Photoactivation of the Photoactive Yellow Protein: Why
Photon Absorption Triggers a Trans-to-Cis Isomerization of
the Chromophore in the Protein
Gerrit Groenhof,
†
Mathieu Bouxin-Cademartory,
§
Berk Hess,
‡
Sam P. de Visser,
§
Herman J. C. Berendsen,
†
Massimo Olivucci,
|
Alan E. Mark,
†
and
Michael A. Robb*
,§
Contribution from the Departments of Biophysical Chemistry and Applied Physics,
UniVersity of Groningen, Nijenborg 4, 9747 AG Groningen, The Netherlands,
Chemistry Department, Imperial College London, London SW7 2AZ, United Kingdom, and
Dipartimento di Chimica, UniVersita` di Siena, Via Aldo Moro, I-53100 Siena, Italy
Received November 12, 2003; E-mail: mike.robb@imperial.ac.uk
Abstract:
Atomistic QM/MM simulations have been carried out on the complete photocycle of Photoactive
Yellow Protein, a bacterial photoreceptor, in which blue light triggers isomerization of a covalently bound
chromophore. The “chemical role” of the protein cavity in the control of the photoisomerization step has
been elucidated. Isomerization is facilitated due to preferential electrostatic stabilization of the chromophore’s
excited state by the guanidium group of Arg52, located just above the negatively charged chromophore
ring. In vacuo isomerization does not occur. Isomerization of the double bond is enhanced relative to
isomerization of a single bond due to the steric interactions between the phenyl ring of the chromophore
and the side chains of Arg52 and Phe62. In the isomerized configuration (ground-state cis), a proton transfer
from Glu46 to the chromophore is far more probable than in the initial configuration (ground-state trans).
It is this proton transfer that initiates the conformational changes within the protein, which are believed to
lead to signaling.
Introduction
A wide variety of organisms have evolved mechanisms to
detect and respond to visible light. In many cases, the biological
response is mediated by structural changes that follow photon
absorption in the protein complex. The initial step in such cases
is normally the photoisomerization of a highly conjugated
prosthetic group. How this leads to large-scale structural changes
of the whole complex is, however, poorly understood. Here,
we report atomistic QM/MM simulations of the photocycle of
the Photoactive Yellow Protein (PYP), a bacterial photoreceptor.
The simulations uncover the detailed sequence of structural
changes that follow photon absorption, including the photo-
isomerization of the covalently bound chromophore and the
intramolecular proton transfer, which leads to the formation of
the signaling state. The results of the simulations (which are
consistent with experimental observations) provide detailed
structural and dynamic information at a “resolution” well beyond
that achievable experimentally. The “chemical role” of the
protein cavity in the control of the photoisomerization has been
elucidated. Thus, the key residues in the protein have been
identified, and the mechanism by which they control the
necessary conformational changes that lead ultimately to signal
transduction in PYP has been documented.
PYP is the primary photoreceptor for the negative photo-
tactic response of Halorhodospira halophila.
1,2
It has been
extensivelystudied both as a model photoreceptor protein and
as a structural prototype for the PAS class of signal transduc-
tion proteins.
3
Blue light induces a trans-to-cis isomerization
of a double bond in the covalently bound p-coumaric acid
chromophore
4-9
(Figure 1). In the resulting metastable state, a
change in the protonation state of the chromophore triggers
major conformational changes in the protein which are believed
to give rise to signal transduction.
10-12
Structural studies of
†
Dept. of Biophysical Chemistry, University of Groningen.
‡
Micromechanics of Materials Group, Dept. of Applied Physics,
University of Groningen.
§
Imperial College London.
|
Universita` di Siena.
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Published on Web 03/11/2004
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J. AM. CHEM. SOC. 2004,
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, 4228-4233 10.1021/ja039557f CCC: $27.50 © 2004 American Chemical Society
