Xiaokun Shu

Zhejiang University

Author Statistics

Papers

Citation

H-Index

i-10 index

Research Trends

Author Order

Document Type

Co-Authors

Roger Y. Tsien

University of California, San Diego

Chan-I Chung

University of California, San Francisco

Junjiao Yang

Huazhong Agricultural University

Tsz‐Leung To

Massachusetts General Hospital

Mark H. Ellisman

University of California, San Diego

Antoine Royant

Institut de Biologie Structurale

Varda Lev-Ram

University of California, San Diego

Céline Lafaye

University of Lausanne

Thomas J. Deerinck

University of California, San Diego

S. James Remington

University of Oregon

Cooperative Institutions

University of California, San Francisco

101

University of California, San Diego

Howard Hughes Medical Institute

Zhejiang University

Stanford University

Chinese Academy of Sciences

Harvard University

University of Oregon

University of California, Berkeley

Centre National de la Recherche Scientifique

Author Statistics

Papers

Citation

H-Index

i-10 index

Research Field

YAP charge patterning mediates signal integration through transcriptional co-condensates

Orion D. Weiner Kirstin Meyer Klaus Yserentant Rasmi Cheloor-Kovilakam Kiersten M. Ruff

Abstract Transcription factor dynamics are used to selectively engage gene regulatory programs. Biomolecular condensates have emerged as an attractive signaling module in this process, but the underlying mechanisms are not well-understood. Here, we probed the molecular basis of YAP signal integration through transcriptional condensates. Leveraging light-sheet single-molecule imaging and synthetic condensates, we demonstrate charge-mediated co-condensation of the transcriptional regulators YAP and Mediator into transcriptionally active condensates in stem cells. IDR sequence analysis and YAP protein engineering demonstrate that the signaling specificity of YAP is established, in part, through complementary electrostatic interactions between negatively charged blocks within YAP and positively charged blocks within Mediator. YAP/Mediator co-condensation is counteracted by negative feedback from transcription, driving an adaptive transcriptional response that is well-suited for decoding dynamic inputs. Our work reveals a molecular framework for YAP condensate formation and sheds new light on the function of YAP condensates for emergent gene regulatory behavior.

SIGNAL (programming language)

10.21203/rs.3.rs-5228191/v1

Cite

Citations (0)

Enhancing Intracellular Accumulation and Target Engagement of PROTACs with Reversible Covalent Chemistry

bioRxiv (Cold Spring Harbor Laboratory) (2019)

Wenhao Guo Xiaoli Qi Xin Yu Yang Liu Chan-I Chung

Abstract Current efforts in the proteolysis targeting chimera (PROTAC) field mostly focus on choosing an appropriate E3 ligase for the target protein, improving the binding affinities towards the target protein and the E3 ligase, and optimizing the PROTAC linker. However, due to the large molecular weights of PROTACs, their cellular uptake remains an issue. Through comparing how different warhead chemistry, reversible noncovalent (RNC), reversible covalent (RC), and irreversible covalent (IRC) binders, affects the degradation of Bruton’s Tyrosine Kinase (BTK), we serendipitously discover that cyano-acrylamide-based reversible covalent chemistry can significantly enhance the intracellular accumulation and target engagement of PROTACs and develop RC-1 as a reversible covalent BTK PROTAC with a high target occupancy as its corresponding kinase inhibitor and effectiveness as a dual functional inhibitor and degrader, a different mechanism-of-action for PROTACs. Importantly, this reversible covalent strategy is generalizable to improve other PROTACs, opening a path to enhance PROTAC efficacy.

Linker

Target protein

10.1101/2019.12.30.873588

Cite

Citations (7)

Author Correction: MYC phase separation selectively modulates the transcriptome

Nature Structural & Molecular Biology (2024)

Junjiao Yang Chan-I Chung Jessica Koach Hongjiang Liu Ambuja Navalkar

During the final steps of figure preparation, a conversion error was introduced in Fig.

10.1038/s41594-024-01351-1

Cite

Citations (1)

A Genetically Encoded Tag for Correlated Light and Electron Microscopy of Intact Cells, Tissues, and Organisms

PLoS Biology (2011)

Xiaokun Shu Varda Lev-Ram Thomas J. Deerinck Yingchuan Qi Ericka B. Ramko

Electron microscopy (EM) achieves the highest spatial resolution in protein localization, but specific protein EM labeling has lacked generally applicable genetically encoded tags for in situ visualization in cells and tissues. Here we introduce "miniSOG" (for mini Singlet Oxygen Generator), a fluorescent flavoprotein engineered from Arabidopsis phototropin 2. MiniSOG contains 106 amino acids, less than half the size of Green Fluorescent Protein. Illumination of miniSOG generates sufficient singlet oxygen to locally catalyze the polymerization of diaminobenzidine into an osmiophilic reaction product resolvable by EM. MiniSOG fusions to many well-characterized proteins localize correctly in mammalian cells, intact nematodes, and rodents, enabling correlated fluorescence and EM from large volumes of tissue after strong aldehyde fixation, without the need for exogenous ligands, probes, or destructive permeabilizing detergents. MiniSOG permits high quality ultrastructural preservation and 3-dimensional protein localization via electron tomography or serial section block face scanning electron microscopy. EM shows that miniSOG-tagged SynCAM1 is presynaptic in cultured cortical neurons, whereas miniSOG-tagged SynCAM2 is postsynaptic in culture and in intact mice. Thus SynCAM1 and SynCAM2 could be heterophilic partners. MiniSOG may do for EM what Green Fluorescent Protein did for fluorescence microscopy.

Yellow fluorescent protein

Protein tag

10.1371/journal.pbio.1001041

Cite

Citations (811)

Structure of Infrared Fluorescent Protein IFP2.0

Céline Lafaye Dehuan Yu Marjolaine Noirclerc‐Savoye Xiaokun Shu Antoine Royant

Fluorescent protein

10.2210/pdb4cqh/pdb

Cite

Citations (0)

A rapid fluorogenic GPCR–β‐arrestin interaction assay

Protein Science (2018)

Qiang Zhang Yaowu Zheng Shaun R. Coughlin Xiaokun Shu

Detection of protein-protein interactions involved in signal transduction in live cells and organisms has a variety of important applications. We report a fluorogenic assay for G protein-coupled receptor (GPCR)-β-arrestin interaction that is genetically encoded, generalizes to multiple GPCRs, and features high signal-to-noise because fluorescence is absent until its components interact upon GPCR activation. Fluorescence after protease-activated receptor-1 activation developed in minutes and required specific serine-threonine residues in the receptor carboxyl tail, consistent with a classical G protein-coupled receptor kinase dependent β-arrestin recruitment mechanism. This assay provides a useful complement to other in vivo assays of GPCR activation.

Arrestin

10.1002/pro.3385

Cite

Citations (16)

Photo-oxidation Using MiniSOG with EM Preparation of Transfected Culture Cells v1

Mason R. Mackey Xiaokun Shu Varda Lev-Ram Thomas J. Deerinck Yingchuan Qi

Abstract taken from Plos Biology Journal: A Genetically Encoded Tag for Correlated Light and Electron Microscopy of Intact Cells, Tissues, and Organisms Electron microscopy (EM) achieves the highest spatial resolution in protein localization, but specific protein EM labeling has lacked generally applicable genetically encoded tags for in situ visualization in cells and tissues. Here we introduce “miniSOG” (for mini Singlet Oxygen Generator), a fluorescent flavoprotein engineered fromArabidopsisphototropin 2. MiniSOG contains 106 amino acids, less than half the size of Green Fluorescent Protein. Illumination of miniSOG generates sufficient singlet oxygen to locally catalyze the polymerization of diaminobenzidine into an osmiophilic reaction product resolvable by EM. MiniSOG fusions to many well-characterized proteins localize correctly in mammalian cells, intact nematodes, and rodents, enabling correlated fluorescence and EM from large volumes of tissue after strong aldehyde fixation, without the need for exogenous ligands, probes, or destructive permeabilizing detergents. MiniSOG permits high quality ultrastructural preservation and 3-dimensional protein localization via electron tomography or serial section block face scanning electron microscopy. EM shows that miniSOG-tagged SynCAM1 is presynaptic in cultured cortical neurons, whereas miniSOG-tagged SynCAM2 is postsynaptic in culture and in intact mice. Thus SynCAM1 and SynCAM2 could be heterophilic partners. MiniSOG may do for EM what Green Fluorescent Protein did for fluorescence microscopy. https://doi.org/10.1371/journal.pbio.1001041

Yellow fluorescent protein

Protein tag

Immunoelectron microscopy

10.17504/protocols.io.eq2lynj8pvx9/v1

Cite

Citations (0)

Structural Determinants of Improved Fluorescence in a Family of Bacteriophytochrome-Based Infrared Fluorescent Proteins: Insights from Continuum Electrostatic Calculations and Molecular Dynamics Simulations

Biochemistry (2016)

Mikołaj Feliks Céline Lafaye Xiaokun Shu Antoine Royant Martin J. Field

Using X-ray crystallography, continuum electrostatic calculations, and molecular dynamics simulations, we have studied the structure, protonation behavior, and dynamics of the biliverdin chromophore and its molecular environment in a series of genetically engineered infrared fluorescent proteins (IFPs) based on the chromophore-binding domain of the Deinococcus radiodurans bacteriophytochrome. Our study suggests that the experimentally observed enhancement of fluorescent properties results from the improved rigidity and planarity of the biliverdin chromophore, in particular of the first two pyrrole rings neighboring the covalent linkage to the protein. We propose that the increases in the levels of both motion and bending of the chromophore out of planarity favor the decrease in fluorescence. The chromophore-binding pocket in some of the studied proteins, in particular the weakly fluorescent parent protein, is shown to be readily accessible to water molecules from the solvent. These waters entering the chromophore region form hydrogen bond networks that affect the otherwise planar conformation of the first three rings of the chromophore. On the basis of our simulations, the enhancement of fluorescence in IFPs can be achieved either by reducing the mobility of water molecules in the vicinity of the chromophore or by limiting the interactions of the nearby protein residues with the chromophore. Finally, simulations performed at both low and neutral pH values highlight differences in the dynamics of the chromophore and shed light on the mechanism of fluorescence loss at low pH.

Chromophore

Planarity testing

Biliverdin

10.1021/acs.biochem.6b00295

Cite

Citations (25)

Major methods and technologies for assessing cell death

Elsevier eBooks (2021)

Tsz‐Leung To Xiaokun Shu

10.1016/b978-0-12-814208-0.00001-4

Cite

Citations (1)