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 4 7 3 879.19 0.24 2 5 11 6 496.86 27.28 3 5 13 8 496.87 27.29 4 6 11 5 642.50 29.07 5 8 11 3 858.49 3.45 6 9 15 6 805.68 3.83 7 11 14 3 858.23 2.27 8 11 15 4 831.91 0.61 9 12 15 3 850.49 1.35 10 12 16 4 831.90 0.60 11 13 16 3 846.90 3.40 12 13 17 4 845.60 3.80 13 14 17 3 853.43 0.12 14 14 18 4 850.73 1.23 15 14 248 234 34.65 0.32 16 15 18 3 865.24 4.66 17 15 19 4 842.16 3.06 18 16 19 3 850.74 1.23 19 16 20 4 845.14 1.56 20 17 20 3 850.68 4.33 21 17 21 4 845.14 1.55 22 17 248 231 37.16 0.94 23 18 21 3 859.96 0.32 24 18 22 4 840.21 0.94 25 18 246 228 46.99 0.15 26 18 247 229 43.91 0.31 27 18 248 230 37.43 1.07 28 19 22 3 846.02 3.84 29 19 23 4 840.24 0.95 30 20 23 3 846.32 3.92 31 20 24 4 841.71 2.81 32 21 24 3 850.88 2.35 33 21 25 4 841.72 2.81 34 21 244 223 47.36 0.12 35 21 247 226 47.32 0.18 36 21 248 227 47.16 0.12 37 22 25 3 851.82 1.88 38 22 26 4 838.90 1.62 39 22 244 222 49.11 0.70 40 22 245 223 47.73 0.01 41 22 246 224 47.45 0.18 42 23 26 3 861.26 2.66 43 23 27 4 836.72 0.54 44 24 27 3 864.59 1.82 45 24 28 4 843.34 2.76 46 24 244 220 50.46 0.12 47 25 28 3 859.87 0.54 48 25 29 4 848.25 0.33 49 25 115 90 138.00 34.20 50 25 158 133 262.37 20.71 51 25 159 134 146.18 38.43 52 25 244 219 50.23 0.22 53 25 245 220 50.22 0.23 54 26 29 3 848.25 0.33 55 26 30 4 843.34 2.76 56 27 30 3 843.34 2.76 57 27 32 5 821.76 2.35 58 27 33 6 676.86 4.45 59 28 33 5 643.77 10.12 60 28 34 6 641.50 11.23 61 28 116 88 231.63 0.85 62 28 183 155 242.41 0.35 63 29 116 87 228.19 2.57 64 29 183 154 248.86 1.22 65 29 184 155 257.20 0.60 66 30 33 3 834.32 6.53 67 30 183 153 290.45 0.97 68 31 56 25 564.43 100.97 69 31 57 26 541.49 109.72 70 31 183 152 290.48 0.96 71 31 184 153 290.48 0.96 72 31 185 154 290.38 0.91 73 31 191 160 289.25 0.55 74 32 56 24 564.60 101.03 75 33 56 23 564.63 101.04 76 33 183 150 337.04 0.62 77 34 54 20 565.81 100.45 78 34 55 21 564.91 100.90 79 34 116 82 401.45 25.48 80 34 183 149 338.51 1.34 81 35 54 19 565.91 100.41 82 35 55 20 565.84 100.45 83 35 57 22 565.13 100.85 84 35 58 23 564.79 100.98 85 35 59 24 564.71 100.94 86 35 114 79 408.53 21.95 87 35 116 81 406.05 23.18 88 35 117 82 401.45 25.48 89 35 183 148 338.51 1.34 90 36 53 17 567.56 99.63 91 36 54 18 565.91 100.41 92 36 59 23 565.84 100.46 93 36 113 77 412.54 22.12 94 36 114 78 408.67 21.88 95 37 52 15 570.19 98.38 96 37 53 16 569.22 98.85 97 37 59 22 565.97 100.44 98 37 60 23 565.95 100.42 99 37 61 24 568.62 99.06 100 37 111 74 415.68 21.02 101 37 112 75 415.23 20.93 102 37 113 76 412.56 22.12 103 37 179 142 366.96 0.20 104 38 50 12 570.92 98.11 105 38 51 13 570.40 98.36 106 38 52 14 570.20 98.38 107 38 61 23 570.25 98.29 108 38 111 73 415.71 21.02 109 38 112 74 415.32 20.91 110 38 114 76 415.28 20.91 111 38 224 186 195.90 0.26 112 38 230 192 193.36 0.48 113 38 231 193 193.28 0.47 114 39 50 11 570.94 98.12 115 39 51 12 570.81 98.16 116 39 61 22 570.23 98.27 117 39 109 70 433.68 29.39 118 39 110 71 426.90 26.07 119 39 111 72 419.16 22.39 120 39 177 138 373.49 0.49 121 39 179 140 370.50 1.57 122 40 48 8 574.15 96.67 123 40 49 9 571.10 98.09 124 40 50 10 570.96 98.11 125 40 109 69 438.63 31.87 126 40 110 70 426.94 26.05 127 40 112 72 426.91 26.07 128 40 220 180 195.97 0.26 129 40 224 184 196.03 0.28 130 40 225 185 195.96 0.26 131 40 232 192 193.31 0.48 132 41 48 7 576.62 95.45 133 41 49 8 573.99 96.65 134 41 106 65 457.18 34.97 135 41 108 67 455.52 35.39 136 41 109 68 449.77 35.41 137 42 47 5 608.47 79.65 138 42 48 6 583.29 92.11 139 42 106 64 457.49 34.84 140 42 107 65 457.34 34.88 141 42 108 66 456.85 34.78 142 42 109 67 455.53 35.39 143 42 110 68 455.51 35.39 144 42 165 123 419.99 16.34 145 42 232 190 195.63 0.41 146 43 46 3 853.18 1.29 147 43 47 4 724.50 21.64 148 43 48 5 607.24 80.27 149 43 49 6 607.24 80.27 150 43 68 25 574.38 93.27 151 43 69 26 574.35 93.25 152 43 70 27 574.26 93.20 153 43 104 61 457.56 34.85 154 43 105 62 457.55 34.84 155 43 106 63 457.51 34.84 156 43 107 64 457.49 34.84 157 43 213 170 289.11 0.67 158 44 103 59 458.33 34.45 159 44 107 63 457.41 34.91 160 45 70 25 577.28 91.78 161 46 215 169 288.69 0.68 162 46 216 170 288.49 0.60 163 47 70 23 577.35 91.72 164 47 213 166 289.03 0.66 165 47 214 167 288.73 0.68 166 47 215 168 288.52 0.61 167 47 216 169 286.67 0.48 168 48 213 165 288.73 0.68 169 48 214 166 288.72 0.68 170 48 217 169 250.00 2.10 171 48 220 172 209.71 3.08 172 49 67 18 578.08 91.39 173 49 68 19 577.47 91.66 174 49 211 162 289.07 0.66 175 49 212 163 288.74 0.68 176 49 213 164 288.69 0.67 177 50 210 160 289.09 0.66 178 50 211 161 288.74 0.68 179 50 212 162 288.73 0.68 180 50 214 164 288.66 0.66 181 50 220 170 196.00 0.27 182 50 224 174 195.99 0.26 183 51 61 10 581.04 92.92 184 51 63 12 581.07 92.89 185 51 68 17 578.02 91.34 186 51 209 158 289.09 0.67 187 51 210 159 288.74 0.67 188 51 211 160 288.71 0.67 189 52 61 9 581.30 92.80 190 52 209 157 288.73 0.67 191 52 210 158 288.73 0.67 192 52 224 172 195.72 0.17 193 53 59 6 631.24 67.84 194 53 60 7 602.93 81.98 195 53 61 8 581.32 92.79 196 53 207 154 289.06 0.66 197 53 208 155 288.75 0.68 198 53 209 156 288.70 0.66 199 54 59 5 773.30 3.17 200 54 207 153 288.73 0.67 201 54 208 154 288.73 0.67 202 55 58 3 885.52 1.03 203 55 59 4 773.32 3.17 204 55 203 148 289.38 0.64 205 55 207 152 288.71 0.67 206 56 203 147 289.28 0.59 207 57 182 125 375.05 9.89 208 57 183 126 373.21 10.28 209 57 191 134 289.73 0.65 210 57 196 139 289.66 0.59 211 57 199 142 289.49 0.61 212 57 200 143 289.45 0.60 213 57 203 146 289.35 0.64 214 58 181 123 379.87 7.49 215 58 182 124 373.42 10.37 216 58 183 125 373.22 10.27 217 58 200 142 289.48 0.61 218 58 204 146 289.35 0.64 219 59 113 54 425.99 15.47 220 59 180 121 380.11 7.43 221 59 181 122 379.87 7.52 222 60 179 119 380.32 7.36 223 60 180 120 380.13 7.29 224 61 178 117 381.53 6.93 225 61 179 118 381.49 6.93 226 62 177 115 382.49 6.50 227 62 178 116 382.36 6.55 228 63 67 4 835.58 2.57 229 63 68 5 830.74 0.16 230 63 176 113 384.89 5.98 231 63 177 114 384.68 6.07 232 63 209 146 289.37 0.62 233 64 67 3 846.45 2.87 234 64 68 4 835.59 2.56 235 64 176 112 384.90 5.98 236 65 68 3 852.09 0.04 237 65 69 4 836.18 2.27 238 65 86 21 486.05 27.42 239 65 89 24 486.44 27.23 240 65 90 25 486.46 27.23 241 65 105 40 463.45 31.85 242 65 129 64 425.84 13.85 243 65 174 109 387.10 5.54 244 65 175 110 386.94 5.57 245 65 176 111 385.00 6.00 246 66 69 3 852.09 0.04 247 66 86 20 486.14 27.38 248 66 90 24 486.54 27.21 249 68 106 38 463.33 31.89 250 68 109 41 462.22 32.05 251 68 175 107 387.09 5.54 252 68 177 109 385.25 6.20 253 69 82 13 486.28 27.32 254 69 85 16 486.47 27.23 255 69 86 17 486.48 27.22 256 69 104 35 463.50 31.85 257 69 106 37 463.44 31.85 258 70 104 34 463.50 31.86 259 70 213 143 289.11 0.61 260 71 77 6 535.10 21.48 261 71 213 142 289.24 0.64 262 72 75 3 848.58 3.67 263 72 76 4 830.39 3.08 264 72 77 5 654.33 23.71 265 72 213 141 289.30 0.65 266 77 82 5 831.48 0.32 267 78 81 3 849.12 0.61 268 78 82 4 831.48 0.32 269 78 99 21 489.01 27.30 270 79 82 3 858.71 4.02 271 79 83 4 834.73 0.62 272 80 83 3 856.33 5.21 273 80 84 4 848.27 1.61 274 81 84 3 855.89 5.42 275 81 85 4 848.27 1.61 276 81 97 16 489.16 27.36 277 81 98 17 489.14 27.35 278 81 99 18 489.11 27.34 279 82 85 3 848.27 1.61 280 82 86 4 848.27 1.61 281 82 99 17 489.10 27.34 282 82 102 20 471.18 35.24 283 82 104 22 464.13 31.75 284 83 86 3 853.48 0.98 285 83 87 4 844.26 3.62 286 84 87 3 845.81 4.38 287 84 88 4 848.92 0.70 288 84 95 11 489.39 27.41 289 84 96 12 489.39 27.42 290 84 97 13 489.20 27.34 291 85 88 3 850.27 3.17 292 85 89 4 847.12 1.59 293 85 97 12 489.16 27.36 294 85 99 14 489.11 27.34 295 85 102 17 488.28 27.19 296 86 89 3 850.27 3.17 297 86 90 4 843.58 0.15 298 87 90 3 856.16 0.22 299 87 91 4 838.02 2.95 300 87 94 7 501.07 28.31 301 87 95 8 489.74 27.28 302 88 91 3 848.05 2.08 303 88 92 4 818.63 12.29 304 88 93 5 727.10 6.48 305 88 94 6 497.78 26.66 306 88 95 7 489.76 27.29 307 89 129 40 426.58 13.62 308 89 174 85 388.06 5.64 309 90 129 39 426.56 13.63 310 90 130 40 426.56 13.63 311 91 94 3 837.19 4.16 312 99 102 3 897.13 2.52 313 100 171 71 505.36 27.03 314 101 105 4 860.09 2.83 315 101 107 6 834.09 5.58 316 101 171 70 505.35 27.03 317 102 105 3 866.44 0.45 318 105 171 66 552.81 51.02 319 105 174 69 505.69 64.67 320 106 109 3 921.15 4.88 321 106 168 62 553.51 50.91 322 107 167 60 553.93 50.77 323 107 168 61 553.48 50.93 324 107 169 62 553.38 50.91 325 108 165 57 554.18 50.76 326 108 166 58 554.09 50.80 327 108 167 59 553.92 50.77 328 108 168 60 553.52 50.97 329 109 165 56 554.11 50.80 330 109 166 57 554.05 50.82 331 109 168 59 553.65 50.99 332 109 175 66 515.60 69.73 333 109 177 68 513.33 68.81 334 110 163 53 554.28 50.81 335 110 164 54 554.13 50.81 336 110 165 55 554.05 50.84 337 110 232 122 193.29 0.47 338 110 233 123 193.25 0.46 339 111 124 13 554.23 50.30 340 111 150 39 554.30 50.86 341 111 163 52 554.30 50.86 342 111 164 53 554.13 50.81 343 111 166 55 554.10 50.84 344 111 177 66 513.79 70.64 345 111 179 68 508.42 70.53 346 112 153 41 555.28 51.03 347 112 162 50 554.77 50.91 348 112 163 51 554.22 50.90 349 112 231 119 193.27 0.47 350 112 232 120 193.13 0.48 351 112 233 121 192.97 0.56 352 113 117 4 818.51 4.13 353 113 122 9 603.86 26.02 354 113 150 37 555.11 50.79 355 113 161 48 555.73 50.84 356 113 162 49 554.78 50.91 357 113 179 66 511.20 71.90 358 113 180 67 510.26 72.34 359 113 181 68 503.15 73.60 360 114 117 3 876.74 5.54 361 114 162 48 555.74 50.86 362 115 159 44 555.97 50.88 363 115 160 45 555.90 50.87 364 115 161 46 555.82 50.85 365 115 162 47 555.82 50.85 366 115 184 69 497.34 72.55 367 116 183 67 498.18 72.97 368 116 184 68 497.20 72.61 369 117 122 5 822.27 5.25 370 117 162 45 556.00 50.88 371 117 181 64 510.08 72.45 372 117 182 65 503.98 75.44 373 117 183 66 498.18 72.97 374 117 184 67 498.17 72.97 375 118 121 3 862.94 1.54 376 118 122 4 844.14 0.26 377 118 182 64 505.06 74.84 378 118 184 66 496.56 72.17 379 119 122 3 851.62 1.83 380 119 147 28 556.41 50.80 381 119 150 31 556.27 50.78 382 121 181 60 510.34 72.39 383 121 182 61 510.20 72.39 384 122 145 23 556.94 50.67 385 122 146 24 556.85 50.68 386 122 147 25 556.44 50.80 387 122 150 28 556.50 50.84 388 122 179 57 511.56 71.93 389 122 180 58 511.25 71.95 390 122 181 59 510.23 72.38 391 123 143 20 557.16 50.64 392 123 144 21 557.12 50.63 393 123 145 22 556.97 50.66 394 123 179 56 511.56 71.93 395 123 180 57 511.42 71.89 396 124 143 19 557.16 50.64 397 124 144 20 557.13 50.63 398 124 146 22 556.99 50.65 399 124 164 40 556.29 50.94 400 124 166 42 556.21 50.93 401 124 177 53 514.05 70.76 402 124 178 54 512.49 71.52 403 124 179 55 511.56 71.93 404 125 142 17 557.21 50.66 405 125 143 18 557.19 50.65 406 125 177 52 514.26 70.66 407 125 178 53 514.01 70.77 408 126 133 7 557.51 50.54 409 126 166 40 555.39 51.39 410 126 175 49 516.63 70.24 411 126 176 50 516.39 70.16 412 126 177 51 514.20 70.70 413 127 132 5 607.84 25.42 414 127 133 6 557.44 50.52 415 127 175 48 516.67 70.22 416 127 176 49 516.59 70.24 417 128 131 3 844.86 2.89 418 128 132 4 669.98 9.65 419 128 174 46 516.93 70.26 420 128 175 47 516.70 70.23 421 128 176 48 516.67 70.22 422 129 174 45 516.94 70.27 423 131 176 45 516.61 70.20 424 132 135 3 878.48 0.72 425 132 136 4 784.64 2.41 426 132 137 5 698.55 19.23 427 132 140 8 646.06 14.25 428 133 137 4 834.31 6.87 429 133 140 7 646.06 14.25 430 133 141 8 646.06 14.25 431 133 142 9 616.11 25.41 432 134 139 5 735.40 25.39 433 134 140 6 646.08 14.26 434 135 139 4 850.70 2.69 435 136 139 3 854.93 0.57 436 136 140 4 824.19 1.57 437 137 140 3 841.80 2.96 438 146 149 3 861.27 7.63 439 146 150 4 842.72 0.15 440 146 164 18 556.76 51.15 441 147 150 3 852.38 1.16 442 149 164 15 556.77 51.16 443 150 162 12 558.62 50.34 444 150 163 13 556.79 51.16 445 150 164 14 556.77 51.15 446 150 179 29 512.39 71.48 447 151 162 11 559.78 49.84 448 151 163 12 558.58 50.31 449 151 233 82 193.24 0.46 450 151 237 86 156.41 7.54 451 152 159 7 560.85 49.80 452 152 161 9 560.34 49.92 453 152 162 10 559.80 49.84 454 153 159 6 560.88 49.81 455 153 160 7 560.84 49.81 456 153 161 8 560.59 49.80 457 153 162 9 560.29 49.95 458 153 163 10 560.20 50.00 459 153 231 78 193.29 0.48 460 153 232 79 193.22 0.46 461 153 233 80 193.03 0.51 462 153 239 86 135.69 2.16 463 153 240 87 135.68 2.15 464 154 158 4 663.96 22.23 465 154 159 5 570.82 44.84 466 154 160 6 560.88 49.81 467 154 239 85 135.72 2.15 468 155 158 3 839.54 3.52 469 155 160 5 646.50 13.48 470 155 239 84 135.73 2.15 471 155 240 85 135.71 2.14 472 155 241 86 135.55 2.16 473 155 243 88 130.51 1.68 474 156 243 87 130.64 1.75 475 156 247 91 118.40 6.91 476 158 243 85 118.77 6.90 477 158 244 86 118.92 6.82 478 158 245 87 118.12 6.90 479 158 247 89 107.08 1.51 480 159 162 3 961.96 5.87 481 160 231 71 193.13 0.45 482 160 240 80 135.58 2.14 483 160 241 81 130.49 1.70 484 160 242 82 128.18 2.85 485 160 243 83 118.64 6.84 486 161 231 70 193.16 0.46 487 163 233 70 193.06 0.51 488 166 175 9 517.47 70.61 489 166 177 11 515.46 69.77 490 168 173 5 627.76 16.89 491 168 175 7 626.44 16.23 492 169 173 4 843.61 10.91 493 170 173 3 855.08 5.17 494 185 189 4 838.25 4.59 495 185 191 6 667.25 2.73 496 189 195 6 700.75 14.89 497 189 196 7 643.28 13.88 498 190 193 3 831.66 6.20 499 191 196 5 644.95 13.22 500 191 197 6 643.28 13.88 501 191 200 9 637.20 16.90 502 192 197 5 643.27 13.88 503 192 200 8 637.23 16.91 504 193 196 3 858.50 7.18 505 193 197 4 775.89 3.72 506 194 197 3 842.93 1.05 507 196 199 3 847.16 1.50 508 196 200 4 845.13 2.52 509 197 200 3 847.16 1.50 510 197 201 4 845.16 2.50 511 198 201 3 847.16 1.50 512 198 202 4 845.31 2.43 513 199 202 3 854.99 3.54 514 199 203 4 834.40 3.03 515 200 203 3 844.32 1.95 516 200 204 4 836.81 1.82 517 201 204 3 854.14 2.00 518 201 205 4 852.99 2.58 519 202 205 3 859.88 3.75 520 202 206 4 833.66 3.39 521 203 206 3 840.46 0.01 522 203 207 4 833.19 3.51 523 204 207 3 860.05 0.45 524 210 224 14 195.72 0.17 525 214 219 5 740.72 18.68 526 214 220 6 687.12 17.71 527 214 224 10 667.23 27.65 528 215 219 4 825.58 4.67 529 216 219 3 853.86 2.82 530 216 220 4 837.85 10.82 531 217 220 3 838.62 10.44 532 217 221 4 832.39 8.09 533 217 232 15 326.14 65.50 534 217 234 17 193.33 0.48 535 217 235 18 193.31 0.48 536 218 221 3 847.05 5.17 537 218 222 4 832.38 8.09 538 219 222 3 851.69 1.56 539 219 223 4 813.49 2.55 540 220 223 3 851.69 1.56 541 220 224 4 798.29 9.73 542 220 225 5 739.19 16.73 543 220 232 12 579.59 46.89 544 221 225 4 752.99 9.83 545 221 226 5 795.20 11.28 546 221 227 6 799.95 8.90 547 221 232 11 513.34 28.09 548 221 240 19 135.80 2.04 549 222 227 5 814.97 1.40 550 223 227 4 818.38 0.30 551 224 227 3 879.89 4.46 552 224 228 4 842.61 9.97 553 224 230 6 752.62 9.64 554 225 228 3 867.73 1.96 555 225 229 4 840.77 10.89 556 225 230 5 728.54 11.58 557 225 231 6 728.28 11.70 558 225 232 7 725.56 11.07 559 225 240 15 135.28 1.83 560 226 229 3 852.20 5.18 561 229 242 13 132.87 1.20 562 230 241 11 134.30 1.74 563 231 240 9 134.99 1.84 564 231 241 10 130.49 1.70 565 232 239 7 135.83 2.08 566 232 240 8 135.00 1.84 567 233 237 4 690.31 2.79 568 233 238 5 528.28 37.80 569 233 239 6 135.84 2.07 570 234 237 3 828.28 3.23 571 234 238 4 651.04 14.08 572 234 240 6 372.01 115.94 573 243 247 4 839.12 11.38 574 244 247 3 852.30 4.79