Oriented immobilization of farnesylated proteins by the thiol-ene reaction

Article abstract of DOI:10.1002/anie.200906190

figure presented Anchoring the protein: Proteins were immobilized rapidly under mild conditions by thiol-ene photocoupling between S-farnesyl groups attached to a genetically encodable CAAX-box tetrapeptide sequence (A is aliphatic) at the C terminus of the protein and surface-exposed thiols (see scheme). This method enables the oriented covalent immobilization of proteins directly from expression lysates without additional purification or derivatization steps.

Full text of DOI:10.1002/anie.200906190

Communications
DOI: 10.1002/anie.200906190
Protein Microarrays
Oriented Immobilization of Farnesylated Proteins by the Thiol-Ene
Reaction**
Dirk Weinrich, Po-Chiao Lin, Pascal Jonkheijm, Uyen T. T. Nguyen, Hendrik Schrꢀder,
Christof M. Niemeyer, Kirill Alexandrov, Roger Goody, and Herbert Waldmann*
Protein biochips are of high interest for various fields of
biotechnology, such as bioanalytics, proteomics, biocatalysis,
and biomaterials.[1–8] For protein-biochip preparation, the
oriented (i.e. site-specific) covalent attachment of proteins to
surfaces is important because it ensures homogeneous surface
coverage and accessibility to the active site of the protein.[9–11]
Moreover, the structural sensitivity of proteins calls for
chemical transformations that proceed under mild conditions
and are compatible with all functional groups present in
proteins.[1,2,12–15] The availability of a method for the fast,
oriented, and covalent immobilization of expressed proteins
from lysates would be of great value. This approach has been
demonstrated previously on the basis of protein transsplic-
ing,[16,17] phosphopantetheinyl transferase catalysis,[18] and O6-
alkylguanine-DNA alkyltransferase (SNAP tag).[19,20] We
recently described the use of the photochemical thiol-ene
reaction for the covalent surface patterning of small biomol-
ecules.[21] We now report that this transformation can be
employed for the fast, oriented, and covalent immobilization
of proteins under mild conditions, and that it provides a novel
means for the direct immobilization of proteins from lysates
without any additional chemical derivatization or purification
steps.
For the thiol-ene reaction to be applied to proteins, an
olefin must be introduced into the protein of interest. In cells,
various proteins are posttranslationally S-farnesylated at C-
terminal cysteine groups by protein farnesyltransferase
(FTase).[22] FTase employs farnesyl pyrophosphate (Fpp) as
the farnesyl donor and recognizes a C-terminal “CAAX-box”
tetrapeptide sequence (C is cysteine, A is an aliphatic amino
acid, X is one of a variety of amino acids). The reaction can
also be performed in vitro (Figure 1a).[23] The FTase-cata-
lyzed transfer of synthetic alkyne- or azide-functionalized
farnesyl analogues in combination with the Huisgen [3+2]
cycloaddition and Staudinger ligation has been explored for
the immobilization of proteins.[24,25]
We reasoned that the equipment of proteins with a
genetically encodable CAAX tag would enable farnesylation
in vitro or in vivo and subsequent photochemical thioether-
bond formation between an olefin of the isoprenoid and
surface-exposed thiols (Figure 1b).
For a proof-of-principle study, we chose the H-, N-, and K-
Ras GTPases, which play major roles in cellular signaling and
are among the most important human oncogene products.[26]
All Ras isoforms bear the CAAX box and require lipidation
for correct function and localization in eukaryotic cells.[27]
Full-length H-Ras, N-Ras, and K-Ras were farnesylated in
vitro with recombinant FTase, as described previously.[28]
Complete farnesylation of H-, N-, and K-RasFar was verified
by means of MALDI MS. By using an experimental setup
established earlier for small molecules,[21] the farnesylated
proteins were drop-cast onto thiol-functionalized SiOx/Si
slides with an intermediate poly(amidoamine) (PAMAM)
dendrimer layer (for an illustration of the slide preparation,
see Scheme S2 in the Supporting Information). To this end,
the protein solution was deposited on the slide surface and
covered with a photomask (Figure 1c). A thin liquid-contain-
ing chamber was obtained which prevented the drying out and
denaturation of the protein. Following exposure to UV light
at a wavelength of 365 nm for 10 minutes (6 JcmÀ2) and
subsequent washing to remove unbound material, the slides
were incubated with a Cy3-labeled antibody directed against
Ras isoforms. Ras-positive microstructures were successfully
detected with a fluorescence microarray scanner (Figure 1d;
see also Figure S3 in the Supporting Information). The
antibody employed recognizes an a helix of the Ras proteins
close to the active site and thus indicates that the immobilized
Ras proteins are correctly folded.[29,30] However, immobiliza-
tion efficiencies varied strongly. Whereas K-RasFar immobi-
lization led to highly fluorescent microstructures, the inten-
[*] Dr. D. Weinrich, Dr. P.-C. Lin, Prof. Dr. H. Waldmann
Abteilung fꢀr Chemische Biologie
Max-Planck-Institut fꢀr Molekulare Physiologie
Otto-Hahn-Strasse 11, 44227 Dortmund (Germany)
and
Fakultꢁt Chemie, Chemische Biologie
Technische Universitꢁt Dortmund
Otto-Hahn-Strasse 6, 44227 Dortmund (Germany)
Fax: (+49)231-133-2499
E-mail: herbert.waldmann@mpi-dortmund.mpg.de
Dr. P. Jonkheijm
MESA+ Institute for Nanotechnology
University of Twente (Netherlands)
Dr. U. T. T. Nguyen, Prof. Dr. R. Goody
Abteilung fꢀr Physikalische Biochemie
Max-Planck-Institut fꢀr Molekulare Physiologie (Germany)
Dr. H. Schrꢂder, Prof. Dr. C. M. Niemeyer
Fakultꢁt Chemie, Biologisch-Chemische Mikrostrukturtechnik
Technische Universitꢁt Dortmund (Germany)
Prof. Dr. K. Alexandrov
Institute for Molecular Bioscience, The University of Queensland
St Lucia QLD 4072 (Australia)
[**] This research was supported by the Deutsche Forschungsgemein-
schaft and the Fonds der Chemischen Industrie. It was also
supported in part by Deutsche Forschungsgemeinschaft grant AL
484/5-4 and a Heisenberg Fellowship to K.A.
Supporting information for this article is available on the WWW
under http://dx.doi.org/10.1002/anie.200906190.
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carboxylic acid groups on
the surface might have
attracted the positively
charged K-Ras C terminus
(abbreviated as KRT) to
increase the concentration
of K-RasFar locally and
thus promote its more effi-
cient immobilization (Fig-
ure 3a). This interaction
would also explain the
slightly higher photoimmo-
bilization
efficiency
observed for H-RasFar
when compared to N-
RasFar, since the C termi-
nus of H-Ras also contains
one lysine residue. A con-
trol experiment in which
C termini
with
lysine
stretches of varying lengths
were used confirmed this
hypothesis (see Figure S5 in
the Supporting Informa-
tion). Different CAAX-
box sequences did not
show strong differences in
immobilization efficiency
(see Figure S6 in the Sup-
porting Information).[31]
We therefore hypothe-
sized that for efficient
immobilization on thiol–
PAMAM surfaces, proteins
of interest should not only
be equipped with a CAAX
box but also with a polyba-
sic, KRT-like amino acid
sequence. To investigate
this hypothesis, we gener-
ated and farnesylated a var-
iant of the fluorescent
mCherry protein with a tet-
Figure 1. a) Farnesylation of proteins by farnesyltransferase (FTase). FTase recognizes the four amino acid
CAAX-box motif at the C terminus of the protein and transfers a farnesyl residue onto the cysteine side chain
by using farnesyl pyrophosphate (Fpp) as a lipid donor. b) Proposed mechanism for the thiol-ene photo-
immobilization of farnesylated proteins. c) Schematic depiction of the thiol-ene photomicrostructuring of
farnesylated Ras isoforms. d) Fluorescence images obtained after the photomicrostructuring of farnesylated
Ras isoforms. Average relative fluorescence intensities obtained from cross-sections of the microstructure
lines (white lines) are indicated.
ralysine-based
C terminus in vitro (H6-
mCherry-4KRT; Fig-
KRT-like
ure 2b). Protein expression
of mCherry modified with
the hexalysine-based KRT-
sities observed for H-RasFar and N-RasFar were only about
5% of the value for K-RasFar.
like C terminus (abbreviated as 6KRT) failed. However, a
control experiment demonstrated that a stretch of four lysine
residues in the protein C terminus was sufficient to enable
immobilization (see Figure S5 in the Supporting Informa-
tion).
To enable the comparison of different parameters in
parallel, we attempted microarray generation instead of
photomicrostructuring. Farnesylated H6-mCherry-4KRT
(H6-mCherry-4KRTFar) was spotted onto a thiol–PAMAM-
functionalized SiOx/Si slide together with nonfarnesylated H6-
The three Ras isoforms share a high sequence identity in
the globular part (amino acids 1–171) but differ at the
C terminus (Figure 2a). Notably, K-Ras contains a polybasic
lysine stretch at the C terminus that is not present in H- and
N-Ras. Since the thiol-functionalized SiOx/Si slides employed
were prepared from carboxylic acid functionalized poly(ami-
doamine) (PAMAM) dendrimers (see Scheme S2 in the
Supporting Information),[21] we reasoned that remaining
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Figure 2. a) C termini of H-Ras, N-Ras, and K-Ras. The CAAX box (the FTase-recognition motif and farnesylation site) and the polybasic stretch of
K-Ras, which does not occur in H-Ras and N-Ras, are indicated. The protein core (1–171) is highly similar for all three isoforms. b) Engineered
variants of mCherry and Rab6A incorporating polybasic C termini resembling the K-Ras C terminus (KRT) with CAAX-box farnesylation sites.
mCherry-4KRTand H6-mCherry lacking a prenylatable tag as
controls. Following exposure to UV light at 365 nm, immo-
bilized protein was detected by fluorescence scanning (for an
illustration of the general work flow see Figure S4 in the
with purified H6-mCherry-4KRTFar as a control. After
exposure to UV light at 365 nm, H6-mCherry-4KRTFar
immobilization was confirmed by fluorescence scanning
(Figure 4a). Hence, the photoimmobilization of farnesylated,
KRT-bearing proteins is possible directly from expression
lysates, thereby obviating laborious purification steps. The
nonspecific, covalent immobilization of other lysate proteins
can be ruled out owing to the absence of KRT sequences.
To extend the method, we investigated the coexpression
of KRT-modified proteins with FTase; this process would
directly yield S-farnesylated expressed proteins owing to the
presence of the genetically encoded CAAX box and thereby
enable thiol-ene photoimmobilization directly from expres-
sion lysates without further purification or modification.
E. coli synthesizes Fpp endogenously but does not have an
endogenous protein farnesyltransferase. Therefore, a suitable
vector incorporating both FTase subunits was coexpressed in
E. coli together with the vector encoding H6-mCherry-4KRT.
SDS-PAGE analysis proved the overexpression of the three
desired proteins (see Figure S1a in the Supporting Informa-
tion). To determine whether sufficient E. coli Fpp and active
FTase were available in the colysate, we generated a micro-
array with and without the addition of Fpp and FTase. As a
modification, a longer thiol linker was used for surface
functionalization, since with this linker photoimmobilization
efficiency increased. Additionally, the UV-light-exposure
time was extended to 20 minutes (12 JcmÀ2). H6-mCherry-
4KRT lysate which did not contain any FTase was used as a
control. The unmodified colysate as well as colysate with
additional Fpp or Fpp/FTase showed high immobilization
efficiency, whereas an approximately tenfold lower immobi-
lization efficiency was observed for the control (Figure 4b,c).
These results demonstrate that the immobilization of KRT-
modified proteins is possible directly from E. coli expression
lysate after coexpression with FTase and by taking advantage
of E. coli Fpp. The addition of Fpp and Fpp/FTase to the
colysate did not improve immobilization efficiency, which
indicates that sufficient amounts of FTase and endogenous
Fpp were generated in vivo. The approach was also success-
fully extended to Ypt1, the yeast analogue of Rab1 (see
Figure S7 in the Supporting Information).
Supporting
Information).
Farnesylated
H6-mCherry-
4KRTFar was immobilized efficiently, whereas only trace
amounts of the controls were detected (Figure 3b,c). This
result supports the hypothesis that the C-terminal KRT-like
sequence strongly enhances thiol-ene photoimmobilization of
farnesylated proteins. In contrast, the N-terminal polyhisti-
dine sequence does not seem to influence protein immobili-
zation, since H6-mCherry, which only bears the polyhistidine
tag, was immobilized poorly.
To demonstrate the applicability of this method to other
protein classes, we investigated the immobilization of Rab
proteins. Rab proteins play decisive roles in vesicular trans-
port,[32,33] whereby Rab6A is involved in vesicular transport
originating from the Golgi apparatus.[34] A suitable Rab6A
variant with a C-terminal KRT sequence that incorporated a
hexalysine stretch (Rab6A-6KRT) was generated and farne-
sylated in vitro. In this case, the hexalysine-based KRT-like
C terminus posed no problems during expression. For immo-
bilization, farnesylated Rab6A-KRT (Rab6A-6KRTFar) was
spotted onto a thiol–PAMAM-functionalized SiOx/Si slide
together with Rab6A as a negative control and photoimmo-
bilized as described above. The Rab6A microarray was then
incubated with a fusion protein consisting of enhanced green
fluorescent protein (eGFP) and the minimal Rab6A-binding
domain of bicaudalD2 (eGFP–bicaudalD2);[34,35] this fusion
protein could be detected by fluorescence scanning. Figure 3d
shows that Rab6A-6KRTFar was immobilized with high
efficiency, whereas the nonspecific immobilization of Rab6A
was minimal. Successful recognition by the Rab6A cognate
effector bicaudalD2 clearly demonstrated that thiol-ene
photoimmobilization yielded correctly folded and functional
proteins on the slide surface.
With a view to determine whether this strategy would
enable the immobilization of proteins obtained directly from
crude cellular lysate, H6-mCherry-4KRT expression lysate
was generated and clarified by ultracentrifugation. H6-
mCherry-4KRT was then farnesylated in the lysate by using
FTase and Fpp. The lysate was spotted onto a thiol-
functionalized slide without any further purification together
In conclusion, the photochemical thiol-ene reaction
between S-farnesyl groups attached to a genetically encod-
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Figure 3. a) Preparation of thiol-functionalized slides from carboxylic acid functionalized slides and charge-mediated interaction with farnesylated
K-Ras which could facilitate photoimmobilization. b) Fluorescence intensity observed for an H6-mCherry-4KRTFar microarray with H6-mCherry-
4KRT and H6-mCherry as controls. c) Fluorescence image of a subsection of the H6-mCherry-4KRTFar microarray described in (b). d) Fluorescence
intensity observed for a Rab6A-6KRTFar/eGFP–bicaudalD2 microarray with native Rab6A as a control.
able CAAX box at the C terminus of proteins and surface-
exposed thiols on PAMAM-functionalized surfaces provides
a method for the oriented and covalent immobilization of
functional proteins under mild conditions in as little as
10 minutes. The natural farnesyl residue can be introduced
into proteins by enzymatic farnesylation in vitro or in vivo by
means of coexpression with FTase and by taking advantage of
the endogenous E. coli Fpp pool. This method opens up the
opportunity to immobilize proteins directly from expression
lysates without additional isolation, purification, or chemical-
derivatization steps otherwise required for oriented and
covalent immobilization.
Received: November 3, 2009
Published online: January 12, 2010
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Keywords: farnesylation · immobilization ·
photochemical reactions · protein microarrays ·
thiol-ene reaction
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DOI:
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cbic.200900559). We observed that the presence of an inter-
mediate PAMAM dendrimer layer leads to about a fivefold
increase in immobilization efficiency, as compared to other
surfaces coatings. Although preliminary studies on the direct
thiol-ene immobilization of KRT proteins suggest that the
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