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 3 599.92 3.59 2 3 7 4 594.61 0.94 3 3 34 31 57.83 1.36 4 4 7 3 610.79 1.85 5 4 8 4 589.88 5.51 6 4 42 38 46.37 0.28 7 4 43 39 47.08 0.08 8 5 8 3 605.54 0.93 9 5 9 4 598.87 3.78 10 6 9 3 603.68 1.39 11 6 10 4 598.88 3.77 12 7 10 3 610.81 2.70 13 7 11 4 593.75 1.22 14 7 28 21 59.47 2.00 15 7 32 25 59.54 2.00 16 7 34 27 59.07 1.79 17 7 39 32 52.75 1.29 18 7 43 36 51.92 1.28 19 7 49 42 50.58 0.75 20 8 11 3 611.39 2.41 21 8 12 4 600.36 4.53 22 8 43 35 51.94 1.29 23 8 49 41 50.56 0.76 24 8 52 44 50.48 0.74 25 8 53 45 50.40 0.78 26 9 12 3 608.00 0.70 27 9 13 4 600.25 4.58 28 10 13 3 597.75 3.33 29 10 14 4 597.73 3.33 30 10 31 21 59.79 1.89 31 10 32 22 59.78 1.89 32 11 14 3 602.83 0.78 33 11 15 4 597.63 3.38 34 11 28 17 60.09 1.74 35 11 49 38 51.98 1.32 36 11 53 42 51.76 1.39 37 12 15 3 607.35 1.66 38 12 16 4 597.73 3.31 39 12 53 41 51.77 1.39 40 12 57 45 51.73 1.38 41 13 16 3 610.49 3.26 42 13 17 4 596.89 3.04 43 14 17 3 596.95 3.01 44 14 18 4 570.71 6.12 45 14 19 5 526.37 13.80 46 14 23 9 96.74 2.26 47 14 27 13 80.56 0.39 48 14 28 14 67.38 0.99 49 14 31 17 64.75 0.32 50 15 19 4 463.68 2.68 51 15 20 5 463.67 2.69 52 15 23 8 101.73 0.11 53 15 46 31 55.80 0.92 54 15 50 35 52.25 1.44 55 15 53 38 52.23 1.27 56 15 95 80 51.76 1.38 57 15 98 83 51.91 1.31 58 16 94 78 51.76 1.38 59 16 95 79 51.76 1.38 60 18 22 4 525.36 5.66 61 18 23 5 469.22 0.07 62 19 22 3 591.87 4.48 63 19 23 4 580.19 1.36 64 19 101 82 54.30 0.56 65 20 23 3 627.11 8.12 66 20 46 26 55.98 0.98 67 20 47 27 55.95 0.99 68 20 50 30 55.26 1.03 69 20 98 78 54.19 0.55 70 20 101 81 54.30 0.56 71 20 102 82 54.31 0.57 72 20 106 86 55.97 0.98 73 21 46 25 56.02 1.01 74 21 101 80 55.29 0.99 75 21 105 84 55.83 0.95 76 22 27 5 601.47 0.61 77 23 27 4 601.46 0.61 78 23 46 23 55.95 0.99 79 24 27 3 608.86 2.87 80 24 28 4 601.78 0.46 81 24 46 22 55.91 0.97 82 25 28 3 606.56 2.42 83 25 29 4 601.45 0.60 84 25 46 21 55.77 0.95 85 26 29 3 602.70 0.16 86 26 30 4 598.24 0.99 87 27 30 3 610.97 1.82 88 27 31 4 595.60 1.94 89 28 31 3 611.58 1.52 90 28 32 4 595.40 2.04 91 28 49 21 55.34 0.77 92 29 32 3 610.01 2.31 93 29 33 4 595.40 2.04 94 29 34 5 442.46 15.15 95 29 35 6 105.17 1.82 96 29 36 7 99.69 3.35 97 29 39 10 84.28 4.33 98 34 38 4 607.94 1.92 99 35 38 3 627.85 1.57 100 36 39 3 667.06 1.34 101 39 43 4 102.59 3.04 102 40 43 3 577.13 7.28 103 40 44 4 108.72 0.70 104 42 48 6 568.79 3.52 105 43 48 5 569.17 3.33 106 43 49 6 445.98 1.15 107 43 52 9 441.43 1.15 108 44 48 4 576.38 0.33 109 45 48 3 582.28 2.89 110 45 49 4 603.54 0.03 111 46 49 3 603.55 0.03 112 46 50 4 590.09 6.75 113 47 50 3 603.54 0.03 114 47 51 4 590.15 6.78 115 47 102 55 386.56 0.10 116 47 106 59 388.32 0.94 117 47 112 65 385.20 0.77 118 48 51 3 604.03 0.28 119 48 52 4 595.88 4.05 120 48 115 67 386.27 0.23 121 49 52 3 603.47 0.26 122 49 53 4 601.89 1.32 123 50 53 3 603.33 0.60 124 50 54 4 601.89 1.32 125 50 98 48 391.48 0.33 126 50 99 49 391.46 0.33 127 50 102 52 391.61 0.40 128 51 54 3 603.33 0.60 129 51 55 4 601.89 1.32 130 51 102 51 391.63 0.40 131 51 112 61 391.10 0.27 132 51 115 64 390.23 0.29 133 51 116 65 389.63 0.31 134 52 55 3 602.76 0.90 135 52 56 4 596.23 4.14 136 53 56 3 603.74 0.39 137 53 57 4 602.76 0.88 138 53 95 42 391.98 0.39 139 54 57 3 603.38 0.57 140 54 58 4 602.45 0.71 141 54 95 41 392.17 0.32 142 54 99 45 391.87 0.38 143 54 116 62 391.73 0.35 144 54 119 65 391.67 0.35 145 55 58 3 609.47 3.67 146 55 59 4 602.87 0.49 147 55 119 64 391.55 0.39 148 55 122 67 391.55 0.39 149 56 59 3 611.69 2.55 150 56 60 4 602.86 0.48 151 57 60 3 607.10 2.60 152 57 61 4 602.68 0.35 153 57 91 34 392.57 0.31 154 57 92 35 392.27 0.28 155 57 95 38 392.27 0.28 156 58 61 3 602.90 0.45 157 58 62 4 602.69 0.34 158 58 92 34 392.66 0.16 159 58 119 61 391.75 0.36 160 58 122 64 391.59 0.40 161 58 123 65 391.49 0.35 162 59 62 3 605.75 1.19 163 59 63 4 601.03 0.48 164 59 122 63 391.62 0.37 165 60 63 3 610.31 4.15 166 60 64 4 601.01 0.49 167 60 91 31 393.37 0.37 168 61 64 3 601.16 0.58 169 61 65 4 597.71 2.15 170 61 82 21 393.92 0.35 171 61 85 24 393.81 0.35 172 61 86 25 393.76 0.33 173 61 89 28 393.57 0.36 174 61 91 30 393.38 0.38 175 61 92 31 393.37 0.37 176 61 93 32 393.37 0.38 177 62 65 3 598.64 1.68 178 62 66 4 597.70 2.15 179 62 122 60 391.75 0.36 180 62 126 64 391.19 0.21 181 63 66 3 597.46 2.02 182 63 67 4 599.09 2.84 183 64 67 3 599.74 2.52 184 64 68 4 599.72 2.53 185 64 89 25 393.62 0.36 186 64 90 26 393.61 0.36 187 64 91 27 393.57 0.36 188 65 68 3 599.75 2.52 189 65 69 4 599.08 2.85 190 65 78 13 394.25 0.29 191 65 81 16 394.18 0.30 192 65 82 17 394.01 0.31 193 65 85 20 393.87 0.35 194 65 126 61 391.51 0.37 195 65 130 65 390.48 0.01 196 66 69 3 617.33 0.76 197 66 70 4 608.76 2.08 198 67 70 3 642.30 2.27 199 68 71 3 633.16 1.36 200 68 81 13 394.24 0.29 201 68 85 17 394.08 0.27 202 69 72 3 622.22 4.66 203 69 78 9 394.38 0.32 204 69 81 12 394.22 0.29 205 71 81 10 394.39 0.34 206 72 77 5 557.51 0.47 207 72 78 6 476.10 40.24 208 72 81 9 394.41 0.33 209 73 77 4 595.83 1.26 210 73 78 5 585.68 3.81 211 74 77 3 612.98 0.57 212 74 78 4 595.83 1.26 213 74 139 65 335.62 1.41 214 75 78 3 591.83 0.74 215 75 79 4 588.20 2.56 216 75 130 55 391.12 0.16 217 75 133 58 390.22 0.14 218 75 134 59 372.84 0.75 219 75 137 62 348.95 1.42 220 75 139 64 334.20 0.87 221 75 140 65 334.20 0.87 222 76 79 3 611.76 3.56 223 76 80 4 594.39 0.55 224 76 139 63 334.19 0.88 225 76 140 64 330.89 2.52 226 76 183 107 227.46 0.28 227 77 80 3 601.66 1.65 228 77 81 4 591.87 0.64 229 78 81 3 597.79 3.58 230 78 82 4 591.86 0.63 231 78 130 52 391.09 0.16 232 79 82 3 607.85 1.45 233 79 83 4 591.87 0.62 234 79 127 48 391.86 0.38 235 79 130 51 391.03 0.18 236 79 131 52 390.75 0.06 237 79 152 73 240.42 1.06 238 79 178 99 233.28 0.42 239 79 179 100 229.96 0.55 240 79 182 103 227.50 0.27 241 79 183 104 227.46 0.28 242 80 83 3 602.64 4.05 243 80 84 4 587.60 2.75 244 80 176 96 234.18 0.06 245 80 179 99 229.97 0.56 246 80 180 100 229.97 0.55 247 80 183 103 227.46 0.28 248 81 84 3 596.08 3.04 249 81 85 4 586.98 2.46 250 82 85 3 604.95 0.27 251 82 86 4 591.87 1.16 252 82 93 11 393.93 0.48 253 82 126 44 391.84 0.38 254 82 127 45 391.82 0.37 255 82 130 48 390.75 0.06 256 83 86 3 612.57 3.46 257 83 127 44 391.85 0.38 258 83 156 73 240.19 1.02 259 83 175 92 234.28 0.01 260 83 179 96 229.89 0.52 261 84 87 3 624.80 1.86 262 84 88 4 603.37 0.86 263 84 172 88 234.54 0.08 264 84 175 91 234.31 0.01 265 84 176 92 234.28 0.00 266 85 88 3 603.36 0.86 267 85 89 4 597.32 3.87 268 86 89 3 614.77 3.60 269 86 93 7 392.95 0.04 270 86 156 70 239.85 1.06 271 86 160 74 237.43 0.10 272 87 160 73 237.46 0.12 273 87 168 81 234.60 0.09 274 87 171 84 234.56 0.09 275 87 172 85 234.54 0.08 276 87 175 88 234.36 0.01 277 88 172 84 234.54 0.08 278 90 94 4 584.20 4.92 279 91 94 3 626.86 2.62 280 92 95 3 605.38 1.65 281 92 96 4 598.07 2.00 282 92 99 7 557.80 0.04 283 92 123 31 391.70 0.35 284 93 96 3 605.37 1.64 285 93 157 64 237.62 0.06 286 93 160 67 237.30 0.04 287 95 98 3 607.04 0.91 288 95 99 4 602.01 3.42 289 96 99 3 607.04 0.91 290 96 100 4 592.50 1.34 291 96 157 61 237.62 0.06 292 96 161 65 237.13 0.00 293 97 100 3 607.40 0.72 294 97 101 4 597.83 4.00 295 97 161 64 237.18 0.01 296 98 101 3 607.33 0.75 297 98 102 4 597.82 4.00 298 99 102 3 597.82 4.00 299 99 103 4 590.77 0.48 300 100 103 3 597.85 3.25 301 100 104 4 590.71 0.47 302 101 104 3 595.22 2.72 303 101 105 4 584.98 0.79 304 102 105 3 592.63 2.58 305 102 106 4 578.06 2.66 306 102 112 10 392.53 0.52 307 102 116 14 392.34 0.46 308 103 107 4 535.08 11.21 309 103 116 13 392.35 0.46 310 103 117 14 392.35 0.46 311 103 120 17 392.34 0.46 312 106 109 3 629.25 1.94 313 106 112 6 449.38 15.14 314 107 113 6 392.55 0.52 315 108 113 5 580.25 3.33 316 109 112 3 621.37 5.56 317 109 113 4 599.44 3.63 318 110 113 3 599.38 3.66 319 110 114 4 580.43 3.41 320 111 115 4 600.50 3.08 321 112 115 3 611.96 0.72 322 112 116 4 581.63 4.02 323 113 116 3 586.35 6.37 324 113 117 4 579.14 5.26 325 114 117 3 616.27 2.64 326 114 118 4 597.85 4.09 327 115 118 3 593.60 3.50 328 115 119 4 594.06 3.73 329 116 119 3 609.44 1.10 330 116 120 4 607.41 2.12 331 117 120 3 602.36 0.42 332 117 121 4 608.68 2.71 333 118 121 3 610.12 2.00 334 119 122 3 620.52 0.21 335 119 123 4 608.67 2.71 336 120 123 3 608.67 2.71 337 120 124 4 601.60 6.25 338 121 124 3 606.93 0.42 339 121 125 4 588.57 0.27 340 122 125 3 606.64 0.57 341 122 126 4 591.34 1.11 342 123 127 4 619.81 0.20 343 123 153 30 239.93 1.03 344 123 154 31 239.96 1.04 345 123 157 34 239.78 1.08 346 124 127 3 610.79 4.70 347 124 128 4 592.36 1.64 348 124 149 25 240.25 1.03 349 124 150 26 240.22 1.03 350 124 153 29 240.01 1.04 351 125 128 3 592.33 1.66 352 125 129 4 583.53 6.05 353 126 129 3 608.16 3.38 354 126 130 4 595.29 2.29 355 127 130 3 596.00 1.94 356 127 131 4 580.60 5.05 357 127 149 22 240.29 1.05 358 127 152 25 240.27 1.05 359 127 153 26 240.25 1.05 360 127 156 29 240.27 1.05 361 128 131 3 609.48 4.98 362 128 132 4 578.51 4.10 363 128 145 17 240.44 1.05 364 128 146 18 240.41 1.03 365 128 149 21 240.28 1.05 366 129 132 3 601.95 1.31 367 129 133 4 578.72 4.21 368 130 133 3 608.10 5.67 369 130 134 4 592.30 3.45 370 130 140 10 359.51 17.17 371 131 134 3 600.32 0.56 372 131 135 4 598.16 0.53 373 131 140 9 329.44 2.18 374 131 145 14 240.48 1.07 375 131 148 17 240.46 1.05 376 131 149 18 240.44 1.05 377 131 152 21 240.44 1.05 378 131 182 51 227.68 0.26 379 131 183 52 227.46 0.28 380 131 186 55 197.53 6.55 381 132 135 3 605.59 3.18 382 132 136 4 598.17 0.53 383 133 136 3 598.16 0.53 384 133 137 4 592.25 3.45 385 134 137 3 590.98 1.48 386 134 138 4 586.68 0.67 387 134 139 5 544.97 14.95 388 134 140 6 442.81 8.32 389 135 138 3 584.60 0.36 390 135 140 5 517.66 28.59 391 135 141 6 329.44 2.18 392 135 142 7 329.20 2.08 393 135 145 10 294.88 1.09 394 140 183 43 227.59 0.21 395 142 145 3 610.72 5.65 396 142 148 6 542.97 5.23 397 142 186 44 221.61 1.05 398 144 147 3 606.55 5.21 399 144 148 4 590.77 2.56 400 145 148 3 600.73 8.13 401 145 149 4 578.48 3.55 402 146 149 3 597.00 0.63 403 146 150 4 590.74 2.58 404 147 150 3 597.16 0.55 405 147 151 4 591.31 2.85 406 148 151 3 582.09 5.25 407 148 152 4 578.54 3.53 408 148 182 34 227.54 0.28 409 148 186 38 152.98 1.44 410 149 152 3 596.39 0.31 411 149 153 4 577.79 0.20 412 150 153 3 587.24 4.27 413 150 154 4 587.94 5.21 414 151 154 3 596.91 0.83 415 151 155 4 577.85 0.17 416 151 182 31 227.53 0.28 417 152 155 3 605.98 3.27 418 152 156 4 590.48 2.64 419 152 182 30 227.47 0.27 420 153 156 3 598.17 0.21 421 153 157 4 591.69 2.05 422 154 157 3 596.78 0.48 423 154 158 4 589.32 0.85 424 155 158 3 596.78 0.49 425 155 159 4 589.32 0.85 426 155 178 23 232.23 0.54 427 156 159 3 609.35 5.50 428 156 160 4 589.31 0.84 429 156 175 19 234.33 0.02 430 156 178 22 232.22 0.54 431 157 160 3 596.38 4.38 432 157 161 4 588.94 0.66 433 158 161 3 612.23 4.05 434 158 162 4 583.00 2.31 435 159 163 4 588.94 0.66 436 159 175 16 234.38 0.01 437 159 178 19 233.80 0.17 438 160 163 3 625.27 3.92 439 160 171 11 234.58 0.07 440 160 175 15 234.37 0.00 441 161 164 3 625.27 3.92 442 163 166 3 614.32 1.52 443 163 171 8 234.62 0.07 444 164 171 7 520.70 1.11 445 166 170 4 588.80 1.20 446 166 171 5 586.64 2.24 447 167 170 3 590.42 2.00 448 167 171 4 586.84 2.18 449 168 171 3 590.42 2.00 450 168 172 4 586.92 2.14 451 169 172 3 607.02 3.86 452 169 173 4 595.38 2.11 453 170 173 3 605.37 2.88 454 170 174 4 597.38 1.12 455 171 174 3 605.37 2.88 456 171 175 4 588.89 3.12 457 172 175 3 605.37 2.88 458 172 176 4 585.99 5.00 459 173 176 3 606.58 1.89 460 173 177 4 585.99 5.00 461 174 177 3 600.09 5.13 462 174 178 4 583.17 3.60 463 175 178 3 590.09 0.14 464 175 179 4 586.90 1.73 465 176 179 3 593.61 1.82 466 176 180 4 580.14 3.05 467 177 180 3 599.10 1.30 468 177 181 4 585.49 0.09 469 178 181 3 593.20 3.19 470 178 182 4 586.08 0.38 471 179 182 3 597.75 2.02 472 179 183 4 587.69 1.54 473 180 183 3 608.23 4.65 474 180 184 4 590.48 0.14 475 181 184 3 604.49 1.02 476 181 185 4 594.56 2.18 477 182 185 3 599.33 0.20 478 182 186 4 594.57 2.18 479 183 186 3 601.57 1.31 480 184 187 3 619.35 1.28