Xiaokun Shu, PhD
Professor
Pharmaceutical Chemistry
School of Pharmacy

The cells' inner life is like a glowing beautiful world of Avatar, after we label many proteins in the cell with multicolor fluorescent reporters.

Our research interests span the fields of Physical Biology, Chemical Biology, Structural Biology, Protein Engineering, Cell & Molecular Biology, Developmental Biology, and Drug Discovery. We apply Physics, Chemistry and Engineering to design biological tools for visualizing and manipulating dynamic cell signaling in vivo in order to understand animal development and homeostasis, because dynamical features of signaling are the essence of living organisms. Effector proteins such as proteases and kinases regulate almost every major signaling pathways, and protein-protein interactions (PPIs) define specificity of signal transduction from extracellular cues to the appropriate intracellular effector proteins. We have developed new classes of fluorescent reporters of proteases, kinases, and PPIs. These reporters achieve large dynamic range, high brightness and fast kinetics, in addition being genetically encoded requiring no exogenous cofactor for non-invasive imaging. Our reporters enable robust and rapid imaging of dynamic signaling in living cells and animals with unexpected fun, identifying small molecules that inhibit dysregulated signaling in disease such as cancer. Other biological tools we are developing include: chemogenetic tools for manipulating protein interaction and liquid-liquid phase separation; a genetically encoded photosensitizer for activating caspase and apoptosis signaling and ablating single cells in live animals; singlet oxygen-mediated proximity labeling technologies for identifying weak and transient PPIs by mass spectrometry. We are applying these novel technologies to explore exciting biology and therapeutics. We also collaborate with many biologists and chemists. We have shared our tools by depositing them to not-for-profit organizations, e.g. Addgene, Bloomington Stock Center.

Together let's explore fascinating biology and discover life-saving therapeutics while having fun in the biological adventures!

• Polarized focal adhesion kinase activity within a focal adhesion during cell migration.
  Nature chemical biology 2023 Li X, Combs JD, Salaita K, Shu X
• ATM-SPARK: A GFP phase separation-based activity reporter of ATM.
  Science advances 2023 Li X, Chung CI, Yang J, Chaudhuri S, Munster PN, Shu X
• Fluorogenic reporter enables identification of compounds that inhibit SARS-CoV-2.
  Nature microbiology 2023 Yang J, Xiao Y, Lidsky PV, Wu CT, Bonser LR, Peng S, Garcia-Knight MA, Tassetto M, Chung CI, Li X, Nakayama T, Lee IT, Nayak JV, Ghias K, Hargett KL, Shoichet BK, Erle DJ, Jackson PK, Andino R, Shu X
• Riboflavin-binding proteins for singlet oxygen production.
  Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology 2022 Lafaye C, Aumonier S, Torra J, Signor L, von Stetten D, Noirclerc-Savoye M, Shu X, Ruiz-González R, Gotthard G, Royant A, Nonell S
• Chapter 4 Major methods and technologies for assessing cell death.
  2022 Tsz-Leung To, Xiaokun Shu
• Ethacridine inhibits SARS-CoV-2 by inactivating viral particles.
  PLoS pathogens 2021 Li X, Lidsky PV, Xiao Y, Wu CT, Garcia-Knight M, Yang J, Nakayama T, Nayak JV, Jackson PK, Andino R, Shu X
• Ethacridine inhibits SARS-CoV-2 by inactivating viral particles in cellular models.
  bioRxiv : the preprint server for biology 2020 Li X, Lidsky P, Xiao Y, Wu CT, GarciaKnight M, Yang J, Nakayama T, Nayak JV, Jackson PK, Andino R, Shu X
• Enhancing intracellular accumulation and target engagement of PROTACs with reversible covalent chemistry.
  Nature communications 2020 Guo WH, Qi X, Yu X, Liu Y, Chung CI, Bai F, Lin X, Lu D, Wang L, Chen J, Su LH, Nomie KJ, Li F, Wang MC, Shu X, Onuchic JN, Woyach JA, Wang ML, Wang J
• Imaging dynamic cell signaling in vivo with new classes of fluorescent reporters.
  Current opinion in chemical biology 2019 Shu X
• Designing a Green Fluorogenic Protease Reporter by Flipping a Beta Strand of GFP for Imaging Apoptosis in Animals.
  Journal of the American Chemical Society 2019 Zhang Q, Schepis A, Huang H, Yang J, Ma W, Torra J, Zhang SQ, Yang L, Wu H, Nonell S, Dong Z, Kornberg TB, Coughlin SR, Shu X
• Tailing miniSOG: structural bases of the complex photophysics of a flavin-binding singlet oxygen photosensitizing protein.
  Scientific reports 2019 Torra J, Lafaye C, Signor L, Aumonier S, Flors C, Shu X, Nonell S, Gotthard G, Royant A
• Dynamic Imaging of Small Molecule Induced Protein-Protein Interactions in Living Cells with a Fluorophore Phase Transition Based Approach.
  Analytical chemistry 2018 Chung CI, Zhang Q, Shu X
• Designed peptides that assemble into cross-α amyloid-like structures.
  Nature chemical biology 2018 Zhang SQ, Huang H, Yang J, Kratochvil HT, Lolicato M, Liu Y, Shu X, Liu L, DeGrado WF
• A rapid fluorogenic GPCR-β-arrestin interaction assay.
  Protein science : a publication of the Protein Society 2018 Zhang Q, Zheng YW, Coughlin SR, Shu X
• De Novo Design of Cross-a Amyloid-Like Fibrils with Cellular Activity.
  Biophysical Journal 2018 Shao-Qing Zhang, Lijun Liu, Junjiao Yang, Marco Lolicato, Huong Kratochvil, Xiaokun Shu, William F. DeGrado
• Visualizing Dynamics of Cell Signaling In Vivo with a Phase Separation-Based Kinase Reporter.
  Molecular cell 2018 Zhang Q, Huang H, Zhang L, Wu R, Chung CI, Zhang SQ, Torra J, Schepis A, Coughlin SR, Kornberg TB, Shu X
• Visualizing Dynamics of Cell Signaling In Vivo with a Phase Separation-Based Kinase Reporter.
  Molecular cell 2018 Zhang Q, Huang H, Zhang L, Wu R, Chung CI, Zhang SQ, Torra J, Schepis A, Coughlin SR, Kornberg TB, Shu X
• Detecting Activity at Different Length Scales: From Subdiffraction to Whole-Animal Activity.
  Biochemistry 2017 To TL, Shu X
• Precision Optogenetic Tool for Selective Single- and Multiple-Cell Ablation in a Live Animal Model System.
  Cell chemical biology 2017 Makhijani K, To TL, Ruiz-González R, Lafaye C, Royant A, Shu X
• The Growing and Glowing Toolbox of Fluorescent and Photoactive Proteins.
  Trends in biochemical sciences 2016 Rodriguez EA, Campbell RE, Lin JY, Lin MZ, Miyawaki A, Palmer AE, Shu X, Zhang J, Tsien RY
• Erratum: Corrigendum: A far-red fluorescent protein evolved from a cyanobacterial phycobiliprotein.
  Nature Methods 2016 Erik A Rodriguez, Geraldine N Tran, Larry A Gross, Jessica L Crisp, Xiaokun Shu, John Y Lin, Roger Y Tsien
• A far-red fluorescent protein evolved from a cyanobacterial phycobiliprotein.
  Nature methods 2016 Rodriguez EA, Tran GN, Gross LA, Crisp JL, Shu X, Lin JY, Tsien RY
• 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 Feliks M, Lafaye C, Shu X, Royant A, Field M
• Rational Design of a GFP-Based Fluorogenic Caspase Reporter for Imaging Apoptosis In Vivo.
  Cell chemical biology 2016 To TL, Schepis A, Ruiz-González R, Zhang Q, Yu D, Dong Z, Coughlin SR, Shu X
• Photoactivatable protein labeling by singlet oxygen mediated reactions.
  Bioorganic & medicinal chemistry letters 2016 To TL, Medzihradszky KF, Burlingame AL, DeGrado WF, Jo H, Shu X
• Structure-guided design of a reversible fluorogenic reporter of protein-protein interactions.
  Protein science : a publication of the Protein Society 2016 To TL, Zhang Q, Shu X
• Rational design of a monomeric and photostable far-red fluorescent protein for fluorescence imaging in vivo.
  Protein science : a publication of the Protein Society 2015 Yu D, Dong Z, Gustafson WC, Ruiz-González R, Signor L, Marzocca F, Borel F, Klassen MP, Makhijani K, Royant A, Jan YN, Weiss WA, Guo S, Shu X
• A naturally monomeric infrared fluorescent protein for protein labeling in vivo.
  Nature methods 2015 Yu D, Baird MA, Allen JR, Howe ES, Klassen MP, Reade A, Makhijani K, Song Y, Liu S, Murthy Z, Zhang SQ, Weiner OD, Kornberg TB, Jan YN, Davidson MW, Shu X
• Rationally designed fluorogenic protease reporter visualizes spatiotemporal dynamics of apoptosis in vivo.
  Proceedings of the National Academy of Sciences of the United States of America 2015 To TL, Piggott BJ, Makhijani K, Yu D, Jan YN, Shu X
• Singlet oxygen triplet energy transfer-based imaging technology for mapping protein-protein proximity in intact cells.
  Nature communications 2014 To TL, Fadul MJ, Shu X
• An improved monomeric infrared fluorescent protein for neuronal and tumour brain imaging.
  Nature communications 2014 Yu D, Gustafson WC, Han C, Lafaye C, Noirclerc-Savoye M, Ge WP, Thayer DA, Huang H, Kornberg TB, Royant A, Jan LY, Jan YN, Weiss WA, Shu X
• Self-assembly of VPS41 promotes sorting required for biogenesis of the regulated secretory pathway.
  Developmental cell 2013 Asensio CS, Sirkis DW, Maas JW, Egami K, To TL, Brodsky FM, Shu X, Cheng Y, Edwards RH
• Singlet Oxygen Triplet Energy Transfer (STET) Based Imaging Technologies for Mapping Protein-Protein Proximity and Interactions in Intact Cells.
  Biophysical Journal 2013 Tsz-Leung To, Xiaokun Shu
• Fluorescent and photo-oxidizing TimeSTAMP tags track protein fates in light and electron microscopy.
  Nature neuroscience 2012 Butko MT, Yang J, Geng Y, Kim HJ, Jeon NL, Shu X, Mackey MR, Ellisman MH, Tsien RY, Lin MZ
• A structural basis for the assembly and functions of a viral polymer that inactivates multiple tumor suppressors.
  Cell 2012 Ou HD, Kwiatkowski W, Deerinck TJ, Noske A, Blain KY, Land HS, Soria C, Powers CJ, May AP, Shu X, Tsien RY, Fitzpatrick JA, Long JA, Ellisman MH, Choe S, O'Shea CC
• Advances in Correlated Light and Electron Microscopy Imaging Probes.
  Microscopy and Microanalysis 2012 T.J. Deerinck, E. Bushong, R. Tsien, M. Ellisman, X. Shu
• Photo-inducible cell ablation in Caenorhabditis elegans using the genetically encoded singlet oxygen generating protein miniSOG.
  Proceedings of the National Academy of Sciences of the United States of America 2012 Qi YB, Garren EJ, Shu X, Tsien RY, Jin Y
• Picking faces out of a crowd: genetic labels for identification of proteins in correlated light and electron microscopy imaging.
  Methods in cell biology 2012 Ellisman MH, Deerinck TJ, Shu X, Sosinsky GE
• Bridging Gaps in Imaging by Applying EM Tomography and Serial Block Face SEM, Including a New Genetically Encoded Tag for Correlated Light and 3D Electron Microscopy of Intact Cells, Tissues and Organisms: Integrating the Resulting Correlated Image Data Using the Whole Brain Catalog.
  Microscopy and Microanalysis 2011 M Ellisman, X Shu, V Lev-Ram, T Deerinck, R Tsien, S Lamont, J Martinez, M Berlanga, E Bushong, M Martone, S Larson
• A genetically encoded tag for correlated light and electron microscopy of intact cells, tissues, and organisms.
  PLoS biology 2011 Shu X, Lev-Ram V, Deerinck TJ, Qi Y, Ramko EB, Davidson MW, Jin Y, Ellisman MH, Tsien RY
• Enhancing Serial Block-Face Scanning Electron Microscopy to Enable High Resolution 3-D Nanohistology of Cells and Tissues.
  Microscopy and Microanalysis 2010 TJ Deerinck, EA Bushong, V Lev-Ram, X Shu, RY Tsien, MH Ellisman
• Genetically Encoded Singlet Oxygen Generator (SOG) Requiring No Exogenous Cofactors.
  Biophysical Journal 2010 Xiaokun Shu, Varda Lev-Ram, Guido M. Gaietta, Thomas J. Deerinck, Ericka B. Ramko, Michael W. Davidson, Mark H. Ellisman, Roger Y. Tsien
• Mammalian expression of infrared fluorescent proteins engineered from a bacterial phytochrome.
  Science (New York, N.Y.) 2009 Shu X, Royant A, Lin MZ, Aguilera TA, Lev-Ram V, Steinbach PA, Tsien RY
• Unique interactions between the chromophore and glutamate 16 lead to far-red emission in a red fluorescent protein.
  Protein science : a publication of the Protein Society 2009 Shu X, Wang L, Colip L, Kallio K, Remington SJ
• An alternative excited-state proton transfer pathway in green fluorescent protein variant S205V.
  Protein science : a publication of the Protein Society 2007 Shu X, Leiderman P, Gepshtein R, Smith NR, Kallio K, Huppert D, Remington SJ
• Ultrafast excited-state dynamics in the green fluorescent protein variant S65T/H148D. 1. Mutagenesis and structural studies.
  Biochemistry 2007 Shu X, Kallio K, Shi X, Abbyad P, Kanchanawong P, Childs W, Boxer SG, Remington SJ
• Ultrafast excited-state dynamics in the green fluorescent protein variant S65T/H148D. 2. Unusual photophysical properties.
  Biochemistry 2007 Shi X, Abbyad P, Shu X, Kallio K, Kanchanawong P, Childs W, Remington SJ, Boxer SG
• Ultrafast excited-state dynamics in the green fluorescent protein variant S65T/H148D. 3. Short- and long-time dynamics of the excited-state proton transfer.
  Biochemistry 2007 Leiderman P, Genosar L, Huppert D, Shu X, Remington SJ, Solntsev KM, Tolbert LM
• Novel chromophores and buried charges control color in mFruits.
  Biochemistry 2006 Shu X, Shaner NC, Yarbrough CA, Tsien RY, Remington SJ
• Kindling fluorescent protein from Anemonia sulcata: dark-state structure at 1.38 A resolution.
  Biochemistry 2005 Quillin ML, Anstrom DM, Shu X, O'Leary S, Kallio K, Chudakov DM, Remington SJ
• Surface alloying of immiscible metals induced by surface state shift
  Surface Science 2003 X.K.Shu, P. Jiang, J.G. Che