Angewandte
Communications
Chemie
Structure Elucidation
A Reactive, Rigid GdIII Labeling Tag for In-Cell EPR Distance
Measurements in Proteins
Yin Yang+, Feng Yang+, Yan-Jun Gong, Jia-Liang Chen, Daniella Goldfarb,* and Xun-
Cheng Su*
Abstract: The cellular environment of proteins differs consid-
erably from in vitro conditions under which most studies of
protein structures are carried out. Therefore, there is a growing
interest in determining dynamics and structures of proteins in
the cell. A key factor for in-cell distance measurements by the
double electron–electron resonance (DEER) method in pro-
teins is the nature of the used spin label. Here we present
a newly designed GdIII spin label, a thiol-specific DOTA-
derivative (DO3MA-3BrPy), which features chemical stability
and kinetic inertness, high efficiency in protein labelling,
a short rigid tether, as well as favorable spectroscopic proper-
ties, all are particularly suitable for in-cell distance measure-
ments by the DEER method carried out at W-band frequencies.
The high performance of DO3MA-3BrPy-GdIII is demon-
strated on doubly labelled ubiquitin D39C/E64C, both in vitro
and in HeLa cells. High-quality DEER data could be obtained
in HeLa cells up to 12 h after protein delivery at in-cell protein
concentrations as low as 5–10 mm.
and it is generally applicable to a limited number of
proteins.[1a,2] DEER is a method that provides distance
distributions between pairs of, usually identical, spin labels
that are attached to a bio-macromolecule at well-defined
sites.[3] Its distance accessibility is usually in the 1.6–8 nm
range[3] and can increase to 16 nm if the protein is deuter-
ated.[4] Owing to its inherently high absolute sensitivity as
compared with NMR spectroscopy, and its insensitivity to
protein size and background signals, DEER can become an
efficient method for in-cell structural studies of proteins.[5]
The first in-cell DEER experiments using standard nitro-
xide spin labels were reported in oocytes, where the low
stability of the nitroxide radicals in the reducing cellular
environment was noted.[5a] This is not a problem when the
nitroxide spin label is exposed to the outside of the cell
environment,[6] but otherwise it pauses a significant limitation
on this methodology. Thus, for the in-cell DEER method to
become a significant and viable technique, stable spin labels
are required to explore the protein interactions and dynamics
in the cell. New nitroxide spin labels are currently under
development but so far they have not been demonstrated in
in-cell DEER experiments.[7] Recently, RIDME distance
measurements between a trityl spin label and intrinsic FeIII
in CP450, requiring 80 h accumulation time, was reported in
oocytes.[8] An attractive alternative approach is to use GdIII-
based spin labels, which have already been reported for many
in vitro GdIII–GdIII DEER applications.[9]
C
haracterization of the dynamics, interactions and struc-
tures of proteins is an important way of delineating their
functions. Current biophysical methods used to explore
protein dynamics and structures are generally applied in vitro,
under conditions that differ considerably from the cellular
milieu. In the cell, molecular crowding, sub-organelle local-
ization, post-translational modifications, and specific and
non-specific associations with cellular components may
inevitably affect the structure and conformational equilibria
of proteins.[1] Therefore, effective methods for exploring the
atomic resolution structure and dynamics of proteins in their
native cellular environment are highly desirable. Currently,
NMR spectroscopy is probably the most effective method for
determining structure and dynamics in the cell at atomic
resolution. However, its low sensitivity invariably requires
expensive isotope labeling and high protein concentrations,
We have recently reported on in-cell W-band GdIII–GdIII
DEER distance measurements of maleimide-DOTA-GdIII-
labeled proteins in human HeLa cells.[10] The drawback of the
maleimide-DOTA tag is its rather long and flexible tether. In
addition, there were reports that thiomaleimide conjugates do
not exhibit long-term stability in cells due to the thiol
exchange with glutathione and the hydrolysis of succinimide
ring.[11] Q-band DEER experiments on a 4-vinyl PyMTA-
GdIII conjugated peptide injected into oocytes was reported as
well.[12] However, the low reactivity of this tag towards protein
thiols results in unfavorable labeling conditions for a pro-
tein.[13] More recently, a lanthanide binding peptide was fused
into a helical bundle peptide both at the N- and C-termini,
GdIII was supplemented with high concentration (100 to
500 mm) through the growing media and W-band in-cell
spectra were recorded.[14] The main problem with this
approach is the low binding constant of GdIII and the long
measurement time (72 h) owing to the background of large
amounts of free GdIII, which affects the signal-to-noise ratio.
In general, efficient in-cell DEER measurements require
high stability of the spin label, a stable linker between the
protein of interest and the spin label and a minimal size of the
[*] Dr. Y. Yang,[+] Prof. D. Goldfarb
Department of Chemical Physics
Weizmann Institute of Science
Rehovot 76100 (Israel)
E-mail: daniella.goldfarb@weizmann.ac.il
F. Yang,[+] Y. J. Gong, J. L. Chen, Prof. X.-C. Su
State Key Laboratory of Elemento-organic Chemistry
Collaborative Innovation Center of Chemical Science and
Engineering (Tianjin), Nankai University
Tianjin 300071 (China)
E-mail: xunchengsu@nankai.edu.cn
[+] These authors contributed equally to this work.
Supporting information for this article can be found under:
Angew. Chem. Int. Ed. 2017, 56, 1 – 6
ꢀ 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
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