Info

All the sequence analyses were performed on the multiple sequence alignments deposited at the GPCRDB (v6.1) (69).

All the sequence analyses were performed on the multiple sequence alignments deposited at the GPCRDB (v6.1) (69).

Fig. 2. The gauche-conformation of Ser and Thr can disrupt the hydrogen bond network of TMHs. Whereas, in principle, this conformation allows two possible hydrogen bonds, with the carbonyls at i-3 and i-4 positions (relative to the Ser/Thr) the gauche+ conformation only permits the interaction with the carbonyl one turn away at i-4. Finally, the trans-conformation excludes the possibility of intrahelical hydrogen bonds. All the figures of molecular models have been created using MolScript v2.1.1 (70) and Raster 3D v2.5 (71).

Fig. 2. The gauche-conformation of Ser and Thr can disrupt the hydrogen bond network of TMHs. Whereas, in principle, this conformation allows two possible hydrogen bonds, with the carbonyls at i-3 and i-4 positions (relative to the Ser/Thr) the gauche+ conformation only permits the interaction with the carbonyl one turn away at i-4. Finally, the trans-conformation excludes the possibility of intrahelical hydrogen bonds. All the figures of molecular models have been created using MolScript v2.1.1 (70) and Raster 3D v2.5 (71).

of these intrahelical hydrogen bonding interactions by Ser and Thr residues. Therefore, the enhanced force applied on the helical structure may induce larger conformational changes in TMHs than are observed in water-soluble proteins.

The additional hydrogen bond formed between the hydroxyl group of Ser and Thr side-chains in its gauche- conformation and the peptide carbonyls in the previous turn of the helix (Fig. 2) disrupts the hydrogen bond network that stabilizes TMHs, inducing or stabilizing a bend or kink in the helix (44). This seemingly small distortion results in a significant displacement of the residues located a few turns away in the helix. Moreover, the effect of other nearby polar residues—either consecutive or located on the same face of the helix (i.e., three/four residues apart)—can increase the magnitude of this structural effect.

2.3. Ser and Thr Can Modulate the Structure of Pro-Kinked Transmembrane a-Helices

Larger conformational changes can be induced in a-helical structures when the two helix-disrupting motifs reviewed earlier occur together. In these cases, Ser or Thr residues can significantly modulate the structure of

Pro-kinked TMHs as a result of changes induced in the hydrogen bond network of the disrupted turn; this results in a synergistic distortion of the helical structure (25). Importantly, sequence motifs of Pro with a nearby Ser or Thr are common in transmembrane helical segments—particularly within the transmembrane bundle of rhodopsin-like GPCRs. Statistical analyses show that there is a clear tendency for Ser and Thr residues to be found at positions one to two residues preceding Pro, with the exception of the SerPro motif (Tables 2 and 3). Analysis of molecular dynamics simulations of Pro-kinked a-helices containing Ser or Thr residues has revealed possible structural roles for these sequence motifs. Ser and Thr residues in the gauche-side-chain conformation can hydrogen bond either of the two carbonyls from the previous turn (three or four positions before in the sequence) (43). Our simulations demonstrate how this different pattern of interaction results in a different rearrangement of the hydrogen bond network in the helical turn (Fig. 3). These differences can be translated into a local change in the opening of the helix and into an overall change of the helical bend angle. The precise modulation of the structure depends on the relative position of Ser/ Thr and Pro residues, the side-chain conformation of the polar residues, and the nature of the intrahelical hydrogen bond between these residues and the backbone carbonyls in the preceding turn of the helix. The changes in the local structure are diverse and can either increase or decrease the bend of the helix compared to the standard Pro-kink. In (Ser/Thr)-X1-Pro and (Ser/Thr)-Pro motifs, an increase of the bend is measured, which apparently is caused by the additional hydrogen bond formed between the side-chain of Ser/Thr and the backbone carbonyl oxygen. In contrast, a decrease of the helical bend angle is observed in (Ser/Thr)-X-X-Pro, Pro-X-(Ser/Thr), and Pro-X-X-(Ser/Thr) motifs, either because of reducing the steric clash between the pyrrolidine ring of Pro and the helical backbone or because of the addition of a constraint in the form of a hydrogen bond in the curved-in face of the helix. In the case of Ser-Pro and Ser-X-Pro motifs, a change in the direction of the helix is observed when the Ser is in the gauche-rotamer (i.e., when the hydroxyl group of Ser hydrogen bonds the backbone carbonyl three positions before in the sequence), which appears to induce a strongly distorted helical turn.

Interestingly, a follow-up of these findings shows that changes in the local hydrogen bond network of the helix, triggered by a change in the Ser or Thr side-chain conformation and amplified by the presence of a nearby Pro residue, can lead to conformational modification of the entire helix in a dynamic fashion. Figure 4 shows the conformations of helices with different Ser/Thr and Pro combinations, in different side-chain conformations of the polar

Table 2

Observed and Expected Number of Occurrences of the (S/T)xxP, (S/T)xP, (S/T)P, P(S/T), Px(S/T), and Pxx(S/T) Motifs in a Nonhomologous Database of Transmembrane Helices

Table 2

Observed and Expected Number of Occurrences of the (S/T)xxP, (S/T)xP, (S/T)P, P(S/T), Px(S/T), and Pxx(S/T) Motifs in a Nonhomologous Database of Transmembrane Helices

Pair

Observed

Expected

Odds ratio

Significance

SxxP

0 0

Post a comment