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Shu

Xiaokun Shu, PhD

Professor
Pharmaceutical Chemistry
Address: 
555 Mission Bay Blvd South, Rm 452Y
UCSF Box 3122
San Francisco, CA 94158
United States
Phone: 
Research Interests: 
Reading, mapping and manipulating signaling networks

Research Summary:
Protein Rational Design and Directed Evolution for Biology and Medicine Summary: We are developing technologies to bridge the gap between clinical medicine and molecular biology. Their successful use in biomedicine will significantly improve treatment of disease.

Publications: 

A Convergent Approach to Resorcinolic Macrolides to Expand Structural Diversity.

Chemistry (Weinheim an der Bergstrasse, Germany)

Lombera JMM, Feng X, Shu X, Seiple IB

BPS2025 - YAP charge patterning mediates signal integration through transcriptional co-condensates.

Biophysical Journal

Kirstin Meyer, Klaus Yserentant, Rasmi Cheloor-Kovilakam, Kiersten Ruff, Chung Chan-I, Xiaokun Shu, Bo Huang, Orion Weiner

BPS2025 - YAP charge patterning mediates signal integration through transcriptional co-condensates.

Biophysical Journal

Kirstin Meyer, Klaus Yserentant, Rasmi Cheloor-Kovilakam, Kiersten Ruff, Chung Chan-I, Xiaokun Shu, Bo Huang, Orion Weiner

Author Correction: MYC phase separation selectively modulates the transcriptome.

Nature structural & molecular biology

Yang J, Chung CI, Koach J, Liu H, Navalkar A, He H, Ma Z, Zhao Q, Yang X, He L, Mittag T, Shen Y, Weiss WA, Shu X

Opposing GPCR signaling programs protein intake setpoint in Drosophila.

Cell

Wu G, Ma T, Hancock CE, Gonzalez S, Aryal B, Vaz S, Chan G, Palarca-Wong M, Allen N, Chung CI, Shu X, Liu Q

YAP charge patterning mediates signal integration through transcriptional co-condensates.

bioRxiv : the preprint server for biology

Meyer K, Yserentant K, Cheloor-Kovilakam R, Ruff KM, Chung CI, Shu X, Huang B, Weiner OD

MYC phase separation selectively modulates the transcriptome.

Nature structural & molecular biology

Yang J, Chung CI, Koach J, Liu H, Navalkar A, He H, Ma Z, Zhao Q, Yang X, He L, Mittag T, Shen Y, Weiss WA, Shu X

Phase separation of YAP-MAML2 differentially regulates the transcriptome.

Proceedings of the National Academy of Sciences of the United States of America

Chung CI, Yang J, Yang X, Liu H, Ma Z, Szulzewsky F, Holland EC, Shen Y, Shu X

A genome-wide gene-environment interaction study of breast cancer risk for women of European ancestry.

Breast cancer research : BCR

Middha P, Wang X, Behrens S, Bolla MK, Wang Q, Dennis J, Michailidou K, Ahearn TU, Andrulis IL, Anton-Culver H, Arndt V, Aronson KJ, Auer PL, Augustinsson A, Baert T, Freeman LEB, Becher H, Beckmann MW, Benitez J, Bojesen SE, Brauch H, Brenner H, Brooks-Wilson A, Campa D, Canzian F, Carracedo A, Castelao JE, Chanock SJ, Chenevix-Trench G, CTS Consortium, Cordina-Duverger E, Couch FJ, Cox A, Cross SS, Czene K, Dossus L, Dugué PA, Eliassen AH, Eriksson M, Evans DG, Fasching PA, Figueroa JD, Fletcher O, Flyger H, Gabrielson M, Gago-Dominguez M, Giles GG, González-Neira A, Grassmann F, Grundy A, Guénel P, Haiman CA, Håkansson N, Hall P, Hamann U, Hankinson SE, Harkness EF, Holleczek B, Hoppe R, Hopper JL, Houlston RS, Howell A, Hunter DJ, Ingvar C, ABCTB Investigators, kConFab Investigators, Isaksson K, Jernström H, John EM, Jones ME, Kaaks R, Keeman R, Kitahara CM, Ko YD, Koutros S, Kurian AW, Lacey JV, Lambrechts D, Larson NL, Larsson S, Le Marchand L, Lejbkowicz F, Li S, Linet M, Lissowska J, Martinez ME, Maurer T, Mulligan AM, Mulot C, Murphy RA, Newman WG, Nielsen SF, Nordestgaard BG, Norman A, O'Brien KM, Olson JE, Patel AV, Prentice R, Rees-Punia E, Rennert G, Rhenius V, Ruddy KJ, Sandler DP, Scott CG, Shah M, Shu XO, Smeets A, Southey MC, Stone J, Tamimi RM, Taylor JA, Teras LR, Tomczyk K, Troester MA, Truong T, Vachon CM, Wang SS, Weinberg CR, Wildiers H, Willett W, Winham SJ, Wolk A, Yang XR, Zamora MP, Zheng W, Ziogas A, Dunning AM, Pharoah PDP, García-Closas M, Schmidt MK, Kraft P, Milne RL, Lindström S, Easton DF, Chang-Claude J

Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project.

Molecular cell

Dekker J, Alber F, Aufmkolk S, Beliveau BJ, Bruneau BG, Belmont AS, Bintu L, Boettiger A, Calandrelli R, Disteche CM, Gilbert DM, Gregor T, Hansen AS, Huang B, Huangfu D, Kalhor R, Leslie CS, Li W, Li Y, Ma J, Noble WS, Park PJ, Phillips-Cremins JE, Pollard KS, Rafelski SM, Ren B, Ruan Y, Shav-Tal Y, Shen Y, Shendure J, Shu X, Strambio-De-Castillia C, Vertii A, Zhang H, Zhong S

Polarized focal adhesion kinase activity within a focal adhesion during cell migration.

Nature chemical biology

Li X, Combs JD, Salaita K, Shu X

ATM-SPARK: A GFP phase separation-based activity reporter of ATM.

Science advances

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

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

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

Ethacridine inhibits SARS-CoV-2 by inactivating viral particles.

PLoS pathogens

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

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

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

Designing a Green Fluorogenic Protease Reporter by Flipping a Beta Strand of GFP for Imaging Apoptosis in Animals.

Journal of the American Chemical Society

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

Torra J, Lafaye C, Signor L, Aumonier S, Flors C, Shu X, Nonell S, Gotthard G, Royant A

Designed peptides that assemble into cross-α amyloid-like structures.

Nature chemical biology

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

Zhang Q, Zheng YW, Coughlin SR, Shu X

De Novo Design of Cross-a Amyloid-Like Fibrils with Cellular Activity.

Biophysical Journal

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

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

Zhang Q, Huang H, Zhang L, Wu R, Chung CI, Zhang SQ, Torra J, Schepis A, Coughlin SR, Kornberg TB, Shu X

Precision Optogenetic Tool for Selective Single- and Multiple-Cell Ablation in a Live Animal Model System.

Cell chemical biology

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

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

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

Rodriguez EA, Tran GN, Gross LA, Crisp JL, Shu X, Lin JY, Tsien RY

Rational Design of a GFP-Based Fluorogenic Caspase Reporter for Imaging Apoptosis In Vivo.

Cell chemical biology

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

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

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

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

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

To TL, Piggott BJ, Makhijani K, Yu D, Jan YN, Shu X

An improved monomeric infrared fluorescent protein for neuronal and tumour brain imaging.

Nature communications

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

Asensio CS, Sirkis DW, Maas JW, Egami K, To TL, Brodsky FM, Shu X, Cheng Y, Edwards RH

Fluorescent and photo-oxidizing TimeSTAMP tags track protein fates in light and electron microscopy.

Nature neuroscience

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

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

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

Qi YB, Garren EJ, Shu X, Tsien RY, Jin Y

A genetically encoded tag for correlated light and electron microscopy of intact cells, tissues, and organisms.

PLoS biology

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

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

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.)

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

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

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

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

Shi X, Abbyad P, Shu X, Kallio K, Kanchanawong P, Childs W, Remington SJ, Boxer SG

Novel chromophores and buried charges control color in mFruits.

Biochemistry

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

Quillin ML, Anstrom DM, Shu X, O'Leary S, Kallio K, Chudakov DM, Remington SJ

Faculty Type: 
Core CVRI Faculty