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 13 61 48 488.17 2.64 2 13 87 74 389.54 2.18 3 13 129 116 128.40 2.65 4 14 37 23 582.97 0.76 5 14 38 24 582.90 0.80 6 14 39 25 582.90 0.80 7 14 60 46 516.97 1.70 8 15 39 24 582.91 0.80 9 15 41 26 582.80 0.84 10 15 57 42 517.15 1.68 11 15 58 43 517.13 1.69 12 15 59 44 517.00 1.70 13 15 60 45 517.00 1.70 14 15 61 46 516.99 1.70 15 16 39 23 583.00 0.77 16 16 40 24 582.92 0.81 17 16 41 25 582.88 0.81 18 16 42 26 582.88 0.81 19 16 59 43 517.08 1.69 20 16 61 45 516.99 1.70 21 17 41 24 582.97 0.78 22 17 42 25 582.81 0.84 23 17 43 26 582.79 0.84 24 17 50 33 517.27 1.73 25 17 53 36 517.24 1.69 26 17 54 37 517.16 1.68 27 17 59 42 517.12 1.68 28 17 61 44 517.04 1.70 29 17 62 45 516.99 1.71 30 17 63 46 516.98 1.71 31 18 26 8 583.57 0.83 32 18 29 11 583.45 0.80 33 18 30 12 583.45 0.81 34 18 33 15 583.44 0.80 35 18 40 22 583.03 0.77 36 18 42 24 582.90 0.81 37 18 43 25 582.77 0.83 38 18 44 26 582.77 0.83 39 18 63 45 516.99 1.71 40 19 44 25 582.77 0.83 41 19 50 31 517.49 1.69 42 19 63 44 517.04 1.70 43 19 64 45 516.95 1.71 44 19 65 46 516.96 1.71 45 19 68 49 488.67 0.01 46 20 25 5 616.75 3.81 47 20 26 6 583.86 0.96 48 20 44 24 582.85 0.80 49 20 45 25 582.77 0.83 50 20 65 45 516.97 1.71 51 20 68 48 492.65 1.99 52 20 91 71 428.95 0.88 53 21 26 5 616.81 3.83 54 21 45 24 582.84 0.80 55 22 25 3 644.38 2.83 56 22 26 4 629.73 0.31 57 23 26 3 640.95 1.74 58 23 27 4 629.74 0.31 59 24 27 3 641.12 1.82 60 24 28 4 629.73 0.32 61 25 28 3 644.36 0.20 62 25 29 4 616.86 3.81 63 25 91 66 428.95 0.91 64 25 114 89 333.13 0.83 65 25 116 91 321.31 2.19 66 26 29 3 644.36 0.20 67 26 30 4 621.84 4.67 68 26 43 17 583.06 0.77 69 27 30 3 635.71 4.52 70 27 31 4 617.80 3.76 71 28 31 3 640.26 1.76 72 28 32 4 626.45 0.56 73 29 32 3 639.89 0.95 74 29 33 4 627.91 0.17 75 29 63 34 517.02 1.71 76 29 91 62 428.87 0.89 77 29 116 87 305.44 5.82 78 29 121 92 274.19 1.42 79 30 33 3 640.75 0.52 80 30 34 4 624.89 1.33 81 30 40 10 583.20 0.77 82 30 43 13 583.10 0.76 83 31 34 3 639.61 1.08 84 31 35 4 623.86 1.06 85 32 35 3 649.38 2.25 86 32 36 4 635.44 4.71 87 32 116 84 294.42 11.33 88 32 117 85 274.40 1.35 89 32 118 86 274.19 1.42 90 32 121 89 274.15 1.44 91 33 36 3 640.62 2.12 92 33 37 4 635.42 4.72 93 33 38 5 597.75 5.34 94 33 40 7 585.92 0.58 95 33 63 30 517.00 1.70 96 33 121 88 274.10 1.42 97 33 125 92 273.70 1.48 98 34 37 3 623.62 1.88 99 34 38 4 617.72 2.22 100 34 40 6 585.92 0.58 101 36 122 86 274.00 1.38 102 38 61 23 517.02 1.70 103 38 125 87 273.50 1.42 104 40 43 3 718.66 0.36 105 41 57 16 517.15 1.68 106 41 59 18 517.02 1.70 107 42 53 11 517.24 1.69 108 44 49 5 554.24 16.68 109 44 50 6 517.50 1.69 110 44 53 9 517.46 1.67 111 45 68 23 503.37 3.04 112 45 69 24 488.66 0.01 113 46 49 3 637.77 3.15 114 46 50 4 630.68 2.91 115 46 68 22 493.03 2.15 116 46 69 23 488.66 0.01 117 46 70 24 486.66 1.01 118 47 50 3 634.03 4.58 119 47 51 4 630.69 2.90 120 47 68 21 493.03 2.15 121 47 69 22 493.01 2.15 122 47 71 24 450.66 1.08 123 47 76 29 429.81 0.80 124 48 51 3 634.53 0.97 125 48 52 4 630.69 2.90 126 48 71 23 450.66 1.08 127 49 52 3 634.94 0.76 128 49 53 4 630.66 2.90 129 50 53 3 640.67 0.24 130 50 54 4 625.02 2.80 131 50 80 30 429.74 0.79 132 51 54 3 638.86 1.16 133 51 55 4 625.03 2.81 134 51 71 20 472.12 1.08 135 51 76 25 429.81 0.80 136 51 79 28 429.76 0.80 137 51 80 29 429.74 0.79 138 52 55 3 644.51 1.67 139 52 56 4 615.08 7.77 140 53 56 3 636.65 3.02 141 53 57 4 608.47 0.26 142 54 58 4 596.66 1.88 143 54 59 5 553.42 19.75 144 54 62 8 517.11 1.68 145 54 80 26 429.69 0.80 146 54 85 31 429.22 0.86 147 55 58 3 640.83 0.93 148 55 83 28 429.38 0.83 149 55 85 30 429.20 0.87 150 58 85 27 429.21 0.87 151 59 62 3 689.13 3.43 152 59 85 26 429.20 0.87 153 59 86 27 429.13 0.84 154 60 86 26 429.11 0.83 155 60 87 27 429.11 0.83 156 61 86 25 429.12 0.84 157 61 87 26 429.09 0.84 158 61 89 28 429.06 0.84 159 61 125 64 273.69 1.47 160 62 80 18 429.62 0.83 161 62 86 24 429.23 0.86 162 62 87 25 429.13 0.85 163 62 88 26 429.06 0.85 164 62 89 27 429.05 0.84 165 63 89 26 429.05 0.84 166 63 91 28 428.88 0.89 167 63 121 58 274.14 1.44 168 63 125 62 273.91 1.38 169 64 89 25 429.12 0.85 170 64 90 26 428.92 0.89 171 64 91 27 428.88 0.90 172 65 68 3 655.91 0.05 173 65 73 8 430.05 0.73 174 65 90 25 429.09 0.85 175 65 91 26 428.89 0.89 176 65 114 49 334.78 0.60 177 66 73 7 430.19 0.74 178 66 74 8 430.05 0.73 179 66 90 24 429.11 0.85 180 66 91 25 429.09 0.85 181 66 92 26 429.05 0.85 182 66 96 30 382.55 5.48 183 66 99 33 349.49 6.67 184 66 100 34 337.41 0.64 185 67 96 29 414.98 1.70 186 67 99 32 349.85 6.82 187 68 71 3 654.70 0.52 188 68 72 4 430.91 0.53 189 68 73 5 430.36 0.78 190 71 75 4 623.12 0.72 191 71 76 5 601.06 2.11 192 71 79 8 596.32 4.03 193 72 75 3 635.77 0.55 194 72 76 4 621.81 0.08 195 73 76 3 637.72 0.42 196 73 77 4 616.12 2.92 197 74 77 3 635.60 1.51 198 74 78 4 616.16 2.91 199 74 90 16 429.29 0.83 200 74 99 25 337.62 0.72 201 74 100 26 337.41 0.64 202 74 103 29 336.49 0.95 203 74 109 35 336.39 0.94 204 75 78 3 633.56 2.56 205 75 79 4 622.18 5.88 206 76 79 3 635.24 0.64 207 76 80 4 624.52 4.71 208 77 80 3 635.21 0.62 209 77 81 4 624.53 4.73 210 77 88 11 429.30 0.83 211 77 90 13 429.25 0.84 212 77 109 32 336.25 0.97 213 78 81 3 635.23 0.61 214 78 82 4 630.59 1.70 215 78 106 28 336.33 0.96 216 78 109 31 336.33 0.94 217 79 82 3 635.23 0.61 218 79 83 4 635.15 0.59 219 80 83 3 635.47 0.74 220 80 84 4 635.15 0.58 221 80 85 5 601.12 1.94 222 80 88 8 429.30 0.83 223 81 84 3 640.81 0.35 224 81 88 7 429.30 0.83 225 81 107 26 336.25 0.97 226 81 108 27 336.25 0.97 227 81 109 28 336.25 0.96 228 84 107 23 336.25 0.97 229 84 132 48 261.14 1.44 230 84 135 51 248.02 1.92 231 84 139 55 212.74 5.61 232 85 132 47 258.77 0.26 233 86 132 46 258.72 0.26 234 87 128 41 269.31 0.74 235 87 129 42 268.01 1.24 236 87 132 45 258.67 0.28 237 88 109 21 335.90 0.96 238 88 110 22 335.89 0.96 239 88 128 40 270.17 1.16 240 89 110 21 335.83 0.96 241 89 112 23 335.70 0.96 242 89 124 35 274.00 1.37 243 89 125 36 273.94 1.36 244 89 128 39 270.87 1.49 245 90 100 10 337.23 0.63 246 90 109 19 336.25 0.97 247 90 110 20 335.94 0.93 248 90 111 21 335.81 0.95 249 90 112 22 335.75 0.98 250 91 112 21 335.69 0.96 251 91 114 23 334.24 0.34 252 91 116 25 332.41 1.19 253 92 96 4 613.81 1.33 254 92 97 5 484.56 60.16 255 92 111 19 336.03 0.97 256 92 112 20 335.94 0.93 257 92 113 21 335.67 0.96 258 92 114 22 335.57 0.98 259 93 96 3 640.38 3.26 260 93 97 4 615.32 2.09 261 93 114 21 335.62 0.94 262 94 97 3 635.88 5.51 263 94 113 19 335.94 0.93 264 96 99 3 650.09 2.43 265 97 100 3 641.95 2.52 266 97 101 4 626.82 0.14 267 97 111 14 336.23 1.02 268 98 101 3 633.47 3.46 269 98 102 4 624.12 1.21 270 99 102 3 634.45 1.16 271 99 103 4 624.13 1.21 272 100 103 3 622.65 4.26 273 100 104 4 620.33 3.10 274 100 109 9 336.45 0.97 275 100 111 11 336.25 0.99 276 101 111 10 336.43 0.98 277 102 105 3 666.07 0.15 278 103 106 3 656.88 2.40 279 103 109 6 352.69 7.08 280 104 107 3 624.85 5.94 281 104 108 4 616.03 5.78 282 104 109 5 336.57 0.98 283 104 131 27 273.35 1.41 284 104 152 48 112.20 1.75 285 108 131 23 268.19 1.29 286 108 132 24 267.90 1.27 287 108 135 27 258.67 0.27 288 109 131 22 268.19 1.29 289 110 124 14 274.16 1.44 290 110 127 17 273.91 1.37 291 110 128 18 273.44 1.39 292 110 131 21 269.66 0.85 293 112 116 4 654.74 1.29 294 112 120 8 274.53 1.43 295 112 121 9 274.48 1.40 296 112 124 12 274.21 1.43 297 113 116 3 688.91 1.15 298 116 120 4 609.75 3.47 299 117 120 3 635.73 3.01 300 117 121 4 627.66 1.02 301 118 121 3 634.62 1.69 302 118 122 4 627.67 1.02 303 119 123 4 647.52 3.61 304 120 123 3 655.28 0.28 305 120 124 4 639.25 0.06 306 121 124 3 647.10 3.82 307 121 125 4 633.49 2.82 308 122 125 3 647.06 3.84 309 122 126 4 639.25 0.06 310 123 126 3 637.17 0.53 311 123 127 4 629.07 0.61 312 124 127 3 637.17 0.52 313 124 128 4 624.96 2.67 314 125 128 3 638.17 0.63 315 125 129 4 624.63 2.83 316 126 129 3 643.94 3.52 317 126 130 4 627.48 1.41 318 126 171 45 86.53 0.97 319 127 130 3 632.20 2.35 320 127 131 4 627.47 1.40 321 127 170 43 86.57 0.99 322 127 171 44 86.53 0.97 323 128 131 3 650.24 1.87 324 128 132 4 623.16 1.04 325 129 132 3 628.59 0.66 326 129 133 4 626.56 0.68 327 130 133 3 647.25 2.15 328 130 134 4 623.07 1.01 329 130 171 41 86.56 0.99 330 130 174 44 86.53 0.97 331 131 134 3 628.64 0.16 332 131 135 4 617.57 1.74 333 131 170 39 86.72 0.97 334 132 135 3 635.44 0.67 335 132 136 4 618.06 1.50 336 133 136 3 644.15 3.69 337 133 137 4 618.05 1.50 338 133 174 41 86.57 0.98 339 134 137 3 648.48 1.53 340 134 138 4 618.43 1.30 341 134 152 18 110.92 1.45 342 134 155 21 109.88 1.30 343 134 156 22 109.77 1.35 344 134 159 25 109.17 1.09 345 134 174 40 86.58 0.98 346 135 138 3 648.48 1.53 347 135 139 4 618.42 1.29 348 135 152 17 110.91 1.46 349 136 139 3 633.21 6.11 350 136 140 4 618.41 1.29 351 137 140 3 636.11 0.52 352 137 141 4 615.54 0.29 353 137 174 37 86.83 0.95 354 137 178 41 86.47 1.03 355 137 188 51 72.30 1.57 356 138 141 3 638.56 3.43 357 138 142 4 613.77 0.59 358 138 148 10 115.03 0.23 359 138 151 13 111.24 1.49 360 138 152 14 111.00 1.42 361 138 155 17 110.94 1.45 362 138 188 50 72.30 1.57 363 139 148 9 120.33 2.31 364 141 187 46 72.30 1.57 365 141 188 47 72.31 1.57 366 142 147 5 614.33 1.85 367 142 148 6 321.98 60.83 368 142 151 9 128.41 1.74 369 143 147 4 632.46 3.56 370 143 148 5 627.22 2.21 371 144 147 3 642.62 1.83 372 144 148 4 627.23 2.21 373 145 148 3 631.72 1.28 374 145 149 4 627.23 2.21 375 146 149 3 645.26 2.83 376 146 150 4 627.24 2.19 377 147 150 3 643.22 4.11 378 147 151 4 621.64 0.58 379 148 151 3 631.63 4.42 380 148 152 4 625.87 1.56 381 149 152 3 646.73 8.47 382 149 153 4 629.94 3.60 383 150 153 3 629.94 3.60 384 150 154 4 629.94 3.60 385 151 154 3 634.57 5.91 386 151 155 4 625.85 1.55 387 151 189 38 72.30 1.57 388 152 155 3 629.48 0.26 389 152 156 4 625.83 1.55 390 153 156 3 620.43 1.10 391 153 157 4 617.59 2.53 392 154 157 3 630.05 0.01 393 154 158 4 630.06 0.01 394 154 189 35 72.33 1.57 395 154 192 38 69.66 0.34 396 154 193 39 69.31 0.51 397 154 196 42 61.77 0.64 398 155 158 3 638.09 1.91 399 155 159 4 623.25 3.43 400 155 174 19 87.50 0.96 401 155 177 22 87.41 0.99 402 155 188 33 72.33 1.57 403 155 192 37 69.58 0.29 404 156 159 3 641.77 0.07 405 156 160 4 623.27 3.42 406 157 160 3 641.77 0.07 407 157 161 4 629.28 6.18 408 157 196 39 61.77 0.64 409 158 161 3 638.40 1.62 410 158 162 4 638.40 1.62 411 158 177 19 88.31 0.59 412 158 192 34 69.16 0.51 413 158 195 37 61.80 0.64 414 158 196 38 61.77 0.64 415 159 162 3 631.71 1.73 416 159 163 4 613.03 1.95 417 159 170 11 97.22 0.19 418 159 173 14 88.38 0.60 419 159 174 15 88.38 0.60 420 159 177 18 88.36 0.60 421 160 163 3 626.56 1.82 422 160 164 4 613.04 1.94 423 161 164 3 636.57 3.76 424 161 165 4 607.22 2.12 425 161 195 34 62.65 0.21 426 161 196 35 61.78 0.64 427 161 199 38 41.74 1.43 428 161 200 39 39.56 0.64 429 162 166 4 606.97 2.01 430 162 167 5 392.35 105.30 431 162 168 6 126.68 2.04 432 162 173 11 92.13 2.37 433 162 176 14 88.67 0.65 434 162 177 15 88.67 0.65 435 162 195 33 61.81 0.63 436 162 199 37 41.73 1.43 437 163 167 4 150.18 1.24 438 163 168 5 126.61 2.08 439 163 169 6 126.60 2.08 440 163 170 7 125.59 1.62 441 163 173 10 101.88 5.56 442 165 199 34 41.73 1.43 443 166 199 33 40.22 0.67 444 169 172 3 628.32 0.97 445 169 173 4 612.61 1.81 446 170 173 3 627.41 1.05 447 170 174 4 624.77 2.69 448 171 174 3 631.45 0.64 449 171 175 4 623.22 3.48 450 172 175 3 628.72 0.74 451 172 176 4 623.22 3.48 452 173 176 3 633.72 1.76 453 173 177 4 629.11 0.56 454 174 177 3 635.51 1.58 455 174 178 4 629.11 0.56 456 174 188 14 99.50 12.02 457 175 178 3 631.28 0.53 458 175 179 4 626.25 1.99 459 176 179 3 640.27 0.80 460 176 180 4 631.90 4.98 461 176 191 15 90.95 10.17 462 176 195 19 63.14 0.12 463 177 180 3 639.18 1.34 464 177 181 4 618.24 1.88 465 177 188 11 99.51 12.01 466 177 191 14 69.81 0.39 467 178 181 3 636.42 2.73 468 178 182 4 618.24 1.88 469 178 188 10 99.53 12.03 470 179 182 3 635.70 2.37 471 179 183 4 620.87 0.57 472 180 183 3 624.49 2.37 473 180 184 4 618.21 1.89 474 180 191 11 92.08 9.63 475 181 184 3 636.50 2.73 476 181 185 4 613.88 0.26 477 181 186 5 194.00 7.52 478 181 187 6 151.33 8.15 479 181 188 7 130.22 2.41 480 181 191 10 100.61 5.36 481 182 185 3 613.88 0.26 482 186 190 4 621.47 0.35 483 186 191 5 614.48 2.02 484 187 190 3 622.00 0.08 485 187 191 4 619.65 0.56 486 188 191 3 622.13 0.15 487 188 192 4 619.64 0.55 488 189 192 3 626.31 1.21 489 189 193 4 619.89 0.68 490 190 193 3 638.14 4.71 491 190 194 4 624.99 1.86 492 191 194 3 627.27 0.72 493 191 195 4 624.50 1.62 494 192 195 3 628.22 4.53 495 192 196 4 619.18 4.29 496 193 196 3 629.26 4.00 497 193 197 4 616.35 2.87 498 194 197 3 620.64 3.55 499 194 198 4 616.29 2.90 500 195 198 3 629.98 5.25 501 195 199 4 604.38 6.51 502 196 199 3 631.38 4.70 503 196 200 4 204.38 2.48