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Published online on May 3, 2005, 10.1073/pnas.0409035102
PNAS | May 17, 2005 | vol. 102 | no. 20 | 7145-7150
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From The Cover
BIOCHEMISTRY
Visualizing reaction pathways in photoactive yellow protein from nanoseconds to seconds

Hyotcherl Ihee *, {dagger} §, ¶, Sudarshan Rajagopal {dagger} §, Vukica Srajer ||, Reinhard Pahl ||, Spencer Anderson ||, Marius Schmidt **, Friedrich Schotte {dagger}{dagger}, Philip A. Anfinrud {dagger}{dagger}, Michael Wulff §§, and Keith Moffat {dagger}, ||, ¶¶

*Department of Chemistry and School of Molecular Science (BK21), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, South Korea; {dagger}Department of Biochemistry and Molecular Biology, ||Center for Advanced Radiation Sources, and ¶¶Institute for Biophysical Dynamics, University of Chicago, 920 East 58th Street, Chicago, IL 60637; **Physik-Department E17, Technische Universitaet München, 85747 Garching, Germany; {dagger}{dagger}National Institutes of Health, Bethesda, MD 20982; and §§European Synchrotron Radiation Facility, Grenoble Cedex 9, France

Edited by Gregory A. Petsko, Brandeis University, Waltham, MA, and approved March 18, 2005 (received for review December 6, 2004)

Determining 3D intermediate structures during the biological action of proteins in real time under ambient conditions is essential for understanding how proteins function. Here we use time-resolved Laue crystallography to extract short-lived intermediate structures and thereby unveil signal transduction in the blue light photoreceptor photoactive yellow protein (PYP) from Halorhodospira halophila. By analyzing a comprehensive set of Laue data during the PYP photocycle (forty-seven time points from one nanosecond to one second), we track all atoms in PYP during its photocycle and directly observe how absorption of a blue light photon by its p-coumaric acid chromophore triggers a reversible photocycle. We identify a complex chemical mechanism characterized by five distinct structural intermediates. Structural changes at the chromophore in the early, red-shifted intermediates are transduced to the exterior of the protein in the late, blue-shifted intermediates through an initial "volume-conserving" isomerization of the chromophore and the progressive disruption of hydrogen bonds between the chromophore and its surrounding binding pocket. These results yield a comprehensive view of the PYP photocycle when seen in the light of previous biophysical studies on the system.

intermediates | mechanism | signal transduction | time-resolved crystallography | singular value decomposition

This paper was submitted directly (Track II) to the PNAS office.

Freely available online through the PNAS open access option.

Abbreviations: PYP, photoactive yellow protein; APS, Advanced Photon Source; ESRF, European Synchrotron Radiation Facility; SVD, singular value decomposition.

Data deposition: The structures reported in this paper have been deposited in the Protein Data Bank, www.pdb.org [PDB ID codes 1TS8 (ICP), 1TS7 (pRCW + pRE46Q), 1TS6 (pB1), and 1TS0 (pB2)].

§ H.I. and S.R. contributed equally to this work.

To whom correspondence should be addressed. E-mail: hyotcherl.ihee{at}kaist.ac.kr.

© 2005 by The National Academy of Sciences of the USA


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