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 12 210 198 48.17 1.48 2 12 211 199 47.79 1.56 3 12 212 200 47.63 1.50 4 13 18 5 717.40 1.01 5 13 204 191 55.63 0.02 6 13 209 196 49.77 0.80 7 13 210 197 48.27 1.54 8 14 17 3 746.36 2.55 9 14 18 4 721.64 3.02 10 15 18 3 738.14 4.64 11 15 19 4 720.68 2.54 12 15 211 196 49.80 0.79 13 15 215 200 48.27 1.46 14 15 216 201 48.16 1.49 15 15 219 204 45.48 0.14 16 16 19 3 721.64 3.02 17 16 20 4 728.94 6.67 18 16 219 203 46.77 0.58 19 17 20 3 737.67 2.31 20 17 21 4 729.12 6.58 21 17 209 192 64.52 0.40 22 18 21 3 746.07 6.50 23 18 22 4 729.12 6.58 24 18 28 10 210.86 3.73 25 18 160 142 234.40 0.59 26 18 209 191 62.75 1.38 27 18 211 193 57.77 0.79 28 19 22 3 745.97 6.55 29 19 23 4 729.38 1.74 30 19 160 141 235.41 0.01 31 19 163 144 238.57 0.24 32 19 164 145 238.67 0.29 33 19 219 200 57.77 0.78 34 20 23 3 745.97 6.55 35 20 24 4 733.58 3.85 36 21 24 3 733.58 3.85 37 21 25 4 733.57 3.85 38 21 26 5 688.68 5.08 39 21 28 7 404.30 83.05 40 21 209 188 71.38 0.73 41 22 25 3 740.42 0.14 42 22 26 4 714.90 2.40 43 22 28 6 404.30 83.05 44 22 43 21 238.75 0.28 45 22 44 22 238.75 0.28 46 22 45 23 238.75 0.28 47 22 160 138 238.83 0.26 48 22 161 139 259.15 2.16 49 22 164 142 267.85 1.38 50 22 166 144 268.07 1.44 51 23 164 141 267.85 1.38 52 23 166 143 268.22 1.36 53 25 44 19 268.85 1.06 54 25 53 28 268.67 1.15 55 26 44 18 268.86 1.06 56 27 42 15 268.85 1.06 57 27 43 16 268.86 1.06 58 27 44 17 268.86 1.06 59 27 53 26 268.85 1.06 60 27 56 29 268.85 1.06 61 27 57 30 268.85 1.06 62 27 208 181 130.84 0.03 63 28 41 13 268.97 1.03 64 28 42 14 268.92 1.03 65 28 43 15 268.94 1.02 66 28 160 132 269.27 1.08 67 28 209 181 130.82 0.03 68 29 40 11 269.00 1.03 69 29 41 12 268.97 1.03 70 29 42 13 268.95 1.02 71 29 175 146 268.50 1.09 72 29 199 170 131.37 0.04 73 29 202 173 131.40 0.01 74 29 203 174 131.13 0.01 75 29 208 179 131.12 0.01 76 29 209 180 130.85 0.03 77 29 210 181 130.80 0.03 78 29 211 182 130.81 0.02 79 30 40 10 269.01 1.03 80 30 41 11 269.04 1.04 81 30 43 13 269.12 1.07 82 30 153 123 269.07 1.04 83 30 156 126 269.27 1.09 84 30 160 130 269.52 1.03 85 30 211 181 130.81 0.03 86 30 213 183 130.75 0.01 87 30 216 186 113.24 0.58 88 31 39 8 269.22 1.07 89 31 40 9 269.07 1.06 90 31 153 122 269.25 1.08 91 31 196 165 134.75 0.91 92 31 199 168 131.73 0.09 93 31 210 179 131.14 0.01 94 31 211 180 130.86 0.03 95 31 212 181 130.80 0.02 96 31 213 182 130.78 0.01 97 32 36 4 707.06 6.42 98 32 37 5 349.69 41.13 99 32 38 6 269.31 1.07 100 32 39 7 269.25 1.08 101 32 151 119 269.27 1.08 102 32 153 121 269.25 1.08 103 32 213 181 130.80 0.02 104 33 36 3 724.87 3.12 105 33 37 4 688.12 3.04 106 33 38 5 269.34 1.08 107 34 38 4 269.35 1.09 108 36 150 114 290.00 0.90 109 36 151 115 289.33 0.74 110 36 152 116 287.06 0.38 111 37 153 116 289.53 0.65 112 37 195 158 135.71 1.01 113 38 195 157 135.18 1.06 114 39 153 114 290.56 0.84 115 39 174 135 278.95 0.26 116 39 193 154 135.71 0.99 117 39 195 156 134.97 0.96 118 40 153 113 290.82 0.78 119 40 174 134 283.57 0.10 120 40 175 135 280.61 1.08 121 40 199 159 131.68 0.12 122 41 153 112 290.84 0.78 123 41 172 131 290.49 0.83 124 41 173 132 289.41 0.48 125 41 174 133 286.58 1.40 126 41 175 134 283.57 0.11 127 42 56 14 290.71 0.75 128 42 57 15 290.44 0.83 129 42 60 18 290.44 0.83 130 42 172 130 290.81 0.77 131 42 173 131 290.50 0.83 132 42 175 133 289.59 0.42 133 42 202 160 131.44 0.01 134 42 208 166 131.12 0.01 135 43 153 110 291.16 0.74 136 43 156 113 291.75 0.46 137 43 157 114 291.75 0.46 138 43 160 117 294.37 1.73 139 43 170 127 293.98 1.56 140 43 171 128 291.14 0.76 141 43 172 129 290.83 0.76 142 44 49 5 323.05 15.62 143 44 53 9 295.01 1.90 144 44 57 13 293.44 1.83 145 44 170 126 294.32 1.73 146 44 171 127 291.76 0.46 147 45 49 4 717.52 2.96 148 45 166 121 333.03 0.62 149 45 170 125 294.37 1.73 150 46 49 3 734.60 2.77 151 46 118 72 314.28 2.11 152 46 119 73 332.82 0.73 153 46 122 76 332.88 0.70 154 46 169 123 329.14 1.20 155 46 170 124 301.49 3.45 156 46 171 125 298.61 3.40 157 47 119 72 333.58 0.95 158 47 122 75 332.94 0.67 159 47 166 119 333.91 1.06 160 47 167 120 333.48 0.84 161 48 119 71 336.82 0.29 162 49 53 4 718.37 1.86 163 49 54 5 718.36 1.87 164 49 115 66 337.68 0.53 165 49 118 69 337.63 0.55 166 49 119 70 337.68 0.53 167 49 171 122 336.47 0.45 168 50 53 3 727.23 2.56 169 50 54 4 725.24 1.57 170 50 115 65 339.91 0.01 171 51 54 3 732.77 1.75 172 51 55 4 725.55 1.43 173 51 111 60 341.53 0.18 174 51 112 61 341.49 0.20 175 51 115 64 340.50 0.17 176 52 55 3 730.43 0.58 177 52 56 4 726.27 1.07 178 53 56 3 735.31 1.86 179 53 57 4 726.29 1.08 180 54 57 3 731.61 3.43 181 54 58 4 726.29 1.08 182 54 65 11 342.50 0.36 183 54 111 57 342.70 0.35 184 54 114 60 342.73 0.33 185 54 115 61 342.72 0.33 186 54 118 64 342.75 0.34 187 54 171 117 342.32 0.43 188 55 58 3 732.52 3.25 189 55 59 4 726.27 1.09 190 55 111 56 342.69 0.35 191 56 59 3 746.50 0.67 192 56 60 4 726.86 2.68 193 56 202 146 131.16 0.01 194 56 206 150 131.04 0.01 195 57 60 3 752.88 3.23 196 57 61 4 724.78 1.67 197 57 65 8 342.58 0.35 198 57 171 114 342.61 0.35 199 57 172 115 342.55 0.34 200 57 173 116 341.72 0.04 201 58 61 3 747.13 0.35 202 58 65 7 342.56 0.35 203 58 114 56 428.43 0.81 204 59 178 119 332.47 0.55 205 60 175 115 337.63 0.54 206 60 176 116 336.82 0.36 207 60 202 142 131.16 0.01 208 60 206 146 131.12 0.01 209 61 65 4 738.41 3.55 210 61 173 112 342.41 0.27 211 61 174 113 341.62 0.01 212 61 175 114 337.85 0.42 213 61 176 115 336.82 0.35 214 62 173 111 342.96 0.54 215 62 174 112 342.23 0.18 216 62 176 114 337.86 0.42 217 63 114 51 504.50 0.71 218 63 173 110 347.25 2.67 219 64 173 109 357.64 1.20 220 65 114 49 504.51 0.70 221 65 137 72 502.93 1.18 222 65 138 73 502.16 1.55 223 65 171 106 389.74 1.97 224 65 172 107 388.53 2.06 225 65 173 108 362.83 0.73 226 66 94 28 502.16 1.55 227 66 138 72 502.17 1.56 228 66 140 74 502.86 1.15 229 66 171 105 389.74 1.97 230 66 172 106 389.17 1.75 231 67 121 54 504.81 0.70 232 67 137 70 504.52 0.71 233 67 138 71 504.14 0.71 234 67 139 72 502.97 1.20 235 67 140 73 502.96 1.20 236 67 169 102 390.31 1.96 237 67 170 103 390.22 1.96 238 67 171 104 389.75 1.97 239 68 140 72 502.97 1.20 240 68 154 86 390.81 1.54 241 68 158 90 390.73 1.75 242 68 169 101 390.38 1.93 243 68 170 102 390.27 1.95 244 68 171 103 390.25 1.95 245 68 172 104 390.23 1.96 246 69 73 4 719.53 3.69 247 69 74 5 716.53 2.21 248 69 77 8 701.90 0.87 249 69 79 10 532.76 13.24 250 69 121 52 505.05 0.76 251 69 139 70 504.58 0.70 252 69 140 71 504.32 0.74 253 69 141 72 502.97 1.20 254 69 142 73 502.91 1.17 255 69 158 89 391.00 1.63 256 69 168 99 390.50 1.91 257 69 169 100 390.35 1.92 258 70 73 3 728.71 0.63 259 70 74 4 726.93 0.01 260 70 158 88 391.19 1.60 261 70 168 98 390.55 1.90 262 71 74 3 738.19 2.40 263 71 75 4 732.00 5.43 264 71 141 70 504.49 0.67 265 71 142 71 504.41 0.68 266 71 144 73 502.07 1.51 267 72 75 3 738.05 2.52 268 72 76 4 724.07 1.44 269 73 76 3 732.00 5.42 270 73 77 4 718.06 1.54 271 73 167 94 390.59 1.89 272 73 168 95 390.45 1.85 273 73 169 96 390.38 1.90 274 74 77 3 747.21 2.15 275 74 78 4 718.02 1.55 276 74 79 5 662.67 7.71 277 74 95 21 504.84 0.71 278 74 141 67 504.57 0.73 279 75 78 3 718.01 1.55 280 76 128 52 553.84 2.16 281 77 121 44 553.74 2.14 282 77 126 49 553.85 2.16 283 77 127 50 553.83 2.16 284 77 128 51 553.84 2.16 285 77 131 54 553.83 2.15 286 77 133 56 554.48 2.10 287 78 128 50 554.00 2.24 288 78 133 55 554.48 2.11 289 79 95 16 554.53 2.08 290 79 96 17 554.45 2.08 291 79 98 19 554.40 2.10 292 79 121 42 554.10 2.25 293 79 133 54 554.52 2.10 294 79 139 60 548.45 1.34 295 80 95 15 554.66 2.09 296 80 96 16 554.56 2.12 297 81 93 12 554.75 2.07 298 81 94 13 554.73 2.08 299 81 95 14 554.68 2.08 300 81 141 60 547.08 1.31 301 82 94 12 554.76 2.07 302 82 95 13 554.72 2.08 303 82 96 14 554.71 2.08 304 82 138 56 553.62 1.88 305 83 86 3 744.13 0.49 306 86 92 6 554.86 2.06 307 88 91 3 624.42 0.72 308 90 150 60 393.82 2.12 309 91 150 59 393.88 2.14 310 92 140 48 552.28 1.54 311 92 150 58 393.84 2.12 312 93 140 47 550.46 0.63 313 93 141 48 549.71 0.82 314 94 138 44 552.51 1.57 315 94 139 45 550.57 0.67 316 94 140 46 549.72 0.83 317 95 139 44 550.44 0.60 318 96 133 37 620.10 1.54 319 96 134 38 619.88 1.47 320 96 139 43 550.56 0.66 321 97 133 36 621.01 1.10 322 97 134 37 620.00 1.52 323 97 135 38 619.78 1.43 324 97 137 40 606.52 0.69 325 97 138 41 564.45 6.28 326 97 139 42 550.58 0.67 327 98 121 23 623.65 0.97 328 98 131 33 622.11 1.34 329 98 132 34 621.39 1.13 330 98 133 35 621.16 1.17 331 98 135 37 619.92 1.48 332 98 136 38 619.90 1.49 333 98 137 39 618.26 1.01 334 98 139 41 598.75 5.88 335 99 108 9 623.83 0.96 336 99 117 18 623.75 0.98 337 99 131 32 622.58 1.17 338 99 132 33 621.92 1.25 339 99 135 36 620.11 1.54 340 99 136 37 620.10 1.55 341 100 105 5 624.00 1.02 342 100 116 16 623.77 0.98 343 100 117 17 623.76 0.98 344 100 120 20 623.75 0.98 345 100 130 30 622.88 1.22 346 100 132 32 622.58 1.17 347 101 120 19 623.78 0.98 348 101 129 28 623.05 1.18 349 101 130 29 622.88 1.22 350 101 131 30 622.86 1.21 351 101 132 31 622.76 1.17 352 102 105 3 738.26 4.68 353 102 116 14 623.88 1.01 354 102 120 18 623.85 1.00 355 104 112 8 624.63 1.05 356 104 116 12 624.17 1.05 357 105 108 3 753.18 2.41 358 105 113 8 624.30 1.01 359 105 116 11 624.26 1.02 360 105 132 27 622.96 1.18 361 106 113 7 681.57 5.79 362 107 113 6 681.59 5.79 363 107 136 29 622.43 1.28 364 108 113 5 681.59 5.79 365 108 114 6 690.02 1.57 366 108 136 28 622.33 1.28 367 109 113 4 715.69 9.25 368 109 114 5 708.28 1.29 369 109 136 27 622.33 1.28 370 110 113 3 729.74 2.23 371 110 114 4 723.06 5.57 372 111 114 3 746.37 5.79 373 111 115 4 729.67 2.21 374 112 115 3 749.10 4.44 375 112 116 4 729.68 2.21 376 113 116 3 740.82 3.36 377 113 117 4 729.68 2.21 378 114 117 3 740.77 2.44 379 114 118 4 729.60 2.23 380 114 136 22 622.25 1.26 381 114 137 23 622.09 1.20 382 115 118 3 739.94 2.86 383 115 119 4 726.23 1.28 384 116 119 3 739.97 2.88 385 116 120 4 737.18 4.27 386 117 120 3 739.62 3.05 387 117 121 4 735.44 5.14 388 117 137 20 620.61 1.94 389 118 121 3 739.63 3.05 390 118 122 4 735.43 5.13 391 118 137 19 620.54 1.98 392 118 171 53 389.70 1.97 393 119 122 3 739.62 3.06 394 119 123 4 718.27 3.40 395 120 123 3 731.28 1.49 396 120 126 6 623.16 1.17 397 120 130 10 623.03 1.17 398 120 131 11 623.03 1.17 399 121 126 5 623.14 1.16 400 121 131 10 622.95 1.18 401 121 137 16 620.37 1.96 402 121 139 18 618.24 1.22 403 121 169 48 390.19 1.94 404 122 167 45 390.44 1.89 405 122 169 47 390.19 1.95 406 123 126 3 728.81 2.00 407 123 167 44 390.46 1.88 408 124 167 43 390.48 1.88 409 125 130 5 748.47 2.12 410 126 130 4 739.51 0.24 411 126 131 5 739.51 0.24 412 127 130 3 757.86 0.94 413 127 131 4 752.95 1.52 414 128 131 3 764.31 0.89 415 128 133 5 746.36 3.18 416 140 154 14 391.01 1.59 417 140 172 32 390.24 1.96 418 141 154 13 391.18 1.56 419 142 154 12 391.18 1.56 420 142 155 13 391.18 1.57 421 142 158 16 391.24 1.60 422 143 146 3 743.16 7.22 423 143 149 6 657.58 18.39 424 143 150 7 393.75 2.08 425 143 155 12 391.37 1.59 426 145 149 4 658.73 17.84 427 146 149 3 756.31 9.70 428 146 150 4 714.25 7.00 429 146 155 9 393.18 1.89 430 146 159 13 392.47 1.55 431 147 150 3 727.16 0.56 432 147 151 4 666.65 13.88 433 147 155 8 393.20 1.89 434 147 156 9 393.20 1.88 435 147 159 12 392.48 1.55 436 147 213 66 130.48 0.05 437 147 216 69 126.63 0.56 438 147 217 70 119.19 1.79 439 147 220 73 112.95 0.62 440 148 217 69 125.85 0.22 441 148 220 72 113.08 0.65 442 148 221 73 112.75 0.66 443 148 224 76 91.57 0.55 444 148 225 77 82.92 1.34 445 148 226 78 23.98 1.74 446 148 227 79 16.50 0.36 447 149 227 78 16.82 0.28 448 150 154 4 760.18 1.86 449 150 155 5 692.80 1.53 450 151 213 62 130.58 0.00 451 151 217 66 125.96 0.21 452 152 155 3 745.50 0.79 453 152 156 4 733.93 2.85 454 152 213 61 130.75 0.00 455 153 156 3 738.29 0.67 456 153 157 4 738.28 0.68 457 153 172 19 390.67 1.99 458 153 213 60 130.37 0.00 459 154 157 3 737.85 0.48 460 154 158 4 731.88 2.52 461 154 172 18 390.64 2.00 462 155 158 3 731.90 2.54 463 155 159 4 727.77 0.47 464 156 159 3 728.02 0.36 465 156 160 4 726.64 1.08 466 156 213 57 130.08 0.07 467 156 216 60 116.06 0.23 468 157 160 3 732.75 2.73 469 157 161 4 726.69 1.06 470 157 170 13 390.76 1.99 471 158 161 3 731.39 0.54 472 158 162 4 726.69 1.06 473 159 162 3 729.45 2.43 474 159 163 4 726.69 1.05 475 159 216 57 117.23 2.60 476 159 220 61 97.59 0.31 477 160 163 3 730.20 2.81 478 160 164 4 716.32 4.13 479 160 216 56 113.22 0.60 480 161 164 3 727.43 1.42 481 161 165 4 711.52 1.74 482 161 166 5 509.52 56.75 483 161 167 6 398.47 5.67 484 161 168 7 391.03 2.05 485 161 169 8 391.03 2.05 486 161 170 9 390.95 2.04 487 162 165 3 735.47 0.17 488 162 220 58 104.20 3.00 489 163 216 53 117.72 2.83 490 163 219 56 110.79 1.50 491 163 220 57 97.59 0.31 492 174 193 19 135.68 0.98 493 175 193 18 135.68 0.97 494 175 194 19 135.47 0.92 495 175 202 27 131.44 0.01 496 176 192 16 135.73 0.99 497 176 193 17 135.68 0.97 498 176 194 18 135.65 0.98 499 177 191 14 135.87 1.04 500 177 192 15 135.78 1.01 501 177 193 16 135.71 0.99 502 177 194 17 135.66 0.98 503 178 188 10 137.10 1.25 504 178 191 13 135.89 1.05 505 179 188 9 137.11 1.26 506 179 189 10 137.10 1.25 507 179 190 11 136.76 1.27 508 179 191 12 135.88 1.06 509 180 188 8 137.13 1.26 510 180 189 9 137.12 1.26 511 180 190 10 137.12 1.26 512 181 188 7 137.25 1.23 513 182 185 3 733.91 1.94 514 182 187 5 143.00 1.21 515 182 188 6 140.11 2.65 516 182 189 7 137.28 1.24 517 188 191 3 782.07 3.04 518 194 198 4 719.40 5.21 519 194 199 5 693.68 1.69 520 194 202 8 669.22 2.74 521 195 198 3 745.06 2.51 522 195 199 4 719.41 5.21 523 196 199 3 734.96 2.54 524 196 200 4 724.09 2.90 525 197 200 3 731.98 3.04 526 197 201 4 727.81 5.13 527 198 201 3 731.81 3.14 528 198 202 4 719.41 5.23 529 199 202 3 719.58 5.17 530 199 203 4 725.39 2.25 531 200 203 3 747.95 4.08 532 200 204 4 716.13 4.71 533 200 210 10 136.96 2.85 534 201 204 3 740.64 4.42 535 201 205 4 716.03 4.77 536 202 205 3 741.65 1.00 537 202 206 4 738.36 0.65 538 202 208 6 707.38 0.91 539 203 206 3 742.38 2.66 540 203 207 4 717.69 1.56 541 203 208 5 687.55 0.21 542 203 210 7 518.32 58.42 543 204 207 3 731.03 3.02 544 204 208 4 713.16 3.83 545 204 210 6 686.75 0.59 546 211 216 5 700.59 1.30 547 212 215 3 724.62 2.81 548 212 216 4 711.11 3.95 549 213 216 3 734.50 9.58 550 213 217 4 715.61 1.69 551 214 217 3 754.43 0.39 552 214 218 4 715.69 1.65 553 215 218 3 729.60 7.13 554 215 219 4 717.69 2.66 555 216 219 3 740.53 0.57 556 216 220 4 725.90 6.76 557 217 220 3 727.64 5.89 558 217 221 4 725.86 6.78 559 218 221 3 730.82 3.87 560 218 222 4 719.14 1.97 561 219 222 3 743.62 3.31 562 220 223 3 746.15 3.79 563 220 224 4 709.90 1.90 564 221 224 3 718.38 9.31 565 221 225 4 422.69 9.16 566 221 226 5 422.12 9.45