BSDB

The conformational change and the identification of the mechanical clamp for proteins can be derived by looking at the unfolding scenario. A unfolding scenario shows distance d_u at which a given native contact is broken for the last time. Contacts in the scenario diagrams are identified by the sequential distance |j - i|. A contact is said to be broken if the distance between amino acids i and j exceeds 1.5σ_ij. An accumulation of many contacts unfolding events at a value of d_u indicates emergence of a force peak. In such figure the y-axis shows the sequential separation between two amino acids that make a native contact. The x-axis indicates at which displacement of the pulling tip the contact is broken for the last time. Notice that thermal fluctuations may reinstate a broken contact temporarily and that’s why we seek the last, and thus definitive, rupture event.

As an example we show the unfolding diagram for the first chain of protein 1c4p. This protein contains an α helix (196-210), denoted as I, and eight β strands, denoted as A through H, as labelled consecutively from the N to C termini. These β strands form three β sheets: a, b, and c. The a sheet comprises four strands (A, B, G, E), b sheet two ( C, F), and c-sheet also two ( D, H). These letters are indicated on the unfolding scenario figure and show which secondary structures are involved in a contact that is broken at the distance d_u. The data symbols marked by asterisks correspond to contacts which do not involve any secondary structures. The remaining symbols are diversified and have a meaning identified by the letter symbols placed next to them. The force peak at about 140 Å involves a near simultaneous rupture of the contacts which relate to the terminal strands A and G: A+G (meaning between A and G), A+I, G+I (i.e. with the helix) as well as D+H, A+B, E+G, D+G, C+G, and A+C. Breaking these contacts results in destroying the a β-sheet. Later on, the remaining contacts, such as C+F in the b sheet are broken and the helix is the last to unravel.

ICN I J |I-J| Displacement error 1 12 181 169 36.84 0.68 2 12 182 170 37.61 0.84 3 12 183 171 37.61 0.84 4 12 197 185 39.15 0.60 5 12 231 219 36.48 0.86 6 13 181 168 38.15 1.10 7 13 197 184 39.56 0.41 8 13 199 186 39.16 0.61 9 13 200 187 39.56 0.42 10 14 17 3 774.46 2.44 11 14 180 166 38.15 1.10 12 14 181 167 38.16 1.10 13 15 18 3 735.04 0.52 14 15 23 8 657.52 2.96 15 15 169 154 38.38 1.00 16 15 171 156 39.03 0.68 17 15 173 158 38.39 1.01 18 15 177 162 38.23 1.08 19 15 179 164 38.32 1.04 20 15 180 165 38.16 1.10 21 15 199 184 39.81 0.30 22 18 22 4 716.21 2.92 23 18 23 5 715.98 3.02 24 18 26 8 699.46 4.12 25 18 199 181 40.66 0.68 26 19 22 3 720.44 2.17 27 19 23 4 716.27 2.93 28 19 204 185 94.25 2.94 29 20 24 4 717.87 3.45 30 21 24 3 725.75 0.48 31 21 25 4 717.88 3.45 32 21 204 183 94.97 2.74 33 21 205 184 95.95 2.72 34 22 25 3 728.08 0.18 35 22 26 4 719.73 2.51 36 22 203 181 94.97 2.75 37 22 204 182 94.97 2.74 38 23 26 3 734.12 2.85 39 23 27 4 719.74 2.50 40 23 170 147 94.67 2.87 41 23 171 148 94.92 2.75 42 23 172 149 95.17 3.09 43 23 199 176 94.49 2.94 44 24 27 3 730.55 1.05 45 24 28 4 719.60 2.44 46 25 28 3 725.44 0.48 47 25 29 4 719.26 2.31 48 25 204 179 99.62 2.18 49 25 205 180 99.63 2.18 50 25 209 184 99.58 2.14 51 26 29 3 731.68 5.29 52 26 30 4 718.84 2.13 53 26 170 144 99.43 2.11 54 26 201 175 99.62 2.18 55 26 209 183 99.63 2.18 56 27 31 4 716.90 3.08 57 27 32 5 715.61 3.73 58 27 164 137 99.45 2.11 59 27 170 143 99.39 2.14 60 27 171 144 99.44 2.11 61 28 31 3 732.88 2.81 62 28 32 4 695.75 6.05 63 28 33 5 671.68 2.43 64 29 33 4 671.68 2.42 65 29 90 61 107.75 0.35 66 29 157 128 107.53 0.44 67 29 206 177 107.76 0.35 68 29 209 180 107.71 0.34 69 29 210 181 107.73 0.35 70 30 157 127 107.50 0.42 71 30 160 130 107.44 0.42 72 30 161 131 107.47 0.43 73 30 170 140 107.45 0.42 74 30 212 182 107.73 0.36 75 30 213 183 107.72 0.38 76 31 161 130 107.45 0.42 77 31 164 133 107.44 0.42 78 31 165 134 107.45 0.42 79 34 91 57 112.00 0.04 80 35 88 53 112.04 0.03 81 35 89 54 111.48 0.10 82 35 90 55 111.42 0.14 83 35 157 122 111.33 0.14 84 35 161 126 111.46 0.07 85 36 57 21 136.94 0.67 86 36 87 51 112.06 0.03 87 36 88 52 112.05 0.03 88 36 89 53 112.03 0.04 89 36 91 55 112.04 0.03 90 36 107 71 112.04 0.03 91 37 87 50 112.07 0.03 92 37 88 51 112.05 0.03 93 38 57 19 147.08 0.87 94 38 86 48 118.53 0.74 95 38 87 49 112.28 0.04 96 39 86 47 122.38 0.76 97 40 84 44 147.78 0.65 98 40 85 45 147.60 0.73 99 40 86 46 147.22 0.90 100 40 114 74 147.59 0.72 101 41 54 13 363.88 96.35 102 41 57 16 168.83 1.90 103 41 84 43 161.90 1.27 104 41 85 44 149.81 0.36 105 41 87 46 147.60 0.73 106 42 82 40 178.36 0.45 107 42 83 41 177.70 0.62 108 42 84 42 163.01 1.02 109 43 52 9 715.62 3.99 110 43 53 10 641.02 3.60 111 43 54 11 366.60 95.00 112 43 81 38 178.46 0.42 113 43 82 39 181.02 1.70 114 44 81 37 182.11 1.16 115 44 82 38 182.19 1.12 116 45 52 7 791.50 3.04 117 45 53 8 713.03 4.54 118 46 52 6 867.50 2.17 119 46 74 28 221.05 0.14 120 46 77 31 212.09 2.33 121 46 81 35 222.15 0.74 122 47 68 21 223.85 0.20 123 47 98 51 223.37 0.05 124 49 74 25 224.33 0.24 125 50 70 20 224.25 0.25 126 50 71 21 224.27 0.23 127 50 73 23 224.30 0.24 128 50 74 24 224.34 0.24 129 50 77 27 224.36 0.24 130 50 214 164 224.25 0.24 131 51 68 17 224.31 0.26 132 51 69 18 224.28 0.25 133 51 70 19 224.23 0.25 134 51 71 20 224.27 0.24 135 51 77 26 224.37 0.25 136 52 68 16 224.22 0.26 137 52 69 17 224.27 0.26 138 52 71 19 224.27 0.24 139 52 77 25 224.34 0.26 140 52 80 28 224.37 0.27 141 52 81 29 224.35 0.27 142 53 67 14 224.06 0.24 143 53 68 15 223.85 0.20 144 54 57 3 728.71 0.33 145 54 66 12 224.33 0.26 146 54 67 13 224.23 0.25 147 54 69 15 224.29 0.25 148 54 85 31 224.31 0.27 149 54 87 33 224.15 0.20 150 55 66 11 224.34 0.25 151 56 65 9 224.38 0.26 152 56 66 10 224.41 0.26 153 57 65 8 224.68 0.22 154 57 66 9 224.47 0.26 155 57 67 10 224.43 0.26 156 57 87 30 224.37 0.26 157 58 64 6 224.70 0.23 158 58 65 7 224.69 0.22 159 58 66 8 224.69 0.22 160 58 67 9 224.67 0.22 161 58 91 33 224.50 0.24 162 58 105 47 224.68 0.22 163 63 103 40 264.24 1.07 164 64 91 27 238.58 0.97 165 64 93 29 231.40 1.64 166 64 103 39 264.36 1.02 167 64 105 41 230.72 0.43 168 65 103 38 264.74 1.08 169 66 100 34 265.35 1.07 170 66 103 37 265.21 1.03 171 66 104 38 264.73 1.08 172 66 105 39 264.75 1.09 173 67 87 20 264.81 1.04 174 67 91 24 264.75 1.08 175 67 104 37 265.11 1.06 176 67 105 38 264.76 1.09 177 67 106 39 264.77 1.09 178 67 107 40 264.76 1.08 179 68 97 29 265.39 1.07 180 68 98 30 265.38 1.06 181 68 104 36 265.37 1.08 182 68 105 37 265.30 1.05 183 68 106 38 264.79 1.10 184 68 107 39 264.92 1.03 185 69 87 18 265.23 1.07 186 69 107 38 264.92 1.03 187 69 109 40 265.05 1.02 188 69 111 42 265.30 1.10 189 70 107 37 265.35 1.09 190 70 108 38 265.25 1.06 191 70 109 39 265.33 1.09 192 70 214 144 265.27 1.07 193 71 76 5 697.90 1.17 194 71 77 6 696.78 0.30 195 71 109 38 265.33 1.09 196 71 111 40 265.43 1.07 197 71 214 143 265.27 1.07 198 71 216 145 265.32 1.09 199 72 76 4 728.23 0.88 200 72 214 142 265.33 1.09 201 72 215 143 265.33 1.10 202 73 76 3 740.46 2.52 203 73 77 4 723.03 1.62 204 74 77 3 723.03 1.62 205 74 78 4 723.02 1.62 206 75 78 3 737.74 1.17 207 75 79 4 726.02 0.12 208 76 79 3 735.58 0.96 209 76 80 4 726.77 0.50 210 76 215 139 265.45 1.06 211 76 216 140 265.45 1.06 212 77 80 3 734.22 0.21 213 77 81 4 725.99 0.10 214 78 81 3 731.58 1.09 215 79 83 4 729.86 1.03 216 79 113 34 274.80 3.47 217 80 83 3 720.32 1.10 218 80 85 5 671.72 1.64 219 80 111 31 265.71 1.03 220 80 112 32 265.96 0.94 221 80 113 33 274.81 3.47 222 80 216 136 265.58 1.03 223 83 113 30 323.75 0.92 224 84 113 29 323.78 0.92 225 84 114 30 323.76 0.91 226 85 111 26 323.85 0.91 227 85 112 27 323.79 0.93 228 85 113 28 323.78 0.92 229 85 114 29 323.76 0.92 230 86 110 24 323.94 0.95 231 86 111 25 323.91 0.93 232 86 112 26 323.86 0.91 233 86 114 28 323.80 0.92 234 86 147 61 323.69 0.86 235 87 107 20 323.95 0.94 236 87 110 23 323.94 0.95 237 87 111 24 323.92 0.93 238 88 110 22 323.94 0.95 239 88 154 66 323.54 0.85 240 88 157 69 323.54 0.85 241 88 158 70 323.54 0.85 242 89 107 18 324.00 0.95 243 89 153 64 323.58 0.84 244 89 157 68 323.56 0.86 245 90 107 17 324.04 0.94 246 90 153 63 323.85 0.91 247 90 157 67 323.60 0.83 248 90 210 120 323.92 0.95 249 91 105 14 556.12 6.92 250 91 106 15 324.20 0.90 251 91 107 16 324.05 0.93 252 92 96 4 700.47 0.01 253 92 105 13 556.13 6.92 254 92 106 14 556.12 6.92 255 92 108 16 572.45 1.25 256 92 206 114 323.99 0.95 257 92 207 115 324.01 0.96 258 92 210 118 324.12 0.90 259 93 96 3 715.86 0.18 260 94 205 111 324.23 0.90 261 95 205 110 324.26 0.91 262 95 207 112 324.24 0.90 263 108 153 45 325.65 1.27 264 108 207 99 325.53 1.26 265 108 210 102 325.50 1.25 266 108 211 103 325.55 1.25 267 108 213 105 325.62 1.25 268 108 214 106 325.60 1.24 269 109 153 44 325.70 1.24 270 109 213 104 325.67 1.26 271 109 216 107 325.66 1.26 272 110 151 41 325.72 1.24 273 110 153 43 325.70 1.24 274 110 216 106 325.80 1.27 275 111 216 105 325.83 1.26 276 112 117 5 694.40 7.76 277 112 147 35 325.99 1.23 278 112 149 37 325.95 1.25 279 113 117 4 717.15 0.89 280 114 117 3 741.23 4.71 281 117 147 30 366.14 0.71 282 117 148 31 366.13 0.71 283 117 149 32 366.13 0.71 284 118 146 28 379.73 2.81 285 119 123 4 738.45 2.65 286 119 145 26 388.63 0.68 287 119 146 27 388.01 0.96 288 119 147 28 400.97 2.36 289 119 148 29 397.26 0.51 290 119 221 102 413.10 1.17 291 122 144 22 463.31 0.66 292 122 145 23 463.30 0.66 293 122 146 24 463.41 0.61 294 123 144 21 463.59 0.74 295 123 145 22 463.56 0.73 296 123 221 98 464.07 0.74 297 123 222 99 464.11 0.76 298 123 223 100 464.10 0.75 299 123 224 101 464.08 0.74 300 124 140 16 463.42 0.66 301 124 143 19 463.62 0.76 302 124 144 20 463.63 0.76 303 125 143 18 463.83 0.72 304 125 145 20 464.14 0.73 305 125 155 30 463.94 0.70 306 125 224 99 464.10 0.75 307 125 225 100 464.06 0.74 308 125 226 101 464.05 0.74 309 126 140 14 464.10 0.74 310 126 224 98 464.11 0.75 311 126 225 99 464.07 0.74 312 126 226 100 464.06 0.74 313 127 138 11 464.16 0.73 314 127 142 15 464.19 0.74 315 127 143 16 464.19 0.74 316 127 159 32 464.08 0.74 317 127 226 99 464.07 0.74 318 127 228 101 464.05 0.74 319 128 135 7 566.55 4.69 320 128 225 97 464.18 0.74 321 128 226 98 464.11 0.75 322 128 227 99 464.07 0.74 323 128 228 100 464.07 0.74 324 129 135 6 566.55 4.69 325 129 136 7 519.37 28.27 326 129 138 9 502.35 19.78 327 129 162 33 464.23 0.73 328 129 163 34 464.19 0.74 329 129 167 38 464.19 0.74 330 129 228 99 464.08 0.74 331 129 230 101 464.06 0.74 332 130 133 3 714.29 2.19 333 130 134 4 684.49 1.15 334 130 135 5 557.88 9.84 335 130 227 97 464.18 0.74 336 130 228 98 464.10 0.74 337 130 229 99 464.07 0.74 338 130 230 100 464.06 0.74 339 131 134 3 728.76 8.04 340 131 136 5 606.73 2.04 341 131 167 36 464.20 0.74 342 131 178 47 464.09 0.73 343 131 179 48 464.06 0.74 344 131 230 99 464.06 0.74 345 131 231 100 464.06 0.74 346 131 232 101 464.05 0.74 347 132 230 98 464.10 0.75 348 132 231 99 464.06 0.74 349 132 232 100 464.06 0.74 350 136 167 31 464.24 0.72 351 137 166 29 464.29 0.73 352 138 142 4 717.53 0.48 353 138 162 24 464.31 0.72 354 139 142 3 721.39 1.45 355 139 162 23 464.34 0.71 356 139 166 27 464.31 0.72 357 141 144 3 755.40 3.42 358 142 158 16 464.75 0.76 359 142 162 20 464.38 0.72 360 143 155 12 464.75 0.77 361 143 158 15 464.75 0.77 362 143 159 16 464.69 0.79 363 143 226 83 464.66 0.81 364 144 158 14 464.80 0.78 365 145 150 5 630.81 11.09 366 145 154 9 544.21 8.25 367 145 155 10 495.08 15.89 368 145 221 76 468.85 2.54 369 147 150 3 720.50 0.61 370 147 154 7 685.38 1.20 371 147 221 74 502.65 3.50 372 148 220 72 505.00 2.33 373 148 221 73 502.67 3.49 374 149 219 70 505.19 2.38 375 150 154 4 720.25 0.48 376 150 155 5 715.38 0.32 377 150 218 68 505.85 2.10 378 150 219 69 505.38 2.30 379 150 221 71 505.13 2.29 380 151 154 3 727.99 0.56 381 151 155 4 718.62 1.30 382 151 217 66 506.06 2.10 383 151 218 67 505.88 2.10 384 152 155 3 723.58 1.40 385 152 156 4 718.61 1.30 386 152 186 34 505.05 2.35 387 152 194 42 505.22 2.41 388 152 196 44 505.00 2.35 389 152 217 65 506.12 2.08 390 152 219 67 506.24 2.14 391 153 156 3 719.63 1.24 392 153 157 4 715.38 0.32 393 153 213 60 506.06 2.10 394 154 158 4 729.16 0.44 395 155 158 3 747.31 1.98 396 155 159 4 723.78 3.06 397 155 186 31 506.30 2.21 398 155 219 64 508.92 2.32 399 155 224 69 508.47 2.50 400 155 226 71 506.60 2.35 401 156 159 3 729.10 0.40 402 156 160 4 723.78 3.06 403 156 184 28 506.15 2.23 404 156 186 30 508.05 2.41 405 156 196 40 506.24 2.19 406 156 213 57 509.00 2.27 407 157 161 4 726.19 1.85 408 158 161 3 730.82 0.42 409 158 162 4 733.16 1.60 410 159 162 3 737.33 3.38 411 159 163 4 733.12 1.62 412 159 184 25 508.72 2.39 413 159 226 67 508.72 2.44 414 159 228 69 508.31 2.53 415 160 163 3 733.16 1.60 416 160 164 4 733.10 1.62 417 160 170 10 623.53 8.46 418 160 184 24 508.82 2.42 419 160 196 36 509.00 2.36 420 160 198 38 508.72 2.37 421 161 164 3 732.68 1.84 422 161 165 4 721.06 7.65 423 162 165 3 717.72 1.30 424 162 166 4 711.99 4.16 425 162 167 5 708.23 2.48 426 163 167 4 689.24 2.44 427 163 168 5 686.77 1.21 428 163 169 6 635.83 2.35 429 163 198 35 511.33 3.48 430 163 228 65 508.90 2.41 431 163 230 67 508.73 2.38 432 164 168 4 640.54 0.00 433 164 169 5 632.64 3.94 434 164 170 6 627.74 6.37 435 167 178 11 547.89 3.60 436 167 179 12 547.88 3.60 437 167 230 63 508.99 2.35 438 168 171 3 720.96 3.15 439 168 176 8 569.35 7.02 440 168 177 9 547.94 3.60 441 169 179 10 522.76 8.80 442 169 198 29 513.60 4.21 443 169 199 30 511.90 3.37 444 170 198 28 511.88 3.35 445 170 199 29 511.88 3.35 446 171 175 4 681.60 11.39 447 171 176 5 600.61 2.22 448 171 177 6 556.67 0.63 449 172 175 3 729.07 8.23 450 172 177 5 570.37 6.52 451 173 177 4 571.36 6.03 452 173 180 7 570.35 6.53 453 177 180 3 806.33 0.51 454 178 232 54 508.95 2.31 455 179 230 51 509.50 2.12 456 179 231 52 509.09 2.31 457 179 232 53 508.94 2.31 458 180 199 19 523.70 0.44 459 180 231 51 509.94 1.91 460 180 232 52 509.03 2.29 461 180 233 53 509.01 2.29 462 181 199 18 523.91 0.39 463 181 230 49 510.20 1.87 464 181 231 50 509.94 1.90 465 181 233 52 509.09 2.31 466 182 197 15 524.39 0.40 467 182 198 16 524.17 0.48 468 182 199 17 524.10 0.45 469 182 229 47 510.47 1.84 470 182 230 48 510.19 1.88 471 182 231 49 510.19 1.88 472 183 195 12 525.46 0.58 473 183 196 13 524.76 0.26 474 183 197 14 524.39 0.40 475 183 198 15 524.21 0.47 476 183 228 45 513.19 0.66 477 183 229 46 511.66 1.34 478 184 195 11 525.50 0.57 479 184 196 12 525.43 0.57 480 184 198 14 524.71 0.24 481 184 226 42 514.35 0.47 482 184 227 43 514.12 0.51 483 184 228 44 513.21 0.65 484 185 193 8 526.01 0.64 485 185 194 9 525.88 0.58 486 185 195 10 525.61 0.54 487 185 226 41 514.66 0.62 488 185 227 42 514.16 0.53 489 185 229 44 514.13 0.51 490 186 193 7 526.01 0.64 491 186 194 8 525.93 0.60 492 186 196 10 525.94 0.60 493 186 219 33 515.97 0.63 494 186 224 38 515.51 0.47 495 186 225 39 515.12 0.54 496 186 226 40 514.67 0.62 497 187 193 6 526.23 0.53 498 187 224 37 515.51 0.47 499 187 225 38 515.34 0.45 500 187 227 40 514.87 0.62 501 188 191 3 755.28 9.25 502 188 193 5 531.49 3.15 503 188 224 36 515.52 0.47 504 189 223 34 515.67 0.51 505 189 224 35 515.62 0.48 506 194 217 23 516.22 0.58 507 196 213 17 518.16 0.77 508 197 200 3 710.74 5.98 509 198 228 30 513.37 0.57 510 198 230 32 511.48 1.32 511 201 209 8 567.14 4.70 512 202 208 6 616.10 6.44 513 202 209 7 607.93 9.07 514 203 208 5 618.72 6.46 515 203 209 6 617.38 5.79 516 204 209 5 668.38 3.10 517 205 208 3 744.61 2.58 518 205 209 4 680.77 6.75 519 206 209 3 722.16 1.16 520 206 210 4 689.53 2.03 521 207 211 4 721.63 1.02 522 208 211 3 731.45 0.04 523 209 212 3 765.39 0.23 524 210 213 3 752.88 0.88 525 211 214 3 741.02 4.80 526 213 216 3 732.25 1.76 527 219 224 5 700.73 0.89 528 220 224 4 707.08 2.27 529 221 224 3 748.77 3.00