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 1 100 99 393.51 0.62 2 1 101 100 393.51 0.62 3 2 24 22 541.79 0.87 4 2 25 23 541.56 0.92 5 2 26 24 541.19 0.87 6 2 61 59 539.80 0.38 7 2 97 95 394.51 0.56 8 2 98 96 394.30 0.49 9 2 99 97 393.53 0.62 10 2 100 98 393.51 0.62 11 2 101 99 393.51 0.62 12 3 24 21 541.81 0.86 13 3 25 22 541.71 0.88 14 3 27 24 541.45 0.86 15 3 30 27 541.34 0.83 16 3 99 96 394.04 0.50 17 3 101 98 393.51 0.62 18 3 103 100 393.51 0.62 19 3 140 137 259.75 0.47 20 4 23 19 542.35 0.72 21 4 24 20 541.82 0.86 22 4 92 88 395.05 0.49 23 4 99 95 394.30 0.49 24 4 101 97 393.62 0.65 25 4 102 98 393.53 0.62 26 4 103 99 393.53 0.62 27 4 140 136 259.82 0.48 28 5 22 17 543.08 0.40 29 5 23 18 542.96 0.43 30 5 103 98 393.53 0.62 31 5 140 135 259.87 0.47 32 5 141 136 259.64 0.48 33 5 144 139 257.89 0.14 34 6 20 14 544.15 0.28 35 6 21 15 543.73 0.30 36 6 22 16 543.06 0.41 37 6 88 82 395.48 0.48 38 6 91 85 395.36 0.44 39 6 92 86 395.25 0.48 40 6 102 96 394.34 0.51 41 6 103 97 393.92 0.56 42 6 104 98 393.53 0.62 43 6 105 99 393.51 0.62 44 6 141 135 259.82 0.48 45 6 144 138 257.93 0.14 46 7 20 13 544.15 0.27 47 7 21 14 544.14 0.28 48 7 88 81 395.79 0.52 49 7 105 98 393.56 0.64 50 7 141 134 259.98 0.44 51 7 145 138 257.92 0.14 52 8 18 10 544.44 0.24 53 8 19 11 544.24 0.29 54 8 20 12 544.16 0.27 55 8 84 76 395.94 0.57 56 8 88 80 395.83 0.54 57 8 148 140 252.24 0.48 58 9 19 10 544.34 0.27 59 9 148 139 256.37 0.52 60 9 149 140 252.23 0.48 61 9 152 143 233.50 0.53 62 10 170 160 160.95 1.19 63 11 18 7 544.59 0.21 64 11 170 159 161.03 1.17 65 12 71 59 539.50 0.29 66 12 80 68 396.29 0.55 67 12 170 158 161.06 1.19 68 12 171 159 161.02 1.17 69 13 18 5 545.76 0.41 70 13 70 57 539.65 0.30 71 13 71 58 539.57 0.30 72 13 152 139 254.33 0.51 73 13 169 156 161.08 1.19 74 13 170 157 161.02 1.17 75 14 70 56 539.67 0.30 76 14 71 57 539.65 0.30 77 14 73 59 537.52 0.69 78 14 169 155 161.09 1.17 79 14 170 156 161.05 1.17 80 14 171 157 161.04 1.17 81 14 180 166 136.75 0.19 82 14 194 180 72.95 0.10 83 15 70 55 539.72 0.33 84 15 152 137 256.66 0.59 85 15 159 144 214.38 0.91 86 15 166 151 162.43 0.95 87 15 169 154 161.09 1.17 88 15 176 161 142.59 0.39 89 15 179 164 139.14 0.06 90 15 180 165 136.71 0.17 91 15 193 178 72.98 0.11 92 15 194 179 72.92 0.10 93 16 70 54 539.72 0.34 94 16 152 136 252.22 0.48 95 16 156 140 222.96 1.07 96 16 159 143 206.47 0.14 97 17 67 50 540.01 0.34 98 17 68 51 539.75 0.35 99 17 152 135 251.62 0.65 100 17 155 138 230.22 0.52 101 18 66 48 540.04 0.33 102 18 67 49 539.84 0.31 103 18 68 50 539.73 0.36 104 18 69 51 539.68 0.34 105 18 87 69 395.97 0.56 106 19 65 46 540.03 0.33 107 19 66 47 539.88 0.29 108 19 67 48 539.74 0.35 109 19 148 129 254.00 0.36 110 19 151 132 250.83 1.03 111 19 152 133 233.87 0.04 112 20 65 45 539.96 0.31 113 20 66 46 539.74 0.35 114 20 68 48 539.69 0.34 115 20 87 67 395.91 0.56 116 20 88 68 395.88 0.56 117 20 91 71 395.64 0.45 118 21 64 43 539.96 0.31 119 21 65 44 539.69 0.34 120 21 144 123 257.92 0.15 121 21 147 126 254.17 0.43 122 21 148 127 252.12 0.51 123 22 63 41 539.96 0.31 124 22 64 42 539.77 0.38 125 22 91 69 395.30 0.47 126 22 92 70 395.22 0.46 127 22 95 73 394.84 0.52 128 23 60 37 540.06 0.33 129 23 62 39 539.95 0.31 130 23 63 40 539.70 0.34 131 23 140 117 259.88 0.47 132 23 144 121 257.82 0.14 133 23 147 124 252.25 0.48 134 24 60 36 539.98 0.32 135 24 61 37 539.96 0.31 136 24 62 38 539.75 0.35 137 24 95 71 394.72 0.58 138 24 97 73 394.53 0.57 139 24 99 75 394.19 0.43 140 25 30 5 628.00 6.75 141 25 33 8 577.29 0.90 142 25 60 35 539.95 0.31 143 25 61 36 539.94 0.31 144 25 140 115 259.80 0.49 145 26 29 3 705.87 1.46 146 26 30 4 694.90 0.69 147 26 61 35 539.93 0.32 148 27 30 3 706.11 1.41 149 27 31 4 715.56 0.70 150 28 31 3 743.27 2.66 151 29 32 3 723.84 0.82 152 29 59 30 540.08 0.26 153 30 33 3 718.09 0.57 154 30 34 4 708.09 4.43 155 30 139 109 259.97 0.44 156 31 34 3 714.29 2.46 157 31 35 4 693.29 0.03 158 32 35 3 695.87 1.29 159 32 36 4 693.32 0.03 160 32 59 27 540.19 0.25 161 33 36 3 695.00 0.81 162 33 37 4 693.32 0.04 163 33 38 5 668.77 7.88 164 33 56 23 540.24 0.24 165 33 59 26 540.22 0.25 166 33 139 106 260.01 0.43 167 33 140 107 260.00 0.43 168 33 143 110 259.45 0.49 169 34 37 3 693.23 0.07 170 34 139 105 260.01 0.43 171 36 52 16 540.91 0.13 172 36 55 19 540.89 0.12 173 36 56 20 540.86 0.12 174 36 59 23 540.71 0.18 175 37 40 3 690.20 1.28 176 37 41 4 690.20 1.28 177 38 41 3 694.96 1.11 178 38 52 14 540.96 0.11 179 38 56 18 540.91 0.12 180 38 139 101 260.06 0.43 181 38 142 104 259.97 0.44 182 38 143 105 259.94 0.45 183 38 146 108 257.92 0.15 184 39 142 103 259.99 0.43 185 41 44 3 660.10 1.02 186 41 49 8 546.95 0.60 187 41 52 11 543.71 1.31 188 41 146 105 259.57 0.51 189 42 49 7 632.15 1.03 190 42 135 93 288.62 4.00 191 42 136 94 287.56 3.64 192 44 48 4 690.57 0.52 193 44 49 5 669.64 6.24 194 44 52 8 641.28 3.51 195 45 48 3 692.36 1.42 196 45 49 4 691.58 0.99 197 46 49 3 692.38 1.40 198 46 50 4 698.95 2.60 199 47 50 3 710.57 0.70 200 47 51 4 701.02 1.55 201 48 51 3 701.03 1.55 202 48 52 4 701.02 1.55 203 49 52 3 701.02 1.55 204 49 53 4 693.91 2.00 205 49 146 97 259.56 0.51 206 49 149 100 257.89 0.16 207 49 150 101 256.49 0.36 208 50 53 3 693.91 2.00 209 50 54 4 693.90 2.00 210 50 150 100 253.88 0.42 211 50 154 104 227.06 1.07 212 51 54 3 705.69 1.06 213 51 55 4 691.84 0.99 214 52 55 3 690.70 1.56 215 52 56 4 690.21 1.41 216 52 146 94 259.00 0.35 217 53 56 3 697.38 2.19 218 53 57 4 692.96 0.37 219 53 65 12 540.23 0.28 220 53 146 93 258.31 0.01 221 53 147 94 257.82 0.13 222 53 150 97 249.36 0.58 223 53 154 101 227.06 1.07 224 54 57 3 693.76 0.76 225 54 58 4 691.53 1.08 226 55 58 3 711.65 0.27 227 55 59 4 701.54 3.84 228 56 59 3 701.63 3.88 229 56 60 4 700.88 4.17 230 56 143 87 259.51 0.51 231 56 146 90 257.91 0.17 232 57 60 3 701.55 3.84 233 57 63 6 611.83 9.02 234 57 147 90 257.68 0.07 235 60 63 3 757.11 0.12 236 60 147 87 256.86 0.09 237 62 95 33 394.68 0.59 238 62 96 34 394.55 0.56 239 62 97 35 394.51 0.57 240 63 95 32 394.68 0.59 241 63 147 84 254.16 0.45 242 64 91 27 395.45 0.48 243 64 94 30 395.14 0.44 244 64 95 31 394.70 0.66 245 65 147 82 254.18 0.44 246 65 151 86 234.20 0.14 247 66 90 24 395.89 0.57 248 66 91 25 395.67 0.46 249 67 151 84 250.83 1.04 250 68 87 19 395.96 0.56 251 69 195 126 72.86 0.09 252 70 195 125 72.89 0.10 253 71 75 4 626.27 16.39 254 71 80 9 396.85 0.65 255 71 195 124 72.90 0.10 256 72 75 3 679.33 2.79 257 72 195 123 72.89 0.10 258 72 196 124 72.86 0.10 259 72 197 125 71.89 0.31 260 72 198 126 69.09 0.20 261 73 194 121 73.01 0.12 262 73 195 122 72.95 0.11 263 73 196 123 72.88 0.10 264 73 198 125 72.08 0.22 265 73 201 128 50.56 0.28 266 73 211 138 17.92 0.42 267 73 212 139 17.78 0.38 268 74 77 3 701.03 4.43 269 74 198 124 70.91 0.07 270 74 199 125 55.46 1.88 271 74 201 127 50.12 0.12 272 74 212 138 17.71 0.34 273 75 80 5 687.91 3.08 274 76 79 3 784.28 1.83 275 76 80 4 687.91 3.08 276 76 82 6 667.44 7.15 277 76 83 7 648.00 3.85 278 77 80 3 690.52 3.35 279 77 171 94 160.83 1.28 280 79 82 3 743.43 0.03 281 80 83 3 749.39 0.59 282 81 84 3 701.77 0.19 283 81 107 26 394.31 0.50 284 81 109 28 394.09 0.44 285 83 86 3 691.01 1.90 286 83 87 4 687.13 3.69 287 84 87 3 698.64 1.92 288 84 88 4 687.27 3.63 289 84 107 23 394.15 0.42 290 84 114 30 302.17 0.26 291 85 88 3 702.32 3.90 292 85 89 4 687.79 3.35 293 85 114 29 302.03 0.20 294 85 117 32 301.93 0.18 295 85 118 33 301.63 0.14 296 85 121 36 301.55 0.15 297 86 89 3 703.97 3.07 298 86 90 4 687.78 3.34 299 86 121 35 301.54 0.15 300 87 90 3 702.29 3.91 301 87 91 4 688.43 3.02 302 88 91 3 695.43 6.46 303 88 92 4 688.43 3.02 304 88 104 16 394.50 0.57 305 88 105 17 394.33 0.49 306 88 114 26 302.03 0.20 307 88 118 30 301.62 0.14 308 89 92 3 697.13 5.61 309 89 93 4 688.42 3.01 310 89 118 29 301.62 0.14 311 89 121 32 301.13 0.26 312 89 122 33 301.01 0.29 313 90 93 3 701.43 3.97 314 90 94 4 688.43 3.00 315 91 94 3 701.43 3.97 316 91 95 4 686.51 2.04 317 92 95 3 705.73 1.82 318 92 102 10 394.50 0.57 319 92 118 26 301.44 0.12 320 92 122 30 300.77 0.17 321 92 124 32 300.64 0.20 322 93 98 5 665.49 0.24 323 93 121 28 301.13 0.26 324 93 122 29 300.77 0.17 325 93 123 30 300.72 0.19 326 93 124 31 300.64 0.19 327 95 98 3 722.55 2.86 328 95 99 4 723.18 2.54 329 98 123 25 300.38 0.23 330 98 124 26 299.74 0.15 331 99 102 3 740.86 3.08 332 99 124 25 300.04 0.33 333 99 126 27 299.08 0.32 334 100 126 26 298.94 0.37 335 100 127 27 298.80 0.30 336 101 127 26 298.83 0.29 337 102 122 20 300.72 0.18 338 102 124 22 300.36 0.23 339 102 126 24 299.23 0.39 340 102 127 25 299.08 0.32 341 102 128 26 298.79 0.29 342 102 129 27 298.76 0.29 343 103 129 26 298.81 0.30 344 103 138 35 260.00 0.45 345 103 140 37 259.93 0.45 346 103 141 38 259.75 0.47 347 104 114 10 301.62 0.15 348 104 118 14 301.44 0.12 349 104 129 25 299.09 0.32 350 104 130 26 298.64 0.23 351 104 131 27 298.66 0.24 352 104 134 30 260.40 0.49 353 104 141 37 259.87 0.47 354 105 131 26 298.74 0.28 355 105 133 28 294.15 1.44 356 105 134 29 261.24 0.07 357 105 141 36 259.97 0.44 358 106 109 3 714.27 1.24 359 106 111 5 301.94 0.14 360 106 114 8 301.74 0.09 361 106 130 24 299.17 0.28 362 106 131 25 298.88 0.21 363 106 132 26 298.73 0.27 364 108 132 24 299.07 0.31 365 109 114 5 651.72 3.62 366 109 132 23 299.32 0.33 367 110 113 3 688.68 0.76 368 110 114 4 665.07 8.61 369 111 114 3 687.58 6.62 370 111 115 4 668.38 6.96 371 111 130 19 299.78 0.20 372 111 131 20 299.67 0.18 373 111 132 21 299.67 0.18 374 112 116 4 668.39 6.95 375 113 116 3 694.50 3.89 376 113 117 4 677.65 11.58 377 114 117 3 700.04 1.11 378 114 118 4 682.12 9.34 379 114 130 16 299.85 0.12 380 115 118 3 693.75 3.52 381 115 119 4 696.93 1.35 382 115 128 13 300.29 0.21 383 115 129 14 300.25 0.21 384 115 130 15 299.87 0.13 385 116 119 3 698.05 1.91 386 116 120 4 696.99 1.38 387 117 120 3 704.87 2.56 388 117 121 4 697.06 1.36 389 118 121 3 697.06 1.36 390 118 122 4 697.06 1.36 391 118 128 10 300.30 0.21 392 119 122 3 713.98 4.33 393 119 128 9 300.30 0.21 394 122 126 4 715.03 1.74 395 122 128 6 614.25 13.29 396 131 134 3 711.08 2.00 397 131 137 6 666.20 2.71 398 131 138 7 657.30 0.15 399 132 137 5 692.49 2.59 400 133 136 3 725.49 1.88 401 133 137 4 696.81 0.43 402 134 137 3 692.09 2.79 403 134 138 4 681.91 2.29 404 134 141 7 407.92 4.44 405 135 141 6 407.94 4.42 406 135 142 7 259.94 0.45 407 135 145 10 259.30 0.35 408 138 141 3 697.64 0.19 409 138 142 4 677.25 0.85 410 139 142 3 677.33 0.83 411 139 143 4 677.26 0.85 412 140 143 3 699.13 0.03 413 140 144 4 677.30 0.84 414 141 144 3 698.61 0.29 415 141 145 4 701.91 1.38 416 142 145 3 704.72 0.01 417 142 146 4 701.94 1.37 418 143 146 3 711.14 1.32 419 143 147 4 703.64 0.51 420 144 147 3 709.01 2.39 421 144 148 4 703.64 0.51 422 145 148 3 708.98 2.16 423 145 149 4 701.89 1.38 424 146 149 3 710.04 5.46 425 146 150 4 691.66 3.33 426 147 150 3 717.12 1.92 427 147 151 4 698.58 0.04 428 148 151 3 709.81 5.58 429 148 152 4 679.50 0.01 430 149 152 3 696.65 3.83 431 149 153 4 678.57 0.16 432 150 153 3 698.31 1.02 433 150 154 4 689.29 5.53 434 151 154 3 710.66 5.14 435 151 155 4 695.76 2.31 436 152 155 3 710.66 5.14 437 152 156 4 699.68 0.35 438 152 168 16 161.10 1.17 439 152 169 17 161.09 1.17 440 152 170 18 161.06 1.16 441 153 156 3 700.70 0.85 442 153 157 4 677.47 0.33 443 154 157 3 700.55 0.80 444 154 158 4 676.36 0.86 445 155 158 3 700.40 0.87 446 155 159 4 678.96 0.29 447 156 159 3 698.35 0.97 448 156 160 4 686.88 1.90 449 156 166 10 162.40 0.95 450 157 160 3 695.97 5.15 451 157 161 4 694.68 5.79 452 158 161 3 708.07 1.12 453 158 162 4 694.68 5.79 454 159 162 3 702.49 1.89 455 159 163 4 678.50 2.29 456 159 166 7 485.57 34.50 457 159 193 34 72.97 0.12 458 160 163 3 686.30 2.19 459 160 164 4 644.88 2.74 460 160 165 5 654.90 7.77 461 160 166 6 396.14 115.90 462 160 167 7 396.14 115.90 463 163 166 3 736.32 2.23 464 163 179 16 141.60 0.78 465 163 183 20 126.69 1.45 466 163 191 28 88.59 0.81 467 163 192 29 88.47 0.86 468 163 193 30 84.75 0.72 469 165 175 10 154.58 0.61 470 165 179 14 142.06 0.57 471 166 176 10 143.62 0.10 472 166 179 13 138.12 0.69 473 167 173 6 160.50 1.17 474 167 175 8 143.72 0.10 475 167 176 9 143.63 0.10 476 168 173 5 160.49 1.18 477 168 175 7 148.92 0.16 478 168 176 8 143.63 0.10 479 169 176 7 142.56 0.41 480 170 173 3 683.75 3.79 481 170 176 6 142.56 0.41 482 171 177 6 142.27 0.52 483 173 176 3 708.55 2.69 484 173 177 4 682.02 4.85 485 174 177 3 693.77 4.71 486 174 178 4 684.22 3.75 487 175 178 3 695.09 4.07 488 175 179 4 677.88 2.52 489 176 179 3 689.97 6.63 490 176 180 4 683.26 3.10 491 177 180 3 708.88 2.83 492 177 181 4 685.35 4.13 493 177 201 24 60.95 1.73 494 177 202 25 56.05 2.62 495 177 211 34 25.41 0.55 496 178 181 3 685.36 4.13 497 178 182 4 685.34 4.13 498 179 182 3 715.70 2.73 499 179 183 4 685.34 4.13 500 179 191 12 93.18 0.10 501 179 193 14 93.06 0.10 502 180 183 3 696.36 1.36 503 180 184 4 692.41 0.60 504 180 190 10 93.04 0.10 505 180 191 11 93.03 0.13 506 180 194 14 85.41 0.54 507 180 211 31 27.23 0.21 508 181 184 3 690.37 0.42 509 181 185 4 684.38 2.56 510 181 203 22 52.38 0.78 511 181 204 23 50.24 0.10 512 181 211 30 27.82 0.43 513 182 185 3 695.59 3.04 514 182 186 4 683.12 1.90 515 183 186 3 698.54 1.55 516 183 187 4 664.62 4.04 517 183 189 6 620.70 5.83 518 183 190 7 99.43 2.31 519 183 191 8 93.25 0.12 520 183 192 9 98.83 2.61 521 184 187 3 691.82 0.32 522 184 188 4 636.58 13.76 523 184 189 5 420.70 2.72 524 184 190 6 99.45 2.31 525 184 210 26 31.85 0.35 526 185 205 20 50.23 0.10 527 185 206 21 50.20 0.10 528 190 194 4 659.73 4.21 529 190 210 20 30.11 0.49 530 190 211 21 27.73 0.48 531 191 194 3 717.57 3.10 532 199 212 13 19.16 0.21 533 200 212 12 19.11 0.21 534 201 211 10 25.34 0.41 535 201 212 11 21.71 0.32 536 202 211 9 27.37 0.34 537 203 209 6 34.20 0.46 538 203 210 7 30.79 0.98 539 203 211 8 27.13 0.46 540 204 208 4 458.99 72.29 541 204 209 5 34.47 0.33 542 205 208 3 710.51 5.11 543 205 210 5 93.19 1.16