopher J. Donnelly, Xin Zhang, Amantha Thathiah
Communications Biology, 2024
Unveiling intracellular phase separation: advances in optical imaging of biomolecular condensates
Yinfeng Guo, Xin Zhang
Trends in Biochemical Sciences, 2024
Tailoring the pKa of Fluorescence Lifetime Imaging Probes to Visualize Aggrephagy and Resolve Its Microenvironmental Viscosity
Yu Wei, Xiaochen Gao, Jiabao Fang, Yu Xiao, Jiachen Liu, Yu Liu, Xin Zhang, Baoxing Shen
Analytical Chemistry, 2024
Biomolecular condensates and disease pathogenesis
Ke Ruan, Ge Bai, Yanshan Fang, Dan Li, Tingting Li, Xingguo Liu, Boxun Lu, Qing Lu, Zhou Songyang, Shuguo Sun, Zheng Wang, Xin Zhang, Wen Zhou, Hong Zhang
Science China Life Sciences, 2024
Chemical Control of Fluorescence Lifetime towards Multiplexing Imaging
Junbao Ma, Feng Luo, Chia‐Heng Hsiung, Jianan Dai, Zizhu Tan, Songtao Ye, Lina Ding, Baoxing Shen, Xin Zhang
Angewandte Chemie International Edition, 2024
Ionic Effect on the Microenvironment of Biomolecular Condensates
Longchen Zhu, Yifei Pan, Ziyi Hua, Yu Liu, Xin Zhang
Journal of the American Chemical Society, 2024
A Cell-Permeable Photosensitizer for Selective Proximity Labeling and Crosslinking of Aggregated Proteome
Huan Feng, Qun Zhao, Nan Zhao, Zhen Liang, Yanan Huang, Xin Zhang, Lihua Zhang, Yu Liu
Advanced Science, 2024
NRhFluors: Quantitative Revealing the Interaction between Protein Homeostasis and Mitochondria Dysfunction via Fluorescence Lifetime Imaging
Yubo Huang, Meiyi Chang, Xiaochen Gao, Jiabao Fang, Wenjing Ding, Jiachen Liu, Baoxing Shen, Xin Zhang
ACS Central Science, 2024
High-Fidelity Assay Based on Turn-Off Fluorescence to Detect the Perturbations of Cellular Proteostasis
Conner Hoelzel, Yulong Bai, Mengdie Wang, Yu Liu, Xin Zhang
ACS Bio and Med Chem Au, 2024
Micropolarity governs the structural organization of biomolecular condensates
Songtao Ye, Andrew P. Latham, Yuqi Tang, Chia-Heng Hsiung, Junlin Chen, Feng Luo, Yu Liu, Bin Zhang, Xin Zhang
Nature Chemical Biology, 2024
Detecting protein−protein interaction during liquid−liquid phase separation using fluorogenic protein sensors
Yanan Huang, Junlin Chen, Chia-Heng Hsiung, Yulong Bai, Zizhu Tan, Songtao Ye, Xin Zhang
Molecular Biology of the Cell, 2024
Design and Application of Fluorescent Probes to Detect Cellular Physical Microenvironments
Junbao Ma, Rui Sun, Kaifu Xia, Qiuxuan Xia, Yu Liu, Xin Zhang
Chemical Reviews, 2024
Seeing Is Believing: Advances in Biological Imaging
Xin Zhang, Squire J. Booker
ACS Bio and Med Chem Au, 2024
Installing hydrogen bonds as a general strategy to control viscosity sensitivity of molecular rotor fluorophores: Special Collection: Aggregation-Induced Processes and Functions
Baoxing Shen, Lihua Liu, Yubo Huang, Jichun Wu, Huan Feng, Yu Liu, He Huang, Xin Zhang
Aggregate, 2024
Measuring Solvent Exchange in Silica Nanoparticles with Rotor-Based Fluorophore
Xuejun Cheng, Yingming Pu, Songtao Ye, Xiao Xiao, Xin Zhang, Hongyu Chen
Advanced Materials, 2024
Regulation of micro- and small-exon retention and other splicing processes by GRP20 for flower development
Jun Wang, Xinwei Ma, Yi Hu, Guanhua Feng, Chunce Guo, Xin Zhang, Hong Ma
Nature Plants, 2024
Chemical Regulation of Fluorescence Lifetime
Jianan Dai, Xin Zhang
Chemical and Biomedical Imaging, 2023
Navigating the terrain of protein aggregation and phase separation - A chemical biology perspective
Cong Liu, Xin Zhang
Current Opinion in Chemical Biology, 2023
Advanced Techniques for Detecting Protein Misfolding and Aggregation in Cellular Environments
Yulong Bai, Shengnan Zhang, Hui Dong, Yu Liu, Cong Liu, Xin Zhang
Chemical Reviews, 2023
Aggregation-Induced Emission (AIE), Life and Health
Haoran Wang, Qiyao Li, Parvej Alam, Haotian Bai, Vandana Bhalla, Martin R. Bryce, Mingyue Cao, Chao Chen, Sijie Chen, Xirui Chen, Yuncong Chen, Zhijun Chen, Dongfeng Dang, Dan Ding, Siyang Ding, Yanhong Duo, Meng Gao, Wei He, Xuewen He, Xuechuan Hong, Yuning Hong, Jing-Jing Hu, Rong Hu, Xiaolin Huang, Tony D. James, Xingyu Jiang, Gen-ichi Konishi, Ryan T. K. Kwok, Jacky W. Y. Lam, Chunbin Li, Haidong Li, Kai Li, Nan Li, Wei-Jian Li, Ying Li, Xing-Jie Liang, Yongye Liang, Bin Liu, Guozhen Liu, Xingang Liu, Xiaoding Lou, Xin-Yue Lou, Liang Luo, Paul R. McGonigal, Zong-Wan Mao, Guangle Niu, Tze Cin Owyong, Andrea Pucci, Jun Qian, Anjun Qin, Zijie Qiu, Andrey L. Rogach, Bo Situ, Kazuo Tanaka, Youhong Tang, Bingnan Wang, Dong Wang, Jianguo Wang, Wei Wang, Wen-Xiong Wang, Wen-Jin Wang, Xinyuan Wang, Yi-Feng Wang, Shuizhu Wu, Yifan Wu, Yonghua Xiong, Ruohan Xu, Chenxu Yan, Saisai Yan, Hai-Bo Yang, Lin-Lin Yang, Mingwang Yang, Ying-Wei Yang, Juyoung Yoon, Shuang-Quan Zang, Jiangjiang Zhang, Pengfei Zhang, Tianfu Zhang, Xin Zhang, Xin Zhang, Na Zhao, Zheng Zhao, Jie Zheng, Lei Zheng, Zheng Zheng, Ming-Qiang Zhu, Wei-Hong Zhu, Hang Zou, Ben Zhong Tang
ACS Nano, 2023
Protein amyloid aggregate: Structure and function
Qianhui Xu, Yeyang Ma, Yunpeng Sun, Dan Li, Xin Zhang, Cong Liu
Aggregate, 2023
A dual-functional BODIPY-based molecular rotor probe reveals different viscosity of protein aggregates in live cells
Baoxing Shen, Kwan Ho Jung, Songtao Ye, Conner A. Hoelzel, Charles H. Wolstenholme, He Huang, Yu Liu, Xin Zhang
Aggregate, 2023
Developing an Affinity-Based Chemical Proteomics Method to In Situ Capture Amorphous Aggregated Proteome and Profile Its Heterogeneity in Stressed Cells
Di Shen, Qun Zhao, Mengdie Wang, Bowen Zhong, Wenhan Jin, Yanan Huang, Hao Jin, Biao Jing, Wang Wan, Xin Zhang, Lihua Zhang, Yu Liu
Analytical Chemistry, 2023
Tailoring the positive and negative solvatochromism for chalcone analogues to detect heterozygous protein co-aggregation
Bai Yulong, Wan Wang, Huang Yanan, Wu Jichun, Liu Lihua, Jing Biao, Chen Junlin, Zhang Xin, Liu Yu
Chemical Communications, 2023
Identification of a novel transthyretin mutation D39Y in a cardiac amyloidosis patient and its biochemical characterizations
Qunchao Ma, Mengdie Wang, Yanan Huang, Ying Nie, Xin Zhang, Dan Dan Yang, Zhuo Wang, Siyin Ding, Ningjing Qian, Yu Liu, Xiaohong Pan
Frontiers in Cardiovascular Medicine, 2023
Enabling Photo-Crosslinking and Photo-Sensitizing Properties for Synthetic Fluorescent Protein Chromophores
Huan Feng, Qun Zhao, Beirong Zhang, Hang Hu, Meng Liu, Kaifeng Wu, Xiaosong Li, Xin Zhang, Lihua Zhang, Yu Liu
Angewandte Chemie International Edition, 2023
Biochemical and biophysical properties of an unreported T96R mutation causing transthyretin cardiac amyloidosis
Meng Jiang, Mengdie Wang, Zhengyu Tao, Yezi Chai, Qiming Liu, Qifan Lu, Qizhen Wu, Xiaoying Ying, Yanan Huang, Ying Nie, Yuqi Tang, Xin Zhang, Yu Liu, Jun Pu
Amyloid, 2023
In situ monitoring of protein aggregation via clusteroluminescence
Zhiming Zhang, Longchen Zhu, Jiahui Feng, Haoke Zhang, Xin Zhang, Jing Zhi Sun, Ben Zhong Tang
Materials Chemistry Frontiers, 2022
Fluorogenic toolbox for visualizing protein aggregation: From designing principles to biological application
Lihua Liu, Yubo Huang, Yufeng Zhou, Yu Zhao, Jinzhi Qi, Xin Zhang, Baoxing Shen
Trac Trends in Analytical Chemistry, 2022
Stress-induced protein disaggregation in the endoplasmic reticulum catalysed by BiP
Eduardo Pinho Melo, Tasuku Konno, Ilaria Farace, Mosab Ali Awadelkareem, Lise R. Skov, Fernando Teodoro, Teresa P. Sancho, Adrienne W. Paton, James C. Paton, Matthew Fares, Pedro M. R. Paulo, Xin Zhang, Edward Avezov
Nature Communications, 2022
Xanthone-based solvatochromic fluorophores for quantifying micropolarity of protein aggregates
Lushun Wang, Chia-Heng Hsiung, Xiaojing Liu, Shichao Wang, Axel Loredo, Xin Zhang, Han Xiao
Chemical Science, 2022
Visualizing the Multistep Process of Protein Aggregation in Live Cells
Songtao Ye, Chia-Heng Hsiung, Yuqi Tang, Xin Zhang
Accounts of Chemical Research, 2022
Four-dimensional nuclear speckle phase separation dynamics regulate proteostasis
William Dion, Heather Ballance, Jane Lee, Yinghong Pan, Saad Irfan, Casey Edwards, Michelle Sun, Jing Zhang, Xin Zhang, Silvia Liu, Bokai Zhu
Science Advances, 2022
Direct visualization and profiling of protein misfolding and aggregation in live cells
Sicheng Tang, Wenting Wang, Xin Zhang
Current Opinion in Chemical Biology, 2021
Generation of pancreatic progenitors from human pluripotent stem cells by small molecules
Yuqian Jiang, Chuanxin Chen, Lauren N. Randolph, Songtao Ye, Xin Zhang, Xiaoping Bao, Xiaojun Lance Lian
Stem Cell Reports, 2021
When aggregation-induced emission meets protein aggregates
Sicheng Tang, Songtao Ye, Xin Zhang
National Science Review, 2021
N-terminal Domain of TDP43 Enhances Liquid-Liquid Phase Separation of Globular Proteins
G. Campbell Carter, Chia-Heng Hsiung, Leman Simpson, Haopeng Yang, Xin Zhang
Journal of Molecular Biology, 2021
A General Strategy to Control Viscosity Sensitivity of Molecular Rotor-Based Fluorophores
S. Ye, H. Zhang, Jinyu Fei, Charles H Wolstenholme, X. Zhang
Angewandte Chemie International Edition, 2021
AggFluor: Fluorogenic Toolbox Enables Direct Visualization of the Multi-Step Protein Aggregation Process in Live Cells
Charles H. Wolstenholme, Hang Hu, Songtao Ye, Brian E. Funk, Divya Jain, Chia-Heng Hsiung, Gang Ning, Yu Liu, Xiaosong Li, Xin Zhang
Journal of the American Chemical Society, 2020
Visualizing and Manipulating Biological Processes by Using HaloTag and SNAP-Tag Technologies
Conner A. Hoelzel, Xin Zhang
Chembiochem, 2020
A General Strategy to Enhance Donor-Acceptor Molecules Using Solvent-Excluding Substituents
X. Zhang, Conner A Hoelzel, Hang Hu, Charles H Wolstenholme, Basel A Karim, Kyle T. Munson, Kwan Ho Jung, Y. Liu, H. Yennawar, J. Asbury, X. Li
Angewandte Chemie International Edition, 2020
Fluorogenic detection of protein aggregates in live cells using the AggTag method
Kwan Ho Jung, Xin Zhang
Methods in Enzymology, 2020
Super-Resolution Optical Lithography with DNA
Shi Ho Kim, Yu Liu, Conner Hoelzel, Xin Zhang, Tae-Hee Lee
Nano Letters, 2019
A Fluorogenic AggTag Method Based on Halo- and SNAP-Tags to Simultaneously Detect Aggregation of Two Proteins in Live Cells
Kwan Ho Jung, Sojung F. Kim, Yu Liu, Xin Zhang
Chembiochem, 2019
Quantification of Cellular Proteostasis in Live Cells by Fluorogenic Assay Using the AgHalo Sensor
Matthew Fares, X. Zhang
Current Protocols in Chemical Biology, 2019
Monitoring proteome stress in live cells using halotag-based fluorogenic sensor
Yu Liu, Matthew Fares, Xin Zhang
Methods in Molecular Biology, 2019
A SNAP-tag fluorogenic probe mimicking the chromophore of the red fluorescent protein Kaede
Kwan Ho Jung, Matthew Fares, Leeann S Grainger, Charles H Wolstenholme, Anna Hou, Y. Liu, X. Zhang
Organic and Biomolecular Chemistry, 2019
A HaloTag-Based Multicolor Fluorogenic Sensor Visualizes and Quantifies Proteome Stress in Live Cells Using Solvatochromic and Molecular Rotor-Based Fluorophores
Yu Liu, Kun Miao, Yinghao Li, Matthew Fares, Shuyuan Chen, Xin Zhang
Biochemistry, 2018
Inverted solvatochromic Stokes shift in GFP-like chromophores with extended conjugation
Hang Hu, Charles H Wolstenholme, Xin Zhang, X. Li
Chinese Journal of Chemical Physics, 2018
NMR Measurements Reveal the Structural Basis of Transthyretin Destabilization by Pathogenic Mutations
Benjamin I. Leach, Xin Zhang, Jeffery W. Kelly, H. Jane Dyson, Peter E. Wright
Biochemistry, 2018
Modulation of Fluorescent Protein Chromophores to Detect Protein Aggregation with Turn-On Fluorescence
Yu Liu, Charles H. Wolstenholme, Gregory C. Carter, Hongbin Liu, Hang Hu, Leeann S. Grainger, Kun Miao, Matthew Fares, Conner A. Hoelzel, Hemant P. Yennawar, Gang Ning, Manyu Du, Lu Bai, Xiaosong Li, Xin Zhang
Journal of the American Chemical Society, 2018
Role of HSP90 in the Regulation of de Novo Purine Biosynthesis
Anthony M. Pedley, Georgios I. Karras, Xin Zhang, Susan Lindquist, Stephen J. Benkovic
Biochemistry, 2018
Carbon nitride nanothread crystals derived from pyridine
Xiang Li, Tao Wang, Pu Duan, Maria Baldini, Haw-Tyng Huang, Bo Chen, Stephen J. Juhl, Daniel Koeplinger, Vincent H. Crespi, Klaus Schmidt-Rohr, Roald Hoffmann, Nasim Alem, Malcolm Guthrie, Xin Zhang, John V. Badding
Journal of the American Chemical Society, 2018
Heat Shock Protein Reports on Proteome Stress
Yu Liu, Xin Zhang
Biotechnology Journal, 2018
A Molecular Rotor-Based Halo-Tag Ligand Enables a Fluorogenic Proteome Stress Sensor to Detect Protein Misfolding in Mildly Stressed Proteome
Matthew Fares, Yinghao Li, Yu Liu, Kun Miao, Zi Gao, Yufeng Zhai, Xin Zhang
Bioconjugate Chemistry, 2018
AgHalo: A Facile Fluorogenic Sensor to Detect Drug-Induced Proteome Stress
Yu Liu, Matthew Fares, Noah P. Dunham, Zi Gao, Kun Miao, Xueyuan Jiang, Samuel S. Bollinger, Amie K. Boal, Xin Zhang
Angewandte Chemie International Edition, 2017
The Cation−π Interaction Enables a Halo-Tag Fluorogenic Probe for Fast No-Wash Live Cell Imaging and Gel-Free Protein Quantification
Yu Liu, Kun Miao, Noah P. Dunham, Hongbin Liu, Matthew Fares, Amie K. Boal, Xiaosong Li, Xin Zhang
Biochemistry, 2017
Fluorescence Turn-On Folding Sensor to Monitor Proteome Stress in Live Cells
Yu Liu, Xin Zhang, Wentao Chen, Yun Lei Tan, Jeffery W. Kelly
Journal of the American Chemical Society, 2015
Individual and collective contributions of chaperoning and degradation to protein homeostasis in E. coli
Younhee Cho, Xin Zhang, Kristine Faye R. Pobre, Yu Liu, David L. Powers, Jeffery W. Kelly, Lila M. Gierasch, Evan T. Powers
Cell Reports, 2015
De Novo-designed enzymes as small-molecule-regulated fluorescence imaging tags and fluorescent reporters
Yu Liu, Xin Zhang, Yun Lei Tan, Gira Bhabha, Damian C. Ekiert, Yakov Kipnis, Sinisa Bjelic, David Baker, Jeffery W. Kelly
Journal of the American Chemical Society, 2014
Heat-shock response transcriptional program enables high-yield and high-quality recombinant protein production in Escherichia coli
Xin Zhang, Yu Liu, Joseph C. Genereux, Chandler Nolan, Meha Singh, Jeffery W. Kelly
ACS Chemical Biology, 2014
Chaperonins resculpt folding free energy landscapes to avoid kinetic traps and accelerate protein folding
Xin Zhang, Jeffery W. Kelly
Journal of Molecular Biology, 2014
Small molecule probes to quantify the functional fraction of a specific protein in a cell with minimal folding equilibrium shifts
Y. Liu, Y. L. Tan, X. Zhang, G. Bhabha, D. C. Ekiert, J. C. Genereux, Y. Cho, Y. Kipnis, S. Bjelic, D. Baker, J. W. Kelly
Proceedings of the National Academy of Sciences of the United States of America, 2014
Fidelity of cotranslational protein targeting by the signal recognition particle
Xin Zhang, Shu-ou Shan
Annual Review of Biophysics, 2014
Preface
Advances in Experimental Medicine and Biology, 2014
Mechanisms of transthyretin inhibition of β-amyloid aggregation in vitro
X. Li, X. Zhang, A. R. A. Ladiwala, D. Du, J. K. Yadav, P. M. Tessier, P. E. Wright, J. W. Kelly, J. N. Buxbaum
Journal of Neuroscience, 2013
Bio-inspired protein-gold nanoconstruct with core-void-shell structure: Beyond a chemo drug carrier
Xiangyou Liu, Wei Wei, Shijiao Huang, Shrong-Shi Lin, Xin Zhang, Chuanmao Zhang, Yuguang Du, Guanghui Ma, Mei Li, Stephen Mann, Ding Ma
Journal of Materials Chemistry B, 2013
Signal recognition particle: An essential protein-targeting machine
David Akopian, Kuang Shen, Xin Zhang, Shu-ou Shan
Annual Review of Biochemistry, 2013
Structural basis of signal sequence surveillance and selection by the SRP-FtsY complex
Ottilie von Loeffelholz, Kèvin Knoops, Aileen Ariosa, Xin Zhang, Manikandan Karuppasamy, et al.
Nature Structural and Molecular Biology, 2013
Apoferritin-ceo2 nano-truffle that has excellent artificial redox enzyme activity
Xiangyou Liu, Wei Wei, Quan Yuan, Xin Zhang, Ning Li, et al.
Chemical Communications, 2012
Molecular dynamics simulations reveal structural coordination of Ffh-FtsY heterodimer toward GTPase activation
Ming‐Jun Yang, Xin Zhang
Proteins Structure Function and Bioinformatics, 2011
Synergistic actions between the SRP RNA and translating ribosome allow efficient delivery of the correct cargos during cotranslational protein targeting KUANG
Kuang Shen, Xin Zhang, Shu-ou Shan
RNA, 2011
Direct visualization reveals dynamics of a transient intermediate during protein assembly
Xin Zhang, Vinh Q. Lam, Yun Mou, Tetsunari Kimura, Jaeyoon Chung, et al.
Proceedings of the National Academy of Sciences of the United States of America, 2011
Molecular dynamics simulation reveals preorganization of the chloroplast FtsY towards complex formation induced by GTP binding
Ming-Jun Yang, Xue-Qin Pang, Xin Zhang, Ke-Li Han
Journal of Structural Biology, 2011
Molecular dynamics simulation of SRP GTPases: Towards an understanding of the complex formation from equilibrium fluctuations
Mingjun Yang, Xin Zhang, Keli Han
Proteins Structure Function and Bioinformatics, 2010
Sequential checkpoints govern substrate selection during cotranslational protein targeting
X. Zhang, R. Rashid, K. Wang, S. o. Shan
Science, 2010
Signal recognition particle (SRP) and SRP receptor: A new paradigm for multistate regulatory GTPases
Shu-ou Shan, Sandra L. Schmid, Xin Zhang
Biochemistry, 2009
Determination of the structure form of the fourth ligand of zinc in acutolysin a using combined quantum mechanical and molecular mechanical simulation
Emilia L. Wu, Kin-Yiu Wong, Xin Zhang, Keli Han, Jiali Gao
Journal of Physical Chemistry B, 2009
Multiple conformational switches in a GTPase complex control co-translational protein targeting
Xin Zhang, Christiane Schaffitzel, Nenad Ban, Shu-ou Shan
Proceedings of the National Academy of Sciences of the United States of America, 2009
Demonstration of a Multistep Mechanism for Assembly of the SRP·SRP Receptor Complex: Implications for the Catalytic Role of SRP RNA
Xin Zhang, Simon Kung, Shu-ou Shan
Journal of Molecular Biology, 2008
High-order symplectic integration in quasi-classical trajectory simulation: Case study for O( 1D) + H 2
Xin Zhang, Ke‐Li Han
International Journal of Quantum Chemistry, 2006
First principles quantum dynamics study reveals subtle resonance in polyatomic reaction: The case of F + CH4 → HF + CH3
Tianshu Chu, Xin Zhang, Liping Ju, Li Yao, Ke-Li Han, et al.
Chemical Physics Letters, 2006
Ab initio study of the H + ClONO2 reaction
Xiaofang Chen, Xin Zhang, Keli Han, António J.C. Varandas
Chemical Physics Letters, 2006
Theoretical study of the mechanism for spin-forbidden quenching process O(1D) + CO2(1Σg+) → O(3P) + CO2(1Σg +)
Guanghui Yang, Li Yao, Xin Zhang, Qingtian Meng, Ke‐Li Han
International Journal of Quantum Chemistry, 2005
A modified potential energy surface for the C2H + H2 → C2H2 + H reaction and a theoretical study on its rate constants
Li-Ping Ju, Ting-Xian Xie, Xin Zhang, Ke-Li Han
Chemical Physics Letters, 2005
A quantum wave-packet study of intersystem crossing effects in the O (P 2,1,0 3, D21) + H2 reaction
Tian-Shu Chu, Xin Zhang, Ke-Li Han
Journal of Chemical Physics, 2005
Theoretical study on analytical potential function and spectroscopic parameters for CaF molecule
Chuan-Lu Yang, Xin Zhang, Ke-Li Han
Journal of Molecular Structure THEOCHEM, 2004
Analytical potential energy function and spectroscopic parameters for the ground and excited states of NaH
Chuan-Lu Yang, Xin Zhang, Ke-Li Han
Journal of Molecular Structure THEOCHEM, 2004
Ab initio geometries, electronic structures of MgB2 molecule
Chuan-Lu Yang, Xin Zhang, Ke-Li Han
Journal of Molecular Structure THEOCHEM, 2004
Theoretical Study on the Formation Mechanism of Iso-CH2I-Cl
Guanghui Yang, Qingtian Meng, Xin Zhang, Keli Han
International Journal of Quantum Chemistry, 2004
Quantum dynamics study of isotope effect for H+CH4 reaction using the SVRT model
Xin Zhang, Guang-Hui Yang, Ke-Li Han, M. L. Wang, John Z. H. Zhang
Journal of Chemical Physics, 2003
MRCI potential curve and analytical potential energy function of the ground state of H2
Chuan-Lu Yang, Yu-Jun Huang, Xin Zhang, Ke-Li Han
Journal of Molecular Structure THEOCHEM, 2003
SVRT calculation for bond-selective reaction H+HOD→H2+OD, HD+OH
Xin Zhang, KeLi Han, John Z. H. Zhang
Journal of Chemical Physics, 2002

Xin Zhang

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