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Biophys J, August 2000, p. 767-775, Vol. 79, No. 2




and
¶
*National High Magnetic Field Laboratory,
Institute
of Molecular Biophysics, ¶Department of Chemistry, and
Department of Mathematics, Florida State University,
Tallahassee, Florida 32306; and §Department of
Biochemistry and Cellular Biology, State University of New York, Stony
Brook, New York 11794 USA
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ABSTRACT |
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The M2 protein from the influenza A virus forms a proton channel in the virion that is essential for infection. This tetrameric protein appears to form a four-helix bundle spanning the viral membrane. Here the solid-state NMR method, 2D polarization inversion spin exchange at magic angle (PISEMA), has been used to obtain multiple constraints from specifically amino acid-labeled samples. The improvement of spectral resolution from 2D PISEMA over 1D methods and 2D separated local field methods is substantial. The reliability of the method is validated by comparison of anisotropic chemical shift and heteronuclear dipolar interactions from single site labeled samples. The quantitative interpretation of the high-resolution constraints confirms the helix tilt to be within the range of previous experimental determinations (32°-38°). The binding of the channel inhibitor, amantadine, results in no change in the backbone structure at position Val27,28, which is thought to be a potential binding site for the inhibitor.
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INTRODUCTION |
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The efficient utilization of structural
constraints and incorporation of all structural information into
structural modeling is an ongoing challenge. The solid-state NMR
method, polarization inversion spin exchange at magic angle (PISEMA),
which correlates 15N-1H dipolar interactions
with 15N chemical shifts (Wu et al., 1994
), provides
high-resolution orientational constraints. Here these constraints are
obtained for the transmembrane peptide of M2 protein from influenza A
virus, M2-TMP. Through assignments made by single-site labels, these high-resolution constraints are combined with the known
-helical structure of M2-TMP to enhance a structural model and to
determine specific torsion angles.
While distance and torsional constraints can be obtained by solid-state
NMR from unoriented samples, orientational constraints in this paper
are obtained from samples uniformly aligned with respect to the
magnetic field axis of the NMR spectrometer. Such constraints have
numerous advantages for assembling structures and for obtaining a
structure that is oriented with respect to its environment
in this
molecular system, a lipid bilayer (Fu and Cross, 1999
; Quine, 1999
).
The two-dimensional PISEMA pulse sequence, developed by Opella and
co-workers, has been successfully used to obtain anisotropic 15N chemical shifts and directly bonded
15N-1H dipolar interactions (Wu et al., 1994
;
Marassi et al., 1997
; Tian et al., 1998
). This spectroscopy of
uniformly aligned samples yields much improved dipolar resolution and a
favorable dipolar scaling factor (0.816) compared to earlier separated
local field (SLF) spectroscopy (Hester et al., 1976
; Waugh, 1976
). The
scheme uses conventional I-S cross-polarization (CP) followed by
frequency-switched Lee-Goldburg (LG) cycles (Bielecki et al., 1990
; Lee
and Goldburg, 1965
). During the LG cycles, the I-spins are locked along
the magic angle, 54.74° relative to the magnetic field, and matched by a phase-alternated spin-lock field applied to the S-spins. The
Fourier transform of the NMR signal against acquisition time, t2, and evolution time,
t1, yields a 2D spectrum with chemical shifts in
the
2 dimension and dipolar splittings in the
1 dimension.
The M2 protein (97 amino acids) from the influenza A virus is an
integral membrane protein with proton channel activity in the viral
coat (Lamb et al., 1994
; Wang et al., 1994
). Its single transmembrane
-helix is contained within the 25-amino acid peptide M2-TMP
(residues 22-46), which has been reported to show channel activity
similar to that of native M2 protein (Duff and Ashley, 1992
). However,
recent studies of various truncated proteins have brought this result
into question (Tobler et al., 1999
). The transmembrane portion of both
M2 and M2-TMP primarily adopts an
-helical structure, and M2 forms a
homotetramer in lipid environments, as characterized by several studies
(Duff et al., 1992
; Holsinger and Lamb, 1991
; Sakguchi et al., 1997;
Kovacs and Cross, 1997
). M2-TMP also appears to form an oligomer. The
helix tilt of a monomer should be sensitive to the thickness of the
lipid bilayer, but M2-TMP has been shown to be quite insensitive to a
change in bilayer thickness (Kovacs et al., 2000
). Therefore, the helix
tilt appears to be an intrinsic propensity of an oligomer. In addition,
the oligomer is not a heterogeneous aggregate, inasmuch as single site
labels give rise to a single identical resonance from each monomer.
M2-TMP is therefore presumed to be a tetrameric state, similar to M2
protein, but the oligomeric state of M2-TMP has not been specifically defined.
In previous investigations of isotopically labeled M2-TMP,
orientational constraints derived from NMR and infrared spectroscopy were interpreted to show that the helices are tilted by 32°-38° with respect to the lipid bilayer normal (Kovacs and Cross, 1997
; Kukol
et al., 1999
; Kovacs et al., 2000
). Moreover, model building of the
tetramer suggested that the
-helical bundle is left-handed (Kovacs
and Cross, 1997
). The channel function of M2 can be blocked by
amantadine, potentially through binding to a specific sequence (residues 27-31) in its transmembrane domain (Skehel, 1992
; Hay, 1992
;
Wang et al., 1993
). Here a preliminary binding experiment of amantadine
with M2-TMP is described.
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MATERIALS AND METHODS |
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Sample preparation
Several 15N-labeled amino acids were purchased from
Cambridge Isotope Lab (Cambridge, MA). M2-TMP
(NH2-Ser22-Ser23-Asp24-Pro25-Leu26- Val27-Val28-Ala29-Ala30-Ser31-Ile32-Ile33-Gly34-Ile35-Leu36-His37-Leu38- Ile39-Leu40-Trp41-Ile42-Leu43-Asp44-Arg45-Leu46-CO2H)
was obtained by solid-phase synthesis, using fluorenoylmethoxy carbonyl
chemistry on an Applied Biosystems 430A Synthesizer. Amino acid
blocking, purification, and characterization of the peptides were
performed as previously described (Kovacs et al., 2000
).
To orient a lipid bilayer preparation, M2-TMP and dimyristoylphosphatidylcholine (DMPC) or dioleoylphosphatidylcholine (DOPC) were codissolved in trifluoroethanol (TFE) with a peptide-to-lipid molar ratio of 1:8 and 1:30, respectively. Then the sample was spread onto ~60 thin glass plates (75 µm × 10.5 mm × 10.5 mm). After vacuum drying to remove TFE, the glass plates were stacked into a glass tube (11 mm × 11 mm), and the samples were hydrated with high-performance liquid chromatography-grade water (~50% by weight). Finally, the samples were sealed and incubated at ~45°C for several days.
NMR experiments
The NMR measurements were performed on a spectrometer with a 9.4-T magnet, operating at a 15N Larmor frequency of 40.585 MHz. The probe was constructed in house and has a rectangular coil suited to the sample size. The oriented M2-TMP samples were placed with the order axis (i.e., the lipid bilayer normal) parallel to the magnetic field axis. All 15N chemical shifts are relative to the resonance for a saturated solution of 15NH4NO3 at 0 ppm.
For the PISEMA experiment, the cross-polarization (CP) period was 1 ms. The rf field strengths were typically 31.4 kHz for the CP match and 38.5 kHz for the Lee-Goldburg (LG) condition, corresponding to a LG time interval of tm = 26 µs. A delay of 1 µs was used at the onset of each ±LG cycle to compensate for the frequency synthesizer (Programmed Test Sources type) switch time, which was found to be critical for achieving the theoretical dipolar scaling factor (0.816). The t1 value was incremented from 0 to 24 Lee-Goldburg cycles, and the refocused 15N-signal was acquired with ~2000 transients for each t1 increment. For data processing, 512 and 256 points in the t2 and t1 dimensions were used, respectively, and exponential line broadening of 100 Hz was used in the t2 dimension, but not in the t1 dimension. The spectral symmetry in the dipolar dimension was achieved by setting the imaginary portion of the data points to zero before the Fourier transform against t1.
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ANALYSIS OF 2D SPECTRA |
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For spectral analysis, several relevant orientation reference
frames are defined (Fig. 1) as follows:
P, the 15N chemical shift anisotropy (CSA)
principal axis frame with the principal tensor elements
11,
22,
33; Nh,
the frame of the 15N-1H dipolar interaction
tensor with its unique z axis along the 15N-1H bond; D, the director frame
with its z axis along the lipid bilayer normal. Any two of
these coordinate systems are related by Euler rotations
(
,
,
).
|
In our oriented samples, the z axis of the director frame is
parallel to the magnetic field, B0, and the
observed chemical shift can be written in terms of tensor magnitudes
and orientations as
|
(1) |
PD,
PD relate
the CSA principal axis frame to the sample director frame. Notice
that
PD = 0.
The 15N-1H dipolar splitting can be described
by
|
(2) |

= (µ0/4
)
(
H
Nh/2
rNH3)
is the dipolar coupling constant;
H and
N
are the gyromagnetic ratios of 1H and 15N,
respectively; h is Planck's constant; and
rNH is the N-H bond length. The angle
is the
polar angle relating the N-H internuclear vector to
B0. Correlating with the CSA frame
yields
|
(3) |
|
PD,
PD) and
(
PNh,
PNh) refer to the transformation
from the CSA principal axis frame to the director frame and to the
dipolar tensor frame, respectively.
Taking the 15N-1H dipolar coupling constant to
be 
= 10.735 kHz, based on an N-H bond length of
1.041 Å, and assuming that the 15N amide tensor
orientations relative to the 15N-1H bond are
typically
PNh = 0°,
PNh = 17° (Mai et al., 1993
), Eqs. 1-3 can be solved for each site, using
pairs of (
obs, 
) values obtained from 2D PISEMA
and the corresponding CSA tensor values
11,
22,
33. The resulting
and
(
PD,
PD) values relate the N-H bond and
the CSA principal axis frame, respectively, to the director
z axis. These angles give important orientational constraints for structural analysis. In general, four possible
PD,
PD solutions, (±
PD,
PD), (
±
PD,
PD), may be derived from the combination of Eqs. 1-3,
while two solutions, (
,
), may be derived from a
positive dipolar splitting value according to Eq. 2. For two adjacent
residues, such as Val27-28 and Ile32-33, the
orientations of the principal axis frames for each residue can be used
to obtain a list of possible
,
torsion angles that correspond to
the data for those residues.
The PAF1 is defined as the CSA principal axis frame for the
first residue (either Val27 or Ile32) with the
B0 orientation (
PD1,
PD1), and the PAF2 is the CSA principal axis
frame for the second residue (Val28 or Ile33)
with the B0 orientation (
PD2,
PD2). For the peptide plane geometry in Fig.
2, the supplements of the bond angles
C
-C1-N and C1-N-C
are 65° and 59°, respectively, and the tetrahedral geometry at
C
is such that the supplement of the angle
N-C
-C is 70°. Unit vectors in the direction of the
C1-N and N-C
bonds in PAF1 are
denoted by u1 and u2, and
the unit vectors in the direction of the
C
-C1 and C1-N bonds in
PAF2 are denoted by u3 and
u4.
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Based on four possible
PD,
PD solutions
for each pair of residues, the torsion angles can now be computed by
using orientational constraints and a torsion angle
identity:
|
|
(4) |
|
(5) |
|
180° and 180°
formed by the x axis and the point (x, y) in the
plane. The key for minimizing ambiguities is to compute the torsion
angles by using only dot products of vectors, to avoid the need for
changing frames between PAF1 and PAF2. The
necessary dot products are
|
(6) |
|
(7) |
|
PD1,
PD1) and
(
PD2,
PD2). Here we will minimize this
set based on the known
-helical secondary structure.
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RESULTS AND DISCUSSION |
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The chemical shift tensor element magnitudes have been determined
by using single site labeled samples of M2-TMP. While the tensors were
not determined in a hydrated lipid bilayer environment, they were
determined as a powder prepared from a trifluoroethanol solution in
which the samples are
-helical. Therefore, the tensors are
characterized for the sites of interest in the conformation of interest
(Table 1).
|
The PISEMA spectra of oriented M2-TMP samples with selective 15N-labeling are displayed in Figs. 3, 5, and 6. The 2D contour plots display 15N chemical shifts in the horizontal dimension and 15N-1H dipolar splittings in the vertical dimension, with the scale expanded by 1.22 to account for the experimental scaling of the dipolar dimension.
|
Fig. 3 shows the PISEMA spectrum of 15N-Ile32,33,35,39,42-labeled M2-TMP in hydrated DMPC lipid bilayers. For comparison, the conventional 1D chemical shift spectrum for this sample is shown at the top. While the peaks of four Ile sites between 118 and 129 ppm cannot be resolved in the 1D spectrum, they are resolved in this 2D spectrum and in the corresponding dipolar slices on the left side.
The spectral results are compared in Table
2 to the chemical shift data from single
site labeled M2-TMP in similar bilayer preparations (spectra not
shown). The assignments for Ile33, Ile35, and
Ile42 and Val27 and Val28 are
achieved from the single site labels. However, without the single site
dipolar information, the assignments for Ile32 and
Ile39 are tentative, based on a novel assignment strategy
that recognizes a helical wheel pattern of resonances in the PISEMA
spectra (Wang et al., 2000
). Note that, while the chemical shift for
Ile42 is within the error bar for Ile39 and
Ile32, the dipolar splitting from the single site label for
Ile42 of 13.8 kHz confirms this assignment.
|
Normally, the sign of the dipolar splitting is considered to be
ambiguous if 
is less than half-maximum (see Eq. 2). Fig. 4, however, shows that these peptide
samples undergo an axial motion about the bilayer normal. Consequently,
when this peptide sample is oriented with the bilayer normal
perpendicular to the field, a single sharp line is observed rather than
a powder pattern (a powder pattern would be seen if axial motion had
not occurred). This means that the motionally averaged 15N
chemical shift and 15N-1H dipolar tensors are
collinear. Because all of the
obs obtained are greater
than their corresponding
iso values (Table 1), the 
values are all positive (Tian et al., 1998
). This substantially reduces the potential structural ambiguities in the following analysis.
Note that such a motion about an axis parallel to
B0 for all of our samples, except Fig. 4
B, has no effect on the NMR observables.
|
Based on these data, a variety of qualitative results can be
identified. First, as previously noted (Kovacs and Cross, 1997
; Kukol
et al., 1999
; Kovacs et al., 2000
), the chemical shift and dipolar
splitting values are not consistent with either a helix parallel to the
bilayer normal or one perpendicular to it. Because the N-H axis and
33 tensor elements are approximately parallel to the
helix axis, helices that are parallel to the bilayer normal give rise
to chemical shifts near
33 and to 
values that are nearly maximal. In contrast, helices that are perpendicular give rise
to chemical shifts near
11/
22 and dipolar
splittings that are at half-maximum and negative. The observed
orientational constraints are variable and far from these extreme
values; therefore, the helix has a considerable tilt.
Second, the substantial variation in dipolar splitting for nearly the
same chemical shift (e.g., Ile42 versus Ile39)
illustrates the noncollinearity of the static 15N chemical
shift and 15N-1H dipolar tensors. The
33 element is typically 17° from the N-H axis
(Harbison et al., 1984
; Oas et al., 1987; Mai et al., 1993
). Third, the
similarity of the orientational constraints for residues i
and i + 7 (e.g., Ile32 and
Ile39, Ile35 and Ile42) suggests
considerable uniformity for this
-helix. Even differences such as
8.8 kHz versus 4.4 kHz in dipolar splitting suggest a difference as
small as 8° in the orientation of the N-H axis.
To investigate the structural influence of the channel inhibitor
amantadine, the PISEMA spectra of oriented
15N-Val27,28-labeled M2-TMP in hydrated DMPC
bilayers with and without amantadine were acquired. For comparison,
they are shown in Fig. 5 as overlaid spectra. The two splittings from Val27 and
Val28 are well resolved in both chemical shift and dipolar
dimensions. From conductivity measurements (Wang et al., 1993
), the
binding constant for amantadine has been established to be 3 × 106 M
1. Therefore, the addition of an equal
molar amount of M2-TMP and amantadine should result in a predominance
of the complex. It has been suggested that amantadine binds in the
vicinity of the Val27,28 residues along the channel pore
(Skehel, 1992
; Hay, 1992
; Wang et al., 1993
). From our previous results
and model (Kovacs and Cross, 1997
), Val27 should line the
pore of the channel, while Val28 is oriented toward an
adjacent helix. The observed differences in the dipolar splittings and
in the chemical shifts are within their error bars for these two
preparations, as clearly seen in the dipolar and chemical shift slices
through the PISEMA spectra. Consequently, there is no evidence for a
significant structural or orientational change for either site upon
amantadine binding. Therefore, no evidence is presented here for
amantadine interacting at these sites and directly blocking the channel
pore. However, the lack of a change in the backbone structure and
orientation does not refute this possibility, because amantadine is
likely to be interacting directly with the side chains and not the
backbone.
|
The improvement in spectral resolution shown in the chemical shift slices of the PISEMA spectra compared to the one-dimensional (1D) chemical shift spectra is nearly a factor of 2. Several different lipid environments and molar ratios have been tried to improve the 1D spectral resolution; however, little effect has been observed. PISEMA spectra of 15N-Val27-labeled M2-TMP in DOPC and DMPC bilayers are shown in Fig. 6. The slight difference in chemical shift and dipolar splitting possibly reflects a very small change in helix tilt due to the increased hydrophobic thickness of the DOPC bilayers. No difference, however, is seen in the linewidths, although they are substantially better than the 1D chemical shift spectra. Data from a T2 measurement on this sample in DOPC yields a T2 value of 750 µs, which suggests an intrinsic line width of 10 ppm (Fig. 7).
|
|
The line width in 1D spectra or in a projection of the PISEMA spectra
in the chemical shift dimension displays a resonance width of ~20
ppm. In the 2D PISEMA spectra the heterogeneous broadening appears
along a diagonal axis through 0 kHz at
iso = 96 ppm. Heterogeneous broadening in these 2D spectra will be constrained within the powder pattern of an unoriented sample, and because of the
global motion this powder pattern lies on these diagonal axes. Thus the
improved resolution in the chemical shift slices of the 2D PISEMA
spectra (Fig. 6) results from a minimization of the heterogeneous broadening.
In Table 2, the
angles derived from dipolar splittings are
presented with the
PD and
PD angles
determined with Eqs. 1-3. In Fig. 8, the
dipolar splitting (a) and chemical shift (b) are plotted as a function of orientation angles
PD,
PD (ranging from 0 to 360° and 0 to 180°
respectively), using the 
,
PNh,
PNh values mentioned above and typical
11,
22,
33 values from the
powder pattern of 15N-Val27-labeled M2-TMP.
Both 
and
obs change more dramatically as a
function of
PD than as a function of
PD.
For
obs, this reflects the small asymmetry parameter of
the amide 15N CSA (typically
0.2). If
equaled 0,
11 would equal
22 and
PD would have no effect on
obs. For

, it reflects the effect of both
and
PNh. If
PNh were also zero, then 
essentially would be
independent of
PD. Because
PNh is
significant (typically 17°), the influence of
PD on

generally is more pronounced. This partially explains why the
five Ile sites, particularly Ile32, Ile39, and
Ile42, could not be resolved by their chemical shifts
alone, but were resolvable by their dipolar splittings.
|
Because there is a limited data set from which it is not yet possible
to calculate a unique molecular structure, we will take advantage of
the knowledge that this polypeptide is predominantly
-helical (Duff
et al., 1992
; Kovacs and Cross, 1997
), that the helices have an average
tilt of 37° ± 3° (Kovacs et al., 2000
), and that the
-helical
geometry is well defined (Quine, 1999
; Kovacs et al., 2000
). The
ambiguity in
presented in Table 2 places the N-H orientation
between 0° and 54.7° or 125.7° and 180°. For an
-helix the
values must all be in one range or the other, because the N-H bond
makes an angle in the range of ±17° with respect to the helix axis,
which in turn makes an angle of 37° with the magnetic field axis.
Moreover, this same argument eliminates all
PD values
greater than 90°. Therefore, only a single sign ambiguity remains in
PD for each of the peptide planes, as shown in Table
3.
|
Many of the possible torsion angles calculated from Eqs. 4-7 can be
eliminated based on steric hindrance information for Val and Ile
residues in the
-helical region. Based on Ramachandran plots,
-branched amino acids have a more limited
-helical region than do
other amino acids. In this analysis, the allowed
-helical region is
taken from Creighten (1984)
. In Table 3, torsion angles within these
dimensions are in boldface; borderline values within 10° of this
region are in plain type and outlying values are italicized. The most
probable torsion angles, thus, are limited to (
83°,
60°) and
(
136°,
60°) for Val27 and (
81°,
30°) for
Ile32.
The transformation from one peptide plane to the next is defined by a
(
,
) torsion angle pair. From this transformation, the local
helix axis direction vector for two adjacent peptide planes can be
computed (Quine, 1999
). Using
PD and
PD
to define the magnetic field direction vector B, the tilt
angle,
, can be obtained from the dot product of the helix axis
direction vector and B. Comparing computed tilts with the
accepted tilt of 37° ± 3° provides another way to filter the
possible orientations of B. In Table 3, tilts within the
range of 37° ± 10° are in boldface; borderline values (37° ± 15°) are in plain type; and outlying values are italicized. Tilt
calculations for Val27 support the validity of the (
,
) solutions and
PD,
PD solutions while
solving the chirality ambiguity. For Ile32, the unique
torsion angle solution is supported and the chirality is solved.
Enhancement of spectral resolution has been achieved through 2D PISEMA
of oriented M2-TMP samples. Information about 15N chemical
shift and 15N-1H dipolar interactions can be
analyzed to derive specific site orientations leading to specific
peptide plane orientations. In turn, these orientations lead to the
structural solution for backbone peptide
,
torsion angles in the
transmembrane domain of M2 transmembrane peptide. From this solution
set, helix axis orientations consistent with those previously described
were found. Furthermore, the M2-TMP structure at residues
Val27,28 appears not to be distorted by amantadine binding.
| |
ACKNOWLEDGMENTS |
|---|
The authors are indebted to the staff of National High Magnetic Field Laboratory NMR facility (A. Blue) and the staff of the Bioanalytical Synthesis and Service Laboratory (H. Hendricks and U. Goli) for their expertise and maintenance of the instruments essential for this effort.
This work has been supported by National Science Foundation (NSF) grant DMB 99-86036 to TAC and JRQ and by a NSF training grant supporting JKD (DBI 96-02233). This work was largely performed at the National High Magnetic Field Laboratory, supported by a NSF Cooperative Agreement (DMR-9527035) and the State of Florida.
| |
FOOTNOTES |
|---|
Received for publication 20 December 1999 and in final form 11 April 2000.
Address reprint requests to Dr. Timothy A. Cross, National High Magnetic Field Laboratory, Florida State University, 1800 E. Paul Dirac Drive, Tallahassee, FL 32306-4005. Tel.: 850-644-0917; Fax: 850-644-1366; E-mail: cross{at}magnet.fsu.edu.
| |
REFERENCES |
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from the relative orientations of backbone N-H and C-H bonds by solid-state NMR.
J. Phys. Chem.
B101:5869-5874
Biophys J, August 2000, p. 767-775, Vol. 79, No. 2
© 2000 by the Biophysical Society 0006-3495/00/08/767/09 $2.00
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