hahn lab

Tools listed by protein target

The list below shows the target protein followed by different methods we have applied. Click the method or go to the get tools page to see caveats and advantages for each method. References are being added for each molecule. Check back for multiple new biosensors and optogenetic tools currently submitted, or write Dr. Hahn to ask what has been targeted.

Visualizing protein activity - biosensors

AR = affinity reagent, a protein or protein fragment that binds selectively to a given state of the target molecule.

  • Src family proteins sensed as a group (dye-labeled AR)
  • FAK (biosensor in collaboration with Schaller group)

Activating proteins with light

Inhibiting proteins with light

Engineered activation by membrane-permeable small molecules

Notes:

  • Currently responds to rapamycin and rapmycin analogs that do not interact with mTor.
  • We can use a light-activated rapamycin to control with light.
  • Activation is irreversible. Karginov lab has developed a reversible version.
  • Src when activated interacts only with p130Cas (RapR TAP)
  • Src when activated interacts only with FAK (RapR TAP)
  • Src is driven to the membrane (RapR TAP)

Other light-controlled techniques

  • Light induced translocation into or out of the nucleus (embedded peptide and/or Zdk, in collaboration with Kuhlman lab)
  • Light-controlled microtubule tip labeling (Zdk and Eb3, with Wittman lab)

Some references, soon to be associated with above tools

  1. Hahn, K.M., A.S. Waggoner and D.L. Taylor.  A calcium-sensitive fluorescent analog of calmodulin based on a novel calmodulin- binding fluorophore.  J. Biol. Chem.265: 20335-20345, 1990. Online article | PDF
  2. Hahn, K.M., R. DeBiasio and D.L. Taylor.  Patterns of elevated free calcium and calmodulin activation in living cells. Nature, 359:736-738, 1992. Online article | PDF
  3. Hahn, K.M., P.A. Conrad, J. Chao, D.L. Taylor and A.S. Waggoner.  A photocrosslinking, fluorescent indicator of mitochondrial membrane potential.  J. Histochem. Cytochem.41: 631-634, 1993. Online article | PDF
  4. Bark, S. J., and K.M. Hahn. Fluorescent indicators of peptide cleavage inside living cells. Methods, 20: 429-435, 2000. Online article | PDF
  5. Chamberlain, C.E., Kraynov, V. and Hahn, K.M. Imaging spatiotemporal dynamics of Rac activation in vivo with FLAIR. Methods Enzymol.325: 389-400, 2000. Online article | PDF
  6. Kraynov, V. S., Chamberlain, C. E., Bokoch, G. M., Schwartz, M. A., Slabaugh, S., and K. M. Hahn. Localized Rac activation dynamics visualized in living cells. Science, 290:333-337, 2000. Online article PDF
  7. Nalbant, P., L. Hodgson, V. Kraynov, A. Toutchkine, K.M. Hahn. Activation of Endogenous Cdc42 Visualized in Living Cells. Science,305:1615-1619, 2004. Online article PDF
  8. Pertz, O., L. Hodgson, R. R. Klemke, and K.M. Hahn. Spatio-temporal dynamics of RhoA activity in migrating cells. Nature,  440(7087):1069-1072, 2006. Online article PDF
  9. Hodgson, L. Nalbant, P. Shen, F., and Hahn, K. Imaging and photobleach correction of Mero-CBD, sensor of endogenous Cdc42 activation. Methods Enzymol., 406:140-156, 2006. Online article | PDF`
  10. Cai, X., Lietha, D. Ceccarelli, D.F., Karginov, A.V., Rajfur, Z., Jacobson, K., Hahn, K.M., Eck, M.J., and Schaller, M.D. Spatial and temporal regulation of focal adhesion kinase activity in living cells. Mol. Cell Biol. 28:201-14, 2008. PMC2223290. Online article | Free PMC article
  11. Garrett, S.C., Hodgson, L., Rybin, A., Toutchkine, A., Hahn, K.M., Lawrence, D.S., and Bresnick, A.R. A Biosensor of S100A4 Metastasis Factor Activation: Inhibitor screening and Cellular Activation Dynamics. Biochemistry, 47:986-996, 2008. PMC3227476. Online article | Free PMC article
  12. Machacek, M., Hodson, L., Welch, C., Elliot, H., Pertz, O., Nalbant, P., Abell, A., Johnson, G., *Hahn, K.M. and *Danuser, G. Coordination of Rho GTPase activities during cell protrusion. Nature, 461: 99-103, 2009. PMC2885353. Online article | Free PMC article
  13. Wu, Y, Frey, D., Lungu, O. I., Jaehrig, A., Schlichting, I., Kuhlman, B. and Hahn, K.M. A genetically-encoded photoactivatable Rac reveals spatiotemporal coordination of Rac and Rho during cell motility. Nature, 461: 104-110, 2009. PMC2766670. Online article | Free PMC article
  14. Yoo, S.K., Deng, Q.,  Cavnar, P. J.,  Wu,Y.I.,  Hahn, K.M., Huttenlocher, A. Differential Regulation of Protrusion and Polarity by PI(3)K during Neutrophil Motility in Live Zebrafish.  Developmental Cell, 18(2):226-236, 2010. PMC2824622. Online article Free PMC article
  15. Karginov, A.V., Ding, F., Kota, P., Dokholyan, N.V., and Hahn, K.M. Engineered allosteric activation of kinases in living cells. Nature Biotech, July; 28(7):743-7, 2010. PMC2902629. Online article Free PMC article
  16. Wang, X., He L, Wu, Y.I., Hahn, K.M., and Montell, D.J. Light-mediated activation reveals a key role for Rac in collective guidance of cell movement in vivo. Nature Cell Biol., 12(6):591-7, 2011. PMC2929827. Online article Free PMC article
  17. Karginov, A.V., Zou, Y., Shirvanyants, D., Kota, P., Dokholyan, N.V., Young, D.D., *Hahn, K.M.  and *Deiters, A. Light regulation of protein dimerization and kinase activity in living cells using photocaged rapamycin and engineered FKBPJ. Am. Chem. Soc., 133: 420-423, 2011. PMC3133816. Online article | Free PMC article
  18. Gulyani, A., Vitriol, E., Allen, R., Wu, J., Gremyachinskiy, D., Lewis, S., Dewar, B., Graves, L.M., Kay, B.K., Kuhlman, B., Elston T., and Hahn, K.M.  A biosensor generated via high-throughput screening quantifies cell edge Src dynamics. Nature Chem. Biol., 7: 437-444, 2011.  PMC3135387. Online article. | Free PMC article
  19. Wu, Y.I., Wang, X., He, L., Montell, D. and Hahn, K.M. Spatiotemporal control of small GTPases with light using the LOV domain. Methods Enzymol., 497: 393-407, 2011.  PMC3407667. Online article | Free PMC article
  20. Karginov, A.V. and Hahn, K.M. Allosteric activation of kinases: design and application of RapR kinases. Curr. Protoc. Cell Biol., 53: 14.13.1 – 14.13.16, 2011. PMC3269071. Online article | Free PMC article
  21. Hinde, E., Digman, M.A., Welch, C., Hahn, K.M. and Gratton, E. Biosensor FRET detection by the phasor approach to Fluorescence Lifetime Imaging Microscopy (FLIM). Microsc. Res. Tech., 75(3): 271-281, 2012.  PMC3523109 . Online article | Free PMC article
  22. Lungu, O.I., Hallett R.A., Choi E.J., Aiken M.J., *Hahn K.M., *Kuhlman B. Designing Photoswitchable Peptides Using the AsLOV2 Domain. Chemistry and Biology, 19(4):507-17, 2012. PMC334866. Online article | Free PMC article
  23. Dietz, D.M., Sun, H., Lobo, M.K., Cahill, M.E., Chadwick, B., Gao, V., Koo, J.W., Mazei-Robison, M.S., Dias, C., Maze, I., Damez-Werno, D., Dietz, K.C., Scobie, K.N., Ferguson, D., Christoffel, D., Ohnishi, Y., Hodes, G.E., Zheng, Y., Neve, R.L., Hahn, K.M., Russo, S.J. and Nestler, E.J. Rac1 is essential in cocaine-induced structural plasticity of nucleus accumbens neurons. Nature Neurosci., 15(6): 891-896, 2012.  PMC3565539. Online article | Free PMC article
  24. MacNevin, C.J., Gremyachinskiy, D., Hsu, C.W., Li L., Rougie, M., Davis, T.T., Hahn, K.M. Environment-sensing merocyanine dyes for live cell imaging applications. Bioconjug. Chem. 24(2):215-23, 2013. PMC3667669. Online article | Free PMC article
  25. Dagliyan, O., Shirvanyants, D., Karginov, A.V., Ding, F., Fee, L., Chandrasekaran, S.N., Freisinger, C.M., Smolen, G.A., Huttenlocher, A., *Hahn, K.M., *Dokholyan, N.V. Rational design of a ligand-controlled protein conformational switch. Proc. Natl. Acad. Sci. U.S.A.,110(17):6800-4, 2013. PMC3637791. Online article Free PMC article
  26. Konze, K.D., Ma, A., Li, F., Barsyte-Lovejoy, D., Parton, T., Macnevin, C.J., Liu, F., Gao, C., Huang, X.P., Kuznetsova, E., Rougie, M., Jiang, A., Pattenden, S.G., Norris, J.L., James, L.I., Roth, B.L., Brown, P.J., Frye, S.V., Arrowsmith, C.H., Hahn, K.M., Wang, G.G., Vedadi, M. and Jin, J. An orally bioavailable chemical probe of the lysine methyltransferases EZH2 and EZH1ACS Chem. Biol., 8(6): 1324–1334,2013. PMC3773059. Online article | Free PMC article
  27. Rao, M.V., Chu, P.H., Hahn, K.M. and Zaidel-Bar, R.  An optogenetic tool for the activation of endogenous diaphanous-related formins induces thickening of stress fibers without an increase in contractility. Cytoskeleton, 70(7): 394-407, 2013. PMC4064713.Online article | Free PMC article
  28. Zawistowski, J.S., Sabouri-Ghomi, M., *Danuser, G., *Hahn, K.M. and *Hodgson, L. A. RhoC biosensor reveals differences in the activation kinetics of RhoA and RhoC in migrating cells. PLoS One, 8(11): e79877, 2013. PMC3818223. Online article | Free PMC article
  29. Karginov, A., Tsygankov, D., Berginski, M., Chu, P-H., Trudeau, E., Yi, J.J., Gomez, Shawn, Elston, T.C. and Hahn, K.M. Dissecting motility signaling through activation of specific Src-effector complexesNature Chem. Bio., 10(4):286-90, 2014.  PMC4064790. Online article Free PMC article
  30. Yi, J.J., Wang, H., Vilela, M., Danuser, G., and Hahn, K.M. Manipulation of endogenous kinase activity in living cells using photoswitchable inhibitory peptides. ACS Synth. Biol., 3(11):788-95, 2014. PMC4277778. Online article | Free PMC article
  31. Chu, P-H., Tsygankov, D., Berginski, M.E., Dagliyan, O., Gomez, S.M., Elston, T.C., Karginov, A.V. and Hahn, K.M. Engineered kinase activation reveals unique morphodynamic phenotypes and associated trafficking for Src family isoforms. Proc. Natl. Acad. Sci. U.S.A.,111(34): 12420–12425, 2014. PMC4151743. Online article | Free PMC article
  32. Yumerefendi, H., Dickinson, D.J., Wang, H., Zimmerman, S., Bear, J.E., Goldstein, B., *Hahn, K. and *Kuhlman, B. Control of protein activity and cell fate specification via light-mediated nuclear translocation. PLoS One, 10(6): e0128443, 2015. PMC4471001. Online article | Free PMC article
  33. Hayashi-Takagi, A., Yagishita, S., Nakamura, M., Shirai, F., Wu, Y.I., Loshbaugh, A.L., Kuhlman, B., Hahn, K.M., and Kasai, H. Labelling and optical erasure of synaptic memory traces in the motor cortex. Nature, 525(7569): 333-8, 2015.  PMC4634641. Online article |Free PMC article
  34. Gentry, L.R., Karginov, A.V., Hahn, K.M. and Der, C.J. Characterization of an engineered Src kinase to study Src signaling and biology. Methods Mol. Biol., 1360: 157-167, 2016. PMC4621786. Online article | Free PMC article
  35. MacNevin, C.J., Toutchkine, A., Marston, D.J., Hsu, C.W., Tsygankov, D., Li, L., Liu, B., Qi, T., Nguyen, D.V. and Hahn, K.M. Ratiometric imaging using a single dye enables simultaneous visualization of Rac1 and Cdc42 activation. J. Am. Chem. Soc., 138(8): 2571-2575, 2016. PMC4825053. Online article Free PMC article
  36. Yumerefendi, H., Lerner, A.M., Zimmerman, S.P., Hahn, K.M., Bear, J.E., Strahl, B.D. and Kuhlman, B. Light-induced nuclear export reveals rapid dynamics of epigenetic modifications. Nature Chem. Biol., 12(6): 399-401, 2016. PMC488806. Online article | Free PMC article
  37. *Hodgson, L., *Spiering, D., Sabouri-Ghomi, M., DerMardirossian, C., *Danuser, G., and *Hahn, K.M. FRET binding antenna reports spatioteGDI-Cdc42 GTPase interactions. Nature Chem. Biol., 12(10): 802-9, 2016. PMC5030135. Online article | Free PMC article
  38. Wang, W., Vilela, M., Winkler, A., Tarnawski, T. Schlichting, I., Yumerefendi, H., Kuhlman, B., Liu, R., Danuser, G., and Hahn, K.M. LOVTRAP, An Optogenetic System for Photo-induced Protein Dissociation. Nature Methods, 13(9): 755-8, 2016PMC5137947. Online article Free PMC article
  39. Wang, H. and Hahn, K.M. LOVTRAP: a versatile method to control protein function with light. Curr. Protoc. Cell Biol., 73: 21.10.1 - 21.10.14, 2016. PMC5137945. Online article | Free PMC arqticle
  40. Dagliyan, O., Tarnawski, M., Chu, P-H., Shirvanyants, D., Schlichting, I., *Dokholyan, N.V., and *Hahn, K.M. Engineering extrinsic disorder to control protein activity in living cells. Science, 354(6318): 1441-1444, 2016. PMC5362825. View free in Science online: Full text PDF Free PMC article
  41. Dagliyan, O., Karginov, A.V., Yagishita, S., Gale, M.E., Wang, H., DerMardirossian, C., Wells, C.M., Dokholyan, N.V., Kasai, H. and Hahn, K.M. Engineering Pak1 Allosteric Switches. ACS Synth. Biol., 6 (7): 1257–1262, 2017. PMC5562282. Online article | Free PMC article
  42. Van Haren, J., Charafeddine, R.A., Ettinger, A., Wang, H., Hahn, K.M., and Wittman, T. Local Control of Intracellular Microtubule Dynamics by EB1 Photo-Dissociation. Nature Cell Biol., 20(3):252261, 2018. PMC5826794. Online article | Free PMC article
  43. Yumerefendi, H., Wang, H., Dickinson, D.J., Lerner, A., Malkus, P., Goldstein, B., Hahn, K., and Kuhlman, B. Light-dependent cytoplasmic recruitment enhances the dynamic range of a nuclear import photoswitch.Chembiochem., 9(12):1319-1325, 2018. PMC6013380. Online article | Free PMC article
  44. Dagliyan, O., Krokhotin, A., Ozkan-Dagliyan, I., Deiters, A., Der, C.J., Hahn, K.M. and Dokholyan, N.V. Computational design of chemogenetic and optogenetic split proteins. Nature Communications, 9: 1-8, 2018. Doi: 10.1038/s41467-018-06531-4. online article | Free PMC article
  45. MacNevin, C.J., Watanabe, T., Weitzman, M., Gulyani, A., Fuehrer, S., Pinkin, N.K., Tian, X., Liu, F., Jin, J., and Hahn, K.M. Membrane-Permeant, Environment-Sensitive Dyes Generate Biosensors within Living Cells. J. Am. Chem. Soc. 141(18):7275-7282., 2019. Online article
  46. Dagliyan, O., Dokholyan, N.V., and Hahn, K.M. Engineering proteinsfor allosteric control by light or ligands. Nature Protocols, 2019 Jun;14(6): 1863-1883. doi: 10.1038/s41596-019-0165-3. [Epub before print] Online article

 

~ Updated 03/10/2021

© UNC Department of Pharmacology