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 3 599.91 3.59 2 3 7 4 591.90 0.42 3 3 34 31 53.18 0.74 4 3 38 35 52.95 0.83 5 4 8 4 601.79 0.44 6 4 42 38 52.16 1.02 7 4 43 39 48.97 0.00 8 5 8 3 606.49 0.46 9 5 9 4 603.74 1.42 10 6 9 3 610.81 2.69 11 6 10 4 598.43 4.08 12 7 10 3 610.81 2.71 13 7 11 4 596.80 3.15 14 7 28 21 57.21 0.28 15 7 32 25 57.21 0.28 16 7 34 27 57.17 0.27 17 7 39 32 55.22 0.07 18 7 43 36 54.04 0.66 19 7 49 42 53.15 0.74 20 8 11 3 613.79 1.21 21 8 12 4 599.97 4.72 22 8 43 35 54.78 0.28 23 8 49 41 53.18 0.73 24 8 52 44 52.96 0.78 25 8 53 45 52.91 0.79 26 8 56 48 52.77 0.86 27 9 12 3 609.42 0.01 28 9 13 4 605.36 2.02 29 10 13 3 609.42 0.01 30 10 14 4 602.83 0.76 31 10 31 21 57.37 0.30 32 10 32 22 57.29 0.31 33 11 14 3 602.84 0.75 34 11 15 4 602.81 0.76 35 11 28 17 57.38 0.34 36 11 49 38 55.26 0.04 37 11 53 42 54.67 0.03 38 12 15 3 610.64 0.01 39 12 16 4 602.82 0.76 40 12 53 41 54.95 0.10 41 12 57 45 54.62 0.04 42 13 16 3 613.19 1.91 43 13 17 4 598.75 1.26 44 14 17 3 602.65 0.70 45 14 18 4 587.97 1.64 46 14 19 5 571.56 6.57 47 14 23 9 107.23 6.49 48 14 27 13 72.50 2.06 49 14 28 14 70.52 3.02 50 15 18 3 608.35 1.14 51 15 19 4 570.84 6.90 52 15 20 5 513.00 22.03 53 15 23 8 110.87 4.67 54 15 46 31 57.04 0.29 55 15 50 35 55.45 0.06 56 15 53 38 55.37 0.01 57 15 95 80 54.99 0.06 58 15 98 83 55.19 0.01 59 16 94 78 54.78 0.01 60 16 95 79 54.79 0.01 61 18 22 4 542.50 3.99 62 18 23 5 464.98 27.27 63 19 22 3 593.92 5.50 64 19 23 4 555.97 10.71 65 19 98 79 55.34 0.03 66 19 101 82 55.47 0.04 67 20 23 3 630.83 6.25 68 20 46 26 57.09 0.28 69 20 47 27 57.01 0.29 70 20 50 30 56.45 0.41 71 20 98 78 55.36 0.02 72 20 101 81 55.48 0.04 73 20 102 82 55.55 0.00 74 20 106 86 56.41 0.40 75 21 101 80 55.63 0.01 76 21 105 84 56.43 0.39 77 23 46 23 57.06 0.29 78 24 27 3 600.52 1.72 79 24 28 4 594.45 4.75 80 24 46 22 57.03 0.27 81 25 28 3 594.45 4.76 82 25 29 4 594.45 4.75 83 25 46 21 57.01 0.28 84 26 29 3 602.84 0.56 85 26 30 4 588.25 0.85 86 27 30 3 599.91 0.61 87 27 31 4 592.91 4.12 88 28 31 3 620.95 6.10 89 28 32 4 592.92 4.12 90 28 49 21 56.27 0.31 91 29 32 3 604.36 1.49 92 29 33 4 561.44 9.28 93 29 34 5 494.98 5.53 94 29 39 10 236.06 72.33 95 30 33 3 608.39 2.16 96 34 38 4 607.84 1.98 97 35 38 3 621.39 4.80 98 35 39 4 609.77 1.01 99 36 39 3 619.71 3.96 100 37 40 3 607.84 1.98 101 39 43 4 277.69 77.20 102 39 44 5 251.89 64.27 103 39 49 10 104.80 6.51 104 40 43 3 565.03 4.83 105 40 44 4 251.87 64.26 106 42 48 6 568.03 3.90 107 43 48 5 568.02 3.90 108 43 49 6 414.37 2.10 109 43 52 9 412.64 3.04 110 44 48 4 576.50 0.17 111 45 48 3 590.58 7.04 112 45 49 4 604.07 0.30 113 46 49 3 604.07 0.29 114 46 50 4 604.07 0.30 115 47 50 3 604.06 0.29 116 47 51 4 596.99 3.83 117 47 102 55 373.31 2.81 118 47 106 59 376.63 1.20 119 47 112 65 371.87 3.39 120 48 51 3 604.06 0.29 121 48 52 4 596.99 3.83 122 49 52 3 603.76 0.41 123 49 53 4 601.59 1.18 124 50 53 3 603.35 0.61 125 50 54 4 601.89 1.32 126 50 98 48 378.17 0.91 127 50 99 49 378.12 0.91 128 50 102 52 378.04 0.89 129 51 54 3 601.89 1.32 130 51 55 4 601.89 1.32 131 51 102 51 378.12 0.93 132 51 115 64 377.43 1.02 133 52 55 3 603.76 0.40 134 52 56 4 603.43 0.57 135 53 56 3 607.64 2.34 136 53 57 4 603.42 0.57 137 53 95 42 378.50 0.93 138 54 57 3 609.46 1.44 139 54 58 4 603.02 0.37 140 54 95 41 378.45 0.95 141 54 99 45 378.18 0.91 142 54 119 65 377.57 0.93 143 55 58 3 609.54 3.63 144 55 59 4 603.03 0.38 145 55 122 67 377.54 0.90 146 56 59 3 603.38 0.00 147 56 60 4 602.61 0.39 148 57 60 3 607.33 2.75 149 57 61 4 596.02 3.68 150 57 91 34 378.82 1.01 151 57 92 35 378.77 1.03 152 57 95 38 378.70 0.99 153 58 61 3 605.37 0.30 154 58 62 4 600.56 0.27 155 58 92 34 378.94 0.94 156 58 119 61 377.86 0.89 157 58 122 64 377.60 0.91 158 58 123 65 377.56 0.90 159 59 62 3 604.15 0.92 160 59 63 4 600.57 0.27 161 59 122 63 377.63 0.93 162 60 63 3 610.47 4.08 163 60 64 4 598.45 0.80 164 60 91 31 379.57 0.94 165 61 64 3 602.95 0.32 166 61 65 4 595.33 0.77 167 61 82 21 380.50 0.96 168 61 85 24 380.18 1.08 169 61 86 25 380.08 1.03 170 61 89 28 379.76 0.91 171 61 91 30 379.57 0.93 172 61 92 31 379.56 0.93 173 61 93 32 379.60 0.93 174 62 65 3 600.22 1.68 175 62 66 4 598.47 0.81 176 62 126 64 377.27 0.84 177 63 66 3 605.06 0.16 178 63 67 4 598.47 0.81 179 64 67 3 592.46 3.81 180 64 68 4 590.46 4.81 181 64 89 25 380.10 1.04 182 64 90 26 380.10 1.05 183 64 91 27 379.76 1.01 184 65 68 3 599.18 0.46 185 65 69 4 580.27 4.26 186 65 78 13 381.38 0.92 187 65 81 16 381.24 0.94 188 65 82 17 380.53 0.95 189 65 85 20 380.31 1.02 190 65 126 61 377.36 0.80 191 65 130 65 377.06 0.86 192 66 69 3 610.31 4.27 193 66 70 4 604.98 1.60 194 68 71 3 627.81 4.04 195 68 81 13 381.38 0.92 196 68 85 17 380.76 1.06 197 69 72 3 605.27 1.47 198 69 78 9 381.39 0.92 199 69 81 12 381.38 0.91 200 71 81 10 404.69 12.49 201 72 77 5 553.10 3.38 202 72 78 6 452.78 2.23 203 72 81 9 404.69 12.49 204 73 77 4 595.24 1.55 205 73 78 5 593.29 0.58 206 74 77 3 601.69 1.67 207 74 78 4 595.24 1.55 208 74 139 65 336.20 0.36 209 75 78 3 593.32 0.59 210 75 79 4 593.32 0.59 211 75 130 55 377.23 0.82 212 75 133 58 376.91 0.80 213 75 134 59 370.38 0.48 214 75 137 62 351.17 2.52 215 75 139 64 332.94 1.50 216 75 140 65 332.94 1.50 217 76 79 3 611.84 3.52 218 76 80 4 594.58 0.04 219 76 139 63 327.10 1.42 220 76 140 64 326.12 0.93 221 76 183 107 226.53 0.11 222 77 80 3 604.88 0.04 223 77 81 4 594.56 0.05 224 78 81 3 604.88 0.04 225 78 82 4 592.63 1.02 226 78 130 52 377.08 0.84 227 79 82 3 614.20 1.72 228 79 83 4 592.64 1.02 229 79 127 48 377.96 0.88 230 79 130 51 377.10 0.85 231 79 131 52 377.07 0.85 232 79 152 73 245.78 0.18 233 79 179 100 229.31 0.26 234 79 182 103 227.00 0.30 235 79 183 104 226.47 0.09 236 80 83 3 607.63 1.56 237 80 84 4 592.16 1.26 238 80 176 96 233.40 0.45 239 80 179 99 229.31 0.26 240 80 180 100 229.11 0.35 241 80 183 103 226.61 0.14 242 81 84 3 603.22 0.59 243 81 85 4 592.10 1.25 244 82 85 3 604.95 0.27 245 82 86 4 597.38 3.89 246 82 93 11 408.25 15.11 247 82 126 44 377.94 0.89 248 82 127 45 377.93 0.88 249 82 130 48 377.07 0.85 250 83 86 3 603.40 0.89 251 83 87 4 603.41 0.89 252 83 127 44 377.94 0.88 253 83 156 73 244.60 0.04 254 83 175 92 233.60 0.35 255 83 179 96 229.10 0.35 256 84 87 3 624.80 1.86 257 84 88 4 603.40 0.89 258 84 172 88 233.73 0.30 259 84 175 91 233.59 0.35 260 84 176 92 233.40 0.44 261 85 88 3 603.40 0.88 262 85 89 4 597.36 3.89 263 86 89 3 616.89 2.54 264 86 93 7 380.33 1.16 265 86 156 70 244.44 0.04 266 86 160 74 243.55 0.11 267 87 160 73 243.53 0.10 268 87 168 81 233.83 0.28 269 87 171 84 233.78 0.30 270 87 172 85 233.63 0.35 271 87 175 88 233.60 0.35 272 88 168 80 233.81 0.29 273 90 94 4 587.45 3.34 274 91 94 3 637.00 1.97 275 92 95 3 624.56 3.77 276 92 96 4 598.90 4.88 277 92 99 7 568.57 5.91 278 92 119 27 377.95 0.89 279 92 123 31 377.89 0.92 280 93 96 3 607.90 0.38 281 93 157 64 244.09 0.00 282 93 160 67 243.41 0.07 283 95 98 3 610.73 2.46 284 95 99 4 597.57 3.85 285 96 99 3 608.39 1.56 286 96 100 4 597.57 3.85 287 96 157 61 244.46 0.10 288 96 161 65 243.33 0.06 289 97 100 3 598.34 3.46 290 97 101 4 598.34 3.46 291 97 161 64 243.53 0.14 292 98 101 3 598.62 3.60 293 98 102 4 589.22 0.30 294 99 102 3 597.83 4.00 295 99 103 4 595.24 2.71 296 99 116 17 378.13 0.96 297 100 103 3 597.86 3.25 298 100 104 4 595.25 2.72 299 100 161 61 243.72 0.23 300 100 162 62 243.72 0.23 301 101 104 3 606.29 0.97 302 101 105 4 596.88 3.74 303 102 105 3 622.39 2.81 304 102 106 4 601.80 5.17 305 102 112 10 383.68 3.56 306 103 106 3 616.63 0.07 307 103 107 4 576.15 3.83 308 103 113 10 383.67 3.58 309 103 116 13 378.17 0.96 310 104 107 3 640.10 5.58 311 106 109 3 599.32 3.56 312 106 112 6 423.23 16.20 313 107 112 5 502.55 4.93 314 107 113 6 423.23 16.20 315 109 112 3 622.06 5.21 316 109 113 4 601.90 4.86 317 110 113 3 612.52 0.45 318 110 114 4 601.93 4.85 319 111 114 3 612.52 0.45 320 111 115 4 609.14 1.24 321 112 115 3 612.51 0.45 322 112 116 4 584.29 1.47 323 113 117 4 583.58 1.10 324 114 117 3 587.62 6.87 325 114 118 4 576.26 4.79 326 115 118 3 588.86 0.40 327 115 119 4 591.38 1.85 328 116 120 4 601.25 0.97 329 117 120 3 603.82 1.16 330 117 121 4 606.59 0.23 331 118 121 3 610.13 2.00 332 118 122 4 610.13 1.99 333 119 122 3 620.53 0.21 334 119 123 4 604.59 4.75 335 120 123 3 605.19 4.46 336 120 124 4 601.61 6.25 337 121 124 3 609.96 2.06 338 121 125 4 588.49 0.31 339 122 125 3 602.38 1.56 340 122 126 4 596.36 1.54 341 123 153 30 245.34 0.01 342 123 154 31 245.34 0.01 343 123 157 34 244.50 0.12 344 124 127 3 610.79 4.70 345 124 128 4 593.03 3.20 346 124 146 22 245.83 0.15 347 124 149 25 245.46 0.01 348 124 150 26 245.41 0.00 349 124 153 29 245.35 0.01 350 125 128 3 593.03 3.20 351 125 129 4 586.90 6.26 352 126 129 3 608.15 3.38 353 126 130 4 585.45 6.99 354 127 130 3 588.83 5.29 355 127 131 4 579.01 4.53 356 127 149 22 245.63 0.09 357 127 152 25 245.43 0.01 358 127 153 26 245.42 0.03 359 127 156 29 245.40 0.02 360 128 131 3 602.72 1.68 361 128 132 4 574.46 6.80 362 128 145 17 246.09 0.24 363 128 146 18 246.08 0.24 364 128 149 21 245.53 0.02 365 129 132 3 612.00 3.72 366 129 133 4 579.95 9.55 367 130 133 3 612.00 3.72 368 130 134 4 583.85 5.75 369 130 140 10 418.01 11.84 370 131 134 3 600.24 0.59 371 131 135 4 597.88 0.39 372 131 140 9 361.14 16.59 373 131 142 11 246.50 0.11 374 131 145 14 246.17 0.24 375 131 148 17 246.13 0.22 376 131 149 18 246.05 0.26 377 131 152 21 245.85 0.17 378 131 182 51 227.70 0.04 379 131 183 52 226.59 0.14 380 131 186 55 202.11 8.85 381 132 135 3 605.30 3.33 382 132 136 4 597.40 0.15 383 132 145 13 246.14 0.23 384 133 136 3 597.88 0.39 385 133 137 4 570.52 5.20 386 134 137 3 589.91 2.00 387 134 138 4 568.89 4.38 388 134 139 5 483.71 15.70 389 134 140 6 478.38 18.34 390 135 138 3 574.26 1.60 391 135 140 5 478.38 18.34 392 135 141 6 325.88 0.95 393 135 142 7 325.81 0.92 394 135 145 10 275.82 10.63 395 140 183 43 226.78 0.19 396 142 145 3 610.72 5.65 397 142 148 6 538.58 1.00 398 142 186 44 221.75 0.98 399 144 147 3 618.52 0.77 400 144 148 4 589.70 3.10 401 145 148 3 606.37 5.31 402 145 149 4 589.72 3.10 403 146 149 3 598.78 1.52 404 146 150 4 590.75 2.58 405 147 150 3 597.16 0.55 406 147 151 4 590.10 2.25 407 148 151 3 593.77 1.52 408 148 152 4 581.89 1.85 409 148 182 34 226.75 0.12 410 148 186 38 156.53 1.85 411 149 152 3 603.67 3.33 412 149 153 4 595.77 0.00 413 150 153 3 606.46 4.52 414 150 154 4 581.91 1.86 415 151 154 3 596.91 0.83 416 151 155 4 581.91 1.86 417 151 182 31 226.72 0.12 418 152 155 3 599.32 6.59 419 152 156 4 590.71 2.53 420 152 182 30 226.66 0.15 421 153 156 3 594.82 1.89 422 153 157 4 582.22 1.71 423 154 157 3 591.77 3.31 424 154 158 4 588.76 1.12 425 155 158 3 592.96 2.72 426 155 159 4 592.46 2.97 427 155 178 23 231.22 0.07 428 156 159 3 609.37 5.49 429 156 160 4 588.74 2.27 430 156 175 19 233.72 0.30 431 156 178 22 229.53 0.33 432 157 160 3 588.75 2.27 433 157 161 4 587.23 1.54 434 158 161 3 612.23 4.05 435 158 162 4 578.70 2.71 436 159 163 4 534.30 6.16 437 159 175 16 233.75 0.29 438 159 178 19 233.00 0.56 439 160 171 11 233.82 0.29 440 160 175 15 233.72 0.29 441 161 164 3 615.28 1.07 442 163 166 3 624.69 0.45 443 163 171 8 390.99 78.84 444 164 171 7 566.91 0.62 445 166 170 4 585.90 3.93 446 166 171 5 576.65 3.80 447 166 174 8 570.37 1.10 448 167 170 3 611.56 8.56 449 167 171 4 588.21 2.78 450 168 171 3 590.32 2.06 451 168 172 4 588.19 2.77 452 169 172 3 604.25 5.25 453 169 173 4 590.62 4.22 454 170 173 3 605.37 2.88 455 170 174 4 599.34 0.14 456 171 174 3 605.37 2.88 457 171 175 4 592.22 3.42 458 172 175 3 605.37 2.88 459 172 176 4 597.52 0.77 460 173 176 3 604.70 2.83 461 173 177 4 597.52 0.76 462 174 177 3 604.40 7.21 463 174 178 4 584.21 1.05 464 175 178 3 604.69 4.09 465 175 179 4 591.78 2.75 466 176 179 3 596.89 0.20 467 176 180 4 590.36 3.46 468 177 180 3 599.11 1.30 469 177 181 4 596.88 0.19 470 178 181 3 601.25 5.65 471 178 182 4 585.80 0.52 472 179 182 3 599.98 0.91 473 179 183 4 587.36 1.29 474 180 183 3 618.88 0.69 475 180 184 4 601.85 5.54 476 181 184 3 605.19 3.89 477 181 185 4 605.17 3.88 478 182 185 3 608.54 2.20 479 182 186 4 605.94 3.50 480 183 186 3 611.08 3.44 481 184 187 3 627.11 2.85