Results
Figure 1 shows the two schematic models (I and II) of interaction for homodimers and homotrimers in the transmembrane domain of integrins that we predicted previously using a computational method ( Lin et al. 2006). To test the validity of these models, we have used here an asparagine scan strategy, targeting five consecutive transmembrane residues spanning the GxxxG-like motif, labeled 1–5 in Figure 1. We have used the transmembrane domains of αM and β2 integrins, which form a known integrin pair ( Hynes 2002). These two transmembrane domains are monomeric in SDS in their native form. Electrophoreses of αM-TM and β2-TM The αM-TM and β2-TM peptides synthesized are shown in Figure 2. In this figure, the location of the GxxxG-like motif is shown by a shaded area (see the figure legend for details). ![Figure 2. Figure 2.](picrender.fcgi?artid=2327277&blobname=930fig2.gif) | Figure 2.Sequences corresponding to the synthesized peptides αM and β2. (A) α-Helical transmembrane (TM) domains of integrin αM. (B) α-Helical TM domains of integrin β2. The five consecutive residues corresponding (more ...) |
Figure 3 shows the SDS electrophoreses of each one of these peptides. Those corresponding to αM ( Fig. 3A) show that the peptide corresponding to the native sequence (labeled SSVGG) is monomeric. In contrast, introduction of asparagine at positions 1 and 5 of the GxxxG-like motif ( NSVGG and SSVG N) produced dimers. Because of the position of the asparagine mutation, the helix–helix interaction in the dimer observed in SDS can only be mediated by the GxxxG-like motif, or model I in Figure 1A. ![Figure 3. Figure 3.](picrender.fcgi?artid=2327277&blobname=930fig3.gif) | Figure 3.SDS-PAGE electrophoreses of the synthetic TMs αM and β2. (A) Electrophoreses corresponding to αM. (B) Electrophoreses corresponding to β2. Lanes run from left to right. The bottom lane represents the molecular weight markers. (more ...) |
Crucially, a dimer was also observed when we introduced the asparagine at position 3 of the motif (SS NGG). In this case, the asparagine is located almost opposite (200° in a canonical α-helix) from positions 1 and 5; therefore, in this case, the helix–helix interaction would be consistent with model II in Figure 1B. As expected, introduction of asparagine at positions 2 and 4 (S NVGG and SSV NG), which are not located on the helix–helix interface in any of the two models (see Fig. 1), produced monomers and some dimers, confirming that these positions only contribute partially to the stabilization of the oligomer. An electrophoretic mobility plot corresponding to these results is shown in the Supplemental material. In addition to those five residues, we introduced asparagine at an additional position in αM. The rationale is that a recent report ( Luo et al. 2004) described an α–α dimer stabilized by a disulfide bond when the mutation W967C was introduced in αIIb. This residue is in phase with position 3 of the GxxxG-like motif, and therefore the interaction described in that dimer must have been consistent with our model II. Residue P1107 in αM is equivalent to W967 in αIIb according to the alignment of α-integrin TM domains ( Lin et al. 2006); therefore, we introduced an asparagine residue in αM at P1107. This peptide is labeled P1107N in Figure 3A. In this case, a clear dimer was also observed, which is consistent with a model II of interaction. The fact that αIIb and αM present this form of interaction suggests that it may be general for the integrin family and related to integrin function. For β2-TM ( Fig. 3B), the SDS electrophoresis results were very similar to those observed for αM-TM. The native sequence (labeled GTVAG) produced only monomers in SDS, whereas introduction of asparagine at positions 1 and 5 of the GxxxG-like motif ( NTVAG and GTVA N) produced only dimers. The position of the asparagine residue in each case implies that the interaction is consistent with model I. Dimers were also observed when we introduced the asparagine at the third position of the motif (GT NAG). In this case, the asparagine is located almost opposite (200° in a canonical α-helix) from positions 1 and 5, and the interaction between β TMs can only be consistent with model II. When asparagine was introduced at positions 2 and 4 (G NVAG and GTV NG), we could observe both monomers and dimers, which suggests that this position only contributes partially to oligomer stabilization because positions 2 and 4 of the motif are not located exactly on the helix–helix interface in either model (see Fig. 1). As in αM-TM, we introduced an additional mutation in order to confirm the result of a recent experiment that found that mutation G708N in β3 induced trimerization and activation in vivo ( Li et al. 2003). From the alignment of β TM sequences ( Lin et al. 2006), we see that the equivalent residue of G708N in the sequence β2 is V715, which we therefore mutated to Asn. Indeed, a dimer was observed ( Fig. 3B, V715N). This result is consistent with a model II type of interaction because this position is seven residues apart (almost in phase) with position 3 of the GxxxG-like motif (see Fig. 2). To further confirm that the helix–helix interactions observed after introducing Asn at position 3 (xxNxx) correspond to model II and are not mediated by the “G” residues in the GxxxG-like motif, we repeated the experiment with two additional mutations where positions 1 and 5 were changed to Phe (FxNxF). If a model I interaction was responsible for the dimers observed, the bulky Phe side chains would destabilize it, producing only monomers. Figure 4 shows that, even in the presence of Phe at positions 1 and 5 (FxNxF), dimers are still present, confirming that the dimerization observed is mediated by Asn at position 3, that is, consistent with model II. ![Figure 4. Figure 4.](picrender.fcgi?artid=2327277&blobname=930fig4.gif) | Figure 4.SDS-PAGE electrophoreses of synthetic TMs of integrin containing Phe mutations in the GxxxG-like motif. Lanes run from left to right, and the typed sequence on the right indicates the integrin type and the position of Asn and Phe mutations in the GxxxG-like (more ...) |
Orientation of the TM α-helices in a lipid bilayer Using site-specific infrared dichroism, SSID ( Arkin et al. 1997; Torres et al. 2000), it is possible to determine the tilt and rotational orientation for transmembrane α-helices in hydrated lipid bilayers. Therefore, we calculated these orientational values experimentally for αM-TM and β2-TM, using the pairs of labeled sequences (numbered 1–3) shown in Figure 2. Each pair contains two consecutive isotopic labels (underlined) that allow calculation of the orientational parameters (see legend in Fig. 2). In this case, the rotational orientation of the α-helices in models I and II turned out to be very similar ( Lin et al. 2006). The reason is that they have opposite interacting faces and also opposite handedness (left or right). Therefore, although it is not possible to know which model (I or II) is present in the lipid bilayer when no asparagine is present, the TM interactions are restrained in the presence of asparagine and the model is known in the mutant sequences. Thus, we only need to confirm that the orientation in each sample (model I or II) is the same, and consistent with that predicted computationally ( Lin et al. 2006).
Figure 5 shows the infrared spectra of a labeled αM-TM synthetic peptide in the regions amide A and I, collected at parallel and perpendicular polarizations. Spectra for other samples were similar and are not shown. The frequency of the bands amide A and amide I, centered at ~3295 and 1655 cm −1, respectively, were consistent with the peptides being completely α-helical. The band corresponding to the isotopic label, 13C= 18O (see arrow), is centered at 1595 cm −1 as expected ( Torres et al. 2000). Dichroic ratios (see Materials and Methods) were obtained for the amide A band and for the label, and are shown in Supplemental Table 1. ![Figure 5. Figure 5.](picrender.fcgi?artid=2327277&blobname=930fig5.gif) | Figure 5.Representative infrared spectra in the amide A and I regions. The spectrum shown corresponds to αM-TM (NSVGG) reconstituted in DMPC bilayers, collected at parallel (solid line) and perpendicular (broken line) polarization. The isotopically labeled (more ...) |
SSID analysis of the raw dichroic data (see Materials and Methods), shown in Supplemental Table 1, produced the helix tilt, β, and rotational orientation. We stress that although a difference in ω between experimental and computational results (~40°) may seem large, we have found for some systems that when analyzing essentially identical models (RMSD < 0.7 Å), the difference in ω may be up to 50°. Therefore, two models cannot be distinguished with confidence if their difference in ω at a particular residue is <50°.
Figure 6 shows that the rotational orientation for residue 1120, ω 1120, (calculated using the pair of sequences labeled “1” in Fig. 2, top panel) in the αM mutant NSVGG was −59° ± 20°. The difference in ω with any of the computational models (dimeric or trimeric) of αM was always smaller than 50°; therefore, the orientation of the α-helices in our sample is compatible with both models I and II. However, given that N is located at position 1 of the motif and found to be a dimer in SDS, the structure should correspond only to a dimeric model I (predicted to have ω = −26°). ![Figure 6. Figure 6.](picrender.fcgi?artid=2327277&blobname=930fig6.gif) | Figure 6.Comparison between experimental (this study) and computationally predicted orientational parameters. (A) The residue used to calculate ω (see black dot in Fig. 2) using SSID is indicated in the first column. Experimental values of ω (and (more ...) |
When Asn is at position 3 (GS NGG), a dimeric model II was found in SDS. For this sample, ω 1120 (calculated with the pair labeled “2” in Fig. 2, top panel) was −75° ± 7°, which is consistent with the predicted orientation of a dimer model II (ω = −92°). When Asn was introduced at N1107, ω 1120 (calculated with the pair labeled “3” in Fig. 2, top panel) was −49° ± 3°, which is similar to the orientation of the other two mutants, although from the position of the mutation, we know that this must correspond to model II. To confirm that the introduction of an asparagine residue at these positions did not affect the stability or orientation of the predicted structure, we repeated our molecular dynamics simulations ( Lin et al. 2006) when Asn mutations were present. We found that the ω angle (rotational orientation) of the conserved models did not change significantly (data not shown). In β2, when Asn was at position 1 (NxxxG), ω 704 was −46° (calculated using the pair labeled “1” in Fig. 2, lower panel). This is compatible with the predicted dimeric models I and II (−13° and −82°, respectively), but because of the location of the Asn residue, the orientation must correspond to model I. For position 3 (GxNxG), ω 704 was −79° (calculated using the pair labeled “2” in Fig. 2, lower panel). This value is only compatible with computational models II (dimer and trimer, with −82° and −110°, respectively), although almost identical to the dimeric form. This is supported by the fact that only dimers were observed in SDS ( Fig. 3). When Asn was introduced at G715N, ω 704 was −89° (calculated with the pair of sequences labeled “3” in Fig. 2, lower panel), again compatible only with computational model II (either dimer or trimer), but we only observed dimers in SDS, which suggests that the structure in lipid bilayers is dimeric, although we cannot eliminate the possibility that a mixture of dimers and trimers (model II) exists in lipid bilayers. The rotational orientation of residue 704 in β2 (ω 704) was also measured in POPC lipid bilayers, which are in a more fluid, liquid crystal, phase at room temperature. For the pair labeled “1” in Figure 2, lower panel, the result was ω 704 = −49° ± 2°, and 17° ± 1° for the helix tilt, entirely consistent with the results obtained in DMPC. |
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