TOPP: A novel nitroxide-labeled amino acid for EPR distance measurements

Article abstract of DOI:10.1002/anie.201103315

A new tool: The amino acid 4-(3,3,5,5-tetramethyl-2,6-dioxo-4- oxylpiperazin-1-yl)-L-phenylglycine (TOPP), which has a rigid nitroxide spin label, can be used for EPR-based distance measurements in peptides. The key feature of the design is the defined orientation of the nitroxide in space with respect to the peptide backbone. EPR measurements provide evidence for the low conformational flexibility of the TOPP label. Copyright

Full text of DOI:10.1002/anie.201103315

DOI: 10.1002/anie.201103315
Spin Labels
TOPP: A Novel Nitroxide-Labeled Amino Acid for EPR Distance
Measurements**
Sven Stoller, Giuseppe Sicoli,* Tatiana Y. Baranova, Marina Bennati, and Ulf Diederichsen*
Electron paramagnetic resonance (EPR) spectroscopy is a
well-established technique for the structural study of biomol-
ecules.[1] In particular, over the past decade distance measure-
ments between methanethiosulfonate spin labels (MTSSL)
attached to cysteine residues of proteins or peptides have
been successfully established.[2] Recently, not only the dis-
tance but also the relative orientation of essential amino acid
radicals rigidly oriented in proteins were measured by pulsed
electron-electron double resonance (PELDOR or DEER)
spectroscopy.[3] To determine the relative orientation of
topological units together with their intermolecular distance,
spin labels with restricted mobility are required.[4] Since the
MTSSL-modified cysteine contains single bond flexibility in
the linker between the backbone and the nitroxide, the amino
acid 2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxyl
(TOAC) is often used as an alternative for a conformationally
rigid label in peptide studies (Figure 1). In TOAC the
nitroxide group is incorporated in a six-membered ring
attached to the backbone a carbon and it provides distance
measurements with higher accuracy.[5] However, TOAC is an
achiral amino acid with a tetrasubstituted a carbon affecting
the peptide secondary structures.[6] Furthermore, the deter-
mination of the relative orientation of two spin-labeled units
is hampered by various TOAC conformations.[7] Thus, for
distance measurements and investigations of the relative
orientation of peptide secondary structures or domains, a spin
label is desirable that can be incorporated into peptides as
regular chiral a-l-amino acid and provides conformational
rigidity such that the nitroxide N–O unit is located at a
defined position in space. However, a chiral amino acid has at
least the Ca–Cb bond as an axis of rotation, a fact that must
be considered in the design of a new spin label with a defined
nitroxide orientation. Furthermore, to facilitate the interpre-
tation of distances it would be advantageous to locate the
nitroxide bond as an elongation of the Ca–Cb axis.
Herein, we report the design and synthesis of the chiral
amino acid 4-(3,3,5,5-tetramethyl-2,6-dioxo-4-oxylpiperazin-
1-yl)-l-phenylglycine (TOPP), in which the nitroxide bond
and the Ca–Cb bond are aligned on the same axis (Figure 1).
Further, we describe the incorporation of TOPP into an
alanine-rich peptide and report EPR distance measurements
in a doubly labeled peptide. The spectroscopic data are
compared with those for the same peptide marked with
conventional MTSSL. The design of TOPP takes advantage
of a planar phenyl ring connected to Ca and para substitution
by a dioxopiperazine that is also kept nearly planar by the
amide functionalities and the geminal methyl residues.
Therefore, a continuous axis from Ca to the nitroxide bond
is expected.[8] The nearly collinear alignment of the nitroxide
and Ca–Cb bond was confirmed by analysis of the N-acetyl
methylamine amino acid derivative of TOPP by means of
DFT calculations (see the Supporting Information).
The key step in the synthesis of the spin-labeled amino
acid Fmoc-TOPP-OH (1) was the copper(II)-catalyzed
Chan–Lam coupling of 3,3,5,5-tetramethylpiperazine-2,6-
dione (2) and boronic acid 3 (Scheme 1). Imide 2 was
synthesized in three steps according to a published synthesis.[9]
Starting from acetone, 2-amino-2-methylpropionitrile was
generated and dimerized under reduced pressure to provide
amine 4. Cyclization of the biscyano amine 4 yielded imide 2
for the Chan–Lam coupling. The synthesis of amino acid
Fmoc-TOPP-OH (1) is based on the functionalization of l-
hydroxyphenylglycine (5). With the introduction of the
carboxybenzyl (Cbz) and benzyl (Bn) protecting groups
Figure 1. Spin labels for EPR structural studies in proteins: MTSSL-
modified cysteine (left), TOAC (middle), and TOPP (right).
[*] Dr. S. Stoller, Dr. T. Y. Baranova, Prof. Dr. M. Bennati,
Prof. Dr. U. Diederichsen
Institut fꢀr Organische und Biomolekulare Chemie
Georg-August-Universitꢁt Gçttingen
Tammannstrasse 2, 37077 Gçttingen (Germany)
E-mail: udieder@gwdg.de
Homepage: http://www.diederichsen.chemie.uni-goettingen.de
phenylglycine derivative,
6 is prone to racemization
Dr. G. Sicoli, Prof. Dr. M. Bennati
(Scheme 1). The reaction conditions throughout the synthesis
were carefully adjusted in this regard. Treatment of 6 with
triflic anhydride delivered enantiomerically pure aryl triflate
7. In order to avoid racemization in subsequent steps, the N-
Cbz group was replaced by two N-Bn protecting groups
generating compound 8. The arylboronic ester 9 was obtained
by borylation of the aryl triflate 8 under Miyaura conditions.
Max-Planck-Institut fꢀr Biophysikalische Chemie
Am Fassberg 11, 37077 Gçttingen (Germany)
E-mail: Giuseppe.Sicoli@mpibpc.mpg.de
[**] We thank the Deutsche Forschungs-gemeinschaft DFG (SFB 803)
for generous support.
Supporting information for this article is available on the WWW
under http://dx.doi.org/10.1002/anie.201103315.
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9743

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purification. The oligomers were charac-
terized by high-resolution ESI mass spec-
trometry, CD spectroscopy, and EPR
measurements.
Since alanine-rich peptides display a
high propensity for forming a helices that
even increases with decreasing temper-
ature,[10] the alanine-rich peptide P1 (Ac-
AAAAK-TOPP-AKAAAAAKAAKA-
TOPP-KAAAA-NH2) containing two
TOPP spin labels was used as a model
system for the EPR distance measure-
ments (Figure 2). The corresponding pep-
tide P2 (Ac-AAAAK-Y-AKAAAAA-
KAAKA-Y-KAAAA-NH2) was pre-
pared as reference in which the TOPP
labels are replaced by tyrosine. Finally, a
third peptide P3 (Ac-AAAAK-MTSSL-
AKAAAAAKAAKA-MTSSL-KAA-
AA-NH2) was synthesized which contains
cysteine for attaching the MTSSL label
instead of the TOPP amino acid.
The a-helical content of peptide P1
twice labeled with TOPP was character-
ized by circular dichroism (CD) and
compared to that of peptide analogues
P2 and P3. The minimum at 208 nm and
the shoulder at 222 nm are typical for an
a-helical peptide conformation.[11] All
peptides provide quite similar CD spectra
in trifluoroethanol (TFE), indicating the
expected helical content (Figure 3). The
TOPP spin label can be incorporated in
peptide helices without conformational
Scheme 1. Synthesis of Fmoc-TOPP-OH (1). TFA=trifluoroacetic acid, DMSO=dimethyl
sulfoxide, dppf=1,1’-bis(diphenylphosphanyl)ferrocene, Fmoc-OSu=N-(9-fluorenylmethoxy-
carbonyloxy)succinimide.
The oxidation of compound 9 with NaIO4 yielded the free
boronic acid 3, which was directly treated with 3,3,5,5-
tetramethylpiperazine-2,6-dione (2) in a copper-mediated
Chan–Lam coupling to assemble the amino acid core
structure 10. The benzyl groups were removed by hydro-
genolysis at 70 psi using Pearlmanꢀs catalyst. The crude
product was submitted to 9-fluorenylmethoxycarbonyl
(Fmoc) protection yielding amino acid 11 with a good optical
purity (> 86% ee, determined by preparation and HPLC
analysis of dipeptides generated by coupling with resin-bound
d-alanine). Oxidation with mCPBA provided the target
compound 1 in an overall yield of 17% over 11 steps.
Also for Fmoc solid-phase peptide synthesis (SPPS)
conditions were required that avoid racemization during
coupling of the activated phenyl glycine derivative 1. HBTU/
HOBt activation was applied except for the spin-labeled
Fmoc-TOPP-OH (1), which was coupled using 3-(diethox-
Figure 2. Model representation of the a-helical structure of peptide P1
(Maestro, version 9.1, Schrçdinger, LLC, New York, 2010).
distortion of the helix and without any indication for
epimerization of the TOPP amino acids during oligomer
synthesis.
Since the a-helical content of alanine-rich peptides
increases with decreasing temperature, the TOPP-labeled
peptide P1 was studied at various temperatures between 20
and À408C by means of continuous-wave (CW) EPR
yphosphoryloxy)-1,2,3-benzotriazin-4(3H)-one
(DEPBT)
and NaHCO3 in THF. Cleavage and deprotection were
achieved with TFA/TIS/H2O (90:5:5) and the respective
peptide containing the spin label TOPP was obtained in its
hydroxylamine form. In order to regenerate the nitroxide
group, the peptide was treated with Cu(OAc)2 prior to HPLC
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Figure 3. CD spectra of peptides P1 (blue), P2 (red), and P3 (black) in
TFE at 208C.
spectroscopy.[10,11] Peptide P1 was dissolved in TFE/glycerol
(90:10) to obtain a cryogenic-type medium. According to the
CW-EPR spectra, decreasing temperature results in reduced
mobility of the spin label, which is caused by the increase in
the a-helical fraction and not only by an increase in viscosity,
as indicated by a control experiment with pure TOPP in the
same medium (see the Supporting Information).
Peptide P1 was dissolved in TFE/EtOH/H2O as well as in
TFE/EtOH/MeOH and slowly cooled down to À808C (before
flash-freezing in liquid nitrogen) in order to increase the
fraction helicity. Analogous results were obtained in different
mixtures (Supporting Information). The EPR distance meas-
urements at the X-band (9 GHz) gave rise to well-defined
dipolar oscillations characterized by several oscillation peri-
ods (Figure 4, blue curve). Furthermore, some Pake pattern
deformation was observed for selected pump and detection
frequencies (see the Supporting Information) indicating the
contribution of orientational selectivity owing to the rigidity
of the label.
Figure 4. Top: Time-domain DEER signal of double-labeled peptide P1
in TFE/EtOH/MeOH (40:40:20). The data points (blue and green
circles) represent the experimental data after background subtraction,
and the red lines are the time-domain simulation of the data
performed with DeerAnalysis2011.[13] Bottom: Best fits of the distance
distribution obtained from Tikhonov regularization (green and blue
curves) The dotted red curves correspond to the best Gaussian fit for
the peptide P3 and a two-Gaussian fit for the peptide P1, respectively.
The DEER experiment was carried out on a Bruker ELEXYSIS 580
pulsed EPR spectrometer at 50 K; p/2Àp=16–32 ns; pELDOR =36 ns;
SPP=50; SRT=5 ms; scans=249; acquisition time: 12 h.
In order to suppress orientational selectivity and extract a
distance distribution, we performed an orientational averag-
ing experiment at 11 field positions. However, the resulting
trace (Supporting Information) did not differ significantly
from the results of the single experiment recorded with
standard PELDOR setup (Figure 4). Analysis of the traces
indicated a narrow distance distribution centered at 2.80 nm
with Dr= 0.26 nm. The distance is consistent with the
estimated distance of 2.7 nm (Figure 2) for two rigid spin
labels linked to a peptide with a-helical conformation (f=
À528, y = À538). A small amount of a heterogeneous
population of structures seems to be formed as indicated by
a second peak (3.15 nm). This population might origin from a
more poorly defined peptide.
A comparative study performed on the peptide P3 led to
an interspin distance of 2.26 nm (Figure 4, green curve). The
distance distribution obtained for this sample is as narrow as
that with the rigid label; this is in contrast to most reported
cases, in which broad distance distributions are usually
observed with MTSSL labels.[12] Nevertheless, the observed
distance between the MTSSL is considerably less than that
between the TOPP labels and must be related to a specific,
unknown conformation of the flexible labels. Simple molec-
ular modeling indicates that there are plausible conforma-
tions in agreement with the observed distance (Supporting
Information); an unambiguous assignment of the spin–spin
distance of 2.26 nm to a preferred conformation would
require more sophisticated modeling. Therefore, the main
advantage associated with the insertion of the TOPP spin
probe as compared to MTSSL is the straightforward assign-
ment of the distance owing to the rigid and readily predictable
structure of the label.
In conclusion, we report the synthesis of a novel, rigid
nitroxide-labeled amino acid TOPP that does not produce
perturbation of the secondary structure, thus, providing a
promising tool for structural studies of peptides and proteins.
The design of the TOPP amino acid is based on the alignment
of the nitroxide with the Ca–Cb amino acid bond on one axis
and the synthetic applicability with respect to racemization at
Ca during amino acid and peptide oligomer synthesis. The
present study illustrates the straightforward assignment of a
spin– spin distance measured by pulsed EPR which is in
contrast to the different and ambiguous result obtained with
the commonly used MTSSL label. Furthermore, the predicted
reduced mobility of the TOPP spin label represents a
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9745

Communications
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potential advantage for its incorporation into transmembrane
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ments at an atomic scale.
Received: May 14, 2011
Published online: September 5, 2011
Keywords: distance measurements · EPR spectroscopy ·
.
nitroxide radicals · peptide conformations · spin labels
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