COMMUNICATION
DOI: 10.1002/chem.201000441
A Photo-Cross-Linking Strategy to Map Sites of Protein–Protein Interactions
Yihui Chen,[b] Yalin Wu,[b] Peter Henklein,[c] Xiaoxu Li,[d] Klaus Peter Hofmann,[a]
Koji Nakanishi,*[b] and Oliver P. Ernst*[a]
Chemical and photochemical cross-linking are potentially
powerful approaches for investigating protein–protein inter-
actions and identification of interaction sites.[1] The ap-
proaches complement high-resolution X-ray diffraction and
NMR spectroscopy methods for three-dimensional protein
structure analysis, especially when proteins are only avail-
able in small amounts or are difficult to crystallize. The
(photo)cross-linked products are typically analyzed by pro-
teolytic digestion and mass spectrometry, yielding, in ideal
cases, sequence and specific amino acid(s) of the interaction
sites. The fast reaction of photo-cross-linking allows its ap-
plication to short-lived protein complexes. To facilitate mass
spectrometric analysis, enrichment of the digested photo-
cross-linked products is desirable. Herein, we describe a
novel photo-cross-linking strategy based on such an enrich-
ment step and capable of mapping sites of protein–protein
interactions. As a test case, we applied the strategy to a
model system represented by the G-protein-coupled recep-
tor (GPCR) rhodopsin and its G protein transducin (Gt).[2]
These two proteins are key enzymes in the visual process
and were chosen previously for (photo)-cross-linking stud-
ies.[3]
GPCRs, also called seven-transmembrane receptors, are
among the most important drug targets and are involved in
many physiological processes by routing extracellular signals
across the cell membrane to different intracellular signaling
pathways.[4] Binding of extracellular ligands causes a confor-
mational change in the GPCR to enable its cytoplasmic
domain to catalyze GDP/GTP exchange in heterotrimeric G
proteins (Gabg); the process that initiates the signaling cas-
cade. Visual signal transduction in the retinal rod cell is a
prototypical sample of G-protein-coupled signaling systems
in which the GPCR rhodopsin with its covalently bound
chromophore 11-cis-retinal acts as a photoreceptor to detect
single photons.[2,5] In its photochemically functional core,
rhodopsin contains the covalently bound ligand 11-cis-reti-
nal, which stabilizes the inactive rhodopsin state. Photon ab-
sorption causes retinal cis!trans isomerization, leading to
in situ formation of an activating ligand in the binding site
and subsequent activation of rhodopsin.
The crystal structures of rhodopsin, as well as that of
opsin, the ligand-free apoprotein, are known.[6] The latter
features a more open conformation of the cytoplasmic
domain, which represents (with respect to G protein cou-
pling) an active GPCR state.[2] For signal transfer to the cog-
nate G protein called transducin (Gt), the C terminus of the
[a] Prof. Dr. K. P. Hofmann, Dr. O. P. Ernst
Institut fꢀr Medizinische Physik und Biophysik
Charitꢁ-Universitꢂtsmedizin Berlin, Charitꢁplatz 1
10117 Berlin (Germany)
Ga subunit, GtaACHTUNTRGNEUNG(340-350) (Figure 1), binds into a central
crevice in the cytoplasmic domain opened in the active re-
ceptor.[7] A second binding site on the G protein is the pre-
nylated C terminus of the Gg subunit. In the case of Gt, the
Fax : (+49)30-450-524952
binding site Gtg
G
ACHTUNGTRENNUNG(60-
[b] Dr. Y. Chen, Dr. Y. Wu, Prof. Dr. K. Nakanishi
Department of Chemistry, Columbia University
New York, NY 10027 (USA)
71)far).[8] The binding site of Gtg
AHCTUNGTRENNUNG
less clear, although there is multiple evidence that it is in-
volved in initial docking to the receptor.[9]
Fax : (+1)212-932-8273
Herein, we set out to determine the binding site of Gtg-
[c] Dr. P. Henklein
AHCTUNGTREG(NNUN 60-71)far on light-activated rhodopsin by preparing a syn-
thetic photoactivable peptide derived from the farnesylated
Gtg C terminus. For this purpose, a derivative of the native
GtgACTHNUGRTENUNG(60-71)far peptide (Scheme 1A, peptide 1) was synthe-
sized, which contained a p-ethynylbenzoyl moiety modified
Phe-64, yielding the photoactivable ethynylated benzophe-
none probe (Scheme 1B, peptide 2). The MALDI-TOF-MS
Institut fꢀr Biochemie, Charitꢁ-Universitꢂtsmedizin Berlin
Charitꢁplatz 1, 10117 Berlin (Germany)
[d] Dr. X. Li
Department of Chemical Engineering, Columbia University
New York, NY 10027 (USA)
Supporting information for this article is available on the WWW
Chem. Eur. J. 2010, 16, 7389 – 7394
ꢃ 2010 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
7389