TABLE 3.
Percentage (%) of the intrahelical hydrogen bond between the OγH side chain of Ser/Thr and the O=Cj-4 and O=Cj-3 carbonyl, and bend angle (mean ± SD) as observed during the molecular dynamics simulations of polyAla α-helices (see Methods)
|
gauche+
|
gauche−
|
|||||||
|---|---|---|---|---|---|---|---|---|
| O=Cj-4
|
O=Cj-3
|
O=Cj-4
|
O=Cj-3
|
|||||
| % | Bend | % | Bend | % | Bend | % | Bend | |
| SAAP | 100 | 15.8 ± 6.4‡ | 0 | – | 94 | 14.2 ± 5.4§ | 6 | – |
| TAAP | 100 | 15.1 ± 7.3§ | 0 | – | 89 | 13.5 ± 4.7§ | 11 | – |
| SAP | 100 | 30.3 ± 11.6§ | 0 | – | 2 | – | 98 | 34.8 ± 9.6§ |
| TAP | 98 | 27.2 ± 7.6§ | 2 | – | 88 | 26.5 ± 7.4§ | 12 | – |
| SP | 99 | 30.5 ± 8.2§ | 1 | – | 67 | 19.6 ± 4.8 | 33 | 49.8 ± 10.1§ |
| TP | 99 | 26.9 ± 6.9§ | 1 | – | 92 | 20.9 ± 6.1 | 8 | – |
| P* | 19.7 ± 7.3 | |||||||
| PS | 100 | 18.9 ± 6.4 | 0 | – | 83 | 17.5 ± 5.8 | 17 | – |
| PT | 100 | 18.9 ± 6.8 | 0 | – | 98 | 19.7 ± 6.5 | 2 | – |
| PAS | 100 | 16.0 ± 6.5‡ | 0 | – | 65 | 14.2 ± 5.6§ | 35 | 14.6 ± 6.6‡ |
| PAT | 100 | 14.1 ± 6.8§ | 0 | – | 93 | 16.4 ± 5.1† | 7 | – |
| PAAS | 100 | 14.0 ± 6.2§ | 0 | – | 35 | 29.6 ± 8.6§ | 65 | 30.0 ± 10.9§ |
| PAAT | 100 | 15.6 ± 6.6‡ | 0 | – | 74 | 24.7 ± 8.8‡ | 26 | 32.4 ± 10.0§ |
*
A Pro-containing polyAla α-helix is used as a control. One-way analysis of variance plus a posteriori two-sided Dunnett's t-tests was employed to contrast if the bend angle of the model peptides differs from the control simulation (†p < 0.05; ‡p < 0.01; §p < 0.001).