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 3 6 3 597.26 8.45 2 3 7 4 591.42 1.40 3 3 34 31 298.87 26.23 4 3 38 35 297.81 26.64 5 4 7 3 593.90 0.51 6 4 8 4 596.55 3.96 7 4 42 38 296.23 26.50 8 4 43 39 296.19 26.49 9 5 8 3 614.11 2.71 10 6 9 3 598.67 2.90 11 6 10 4 596.10 4.19 12 7 10 3 602.45 1.02 13 7 11 4 602.44 1.01 14 7 28 21 300.19 25.89 15 7 32 25 300.24 25.87 16 7 38 31 299.72 25.82 17 7 39 32 299.09 26.04 18 7 43 36 298.99 26.00 19 7 49 42 294.14 24.07 20 8 11 3 602.45 1.02 21 8 12 4 596.16 2.12 22 8 43 35 299.08 25.95 23 8 49 41 294.34 23.96 24 8 52 44 293.80 23.91 25 8 53 45 292.55 23.32 26 8 56 48 291.28 22.68 27 9 12 3 619.28 0.80 28 9 13 4 597.98 3.75 29 10 13 3 616.33 7.96 30 10 14 4 591.99 1.48 31 10 31 21 301.15 25.42 32 10 32 22 300.80 25.59 33 11 14 3 593.87 1.70 34 11 15 4 592.04 1.46 35 11 28 17 300.83 25.57 36 11 49 38 295.91 23.68 37 11 53 42 295.08 23.27 38 12 15 3 600.32 3.02 39 12 16 4 596.92 3.91 40 12 53 41 295.10 23.26 41 12 57 45 292.73 22.00 42 12 91 79 269.41 10.34 43 12 95 83 268.83 9.98 44 13 16 3 603.28 0.73 45 13 17 4 582.38 3.36 46 14 17 3 591.20 5.32 47 14 18 4 579.75 4.67 48 14 19 5 575.52 6.78 49 14 23 9 304.93 25.88 50 14 27 13 303.08 24.91 51 14 28 14 303.09 24.91 52 15 19 4 537.27 3.72 53 15 20 5 501.38 9.52 54 15 23 8 306.58 25.21 55 15 28 13 303.12 24.92 56 15 46 31 302.20 24.53 57 15 50 35 299.44 24.84 58 15 53 38 296.39 23.45 59 15 95 80 269.15 9.83 60 15 98 83 269.12 9.79 61 16 94 78 269.32 9.92 62 16 95 79 269.15 9.83 63 18 22 4 549.09 6.83 64 18 23 5 496.78 32.98 65 19 22 3 589.48 0.21 66 19 23 4 578.98 3.98 67 19 101 82 270.72 8.97 68 20 23 3 634.31 0.15 69 20 46 26 302.43 24.45 70 20 47 27 302.28 24.42 71 20 50 30 301.84 24.55 72 20 98 78 270.62 9.02 73 20 101 81 270.52 8.87 74 20 102 82 270.00 8.62 75 20 105 85 270.09 8.32 76 20 106 86 270.10 8.29 77 21 24 3 633.79 0.40 78 21 101 80 270.91 8.88 79 21 105 84 270.08 8.29 80 22 27 5 599.04 2.66 81 23 27 4 586.66 0.14 82 23 46 23 302.57 24.34 83 24 27 3 601.71 1.32 84 24 28 4 601.71 1.32 85 24 46 22 302.57 24.34 86 25 28 3 602.55 1.65 87 25 29 4 597.13 0.96 88 25 46 21 302.42 24.26 89 26 29 3 612.88 1.97 90 26 30 4 595.04 0.88 91 27 30 3 607.94 4.44 92 27 31 4 597.94 0.57 93 28 31 3 617.78 3.16 94 28 32 4 591.65 2.58 95 28 49 21 301.53 23.79 96 29 32 3 596.42 0.20 97 29 33 4 591.33 2.75 98 29 34 5 514.67 0.67 99 29 35 6 457.09 28.12 100 29 36 7 314.75 30.00 101 29 39 10 303.42 24.70 102 30 33 3 601.72 1.42 103 34 38 4 598.62 0.80 104 35 38 3 609.61 1.40 105 35 39 4 615.40 4.30 106 36 39 3 633.36 3.56 107 37 40 3 614.88 1.18 108 37 41 4 620.63 1.70 109 38 41 3 625.63 0.29 110 38 42 4 604.72 3.90 111 39 42 3 614.68 5.76 112 39 43 4 581.56 5.63 113 39 49 10 304.03 24.61 114 40 43 3 603.38 2.37 115 40 44 4 541.42 5.84 116 43 48 5 570.75 13.86 117 43 49 6 317.39 30.01 118 44 48 4 582.59 7.98 119 45 48 3 590.60 3.98 120 45 49 4 592.45 3.06 121 46 49 3 597.34 0.62 122 46 50 4 596.12 1.23 123 47 50 3 597.33 0.62 124 47 51 4 597.30 0.61 125 47 102 55 338.88 25.84 126 47 106 59 337.23 26.70 127 48 51 3 597.28 0.60 128 48 52 4 597.25 0.58 129 49 52 3 603.58 2.05 130 49 53 4 608.98 0.65 131 50 53 3 622.78 1.27 132 50 54 4 608.99 0.65 133 50 98 48 339.89 25.62 134 50 99 49 339.72 25.70 135 50 102 52 339.12 25.96 136 51 54 3 609.39 0.44 137 51 55 4 608.99 0.65 138 51 102 51 339.17 25.97 139 51 115 64 315.00 37.88 140 51 116 65 314.98 37.90 141 51 118 67 314.96 37.91 142 51 119 68 314.85 37.91 143 52 55 3 609.40 0.45 144 52 56 4 608.95 0.66 145 53 56 3 604.56 2.85 146 53 57 4 604.56 2.85 147 53 95 42 340.25 25.58 148 54 57 3 597.62 0.61 149 54 58 4 596.08 1.37 150 54 95 41 340.51 25.46 151 54 99 45 339.80 25.75 152 54 116 62 315.15 37.88 153 54 119 65 314.85 37.91 154 55 58 3 595.73 1.18 155 55 59 4 589.13 2.10 156 55 118 63 315.02 37.94 157 55 119 64 314.88 37.90 158 55 122 67 314.16 38.12 159 56 59 3 598.80 0.35 160 56 60 4 589.15 2.10 161 57 60 3 599.26 0.12 162 57 61 4 589.13 2.09 163 57 91 34 340.89 25.40 164 57 92 35 340.81 25.42 165 57 95 38 340.64 25.51 166 58 62 4 585.39 2.92 167 58 92 34 340.88 25.41 168 58 119 61 315.00 37.95 169 58 122 64 314.29 38.20 170 58 123 65 314.13 38.13 171 59 62 3 601.45 0.73 172 59 63 4 585.62 2.67 173 59 122 63 314.38 38.23 174 60 63 3 606.91 0.23 175 60 64 4 594.23 1.49 176 60 91 31 341.69 25.41 177 61 64 3 600.73 1.04 178 61 65 4 594.33 1.54 179 61 82 21 342.35 25.54 180 61 85 24 342.15 25.47 181 61 86 25 342.03 25.45 182 61 89 28 341.82 25.39 183 61 91 30 341.69 25.42 184 61 92 31 341.69 25.42 185 61 93 32 341.69 25.41 186 62 65 3 603.59 2.47 187 62 66 4 599.34 0.35 188 62 126 64 313.29 38.41 189 63 66 3 597.81 1.12 190 63 67 4 597.81 1.12 191 64 67 3 610.93 5.44 192 64 68 4 599.66 0.19 193 64 89 25 342.00 25.44 194 64 90 26 341.93 25.44 195 64 91 27 341.73 25.43 196 65 68 3 609.03 0.24 197 65 69 4 598.39 0.45 198 65 78 13 342.85 25.41 199 65 81 16 342.49 25.57 200 65 82 17 342.37 25.53 201 65 85 20 342.21 25.46 202 65 130 65 312.49 38.52 203 66 69 3 607.50 4.20 204 66 70 4 611.39 2.13 205 67 70 3 649.45 0.67 206 68 71 3 620.24 3.74 207 68 85 17 342.46 25.57 208 69 72 3 619.09 1.74 209 69 78 9 342.84 25.41 210 71 81 10 342.94 25.41 211 72 77 5 532.11 9.70 212 72 78 6 454.20 30.20 213 72 81 9 342.94 25.41 214 73 77 4 585.70 0.25 215 73 78 5 585.70 0.24 216 74 77 3 595.80 3.52 217 74 78 4 585.95 0.12 218 74 139 65 263.43 33.12 219 75 78 3 594.27 4.29 220 75 79 4 593.83 3.81 221 75 130 55 313.45 38.31 222 75 133 58 311.92 38.36 223 75 134 59 293.29 37.58 224 75 137 62 274.81 36.10 225 75 139 64 263.41 33.11 226 75 140 65 263.41 33.12 227 76 79 3 612.88 0.52 228 76 80 4 606.32 3.79 229 76 139 63 263.36 33.09 230 76 140 64 254.00 28.41 231 76 183 107 53.00 1.04 232 77 80 3 611.67 1.11 233 77 81 4 600.09 0.68 234 78 81 3 611.65 1.12 235 78 82 4 592.25 3.23 236 78 130 52 312.66 38.55 237 79 82 3 611.65 1.12 238 79 83 4 601.73 1.52 239 79 127 48 314.31 38.27 240 79 130 51 312.66 38.55 241 79 131 52 312.63 38.55 242 79 152 73 76.92 0.73 243 79 179 100 61.11 0.44 244 79 182 103 58.66 0.01 245 79 183 104 50.10 0.68 246 80 83 3 611.41 1.01 247 80 84 4 589.13 3.18 248 80 176 96 71.17 0.06 249 80 179 99 61.13 0.45 250 80 180 100 61.11 0.44 251 80 183 103 51.95 1.57 252 81 84 3 589.14 3.18 253 81 85 4 591.23 2.14 254 82 85 3 605.60 4.08 255 82 86 4 597.60 0.12 256 82 126 44 314.30 38.27 257 82 127 45 314.05 38.18 258 82 130 48 312.61 38.55 259 83 86 3 624.52 3.37 260 83 87 4 618.94 6.16 261 83 127 44 314.22 38.23 262 83 156 73 74.16 0.55 263 83 175 92 71.18 0.05 264 83 179 96 61.11 0.44 265 84 87 3 624.52 3.37 266 84 88 4 608.60 4.59 267 84 172 88 71.35 0.06 268 84 175 91 71.19 0.05 269 84 176 92 71.16 0.06 270 85 88 3 601.96 2.33 271 85 89 4 595.51 5.55 272 86 89 3 625.16 5.36 273 86 93 7 341.97 25.51 274 86 160 74 71.79 0.01 275 87 160 73 71.78 0.01 276 87 171 84 71.34 0.06 277 87 172 85 71.34 0.06 278 87 175 88 71.17 0.06 279 88 172 84 71.32 0.06 280 90 94 4 591.10 4.07 281 91 94 3 631.75 1.19 282 92 95 3 628.50 0.60 283 92 96 4 610.90 3.43 284 92 123 31 314.17 38.15 285 93 96 3 618.09 0.17 286 93 160 67 71.76 0.04 287 95 98 3 609.90 4.16 288 95 99 4 581.13 1.41 289 96 99 3 609.90 4.16 290 96 100 4 599.76 9.22 291 96 157 61 71.77 0.03 292 96 161 65 71.52 0.07 293 97 100 3 606.19 6.01 294 97 101 4 598.06 10.06 295 98 101 3 609.87 4.17 296 98 102 4 604.44 6.88 297 99 102 3 610.12 4.04 298 99 103 4 604.45 6.87 299 100 103 3 607.95 5.12 300 100 104 4 607.96 5.12 301 100 161 61 71.75 0.03 302 101 104 3 614.35 2.16 303 101 105 4 598.46 0.35 304 102 105 3 600.31 1.28 305 102 106 4 598.46 0.35 306 102 112 10 377.44 7.34 307 102 116 14 315.20 37.90 308 103 106 3 609.75 1.57 309 103 107 4 583.27 4.15 310 103 112 9 377.38 7.32 311 103 113 10 377.38 7.32 312 103 116 13 315.21 37.90 313 104 107 3 604.59 2.75 314 106 109 3 608.35 0.87 315 106 112 6 394.09 0.98 316 107 112 5 470.89 8.42 317 109 112 3 619.24 0.68 318 110 113 3 621.73 1.72 319 110 114 4 592.83 4.99 320 111 114 3 614.02 5.57 321 111 115 4 592.85 4.98 322 112 115 3 618.59 0.23 323 112 116 4 579.60 1.64 324 113 116 3 592.86 1.58 325 113 117 4 577.21 0.44 326 115 118 3 585.57 1.83 327 115 119 4 579.91 4.65 328 116 119 3 596.93 1.19 329 116 120 4 573.51 1.46 330 117 120 3 587.15 1.03 331 117 121 4 579.81 1.69 332 118 121 3 612.21 5.11 333 118 122 4 590.68 3.69 334 119 122 3 599.78 5.91 335 119 123 4 587.83 5.12 336 120 123 3 600.24 5.68 337 120 124 4 587.83 5.12 338 121 124 3 604.58 2.77 339 121 125 4 583.73 3.58 340 122 125 3 612.51 0.53 341 123 126 3 644.63 2.27 342 123 153 30 74.55 0.68 343 123 154 31 74.73 0.78 344 123 157 34 74.53 0.69 345 124 127 3 616.60 2.98 346 124 128 4 602.70 0.73 347 124 149 25 75.00 0.69 348 124 150 26 74.98 0.68 349 124 153 29 74.56 0.69 350 125 128 3 603.90 0.62 351 125 129 4 598.07 3.06 352 126 129 3 620.14 1.04 353 126 130 4 592.76 0.41 354 127 130 3 592.76 0.42 355 127 131 4 591.55 0.19 356 127 149 22 75.04 0.70 357 127 152 25 74.98 0.67 358 127 153 26 74.92 0.70 359 127 156 29 74.96 0.68 360 128 131 3 603.09 0.66 361 128 132 4 586.15 2.44 362 128 145 17 76.99 0.73 363 128 146 18 76.99 0.73 364 128 149 21 76.00 1.19 365 129 132 3 585.54 2.10 366 129 133 4 577.20 6.10 367 130 134 4 586.65 2.93 368 130 140 10 253.99 28.41 369 131 134 3 592.19 0.20 370 131 135 4 592.25 5.74 371 131 140 9 253.65 28.25 372 131 145 14 77.07 0.76 373 131 148 17 77.08 0.76 374 131 149 18 76.98 0.75 375 131 152 21 76.99 0.74 376 131 182 51 58.43 0.12 377 131 186 55 34.05 0.18 378 132 135 3 604.29 0.28 379 132 136 4 592.26 5.73 380 132 145 13 77.07 0.76 381 133 136 3 592.95 5.39 382 133 137 4 584.36 9.68 383 134 137 3 592.06 5.83 384 134 138 4 590.56 6.58 385 134 139 5 439.22 4.03 386 134 140 6 403.31 10.55 387 135 138 3 590.77 0.93 388 135 140 5 426.65 1.14 389 135 141 6 253.35 28.36 390 135 142 7 253.34 28.36 391 135 145 10 132.38 0.75 392 140 183 43 58.43 0.12 393 142 145 3 609.60 0.76 394 142 148 6 532.97 12.63 395 142 186 44 36.84 1.56 396 144 147 3 614.51 6.13 397 144 148 4 604.27 0.98 398 145 148 3 604.29 0.98 399 145 149 4 604.28 0.98 400 146 149 3 604.30 0.98 401 146 150 4 604.29 0.98 402 147 150 3 611.71 1.06 403 147 151 4 604.31 0.97 404 148 151 3 602.59 0.12 405 148 152 4 602.58 0.12 406 148 182 34 50.33 0.65 407 148 186 38 34.02 0.18 408 149 152 3 602.59 0.12 409 149 153 4 595.10 3.85 410 150 153 3 606.86 1.24 411 150 154 4 602.13 0.11 412 151 154 3 615.60 5.60 413 151 155 4 586.93 2.71 414 151 182 31 50.19 0.70 415 152 155 3 612.82 1.20 416 152 156 4 586.92 2.70 417 152 182 30 50.12 0.69 418 153 156 3 605.41 2.27 419 153 157 4 591.06 0.84 420 154 157 3 591.08 0.85 421 154 158 4 591.21 0.78 422 155 158 3 605.42 2.27 423 155 159 4 591.23 0.79 424 155 178 23 62.06 0.35 425 156 159 3 596.84 2.02 426 156 160 4 591.24 0.78 427 156 175 19 71.08 0.07 428 156 178 22 61.18 0.45 429 157 160 3 604.86 1.24 430 157 161 4 586.78 1.45 431 158 161 3 593.15 4.62 432 158 162 4 560.38 11.74 433 159 163 4 530.58 9.40 434 159 175 16 71.10 0.07 435 159 178 19 64.00 0.61 436 160 171 11 79.73 4.13 437 160 175 15 71.00 0.14 438 161 164 3 620.63 2.05 439 163 166 3 632.88 3.15 440 163 171 8 90.25 0.03 441 163 174 11 88.12 1.04 442 164 171 7 506.41 17.61 443 166 170 4 600.25 2.51 444 166 171 5 586.82 0.92 445 167 170 3 621.95 2.71 446 167 171 4 599.75 2.76 447 168 171 3 616.57 5.39 448 168 172 4 599.75 2.76 449 169 172 3 610.25 2.45 450 169 173 4 597.86 1.82 451 170 173 3 593.23 4.13 452 170 174 4 593.01 4.04 453 171 174 3 597.66 2.00 454 171 175 4 582.67 9.20 455 172 175 3 597.29 1.23 456 172 176 4 591.79 1.53 457 173 176 3 602.09 3.62 458 173 177 4 597.30 1.23 459 174 177 3 612.46 0.91 460 174 178 4 591.93 1.60 461 175 178 3 604.97 4.92 462 175 179 4 588.94 3.10 463 176 179 3 604.96 4.92 464 176 180 4 585.28 1.28 465 177 180 3 593.96 3.06 466 177 181 4 593.97 3.06 467 178 181 3 611.46 5.68 468 178 182 4 582.38 8.86 469 179 182 3 612.14 5.33 470 179 183 4 576.14 5.83 471 180 183 3 603.05 0.79 472 180 184 4 598.13 1.56 473 181 184 3 606.79 2.66 474 181 185 4 598.15 1.56 475 182 185 3 607.75 1.56 476 182 186 4 602.96 0.83 477 183 186 3 609.25 0.53 478 183 187 4 608.94 2.17 479 184 187 3 617.56 2.73