Collaborations & Publications

The Palmer Lab is involved in active collaborations with the following labs:

  • Natalie Ahn, CU Biochemistry, CU Biofrontiers Institute – Mass Spectrometry
  • Stephanie Bryant, CU Chemical and Biological Engineering – 3D Tissue Culture Models
  • Pascale Cossart, Institut Pasteur – Listeria Pathogenesis
  • Corrie Detweiler, CU Molecular Cellular and Developmental Biology – Salmonella Infections in Mouse Models
  • Dorota Gryko, Polish Academy of Sciences Institute of Organic Chemistry – Synthesis of Organometallic Compounds
  • Ralph Jimenez, JILA, NIST, CU Chemistry – Optically Integrated Microfluidics
  • Kevin Jones, CU Molecular Cellular Developmental Biology – Calcium and Neurodegeneration
  • Leslie Leinwand, CU Molecular Cellular Developmental Biology, CU Biofrontiers Institute – Cardiomyocyte Biology
  • Rafael Piestun, CU Department of Electrical and Computer Engineering, CU Department of Physics – Optical Radiation
  • Erik Snapp, Albert Einstein College of Medicine – Department of Anatomy and Structural Biology – Quality Control in the Endoplasmic Reticulum
  • Rotem Sorek, Weizmann Institute of Science – Microbial Genomics
  • Sabrina Spencer, CU Biochemistry – Cell Cycle Regulation
  • Alexis Templeton, CU Geological Sciences – Imaging Microbial Biofilms
  • Vladislav Verkusha, Albert Einstein College of Medicine – Department of Anatomy and Structural Biology – Fluorescent Protein Engineering
  • Adrie Von Bockhoven, UC Denver – Zinc in Prostate Cancer

The Palmer Lab is also associated with the following training programs and initiatives:

Palmer Lab Publications:

For most up to date list, click here.

76. Young, A.M. & Palmer, A.E. Methods to illuminate the role of Salmonella effector proteins during infection: A review. Frontiers in Cellular and Infection Microbiology 2017, 7:363.

75. Carter, K.P., Carpenter, M.C., Fiedler, B., Jimenez, R. & Palmer, A.E. Critical comparison of FRET-sensor functionality in the cytosol and endoplasmic reticulum and implications for quantification of ions. Analytical Chemistry 2017.

74. Young, A.M., Minson, M., McQuate, S.E. & Palmer, A.E. Optimized fluorescence complementation platform for visualizing Salmonella effector proteins reveals distinctly different intracellular niches in different cell types. ACS Infectious Diseases 2017, 3(8):575-84.

73. Carpenter, M.C. & Palmer, A.E. Native and engineered sensors for Ca2+ and Zn2+: Lessons from calmodulin and MTF1. Essays in Biochemistry 2017, 61(2):237-43.

72. Lauinger, L., Li, J., Shostak, A., Cemel, I.A., Ha, N., Zhang, Y., Merkl, P.E., Obermeyer, S., Stankovic-Valentin, N., Schafmeier, T., Wever, W.J., Bowers, A.A., Carter, K.P., Palmer, A.E., Tschochner, H., Melchior, F., Deshaies, R.J., Brunner, M. & Diernfellner, A. Thiolutin is a zinc chelator that inhibits the Rpn11 and other JAMM metalloproteases. Nature Chemical Biology 2017, 13(7):709-14.

71. Sanford, L. & Palmer, A.E. Recent advances in development of genetically encoded fluorescent sensors. Methods in Enzymology 2017, 589:1-49.

70. Mo, G.C., Ross, B., Hertel, F., Manna, P., Yang, X., Greenwald, E., Booth, C., Plummer, A.M., Tenner, B., Chen, Z., Wang, Y., Kennedy, E.J., Cole, P.A., Fleming, K.G., Palmer, A., Jimenez, R., Xiao, J., Dedecker, P. & Zhang, J. Genetically encoded biosensors for visualizing live-cell biochemical activity at super-resolution. Nature Methods 2017, 14(4):427-34.

69. Li, J., Yakushi, T., Parlati, F., Mackinnon, A.L., Perez, C., Ma, Y., Carter, K.P., Colayco, S., Magnuson, G., Brown, B., Nguyen, K., Vasile, S., Suyama, E., Smith, L.H., Sergienko, E., Pinkerton, A.B., Chung, T.D.Y., Palmer, A.E., Pass, I., Hess, S., Cohen, S.M. & Deshaies, R.J. Capzimin is a potent and specific inhibitor of proteasome isopeptidase Rpn11. Nature Chemical Biology 2017, 13(5):486-93.

68. Fiedler, B.L., Van Buskirk, S., Carter, K.P., Qin, Y., Carpenter, M.C., Palmer, A.E. & Jimenez, R. Droplet microfluidic flow cytometer for sorting on transient cellular responses of genetically-encoded sensors. Analytical Chemistry 2017, 89(1):711-9.

67. Specht, E.A., Braselmann, E. & Palmer, A.E. A critical and comparative review of fluorescent tools for live-cell imaging. Annual Review of Physiology 2017, 79:93-117.

66. Rodriguez, E.A., Campbell, R.E., Lin, J.Y., Miyawaki, A., Palmer, A.E., Shu, X., Zhang, J. & Tsien, R.Y. The growing and glowing toolbox of fluorescent and photoactive proteins. Trends in Biochemical Sciences 2016, 42(2):111-29.

65. Qin, Y., Sammond, D.W., Braselmann, E., Carpenter, M.C. & Palmer, A.E. Development of an optical Zn2+ probe based on a single fluorescent protein. ACS Chemical Biology 2016, 11(10):2744-51.

64. Palmer, A.E. & Zhang, J. Roger Y. Tsien 1952-2016. Nature Chemical Biology 2016, 12(11):887.

63. Carpenter, M.C., Lo, M.N. & Palmer, A.E. Techniques for measuring cellular zinc. Archives of Biochemistry and Biophysics 2016, 611:20-9.

62. McQuate, S.E., Young, A.M., Silva-Herzog, E., Bunker, E., Hernandez, M., de Chaumont, F., Liu, X., Detweiler, C.S. & Palmer, A.E. Long-term live cell imaging reveals new roles For Salmonella effector proteins SseG and SteA. Cellular Microbiology 2016, 19(1):e12641.

61. Carpenter, M.C. & Palmer, A.E. Unraveling the mystery of the ring: Tracking heme dynamics in living cells. Proc. Natl. Acad. Sci. USA 2016, 113(27):7296-7.

60. Dean, K.M., Davis, L.M., Lubbeck, J.L., Manna, P., Friis, P., Palmer, A.E. & Jimenez, R. High-speed multiparameter photophysical analyses of fluorophore libraries. Analytical Chemistry 2015, 87(10):5026-30.

59. Kim, T.-J., Joo, C., Seong, J., Vafabakhsh, R., Botvinick, E.L., Berns, M.W., Palmer, A.E., Wang, N., Ha, T., Jakobsson, E., Sun, J. & Wang, Y. Distinct mechanisms regulating mechanical force-induced Ca2+ signals at the plasma membrane and the ER in human MSCs. eLife 2015, 4:e04876.

58. Carter, K.P. & Palmer, A.E. Metallobiology: zinc differently. Nature Chemistry 2015, 7(2):96-7.

57. Park, J.G. & Palmer, A.E. Properties and use of genetically encoded FRET sensors for cytosolic and organellar Ca2+ measurements. Cold Spring Harbor Protocols 2015, 2015(1):pdb.top066043.

56. Park, J.G. & Palmer, A.E. Measuring the in situ Kd of a genetically encoded Ca2+ sensor. Cold Spring Harbor Protocols 2015, 2015(1):pdb.prot076554.

55. Park, J.G. & Palmer, A.E. Verifying the function and localization of genetically encoded Ca2+ sensors and converting FRET ratios to Ca2+ concentrations. Cold Spring Harbor Protocols 2015, 2015(1):pdb.prot076547.

54. Dean, K.M., Lubbeck, J.L., Davis, L.M., Regmi, C.K., Chapagain, P.P., Gerstman, B.S., Jimenez, R. & Palmer, A.E. Microfluidics-based selection of red-fluorescent proteins with decreased rates of photobleaching. Integrative Biology : Quantitative Biosciences From Nano to Macro 2014, 7(2):263-73.

53. Farnsworth, N.L., Mead, B.E., Antunez, L.R., Palmer, A.E. & Bryant, S.J. Ionic osmolytes and intracellular calcium regulate tissue production in chondrocytes cultured in a 3D charged hydrogel. Matrix Biology : Journal of the International Society for Matrix Biology 2014, 40:17-26.

52. Dean, K.M. & Palmer, A.E. Advances in fluorescence labeling strategies for dynamic cellular imaging. Nature Chemical Biology 2014, 10(7):512–23.

51. Carter, K.P., Young, A.M. & Palmer, A.E. Fluorescent sensors for measuring metal ions in living systems. Chemical Reviews 2014, 114(8):4564–601.

50. Park, J.G. & Palmer A.E. Quantitative measurement of Ca2+ and Zn2+ in mammalian cells using genetically encoded fluorescent biosensors. Methods in Molecular Biology 2013, 1071:29-47.

49. Stavru, F., Palmer, A.E., Wang, C., Youle, R.J. & Cossart, P. Atypical mitochondrial fission upon bacterial infection. Proc. Natl. Acad. Sci. USA 2013, 110(40):16003–8.

48. Qin, Y., Miranda, J.G., Stoddard, C.I., Dean, K.M., Galati, D.F. & Palmer, A.E. Direct comparison of a genetically encoded sensor and small molecule indicator: Implications for quantification of cytosolic Zn2+. ACS Chemical Biology 2013, 8(11):2366−71.

47. Davis, L.M., Lubbeck, J.L., Dean, K.M., Palmer, A.E. & Jimenez, R. Microfluidic cell sorter for use in developing red fluorescent proteins with improved photostability. Lab on a Chip 2013 13(12), 2320-7.

46. Jeong, J., Walker, J.M., Wang, F., Park, J.G., Palmer, A.E., Guita, C., Rohrbach, M., Steinmann, B. & Eide, D.J. Promotion of vesicular zinc efflux by Zip13 and its implications for spondylocheiro dysplastic Ehlers-Danlos syndrome. Proc. Natl. Acad. Sci. USA 2012, 109(51):E3530-8.

45. Miranda, J.G., Weaver, A.L., Qin, Y., Park, J.G., Stoddard, C.I., Lin, M.Z. & Palmer, A.E. New alternately colored FRET sensors for simultaneous monitoring of Zn2+ in multiple cellular locations. PLoS ONE 2012, 7(11):e49371.

44. Geng, X., Huang, C., Qin, Y., McCombs, J.E., Yuan, Q., Harry, B.L., Palmer, A.E., Xia, N.S. & Xue, D. Hepatitits B virus X protein targets Bcl-2 proteins to increase intracellular calcium, required for virus replication and cell death induction.  Proc. Natl. Acad. Sci. USA 2012, 109(45):18471-6.

43. Park, J.G., Qin, Y. Galati, D.F. & Palmer, A.E. New sensors for quantitative measurement of mitochondrial zinc(II). ACS Chemical Biology 2012, 7(10):1636-40.

42. Dean, K.M., Qin, Y. & Palmer, A.E. Visualizing metal ions in cells: An overview of analytical techniques, approaches, and probes. Biochim. Biophys. Acta. 2012, 1823(9):1406-15.

41. West, D.C., Qin, Y., Peterson, Q.P., Thomas, D.L., Palchaudhuri, R., Morrison, K.C., Lucas, P.W., Palmer, A.E., Fan, T.M. & Hergenrother, P.J. Differential effects of procaspase-3 activating compounds in the induction of cancer cell death. Molecular Pharmaceutics 2012, 9(5):1425-34.

40. Lubbeck, J.L., Dean, K.M., Ma, H., Palmer, A.E. & Jimenez, R. Microfluidic flow cytometer for quantifying photobleaching of fluorescent proteins in cells. Analytical Chemistry 2012, 9(5):1425-34.

39. Ma, H., Gibson, E.A., Dittmer, P.J., Jimenez, R. & Palmer, A.E. High-throughput examination of FRET-detected metal ion response in mammalian cells. J. Am. Chem. Soc. 2012, 134(5):2488-91.

38. Dean K.M., Lubbeck J.L., Binder J.K., Schwall L.R., Jimenez R & Palmer A.E. Analysis of red-fluorescent proteins provides insight into dark-state conversion and photodegradation. Biophysical Journal 2011, 101(4):961-9.

37. Qin, Y., Dittmer, P.J., Park, J.G., Jansen, K.B. & Palmer, A.E. Measuring Steady State and Dynamic ER and Golgi Zn2+ with Genetically Encoded Sensors. Proc. Nat. Acad. Sci. USA 2011, 108(18):7351-6.

36. Palmer, A.E., Qin, Y., Park, J.G. & McCombs, J.E. Design and application of genetically encoded biosensors. Trends in Biotechnology 2011, 29(3):144-52.

35. Perocchi, F., Gohil, V.M., Girgis, H.S., Bao, X.R., McCombs, J.E., Palmer, A.E. & Mootha, V.K. MICU1 encodes a mitochondrial EF hand protein required for Ca(II) uptake. Nature 2010, 467(7313):291-6.

34. Ravier, M.A, Cheng-Xue, R., Palmer, A.E., Henquin, J.C. & Gilon, P. Subplasmalemmal Ca(2+) measurements in mouse pancreatic beta cells support the existence of an amplifying effect of glucose on insulin secretion. Diabetologia 2010, 53(9):1947-57.

33. Ong, D.S., Mu, T.W., Palmer, A.E. & Kelly, J.W. Endoplasmic reticulum Ca2+ increases enhance mutant glucocerebrosidase proteostasis. Nature Chemical Biology 2010, 6(6):424-32.

32. Palmer, A.E. & Dittmer, P.J. SNAP-shots of hydrogen peroxide in cells. Chemistry & Biology 2010, 17(4):318-9.

31. McCombs, J.E., Gibson, E.A. & Palmer, A.E. Using a genetically targeted sensor to investigate the role of presinillin-1 in ER Ca2+ levels and dynamics. Molecular Biosystems 2010, 6(9):1640-9.

30. Van Engelenburg, S.B. & Palmer, A.E. Imaging type-III secretion reveals dynamics and spatial segregation of Salmonella effectors. Nature Methods 2010 7(4):325-30. * This work was highlighted in the Nature Structural Molecular Biology

29. Van Engelenburg, S.B., Nahreini, T. & Palmer, A.E. FACS-based selection of tandem tetracysteine peptides with improved ReAsH brightness in live cells. Chembiochem 2010, 11(4):489-93.

28. Palmer, A.E. & Franz, K.J. Introduction to “cellular metal homeostasis and trafficking”. Chemical Reviews 2009, 109(10):4533-5.

27. Schafer, D., Gibson, E.A., Salim, E.A., Palmer, A.E. & Jimenez R. Microfluidic cell counter with embedded optical fibers fabricated by femtosecond laser ablation and anodic bonding. Optics Express 2009, 17(8):6068-73.

26. Dittmer, P.J., Miranda, J.G., Gorski, J.A. & Palmer, A.E. Genetically encoded sensors to elucidate spatial distribution of cellular zinc. Journal of Biological Chemistry. 2009, 284(24):16289-97.

25. Palmer, A.E. Expanding the repertoire of fluorescent calcium sensors. ACS Chemical Biology 2009, 4(3):157-9.

24. McCombs, J.E. & Palmer, A.E. Measuring calcium dynamics in living cells with genetically encodable calcium indicators. Methods 2008, 46(3):152-9.

23. Wallace, D.J., Borgloh, S.M.z.A., Yang, Y., Bausen, M., Kugler, S., Palmer, A.E., Tsien, R.Y., Sprengel, R., Kerr, J.N.D., Denk, W. & Hasan, M.T. Single-spike detection in vitro and in vivo with a genetic Ca2+ sensor. Nature Methods 2008, 5(9):797-804.

22. Van Engelenburg, S.B. & Palmer, A.E. Quantification of real-time Salmonella effector type III secretion kinetics reveals differential secretion rates for SopE2 and SptP. Chemistry & Biology 2008, 15(6):619-28.

21. Xu, C., Xu, W., Palmer, A.E. & Reed, J.C. BI-1 regulates endoplasmic reticulum Ca2+ downstream of Bcl-2-family proteins. Journal of Biological Chemistry. 2008, 283(17):11477-84.

20. Van Engelenburg, S.B. & Palmer, A.E. Fluorescent sensors of protein function. Current Opinion Chemical Biology 2008, 12(1):60-5.

19. Palmer, A.E. & Tsien, R. Y. Measuring calcium signaling using genetically targetable fluorescent indicators. Nature Protocols 2006, 1(2):1-9.

18. Palmer, A.E., Giacomello, M., Kortemme, T., Hires, S.A., Lev-Ram, V., Baker, D. & Tsien R.Y. Ca2+ indicators based on computationally-redesigned calmodulin-peptide pairs. Chemistry and Biology 2006, 13:521-530

17. Duman, J.G., Chen, L., Palmer A.E. & Hille, B. Contributions of intracellular compartments to calcium dynamics: Implicating an acidic store. Traffic 2006, 7:859-72.

16. Qunitanar, L., Yoon, J., Aznar, C.P., Palmer, A.E., Andersson, K.K., Britt, R.D. & Solomon, E.I. Spectroscopic and electronic structure studies of the trinuclear Cu cluster active site of the multicopper oxidase laccase: nature of its coordination unsaturation. J. Am. Chem. Soc. 2005, 127(40):13832-45.

15. Palmer, A.E., Jin, C., Reed, J.C. & Tsien, R.Y. Bcl-2 mediated alterations in endoplasmic reticulum Ca2+ analyzed with an improved genetically encoded fluorescent sensor. Proc. Natl. Acad. Sci. 2004, 101(50):17404-9.* This work was highlighted in BioTechniques 2005, 38:1, p1 and Nature Reviews Molecular Cell Biology 2005, 6, p92.

14. Shaner, N.C., Campbell, R.E., Steinbach, P.A., Giepmans, B.N.G., Palmer, A.E. & Tsien, R.Y. Improved monomeric red, orange, and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein. Nature Biotechnology 2004, 22:1567-72.

13. Andersson, K.K., Schmidt, P.P., Katterle, B., Strand, K., Palmer, A.E., Lee, S.-K., Solomon, E.I., Graslund, A. & Barra, A.-L. Examples of high frequency EPR studies in bioinorganic chemistry. J. Biol. Inorg. Chem. 2003, 8:235-47.

12. Palmer, A.E., Szilagyi, R.K., Cherry, J.R., Jones, A., Xu, F. & Solomon, E.I. Spectroscopic characterization of the Leu513His variant of fungal laccase: effect of increased axial ligand interaction on the geometric and electronic structure of the Type 1 Cu site. Inorganic Chemistry 2003, 42:4006-17.

11. Campbell, R.E., Tour, O., Palmer, A.E., Steinbach, P.A., Baird, G.S., Zacharias, D.A. & Tsien, R.Y. A monomeric red fluorescent protein. Proc. Natl. Acad. Sci. 2002, 99:7877-82.

10. Palmer, A.E., Quintanar, L., Severance, S., Wang, T.-P., Kosman, D.J. & Solomon, E.I. Spectroscopic characterization and O2 reactivity of the trinuclear Cu cluster of mutants of the multicopper oxidase Fet3p. Biochemistry 2002, 41:6438-48.

9. Palmer, A.E., Lee, S.K. & Solomon E. I. Decay of the peroxide intermediate in laccase: Reductive cleavage of the O-O bond. J. Am. Chem. Soc. 2001, 123:6591-9.

8. Solomon, E.I., Chen, P., Lee, S.K., Metz, M. & Palmer, A.E. Oxygen binding, activation, and reduction to water by copper proteins. Angew. Chemie Int. Ed. 2001, 40(24):4570-90.

7. Machonkin, T.E., Quintanar, L., Palmer, A.E., Hassett, R.F., Severance, S., Kosman, D.J. & Solomon, E.I. Spectroscopic characterization of FET3p, a new member of the multicopper oxidase family. J. Am. Chem. Soc. 2001, 123:5507-17.

6. Palmer, A.E., Randall, D.W., Xu, F. & Solomon, E.I. Spectroscopic studies and electronic structure description of the high potential type 1 copper site in fungal laccase: Insight into the effect of the axial ligand. J. Am. Chem. Soc. 1999, 121:7138-49.

5. Xu, F., Palmer, A.E., Yaver, D.S., Berka, R.M., Gambetta, G.A., Brown, S.H. & Solomon, E.I. Targeted mutations in a Trametes villosa laccase: axial perturbations of the T1 copper. J. Biol. Chem. 1999, 274:12372-5.

4. Wilcox, D.E., Bennett, L.L., Cox, E.H., Haleblian, G., Hill, B.T., Kowack, E.P., Liu, X., Merkel, J.S., Palmer, A.E., Posewitz, M.C., Roy, J.F. & Wetterhahn, K.E. Interaction of metallothionein with carcinogenic metals Ni(II), Cr(VI), and As(III). In: Metallothionein IV. Ed: Klassen, C.D. 1999, Birkhauser: Basel, p 585-594.

3. Solomon, E.I., Palmer, A.E., Sundaram, U.M. & Machonkin, T.E. Spectroscopic studies of O2 intermediates in copper proteins: electronic structure contributions to function in bioinorganic chemistry. In: Spectroscopic Methods in Bioinorganic Chemistry. Eds: Solomon, E.I. and Hodgson, K.O. 1998, ACS: Washington, D.C., p 423-452.

2. Xu, F., Berka, R.M., Wahleithner, J.A., Nelson, B.A., Shuster, J.R., Brown, S.H., Palmer, A.E. & Solomon, E.I. Site directed mutations in fungal laccase: Effect on redox potential, activity, and pH profile. Biochemical J. 1998, 334:63-70

1. Bobilya, D. J., D’Amour, K., Palmer, A., Skeffington, C., Therrien, N. & Tibaduiza, E. C. Isolation and cultivation of porcine brain capillary endothelial cells as an in vitro model of the blood-brain barrier. Methods in Cell Science 1995, 17:25-32.