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 48 479.89 0.03 2 13 87 74 386.76 1.11 3 13 129 116 101.35 0.93 4 14 37 23 576.63 2.18 5 14 38 24 576.55 2.20 6 14 39 25 576.55 2.19 7 14 60 46 509.25 0.89 8 15 39 24 576.55 2.19 9 15 41 26 576.35 2.17 10 15 59 44 509.30 0.90 11 15 60 45 509.28 0.90 12 15 61 46 509.28 0.90 13 16 33 17 576.70 2.18 14 16 38 22 576.68 2.17 15 16 39 23 576.62 2.19 16 16 40 24 576.55 2.19 17 16 41 25 576.51 2.20 18 16 42 26 576.51 2.20 19 16 61 45 509.27 0.90 20 16 63 47 509.25 0.90 21 17 41 24 576.58 2.21 22 17 42 25 576.36 2.17 23 17 43 26 576.36 2.17 24 17 44 27 576.35 2.17 25 17 50 33 509.56 0.92 26 17 53 36 509.58 0.90 27 17 54 37 509.49 0.94 28 17 59 42 509.37 0.89 29 17 61 44 509.32 0.90 30 17 62 45 509.27 0.90 31 17 63 46 509.26 0.90 32 18 42 24 576.58 2.21 33 18 43 25 576.45 2.21 34 18 44 26 576.35 2.17 35 18 63 45 509.27 0.90 36 19 44 25 576.35 2.17 37 19 50 31 509.75 0.90 38 19 63 44 509.32 0.90 39 19 64 45 509.19 0.88 40 19 65 46 509.20 0.88 41 19 68 49 490.88 3.29 42 20 25 5 593.39 3.08 43 20 26 6 577.45 2.03 44 20 44 24 576.54 2.20 45 20 45 25 576.34 2.16 46 20 65 45 509.22 0.87 47 20 68 48 491.84 2.81 48 20 91 71 418.53 0.64 49 21 26 5 593.49 3.05 50 21 45 24 576.48 2.23 51 22 25 3 641.51 0.60 52 22 26 4 610.10 1.92 53 23 26 3 630.29 5.01 54 23 27 4 617.88 1.97 55 24 27 3 625.75 1.33 56 24 28 4 618.98 3.08 57 25 28 3 626.09 1.50 58 25 29 4 618.99 3.09 59 25 91 66 418.49 0.62 60 25 114 89 322.64 1.10 61 25 116 91 309.98 0.24 62 26 29 3 634.98 0.57 63 26 30 4 624.97 3.99 64 26 43 17 576.69 2.19 65 27 30 3 634.79 0.66 66 27 31 4 627.49 2.73 67 28 31 3 645.79 1.43 68 28 32 4 627.49 2.73 69 29 32 3 637.94 2.50 70 29 33 4 627.81 2.89 71 29 63 34 509.31 0.89 72 29 91 62 418.41 0.62 73 29 116 87 294.44 1.87 74 29 121 92 263.86 0.03 75 30 33 3 634.84 0.63 76 30 34 4 627.81 2.89 77 30 40 10 576.91 2.17 78 30 43 13 576.74 2.19 79 31 34 3 630.33 1.64 80 31 35 4 627.81 2.90 81 32 35 3 634.89 0.65 82 32 36 4 627.77 2.91 83 32 116 84 272.79 3.62 84 32 117 85 264.11 0.12 85 32 118 86 263.88 0.03 86 32 121 89 263.86 0.03 87 33 36 3 638.07 0.94 88 33 37 4 619.23 7.17 89 33 38 5 579.73 0.89 90 33 40 7 577.35 2.06 91 33 63 30 509.30 0.89 92 33 121 88 263.85 0.03 93 33 125 92 263.51 0.07 94 34 37 3 634.86 0.67 95 34 38 4 585.06 0.54 96 34 40 6 577.07 2.21 97 36 118 82 263.88 0.03 98 36 122 86 263.80 0.01 99 38 61 23 509.31 0.89 100 38 125 87 263.31 0.12 101 40 43 3 703.05 0.54 102 41 59 18 509.29 0.90 103 44 49 5 509.78 0.91 104 44 50 6 509.74 0.91 105 44 53 9 509.73 0.91 106 45 69 24 472.52 0.73 107 46 49 3 643.36 0.28 108 46 50 4 614.07 4.21 109 46 68 22 495.68 0.92 110 46 69 23 472.51 0.73 111 46 70 24 472.00 0.56 112 47 50 3 629.49 6.66 113 47 51 4 619.22 1.64 114 47 68 21 497.94 0.21 115 47 69 22 495.66 0.91 116 47 71 24 455.18 0.74 117 47 76 29 424.30 1.68 118 48 51 3 642.38 4.20 119 48 52 4 617.69 2.40 120 48 70 22 470.35 1.24 121 48 71 23 459.55 1.44 122 49 52 3 628.79 2.58 123 49 53 4 617.65 2.39 124 50 53 3 629.62 2.16 125 50 54 4 623.03 0.31 126 50 80 30 424.27 1.67 127 51 54 3 632.55 3.62 128 51 55 4 631.64 4.08 129 51 71 20 462.07 1.67 130 51 76 25 424.31 1.69 131 51 79 28 424.29 1.68 132 51 80 29 424.27 1.67 133 52 55 3 638.91 1.93 134 52 56 4 619.54 1.97 135 53 56 3 642.38 1.04 136 53 57 4 609.85 2.87 137 54 57 3 640.36 2.06 138 54 58 4 593.72 4.90 139 54 59 5 580.91 0.78 140 54 62 8 509.56 0.84 141 54 80 26 424.25 1.69 142 54 85 31 423.80 1.87 143 55 58 3 639.17 1.46 144 55 79 24 424.31 1.69 145 55 83 28 423.97 1.82 146 55 85 30 423.80 1.87 147 58 85 27 423.79 1.88 148 59 62 3 676.88 0.35 149 59 86 27 423.70 1.92 150 60 86 26 423.69 1.92 151 60 87 27 423.68 1.92 152 61 86 25 423.69 1.92 153 61 87 26 423.66 1.91 154 61 89 28 423.60 1.88 155 61 125 64 263.31 0.15 156 62 80 18 424.29 1.75 157 62 86 24 423.78 1.88 158 62 87 25 423.67 1.88 159 62 88 26 421.35 0.76 160 62 89 27 419.80 0.01 161 63 89 26 418.99 0.42 162 63 91 28 418.82 0.42 163 63 121 58 263.75 0.09 164 63 125 62 263.38 0.14 165 64 89 25 419.03 0.45 166 64 90 26 418.79 0.44 167 64 91 27 418.78 0.45 168 65 68 3 661.82 11.34 169 65 73 8 424.72 1.75 170 65 90 25 418.89 0.49 171 65 91 26 418.61 0.54 172 65 114 49 324.66 0.34 173 66 73 7 424.77 1.77 174 66 74 8 424.76 1.77 175 66 90 24 418.78 0.58 176 66 91 25 418.69 0.58 177 66 92 26 418.58 0.55 178 66 96 30 377.92 2.11 179 66 99 33 348.76 8.39 180 66 100 34 333.12 0.61 181 67 72 5 441.25 5.73 182 67 96 29 405.66 1.23 183 67 99 32 350.94 7.32 184 68 71 3 665.55 0.46 185 68 72 4 441.21 5.74 186 68 73 5 441.19 5.74 187 71 75 4 611.97 0.86 188 71 76 5 594.08 0.12 189 71 79 8 593.73 0.05 190 72 75 3 627.09 2.92 191 72 76 4 614.69 0.51 192 73 76 3 625.38 0.61 193 73 77 4 610.53 2.60 194 74 77 3 612.40 1.68 195 74 78 4 612.40 1.69 196 74 99 25 333.11 0.68 197 74 100 26 333.05 0.66 198 74 103 29 332.74 0.74 199 74 109 35 332.44 0.67 200 75 78 3 634.44 8.46 201 75 79 4 618.08 1.33 202 76 79 3 624.19 0.03 203 76 80 4 623.70 1.47 204 77 80 3 623.71 1.48 205 77 81 4 616.45 0.49 206 77 88 11 419.11 0.49 207 77 90 13 418.94 0.51 208 77 109 32 332.04 0.56 209 78 81 3 623.70 1.47 210 78 82 4 614.47 0.52 211 78 103 25 332.63 0.71 212 78 106 28 332.47 0.71 213 78 109 31 332.39 0.68 214 79 82 3 622.04 2.30 215 79 83 4 622.05 2.29 216 80 83 3 624.47 1.98 217 80 84 4 622.05 2.29 218 80 85 5 600.71 3.92 219 80 88 8 423.32 1.64 220 81 84 3 622.68 2.88 221 81 88 7 423.34 1.64 222 81 106 25 332.41 0.69 223 81 107 26 332.19 0.64 224 81 108 27 332.04 0.56 225 81 109 28 332.01 0.56 226 82 106 24 332.41 0.69 227 84 106 22 332.47 0.72 228 84 107 23 332.19 0.64 229 84 132 48 256.04 0.53 230 84 135 51 249.61 0.29 231 84 139 55 223.41 3.48 232 85 132 47 254.32 0.98 233 86 132 46 253.94 1.17 234 87 128 41 258.44 0.14 235 87 129 42 258.12 0.16 236 87 132 45 253.55 1.00 237 88 108 20 332.01 0.56 238 88 109 21 331.78 0.54 239 88 110 22 331.78 0.54 240 88 128 40 260.05 0.77 241 89 110 21 331.77 0.54 242 89 112 23 330.86 0.27 243 89 124 35 263.37 0.15 244 89 125 36 263.38 0.15 245 89 128 39 260.95 0.93 246 90 100 10 332.70 0.81 247 90 109 19 331.87 0.53 248 90 110 20 331.81 0.54 249 90 111 21 331.64 0.51 250 90 112 22 331.28 0.34 251 91 112 21 330.87 0.26 252 91 114 23 324.58 0.38 253 91 116 25 322.70 1.06 254 92 96 4 600.63 7.45 255 92 97 5 362.42 1.57 256 92 111 19 331.82 0.55 257 92 112 20 331.74 0.56 258 92 113 21 331.03 0.34 259 92 114 22 326.80 1.27 260 93 96 3 621.95 2.10 261 93 97 4 611.75 1.91 262 93 114 21 330.27 0.16 263 94 97 3 642.15 2.10 264 94 113 19 331.72 0.56 265 96 99 3 641.09 1.50 266 97 100 3 636.09 1.01 267 97 101 4 626.39 2.38 268 97 111 14 332.11 0.55 269 98 101 3 631.32 0.08 270 98 102 4 624.37 1.37 271 99 102 3 634.50 1.51 272 99 103 4 634.50 1.51 273 100 103 3 631.15 3.19 274 100 104 4 623.08 7.22 275 100 109 9 332.52 0.69 276 100 110 10 332.30 0.61 277 100 111 11 332.10 0.54 278 101 104 3 637.62 0.04 279 101 111 10 332.39 0.68 280 103 106 3 643.32 2.98 281 103 109 6 332.56 0.69 282 104 107 3 628.59 3.20 283 104 109 5 332.56 0.68 284 104 131 27 261.56 0.73 285 104 152 48 101.88 5.75 286 105 152 47 101.88 5.75 287 107 135 28 251.14 0.15 288 107 152 45 101.54 5.92 289 108 131 23 257.98 0.21 290 108 132 24 257.84 0.16 291 108 135 27 250.78 0.33 292 109 131 22 258.42 0.14 293 110 127 17 263.33 0.17 294 110 128 18 263.29 0.18 295 110 131 21 258.85 0.05 296 112 116 4 644.12 3.29 297 112 120 8 264.20 0.14 298 112 121 9 264.04 0.18 299 112 124 12 263.70 0.11 300 113 116 3 683.35 1.23 301 116 120 4 575.35 20.50 302 117 120 3 619.73 1.68 303 117 121 4 624.94 5.12 304 118 121 3 626.80 4.19 305 118 122 4 624.94 5.12 306 119 123 4 637.01 0.93 307 120 123 3 647.20 0.33 308 120 124 4 628.24 1.40 309 121 124 3 634.95 1.96 310 121 125 4 621.26 1.22 311 122 125 3 627.38 1.82 312 122 126 4 621.28 1.23 313 123 126 3 623.85 0.05 314 123 127 4 621.28 1.24 315 124 127 3 621.64 1.06 316 124 128 4 621.64 1.06 317 125 128 3 621.66 1.06 318 125 129 4 621.65 1.06 319 126 129 3 621.66 1.07 320 126 130 4 621.40 1.21 321 126 171 45 82.52 0.81 322 126 175 49 82.51 0.81 323 127 130 3 621.68 1.07 324 127 131 4 621.69 1.08 325 127 170 43 82.63 0.78 326 127 171 44 82.53 0.80 327 128 131 3 639.93 1.22 328 128 132 4 621.45 1.23 329 129 132 3 621.38 1.27 330 129 133 4 615.97 3.98 331 130 133 3 621.35 1.29 332 130 134 4 615.97 3.98 333 130 171 41 82.53 0.80 334 130 174 44 82.52 0.81 335 131 134 3 615.92 4.01 336 131 135 4 615.91 4.01 337 131 170 39 82.83 0.77 338 132 135 3 627.69 4.46 339 132 136 4 615.93 4.00 340 133 136 3 614.39 0.20 341 133 137 4 611.25 1.66 342 133 174 41 82.53 0.81 343 134 137 3 628.63 4.20 344 134 138 4 611.25 1.66 345 134 155 21 101.05 5.88 346 134 156 22 100.97 5.91 347 134 159 25 96.62 6.90 348 134 174 40 82.53 0.81 349 135 138 3 613.64 3.30 350 135 139 4 610.78 1.89 351 135 152 17 101.48 5.88 352 136 139 3 615.53 4.25 353 136 140 4 609.48 1.23 354 137 140 3 632.07 3.00 355 137 141 4 604.46 3.75 356 137 174 37 82.72 0.82 357 137 178 41 82.09 0.96 358 137 188 51 64.74 0.46 359 138 141 3 633.13 2.46 360 138 142 4 558.73 19.07 361 138 148 10 101.83 5.84 362 138 151 13 101.73 5.84 363 138 152 14 101.61 5.89 364 138 155 17 101.59 5.88 365 138 188 50 64.77 0.45 366 139 148 9 101.84 5.83 367 142 147 5 606.28 2.19 368 142 148 6 283.83 36.97 369 142 151 9 113.12 0.21 370 143 147 4 620.92 2.27 371 143 148 5 611.39 0.24 372 144 147 3 630.85 7.23 373 144 148 4 618.66 3.39 374 145 148 3 621.56 2.59 375 145 149 4 620.90 2.27 376 146 149 3 624.76 0.98 377 146 150 4 621.57 2.58 378 147 150 3 631.70 0.46 379 147 151 4 617.00 0.48 380 148 151 3 617.61 0.76 381 148 152 4 617.01 0.48 382 149 152 3 635.57 0.16 383 149 153 4 618.12 0.08 384 150 153 3 620.45 0.36 385 150 154 4 614.98 1.65 386 151 154 3 622.90 2.46 387 151 155 4 609.23 1.24 388 151 189 38 64.73 0.45 389 152 155 3 622.16 1.22 390 152 156 4 609.63 1.45 391 153 156 3 620.54 2.02 392 153 157 4 617.85 0.69 393 154 157 3 621.27 1.02 394 154 158 4 617.85 0.69 395 154 189 35 64.83 0.44 396 154 192 38 64.22 0.21 397 154 193 39 64.21 0.21 398 154 196 42 58.30 1.62 399 155 158 3 624.25 0.50 400 155 159 4 617.32 0.42 401 155 174 19 94.67 4.95 402 155 177 22 88.23 1.79 403 155 188 33 64.81 0.45 404 155 192 37 63.79 0.41 405 156 159 3 624.26 0.51 406 156 160 4 615.74 4.77 407 157 160 3 621.36 1.97 408 157 161 4 616.76 4.26 409 157 196 39 58.29 1.64 410 158 161 3 624.73 0.28 411 158 162 4 621.36 1.96 412 158 177 19 95.03 4.75 413 158 192 34 64.22 0.20 414 158 195 37 58.30 1.65 415 158 196 38 58.27 1.64 416 159 162 3 642.27 1.71 417 159 163 4 614.81 1.31 418 159 170 11 116.60 1.57 419 159 173 14 95.06 4.76 420 159 174 15 95.17 4.71 421 159 177 18 95.05 4.76 422 160 163 3 615.25 1.54 423 160 164 4 609.01 1.54 424 161 164 3 618.96 0.07 425 161 165 4 607.82 2.08 426 161 195 34 58.86 1.37 427 161 196 35 58.30 1.65 428 161 199 38 33.69 0.78 429 161 200 39 31.92 1.01 430 162 166 4 313.54 60.88 431 162 167 5 170.47 4.67 432 162 168 6 120.75 0.29 433 162 173 11 116.31 1.43 434 162 176 14 111.90 3.64 435 162 177 15 111.90 3.64 436 162 195 33 58.30 1.65 437 162 199 37 33.69 0.78 438 163 167 4 130.66 0.97 439 163 168 5 120.75 0.29 440 163 169 6 120.75 0.30 441 163 170 7 120.75 0.30 442 163 173 10 116.86 1.65 443 165 199 34 34.82 0.21 444 166 199 33 35.16 0.12 445 168 172 4 601.78 5.78 446 168 173 5 386.11 24.37 447 168 176 8 320.85 57.02 448 169 172 3 615.98 2.43 449 169 173 4 612.22 0.56 450 170 173 3 615.33 2.10 451 170 174 4 610.76 0.17 452 171 174 3 624.64 6.77 453 171 175 4 612.78 1.18 454 172 175 3 616.37 0.60 455 172 176 4 616.37 0.61 456 173 176 3 621.04 1.73 457 173 177 4 616.39 0.60 458 174 177 3 617.29 1.05 459 174 178 4 616.40 0.60 460 174 188 14 102.12 6.33 461 175 178 3 617.28 0.17 462 175 179 4 616.40 0.60 463 176 179 3 617.58 1.18 464 176 180 4 614.95 1.33 465 176 184 8 512.71 39.12 466 176 191 15 96.27 3.55 467 176 195 19 96.22 3.57 468 177 180 3 616.15 1.89 469 177 181 4 614.99 1.31 470 177 188 11 102.09 6.35 471 177 191 14 96.22 3.56 472 178 181 3 625.24 1.69 473 178 182 4 614.97 1.31 474 178 188 10 102.15 6.35 475 179 182 3 617.66 0.01 476 179 183 4 614.88 1.28 477 180 183 3 616.47 2.06 478 180 184 4 613.00 2.22 479 180 191 11 96.28 3.56 480 181 184 3 619.67 0.12 481 181 185 4 556.66 17.12 482 181 186 5 277.52 34.91 483 181 187 6 130.78 2.14 484 181 188 7 127.41 2.92 485 181 191 10 96.33 3.54 486 182 185 3 604.06 6.57 487 184 191 7 268.44 40.87 488 186 190 4 613.43 3.41 489 186 191 5 598.18 11.02 490 187 190 3 625.69 2.43 491 187 191 4 623.87 1.82 492 188 191 3 625.28 1.11 493 188 192 4 623.87 1.82 494 189 192 3 623.88 1.82 495 189 193 4 623.84 1.83 496 190 193 3 623.83 1.84 497 190 194 4 623.82 1.85 498 191 194 3 624.26 1.61 499 191 195 4 623.77 1.85 500 192 195 3 623.12 1.05 501 192 196 4 606.53 6.78 502 193 196 3 630.02 4.50 503 193 197 4 612.73 2.56 504 194 197 3 628.55 5.23 505 194 198 4 605.34 6.26 506 195 198 3 629.74 4.64 507 195 199 4 590.16 1.05 508 196 199 3 629.80 4.61 509 196 200 4 279.38 47.62