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Biophys J, December 2002, p. 3336-3350, Vol. 83, No. 6

and
*Institute of Molecular Biology, 07745 Jena, Germany; and
National High Magnetic Field Laboratory, Tallahassee,
Florida 32310 USA
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ABSTRACT |
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The response of membrane-associated peptides toward the
lipid environment or other binding partners can be monitored by
solid-state NMR of suitably labeled side chains. Tryptophan is a
prominent amino acid in transmembrane helices, and its
19F-labeled analogues are generally biocompatible and cause
little structural perturbation. Hence, we use 5F-Trp as a highly
sensitive NMR probe to monitor the conformation and dynamics of the
indole ring. To establish this 19F-NMR strategy, gramicidin
A was labeled with 5F-Trp in position 13 or 15, whose
1/
2 torsion angles are known from
previous 2H-NMR studies. First, the alignment of the
19F chemical shift anisotropy tensor within the membrane
was deduced by lineshape analysis of oriented samples. Next, the three
principal axes of the 19F chemical shift anisotropy tensor
were assigned within the molecular frame of the indole ring. Finally,
determination of
1/
2 for 5F-Trp in the
lipid gel phase showed that the side chain alignment differs by up to
20° from its known conformation in the liquid crystalline state. The
sensitivity gain of 19F-NMR and the reduction in the amount
of material was at least 10-fold compared with previous
2H-NMR studies on the same system and 100-fold compared
with 15N-NMR.
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INTRODUCTION |
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Because the three-dimensional structure of most
membrane-bound proteins is not yet accessible, it is often useful to
focus on specific molecular segments. For example, the conformation of
a prosthetic group or ligand may bear functionally relevant information
on a membrane-associated receptor, and the behavior of a protein side
chain may yield valuable insight about its immersion in the membrane or
its interaction with other binding partners. In many cases a
substantial response in the conformation or motional freedom of certain
side chains is expected, for example when an amphiphilic peptide
associates peripherally with the lipid bilayer, when lateral protein
aggregates are formed in the membrane, or when the lipid phase state is
altered. These effects are readily monitored, for example, by analyzing
the intrinsic fluorescence of aromatic side chains. Tryptophan (Trp) in
particular is a sensitive reporter of local dynamics, hydrophobicity,
and anisotropic interactions of membrane-associated proteins. For
example, Raman studies and fluorescence spectroscopy have been used to
monitor the alignment and environmental response of Trp side chains in
gramicidin A (Scarlata, 1988
, 1991
; Takeuchi et al., 1990
; Maruyama and
Takeuchi, 1998
). In other membrane proteins, Trp fluorescence spectra
have been correlated with different microenvironments (Reshetnyak and Burnstein, 2001
; Reshetnyak et al., 2001
), and multiexponential decays
have been interpreted in terms of discrete rotamer populations (Clayton
and Sawyer, 1999a
,b
). However, the information content of such
fluorescence analysis is still under debate (Ladokhin and White, 2001
),
as it is not straightforward to describe the absolute alignment of the
Trp side chain nor to characterize its axes of motional averaging.
The only direct approach to observe the structure of a side chain in a
noncrystalline membrane protein or fiber is afforded by solid-state NMR
spectroscopy (Watts et al., 1995
; Opella 1997
; Marassi and Opella,
1998
; Fu and Cross, 1999
). The detailed alignment and motional
averaging of specific side chains have been addressed, for example, in
gramicidin A (Killian, 1992
; Hu et al., 1993
, 1995
; Koeppe et al.,
1994
, 1995
; Hu and Cross, 1995
; Ketchem et al., 1997
),
bacteriorhodopsin (Spohn et al., 1983
; Keniry et al., 1984
), various
other peripheral and transmembrane protein segments (Koenig et al.,
1999
; Sharpe and Grant, 2000
; Sharpe et al., 2000
), and silk fibers
(Nicholson et al., 1993
; Asakura et al., 1997
; Demura et al., 1998
;
Kameda et al., 1999a
,b
). To observe a specific protein side chain by
solid-state NMR, most previous studies have relied on selective isotope
labeling with 2H, 13C, or
15N, which are nonperturbing but which have an
inherently low sensitivity compared with 1H-NMR.
To improve sensitivity, 19F has been successfully
used as an alternative probe in proteins, both in liquid state NMR
(Gerig, 1994
, 1998
; Danielson and Falke, 1996
; Luck et al., 1996
; Sun
et al., 1996
; Lau and Gerig, 1997
; Bouchard et al., 1998
; Zemsky et
al., 1999
; Luck and Johnson, 2000
) and solid-state NMR (McDowell et
al., 1993
, 1996
; Feeney et al., 1996
; Klug et al., 1997
; Goetz et al.,
1999
; Ulrich 2000
; Grage et al., 2001
; Murphy et al., 2001
; Salgado et
al., 2002
). In addition to its high sensitivity, which promises to
reduce acquisition times theoretically by two to three orders of
magnitude, 19F possesses a wide dispersion of
isotropic chemical shifts as well as a large chemical shift anisotropy
(CSA), which renders it a highly informative reporter of local
structure (Ulrich, 2000
).
Having recently demonstrated the use of 19F-NMR
to determine the overall alignment and motional averaging of a cyclic
peptide in a membrane (Grage et al., 2001
; Salgado et al., 2002
), here we will illustrate the structure analysis of a
19F-labeled protein side chain. The most relevant
candidate for this kind of investigation is
19F-labeled tryptophan, besides other aromatic
and aliphatic amino acids. Even though the risk of inducing a small
structural or electronic perturbation cannot be completely avoided,
hydrophobic side chains with a single
19F-substituent at the periphery are usually
compatible with the native protein structure. Fluorine-labeled Trp,
Phe, and Leu are indeed the most prominent and least perturbing amino
acids used for 19F-NMR on proteins, as they can
be readily incorporated biosynthetically by supplementing the growth
medium of most expression systems (McDowell et al., 1993
, 1996
; Gerig
1994
; Danielson and Falke, 1996
; Feeney et al., 1996
; Luck et al.,
1996
; Sun et al., 1996
; Klug et al., 1997
; Lau and Gerig, 1997
;
Bouchard et al., 1998
; Goetz et al., 1999
). Many studies have shown
that 5F-Trp, 6F-Trp, 4F-Phe, and
F-Leu hardly affect the surrounding
protein structure (Feeney et al., 1996
; Sun et al., 1996
), and vice
versa that the conformation of these labeled side chains hardly differs
from that of the unlabeled system (Lau and Gerig, 1997
; Cotten, 1998
; Cotten et al., 1999
).
There are several biophysical reasons why a more detailed
characterization especially of Trp in membrane-associated peptides and
proteins is generally desirable. Due to its amphiphilic character, Trp
plays a distinguished role both in integral membrane proteins as well
as in peripheral ones. In transmembrane helices Trp frequently occurs
near the polar-apolar interface, where it helps to anchor the helix at
an appropriate depth within the lipid bilayer (Schiffer et al., 1992
;
de Planque et al., 1998
; Wallace and Janes, 1999
; Morein et al., 2000
;
Rinia et al., 2000
). In ion channels the dipole moments of indole rings
are often aligned toward the channel center to guide the entry of ions
(Hu et al., 1993
, 1995
; Avdonin and Hoshi, 2001
; Townsley et al.,
2001
), and Trp may also stabilize the channel structure (Cotten et al.,
1997
; Okada et al., 2001
). Another role of Trp has been attributed to
its partial membrane immersion, which mediates the peripheral adhesion
of amphiphilic peptides to membranes, as in the case of cecropins (Oh
et al., 2000
), indolicins (Hancock and Diamond, 2000
; Friedrich et al., 2001
), and annexins (Hofmann et al., 2000
). In the latter example, Trp
has also been suggested to modulate the formation of two-dimensional protein arrays on the membrane surface (Pigault et al., 1999
). Trp side
chains have been further proposed to interact with certain lipids
(Killian, 1992
; Mousson et al., 2001
) or to facilitate the lateral
association of transmembrane proteins. Hence, it is of fundamental
interest to be able to monitor directly the conformation and motional
behavior of this special amino acid in membrane proteins by solid-state
NMR, even if this involves the observation of a nonnatural
19F-substituent on the indole ring.
The alignment of a 19F-labeled Trp side chain
with respect to the lipid bilayer surface will be determined here by
analyzing the 19F CSA tensor in a uniaxially
oriented membrane sample, in a similar way as it has been previously
done by 2H-, 13C-, and
15N-NMR (Spohn et al., 1983
; Keniry et al., 1984
;
Killian 1992
; Hu et al., 1993
, 1995
; Nicholson et al., 1993
; Koeppe et
al., 1994
, 1995
; Hu and Cross, 1995
; Lee et al., 1995
; Asakura et al., 1997
; Demura et al., 1998
; Jude et al., 1999
; Kameda et al., 1999a
,b
; Koenig et al., 1999
; Koeppe et al., 2000
; Sharpe and Grant, 2000
; Sharpe et al., 2000
). We note that 19F possesses
a highly asymmetric CSA tensor, in contrast to the axially symmetric
1H-15N dipolar coupling or
the nearly axially symmetric amide 15N CSA and
2H quadrupolar tensors. Therefore, the
19F CSA tensor can be used to fully describe the
three-dimensional alignment of the labeled segment with respect to the
membrane normal in terms of two Euler angles, rather than providing
only a single angular restraint. To extract both Euler angles, the NMR
analysis requires a concerted lineshape analysis of the sample at
several different tilt angles (Ulrich et al., 1992
, 1994
, 1995
; Ulrich
and Watts, 1993
, 1994
; Ulrich and Grage, 1998
), or alternatively magic
angle oriented sample spinning can be used (Glaubitz and Watts, 1998
;
Glaubitz et al., 1999
, 2000
). In principle, all tools for the analysis
of 19F-labels in membranes are at hand, but there
remains an open question concerning 1) the principal axis values in
situ and 2) the alignment of the CSA tensor within the molecular frame.
This fundamental information about 19F CSA
tensors is not yet available for any fluorinated amino acid. Anisotropic values (but not the alignments) of
19F chemical shift tensors have been reported for
various systems including 5F-Trp, but not yet in the framework of any
peptide or protein (Yim and Gilson, 1968
; Mehring et al., 1971
; Luck et al., 1996
). For a few aromatic systems the respective principal tensor
axes have been assigned to the molecular frame, but not yet for the
indole ring of Trp (Snyder, 1965
; Nehring and Saupe, 1970
; Griffin et
al., 1973
; Halstead et al., 1975
; Mehring 1983
; Hiyama et al., 1986
).
To first obtain the fundamental CSA parameters for 5F-Trp and
then to tackle a biologically relevant question by
19F-NMR, we have investigated here a particular
structural aspect of the antimicrobial peptide gramicidin A (gA), which
has attracted much attention over the past decade. The
pentadecapeptide
(HCO-Val-Gly-Ala-DLeu-Ala-DVal-Val-DVal-Trp-DLeu-Trp-DLeu-Trp-DLeu-Trp-NHCH2CH2OH) is known to form dimeric ion channels in membranes (Harold and Baarda,
1967
; Arseniev et al., 1985
; Killian, 1992
). The rim of the
right-handed
-helix is lined with four tryptophans, which play an
important structural role in the membrane-immersion of the peptide
(Killian, 1992
; Hu et al., 1993
; Pascal and Cross, 1993
; Cotten et al.,
1997
) and which are functionally relevant for the conductivity and
selectivity of the ion channel (Becker et al., 1991
; Hu and Cross,
1995
; Hu et al., 1995
; Busath et al., 1998
). The structure of the
peptide in liquid crystalline membranes has been fully resolved by
previous 2H-, 13C-, and
15N-NMR studies, revealing the detailed
conformation and dynamics of the Trp side chains (Macdonald and Seelig,
1988
; Ketchem et al., 1993
, 1997
; Koeppe et al., 1994
, 2000
; Cross et
al., 1999
). In recent functional studies of gA,
19F-substituents were placed in various positions
of the indole rings as a tool to modify their electric dipole moments,
which provided valuable insights into the mechanism of ion transport (Anderson et al., 1998
, 2001
; Busath et al., 1998
; Dorigo et al., 1999
;
Phillips et al., 1999
; Thompson et al., 2001
). Despite some appreciable
electric dipole effects, the structural impact of the fluorine
substitutions on the side chain torsion angles of Trp was found to be
rather small, changing
1 by less than 5°, and
2 by less than 12° (Cotten 1998
; Cotten
et al., 1999
) (for definitions of
1/
2, see Fig.
1). Given this reliable information on
the structure of native gA and its 19F-labeled
analogues, here we have carried out the first direct 19F-NMR analysis of 5F-Trp in a
membrane-associated peptide. That way, it was not only possible to
establish the NMR approach and demonstrate its high sensitivity,
but also to obtain new structural data on the side chain response
in gA toward different phase states of the lipid bilayer.
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MATERIALS AND METHODS |
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Samples
Three types of gramicidin A peptides were examined in this
study: labeled at position 13 with 5F-Trp ["F13-gA"], at position 13 with 5F-(2,4,6,7)2H-Trp ["F(d)13-gA"],
or at position 15 with 5F-(2,4,6,7)2H-Trp
["F(d)15-gA"]. See Fig. 1 for the numbering of the indole ring.
The fluorinated peptides were synthesized by standard solid phase
methods as described previously (Fields et al., 1988
, 1989
; Cotten et
al., 1999
). The peptides were incorporated in
dimyristoylphosphatidylcholine (DMPC) purchased from Avanti Polar
Lipids (Alabaster, AL) and used without further purification.
Nonoriented powder samples of F(d)13-gA and F(d)15-gA were prepared by
codissolving the peptide and DMPC at a peptide:lipid molar ratio of
1:10 in benzene with 5 vol% ethanol. The solvent was removed under
vacuum, and the mixture was hydrated to 50% (weight/total weight) by
adding high-performance liquid chromatography-grade water, as
previously described (Cotten et al., 1999
).
For the oriented samples, DMPC and gA at a 10:1 ratio (using either 9 mg F(d)13-gA, or 2 mg of F(d)15-gA or F13-gA) were cosolubilized in 450 µl of 95:5 vol/vol mixture of benzene/ethanol. The solution was distributed over 15 glass slides of 8 mm × 20 mm × 0.06-mm (Marienfeld, Lauda-Königshofen, Germany). After evaporating the solvent under N2, the slides were dried under vacuum overnight. Samples containing F(d)13-gA and F(d)15-gA were hydrated to 50% by adding high-performance liquid chromatography-grade water to each slide with a micropipette and then stacked. The stack was covered with an additional slide, sealed with epoxide glue along the edges to prevent the sample from drying, and incubated for several days at 45°C. Alternatively, the glass slides with F13-gA were stacked first, then incubated at 98% humidity for 48 h until the sample became transparent, and finally wrapped in parafilm. Both approaches yielded equivalent results in terms of the peptide structure and mobility, although the latter sample had a significantly better mosaic spread.
Instrumentation
Solid-state 19F-NMR spectra were acquired on a 500-MHz Varian Unity Inova spectrometer (19F frequency at 470.3 MHz). A double-tuned (1H/19F) flat-coil probe (2.5 mm × 9 mm) from Doty Scientific (Columbia, SC) was used. The orientation of the flat coil could be adjusted with a goniometer to within 2°. The 19F 90°-pulse length was 2.5 µs, and 1H-decoupling of up to 40 kHz was applied. A Hahn echo with a 25-µs delay was used to acquire free induction decays of 5120 points (zero filled to 16,384) with a 2-µs dwell time over 10 ms. The recycle time was 3 to 4 s, and 5,000 to 10,000 scans were acquired, depending on the phase state and linewidth of the sample. A 100-Hz linebroadening was applied, and all chemical shift values were referenced with respect to CFCl3 at 25°C. T2-relaxation times were measured with an echo sequence over 10 suitably incremented delay times.
The degree of sample orientation was assessed by
31P-NMR using a homebuilt flat-coil
1H/X probe. In the first set of oriented samples
containing F(d)13-gA and F(d)15-gA, ~50% of the material were well
oriented, whereas the sample prepared later from F13-gA was oriented to
90%. An appropriate powder contribution was thus subtracted from the
corresponding 19F-NMR spectra, but this procedure
had no impact on the analysis because the resulting lineshapes of
analogous samples were very similar (despite the different amounts of
powder contribution subtracted). The residual
19F-background signal of the NMR probe was also
subtracted. Because most spectra contained a small signal of
trifluoroacetic acid at
76 ppm, this narrow peak was replaced in the
oriented spectra by a straight connection between
69 and
81 ppm to
avoid any misfit in the lineshape simulations.
Lineshape simulations
The experimental 19F spectra from oriented
samples aligned at a tilt angle
in the magnetic field were compared
with lineshapes calculated numerically by a C2+
program. This strategy is illustrated in Fig. 1, where the chemical shift anisotropy tensor is successively rotated from one frame of
reference to the next using three angles
,
, and
each. The
starting point in the lineshape simulations was the CSA tensor
P in the principal axis frame (P)
for which the three principal axis values were obtained from the
19F-NMR spectrum of lyophilized gA. First, the
tensor was transferred via the indole ring frame (I) into
the helix frame (H) with the z axis along the gA
axis. Subsequently, the tensor was rotated into a sample frame
(S) that is fixed with its z axis along the glass
plate normal, as the helix axis may deviate from the sample normal due
to "mosaic spread." Finally, the tensor was transferred into the
laboratory frame (L) to account for the macroscopic sample tilt
. The resulting resonance frequency is then given by the (
L)33-component of the
tensor
L in the laboratory frame. For the
complete spectrum, however, it has to be considered that the membrane
environment defines only the gramicidin helix axis direction but not
its azimuthal polarity. This, in addition to the mosaic spread, was
taken into account by averaging over the three Euler angles
HS,
HS, and
HS, which transform the coordinate system H
into S. The lineshapes were constructed from 106
randomly chosen Euler angle sets
HS,
HS, and
HS with
uniformly distributed
HS and
HS. The helix slant
HS was varied according to a Gaussian
distribution p(
HS) ~ sin(
HS)
exp[
HS2/(2
2)]
around
HS = 0 with a standard deviation of
= 12°, called the mosaic spread. Additional Lorentzian
linebroadening of 1 to 2.5 kHz was applied to the simulated spectra to
account for the intrinsic linewidth, choosing always the same value
within any one tilt series.
Our discussion of the spatial relationship between the
19F CSA tensor and tryptophan is based on the
gramicidin A structure 1MAG.pdb, and on the indole geometry from the
Sybyl database (Sybyl 6.4, Tripos Inc., St. Louis, MO), which is
equivalent to the data used in the 2H-NMR study
of gA by Hu et al. (Hu and Cross, 1995
; Hu et al., 1995
). A different
coordinate set for the Trp geometry had been used in the previous
2H-NMR analysis on
19F-substituted gA by Cotten et al. (Cotten,
1998
; Cotten et al., 1999
). Therefore, those
2H-NMR data were re-evaluated here with the same
indole geometry as Hu et al. to enable an unbiased comparison with our
own 19F-NMR data. It is important to realize that
the precision at which the indole geometry can be derived from the
literature or any database is rather limited and translates into an
uncertainty of ~5° in the
1/
2 rotamer angles of
the side chain.
Root of mean square deviation analysis
The spectral lineshapes of a tilt series were simulated from two
different points of view, as there are two possible ways of describing
the 19F CSA tensor orientation with respect to
the sample fixed frame (S). The first, ab initio approach
makes use of two Euler angles
PS and
PS, which define the principal axis system of
the CSA (P) with respect to the sample S.
Alternatively, in the in situ approach, we start off with the known
backbone structure of gramicidin A, and then the two rotamer angles
1 and
2 are used to
describe the torsions around the C
-C
and C
-C
bonds of Trp,
respectively (for definition of
1 and
2, see International Union of Pure and
Applied Chemistry and International Union of Biochemistry and Molecular
Biology 1970). These two approaches are equivalent in defining the
absolute CSA tensor orientation in S, and they can be
readily interconverted, provided that the alignment of the tensor with
respect to the indole geometry is known. Because this relationship has
not yet been characterized for 19F-labeled Trp,
here we will deduce the CSA tensor alignment and axis assignment by
comparing our 19F-NMR ab initio data set with the
previous 2H-NMR in situ data set. For an unbiased
representation of each set of NMR spectra, it is necessary to carry out
a systematic conformational search and to validate the experimental
data in an objective way. This was done by calculating the root mean
square deviation (rmsd) between the simulated lineshapes and the
experimental spectra of a complete tilt series, either as a function of
PS and
PS (ab
initio), or as a function of
1 and
2 (in situ):
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Minima of the rmsd were calculated to obtain the best-fit ab initio
tensor orientation and the best in situ side chain conformation, respectively. It should be noted that the combination of several lineshapes from a tilt series to yield a single rmsd value is not
unproblematic, because there are various ways how their respective contributions could be weighted in view of their very different spectral widths. Nevertheless, we found that the rmsd minima obtained with a linear weighting procedure correspond to excellent fits of
simulated and experimental lineshapes. Any other, more elaborate weighting models did not move the minima by more than 5°, hence our
rmsd analysis leads to reliable results. Another potential source of
error in the rmsd plots concerns the accuracy in the chemical shift
determination, which is critical when the peak position in the 0°
tilt spectrum lies close to the
22 CSA
tensor value, as it happens to be the case here. In this situation, an error of 1 ppm would translate into a shift of the rmsd minima of
~3° in
PS, hence it is important to care
about good referencing in the oriented samples (R. W. Glaser and
A. S. Ulrich, submitted; R. Ulrich, R. W. Glaser, and A. S. Ulrich, submitted).
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RESULTS |
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The anisotropy of the 19F chemical shift is
characterized by a tensor with the three principal values
11,
22, and
33. Our aim is to determine the two unique
angles
and
, which describe the CSA alignment with respect to
the lipid bilayer, as illustrated in Fig. 1. From these angles, we will
then be able to deduce the conformation of the 5F-Trp side chain (i.e.,
1 and
2 values) to
which this CSA tensor is attached. First, we measure the three principal CSA values of 5F-Trp from nonoriented bilayer samples. Using
aligned samples, contributions of 1H-coupling,
T2-relaxation, and mosaic spread to the
19F linewidth are assessed, and spectra of
protonated and deuterated 5F-Trp samples are compared. Second, a tilted
series of orientation-dependent spectra of uniaxially aligned samples
is analyzed by lineshape simulation to determine the alignment of the
19F CSA tensor with respect to the membrane.
Next, we assign the three principal CSA axes with the aid of the known
coordinates of gA. On this basis, we are able to position the CSA
tensor into the molecular frame of the indole ring. Finally, the side
chain conformation of Trp in the gel phase bilayer can be determined and compared with its alignment known from 2H-NMR
studies of the liquid crystalline phase. A special emphasis of this
work concerns the behavior of gA in the gel state of the membrane where
the peptide is immobilized. Even though structural studies are rarely
performed in the gel state (Scarlata, 1988
, 1991
; Takeuchi et al.,
1990
; Nicholson et al., 1991
; Maruyama and Takeuchi, 1998
), the general
approach presented here will be relevant for any large membrane protein
that does not undergo fast long-axial rotation in the lipid bilayer.
Powder samples
Fig. 2 shows the
19F-NMR spectra for non-oriented samples of
F(d)13-gA (a, b) and F(d)15-gA (c,
d), incorporated into DMPC at a peptide:lipid ratio of 1:10.
When acquired at 35°C, i.e., above the lipid phase transition
temperature, the powder lineshapes (a, c) reflect
axially symmetric CSA tensors. Both span the range from
120.0 ppm to
139.0 ppm, as estimated by a lineshape fitting procedure that takes
linebroadening into account. This axial symmetry reflects the expected
fast reorientation of the peptide about the membrane normal at 35°C
(Macdonald and Seelig, 1988
; Lee et al., 1993
). Motional averaging,
however, obscures the structural information contained in the
anisotropy of the three distinct principal axes of the
19F CSA tensor. Therefore, to apply the proposed
NMR strategy to its full potential, it is important to prevent any
global molecular rotation. The corresponding
19F-NMR spectra at 5°C, where the peptide is
immobilized in the gel phase of the lipid, are displayed in Fig. 2,
b and d. These lineshapes now represent
nonaxially symmetric CSA tensors, whose principal axis values
11,
22, and
33 are extracted from the two edges and the
maximum (Nicholson et al., 1991
). Due to difficulties in chemical shift
referencing in a flat-coil probe (R. W. Glaser and A. S. Ulrich, submitted; R. Ulrich, R. W. Glaser, and A. S. Ulrich,
submitted), absolute errors are on the order of ±2 ppm, but the
relative values are self-consistent within ±1 ppm. For the label in
position 13, the principal axis values are
11 =
80.0 ppm,
22 =
141.5 ppm, and
33 =
156.5 ppm, and for position 15 they are
11 =
81.0 ppm,
22 =
141.0 ppm, and
33 =
157.5 ppm. The
isotropic chemical shifts are calculated to be
iso =
126.0 for F(d)13-gA, and
iso =
126.5 for F(d)15-gA, and the total
width of both respective tensors is 76.5 ppm. The CSA width of the
membrane-embedded peptide at 5°C is smaller than that of lyophilized
gramicidin A (
11
33 = 83 ppm) and of polycrystalline 5F-Trp (87 ppm) (U. Dürr, S. L. Grage, and A. S. Ulrich,
manuscript in preparation). This suggests that the gel phase lipid
environment provides a limited degree of librational freedom for the
Trp side chains, which are nevertheless subject to considerable
intramolecular steric hindrance by neighboring amino acids (Nicholson
et al., 1991
; Koeppe et al., 2000
). Upon cooling the polycrystalline
amino acid down to
60°C, we observed a further increase in its CSA by ~10 ppm, approaching the rigid powder limit (data not shown). This
trend compares well with the reported CSA widths of
15N in the amide groups of gramicidin A from
which the amplitudes of librational motion in the backbone have been
estimated as ±10° at
60°C and up to ±20° in the lipid gel
phase (Nicholson et al., 1991
; Lazo et al., 1993
, 1995
). For the Trp
side chains Hu et al. (1995)
have reported librational amplitudes of
~30° in the liquid crystalline state. In the present study,
however, all three 19F CSA tensor values are
affected by librational motion in a complex way, hence we do not
attempt to attribute the observed averaging to any particular torsional
axis nor to define an order parameter.
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Oriented samples
When a uniaxially oriented sample is aligned horizontally, i.e.,
with its axis parallel to the static magnetic field direction (
= 0°), all labeled sites have the same orientation with respect to
this direction. One specific frequency is selected from the powder
spectrum, resulting in a single narrow peak. The
19F-NMR spectra obtained this way from gA labeled
in position 13 are shown in Fig. 3. The
lineshapes are compared with and without 1H-decoupling, both for protonated (a)
and deuterated (b) 5F-Trp side chains, and each panel
displays data for the two different temperatures of 35°C (liquid
crystalline bilayer) and 5°C (gel phase). We note that the lipid
phase transition has only a small effect on the resonance position
(Fig. 3, a and b), suggesting that the Trp
conformation is quite similar in both the fluid phase and the gel state
environment. If the only consequence of lipid chain melting on gA were
the onset of long-axial rotation, then the signal would remain exactly
at the same frequency. However, there is a small but significant shift
of 2.7 ppm toward the isotropic value in going from 5 to 35°C, which
was confirmed by compiling 19F-NMR data also from
other oriented samples of gA (not shown). This small shift may thus be
attributed to a slight local conformational change or to some
additional motional averaging. It is likely that a slight wobble of the
gA axis plus increased librational freedom of the Trp side chains is
facilitated in the liquid crystalline phase of the lipid. In a
simplistic approach, such motional averaging may be described by an
isotropic order parameter Smol. Its
value can be estimated from the ratio of the observed CSA width of 19 ppm at 35°C (Fig. 2, a and c) over the
theoretically expected CSA width {19 ppm + 3/2 × 2.7 ppm},
provided there is no conformational change. The resulting value of
Smol
0.8 appears reasonable for the side chain of a transmembrane peptide, but it must only be regarded
as a rough indicator of the extent of motional averaging. It will be
shown below that the Trp torsion angles indeed respond slightly to the
lipid phase state, hence it is not possible here to discriminate
between motional effects and conformational changes.
|
The observed linewidths (at half height) of the oriented spectra are
plotted in Fig. 3, c and d as a function of the
1H-decoupling field strength
B1. Fig. 3 c illustrates the
line-narrowing effect of motional averaging due to global peptide
rotation in the liquid crystalline phase, and Fig. 3 d
compares the linewidths of protonated and deuterated indole rings at
5°C. 1H-decoupling is obviously essential for
achieving optimal resolution. The nondecoupled linewidths of ~11 kHz
start to decrease significantly when rather low decoupling power (20 kHz B1 field strength) is applied. Above 40 kHz
of 1H-decoupling field strength, however, the
residual 19F-NMR linewidths of ~2 kHz in the
fluid phase and 4 kHz in the gel state cannot be further improved.
These large line widths cannot be attributed to transverse relaxation,
because the measured T2 relaxation times yield an
intrinsic line width of 1/(
T2)
500 Hz at 35°C, and
1/(
T2)
800 Hz at 5°C,
respectively. Likewise, we exclude susceptibility effects as a primary
contribution, because in other 19F-NMR studies of
oriented samples we obtained line widths between 800 and 1500 Hz using
the same setup (Salgado et al., 2002
; R. W. Glaser and A. S. Ulrich, submitted). The dominant contribution to the considerable
linewidths of gA in our samples stems from the orientational disorder
of the peptide, which was estimated to be ~12° by lineshape
simulation in both the gel state and the fluid phase. This large mosaic
spread does not compare favorably with published data on gA aligned in
liquid crystalline bilayers, where values as little as 0.3° have been
reported (Hu and Cross, 1995
; Hu et al., 1995
). In fact, previous
2H-NMR studies of the same
19F-labeled compounds had also noted a
significant increase in the orientational heterogeneity of the
fluorinated side chains compared with the
19F-free analogues (Cotten et al., 1999
).
Moreover, working in the gel phase seems to reduce the sample quality,
as 15N-NMR studies on gA at low temperature also
encountered a significant linebroadening that could not be explained in
terms of homogeneous relaxation broadening nor by a lack of
1H-decoupling (Nicholson et al., 1991
). It was
argued that bilayer defects in the gel state are not annealed as well
as in the liquid crystalline phase, which leads to a considerable range
of helix orientations that are not motionally averaged.
The substitution of the indole protons by deuterons had no impact on
the linewidth or the 1H-decoupling efficiency in
the gel state (Fig. 3 d). As the dipolar coupling to protons
is usually a considerable source of linebroadening, this observation
suggests strong intra- and intermolecular
1H-19F coupling to nearest
neighbors. Additionally, the dipolar coupling between
19F and the adjacent deuterons also has to be
considered here, at least when working with low
1H-decoupling strengths. Indeed
2H-19F dipolar splittings
of up to 2 kHz have been observed by Cotten et al. (1999)
on the same
labeled samples, serving as a useful marker in assigning the
2H-NMR resonances. At higher
B1 fields the effect of
1H-decoupling on the linewidth diminishes in our
system, because the mosaic spread becomes the major contribution to the
linebroadening. Our more recent experience with other
19F-labeled compounds suggests that it may be
advantageous to keep the neighboring protons, as otherwise simultaneous
1H and 2H decoupling would
become necessary (U. Dürr, S. L. Grage, and A. S. Ulrich, manuscript in preparation).
Lineshape analysis
When an oriented gA sample was placed horizontally into the magnet
(
= 0°), a single resonance line was observed, both at 35°C
and 5°C (Fig. 3, a and b). Given the nonaxially
symmetric CSA, the observed 19F-NMR frequency is
compatible with a manifold of different tensor orientations. When the
peptides are immobilized in the gel phase, this redundancy can be
lifted by tilting the sample at an angle
. As illustrated in Fig.
4, the ensemble of immobilized gA
molecules, which differ in their azimuthal polarity, then gives rise to
a distribution of 19F-NMR frequencies. Tensor
alignments that were indistinguishable at
= 0° now become
distinguishable by their characteristic 19F-NMR
lineshapes, and their Euler angles can be extracted by spectral simulation. In our first ab initio approach, we determine the relation
between the CSA principal axis system (P) and a sample coordinate system (S) with the z axis pointing
along the glass plate normal (see Fig. 1). The CSA orientation is
described by two Euler angles
and
, whereas the third angle
is evenly distributed about the sample normal. Fig.
5 shows the root mean square deviation
(rmsd) between the experimental and calculated spectra, which were
calculated in 1° increments for the entire orientational space
spanned by
and
, for F(d)13-gA (left) and F(d)15-gA (right).
Each plot combines the data from a complete series of tilt angles, as
described in the Materials and Methods section. The rmsd plots possess
several symmetries, corresponding to inherent redundancies in tensor
alignment that cannot be lifted. When considering the symmetry
properties of a nonaxially symmetric CSA tensor, there remains a
fourfold ambiguity for 0°
180° and 0°
180°, which is
correctly displayed in this analysis (Fig. 5).
|
|
The minima in the rmsd plots reflect those particular CSA tensor
orientations relative to the bilayer normal that fit best to the
experimental data. The corresponding angles are
= 80°/
= 79° (plus symmetry-related copies) for both
F(d)13-gA and F13-gA and
= 90°/
= 73° (plus
copies) for F(d)15-gA, within ±5°. Fig. 4 demonstrates an excellent
agreement between the experimental 19F-NMR
spectra and the lineshape simulations obtained with the best-fit values
of
and
for each individual gA sample investigated here. The
protonated and deuterated Trp analogues in position 13 are fit by the
same set of lineshapes, as expected, thus confirming the consistency
and reproducibility of the sample preparation, the acquisition of tilt
series, and the data analysis. Interestingly, the 5F-Trp spectra for
positions 13 and 15 of gA resemble one another, which suggests that
both indole rings must be aligned in a similar way. Previous
2H-NMR studies of gA in the liquid crystalline
state had indeed shown that all four Trp side chains assume a similar
conformation (with the possible exception of Trp-9, about which there
is still some disagreement in the literature) (Hu et al., 1993
, 1995
;
Koeppe et al., 1994
, 2000
; Hu and Cross, 1995
; Cotten et al., 1997
;
Cotten 1998
). These indole orientations are functionally important as their electric dipole moments are aligned uniformly around the channel
mouth to guide the entry of the ions.
CSA tensor assignment
So far, the CSA tensors have been successfully positioned with
respect to the gel state lipid bilayer, but these results do not yet
provide any information about the torsion angles
1 and
2 of the Trp
side chains. To be able to draw such conclusions, the alignment of the
CSA tensor has to be known with respect to the molecular frame of the
indole ring. Such data is not available for 5F-Trp, but we will deduce
this missing information from the previously reported structure of gA
(Hu et al., 1993
, 1995
; Hu and Cross, 1995
; Cotten et al., 1997
; Cotten
1998
). The published coordinates had been derived by
2H-NMR, using the very same gA peptides with
19F-labeled Trp side chains as in this
19F-NMR study. However, the previous
2H-NMR data had been acquired in DMPC bilayers at
40°C rather than in the lipid gel phase. Hence, we may use these
coordinates on the assumption that the Trp side chain conformation is
unaffected by the lipid phase transition, which is true to a first
approximation (as outlined above, Fig. 3, a and
b).
For the simulations of Figs. 4 and 5, the CSA tensor had not been
constrained to the molecular scaffold of gA. As a next step we will now
fix the principal axis of the CSA tensor with respect to the structure
of gA that is known from the previous 2H-NMR
studies. There are six straightforward and plausible possibilities to
place the 19F CSA tensor into Trp: with one axis
pointing along the C-F bond, another orthogonal axis lying in the
indole plane, and the third axis being perpendicular to both.
Lineshapes were simulated for the six possible permutations of the
three axes, and the resulting spectral tilt series are summarized for
F(d)13-gA in Fig. 6. The best agreement
is seen in column 3, with the
22 axis pointing along the C-F bond,
11 lying in-plane of the
indole ring, and
33 aligned perpendicular.
This axis assignment is in accordance with similar
19F CSA tensors that have been described in
single crystal studies of fluorobenzenes and other fluorinated aromatic
compounds (Snyder, 1965
; Nehring and Saupe, 1970
; Griffin et al., 1973
;
Halstead et al., 1975
; Mehring, 1983
; Hiyama et al., 1986
).
|
| |
DISCUSSION |
|---|
|
|
|---|
The aim of this work was to introduce a new
19F-NMR strategy for structural studies in
biomembranes, especially for peptides and proteins with tryptophan side
chains. Incorporation of fluorotryptophan is a structurally
conservative and highly sensitive approach to monitor directly any
changes in the alignment and dynamics of the labeled side chain as well
as the polypeptide on the whole. For example, the symmetry properties
of the 19F-NMR powder lineshape readily reveal
the onset of long-axial peptide rotation, when a membrane sample is
heated through the lipid gel-to-liquid crystalline phase transition
(see Fig. 2). For peptides that are immobilized in the gel state, we
have demonstrated how the alignment of a
19F-labeled Trp side chain can be determined with
respect to the membrane normal. The structure analysis of the indole
ring is based on the anisotropic chemical shift of the
19F-label in a macroscopically oriented sample
that has to be measured at different tilt angles. This approach was
applied to gramicidin A labeled at position 13 or 15 with 5F-tryptophan
that was either protonated or deuterated, - the latter being the same
material that had been recently used in an analogous
2H-NMR study (Cotten et al., 1999
). Based on the
gA coordinates obtained by 2H-NMR in liquid
crystalline DMPC, we were able to assign the principal axes of the
19F CSA tensor in the molecular frame of the
5F-Trp indole ring, notably in the same lipid environment but in the
gel state. The most shielded CSA component
33
of 5F-Trp was found to be perpendicular to the indole plane,
22 to be aligned with the C-F bond, and the
least shielded
11 to be in-plane of the ring
and orthogonal to the C-F bond.
To make the above tensor assignment, we had assumed that the principal
axes of the CSA tensor are symmetrically constrained to the planar
indole ring and to the C-F bond direction. The corresponding best fit
of the predicted lineshapes in Fig. 6 (column 3) does indeed reproduce
all features of the experimental 19F-NMR data
quite well. However, the agreement is not as perfect as for the
unconstrained case seen in Fig. 4, where the CSA tensor had been
treated independently of any molecular framework. A possible explanation for this difference could be a deviation of the CSA principal axes from the ideal symmetry of the indole frame that had
been assumed above. In that case the tensor would nonetheless be
expected to obey the planar symmetry of the indole ring reasonably well, i.e., it should deviate mainly by a rotation around the indole
normal. Allowing for such rotational deviation, however, it was not
possible to find a tensor orientation that obeys the planar indole
symmetry. Instead, we found that the
33-axis
of our CSA tensor would have to be tilted away by ~20° from the
indole normal.
The divergence was estimated by considering the Euler transformation
(
PI,
PI,
PI,) from the principal axis frame
(P) to the indole-fixed frame (I, coinciding with
P in the constrained case) the following way: We positioned
the CSA tensor into the known framework of the gA molecule according to
the Euler angles determined for the unconstrained case. Because the two
systems P and I are indeterminate with regard to
their rotation about the sample normal, their azimuthal difference

=
PS
IS and hence the Euler angles
PI,
PI,
PI are not uniquely defined. An additional
assumption is necessary to closer specify the tensor orientation in the
indole-fixed frame. It is reasonable to choose the remaining free
parameter 
such that the planar indole symmetry is most fully
conserved, i.e., the z axis of P is closest to the z axis of I. This is the case for 
= 0° (or 180°), yielding
PI = 80°,
PI = 19°,
PI =
87° (plus three further, equivalent solutions). The transformation
described by these Euler angles is close to a rotation of
PI about the x axis, which would be
PI = 90°,
PI,
PI =
90°). That way, we estimated that the
tensor's
33-axis is tilted away from the
indole normal by ~20°, hence it does not obey the planar symmetry
of the aromatic ring.
There may be two explanations to account for this apparent discrepancy
between the CSA alignment obtained here ab initio by 19F-NMR on the one hand and the predicted CSA
alignment on the other hand that had been calculated under the
assumption that the tensor is fixed to the molecular coordinates of gA
known from 2H-NMR. First, the
19F CSA tensor could indeed be significantly
tilted out-of-plane of the indole ring due to the influence of
neighboring side chains, the lipid environment, or hydrogen-bonds
formed. However, as the CSA tensor orientation is usually a rather
local property of the environment, a CSA tensor not obeying the planar
indole symmetry seems rather implausible. The few
19F CSA tensor alignments that are known for
aromatic crystalline compounds, where the impact of neighboring groups
is just as likely as in gA, show only small deviations of a few degrees
(Snyder, 1965
; Nehring and Saupe, 1970
; Griffin et al., 1973
; Halstead et al., 1975
; Mehring, 1983
; Hiyama et al., 1986
). As an alternative explanation we therefore propose that the side chain conformation measured here at 5°C differs from the conformation described
previously by 2H-NMR at 40°C. After all, the
previous 5F-Trp coordinates had been obtained in a liquid crystalline
lipid environment, and they were used only to a first approximation for
the current analysis of gA in the gel phase (Hu et al., 1993
, 1995
; Hu
and Cross, 1995
; Cotten et al., 1997
; Cotten, 1998
).
Given the arguments above, we attribute the slight but significant
mismatch of the experimental and simulated spectra in Fig. 6 (column 3)
to genuine differences in the side chain conformation in the different
phase states of the lipid bilayer. Hence, by an in situ analysis of the
5F-Trp alignment, it is possible now to determine directly the torsion
angles
1 and
2 in the
gel phase. The side chain conformation was structurally refined under the following two assumptions: 1) The C
-C
orientation stays the
same below and above the phase transition temperature, meaning that the
structure of the hydrogen-bonded gA backbone does not change; and 2)
the CSA tensor is aligned with its axes pointing along the indole-fixed
frame directions according to the assignment of Fig. 6 (column 3). The
in situ rmsd analysis for F(d)13-gA as a function of the two rotamer
angles
1 and
2 is
shown in Fig. 7. This plot is basically a
translation from the general orientational space spanned by the Euler
angles
and
(as in Fig. 5) into the conformational space of
1 and
2, leaving out those orientations that are not sterically accessible by any
combination of torsion angles. Each of the four sets of minima in the
1/
2 map correspond
precisely to the minima found in the
-
map, meaning that the ab
initio 5F-Trp orientations are indeed readily accessible by rotations
about the C
-C
and C
-C
bonds of the peptide. It is not yet
possible to tell from the 19F-NMR data alone,
which of the symmetry-related solutions corresponds to the actual side
chain conformation in gA, just as the previous 2H-NMR studies had to leave this question open.
Table 1 summarizes the most reasonable
group of solutions in analogy to the 2H-NMR results.
Studies are currently in progress to find the unique solution from
19F-19F dipolar distance
constraints between two 19F-labeled indole rings.
|
|
When comparing the values of
1 and
2 in Table 1 for the liquid crystalline phase
and the gel state, the differences of ~10° to 20° suggest a small
but significant change in the conformation of both Trp-13 and -15 upon
passing through the lipid phase transition. (This does not however
jeopardize the fundamental assignment of the CSA tensor axes in Fig.
6). It is indeed reasonable to suppose that the peptide side chains
will respond to the considerable increase in bilayer thickness in the
gel state, especially as the Trp residues are located in the
hydrophilic-hydrophobic interface of the membrane. In view of the
multiple allowed solutions, it is not yet possible to recognize any
systematic kind of orientational change, such as an adjustment toward
an ideal trans/gauche conformation, or toward a
more parallel alignment of the indole ring with the lipid chains. To
systematically assess the effect of bilayer thickness it would now be
interesting to monitor the Trp behavior in various lipids with
different acyl chain lengths. Because the indole dipole orientations
play a significant role in the function of the gramicidin A ion
channel, previous studies in membrane-mimicking environments have also
paid close attention to the conformation of the tryptophan side chains
(Arseniev et al., 1985
; Ketchem et al., 1997
; Townsley et al., 2001
). A
comparison of the solid-state NMR structure in planar bilayers with
solution state 1H-NMR results in micelles
revealed differences in torsion angles on the same order of magnitude
as those detected here for the change in the lipid phase state. Because
19F-labeling itself induces a slight
conformational change of similar size, however, it is not meaningful to
compare these
1/
2
values further.
With regard to the accuracy of the proposed values, it is important to
point out that different choices of published indole coordinates lead
to an intrinsic uncertainty of ~5° in determining the Trp
conformation. Hence, our results are accurate to within 10°, given
the quality of fit between the experimental
19F-NMR data and the simulated lineshapes. The
values in Table 1 illustrate the influence of choosing a particular set
of indole geometries, namely those used by Hu et al. (Hu and Cross,
1995
; Hu et al., 1995
) and used throughout this publication or by
Cotten et al. (Cotten et al., 1997
; Cotten, 1998
). As noted in the
Materials and Methods section, the indole geometries found in the
literature and in databases differ only very slightly among each other,
but these small differences translate into variations in
1 and
2 of ~5°.
Nonetheless, even if we had based our entire analysis on the indole
geometry used by Cotten et al. (Cotten et al., 1997
; Cotten, 1998
),
this would only have marginally altered the simulated lineshapes on
which the tensor axes assignment is based here, leaving our fundamental
assignment and other basic conclusions unchanged. We also note that our
19F-NMR analysis of the single nonaxially
symmetric CSA tensor has yielded 4 × 4 minima in the full range
between 0° and 360° (e.g., for F(d)13-gA), whereas only 4 × 2 minima were observed in previous 2H-NMR studies.
This finding is consistent with the inherently higher symmetry of the
single 19F CSA tensor compared with two or more
magnetically inequivalent 2H-labels on an indole
ring, yielding a higher information content for the latter case.
Furthermore, in contrast to the 2H-NMR study by
Cotten et al. (Cotten et al., 1999
), all minima in our
1/
2 plots have the
same rmsd value. This means that all of the best-fit conformations in
our unconstrained
/
space are just as readily accessible in the
constrained
1/
2
space. Differences in the depths of the minima would be observed in
cases where only a subset of the absolute minima in
/
space were
accessible in the
1/
2 space.
The strategy of labeling with 19F allowed for
highly sensitive NMR experiments, requiring only small amounts of
material, such as 2 mg peptide. Typical acquisition times were between
4 and 10 h, depending on the spectral lineshape to be measured
(narrow peaks for horizontally oriented samples, or wideline spectra
from tilted samples). These experimental 19F-NMR
conditions call for a direct comparison with previous
2H- and 15N-NMR studies on
similar gA samples. For example, Cotten et al. (Cotten et al., 1997
;
Cotten 1998
) used ~25 mg of the same
19F/2H-labeled peptide to
obtain oriented 2H-NMR spectra in 6 h.
Koeppe et al. (1994
, 1995
, 2000
) have also studied
2H-labeled Trp in gA and used 6 mg (or 12 mg)
peptide to acquire spectra over a period of 1 to 3 days (or 12-36 h,
respectively), and a related study on 2H-labeled
valine in gA needed 50 mg to obtain powder spectra in 8 h (Lee et
al., 1995
). Previous 15N-NMR studies required 1 to 2.5 days (and up to 4 days) to obtain powder-lineshapes with 80 mg
of peptide (Hu et al., 1993
, 1995
; Hu and Cross, 1995
). Given that the
intrinsic sensitivity of an NMR experiment scales with the gyromagnetic
ratio as
5/2 (Ernst et al., 1990
; Abragam,
1996
), 19F theoretically offers a 100-fold
advantage in sensitivity compared with 2H, and
1000-fold compared with 15N. This translates into
an even greater reduction in measurement time if the same amount of
material was to be used (since S/N

H/
N). Furthermore,
our 19F-NMR spectra suffer from a m