Table 5.
Summary of distance proximity constraints on rhodopsin conformations based upon epitope mappings of selected mAbs
| Constraint | |||||||
| Antibody name | No. occurrences | From | To | Avg. block sub. score | Map type | ||
| Intradiskal | |||||||
| B1gN | 1 | N | 2 | V | 11 | 75% | I |
| B1gN | 1 | T | 4 | F | 9 | 75% | I |
| B1gN | 1 | F | 9 | V | 11 | 100% | I |
| B1gN | 1 | V | 11 | F | 24 | 86% | F |
| B1gN | 1 | V | 11 | F | 37 | 88% | F |
| B1gN | 1 | P | 12 | V | 204 | 88% | F |
| B1gN | 1 | F | 13 | D | 190 | 100% | F |
| B1gN | 2 | F | 13 | D | 282 | 100% | V |
| B1gN | 1 | N | 15 | T | 17 | 75% | I |
| B1gN | 1 | N | 15 | Q | 28 | 100% | F |
| B1gN | 2 | N | 15 | Q | 36 | 100% | F |
| B1gN | 1 | N | 15 | Q | 184 | 100% | F |
| B1gN | 1 | N | 15 | Q | 279 | 100% | F |
| B1gN | 13 | K | 16 | G | 18 | 100% | V |
| B1gN | 1 | T | 17 | Y | 29 | 42% | I |
| B1gN | 1 | V | 19 | Q | 28 | 58% | I |
| B1gN | 1 | V | 19 | Y | 30 | 75% | I |
| B1gN | 1 | S | 22 | F | 24 | 100% | F |
| B1gN | 1 | Q | 28 | Y | 191 | 88% | F |
| B1gN | 5 | Y | 30 | A | 32 | 100% | V |
| B1gN | 4 | Y | 30 | I | 189 | 88% | F |
| B1gN | 2 | Q | 36 | Y | 191 | 88% | F |
| B1gN | 1 | Y | 43 | I | 189 | 88% | F |
| B1gN | 1 | Q | 184 | Y | 191 | 88% | F |
| B1gN | 1 | D | 190 | V | 204 | 100% | F |
| B1gN | 1 | Y | 191 | Q | 279 | 88% | F |
| B1gN | 1 | V | 204 | D | 282 | 100% | F |
| B1gN | 1 | S | 281 | F | 283 | 67% | I |
| B1gN | 1 | D | 282 | G | 284 | 50% | I |
| Cyloplasmic group I | |||||||
| K42-41L | 2 | R | 69 | E | 239 | 90% | F |
| K42-41L | 1 | R | 69 | S | 338 | 100% | F |
| K42-41L | 1 | R | 147 | E | 239 | 100% | F |
| K42-41L | 1 | R | 147 | S | 338 | 100% | F |
| K42-41L | 1 | G | 149 | E | 332 | 75% | F |
| K42-41L | 1 | E | 150 | A | 235 | 75% | F |
| K42-41L | 1 | E | 150 | Q | 237 | 81% | F |
| K42-41L | 1 | E | 150 | A | 333 | 75% | F |
| K42-41L | 1 | K | 231 | A | 234 | 67% | I |
| K42-41L | 1 | K | 231 | Q | 238 | 81% | F |
| K42-41L | 1 | E | 232 | A | 234 | 67% | F |
| K42-41L | 1 | A | 233 | Q | 236 | 72% | F |
| K42-41L | 1 | A | 233 | Q | 237 | 70% | I |
| K42-41L | 1 | Q | 237 | E | 239 | 57% | F |
| K42-41L | 1 | Q | 237 | E | 332 | 75% | F |
| K42-41L | 4 | Q | 238 | S | 240 | 69% | F |
| K42-41L | 4 | Q | 238 | L | 328 | 90% | F |
| K42-41L | 4 | E | 239 | K | 245 | 77% | V |
| K42-41L | 1 | E | 239 | R | 314 | 80% | F |
| K42-41L | 3 | S | 240 | K | 248 | 58% | F |
| K42-41L | 1 | K | 245 | E | 247 | 67% | F |
| K42-41L | 1 | K | 245 | E | 249 | 67% | F |
| K42-41L | 1 | K | 245 | S | 343 | 67% | I |
| K42041L | 1 | A | 246 | K | 248 | 67% | I |
| K42-41L | 3 | G | 324 | N | 326 | 75% | F |
| K42-41L | 1 | P | 327 | G | 329 | 83% | I |
| K42-41L | 1 | G | 329 | T | 342 | 100% | I |
| Cytoplasmic group II | |||||||
| K16-111c | |||||||
| K16-111c | 1 | N | 145 | G | 324 | 90% | I |
| K16-111c | 1 | N | 145 | P | 347 | 100% | I |
| K16-111c | 3 | F | 148 | A | 346 | 81% | V |
| K16-111c | 1 | N | 151 | G | 324 | 90% | H |
| K16-111c | 1 | N | 151 | P | 347 | 100% | H |
| K16-111c | 3 | E | 232 | V | 318 | 75% | F |
| K16-111c | 1 | E | 249 | P | 347 | 67% | H |
| K16-111c | 1 | T | 251 | G | 329 | 75% | H |
| K16-111c | 1 | N | 310 | G | 324 | 90% | I |
| K16-111c | 1 | N | 310 | P | 347 | 100% | I |
| K16-111c | 1 | N | 315 | M | 317 | 83% | F |
| K16-111c | 1 | N | 315 | P | 327 | 83% | F |
| K16-111c | 2 | M | 317 | G | 329 | 100% | V |
| K16-111c | 1 | V | 318 | N | 326 | 75% | I |
| K16-111c | 2 | K | 325 | P | 327 | 73% | F |
| K16-111c | 1 | N | 326 | M | 317 | 90% | F |
| K16-111c | 2 | N | 326 | P | 347 | 58% | I |
| K16-111c | 3 | P | 327 | G | 329 | 100% | I |
Additional distance proximity constraints on rhodopsin confirmations, based on the other mAbs mapped are presented in Supplementary Material to this paper.
Epitope maps that contain rhodopsin sequence gaps were used to infer structural proximities in the folded protein, as explained in the text. Average block substitution scores were calculated using the amino acid similarity matrix (based on Table 3) between the phage display consensus epitope and all linearly continuous residues of rhodopsin that are mapped to on either side of a gap. "Map type" describes how the mapping was obtained: F = mapped with FINDMAP, I = mapped by manual Inspection, H = Hybrid of both methods (some residues held constant then mapped by FINDMAP), or V = aVeraged, in cases where the gap is present in multiple mappings from different source types.