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    Xiaokun Shu, PhD

    TitleAssistant 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.


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      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. 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. 2016 Nov 1. PMID: 27814948.
        View in: PubMed
      2. Yu D, Zhang X, Shu XO, Cai H, Li H, Ding D, Hong Z, Xiang YB, Gao YT, Zheng W, Yang G. Dietary glycemic index, glycemic load, and refined carbohydrates are associated with risk of stroke: a prospective cohort study in urban Chinese women. Am J Clin Nutr. 2016 Nov; 104(5):1345-1351. PMID: 27733400.
        View in: PubMed
      3. 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 Aug 1. PMID: 27479328.
        View in: PubMed
      4. 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 Jul 29. PMID: 27471775.
        View in: PubMed
      5. 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.
        View in: PubMed
      6. 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):3359-63. PMID: 27220724.
        View in: PubMed
      7. Warren Andersen S, Zheng W, Sonderman J, Shu XO, Matthews CE, Yu D, Steinwandel M, McLaughlin JK, Hargreaves MK, Blot WJ. Combined Impact of Health Behaviors on Mortality in Low-Income Americans. Am J Prev Med. 2016 Sep; 51(3):344-55. PMID: 27180031.
        View in: PubMed
      8. 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.
        View in: PubMed
      9. 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.
        View in: PubMed
      10. Yu D, Moore SC, Matthews CE, Xiang YB, Zhang X, Gao YT, Zheng W, Shu XO. Plasma metabolomic profiles in association with type 2 diabetes risk and prevalence in Chinese adults. Metabolomics. 2016 Jan; 12. PMID: 27840598.
        View in: PubMed
      11. 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.
      12. 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; 5:4072. PMID: 24905026; PMCID: PMC4091638.
      13. 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; 5:3626. PMID: 24832154; PMCID: PMC4077998.
      14. 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.
      15. 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.
      16. 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.
      17. 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 8; 109(19):7499-504. PMID: 22532663; PMCID: PMC3358873.
      18. 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.
      19. 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.
      20. 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 8; 324(5928):804-7. PMID: 19423828; PMCID: PMC2763207.
      21. 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.
      22. 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.
      23. 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
      24. 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.
      25. 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.
      26. 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
      27. 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
      28. 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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