Zhang complete publications_august 2013

Jin Zhang, Ph.D.
Department of Pharmacology and Molecular Sciences Johns Hopkins University School of Medicine Publications
1. Woodard CL, Goodwin CR, Wan J, Xia S, Hu J, Newman RH, Zhang J,
Hayward, SD, Qian J, Laterra J, Zhu H. Profiling the dynamics of a human phosphorylome reveals new components in HGF/c-Met signaling. PLoS One, 2013, accepted. 2. Burdyga A, Conant A, Haynes L, Zhang J, Jalink K, Sutton R, Neoptolemos J,
Costello E, and Tepikin A. cAMP inhibits migration, ruffling and paxillin accumulation in focal adhesions of pancreatic ductal adenocarcinoma cells: Effects of PKA and EPAC. Biochim Biophys Acta. 2013, in press. 3. Hertel F, Zhang J. Monitoring of post-translational modification dynamics with
genetically encoded fluorescent reporters. Biopolymers 2013, in press. 4. Nunes AR, Holmes AP, Sample V, Kumar P, Cann MJ, Monteiro EC, Zhang J,
Gauda EB. Bicarbonate-Sensitive Soluble and Transmembrane Adenylyl Cyclases in Peripheral Chemoreceptors. Respir Physiol Neurobiol. 2013, 188(2):83-93. 5. Huang J, Yang JR, Zhang J†, Yang J†. Total Synthesis and Structure-Activity
Relationship Study of the Potent cAMP Signaling Agonist (-)-Alotaketal A. †Co-corresponding authors. Org. Biomol. Chem. 2013, 11(19): 3212-22. 6. Newman RE*, Hu J*, Rho H*, Xie Z*, Woodard C, Neiswinger J, Hwang W, Shirley M, Hu S, Cooper C, Jeong JS, Wu G, Lin J, Gao X, Ni Q, Ji H, Desiderio S, Dalby
KN, Birnbaum MJ, Cole PA, Knapp S, Ryazanov A, Zack DJ, Blackshaw S,
Pawson T, Gingras A, Pandey A, Turk BE, Zhang J†, Zhu H†, Qian J†.
Construction of a High-Resolution Map of Phosphorylation Networks in Humans.
*Equal contribution. †Co-corresponding authors. Mol. Syst. Biol. 2013; 9:655
7. Hu J*, Rho HS*, Newman RH*, Hwang W, Neiswinger J, Zhu H†, Zhang J†,
Qian J†. Global analysis of phosphorylation networks in humans. *Equal contribution. †Co-corresponding authors. Biochim Biophys Acta. 2013, S1570-9639(13)00122-2. 8. Depry C, Mehta S, and Zhang J. Multiplexed visualization of dynamic signaling
networks using genetically encoded fluorescent protein-based biosensors. Pflugers Arch. 2013; 465(3): 373-81. 9. Sample V, Ni Q, Mehta S, Inoue T, Zhang J. Controlling Enzymatic Action in
Living Cells with a Kinase-Inducible Bimolecular Switch. ACS Chem Biol. 2013; 8(1): 116-21. 10. Dedecker P, Duwé S, Neely RK, Zhang J. Localizer: fast, accurate, open-source,
and modular software package for superresolution microscopy. J. Biomed. Opt. 2012; 17(12): 126008. 11. Ghigo A, Perino A, Mehel H, Zahradníková A Jr, Morello F, Leroy J, Nikolaev VO, Damilano F, Cimino J, De Luca E, Richter W, Westenbroek R, Catterall WA,
Zhang J, Yan C, Conti M, Gomez AM, Vandecasteele G, Hirsch E, Fischmeister
R. Phosphoinositide 3-kinase γ protects against catecholamine-induced
ventricular arrhythmia through protein kinase A-mediated regulation of distinct
phosphodiesterases. Circulation, 2012; 126(17): 2073-83.
12. Nunes AR, Sample V, Xiang YK, Monteiro EC, Gauda E, Zhang J. Effect of
oxygen on phosphodiesterases (PDE) 3 and 4 isoforms and PKA activity in the superior cervical ganglia. Adv Exp Med Biol. 2012; 758:287-94. 13. Martinez-Ferrando I, Chaerkady R, Zhong J, Molina H, Kishore H, Herbst- Robinson K, Dancy BM, Katju V, Bose R, Zhang J, Pandey A, and Cole PA.
Identification of targets of c-Src tyrosine kinase by chemical complementation
and phosphoproteomics. Mol. Cell Proteomics. 2012; 11(8): 355-69.
14. Dancy BM, Crump NT, Peterson DJ, Mukherjee C, Bowers EM, Ahn Y, Yoshida M, Zhang J, Mahadevan LC, Meyers DJ, Boeke JD, Cole PA. Live cell studies of
p300/CBP Histone Acetyltransferase Activity and Inhibition. ChemBioChem
2012; 13(14): 2113-21.
15. Dedecker P†, Mo GCH, Dertinger T, and Zhang J†. Widely accessible method for
superresolution fluorescence imaging of living systems. †Co-corresponding authors. Proc. Natl. Acad. Sci. USA 2012; 109(27): 10909-14. 16. Ganesan A and Zhang J. How cells process information: Quantification of
spatiotemporal signaling dynamics. Protein Sci. 2012; 21(7): 918-28. 17. Huang J, Yang J, Zhang J† and Yang J†. Total Synthesis of the Potent cAMP
Signaling Agonist (-)-Alotaketal A. †Co-corresponding authors. J. Am. Chem. Soc. 2012; 134(21): 8806-9. 18. Aye-Han NN, Allen MD, Ni Q, and Zhang J. Parallel tracking of cAMP and PKA
signaling dynamics in living cells with FRET-based fluorescent biosensors. Mol. Biosyst. 2012; 8(5):1435-40. 19. Sample V*, DiPilato LM*, Yang J*, Ni Q1, Saucerman JJ† and Zhang J†.
Regulation of Nuclear PKA revealed by spatiotemporal manipulation of cAMP. *Equal contribution. †Co-corresponding authors. Nat. Chem. Biol. 2012; 8(4): 375-82. 20. del Puerto A, Díaz-Hernández J, Tapia M, Gómez-Villafuertes R, Benitez M, Zhang J, Miras-Portugal M, Wandosell F, Díaz-Hernandez M, and Garrido J.
Adenylate cyclase 5 coordinates the action of ADP, P2Y1, P2Y13, and ATP-
gated P2X7 receptors on axonal elongation. J. Cell Sci. 2012; 125 (Pt 1): 176-88.
21. Zhou X, Herbst-Robinson KJ and Zhang J. Visualizing dynamic activities of
signaling enzymes using genetically encodable FRET-based biosensors from designs to applications. Method Enzymol. 2012; 504:317-40. 22. Gao X, Lowry P, Zhou X, Depry C, Wei Z, Wong GW, and Zhang J. PI3K/Akt
signaling requires spatial compartmentalization in plasma membrane microdomains. Proc. Natl. Acad. Sci. USA 2011; 108(35): 14509-14. 23. Chakir K, Depry C, Dimaano VL, Zhu W, Vanderheyden M, Bartunek J, Abraham TP, Tomaselli GF, Liu S, Xiang YK, Zhang M, Takimoto E, Dulin N, Xiao RP,
Zhang J, and Kass DA. Gαs-Biased ß2-Adrenergic Signaling from Restoring
Synchronous Contraction in the Failing Heart. Sci. Transl. Med. 2011; 3(100): 100ra88. 24. Depry C and Zhang J. Using FRET-Based Reporters to Visualize Subcellular
Dynamics of Protein Kinase A Activity. Method Mol. Biol. 2011; 756: 285-94. 25. Herbst KJ, Allen MD, and Zhang J. Spatiotemporally regulated PKA activity is a
critical regulator of growth factor-stimulated ERK signaling in PC12 cells. Mol. Cell Biol. 2011; 31(19): 4063-75. 26. Herbst KJ, Allen MD, and Zhang J. Luminescent kinase activity biosensors
based on a versatile molecular switch. J. Am. Chem. Soc. 2011; 133(15): 5676-9 27. Mehta S and Zhang J. Reporting from the Field ─ Genetically-Encoded
Fluorescent Reporters Uncover Signaling Dynamics in Living Biological Systems. Annu. Rev. Biochem. 2011; 80: 375-401. 28. Newman RH, Fosbrink M and Zhang J. Genetically Encoded Fluorescent
Biosensors for Tracking Signaling Dynamics in Living Cells. Chem. Rev. 2011; 111(5): 3614-66. 29. Wan M, Li J, Herbst K, Zhang J, Yu B, Wu X, Qiu T, Lei W, Lindvall C, Williams
BO, Ma H, Zhang F and Cao X. LRP6 Mediates GPCR-Induced cAMP Generation by Regulation of Gαs Membrane Targeting. Sci. Sig. 2011; 4(164): ra15. 30. Herbst KJ, Coltharp C, Amzel LM and Zhang J. Direct Activation of Epac by
Sulfonylurea is Isoform Selective. Chem. Biol. 2011; 18(2): 243-51. 31. Liu S, Zhang J, and Xiang Y. FRET-based direct detection of dynamic protein
kinase A activity on the sarcoplasmic reticulum in cardiomyocytes. Biochem. Biophys. Res. Commun. 2011; 404(2): 581-6. 32. Ni Q*, Ganesan A*, Aye-Han N*, Gao X, Allen MD, Levchenko A†, and Zhang J†.
Signaling Diversity of PKA via a Ca2+-cAMP-PKA Oscillatory Circuit. *Equal contribution. †Co-corresponding authors. Nat. Chem. Biol. 2011; 7(1): 34-40. 33. Depry C, Allen MD, and Zhang J. Visualization of PKA activity in Plasma
Membrane Microdomains. Mol. BioSyst., 2011, 7(1): 52-8 34. Gildea JJ, Shah I, Weiss R, Casscells ND, McGrath HE, Zhang J, and Felder
RA. HK-2 Human Renal Proximal Tubule Cells as a Model for G Protein-Coupled Receptor Kinase Type 4-Mediated Dopamine 1 Receptor Uncoupling. Hypertension 2010; 56(3): 505-11 35. Depry C and Zhang J. Visualization of kinase activity with FRET-based activity
biosensors. Curr. Protoc. Mol. Biol. 2010; Chapter 18: Unit 18.15. 36. Yamashiro T, Kuge H, Zhang J and Honke K. Calcineurin Mediates The
Angiotensin II-induced Aldosterone Synthesis in the Adrenal Glands by Upregulation of Transcription of The CYP11B2 Gene. J. Biochem. 2010; 148(1):115-23 37. Fosbrink M, Aye-Han N and Zhang J. Visualization of JNK Activity Dynamics
with a Genetically Encoded Fluorescent Biosensor. Proc. Natl. Acad. Sci. USA 2010; 107(12): 5459-64. 38. Gao X and Zhang J. FRET-based activity biosensors to probe
compartmentalized signaling. Chembiochem 2010; 11(2): 147-51 39. DiPilato LM and Zhang J. Fluorescent protein-based biosensors: resolving
spatiotemporal dynamics of signaling. Curr. Opin. Chem. Biol. 2010;14(1): 37-42 40. Gildea JJ, Israel JA, Johnson AK, Zhang J, Jose PA and Felder RA. Caveolin-1
and dopamine-mediated internalization of NaKATPase in human renal proximal tubule cells. Hypertension 2009; 54(5):1070-6. 41. Sample V, Newman RH and Zhang J. The Structure and Function of Fluorescent
Proteins. Chem. Soc. Rev. 2009; 38(10): 2852-64 42. Aye-Han N, Ni Q and Zhang J. Fluorescence Biosensors for Real Time Tracking
of Post-translational Modification Dynamics. Curr. Opin. Chem. Biol. 2009; 13(4): 392-7 43. Herbst K, Ni Q and Zhang J. Dynamic Visualization of Signal Transduction in
Living Cells: from Second Messegners to Kinases. IUBMB Life 2009; 61(9): 902-8 44. DiPilato LM and Zhang J. The role of membrane microdomains in shaping β2-
adrenergic receptor-mediated cAMP dynamics. Mol. BioSyst. 2009; 5(8): 832-7 45. Herbst K, Allen MD and Zhang J. The cAMP-dependent Protein Kinase Inhibitor
H-89 Attenuates the Bioluminescent Signal Produced by Renilla Luciferase. PLoS ONE 2009; 4(5): e5642. 46. Soto D, De Arcangelis V, Zhang J and Xiang Y. Dynamic PKA activities induced
by b adrenoceptors dictate signaling propagation for substrate phosphorylation and myocyte contraction. Circ Res. 2009; 104(6):770-9 47. Seong J, Lu S, Ouyang M, Huang H, Zhang J, Frame MC and Wang Y.
Visualization of Src activity at different compartments of the plasma membrane by FRET imaging. Chem. Biol. 2009; 16(1):48-57 48. Zhang J. The colorful journey of green fluorescent protein. ACS Chem. Biol. 49. Rahdar M, Inoue T, Meyer T, Zhang J, Vazquez F and Devreotes PN. A
phosphorylation-dependent intramolecular interaction regulates the membrane association and activity of the tumor suppressor PTEN. Proc. Natl. Acad. Sci. USA 2009; 106(2):480-5. 50. Ren YR, Pan F, Parvez S, Fleig A, Chong CR, Xu J, Dang Y, Zhang J, Jiang H,
Penner R and Liu JO. Clofazimine inhibits human Kv1.3 potassium channel by perturbing calcium oscillation in T lymphocytes. PLoS ONE 2008; 3(12): e4009 51. Vincent P, Gervasi N and Zhang J. Real-time monitoring of cyclic nucleotide
signaling in neurons using genetically-encoded FRET probes. Brain Cell Biol. 2008; 36: 3-17 52. Ananthanarayanan B, Ni Q and Zhang J. Molecular sensors based on
fluorescence resonance energy transfer to visualize cellular dynamics. Method Cell Biol. 2008; 89: 37-57 53. Lim CJ, Kain KH, Tkachenko E, Goldfinger LE, Gutierrez E, Allen MD, Groisman A, Zhang J and Ginsberg MH. Integrin-mediated Protein Kinase A Activation at
the Leading Edge of Migrating Cells. Mol. Biol. Cell 2008; 19(11): 4930-4941.
54. Szewczuk LM, Tarrant MK, Sample V, Drury WJ 3rd, Zhang J and Cole PA.
Aalysis of Serotonin N-Acetyltransferase Regulation in Vitro and in Live Cells Using Protein Semisynthesis. Biochemistry 2008; 47(39): 10407-19. 55. Gao X and Zhang J. Spatiotemporal Analysis of Differential Akt Regulation in
Plasma Membrane Microdomains. Mol. Biol. Cell 2008; 19(10): 4366-73. 56. DiPilato LM and Zhang J. Second Messengers in Cellular Signaling. Wiley
57. Lu S, Ouyang M, Seong J, Zhang J, Chien S and Wang Y. The spatiotemporal
pattern of Src activation at lipid rafts reveraled by diffusion-corrected FRET imaging. PLoS Comput. Biol. 2008; 4(7): e1000127 58. Newman RH and Zhang J. Small molecules and chemical tools at the interface.
Nat. Chem. Biol. 2008; 4 (7) 4(7): 382-6 59. Newman RH and Zhang J. Visualization of phosphatase activity in living cells
with a FRET-based calcineurin activity sensor. Mol. BioSyst. 2008; 4(6): 496-501. 60. Newman RH and Zhang J. Fucci: street lights on the road to mitosis. Chem. Biol.
61. Violin JD*, DiPilato LM*, Yildrim N*, Elston TC†, Zhang J†, and Lefkowitz RJ†. β2-
Adrenergic Receptor Signaling and Desensitization Elucidated by Quantitative Modeling of Real-Time cAMP Dynamics. *Equal contribution. †Co-corresponding authors J. Biol. Chem. 2008; 283(5): 2949-2961 62. Allen MD and Zhang J. A Tunable FRET Circuit for Engineering Fluorescent
Biosensors. Angew. Chem. Int. Ed Engl. 2008;47(3): 500-2 63. Ananthanarayanan B, Fosbrink M, Rahdar M and Zhang J. Live-Cell Molecular
Analysis of Akt Activation Reveals Roles for Activation Loop Phosphorylation. J. Biol. Chem. 2007; 282(50): 36634-41 64. Ni Q and Zhang J. Dynamic Visualization of Cellular Signaling. A book chapter in
“Advances in Biochemical Engineering/Biotechnology”, edited by Endo I and Nagamune T. Springer, 2007. 65. Zhang J and Allen MD. FRET-based Kinase Biosensors – Illuminating the
Kinome. Mol. Biosyst. 2007; 3: 759-765 66. Maresh J, Zhang J, Tzeng Y, Goodman NA and Lynn DG. Rational Design of
Inhibitors of VirA-VirG Two-Component Signal Transduction. Bioorg. Med. Chem Lett. 2007; 17: 3281-6. 67. Sachs BD, Baillie GS, McCall JR, Passino MA, Schachtrup C, Wallace DA, Dunlop AJ, Mackenzie KF, Klussmann E, Lynch MJ, Sikorski SL, Nuriel T,
Tsigelny I, Zhang J, Houslay MD, Chao MV and Akassoglou K. p75 neurotrophin
receptor regulates tissue fibrosis through inhibition of plasminogen activation via
a PDE4/cAMP/PKA pathway. J. Cell Biol. 2007; 177: 1119-32.
68. Gervasi N, Hepp R, Tricoire L, Sureau F, Zhang J, Lambolez B, Paupardin-
Tritsch D and Vincent P. Subcellular integration of cyclic-AMP-dependant Protein Kinase A activity dynamics in neurons in mouse brain slices. J. Neurosci. 2007; 14: 2744 – 2750. 69. Dunn T, Wang C, Colicos MA, Zaccolo M, DiPilato LM, Zhang J, Tsien RY,
Feller MB. Imaging of cAMP levels and PKA activity reveals that retinal waves drive oscillations in second messenger cascades. J. Neurosci. 2006; 26:12807–12815. 70. DiPilato LM, and Zhang J. FRETting Mice Shed Light on Cardiac Adrenergic
Signaling. Circ. Res. 2006; 99: 1021–1023. 71. Allen MD and Zhang J. Subcellular Dynamics of Protein Kinase A Activity
Visualized by FRET-based Reporters. Biochem. Biophys. Res. Commun. 2006; 348: 716-721. 72. Allen MD, DiPilato LM, Rahdar M, Ren YR, Chong C, Liu JO and Zhang J.
Reading Dynamic Kinase Activity in Living Cells for High-throughput Screening. ACS Chem. Biol. 2006; 1: 371-376. 73. Saucerman JJ, Zhang J, Stenbit AE, Tsien RY and McCulloch AD. Systems
Analysis of PKA-mediated Phosphorylation Gradients in Cardiac Myocytes. Proc. Natl. Acad. Sci. USA 2006; 103: 12923-12928. 74. Ni Q, Titov DV and Zhang J. Analyzing Protein Kinase Dynamics in Living Cells
with FRET reporters. Methods 2006; 40: 279-286. 75. Maresh J*, Zhang J* and Lynn DG. The Innate Immunity of Maize and the
Dynamic Chemical Strategies Regulating Two-Component Signal Transduction in Agrobacterium tumefaciens. ACS Chem. Biol. 2006; 1: 165-175. * Equal contribution. 76. Qiao Y, Molina H, Pandey A, Zhang J and Cole PA. Chemical Rescue of a
Mutant Enzyme in Living Cells. Science 2006; 311: 1293-1297. 77. Ananthanarayanan B, Ni Q, and Zhang J. Signal propagation from membrane
messengers to nuclear effectors revealed by reporters of phosphoinositide dynamics and Akt activity. Proc. Natl. Acad. Sci. USA 2005; 102: 15081-15086. 78. Zhang J*, Hupfeld CJ*, Taylor SS, Olefsky JM, and Tsien RY. Insulin Disrupts
Beta-Adrenergic Receptor Signaling to Protein Kinase A in Adipocytes. Nature 2005; 437: 569-573.*Equal contribution. 79. Kunkel MT, Ni Q, Tsien RY, Zhang J and Newton AC. Spatio-temporal dynamics
of protein kinase B/Akt signaling revealed by a genetically-encoded fluorescent reporter. J. Biol. Chem. 2005; 280: 5581-5587. 80. DiPilato LM, Cheng X, and Zhang J. Fluorescent Indicators of cAMP and Epac
Activation Reveal Differential Dynamics of cAMP Signaling within Discrete Subcellular Compartments. Proc. Natl. Acad. Sci. USA 2004; 101: 16513-16518. 81. Violin JD, Zhang J, Tsien RY and Newton AC. A Genetically Encoded
Fluorescent Reporter Reveals Oscillatory Phosphorylation by Protein Kinase C. J. Cell Biol. 2003; 161: 899-909. 82. Zhang J, Campbell RE, Ting AY and Tsien RY. Creating New Fluorescent
Probes for Cell Biology. Nat. Rev. Mol. Cell Biol. 2002; 3: 906-918. 83. Zhang J, Ma Y, Taylor SS and Tsien RY. Genetically Encoded Reporters of
Protein Kinase A activity Reveal Impact of Substrate Tethering. Proc. Natl. Acad. Sci. USA 2001; 98: 14997-15002. 84. Zhang J, Boone L, Kocz R, Zhang C, Binns AN and Lynn DG. At the
Maize/Agrobacterium Interface: Natural Factors Limiting Host Transformation. Chem. Biol. 2000; 7: 611-621. 85. Campbell AM, Tok J, Zhang J, Wang Y, Stein M, Lynn DG and Binns AN.
Xenognosin Sensing in Virulence: Is there a Phenol Receptor in Agrobacterium tumefaciens? Chem. Biol. 2000; 7: 65-76.

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