Cobalt(II)-responsive DNA binding of a GCN4-bZIP protein containing cysteine residues functionalized. with iminodiacetic acid

Full text of DOI:10.1002/anie.200902888

Angewandte
Chemie
DOI: 10.1002/anie.200902888
Metal Switches
Cobalt(II)-Responsive DNA Binding of a GCN4-bZIP Protein
Containing Cysteine Residues Functionalized with Iminodiacetic
Acid**
Yusuke Azuma, Miki Imanishi, Tomoyuki Yoshimura, Takeo Kawabata, and Shiroh Futaki*
The design of proteins with functions that can be controlled
by external stimuli is a challenge in peptide/protein engineer-
ing.[1] Many natural proteins utilize metal ions to stabilize
their structure and regulate their bioactivity. The structural
engineering of proteins with effective metal coordination to
enable switching between two different structures would thus
increase the feasibility of developing novel protein machi-
neries.[2,3] Our previous studies showed that metal coordina-
tion of iminodiacetic acid (Ida) moieties yielded a significant
decrease in helicity when the Ida moieties were placed at
positions i and i + 2 in helical peptides.[3] This approach is
particularly useful for the functional regulation of proteins
with stable helical structures, as exemplified through recog-
nition switching between leucine zipper peptides derived
from Jun and Fos oncoproteins and through extramembrane
gating control of artificial ion channels.[3] However, due to the
lack of methodology for the effective introduction of Ida
moieties at specific positions in proteins, the application of
this concept has been limited to synthetic peptides.[4]
i + 2 in the leucine zipper segment (bZIP-1a, bZIP-1b) were
designed to destabilize the helical structure of the bZIP
protein by the interaction of Ida with metals to switch DNA
binding (Figure 1). The positions of the Ida modification were
selected as shown in Figure 1c so as to have a minimum effect
on dimer formation in the absence of metals.[7]
We now present a new method for introducing Ida
moieties into proteins. The method involves the specific
modification of cysteine residues by treatment with a new
functionalization agent, N-(2-tosylthioethyl)iminodiacetic
acid (Ts-S-IDA, 5). We demonstrated the practicability of
this approach by modifying a protein derived from the yeast
transcription factor GCN4 with Ida moieties. Successful
switching of the DNA binding in response to a metal was
observed for one the resulting proteins.
The GCN4-bZIP protein (bZIP = basic leucine zipper)
consists of two helical segments. Dimerization through the
leucine zipper segment is critical for binding to the target
DNA segment (AP-1 site) by the basic segment.[5] The well-
studied structure of the protein has been employed as a model
for the design of reversible control of DNA binding through
switching of the dimer formation.[6] In the present study, bZIP
proteins containing a pair of Ida residues at positions i and
[*] Y. Azuma, Dr. M. Imanishi, Dr. T. Yoshimura, Prof. Dr. T. Kawabata,
Prof. Dr. S. Futaki
Figure 1. Design of metal-responsive bZIP proteins. a) Sequences of
the bZIP proteins studied and the target DNA (AP-1). b) Schematic
representation of the bZIP-2/AP-1 complex. c) Helical-wheel projection
of bZIP-2. X is an Ida-modified cysteine residue; wt=wild type.
Institute for Chemical Research, Kyoto University
Uji, Kyoto 611-0011 (Japan)
Fax: (+81)774-32-3038
E-mail: futaki@scl.kyoto-u.ac.jp
[**] This research was supported in part by Grants-in-Aid for Scientific
Research from the Ministry of Education, Culture, Sports, Science,
and Technology of Japan. Y.A. is grateful for a JSPS Research
Fellowship for Young Scientists.
The agent for modification with Ida, Ts-S-IDA (5), was
synthesized readily from 2-bromoethylamine (2) in three
steps (Scheme 1). The treatment of the recombinant proteins
with Ts-S-IDA (1.5 equiv for each cysteine residue) in 10 mm
Supporting information for this article is available on the WWW
under http://dx.doi.org/10.1002/anie.200902888.
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(EMSA), even upon the addition of excess amounts of the
metals (Table 1; see also Figure S2 in the Supporting Infor-
mation).[9] Therefore, we designed an alternative protein,
bZIP-2, with two pairs of Ida moieties in the leucine zipper
segment to cause greater destabilization upon the addition of
a metal (Figure 1).[8]
Table 1: Kd values for the binding of bZIP proteins to AP-1 in the absence
or presence of a metal.
Kd[a] [nm]
Scheme 1. Preparation of Ts-S-IDA (5), an agent for the modification of
proteins with Ida. DIEA=diisopropylethylamine, DMF=N,N-dimethyl-
formamide, Ts=p-toluenesulfonyl.
no metal
CoII
NiII
MnII
bZIP-wt
bZIP-1a
bZIP-1b
bZIP-2
15Æ2.6
24Æ2.7
22Æ3.7
22Æ3.0
21Æ1.0
16Æ1.2
58Æ15
26Æ8.1
17Æ2.0
44Æ4.7
26Æ3.9
50Æ15
23Æ3.1
16Æ2.5
38Æ7.3
27Æ4.6
64Æ10
21Æ2.6
Tris-HCl (pH 7.5; Tris = tris(hydroxymethyl)aminomethane)
at 48C for 1 h yielded the desired bZIP proteins without
difficulty.[8] Monitored by HPLC, the reaction reached
completion almost immediately upon the addition of Ts-S-
IDA (5); no side reactions were detected.
Unexpectedly, CD spectroscopy showed that the addition
of metals in the presence of DNA had only a slight effect on
the structure of bZIP-1a and bZIP-1b (Figure 2a; see also
Figure S1 in the Supporting Information). Similarly, no
significant decrease in the affinity of these proteins for
DNA was observed in an electrophoretic mobility shift assay
>1000[b]
bZIP-2+EDTA
22Æ1.1
[a] The Kd value was determined by an electrophoretic mobility shift
assay, as described in the Supporting Information. All values reported are
the mean of at least three measurements (Æ the standard deviation).
[b] Protein concentration at which the bound fraction of the DNA is
about half the maximum amount (q=0.5).
The CD spectrum of bZIP-2 suggested that this protein
has a helical structure, although its helical content was
somewhat lower than that of the wild-type bZIP protein in the
presence of DNA (the [q]222 values for bZIP-2 and bZIP-wt
were À2.5 ꢀ 10À4 and À3.1 ꢀ 10À4 degcm2 dmolÀ1, respec-
tively), possibly as a result of electrostatic repulsion between
the various Ida moieties (Figure 2b; see also Figure S1d in
the Supporting Information). Analysis by EMSA showed that
bZIP-2 had a similar affinity for the AP-1 site of DNA to that
of the wild type in the absence of metals (the Kd values for
bZIP-2 and bZIP-wt were 22 Æ 3.0 and 15 Æ 2.6 nm, respec-
tively; Figure 3; see also Figure S2a in the Supporting
Information).
A significant decrease in the helical content and affinity
for DNA of bZIP-2 was observed upon the addition of CoII
(Figures 2b and 3). The addition of CoII (30 mm; 1.5 equiv for
each Ida pair) induced a 33% decrease in the helical content.
Metal titration of the protein showed a saturation in the
decrease of the helical content at 2 equivalents of CoII to the
protein (Figure 2b, inset). These results suggested that metal
coordination to each Ida moiety effectively leads to the
structural alteration of bZIP-2. Furthermore, a dramatic
decrease in the affinity of bZIP-2 for the target DNA was
observed in the presence of 30 mm CoII (Kd > 1000 nm;
Figure 3, Table 1): the Kd value of the protein was more
than 45 times higher than in the absence of CoII (Kd = 22 Æ
3.0 nm). The addition of ethylenediaminetetraacetic acid
(EDTA; 300 mm) resulted in complete recovery of the
DNA-binding affinity (Kd = 22 Æ 1.1 nm).[10,11] Thus, the incor-
poration of two pairs of Ida moieties in the protein structure
led to a bZIP protein that interacts reversibly with the target
DNA as a result of CoII binding.
Figure 2. Difference CD spectra of a) bZIP-1a and b) bZIP-2 (10 mm) in
the absence (black) or presence (red) of CoII (30 mm). The spectra
shown were obtained by subtracting the spectra of AP-1 (5 mm). The
inset shows the molar ellipticity at 222 nm, [q]222, of bZIP-2 as a
function of the CoII concentration. [P] is the protein concentration.
To assess the sensitivity of bZIP-2 to CoII during DNA
binding, we carried out a metal-titration experiment with
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proteins with a stable helical struc-
ture. The results obtained in this
study should provide an important
platform for the design of artificial
sensor and regulator proteins.
Received: May 29, 2009
Published online: August 4, 2009
Figure 3. EMSA for bZIP-2 binding to AP-1 in the absence (lanes 1–6) or presence (lanes 7–12) of
CoII (30 mm) and after the addition of excess EDTA (300 mm). From left to right in lanes 1–6 as well
as in lanes 7–12 and lanes 13–18, the protein concentration was 0, 3.3, 10, 30, 90, and 270 nm.
Keywords: biosensors · DNA binding ·
.
helix destabilization · metal switches ·
proteins
bZIP-2 (100 nm; Figure 4). Analysis by EMSA showed an
almost-quantitative CoII-dependent release of bZIP-2 from
AP-1 and thus suggested that bZIP-2 was very sensitive to
[1] a) F. Zhang, A. Zarrine-Afsar, M. S. Al-Abdul-Wahid, R. S.
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[4] Iminodiacetic acid (Ida) moieties can be introduced into
peptides by the selective removal of e-amino protecting groups
of specific lysine residues on a solid support prior to conversion
into Ida.[3] Alternatively, Ida derivatives of lysine may be
introduced as building blocks through solid-phase peptide
synthesis: a) F. Q. Ruan, Y. Q. Chen, P. B. Hopkins, J. Am.
Chem. Soc. 1990, 112, 9403 – 9404; b) I. Hamachi, Y. Yamada, T.
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[7] The inclusion of Ida in sequences at positions a and d was
avoided so as not to hamper the hydrophobic interaction
between the helices. A combination of the e and g positions
(as i and i + 2) was avoided, as it would result in the positioning
of negatively charged Ida moieties in close proximity, at
position e in one helix and position g in the other, and would
thus destabilize dimer formation: a) J. M. Mason, K. M. Arndt,
ChemBioChem 2004, 5, 170 – 176; b) W. D. Kohn, C. M. Kay, D.
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Figure 4. a) EMSA for the binding of bZIP-2 (100 nm) to AP-1 (2 nm)
in the absence (lane 1) or presence (lanes 2–7) of CoII. In lanes 1–7,
the CoII concentration was 0, 50, 100, 150, 200, 250, and 300 nm,
respectively. b) Plot of the fraction of fluorescein-end-labeled DNA
bound to bZIP-2 as a function of the CoII concentration. The data
points represent the average of three experiments (Æ the standard
deviation).
In this study, we established a new method for introducing
Ida moieties into proteins by the development of an efficient
cysteine-modification agent, Ts-S-IDA (5; Scheme 1). We
also demonstrated effective and reversible control of the
DNA binding of GCN4-bZIP with CoII. The difference in the
affinity of bZIP-2 for AP-1 in the absence and presence of
CoII is significantly greater than that observed with other
methods for controlling the DNA binding of GCN4-bZIP.[6]
Furthermore, effective chelation of CoII in the submicromolar
range with Ida enables structural switching of bZIP-2 to
enable bZIP-2 release from AP-1 (Figure 4). The required
concentration of CoII is significantly lower than the required
metal concentrations for the functional switching of previ-
ously reported metal-responsive coiled-coil proteins.[12] The
concept of helix destabilization by the i and i + 2 positioning
of Ida would be applicable to the functional switching of other
[8] The Ida-modified structures of the proteins were confirmed by
ESI-MS. bZIP-1a: m/z calcd for [M+H]+: 7221.43; found:
7221.77; bZIP-1b: m/z calcd for [M+H]+: 7263.50; found:
7263.03; bZIP-2: m/z calcd for [M+H]+: 7609.93; found: 7610.03.
[9] No effect of metal addition was observed for wild-type bZIP (see
Figures S1 and S2 in the Supporting Information).
[10] The simple addition of EDTA led to the recovery of DNA
binding but not to the complete refolding of bZIP-2. Complete
refolding only occurred when the protein was heated to 808C
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and cooled slowly in the presence of EDTA (300 mm; see
[12] a) K. Suzuki, H. Hiroaki, D. Kohda, H. Nakamura, T. Tanaka, J.
Am. Chem. Soc. 1998, 120, 13008 – 13015; b) T. Mizuno, K.
Murao, Y. Tanabe, M. Oda, T. Tanaka, J. Am. Chem. Soc. 2007,
129, 11378 – 11383.
Figure S3 in the Supporting Information). This result suggests
that bZIP-2 may form a metastable structure in the complex with
CoII.
[11] The effects of NiII and MnII on the helix destabilization and
DNA binding of bZIP-2 were less pronounced than the effect of
CoII (see Figure S4 in the Supporting Information).
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