The Contribution of Hydrophobic Interactions to Conformational Changes of Inward/Outward Transmembrane Transport Proteins
Abstract
:1. Introduction
2. Materials and Methods
2.1. Data
2.2. The FOD/FOD-M Models
3. Results
3.1. The Analysis of Individual Examples
- In the center of a protein there is a highly polar residue (for example lysine), which significantly reduces the level of hydrophobicity;
- In the center of a protein is a free space. In this situation, even residues with a high level of hydrophobicity (due to the reduced number of other residues with which interaction is possible) cause a reduction in the value of the observed hydrophobicity O (which is the sum of interactions).
3.1.1. Putative Bacterial Homologue of Ferroportin (BbFPN)
3.1.2. Representative of Solute Carrier 17 (SLC17)
3.1.3. Proton-Coupled Sugar Transporter Xy1E
3.1.4. Multidrug Transporter MdfA
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Inward | Outward | |||||
---|---|---|---|---|---|---|
PDB ID [REF] | Chain Length | Transported Molecules | Transport | Source Organism | Chain Length | PDB ID [REF] |
5AYO [50] | (4–426) | Proton/Fe2+ | Symport | Bdellovibrio bacterovorus | (4–426) | 5AYM [50] |
6E9N [51] | (27–234) (243–443) | Proton/D-galactonate | Symport | E. coli | (24–230) (243–289) (295–442) | 6E9O [51] |
4QIQ [52] | (8–228) (247–471) | Proton/sugar | Symport | E. coli | (5–479) | 4GBY [53] |
4ZP0 [54] | (9–400) | Proton/antibiotic | Antiport | E. coli | (14–400) | 6GVI [55] |
INWARD | OUTWARD | ||||
---|---|---|---|---|---|
PDB ID | RD | K | K | RD | PDB |
6E9N | 0.596 | 0.6 | 0.9 | 0.711 | 6E9O |
4QIQ | 0.693 | 0.8 | 0.9 | 0.697 | 4GBY |
5AYO | 0.725 | 1.1 | 1.0 | 0.711 | 5AYM |
4ZP0 | 0.647 | 0.7 | 0.7 | 0.642 | 6GV1 |
HELIX | OUTWARD PDP ID—5AYM | INWARD PDB ID—5AYO | |||
---|---|---|---|---|---|
TM | FRAGMENT | RD | K | RD | K |
1 | 3–39 | 0.772 | 1.5 | 0.858 | 1.1 |
2 | 42–69 | 0.624 | 0.5 | 0.630 | 0.5 |
3 | 72–104 | 0.681 | 0.3 | 0.610 | 0.5 |
4 | 109–146 | 0.700 | 0.5 | 0.835 | 0.7 |
4” | 138–146 | 0.844 | 0.4 | ||
5 | 147–177 | 0.768 | 1.5 | 0.462 | 0.8 |
6 | 186–218 | 0.593 | 0.5 | 0.580 | 0.4 |
SH1 | 237–242 | 0.557 | 0.1 | ||
7A | 243–255 | 0.803 | 0.8 | 0.805 | 0.6 |
7B | 262–272 | 0.414 | 0.2 | 0.351 | 0.0 |
8 | 276–306 | 0.413 | 0.2 | 0.647 | 0.6 |
9 | 307–330 | 0.759 | 0.8 | 0.616 | 0.5 |
10 | 336–366 | 0.758 | 0.9 | 0.648 | 0.6 |
11 | 367–396 | 0.548 | 0.3 | 0.561 | 0.3 |
12 | 401–424 | 0.243 | 0.0 | 0.590 | 0.4 |
HELIX | OUTWARD PDB ID—6E9O | INWARD PDB ID—6E9N | |||
---|---|---|---|---|---|
TM | FRAGMENT | RD | K | RD | K |
1 | 28–62 | 0.683 | 0.5 | 0.554 | 0.3 |
2 | 64–94 | 0.457 | 0.3 | 0.534 | 0.3 |
3 | 96–114 | 0.800 | 0.8 | 0.670 | 0.5 |
4 | 118–148 | 0.891 | 1.9 | 0.751 | 1.4 |
5 | 152–182 | 0.738 | 0.5 | 0.634 | 0.4 |
6 | 184–206 | 0.578 | 0.4 | 0.465 | 0.2 |
CH1 | 216–226 | 0.286 | 0.1 | 0.270 | 0.0 |
CH2 | 245–253 | 0.478 | 0.3 | 0.501 | 0.3 |
7 | 254–276 | 0.503 | 0.2 | 0.501 | 0.3 |
8 | 291–321 | 0.537 | 0.4 | 0.568 | 0.3 |
9 | 324–349 | 0.714 | 0.7 | 0.445 | 0.2 |
10A | 354–369 | 0.932 | 1.0 | 0.661 | 0.4 |
10B | 375–380 | 0.822 | 0.3 | 0.681 | 0.6 |
11 | 384–414 | 0.600 | 0.3 | 0.502 | 0.2 |
12 | 416–438 | 0.556 | 0.2 | 0.557 | 0.2 |
HELIX | OUTWARD PDB ID—4GBY | INWARD PDB ID—4QIQ | |||
---|---|---|---|---|---|
TM | FRAGMENT | RD | K | RD | K |
1 | 16–47 | 0.684 | 0.6 | 0.672 | 0.5 |
2 | 52–80 | 0.356 | 0.2 | 0.505 | 0.3 |
3 | 81–104 | 0.610 | 0.5 | 0.308 | 0.0 |
EC1 | 118–121 | 0.385 | 0.1 | 0.473 | 0.1 |
4 | 126–155 | 0.419 | 0.1 | 0.457 | 0.2 |
5 | 156–187 | 0.776 | 0.6 | 0.475 | 0.2 |
6 | 190–220 | 0.783 | 0.6 | 0.642 | 0.5 |
IC1 | 223–228 | 0.621 | 0.4 | 0.382 | 0.1 |
IC3 | 247–261 | 0.349 | 0.1 | 0.716 | 1.1 |
7A | 270–291 | 0.899 | 1.6 | 0.734 | 0.9 |
7B | 293–305 | 0.664 | 0.4 | 0.535 | 0.2 |
8 | 310–337 | 0.648 | 0.4 | 0.560 | 0.3 |
9 | 342–366 | 0.657 | 0.6 | 0.523 | 0.3 |
10 | 369–399 | 0.885 | 0.9 | 0.880 | 1.2 |
11 | 402–440 | 0.602 | 0.5 | 0.625 | 0.4 |
12 | 442–461 | 0.425 | 0.2 | 0.455 | 0.2 |
HELIX | OUTWARD PDB ID—6GV1 | INWARD PDB ID—4ZP0 | |||
---|---|---|---|---|---|
TM | FRAGMENT | RD | K | RD | K |
1 | 16–47 | 0.769 | 1.2 | 0.763 | 1.2 |
2 | 52–80 | 0.676 | 0.5 | 0.693 | 0.5 |
3 | 81–101 | 0.506 | 0.2 | 0.362 | 0.1 |
4 | 104–134 | 0.514 | 0.3 | 0.577 | 0.3 |
5 | 135–166 | 0.723 | 0.6 | 0.685 | 0.6 |
6 | 169–192 | 0.308 | 0.1 | 0.331 | 0.2 |
SH1 | 204–217 | 0.415 | 0.2 | 0.283 | 0.1 |
7A | 218–234 | 0.597 | 0.3 | 0.660 | 0.5 |
7B | 234–251 | 0.781 | 0.8 | 0.878 | 0.6 |
8 | 251–281 | 0.427 | 0.2 | 0.276 | 0.1 |
9 | 281–309 | 0.760 | 0.7 | 0.628 | 0.4 |
10 | 309–343 | 0.641 | 0.4 | 0.509 | 0.2 |
11 | 343–375 | 0.629 | 0.4 | 0.557 | 0.8 |
12 | 375–399 | 0.660 | 0.6 | 0.630 | 0.8 |
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Roterman, I.; Stapor, K.; Konieczny, L. The Contribution of Hydrophobic Interactions to Conformational Changes of Inward/Outward Transmembrane Transport Proteins. Membranes 2022, 12, 1212. https://doi.org/10.3390/membranes12121212
Roterman I, Stapor K, Konieczny L. The Contribution of Hydrophobic Interactions to Conformational Changes of Inward/Outward Transmembrane Transport Proteins. Membranes. 2022; 12(12):1212. https://doi.org/10.3390/membranes12121212
Chicago/Turabian StyleRoterman, Irena, Katarzyna Stapor, and Leszek Konieczny. 2022. "The Contribution of Hydrophobic Interactions to Conformational Changes of Inward/Outward Transmembrane Transport Proteins" Membranes 12, no. 12: 1212. https://doi.org/10.3390/membranes12121212
APA StyleRoterman, I., Stapor, K., & Konieczny, L. (2022). The Contribution of Hydrophobic Interactions to Conformational Changes of Inward/Outward Transmembrane Transport Proteins. Membranes, 12(12), 1212. https://doi.org/10.3390/membranes12121212