Properties of TMDs of the constructs used in this study
| Protein . | TMD sequence . | Mode of calculationa . | Number of residues in TMD . | Hydrophobicity (GES scale) . | . | |
|---|---|---|---|---|---|---|
. | . | . | . | Total . | Meanc . | |
| b5 | …DSNSSW WTNWVIPAISALIVALM YR… | TMD (1) | 23 | 27.1 | 1.18 | |
| TMD (2) | 17 | 28.9 | 1.67 | |||
| Syb2 | …K MMIILGVICAIILIIIIVYF ST | TMD (1) | 22 | 54.9 | 2.50 | |
| TMD (2) | 20 | 53.1 | 2.66 | |||
| PTP1B | …KPFL VNMCVATVLTAGAY LCYR… | TMD (1) | 20 | 29.1 | 1.46 | |
| TMD (2) | 14 | 18.7 | 1.34 | |||
| b5-scrambled-ops-28 | …DSNSS WWASAIIATMIPLLVNVW YR… | TMD (1) | 23 | 27.1 | 1.18 | |
| TMD (2) | 18 | 30.1 | 1.71 | |||
| b5-HH-ops-28b | …DSNS SWWTAWVIPLILILVVALM YR… | TMD (1) | 23 | 37.9 | 1.65 | |
| TMD (2) | 19 | 42.2 | 2.22 | |||
| b5-Syb2-ops-28 | …DSNSSW WTNMMIILGVICAIILIIIIV YFYR… | TMD (1) | 29 | 49.6 | 1.71 | |
| TMD (2) | 21 | 48.4 | 2.3 | |||
| b5-Syb2mut-ops-28b | …DSNSSW WTNMMGILGVGCAGIL—-V YFYR… | TMD (1) | 25 | 30.9 | 1.24 | |
| TMD (2) | 17 | 29.7 | 1.75 | |||
| Protein . | TMD sequence . | Mode of calculationa . | Number of residues in TMD . | Hydrophobicity (GES scale) . | . | |
|---|---|---|---|---|---|---|
. | . | . | . | Total . | Meanc . | |
| b5 | …DSNSSW WTNWVIPAISALIVALM YR… | TMD (1) | 23 | 27.1 | 1.18 | |
| TMD (2) | 17 | 28.9 | 1.67 | |||
| Syb2 | …K MMIILGVICAIILIIIIVYF ST | TMD (1) | 22 | 54.9 | 2.50 | |
| TMD (2) | 20 | 53.1 | 2.66 | |||
| PTP1B | …KPFL VNMCVATVLTAGAY LCYR… | TMD (1) | 20 | 29.1 | 1.46 | |
| TMD (2) | 14 | 18.7 | 1.34 | |||
| b5-scrambled-ops-28 | …DSNSS WWASAIIATMIPLLVNVW YR… | TMD (1) | 23 | 27.1 | 1.18 | |
| TMD (2) | 18 | 30.1 | 1.71 | |||
| b5-HH-ops-28b | …DSNS SWWTAWVIPLILILVVALM YR… | TMD (1) | 23 | 37.9 | 1.65 | |
| TMD (2) | 19 | 42.2 | 2.22 | |||
| b5-Syb2-ops-28 | …DSNSSW WTNMMIILGVICAIILIIIIV YFYR… | TMD (1) | 29 | 49.6 | 1.71 | |
| TMD (2) | 21 | 48.4 | 2.3 | |||
| b5-Syb2mut-ops-28b | …DSNSSW WTNMMGILGVGCAGIL—-V YFYR… | TMD (1) | 25 | 30.9 | 1.24 | |
| TMD (2) | 17 | 29.7 | 1.75 | |||
TMDs were defined either as the uncharged sequence close to the C terminus (sequence in between the charged residues, which are shown in bold; TMD (1)) or as the stretch with negative hydrophilicity according to the GES hydropathy scale (Engelman et al., 1986), computed with a window of seven residues (TMD (2)); indicated in italics. The TMD of b5-Syb2-ops-28 differs from the one of native Syb-2 (reported for comparison) in the flanking sequences derived from b5.
The underlined characters in b5-HH-ops-28 and b5-Syb2mut-ops-28 indicate the residues that have been changed from the TMD of b5 and Syb2, respectively. In addition, the TMD of b5-HH-ops-28, which was derived from the rat protein, differs from the rabbit sequence (in b5-ops-28) by an I®V replacement at position 122 of the native polypeptide. This substitution has a negligible effect on the hydrophobicity of the TMD and no effect on translocation efficiency (unpublished data).
Total hydrophobicity/number of residues in TMD.