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 2 6 4 532.34 1.01 2 2 7 5 565.54 17.57 3 2 8 6 532.37 0.99 4 7 11 4 702.33 5.30 5 7 12 5 683.90 3.91 6 8 11 3 715.45 1.27 7 8 12 4 687.66 2.04 8 8 115 107 290.58 0.69 9 9 12 3 684.55 3.59 10 9 13 4 684.54 3.59 11 10 13 3 691.66 2.27 12 10 14 4 686.17 2.77 13 10 112 102 305.10 6.25 14 10 115 105 292.25 0.18 15 11 14 3 689.43 1.15 16 11 15 4 702.45 5.40 17 11 41 30 315.59 1.02 18 11 115 104 305.11 6.25 19 12 15 3 704.82 4.22 20 12 16 4 702.39 5.42 21 13 16 3 714.72 0.72 22 13 17 4 712.12 0.57 23 13 105 92 348.58 1.83 24 13 109 96 348.35 1.90 25 14 17 3 723.33 2.41 26 14 18 4 712.12 0.57 27 14 39 25 349.41 1.51 28 14 41 27 348.08 2.02 29 14 69 55 348.07 2.02 30 14 97 83 350.17 1.51 31 14 102 88 349.62 1.69 32 14 105 91 348.57 1.83 33 14 112 98 346.78 2.27 34 15 18 3 708.02 5.25 35 15 41 26 348.25 1.94 36 15 43 28 348.58 2.27 37 15 95 80 349.75 1.70 38 17 97 80 351.56 0.86 39 17 101 84 351.57 0.86 40 17 105 88 351.36 0.95 41 18 95 77 351.69 0.92 42 18 96 78 351.56 0.86 43 18 97 79 351.56 0.86 44 19 95 76 352.41 0.93 45 19 96 77 352.19 0.98 46 20 43 23 355.12 1.19 47 20 93 73 355.17 1.21 48 20 94 74 353.50 0.86 49 20 95 75 352.53 0.98 50 21 93 72 355.18 1.21 51 21 94 73 355.01 1.25 52 21 96 75 353.86 0.71 53 22 91 69 458.13 1.10 54 22 92 70 363.36 4.01 55 22 93 71 355.45 1.07 56 23 27 4 660.43 10.27 57 23 29 6 525.86 1.88 58 23 88 65 466.36 1.56 59 23 91 68 460.93 0.29 60 23 92 69 431.24 7.94 61 23 94 71 371.88 8.27 62 24 27 3 700.56 3.65 63 24 88 64 485.80 0.93 64 24 91 67 471.34 1.13 65 25 88 63 489.93 1.14 66 25 89 64 489.97 1.14 67 25 90 65 489.89 1.12 68 25 91 66 483.19 2.23 69 26 88 62 505.35 1.71 70 27 87 60 506.15 1.45 71 27 88 61 505.45 1.72 72 28 31 3 746.03 1.06 73 28 85 57 507.24 1.41 74 28 86 58 506.98 1.29 75 28 87 59 506.16 1.44 76 29 47 18 506.97 1.28 77 29 70 41 505.60 1.62 78 29 86 57 507.00 1.29 79 29 88 59 506.90 1.25 80 29 94 65 505.34 1.71 81 30 34 4 701.00 0.28 82 30 40 10 505.60 1.62 83 30 70 40 506.10 1.46 84 30 71 41 505.60 1.62 85 30 82 52 508.42 1.07 86 30 84 54 508.25 1.09 87 30 85 55 507.87 1.28 88 30 86 56 507.28 1.38 89 31 34 3 716.74 1.86 90 31 82 51 508.63 0.98 91 31 85 54 508.05 1.20 92 32 82 50 508.63 0.98 93 32 83 51 508.42 1.07 94 32 84 52 508.17 1.16 95 32 85 53 508.12 1.17 96 33 81 48 510.56 0.85 97 33 82 49 509.42 1.23 98 34 81 47 513.66 0.44 99 34 82 48 512.50 0.12 100 35 80 45 514.08 0.33 101 35 81 46 513.75 0.46 102 36 74 38 514.20 0.39 103 36 80 44 514.17 0.38 104 36 81 45 514.06 0.33 105 36 82 46 513.82 0.44 106 36 99 63 506.81 1.39 107 37 82 45 514.19 0.38 108 37 98 61 506.82 1.39 109 37 99 62 506.81 1.39 110 38 71 33 517.34 1.01 111 38 82 44 514.49 0.44 112 38 96 58 507.27 1.43 113 38 97 59 507.12 1.39 114 38 98 60 506.82 1.39 115 38 99 61 506.82 1.39 116 39 69 30 517.92 0.86 117 39 70 31 517.74 0.89 118 39 71 32 517.34 1.01 119 39 72 33 517.25 0.97 120 39 96 57 507.28 1.43 121 39 97 58 507.17 1.41 122 39 99 60 506.86 1.40 123 39 102 63 504.54 2.46 124 39 116 77 353.56 0.92 125 40 69 29 517.92 0.86 126 40 70 30 517.75 0.88 127 40 71 31 517.72 0.88 128 40 82 42 514.89 0.39 129 40 94 54 507.96 1.22 130 40 95 55 507.44 1.44 131 40 96 56 507.27 1.43 132 41 67 26 518.87 0.84 133 41 68 27 518.13 0.83 134 41 69 28 517.96 0.84 135 41 94 53 507.98 1.22 136 41 95 54 507.92 1.21 137 42 45 3 749.88 0.95 138 42 47 5 677.70 7.09 139 42 64 22 518.98 0.82 140 42 65 23 518.90 0.85 141 42 66 24 518.88 0.84 142 42 67 25 518.86 0.84 143 42 68 26 518.25 0.83 144 42 70 28 518.13 0.83 145 42 93 51 508.50 1.14 146 42 94 52 508.26 1.15 147 43 66 23 518.94 0.87 148 43 93 50 508.56 1.16 149 43 94 51 508.38 1.19 150 43 95 52 508.35 1.19 151 44 66 22 518.99 0.84 152 44 92 48 511.40 1.53 153 44 93 49 509.02 1.38 154 45 65 20 519.24 0.87 155 45 66 21 519.20 0.88 156 45 90 45 514.18 0.34 157 45 91 46 514.12 0.34 158 45 92 47 511.42 1.53 159 46 64 18 519.37 0.86 160 46 65 19 519.24 0.87 161 46 88 42 514.32 0.37 162 46 89 43 514.23 0.35 163 46 90 44 514.19 0.34 164 46 92 46 513.62 0.45 165 47 63 16 519.97 1.10 166 47 64 17 519.74 1.02 167 47 86 39 514.91 0.36 168 47 87 40 514.59 0.36 169 47 88 41 514.31 0.36 170 47 89 42 514.24 0.35 171 47 92 45 513.71 0.50 172 48 60 12 521.25 1.26 173 48 62 14 520.97 1.30 174 48 63 15 520.20 1.10 175 48 86 38 514.95 0.38 176 48 87 39 514.63 0.35 177 49 60 11 521.44 1.34 178 49 61 12 521.21 1.24 179 49 62 13 520.99 1.30 180 49 64 15 520.85 1.26 181 49 84 35 516.88 0.91 182 49 85 36 516.50 0.74 183 49 86 37 514.95 0.38 184 50 58 8 521.56 1.33 185 50 59 9 521.51 1.33 186 50 60 10 521.45 1.34 187 50 61 11 521.45 1.35 188 50 84 34 516.90 0.90 189 50 85 35 516.76 0.87 190 50 87 37 516.28 0.93 191 51 58 7 526.03 0.91 192 51 59 8 521.55 1.33 193 51 61 10 521.52 1.32 194 51 83 32 517.18 0.97 195 51 84 33 516.94 0.90 196 51 85 34 516.91 0.90 197 52 56 4 671.38 7.38 198 52 57 5 530.84 1.48 199 52 58 6 526.03 0.91 200 52 85 33 517.12 0.99 201 52 87 35 517.12 0.99 202 53 56 3 703.58 4.49 203 53 57 4 620.73 17.95 204 58 87 29 516.98 0.98 205 58 174 116 84.20 4.79 206 59 134 75 336.21 0.38 207 59 174 115 73.45 0.59 208 60 63 3 785.88 4.12 209 60 130 70 344.10 1.62 210 60 174 114 73.45 0.59 211 60 175 115 70.62 1.96 212 61 84 23 516.88 0.91 213 61 130 69 344.03 1.65 214 63 89 26 514.31 0.37 215 63 150 87 48.31 0.68 216 63 167 104 49.34 0.26 217 64 68 4 630.64 10.02 218 64 69 5 630.65 10.01 219 64 70 6 579.98 14.98 220 64 123 59 352.98 0.95 221 65 68 3 699.75 4.86 222 67 119 52 353.27 0.88 223 68 119 51 353.27 0.88 224 68 123 55 353.18 0.88 225 69 102 33 506.59 1.44 226 69 112 43 353.75 0.97 227 69 116 47 353.45 0.93 228 69 119 50 353.27 0.88 229 69 123 54 353.24 0.89 230 70 86 16 514.22 0.35 231 70 94 24 507.98 1.21 232 71 82 11 514.73 0.44 233 71 99 28 507.14 1.42 234 72 75 3 699.60 1.22 235 72 99 27 507.11 1.43 236 72 116 44 353.60 0.93 237 72 120 48 353.49 0.95 238 72 123 51 353.41 0.91 239 73 83 10 514.57 0.46 240 73 120 47 353.57 0.92 241 74 77 3 727.59 2.74 242 74 80 6 514.96 0.51 243 74 99 25 507.06 1.40 244 75 99 24 506.76 1.43 245 75 102 27 505.84 1.81 246 75 103 28 500.68 4.38 247 75 116 41 354.19 0.90 248 76 113 37 354.41 0.92 249 76 116 40 354.38 0.92 250 76 120 44 353.84 0.99 251 77 80 3 763.01 3.15 252 78 100 22 506.73 1.38 253 82 99 17 506.82 1.39 254 88 92 4 626.18 14.46 255 97 101 4 679.12 1.30 256 97 102 5 673.63 1.44 257 97 105 8 671.68 0.46 258 98 101 3 692.12 2.89 259 98 102 4 680.99 2.23 260 99 102 3 690.31 1.81 261 99 103 4 682.87 1.42 262 100 103 3 696.99 3.89 263 100 104 4 687.19 0.14 264 101 104 3 691.89 2.48 265 101 105 4 700.84 1.99 266 102 105 3 700.85 1.99 267 102 106 4 702.31 2.71 268 102 112 10 354.34 0.94 269 102 116 14 354.05 0.96 270 103 106 3 709.25 5.84 271 103 107 4 708.91 6.01 272 104 107 3 709.31 5.82 273 104 108 4 708.91 6.01 274 105 108 3 710.14 0.73 275 105 109 4 695.09 4.76 276 106 109 3 694.95 3.77 277 106 110 4 677.56 1.88 278 106 112 6 561.97 6.05 279 106 113 7 550.20 0.25 280 109 112 3 723.34 1.05 281 110 113 3 706.39 1.81 282 110 114 4 697.85 5.39 283 111 114 3 704.70 2.66 284 111 115 4 677.45 1.27 285 112 115 3 702.10 3.27 286 112 116 4 690.50 5.26 287 113 116 3 698.69 1.17 288 113 117 4 690.56 5.25 289 114 117 3 711.25 0.97 290 114 118 4 694.96 3.06 291 115 118 3 711.25 0.96 292 115 119 4 704.88 1.91 293 116 119 3 711.07 0.88 294 116 120 4 704.89 1.91 295 117 120 3 705.16 1.76 296 117 121 4 701.40 3.64 297 118 121 3 702.99 2.85 298 118 122 4 701.38 3.65 299 119 122 3 699.52 2.72 300 119 123 4 696.17 1.05 301 120 123 3 704.56 0.20 302 120 124 4 696.17 1.05 303 121 124 3 697.87 0.21 304 121 125 4 696.08 1.01 305 122 125 3 703.71 3.12 306 122 126 4 694.38 2.08 307 123 126 3 710.34 1.24 308 123 127 4 699.70 0.81 309 124 127 3 702.29 0.48 310 124 128 4 702.28 0.48 311 125 128 3 708.13 2.44 312 125 129 4 703.09 0.88 313 126 129 3 708.94 2.04 314 126 130 4 695.24 4.82 315 127 130 3 709.72 2.42 316 127 131 4 694.90 4.99 317 128 131 3 709.72 2.42 318 128 132 4 702.92 0.98 319 129 132 3 719.70 1.44 320 129 133 4 694.89 5.00 321 130 133 3 707.66 1.39 322 130 134 4 686.39 0.64 323 130 175 45 153.00 1.95 324 131 134 3 696.88 4.40 325 131 135 4 686.04 0.82 326 132 135 3 696.68 3.31 327 132 136 4 681.37 1.51 328 133 136 3 705.58 0.45 329 133 137 4 675.42 3.39 330 133 142 9 196.66 1.51 331 133 145 12 193.94 2.87 332 134 142 8 549.33 5.54 333 134 176 42 154.04 2.18 334 137 141 4 668.56 3.14 335 137 142 5 645.96 8.17 336 137 145 8 615.15 6.35 337 138 141 3 705.88 1.07 338 138 142 4 680.31 1.80 339 139 142 3 707.47 0.73 340 139 143 4 692.46 7.78 341 139 176 37 157.69 0.97 342 139 178 39 157.56 0.93 343 139 182 43 157.14 0.90 344 139 186 47 157.10 0.88 345 140 143 3 707.03 0.51 346 140 144 4 680.66 1.86 347 140 186 46 157.09 0.88 348 140 189 49 157.05 0.86 349 140 190 50 157.05 0.86 350 141 144 3 695.19 6.44 351 141 145 4 688.08 4.24 352 142 145 3 703.43 1.30 353 142 146 4 688.23 4.17 354 142 176 34 157.99 1.02 355 142 177 35 158.19 0.93 356 143 146 3 700.29 1.86 357 143 147 4 688.23 4.17 358 143 172 29 157.88 1.07 359 143 176 33 158.22 0.94 360 143 183 40 157.21 0.85 361 143 186 43 157.15 0.87 362 143 187 44 157.12 0.88 363 143 190 47 157.09 0.88 364 144 147 3 706.00 0.97 365 144 148 4 694.12 6.91 366 144 190 46 157.10 0.88 367 145 148 3 700.68 3.62 368 145 149 4 702.97 2.48 369 146 149 3 696.78 0.94 370 146 150 4 689.18 4.42 371 146 175 29 158.37 0.89 372 146 176 30 158.37 0.89 373 147 150 3 704.94 1.50 374 147 151 4 685.63 2.69 375 147 172 25 158.30 0.93 376 147 187 40 157.24 0.82 377 147 196 49 146.99 1.59 378 147 202 55 142.94 1.75 379 147 204 57 111.66 6.02 380 148 152 4 694.83 1.91 381 148 204 56 111.96 5.88 382 148 206 58 96.17 0.19 383 148 208 60 69.08 6.61 384 149 152 3 702.21 1.79 385 149 153 4 702.21 1.79 386 150 153 3 725.36 0.17 387 150 156 6 392.61 69.41 388 150 165 15 158.70 0.96 389 150 167 17 158.60 0.99 390 151 156 5 451.31 40.05 391 151 163 12 161.82 0.11 392 151 165 14 159.05 0.80 393 151 204 53 139.14 1.46 394 152 206 54 111.95 5.87 395 153 156 3 687.53 3.85 396 156 164 8 176.89 3.09 397 156 165 9 171.80 0.55 398 157 163 6 179.50 1.80 399 157 164 7 176.89 3.09 400 158 162 4 570.50 11.30 401 158 163 5 197.44 6.90 402 159 162 3 639.52 20.75 403 159 163 4 379.29 79.11 404 159 203 44 144.78 1.69 405 161 203 42 144.79 1.71 406 161 205 44 144.58 1.72 407 162 204 42 144.70 1.72 408 162 205 43 144.53 1.72 409 163 203 40 144.69 1.72 410 163 204 41 144.59 1.72 411 163 206 43 143.80 1.35 412 164 201 37 144.83 1.69 413 164 202 38 144.70 1.72 414 164 203 39 144.38 1.65 415 165 201 36 144.63 1.70 416 165 202 37 144.59 1.72 417 165 204 39 144.50 1.70 418 166 201 35 144.57 1.73 419 167 171 4 676.42 1.02 420 167 172 5 665.02 4.67 421 167 200 33 144.68 1.76 422 168 171 3 693.64 2.25 423 168 172 4 692.84 5.14 424 169 172 3 707.87 0.79 425 169 173 4 683.65 2.72 426 169 180 11 172.95 1.07 427 169 183 14 164.66 2.33 428 169 184 15 164.65 2.33 429 169 187 18 164.65 2.33 430 170 173 3 699.24 1.48 431 170 174 4 683.72 2.75 432 170 180 10 172.97 1.07 433 171 174 3 703.39 3.55 434 171 175 4 689.08 3.25 435 172 175 3 702.71 3.56 436 172 176 4 676.80 2.52 437 172 183 11 164.67 2.32 438 172 187 15 164.64 2.33 439 173 176 3 694.71 2.74 440 173 177 4 654.28 2.64 441 173 178 5 453.51 42.58 442 173 183 10 170.08 0.37 443 178 182 4 700.40 0.98 444 178 183 5 680.60 1.60 445 179 182 3 706.47 2.06 446 179 183 4 700.40 0.98 447 180 183 3 710.50 0.04 448 180 184 4 700.36 1.00 449 181 184 3 704.59 1.11 450 181 185 4 700.35 0.99 451 182 185 3 700.48 1.02 452 182 186 4 700.37 1.01 453 183 186 3 700.40 0.99 454 183 187 4 688.68 5.68 455 184 187 3 702.18 2.69 456 184 188 4 697.06 1.50 457 185 188 3 703.32 1.60 458 185 189 4 697.12 1.47 459 186 189 3 698.62 0.91 460 186 190 4 697.11 1.46 461 187 190 3 698.59 0.92 462 187 191 4 691.93 1.14 463 187 196 9 540.55 0.21 464 188 191 3 698.37 0.82 465 188 192 4 691.91 1.13 466 189 192 3 702.20 2.73 467 189 193 4 682.88 3.37 468 190 193 3 703.77 6.29 469 190 194 4 677.90 5.83 470 190 195 5 611.70 8.76 471 190 196 6 544.70 2.29 472 191 194 3 675.04 7.26 473 191 196 5 540.54 0.21 474 191 197 6 381.34 79.39 475 191 198 7 378.81 80.65 476 195 205 10 143.53 15.56 477 196 202 6 193.74 8.34 478 196 203 7 185.16 5.23 479 196 204 8 143.55 15.56 480 197 202 5 185.75 4.96 481 197 203 6 185.22 5.20 482 198 202 4 196.06 0.20