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 1 127 126 201.50 0.41 2 1 158 157 45.55 0.74 3 1 159 158 38.81 0.20 4 1 160 159 38.39 0.41 5 1 162 161 38.27 0.46 6 2 127 125 201.51 0.41 7 2 128 126 201.52 0.41 8 2 158 156 47.88 0.34 9 2 159 157 38.85 0.20 10 2 165 163 36.95 0.65 11 3 121 118 201.50 0.42 12 3 124 121 201.57 0.41 13 3 127 124 201.54 0.41 14 3 128 125 201.52 0.41 15 3 130 127 201.50 0.41 16 3 157 154 50.76 0.78 17 3 158 155 48.58 0.22 18 3 160 157 39.06 0.26 19 4 42 38 313.52 0.94 20 4 43 39 313.51 0.94 21 4 45 41 313.03 1.03 22 4 128 124 201.55 0.40 23 4 129 125 201.52 0.41 24 4 130 126 201.51 0.41 25 4 155 151 55.46 0.16 26 4 156 152 54.52 0.01 27 4 157 153 51.13 0.59 28 4 166 162 37.12 0.58 29 4 168 164 36.93 0.63 30 5 130 125 201.52 0.41 31 5 132 127 201.47 0.41 32 5 136 131 145.55 0.32 33 5 137 132 139.63 0.18 34 5 140 135 123.06 0.70 35 5 155 150 55.48 0.17 36 5 156 151 54.65 0.06 37 5 158 153 53.41 0.04 38 6 38 32 329.94 6.02 39 6 42 36 315.85 1.03 40 6 58 52 329.42 5.78 41 6 129 123 201.61 0.41 42 6 130 124 201.53 0.40 43 6 131 125 201.51 0.41 44 6 132 126 201.50 0.41 45 6 154 148 64.46 0.57 46 6 155 149 55.61 0.24 47 7 14 7 565.59 0.74 48 7 132 125 201.52 0.41 49 7 133 126 201.49 0.42 50 7 134 127 198.28 0.09 51 7 137 130 142.88 0.83 52 7 150 143 82.78 1.46 53 7 151 144 82.52 1.46 54 7 152 145 80.67 0.78 55 7 153 146 78.62 0.94 56 7 154 147 66.50 0.02 57 8 14 6 565.60 0.74 58 8 20 12 361.67 6.80 59 8 27 19 358.59 6.68 60 8 54 46 330.11 6.11 61 8 55 47 329.79 6.27 62 8 58 50 329.92 6.03 63 8 132 124 201.55 0.40 64 8 133 125 201.52 0.41 65 8 152 144 82.25 1.56 66 8 153 145 80.07 0.88 67 9 27 18 358.92 6.82 68 9 31 22 357.65 6.30 69 9 34 25 357.45 6.28 70 9 58 49 349.50 3.60 71 9 152 143 82.27 1.56 72 9 153 144 80.11 0.85 73 10 14 4 565.86 0.88 74 10 15 5 565.59 0.74 75 10 27 17 359.17 6.87 76 10 28 18 359.24 6.86 77 10 30 20 359.18 6.83 78 10 31 21 358.87 6.90 79 10 34 24 358.88 6.90 80 10 152 142 82.33 1.55 81 11 14 3 572.96 1.89 82 11 15 4 570.93 1.66 83 11 20 9 390.96 7.50 84 11 25 14 359.38 6.95 85 11 26 15 359.37 6.94 86 11 27 16 359.29 6.92 87 11 28 17 359.40 6.92 88 11 54 43 359.29 6.92 89 12 15 3 575.95 3.10 90 12 16 4 565.61 0.74 91 12 28 16 359.57 6.84 92 13 16 3 575.65 3.25 93 13 17 4 564.56 0.25 94 13 18 5 501.69 4.90 95 13 19 6 501.69 4.89 96 13 20 7 408.78 1.40 97 13 23 10 391.00 7.49 98 13 25 12 361.68 6.80 99 13 81 68 287.81 0.80 100 13 82 69 272.72 1.59 101 14 20 6 408.44 1.23 102 14 152 138 83.11 1.36 103 16 84 68 272.31 1.77 104 17 84 67 272.61 1.61 105 17 85 68 272.21 1.72 106 18 82 64 272.81 1.54 107 18 83 65 272.67 1.59 108 18 84 66 272.27 1.74 109 19 77 58 310.36 1.91 110 19 80 61 289.87 0.21 111 19 82 63 272.84 1.56 112 19 83 64 272.72 1.57 113 19 85 66 272.20 1.71 114 19 88 69 270.60 0.98 115 19 96 77 248.49 4.86 116 20 23 3 600.22 5.38 117 20 25 5 492.98 8.09 118 20 54 34 409.93 0.79 119 20 74 54 311.95 1.29 120 20 77 57 310.36 1.91 121 21 52 31 410.96 1.21 122 21 54 33 411.80 1.63 123 21 74 53 311.88 1.26 124 21 75 54 311.88 1.26 125 21 77 56 311.68 1.27 126 21 81 60 282.05 3.69 127 22 52 30 410.89 1.25 128 22 73 51 312.10 1.27 129 22 74 52 312.09 1.27 130 22 75 53 312.08 1.27 131 22 76 54 311.78 1.24 132 22 81 59 287.86 0.79 133 22 108 86 246.47 5.24 134 22 116 94 236.30 3.92 135 23 54 31 412.37 1.71 136 23 81 58 282.13 3.65 137 24 52 28 412.23 1.66 138 24 53 29 412.23 1.66 139 24 54 30 412.35 1.71 140 25 54 29 412.38 1.70 141 26 53 27 412.50 1.71 142 27 31 4 558.86 1.68 143 27 32 5 558.29 1.98 144 27 54 27 412.54 1.73 145 27 57 30 412.60 1.75 146 27 58 31 412.59 1.75 147 27 61 34 412.82 1.66 148 28 31 3 571.03 0.42 149 28 32 4 567.07 1.79 150 29 32 3 575.56 2.44 151 29 33 4 567.86 1.41 152 30 33 3 571.12 0.22 153 30 34 4 568.84 2.21 154 30 37 7 566.78 1.63 155 31 34 3 583.88 4.34 156 31 35 4 568.85 2.21 157 32 35 3 580.88 1.18 158 32 36 4 576.83 1.78 159 32 57 25 413.01 1.60 160 32 61 29 413.10 1.60 161 33 36 3 580.77 1.12 162 33 37 4 577.07 1.66 163 34 37 3 582.56 0.23 164 34 38 4 578.75 2.12 165 34 152 118 82.47 1.47 166 34 153 119 80.89 1.13 167 35 38 3 583.39 4.39 168 35 39 4 578.75 2.12 169 35 58 23 413.06 1.58 170 35 61 26 413.16 1.61 171 35 62 27 413.16 1.61 172 36 39 3 583.97 0.49 173 36 61 25 413.14 1.61 174 37 41 4 575.26 2.58 175 37 170 133 36.84 0.64 176 38 41 3 578.56 1.17 177 38 42 4 571.34 2.44 178 38 58 20 413.50 1.70 179 38 62 24 413.45 1.66 180 38 153 115 80.08 0.87 181 38 168 130 36.98 0.65 182 38 170 132 36.81 0.64 183 39 61 22 413.57 1.67 184 39 62 23 413.45 1.66 185 39 63 24 413.50 1.64 186 41 168 127 36.97 0.65 187 41 170 129 36.78 0.61 188 42 64 22 485.94 0.43 189 42 129 87 207.40 2.52 190 42 131 89 207.39 2.52 191 42 155 113 63.36 0.02 192 42 168 126 36.96 0.65 193 43 64 21 486.10 0.45 194 43 129 86 207.74 2.68 195 44 64 20 486.09 0.45 196 45 64 19 486.22 0.43 197 45 127 82 207.97 2.66 198 45 128 83 207.50 2.44 199 45 129 84 207.47 2.45 200 46 127 81 207.98 2.65 201 46 128 82 207.47 2.42 202 46 129 83 207.44 2.41 203 47 64 17 486.23 0.42 204 47 66 19 486.13 0.48 205 47 67 20 486.17 0.48 206 47 129 82 207.21 2.31 207 47 131 84 207.16 2.31 208 48 66 18 486.24 0.46 209 48 67 19 486.17 0.49 210 48 69 21 486.08 0.49 211 48 72 24 472.53 3.00 212 48 120 72 214.66 5.88 213 48 124 76 208.65 2.93 214 48 128 80 207.31 2.33 215 48 129 81 207.21 2.31 216 48 130 82 207.06 2.27 217 48 131 83 206.63 2.10 218 49 55 6 504.91 1.46 219 49 56 7 488.05 0.36 220 49 59 10 486.35 0.46 221 49 66 17 486.28 0.47 222 49 67 18 486.28 0.47 223 49 68 19 486.16 0.50 224 49 69 20 486.15 0.50 225 49 72 23 472.53 3.00 226 49 131 82 206.54 2.04 227 50 55 5 504.93 1.46 228 50 56 6 504.92 1.45 229 50 69 19 486.12 0.48 230 50 72 22 472.54 3.00 231 50 73 23 471.94 3.15 232 50 131 81 206.62 2.00 233 50 132 82 205.55 1.52 234 50 133 83 206.27 1.92 235 51 56 5 547.79 4.62 236 51 68 17 486.23 0.45 237 51 70 19 486.11 0.48 238 51 73 22 479.45 0.25 239 52 55 3 583.63 1.55 240 52 56 4 562.00 0.95 241 52 73 21 479.48 0.27 242 52 133 81 205.52 1.45 243 53 56 3 578.29 0.70 244 53 57 4 558.93 0.58 245 54 57 3 572.87 1.29 246 54 58 4 559.49 0.53 247 54 74 20 479.93 0.48 248 54 133 79 205.49 1.48 249 55 58 3 573.00 1.14 250 55 59 4 566.69 1.45 251 55 131 76 206.59 2.02 252 55 133 78 205.45 1.52 253 56 59 3 576.15 3.77 254 56 60 4 566.70 1.45 255 56 68 12 486.31 0.48 256 57 60 3 578.37 0.60 257 57 61 4 566.71 1.43 258 58 61 3 583.72 7.05 259 58 62 4 566.69 1.44 260 58 131 73 206.57 2.07 261 59 62 3 579.43 1.29 262 59 63 4 566.70 1.44 263 59 64 5 520.21 8.50 264 59 66 7 486.35 0.48 265 59 131 72 206.53 2.07 266 60 63 3 574.24 3.88 267 60 64 4 562.08 0.82 268 62 131 69 207.00 2.31 269 64 129 65 207.25 2.35 270 64 131 67 207.09 2.35 271 69 72 3 585.66 0.58 272 69 120 51 214.77 5.90 273 70 73 3 578.03 0.58 274 70 116 46 223.61 10.10 275 71 116 45 223.34 10.01 276 71 117 46 223.28 10.04 277 71 120 49 215.06 6.04 278 72 120 48 214.77 5.90 279 72 130 58 206.76 2.02 280 72 132 60 205.83 1.65 281 72 133 61 205.83 1.65 282 72 136 64 178.80 14.01 283 73 113 40 223.93 10.17 284 73 116 43 223.67 10.06 285 73 133 60 205.42 1.41 286 73 136 63 179.25 13.77 287 74 113 39 224.05 10.21 288 74 116 42 223.79 10.10 289 74 133 59 204.65 1.02 290 74 134 60 204.70 1.04 291 74 135 61 204.50 1.10 292 74 136 62 190.48 7.97 293 75 108 33 246.40 5.21 294 75 109 34 246.39 5.21 295 75 110 35 246.04 5.07 296 75 113 38 224.05 10.21 297 75 116 41 223.87 10.13 298 76 81 5 548.48 2.02 299 76 104 28 246.93 5.35 300 76 106 30 246.70 5.24 301 76 107 31 246.49 5.24 302 76 108 32 246.40 5.21 303 77 80 3 562.84 1.36 304 77 81 4 548.48 2.02 305 77 96 19 254.55 1.88 306 77 102 25 247.09 5.42 307 77 104 27 246.93 5.35 308 77 107 30 246.49 5.24 309 78 81 3 580.27 2.60 310 78 105 27 247.06 5.41 311 78 106 28 246.63 5.24 312 78 107 29 246.49 5.25 313 79 105 26 247.06 5.41 314 80 83 3 548.41 4.34 315 80 88 8 271.61 1.48 316 80 92 12 270.01 1.25 317 80 102 22 247.63 5.21 318 80 104 24 247.06 5.41 319 80 105 25 247.06 5.41 320 83 88 5 381.70 5.67 321 84 87 3 582.49 3.71 322 84 88 4 536.22 0.38 323 85 88 3 559.37 0.99 324 85 93 8 317.31 10.12 325 85 96 11 305.95 5.46 326 85 97 12 286.25 15.30 327 88 92 4 569.95 3.68 328 88 93 5 540.19 7.35 329 88 96 8 532.71 11.09 330 89 92 3 579.63 2.35 331 89 93 4 569.95 3.68 332 90 93 3 573.46 5.43 333 90 94 4 550.80 2.09 334 91 94 3 570.57 2.02 335 91 95 4 557.85 5.52 336 92 95 3 572.23 2.36 337 92 96 4 557.83 5.53 338 92 102 10 247.66 5.19 339 92 105 13 247.64 5.17 340 93 96 3 568.85 0.03 341 93 97 4 557.85 5.53 342 94 97 3 571.05 1.53 343 94 98 4 550.83 2.02 344 95 98 3 576.95 1.42 345 95 99 4 550.69 1.96 346 95 100 5 521.60 0.08 347 95 101 6 424.65 6.21 348 95 102 7 247.69 5.17 349 96 99 3 553.18 0.70 350 96 102 6 262.24 2.10 351 96 138 42 202.41 0.14 352 97 138 41 202.44 0.15 353 98 142 44 149.19 1.26 354 99 110 11 247.17 4.91 355 99 113 14 247.18 4.90 356 99 114 15 246.95 4.81 357 99 135 36 204.43 0.83 358 99 138 39 198.56 1.79 359 99 139 40 193.00 4.56 360 99 142 43 148.94 1.23 361 100 110 10 247.18 4.91 362 102 109 7 248.00 4.86 363 102 110 8 247.63 4.69 364 103 107 4 558.25 2.81 365 103 108 5 305.94 33.74 366 103 109 6 247.69 4.65 367 104 107 3 566.60 4.29 368 104 108 4 560.93 1.47 369 108 113 5 544.27 4.27 370 108 116 8 532.03 4.35 371 109 112 3 577.61 1.01 372 109 113 4 561.74 0.40 373 110 113 3 577.61 1.01 374 110 114 4 564.24 0.85 375 111 114 3 570.78 2.42 376 111 115 4 570.78 2.42 377 112 115 3 573.90 1.02 378 112 116 4 570.78 2.42 379 113 116 3 575.35 0.29 380 113 117 4 570.77 2.42 381 113 135 22 204.57 1.11 382 113 136 23 186.88 9.90 383 113 139 26 148.79 1.28 384 114 117 3 573.00 1.31 385 114 118 4 563.40 1.26 386 114 139 25 148.30 1.04 387 115 118 3 575.21 2.41 388 115 119 4 560.72 0.08 389 116 119 3 576.68 1.16 390 116 120 4 560.51 0.21 391 117 120 3 583.96 2.48 392 117 121 4 569.03 1.58 393 117 136 19 179.22 13.79 394 117 140 23 143.92 0.24 395 118 121 3 584.72 4.38 396 118 122 4 566.35 2.93 397 118 139 21 178.31 14.10 398 118 140 22 174.93 15.52 399 118 143 25 124.66 0.12 400 118 160 42 48.31 0.07 401 119 122 3 582.85 5.32 402 119 123 4 582.85 5.32 403 120 123 3 582.85 5.32 404 120 124 4 582.85 5.32 405 120 130 10 207.16 2.22 406 121 124 3 584.71 4.32 407 121 130 9 207.27 2.27 408 121 140 19 173.35 16.68 409 121 160 39 48.25 0.05 410 122 160 38 48.51 0.07 411 124 130 6 305.58 32.38 412 132 136 4 565.59 4.60 413 132 137 5 559.19 2.06 414 133 136 3 571.70 1.79 415 133 137 4 565.63 4.58 416 134 137 3 577.20 1.20 417 134 138 4 565.68 4.62 418 135 138 3 582.11 3.60 419 135 139 4 565.69 4.62 420 136 139 3 587.67 0.81 421 136 140 4 565.69 4.61 422 137 140 3 575.43 2.23 423 137 141 4 565.75 4.57 424 137 150 13 83.02 1.36 425 137 156 19 55.47 0.18 426 138 141 3 572.93 0.97 427 138 142 4 565.75 4.56 428 138 148 10 83.11 1.35 429 138 149 11 83.11 1.35 430 139 142 3 574.12 1.57 431 139 143 4 567.75 5.56 432 140 143 3 574.94 1.98 433 140 144 4 569.10 4.89 434 140 158 18 54.15 0.07 435 140 160 20 52.61 0.10 436 141 144 3 567.00 5.94 437 141 145 4 565.74 6.57 438 141 146 5 518.38 3.15 439 141 147 6 345.61 46.39 440 141 148 7 83.45 1.18 441 141 150 9 83.42 1.17 442 141 156 15 55.44 0.17 443 141 158 17 54.61 0.07 444 141 164 23 43.36 1.02 445 141 167 26 38.84 0.20 446 142 145 3 573.99 2.44 447 142 146 4 531.33 1.15 448 143 160 17 53.62 0.07 449 144 158 14 54.34 0.01 450 144 160 16 53.61 0.07 451 144 161 17 52.47 0.13 452 144 162 18 50.84 0.78 453 144 163 19 50.16 0.46 454 144 164 20 50.06 0.49 455 146 164 18 51.01 0.68 456 146 167 21 49.94 0.54 457 147 167 20 46.96 0.78 458 150 154 4 536.45 0.35 459 150 156 6 75.14 0.10 460 150 167 17 38.96 0.30 461 151 154 3 565.45 0.92 462 154 168 14 37.02 0.64 463 154 169 15 36.91 0.64 464 155 167 12 37.12 0.58 465 155 168 13 36.94 0.64 466 156 164 8 38.86 0.21 467 156 166 10 37.13 0.58 468 156 167 11 36.97 0.64 469 157 164 7 38.72 0.24 470 157 165 8 37.15 0.58 471 157 166 9 37.09 0.58 472 158 163 5 301.83 3.60 473 158 164 6 37.12 0.58 474 158 165 7 37.12 0.58 475 159 162 3 603.91 1.30 476 159 163 4 530.56 2.79 477 159 165 6 37.11 0.57 478 164 167 3 704.06 6.15