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Xiaokun Shu, PhD

TitleAssociate Professor
SchoolUCSF School of Pharmacy
DepartmentPharmaceutical Chemistry
Address555 Mission Bay Blvd South
San Francisco CA 94158
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    Collapse Biography 
    Collapse Awards and Honors
    2012NIH Director's New Innovator Award

    Collapse Overview 
    Collapse Overview
    The Shu lab is interested in applying Principles of Physics and Chemistry to develop technologies for Biology. With the completion of human genome project, the next step in understanding biology and disease is to identify protein interactome and to characterize protein machines since protein-protein interaction networks underlie most cellular processes and protein machines carry out every major cellular process and maintain homeostasis of an organism. However, unlike the genome, protein interactome is dynamic and contains weakly associated components, which are difficult to detect. Hence, toward construction of a complete human interactome, we aim to develop new technologies for: 1) identifying weak or transient protein interactions; 2) imaging protein-protein interactions with spatiotemporal resolution. To understand mechanisms of biological processes and disease, we are also interested in developing technologies for: 3) imaging spatiotemporal dynamics of cell signaling including kinase activities in whole-animals; 4) imaging neuronal activities in brain by recording calcium and membrane potential. With these technologies, our ultimate goal is to understand molecular mechanisms of animal development and disease.


    Collapse Research 
    Collapse Research Activities and Funding
    Rational design of a genetically encoded infrared fluorescent protease reporter
    NIH/NIGMS R01GM115399Aug 1, 2015 - Jul 31, 2019
    Role: Principal Investigator
    New principle-based technologies for identifying transient protein interactions
    NIH/NIGMS DP2GM105446Sep 30, 2012 - Jun 30, 2017
    Role: Principal Investigator

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    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. To TL, Shu X. Detecting Activity at Different Length Scales: From Subdiffraction to Whole-Animal Activity. Biochemistry. 2017 Sep 15. PMID: 28915023.
      View in: PubMed
    2. Yang JJ, Yu D, Takata Y, Smith-Warner SA, Blot W, White E, Robien K, Park Y, Xiang YB, Sinha R, Lazovich D, Stampfer M, Tumino R, Aune D, Overvad K, Liao L, Zhang X, Gao YT, Johansson M, Willett W, Zheng W, Shu X. Dietary Fat Intake and Lung Cancer Risk: A Pooled Analysis. J Clin Oncol. 2017 Sep 10; 35(26):3055-3064. PMID: 28742456.
      View in: PubMed
    3. Yu D, Takata Y, Smith-Warner SA, Blot W, Sawada N, White E, Freedman N, Robien K, Giovannucci E, Zhang X, Park Y, Gao YT, Chlebowski RT, Langhammer A, Yang G, Severi G, Manjer J, Khaw KT, Weiderpass E, Liao LM, Caporaso N, Krokstad S, Hveem K, Sinha R, Ziegler R, Tsugane S, Xiang YB, Johansson M, Zheng W, Shu X. Prediagnostic Calcium Intake and Lung Cancer Survival: A Pooled Analysis of 12 Cohort Studies. Cancer Epidemiol Biomarkers Prev. 2017 Jul; 26(7):1060-1070. PMID: 28264875.
      View in: PubMed
    4. Makhijani K, To TL, Ruiz-González R, Lafaye C, Royant A, Shu X. Precision Optogenetic Tool for Selective Single- and Multiple-Cell Ablation in a Live Animal Model System. Cell Chem Biol. 2017 Jan 19; 24(1):110-119. PMID: 28065655.
      View in: PubMed
    5. Rodriguez EA, Campbell RE, Lin JY, Lin MZ, Miyawaki A, Palmer AE, Shu X, Zhang J, Tsien RY. The Growing and Glowing Toolbox of Fluorescent and Photoactive Proteins. Trends Biochem Sci. 2017 Feb; 42(2):111-129. PMID: 27814948.
      View in: PubMed
    6. Hampras SS, Sucheston-Campbell LE, Cannioto R, Chang-Claude J, Modugno F, Dörk T, Hillemanns P, Preus L, Knutson KL, Wallace PK, Hong CC, Friel G, Davis W, Nesline M, Pearce CL, Kelemen LE, Goodman MT, Bandera EV, Terry KL, Schoof N, Eng KH, Clay A, Singh PK, Joseph JM, Aben KK, Anton-Culver H, Antonenkova N, Baker H, Bean Y, Beckmann MW, Bisogna M, Bjorge L, Bogdanova N, Brinton LA, Brooks-Wilson A, Bruinsma F, Butzow R, Campbell IG, Carty K, Cook LS, Cramer DW, Cybulski C, Dansonka-Mieszkowska A, Dennis J, Despierre E, Dicks E, Doherty JA, du Bois A, Dürst M, Easton D, Eccles D, Edwards RP, Ekici AB, Fasching PA, Fridley BL, Gao YT, Gentry-Maharaj A, Giles GG, Glasspool R, Gronwald J, Harrington P, Harter P, Hasmad HN, Hein A, Heitz F, Hildebrandt MA, Hogdall C, Hogdall E, Hosono S, Iversen ES, Jakubowska A, Jensen A, Ji BT, Karlan BY, Kellar M, Kelley JL, Kiemeney LA, Klapdor R, Kolomeyevskaya N, Krakstad C, Kjaer SK, Kruszka B, Kupryjanczyk J, Lambrechts D, Lambrechts S, Le ND, Lee AW, Lele S, Leminen A, Lester J, Levine DA, Liang D, Lissowska J, Liu S, Lu K, Lubinski J, Lundvall L, Massuger LF, Matsuo K, McGuire V, McLaughlin JR, McNeish I, Menon U, Moes-Sosnowska J, Narod SA, Nedergaard L, Nevanlinna H, Nickels S, Olson SH, Orlow I, Weber RP, Paul J, Pejovic T, Pelttari LM, Perkins B, Permuth-Wey J, Pike MC, Plisiecka-Halasa J, Poole EM, Risch HA, Rossing MA, Rothstein JH, Rudolph A, Runnebaum IB, Rzepecka IK, Salvesen HB, Schernhammer E, Schmitt K, Schwaab I, Shu X, Shvetsov YB, Siddiqui N, Sieh W, Song H, Southey MC, Tangen IL, Teo SH, Thompson PJ, Timorek A, Tsai YY, Tworoger SS, Tyrer J, van Altena AM, Vergote I, Vierkant RA, Walsh C, Wang-Gohrke S, Wentzensen N, Whittemore AS, Wicklund KG, Wilkens LR, Wu AH, Wu X, Woo YL, Yang H, Zheng W, Ziogas A, Gayther SA, Ramus SJ, Sellers TA, Schildkraut JM, Phelan CM, Berchuck A, Chenevix-Trench G, Cunningham JM, Pharoah PP, Ness RB, Odunsi K, Goode EL, Moysich KB. Assessment of variation in immunosuppressive pathway genes reveals TGFBR2 to be associated with risk of clear cell ovarian cancer. Oncotarget. 2016 10 25; 7(43):69097-69110. PMID: 27533245.
      View in: PubMed
    7. Rodriguez EA, Tran GN, Gross LA, Crisp JL, Shu X, Lin JY, Tsien RY, et al. A far-red fluorescent protein evolved from a cyanobacterial phycobiliprotein. Nat Methods. 2016 Sep; 13(9):763-9. PMID: 27479328; PMCID: PMC5007177 [Available on 03/01/17].
      View in: PubMed, PubMed Central
    8. Feliks M, Lafaye C, Shu X, Royant A, Field M, et al. 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 Aug 09; 55(31):4263-74. PMID: 27471775.
      View in: PubMed
    9. To TL, Schepis A, Ruiz-González R, Zhang Q, Yu D, Dong Z, Coughlin SR, Shu X. Rational Design of a GFP-Based Fluorogenic Caspase Reporter for Imaging Apoptosis In Vivo. Cell Chem Biol. 2016 Jul 21; 23(7):875-82. PMID: 27447051; PMCID: PMC5026494 [Available on 01/21/17].
      View in: PubMed, PubMed Central
    10. To TL, Medzihradszky KF, Burlingame AL, DeGrado WF, Jo H, Shu X. Photoactivatable protein labeling by singlet oxygen mediated reactions. Bioorg Med Chem Lett. 2016 Jul 15; 26(14):3359-3363. PMID: 27220724; PMCID: PMC4903891 [Available on 07/15/17].
      View in: PubMed, PubMed Central
    11. To TL, Zhang Q, Shu X. Structure-guided design of a reversible fluorogenic reporter of protein-protein interactions. Protein Sci. 2016 Mar; 25(3):748-53. PMID: 26690964; PMCID: PMC4815423 [Available on 03/01/17].
      View in: PubMed, PubMed Central
    12. 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. Rational design of a monomeric and photostable far-red fluorescent protein for fluorescence imaging in vivo. Protein Sci. 2016 Feb; 25(2):308-15. PMID: 26549191; PMCID: PMC4815332 [Available on 02/01/17].
      View in: PubMed, PubMed Central
    13. 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. A naturally monomeric infrared fluorescent protein for protein labeling in vivo. Nat Methods. 2015 Aug; 12(8):763-5. PMID: 26098020; PMCID: PMC4521985.
      View in: PubMed, PubMed Central
    14. To TL, Piggott BJ, Makhijani K, Yu D, Jan YN, Shu X. Rationally designed fluorogenic protease reporter visualizes spatiotemporal dynamics of apoptosis in vivo. Proc Natl Acad Sci U S A. 2015 Mar 17; 112(11):3338-43. PMID: 25733847; PMCID: PMC4371907.
      View in: PubMed, PubMed Central
    15. To TL, Fadul MJ, Shu X. Singlet oxygen triplet energy transfer-based imaging technology for mapping protein-protein proximity in intact cells. Nat Commun. 2014 Jun 06; 5:4072. PMID: 24905026; PMCID: PMC4091638.
      View in: PubMed, PubMed Central
    16. 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. An improved monomeric infrared fluorescent protein for neuronal and tumour brain imaging. Nat Commun. 2014 May 15; 5:3626. PMID: 24832154; PMCID: PMC4077998.
      View in: PubMed, PubMed Central
    17. Asensio CS, Sirkis DW, Maas JW, Egami K, To TL, Brodsky FM, Shu X, Cheng Y, Edwards RH. Self-assembly of VPS41 promotes sorting required for biogenesis of the regulated secretory pathway. Dev Cell. 2013 Nov 25; 27(4):425-37. PMID: 24210660; PMCID: PMC3974617.
      View in: PubMed, PubMed Central
    18. Butko MT, Yang J, Geng Y, Kim HJ, Jeon NL, Shu X, Mackey MR, Ellisman MH, Tsien RY, Lin MZ. Fluorescent and photo-oxidizing TimeSTAMP tags track protein fates in light and electron microscopy. Nat Neurosci. 2012 Dec; 15(12):1742-51. PMID: 23103964; PMCID: PMC3509268.
      View in: PubMed, PubMed Central
    19. 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. A structural basis for the assembly and functions of a viral polymer that inactivates multiple tumor suppressors. Cell. 2012 Oct 12; 151(2):304-19. PMID: 23063122; PMCID: PMC3681303.
      View in: PubMed, PubMed Central
    20. Xu J, Mo Z, Ye D, Wang M, Liu F, Jin G, Xu C, Wang X, Shao Q, Chen Z, Tao Z, Qi J, Zhou F, Wang Z, Fu Y, He D, Wei Q, Guo J, Wu D, Gao X, Yuan J, Wang G, Xu Y, Wang G, Yao H, Dong P, Jiao Y, Shen M, Yang J, Ou-Yang J, Jiang H, Zhu Y, Ren S, Zhang Z, Yin C, Gao X, Dai B, Hu Z, Yang Y, Wu Q, Chen H, Peng P, Zheng Y, Zheng X, Xiang Y, Long J, Gong J, Na R, Lin X, Yu H, Wang Z, Tao S, Feng J, Sun J, Liu W, Hsing A, Rao J, Ding Q, Wiklund F, Gronberg H, Shu X, Zheng W, Shen H, Jin L, Shi R, Lu D, Zhang X, Sun J, Zheng SL, Sun Y. Genome-wide association study in Chinese men identifies two new prostate cancer risk loci at 9q31.2 and 19q13.4. Nat Genet. 2012 Nov; 44(11):1231-5. PMID: 23023329; PMCID: PMC4116636.
      View in: PubMed, PubMed Central
    21. Qi YB, Garren EJ, Shu X, Tsien RY, Jin Y. Photo-inducible cell ablation in Caenorhabditis elegans using the genetically encoded singlet oxygen generating protein miniSOG. Proc Natl Acad Sci U S A. 2012 May 08; 109(19):7499-504. PMID: 22532663; PMCID: PMC3358873.
      View in: PubMed, PubMed Central
    22. Ellisman MH, Deerinck TJ, Shu X, Sosinsky GE. Picking faces out of a crowd: genetic labels for identification of proteins in correlated light and electron microscopy imaging. Methods Cell Biol. 2012; 111:139-55. PMID: 22857927; PMCID: PMC3532940.
      View in: PubMed, PubMed Central
    23. Shu X, Lev-Ram V, Deerinck TJ, Qi Y, Ramko EB, Davidson MW, Jin Y, Ellisman MH, Tsien RY. A genetically encoded tag for correlated light and electron microscopy of intact cells, tissues, and organisms. PLoS Biol. 2011 Apr; 9(4):e1001041. PMID: 21483721; PMCID: PMC3071375.
      View in: PubMed, PubMed Central
    24. Shu X, Royant A, Lin MZ, Aguilera TA, Lev-Ram V, Steinbach PA, Tsien RY. Mammalian expression of infrared fluorescent proteins engineered from a bacterial phytochrome. Science. 2009 May 08; 324(5928):804-7. PMID: 19423828; PMCID: PMC2763207.
      View in: PubMed, PubMed Central
    25. Shu X, Wang L, Colip L, Kallio K, Remington SJ. Unique interactions between the chromophore and glutamate 16 lead to far-red emission in a red fluorescent protein. Protein Sci. 2009 Feb; 18(2):460-6. PMID: 19165727; PMCID: PMC2708057.
      View in: PubMed, PubMed Central
    26. Shu X, Leiderman P, Gepshtein R, Smith NR, Kallio K, Huppert D, Remington SJ. An alternative excited-state proton transfer pathway in green fluorescent protein variant S205V. Protein Sci. 2007 Dec; 16(12):2703-10. PMID: 17965188; PMCID: PMC2222808.
      View in: PubMed, PubMed Central
    27. Leiderman P, Genosar L, Huppert D, Shu X, Remington SJ, Solntsev KM, Tolbert LM. 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 Oct 30; 46(43):12026-36. PMID: 17918961.
      View in: PubMed
    28. 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. 2. Unusual photophysical properties. Biochemistry. 2007 Oct 30; 46(43):12014-25. PMID: 17918960; PMCID: PMC2527858.
      View in: PubMed, PubMed Central
    29. 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. 1. Mutagenesis and structural studies. Biochemistry. 2007 Oct 30; 46(43):12005-13. PMID: 17918959; PMCID: PMC2536499.
      View in: PubMed, PubMed Central
    30. Shu X, Shaner NC, Yarbrough CA, Tsien RY, Remington SJ. Novel chromophores and buried charges control color in mFruits. Biochemistry. 2006 Aug 15; 45(32):9639-47. PMID: 16893165.
      View in: PubMed
    31. Quillin ML, Anstrom DM, Shu X, O'Leary S, Kallio K, Chudakov DM, Remington SJ. Kindling fluorescent protein from Anemonia sulcata: dark-state structure at 1.38 A resolution. Biochemistry. 2005 Apr 19; 44(15):5774-87. PMID: 15823036.
      View in: PubMed
    32. X.K.Shu, P. Jiang, J.G. Che. Surface alloying of immiscible metals induced by surface state shift. Surface Science. 2003; 545(3):199-210.
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