462
P. Shi et al. / Biochemical and Biophysical Research Communications 402 (2010) 461–466
an intermediate. A mixture of Na15NO2 (8.75 g), diethyl malonate
(16 mL), and water (0.75 mL) was placed in a three-necked, round-
bottomed flask, with toluene (24 mL) as solvent. The stirred mixture
was cooled in an ice bath. Glacial acetic acid (10 mL) was then slowly
added. The reaction mixture was warmed to 40–50 °C and
maintained at this temperature for 6 h. The organic layer was then
separated using a separating funnel. An yellow oil (diethyl oximino-
malonate) was obtained after removing the solvent. Reaction of
diethyl oximinomalonate with glacial acetic acid was initiated by
the addition of zinc powder (22 g) and the stirred mixture was kept
at 40–50 °C for 4 h. The 15N-labeled diethyl acetaminomalonate was
obtained as a pure white product by recrystallization from water.
The required 15N-labeled trifluoromethyl-phenylalanine was
synthesized from 15N-labeled diethyl acetaminomalonate and 4-tri-
fluoromethylbenzyl bromide. A solution of diethyl acetamidomalo-
nate (10.0 g) in anhydrous ethanol (125 mL) was added to a sodium
ethoxide solution and the mixture was heated at 50 °C for 1.5 h.
4-Trifluoromethylbenzyl bromide (11.0 g) was then added portion-
wise to the reaction mixture and the reaction was allowed to pro-
ceed for 20 h. The reaction mixture was then cooled to room
temperature and the precipitate was collected by filtration and
added to a mixture of 98% formic acid (50 mL) and concentrated
HCl (50 mL). The resulting mixture was refluxed at 100 °C for 24 h
before the final product of 15N-labeled trifluoromethyl-phenylala-
nine (tfmF) was dried. Details of verification of the identity of the
product and assessment of its purity can be found in the Supporting
Information.
20 min before packing onto a gravity-flow column. Impurities were
washed out by applying 50 mL of washing buffer [50 mM Tris,
500 mM NaCl, 20 mM imidazole, pH 8.0] to the column. The target
proteins were then eluted from the column using elution buffer
[50 mM Tris, 500 mM NaCl, 250 mM imidazole, pH 8.0].
Purified recombinant SH3 proteins were analyzed using
SDS–PAGE (12%, w/v) and concentrated using an Amicon Ultra
15 mL device (5000 MWCO, Millipore). Two rounds of concentra-
tion and dilution in NMR buffer [50 mM NaH2PO4–Na2HPO4, pH
6.5] were applied to the eluted protein sample for imidazole re-
moval and buffer exchange. D2O was added to the SH3 sample to
give a 10% (v/v) final concentration before solution NMR analysis.
2.5. Backbone amide 1H and side-chain 19F chemical shift and
relaxation data analysis
All one-dimensional 15N-filtered 1H NMR spectra were acquired
at 298 K on a Bruker Avance 500 MHz spectrometer equipped with
a triple-resonance cryo-probe. A heteronuclear single-quantum
correlation (HSQC) pulse sequence was applied to implement
15N magnetization filtering. The first free-induction decay (FID)
data, with 2048 complex points for the HSQC experiment, were col-
lected and processed with an exponential window function (line
broadening = 10 Hz) using Bruker data-processing software. Back-
bone amide 15N T1 and T2 relaxation data were acquired using a
1D mode standard HSQC-based pulse sequence on the same Bruker
500 MHz spectrometer [10]. Peak intensities of a total of seven lon-
gitudinal relaxation durations (61.33, 141.6, 242.0, 362.42, 523.0,
753.82 and 1145.2 ms) were measured and regressed against the
durations as a single-exponential function for the T1 data, while peak
intensities of six transverse relaxation durations (17.6, 35.2, 52.8,
70.4, 105.6 and 140.8 ms) were measured and regressed for the T2
data of backbone amide 1H in tfmF–SH3 using Origin software
(OriginLab, Co.).
2.2. Constructs
A DNA fragment encoding the human vinexin SH3 domain was
PCR-amplified from the previously described expression plasmid
[8]. The amplified fragment was inserted into pBAD vector (Invitro-
gen Co.) between the NcoI and XhoI sites. The protein sequence
derived from the plasmid contained a His6-tag attached to the
N terminus of the recombinant SH3 domain.
All one-dimensional 19F NMR spectra were acquired at 298 K on
a Bruker Avance 400 MHz spectrometer equipped with a broad-
band double-resonance probe and the observation channel was
tuned to 19F (376 MHz). One-dimensional 19F chemical shift data
were acquired with 16384 complex points using a simple 1D pulse,
and processed with an exponential window function (line broad-
ening = 10 Hz) using Bruker data-processing software. Side-chain
19F T1 relaxation data were collected with eight longitudinal relax-
ation durations (50, 100, 200, 500, 800, 1000, 1500 and 2000 ms)
using a standard Bruker one-dimensional inverse-recovery pulse
sequence. Side-chain 19F T2 relaxation data were collected with
eight transverse relaxation durations (100, 150, 200, 400, 600,
800, 1200 and 1600 ms) using a standard Bruker 1D Carr–Purcel–
Meiboom–Gill (CPMG) pulse sequence. The intensities of the series
of peaks were measured and regressed for T1 or T2 data for the
side-chain 19F in 15N/19F-tfmF–SH3.
2.3. Incorporation of 15N/19F-labeled trifluoromethyl-phenylalanine
into the SH3 domain of human vinexin protein
In plasmid pBAD-His6-SH3, codons corresponding to Phe7,
Tyr26, and Tyr51 of the SH3 domain were respectively, mutated
to amber stop codon TAG using quick-change site-directed muta-
genesis (Stratagene Co.). The pBAD plasmid coding the mutated
SH3 domain and plasmid pDule-tfmF (containing DNA sequences
coding tRNACUA and tfmF-specific aminoacyl-tRNA synthetase,
kindly provided by Dr. R.A. Mehl, Department of Chemistry, Frank-
lin and Marshall College, Pennsylvania, USA) were co-transformed
into Escherichia coli host cells TOP10 in the presence of 15
lg/mL
tetracycline and 100 g/mL amphicillin, in a similar manner as re-
l
ported previously [7,9]. The transformed bacteria were incubated
in LB medium overnight, then transferred to fresh 2ꢀ YT medium
containing 1 mM 15N/19F-tfmF at 37 °C. Expression of the SH3 pro-
tein was induced using 0.2% arabinose when the OD600 reached 1.0.
3. Results and discussion
3.1. Unnatural amino acid tfmF synthesis
2.4. Protein purification
The reactions shown in Scheme 1 were carried out to incorpo-
rate 15N spin into the unnatural amino acids. 15N spin was intro-
duced at the amide nitrogen of 19F-trifluoromethyl-phenylalanine
Cells were harvested by centrifugation at 6000 rpm for 8 min at
4 °C. Cell pastes were suspended in 40 mL of lysis buffer [50 mM
Tris–HCl, 500 mM NaCl, 3 mM imidazole, pH 8.0]. Cell suspensions
in lysis buffer were probe-sonicated (VC500, Sonics and Materials,
Danbury, CT) at a power level of 30%, 2.0 s pulse on and 4.0 s pulse
off, for a total of 10 min on ice. The lysate was then centrifuged at
16,000 rpm for 20 min at 4 °C. Pellets from the centrifugation were
discarded and the supernatant was mixed with 5 mL of Ni2+-NTA
resin (QIAgen, Valencia, CA). The mixture was rotated at 4 °C for
(
19F-tfmF) from 15N-labeled NaNO2, which provided the original
source of 15N spin (Scheme 1). Before synthesizing 15N/19F-tfmF,
15N-labeled diethyl acetamidomalonate (DEAM), an amino acid
intermediate, was synthesized (Scheme 1, reaction 1). This
15N-amide-labeled DEAM could be used as a common amino acid
intermediate for the further synthesis of many different natural
or unnatural amino acids. Here, 4-trifluoromethylbenzyl bromide