Receptor activation is at the basis of all biological signal transduction events. Malfunctioning of signaling pathways can cause cancer. We study the mechanism of receptor activation using photoactive yellow protein (PYP), a PAS domain photoreceptor, as a powerful model system. PYP exhibits rhodopsin-like photochemistry based on its p-coumaric acid (pCA) chromophore, and has been investigated by X-ray crystallography. We have recently shown that the presence of a protein crystal lattice greatly reduces the structural changes that occur during the formation of the pB photocycle intermediate, the presumed signaling state of PYP. In addition, our preliminary results strongly indicate that the pB intermediate is partially unfolded. In this proposal we will examine the role of partial protein unfolding upon receptor activation as a novel signal transduction mechanism. (i) We will establish the extent of partial protein unfolding during pB formation by NMR spectroscopy, and by two novel methods: light-induced H/D exchange and light-induced differential scanning calorimetry. In addition, we will examine the hypothesis that the pB intermediate is a molten globule state by studying changes in ANS fluorescence, changes in CD spectrum, and changes in the radius of gyration upon pB formation. (ii) We will examine the effects of the presence of a crystal lattice on the kinetics and thermodynamics of the photocycle using both wt- PYP and the E46Q mutant in both P6 3 and P6 5 crystals by flash photolysis at a range of temperatures. (iii) We will test the hypothesis that the Glu46-pCA couple constitutes the built-in default for the light-triggered protein quake in PYP. These experiments will reveal changes in functional dynamics imposed by a crystal lattice, and will determine the role of transient partial protein unfolding as a novel signal transduction mechanism that is anticipated to play a role not only in PYP but also in other signal transduction systems.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM063805-04
Application #
6769520
Study Section
Molecular and Cellular Biophysics Study Section (BBCA)
Program Officer
Basavappa, Ravi
Project Start
2001-07-01
Project End
2005-06-30
Budget Start
2004-07-01
Budget End
2005-06-30
Support Year
4
Fiscal Year
2004
Total Cost
$226,500
Indirect Cost
Name
University of Chicago
Department
Biochemistry
Type
Schools of Medicine
DUNS #
005421136
City
Chicago
State
IL
Country
United States
Zip Code
60637
Kumauchi, Masato; Kaledhonkar, Sandip; Philip, Andrew F et al. (2010) A conserved helical capping hydrogen bond in PAS domains controls signaling kinetics in the superfamily prototype photoactive yellow protein. J Am Chem Soc 132:15820-30
Lee, Byoung-Chul; Kumauchi, Masato; Hoff, Wouter D (2010) Modulating native-like residual structure in the fully denatured state of photoactive yellow protein affects its refolding. J Biol Chem 285:12579-86
Philip, Andrew F; Kumauchi, Masato; Hoff, Wouter D (2010) Robustness and evolvability in the functional anatomy of a PER-ARNT-SIM (PAS) domain. Proc Natl Acad Sci U S A 107:17986-91
Carroll, Elizabeth C; Song, Sang-Hun; Kumauchi, Masato et al. (2010) Subpicosecond Excited-State Proton Transfer Preceding Isomerization During the Photorecovery of Photoactive Yellow Protein. J Phys Chem Lett 1:2793-2799
Philip, Andrew F; Nome, Rene A; Papadantonakis, George A et al. (2010) Spectral tuning in photoactive yellow protein by modulation of the shape of the excited state energy surface. Proc Natl Acad Sci U S A 107:5821-6
Hoff, Wouter D; van der Horst, Michael A; Nudel, Clara B et al. (2009) Prokaryotic phototaxis. Methods Mol Biol 571:25-49
van der Horst, Michael A; Stalcup, T Page; Kaledhonkar, Sandip et al. (2009) Locked chromophore analogs reveal that photoactive yellow protein regulates biofilm formation in the deep sea bacterium Idiomarina loihiensis. J Am Chem Soc 131:17443-51
Lee, Byoung-Chul; Hoff, Wouter D (2008) Proline 54 trans-cis isomerization is responsible for the kinetic partitioning at the last-step photocycle of photoactive yellow protein. Protein Sci 17:2101-10
Philip, Andrew F; Eisenman, Kaury T; Papadantonakis, George A et al. (2008) Functional tuning of photoactive yellow protein by active site residue 46. Biochemistry 47:13800-10
Kumauchi, Masato; Hara, Miwa T; Stalcup, Page et al. (2008) Identification of six new photoactive yellow proteins--diversity and structure-function relationships in a bacterial blue light photoreceptor. Photochem Photobiol 84:956-69

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