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 9 127 119 48.62 0.56 2 10 127 118 49.78 0.38 3 10 128 119 49.59 0.29 4 11 125 115 49.80 0.37 5 11 127 117 49.79 0.37 6 12 23 11 49.80 0.38 7 12 128 117 49.83 0.39 8 12 129 118 49.81 0.39 9 13 21 8 49.91 0.35 10 13 23 10 49.81 0.38 11 13 24 11 49.83 0.39 12 13 124 112 49.84 0.38 13 13 131 119 49.83 0.39 14 14 21 7 245.16 66.34 15 15 20 5 615.98 2.10 16 15 21 6 245.16 66.34 17 16 19 3 814.94 2.44 18 16 20 4 616.61 1.80 19 20 25 5 786.41 2.11 20 21 24 3 821.95 5.92 21 21 25 4 811.69 0.80 22 22 25 3 837.86 2.04 23 22 26 4 811.67 0.79 24 23 26 3 811.69 0.80 25 23 27 4 811.66 0.79 26 23 131 109 343.38 1.73 27 24 27 3 811.67 0.80 28 24 28 4 811.65 0.79 29 24 124 101 343.46 1.74 30 24 131 108 343.51 1.71 31 24 154 132 340.78 1.14 32 25 28 3 813.33 3.45 33 25 29 4 801.93 5.62 34 26 29 3 827.70 8.12 35 26 30 4 810.75 0.35 36 27 30 3 817.77 3.16 37 27 31 4 810.76 0.35 38 27 131 105 344.90 1.65 39 27 132 106 344.91 1.65 40 27 133 107 344.89 1.65 41 27 153 128 344.81 1.69 42 28 31 3 819.18 3.87 43 28 32 4 812.45 3.64 44 28 153 127 344.83 1.68 45 29 32 3 812.56 3.58 46 29 33 4 811.59 4.07 47 30 33 3 825.80 3.04 48 30 34 4 804.92 0.23 49 31 34 3 814.72 4.67 50 31 79 48 345.06 1.68 51 31 80 49 345.10 1.70 52 31 133 103 345.12 1.70 53 31 134 104 345.05 1.68 54 31 135 105 345.04 1.67 55 31 153 124 345.10 1.70 56 31 166 137 330.80 3.03 57 32 166 136 330.80 3.02 58 32 167 137 330.76 3.02 59 32 169 139 330.11 2.74 60 33 167 136 330.80 3.03 61 34 80 46 345.53 1.72 62 34 166 134 331.14 3.05 63 34 167 135 330.99 3.04 64 35 51 16 376.82 0.58 65 35 53 18 375.93 1.11 66 35 66 31 374.62 1.65 67 35 79 44 348.98 2.71 68 35 166 133 331.19 3.04 69 36 50 14 376.85 0.57 70 36 79 43 361.04 1.46 71 36 165 131 331.56 3.19 72 36 166 132 331.19 3.04 73 36 167 133 331.17 3.04 74 36 168 134 331.16 3.04 75 36 200 166 254.33 0.05 76 37 49 12 377.16 0.54 77 37 50 13 376.83 0.57 78 37 77 40 374.37 1.77 79 37 78 41 371.70 1.19 80 37 79 42 367.19 0.93 81 37 164 129 331.68 3.15 82 37 165 130 331.67 3.15 83 38 48 10 377.21 0.52 84 38 49 11 377.19 0.56 85 38 137 100 374.37 1.78 86 38 163 127 331.88 3.09 87 38 164 128 331.69 3.14 88 38 193 157 256.14 0.21 89 38 196 160 255.97 0.21 90 38 197 161 255.86 0.09 91 39 47 8 380.43 1.71 92 39 48 9 377.18 0.54 93 39 137 99 374.53 1.73 94 39 148 111 374.80 1.73 95 39 162 125 340.56 1.22 96 39 163 126 332.03 3.04 97 40 46 6 381.89 1.65 98 40 47 7 380.55 1.66 99 40 148 110 375.36 1.67 100 40 162 124 340.61 1.21 101 40 176 138 322.03 1.86 102 40 180 142 301.62 1.10 103 40 189 151 256.80 0.15 104 40 192 154 256.57 0.17 105 40 193 155 256.26 0.20 106 41 46 5 381.70 1.75 107 41 147 107 376.25 1.88 108 41 147 108 375.45 1.69 109 41 161 122 345.10 1.70 110 41 180 141 310.91 4.46 111 42 45 3 811.64 2.14 112 42 46 4 631.07 2.66 113 42 184 144 261.61 1.39 114 42 186 146 259.12 0.89 115 42 189 149 257.12 0.01 116 43 147 105 377.53 2.51 117 43 182 141 297.99 2.91 118 43 183 142 297.87 2.87 119 43 184 143 268.00 4.39 120 44 147 104 377.72 2.60 121 44 185 143 266.67 3.93 122 44 186 144 259.33 0.82 123 45 147 103 377.72 2.60 124 45 186 143 258.82 0.72 125 45 215 172 253.50 0.05 126 45 216 173 253.15 0.07 127 46 139 94 377.51 2.71 128 46 147 102 377.74 2.62 129 46 186 142 258.82 0.72 130 46 214 170 253.50 0.05 131 46 215 171 253.39 0.04 132 47 189 144 256.92 0.09 133 47 193 148 256.46 0.10 134 47 212 167 253.83 0.01 135 47 213 168 253.65 0.03 136 47 214 169 253.38 0.04 137 48 67 19 377.63 2.80 138 48 75 27 377.66 2.79 139 48 76 28 377.60 2.77 140 48 77 29 377.44 2.81 141 48 139 92 377.62 2.78 142 48 212 166 253.72 0.02 143 48 213 167 253.52 0.07 144 49 211 164 253.74 0.03 145 49 212 165 253.40 0.04 146 50 66 16 377.56 2.86 147 50 67 17 377.60 2.87 148 50 77 27 377.44 2.87 149 50 197 149 255.60 0.02 150 50 210 162 253.79 0.02 151 50 211 163 253.71 0.03 152 51 66 15 377.58 2.87 153 51 202 152 254.79 0.04 154 51 203 153 254.79 0.04 155 51 209 160 253.82 0.01 156 51 210 161 253.77 0.01 157 52 61 9 377.80 2.79 158 52 209 158 253.85 0.01 159 52 209 159 253.80 0.01 160 52 210 160 253.77 0.01 161 52 211 161 253.76 0.01 162 53 203 151 254.78 0.04 163 56 59 3 820.88 5.25 164 60 63 3 834.62 3.56 165 61 64 3 831.09 3.74 166 61 209 149 253.87 0.01 167 62 65 3 839.25 2.06 168 64 211 149 253.84 0.01 169 65 211 148 253.72 0.06 170 65 223 175 103.05 1.69 171 66 77 11 506.54 0.46 172 66 78 12 493.62 6.00 173 66 85 19 493.62 6.00 174 66 211 147 253.72 0.06 175 67 76 9 560.02 25.23 176 67 77 10 557.79 25.08 177 67 85 18 530.08 0.34 178 67 211 146 253.80 0.03 179 67 213 148 253.52 0.08 180 67 223 173 102.76 1.54 181 68 75 7 611.93 0.65 182 68 76 8 611.04 0.27 183 68 85 17 535.09 2.12 184 68 89 21 539.73 0.20 185 68 93 25 546.74 3.42 186 68 221 170 107.77 3.31 187 69 72 3 866.86 2.33 188 69 74 5 674.56 26.78 189 69 75 6 612.35 0.67 190 69 93 24 546.77 3.42 191 69 221 169 107.72 3.29 192 70 74 4 730.80 1.34 193 70 75 5 619.88 1.19 194 70 76 6 617.31 0.10 195 70 89 19 546.69 3.39 196 70 92 22 546.74 3.42 197 70 93 23 546.76 3.42 198 70 112 43 580.26 13.31 199 70 138 69 546.70 3.40 200 71 74 3 821.02 5.12 201 71 96 25 601.84 2.36 202 71 106 36 603.70 1.65 203 71 107 37 603.41 1.78 204 71 112 42 602.04 2.45 205 72 106 35 604.08 1.49 206 72 219 164 108.20 3.45 207 72 220 165 108.19 3.45 208 72 221 166 108.02 3.44 209 73 140 68 600.22 0.10 210 73 141 69 600.14 0.08 211 73 215 144 253.62 0.01 212 73 219 163 108.20 3.45 213 73 220 164 108.11 3.41 214 74 107 34 604.08 1.47 215 74 109 36 604.06 1.47 216 74 112 39 604.06 1.47 217 74 138 65 600.61 0.08 218 74 139 66 600.45 0.10 219 74 140 67 600.22 0.09 220 74 141 68 600.26 0.10 221 74 215 143 253.59 0.03 222 75 138 64 600.62 0.07 223 75 139 65 600.55 0.07 224 75 215 142 253.47 0.09 225 75 221 163 107.63 3.25 226 76 85 9 609.23 1.09 227 76 137 62 600.94 0.01 228 76 138 63 600.62 0.07 229 77 85 8 612.25 2.40 230 77 136 60 601.24 0.05 231 77 137 61 601.04 0.05 232 78 82 4 819.60 0.46 233 78 85 7 619.73 0.62 234 78 134 57 603.69 0.78 235 78 135 58 602.62 0.47 236 78 136 59 601.25 0.04 237 78 165 89 331.55 3.13 238 79 134 56 603.70 0.78 239 79 135 57 603.16 0.51 240 79 165 88 331.19 3.04 241 79 166 89 331.06 3.04 242 80 133 54 604.27 1.02 243 80 134 55 603.91 0.88 244 81 84 3 835.28 0.40 245 81 85 4 821.95 2.57 246 81 133 53 604.29 1.02 247 81 134 54 604.28 1.02 248 82 85 3 821.96 2.58 249 82 86 4 821.95 2.57 250 83 86 3 821.95 2.56 251 83 87 4 821.95 2.56 252 84 87 3 840.70 3.24 253 84 88 4 814.99 0.92 254 84 130 47 606.92 0.15 255 84 132 49 606.72 0.12 256 84 133 50 606.72 0.12 257 84 134 51 606.60 0.16 258 85 88 3 814.96 0.88 259 85 89 4 814.93 0.89 260 85 134 50 606.35 0.30 261 85 136 52 605.53 0.67 262 86 89 3 814.97 0.86 263 86 90 4 814.93 0.89 264 87 90 3 829.10 3.49 265 87 91 4 813.75 0.32 266 87 132 46 606.90 0.20 267 88 91 3 826.09 1.99 268 88 92 4 809.28 0.94 269 88 116 29 607.35 0.02 270 88 119 32 607.31 0.04 271 88 120 33 607.29 0.04 272 88 132 45 606.78 0.14 273 88 134 47 606.60 0.20 274 88 136 49 605.25 0.84 275 89 92 3 812.75 0.80 276 89 93 4 809.30 0.94 277 90 93 3 816.86 1.26 278 90 94 4 809.33 0.96 279 91 94 3 826.91 3.77 280 91 95 4 809.33 0.96 281 91 119 29 607.37 0.03 282 92 95 3 833.46 2.82 283 92 96 4 809.31 0.97 284 92 112 21 607.85 0.18 285 92 116 25 607.46 0.01 286 93 96 3 811.75 0.25 287 93 97 4 814.71 1.73 288 94 97 3 831.68 3.53 289 94 98 4 811.65 0.29 290 95 98 3 824.87 6.94 291 95 99 4 787.06 0.23 292 95 112 18 607.95 0.14 293 95 115 21 607.73 0.10 294 96 100 4 807.94 9.95 295 96 101 5 781.64 2.17 296 96 107 12 609.22 0.30 297 96 112 17 607.95 0.14 298 97 100 3 833.29 2.73 299 97 101 4 758.11 3.75 300 97 102 5 742.01 3.37 301 97 106 10 609.97 0.61 302 98 102 4 758.22 10.73 303 98 102 5 752.99 8.85 304 99 102 4 786.72 0.80 305 100 102 3 804.21 6.79 306 100 103 4 756.87 2.25 307 100 105 6 706.07 1.55 308 100 106 7 655.83 23.55 309 100 107 8 609.88 0.58 310 100 108 9 609.96 0.61 311 100 111 12 609.15 0.38 312 101 103 3 795.13 4.82 313 101 104 4 706.08 1.55 314 101 105 5 662.76 23.21 315 101 106 6 649.79 19.27 316 107 112 5 755.40 2.00 317 108 111 3 832.88 1.33 318 108 112 4 812.30 3.06 319 108 142 34 603.26 1.66 320 109 112 3 827.61 7.05 321 109 113 4 810.48 2.16 322 109 138 29 603.86 1.47 323 109 140 31 603.50 1.61 324 109 141 32 603.49 1.62 325 109 142 33 603.41 1.61 326 109 147 39 600.06 0.07 327 109 149 41 599.83 0.00 328 110 113 3 817.19 5.44 329 110 114 4 809.33 1.51 330 110 145 35 600.28 0.13 331 111 114 3 815.20 1.42 332 111 115 4 810.11 1.90 333 112 115 3 813.28 3.32 334 112 116 4 813.12 3.40 335 113 116 3 819.18 0.38 336 113 117 4 813.09 3.42 337 113 138 25 603.89 1.46 338 113 149 37 600.04 0.07 339 113 151 39 599.79 0.01 340 113 157 45 463.80 3.42 341 114 117 3 819.18 0.37 342 114 118 4 813.07 3.43 343 114 157 44 463.95 3.50 344 115 118 3 819.18 0.36 345 115 119 4 816.81 5.30 346 116 119 3 822.76 2.33 347 116 120 4 816.99 5.21 348 116 136 20 604.17 1.40 349 116 138 22 604.10 1.41 350 117 120 3 822.88 2.27 351 117 121 4 820.74 3.33 352 117 151 35 599.92 0.04 353 117 155 39 529.12 0.12 354 117 157 41 480.12 4.58 355 118 121 3 828.18 0.38 356 118 122 4 820.74 3.33 357 119 122 3 830.85 1.71 358 119 123 4 824.14 5.06 359 120 123 3 828.45 2.91 360 120 124 4 816.14 1.06 361 120 132 12 607.00 0.32 362 120 134 14 606.91 0.32 363 120 136 16 606.77 0.36 364 120 151 32 600.09 0.07 365 120 153 34 599.32 0.21 366 120 155 36 558.05 1.26 367 121 124 3 811.05 1.24 368 121 125 4 806.32 1.55 369 121 155 35 585.09 1.75 370 122 125 3 823.20 2.48 371 122 126 4 796.21 5.27 372 123 129 6 607.39 0.37 373 123 131 8 607.10 0.34 374 123 132 9 607.10 0.34 375 124 131 7 607.10 0.34 376 124 153 30 600.07 0.07 377 126 129 3 855.05 0.10 378 131 153 23 599.98 0.03 379 132 153 22 599.70 0.07 380 134 153 20 599.59 0.10 381 135 151 17 599.74 0.09 382 135 152 18 599.41 0.18 383 135 153 19 599.38 0.20 384 135 165 31 331.18 3.05 385 136 150 15 599.78 0.09 386 136 151 16 599.68 0.06 387 137 148 12 600.06 0.07 388 137 149 13 599.96 0.03 389 137 150 14 599.67 0.06 390 137 163 27 358.59 10.27 391 137 165 29 331.63 3.15 392 138 148 11 600.03 0.07 393 138 149 12 599.75 0.09 394 138 151 14 599.66 0.06 395 139 147 9 600.03 0.07 396 139 148 10 599.68 0.06 397 139 215 77 253.44 0.07 398 140 147 7 600.03 0.07 399 140 147 8 599.90 0.07 400 140 215 76 253.47 0.07 401 141 146 5 600.06 0.07 402 141 147 6 599.99 0.09 403 141 215 75 253.58 0.01 404 141 220 95 108.17 3.44 405 142 145 3 815.30 0.88 406 142 146 4 636.04 0.29 407 147 215 69 253.52 0.04 408 147 216 70 253.50 0.05 409 148 159 11 453.86 1.64 410 148 160 12 443.24 6.94 411 148 162 14 417.72 0.24 412 149 158 9 460.80 4.56 413 149 159 10 453.85 1.64 414 150 157 7 461.12 4.58 415 150 158 8 460.80 4.56 416 150 160 10 456.73 3.47 417 150 163 13 387.68 0.68 418 150 165 15 331.58 3.17 419 151 156 5 485.08 2.08 420 151 157 6 461.06 4.56 421 152 155 3 813.06 7.41 422 152 156 4 645.51 11.88 423 152 158 6 563.29 37.02 424 160 163 3 855.74 2.18 425 161 180 19 298.03 2.90 426 162 176 14 322.03 1.86 427 162 180 18 301.61 1.10 428 163 173 10 322.12 1.88 429 163 176 13 321.57 1.67 430 164 169 5 330.21 2.72 431 164 172 8 324.45 2.08 432 164 173 9 322.15 1.89 433 165 169 4 647.22 11.32 434 166 169 3 818.45 3.16 435 168 171 3 813.54 0.36 436 168 172 4 805.10 2.45 437 169 172 3 811.60 0.80 438 169 173 4 800.13 0.21 439 170 173 3 813.28 0.04 440 170 174 4 808.32 2.43 441 171 174 3 821.13 1.66 442 171 175 4 808.33 2.43 443 172 175 3 809.55 2.04 444 172 176 4 807.74 2.95 445 172 196 24 255.59 0.41 446 173 176 3 820.74 2.77 447 173 177 4 807.74 2.95 448 174 177 3 818.40 2.39 449 174 178 4 807.75 2.94 450 175 178 3 826.32 0.65 451 175 179 4 808.64 1.42 452 175 195 20 256.05 0.30 453 175 196 21 255.94 0.33 454 175 199 24 255.57 0.43 455 176 179 3 817.31 2.91 456 176 180 4 801.86 2.21 457 176 192 16 256.33 0.29 458 176 196 20 255.68 0.46 459 179 192 13 256.45 0.29 460 179 195 16 256.42 0.31 461 180 184 4 832.68 3.43 462 181 184 3 853.29 0.35 463 184 188 4 812.16 6.33 464 184 192 8 789.55 2.66 465 185 188 3 820.70 2.08 466 185 189 4 820.69 2.07 467 186 189 3 820.70 2.08 468 186 190 4 820.70 2.07 469 186 214 28 253.86 0.03 470 187 190 3 822.89 0.97 471 187 191 4 820.70 2.07 472 187 232 60 79.42 0.76 473 188 191 3 820.64 2.10 474 188 192 4 820.62 2.08 475 189 192 3 821.30 2.89 476 189 193 4 816.00 0.22 477 190 193 3 819.27 1.83 478 190 194 4 816.03 0.21 479 190 212 22 253.90 0.01 480 190 214 24 253.75 0.00 481 190 232 57 79.56 0.99 482 191 194 3 819.27 1.82 483 191 195 4 814.03 0.80 484 191 235 59 67.95 0.67 485 191 236 60 47.53 8.70 486 192 195 3 823.74 0.32 487 192 196 4 815.83 0.10 488 193 196 3 824.72 4.42 489 193 197 4 815.83 0.12 490 194 197 3 824.76 4.40 491 194 198 4 816.01 0.03 492 194 206 11 254.22 0.01 493 194 212 18 253.79 0.01 494 194 232 53 77.41 0.06 495 194 233 54 75.05 0.20 496 195 198 3 829.14 2.21 497 195 199 4 826.88 3.33 498 195 236 56 43.99 6.97 499 196 199 3 835.12 0.79 500 196 200 4 826.88 3.33 501 197 200 3 829.93 4.84 502 197 202 4 811.75 2.10 503 197 206 8 329.56 37.76 504 197 210 13 253.84 0.03 505 198 202 3 824.01 4.05 506 198 206 7 329.55 37.77 507 198 236 53 58.97 0.52 508 202 205 3 950.51 1.96 509 202 206 4 783.72 7.10 510 202 210 9 253.83 0.03 511 205 209 5 724.27 8.63 512 206 209 4 770.45 6.55 513 206 210 5 713.53 3.26 514 206 233 43 78.80 1.93 515 207 209 3 826.87 2.57 516 207 210 4 777.97 8.96 517 207 230 39 79.58 1.98 518 207 233 42 78.52 1.79 519 208 226 34 90.16 2.65 520 208 229 37 81.12 1.80 521 208 230 38 80.92 1.70 522 209 226 33 90.17 2.64 523 210 229 34 81.16 1.79 524 211 223 27 102.76 1.54 525 212 223 26 102.77 1.54 526 212 224 27 102.48 1.67 527 213 221 23 107.77 3.32 528 213 222 24 107.31 3.10 529 213 223 25 102.77 1.54 530 214 221 22 107.77 3.33 531 214 222 23 107.62 3.25 532 215 220 20 108.06 3.43 533 215 221 21 107.76 3.32 534 216 220 19 108.10 3.41 535 217 220 18 108.34 3.42 536 217 217 14 110.45 2.90 537 217 218 15 110.22 2.87 538 217 219 16 110.19 2.88 539 217 220 17 108.35 3.42 540 217 217 3 802.53 2.29 541 217 217 4 800.61 2.38 542 217 218 14 110.45 2.90 543 217 219 15 110.25 2.85 544 217 217 3 789.64 8.73 545 217 217 12 110.87 2.75 546 217 218 13 110.79 2.78 547 217 219 12 110.86 2.77 548 217 222 15 110.27 2.84 549 217 217 8 112.94 1.88 550 217 217 9 112.91 1.88 551 217 218 10 110.87 2.77 552 217 219 11 110.87 2.77 553 217 217 3 838.30 6.24 554 217 217 3 841.67 1.13 555 222 228 6 808.57 0.28 556 224 228 4 807.49 0.82 557 224 229 5 807.46 0.83 558 225 228 3 810.34 1.17 559 225 229 4 808.62 0.30 560 226 229 3 812.41 2.19 561 226 230 4 812.07 1.43 562 227 230 3 826.42 4.92 563 227 231 4 808.78 0.39 564 228 232 4 813.89 2.17 565 229 232 3 818.19 0.66 566 229 233 4 812.24 1.34 567 230 233 3 812.40 1.43 568 230 234 4 812.39 1.42 569 232 235 3 816.03 0.39 570 233 236 3 830.95 1.79