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 54 57 3 646.53 3.94 2 54 58 4 632.66 2.81 3 55 58 3 646.63 3.89 4 55 59 4 636.92 0.70 5 56 59 3 654.36 0.61 6 56 60 4 634.86 1.73 7 57 60 3 647.30 4.14 8 57 61 4 635.67 1.32 9 58 61 3 649.75 1.28 10 58 62 4 639.25 0.45 11 59 62 3 645.99 0.59 12 59 63 4 639.22 0.38 13 60 63 3 644.89 0.20 14 60 64 4 639.37 0.40 15 61 64 3 645.15 2.50 16 61 65 4 645.09 2.46 17 61 87 26 516.13 0.35 18 61 88 27 510.01 2.70 19 62 65 3 645.10 2.46 20 62 66 4 645.12 2.48 21 63 66 3 645.12 2.48 22 63 67 4 645.13 2.48 23 64 67 3 656.78 0.76 24 64 68 4 645.11 2.50 25 64 82 18 520.41 2.25 26 64 86 22 519.56 2.04 27 64 88 24 516.94 0.75 28 65 68 3 654.19 2.05 29 65 69 4 645.11 2.50 30 65 83 18 520.15 2.17 31 65 88 23 517.00 0.78 32 66 69 3 653.57 6.75 33 66 70 4 645.10 2.50 34 67 70 3 641.32 4.40 35 67 71 4 642.37 4.92 36 67 82 15 520.81 2.23 37 68 71 3 656.69 2.23 38 68 72 4 642.21 5.00 39 68 79 11 520.81 2.23 40 68 82 14 520.81 2.23 41 68 83 15 520.78 2.24 42 69 72 3 655.62 1.71 43 69 73 4 644.94 3.64 44 69 104 35 519.51 2.55 45 69 105 36 519.36 2.63 46 69 106 37 519.33 2.62 47 70 73 3 647.66 2.31 48 70 74 4 647.66 2.31 49 71 74 3 658.83 3.27 50 71 75 4 634.64 1.20 51 71 79 8 520.98 2.23 52 71 82 11 520.91 2.22 53 72 75 3 656.14 1.93 54 72 76 4 576.13 0.66 55 72 79 7 520.98 2.23 56 72 80 8 520.98 2.23 57 72 100 28 519.90 2.41 58 72 106 34 519.51 2.58 59 72 110 38 519.25 2.57 60 72 111 39 519.24 2.58 61 72 114 42 519.10 2.60 62 73 105 32 519.58 2.58 63 73 106 33 519.50 2.58 64 73 107 34 519.41 2.58 65 73 110 37 519.23 2.56 66 75 78 3 647.12 3.38 67 75 79 4 637.02 1.67 68 76 79 3 649.38 4.65 69 76 80 4 639.10 0.62 70 76 110 34 519.25 2.57 71 76 113 37 519.15 2.60 72 76 114 38 519.05 2.58 73 77 80 3 663.43 2.38 74 77 81 4 639.09 0.62 75 77 114 37 519.10 2.60 76 77 117 40 516.58 2.06 77 77 119 42 462.42 5.13 78 78 81 3 649.99 2.47 79 78 82 4 639.08 0.61 80 79 82 3 648.78 1.86 81 79 83 4 639.08 0.61 82 80 83 3 641.45 1.79 83 80 84 4 641.41 1.81 84 80 89 9 520.59 2.50 85 80 96 16 520.11 2.44 86 80 99 19 520.11 2.47 87 80 114 34 519.10 2.60 88 81 84 3 637.43 0.22 89 81 85 4 637.38 0.21 90 82 85 3 652.42 2.04 91 82 86 4 641.07 3.64 92 83 86 3 656.21 0.14 93 83 87 4 631.27 1.25 94 83 88 5 598.79 14.96 95 83 89 6 520.59 2.50 96 83 99 16 520.10 2.48 97 84 87 3 638.74 4.80 98 84 89 5 572.14 28.27 99 84 91 7 520.50 2.53 100 89 95 6 563.27 3.66 101 89 96 7 535.60 10.18 102 89 99 10 520.65 2.76 103 90 95 5 574.66 9.32 104 90 96 6 599.10 2.89 105 91 96 5 609.50 2.27 106 91 121 30 454.22 2.27 107 92 95 3 641.60 4.88 108 92 96 4 633.89 2.66 109 93 96 3 657.51 1.19 110 93 97 4 633.88 2.66 111 93 121 28 454.25 2.25 112 93 124 31 454.14 2.27 113 93 125 32 454.12 2.28 114 93 128 35 453.67 2.23 115 94 97 3 638.27 0.47 116 94 98 4 633.88 2.66 117 94 128 34 453.44 2.33 118 95 98 3 643.20 2.95 119 95 99 4 638.25 0.48 120 96 99 3 644.42 3.89 121 96 100 4 633.43 1.93 122 96 114 18 519.34 2.70 123 96 121 25 454.26 2.25 124 96 125 29 454.13 2.27 125 97 100 3 651.77 0.21 126 97 101 4 635.00 2.71 127 97 125 28 454.14 2.27 128 97 128 31 453.45 2.33 129 97 129 32 453.31 2.29 130 97 132 35 446.67 1.98 131 98 101 3 644.66 3.77 132 98 102 4 634.97 2.73 133 98 132 34 446.74 2.03 134 99 102 3 648.89 3.65 135 99 103 4 634.86 2.79 136 99 106 7 557.58 4.20 137 100 103 3 634.86 2.79 138 100 106 6 531.86 8.66 139 100 111 11 519.53 2.62 140 100 114 14 519.37 2.71 141 100 115 15 519.33 2.71 142 100 125 25 454.19 2.25 143 100 129 29 453.31 2.29 144 101 129 28 453.31 2.29 145 101 132 31 444.25 0.79 146 101 133 32 444.22 0.78 147 103 106 3 624.77 12.03 148 103 111 8 519.62 2.63 149 106 111 5 624.40 2.25 150 107 110 3 653.61 1.27 151 107 111 4 636.96 2.56 152 108 111 3 646.58 2.25 153 108 112 4 636.96 2.56 154 108 149 41 375.28 0.98 155 108 150 42 375.26 0.97 156 108 151 43 375.19 0.97 157 108 152 44 375.17 0.97 158 108 246 138 26.18 0.30 159 109 112 3 652.34 0.81 160 109 113 4 635.98 3.04 161 109 152 43 375.13 0.98 162 110 113 3 652.34 0.81 163 110 114 4 635.98 3.04 164 111 114 3 657.33 5.03 165 111 115 4 629.51 0.18 166 111 150 39 375.26 0.97 167 111 151 40 375.21 0.98 168 112 115 3 650.41 4.35 169 112 116 4 629.80 0.33 170 112 151 39 375.24 0.98 171 112 152 40 375.19 0.98 172 112 154 42 374.68 0.95 173 112 163 51 374.36 1.01 174 113 116 3 657.53 0.79 175 113 117 4 633.77 1.66 176 114 117 3 667.74 5.78 177 114 122 8 454.25 2.25 178 114 125 11 454.25 2.26 179 115 125 10 454.25 2.26 180 115 126 11 454.11 2.26 181 115 129 14 453.55 2.28 182 115 151 36 375.25 0.98 183 115 163 48 374.35 1.01 184 116 159 43 374.38 0.98 185 116 162 46 374.39 1.00 186 116 163 47 374.37 0.99 187 117 122 5 558.57 13.78 188 117 123 6 579.94 5.88 189 118 123 5 619.22 0.83 190 118 162 44 374.38 1.00 191 119 122 3 654.16 2.27 192 119 123 4 633.98 4.12 193 120 123 3 653.50 2.64 194 120 124 4 635.68 3.27 195 121 124 3 640.47 3.26 196 121 125 4 643.04 0.41 197 122 125 3 654.78 1.99 198 122 126 4 641.19 1.34 199 123 126 3 652.96 1.07 200 123 127 4 640.00 7.55 201 123 162 39 374.41 0.99 202 124 127 3 654.45 0.33 203 124 128 4 638.32 8.40 204 125 128 3 654.46 0.34 205 125 129 4 638.33 8.40 206 126 129 3 653.41 0.85 207 126 130 4 637.41 0.30 208 126 162 36 374.47 1.02 209 126 163 37 374.37 1.01 210 126 166 40 368.17 0.35 211 127 130 3 653.14 0.99 212 127 131 4 638.71 0.17 213 128 131 3 651.48 2.14 214 128 132 4 639.27 0.12 215 129 132 3 659.73 2.73 216 129 133 4 639.28 0.12 217 129 150 21 375.39 0.99 218 129 151 22 375.33 0.99 219 130 133 3 650.26 1.97 220 130 147 17 375.55 0.99 221 130 166 36 368.19 0.35 222 130 167 37 368.15 0.35 223 130 170 40 362.44 0.83 224 131 170 39 362.46 0.83 225 133 146 13 375.56 0.99 226 133 147 14 375.56 0.99 227 133 150 17 375.47 0.98 228 133 170 37 365.08 1.33 229 134 138 4 672.01 3.85 230 134 146 12 375.74 0.93 231 134 170 36 367.89 0.46 232 135 138 3 657.25 0.49 233 135 143 8 375.74 0.93 234 135 146 11 375.81 0.89 235 135 147 12 375.73 0.93 236 135 167 32 374.28 0.96 237 135 170 35 367.98 0.43 238 135 171 36 365.08 1.33 239 135 174 39 338.67 5.32 240 135 175 40 316.25 1.34 241 136 174 38 342.23 3.54 242 136 175 39 334.12 7.59 243 137 175 38 342.24 3.54 244 138 142 4 628.49 4.62 245 138 143 5 600.91 5.87 246 138 146 8 600.36 6.00 247 138 171 33 368.12 0.36 248 139 142 3 646.18 1.74 249 139 143 4 628.52 4.62 250 139 171 32 368.14 0.36 251 139 234 95 99.05 0.36 252 140 143 3 648.86 3.72 253 140 144 4 636.72 1.89 254 140 167 27 374.62 1.03 255 140 171 31 368.03 0.40 256 140 179 39 306.98 1.75 257 140 185 45 252.18 5.58 258 140 188 48 252.02 5.57 259 140 189 49 251.99 5.57 260 140 192 52 251.34 5.30 261 140 234 94 99.05 0.36 262 141 144 3 641.98 0.73 263 141 145 4 638.61 0.95 264 141 192 51 250.87 5.15 265 141 234 93 99.04 0.35 266 141 237 96 98.10 0.31 267 141 238 97 98.08 0.30 268 141 243 102 44.85 0.68 269 142 145 3 645.99 1.27 270 142 146 4 638.61 0.95 271 143 146 3 647.06 1.20 272 143 147 4 638.04 0.66 273 143 167 24 374.26 0.95 274 143 171 28 363.47 0.33 275 144 147 3 644.69 1.20 276 144 148 4 638.02 0.67 277 144 164 20 374.69 1.01 278 144 167 23 371.52 1.05 279 144 189 45 251.45 5.36 280 144 192 48 250.84 5.15 281 144 193 49 246.58 3.62 282 144 243 99 42.72 1.16 283 145 148 3 659.40 1.65 284 145 149 4 647.15 0.07 285 145 237 92 98.06 0.29 286 145 238 93 97.68 0.11 287 145 241 96 53.75 0.04 288 145 242 97 52.62 0.21 289 145 243 98 42.72 1.16 290 146 149 3 659.39 1.65 291 146 150 4 654.85 3.92 292 147 150 3 655.50 3.60 293 147 151 4 654.86 3.93 294 147 163 16 374.66 1.02 295 147 164 17 374.61 1.04 296 147 167 20 368.16 0.35 297 148 151 3 669.75 4.70 298 148 153 5 626.66 3.01 299 148 193 45 243.92 2.29 300 148 243 95 42.72 1.16 301 148 245 97 39.91 1.00 302 148 246 98 39.76 0.93 303 149 244 95 39.96 1.02 304 149 245 96 39.70 0.92 305 149 246 97 34.76 1.51 306 151 163 12 374.50 1.03 307 151 246 95 30.19 1.65 308 152 245 93 37.89 1.85 309 152 246 94 30.30 1.65 310 153 160 7 461.16 44.27 311 153 163 10 374.60 1.04 312 154 159 5 583.19 4.22 313 154 160 6 564.25 0.86 314 154 163 9 466.82 47.08 315 155 160 5 636.13 1.42 316 156 159 3 651.62 2.75 317 156 160 4 636.37 1.31 318 157 160 3 651.62 2.75 319 157 161 4 642.59 1.75 320 158 161 3 651.64 2.77 321 158 162 4 651.63 2.77 322 159 162 3 655.78 0.69 323 159 163 4 645.63 0.23 324 160 163 3 653.49 1.83 325 160 164 4 642.58 1.74 326 160 190 30 251.27 5.37 327 161 164 3 654.00 0.97 328 161 165 4 642.56 1.75 329 161 186 25 252.02 5.58 330 162 165 3 651.90 1.24 331 162 166 4 643.37 1.32 332 163 166 3 644.34 1.05 333 163 167 4 639.86 0.50 334 164 167 3 634.59 1.35 335 164 168 4 635.36 1.69 336 164 186 22 252.01 5.58 337 164 189 25 251.33 5.38 338 164 190 26 251.31 5.37 339 164 193 29 247.09 3.31 340 165 168 3 642.74 1.70 341 165 169 4 635.37 1.69 342 165 186 21 252.01 5.58 343 166 169 3 645.14 0.70 344 166 170 4 635.57 1.78 345 167 170 3 647.76 0.17 346 167 171 4 635.58 1.80 347 167 189 22 251.34 5.38 348 168 171 3 646.68 0.38 349 168 172 4 635.56 1.82 350 168 182 14 252.15 5.59 351 168 185 17 252.06 5.59 352 168 186 18 252.02 5.58 353 169 172 3 654.11 3.33 354 169 173 4 635.55 1.82 355 169 182 13 252.14 5.59 356 170 173 3 648.33 4.57 357 170 174 4 635.40 1.89 358 171 174 3 652.40 5.26 359 171 175 4 624.46 0.26 360 171 178 7 585.69 14.92 361 171 179 8 298.95 2.27 362 171 185 14 252.15 5.58 363 172 175 3 646.65 4.31 364 172 176 4 618.05 1.25 365 172 179 7 295.34 0.46 366 172 182 10 252.17 5.58 367 172 185 13 252.18 5.58 368 173 176 3 657.63 1.18 369 175 178 3 663.44 0.12 370 176 180 4 646.37 0.10 371 177 180 3 695.49 1.39 372 178 230 52 106.44 1.20 373 179 184 5 542.27 0.30 374 179 185 6 258.19 8.54 375 179 188 9 268.86 2.71 376 179 226 47 111.47 1.17 377 179 230 51 108.93 2.43 378 180 222 42 113.41 1.14 379 181 184 3 647.48 7.04 380 181 185 4 629.07 3.53 381 181 222 41 113.28 1.07 382 182 185 3 646.61 7.48 383 182 186 4 616.47 2.52 384 183 186 3 654.85 3.56 385 183 187 4 629.88 2.65 386 184 187 3 645.11 1.31 387 184 188 4 629.89 2.66 388 184 220 36 113.44 1.12 389 184 221 37 113.39 1.12 390 184 226 42 111.62 1.10 391 185 188 3 648.35 0.42 392 185 189 4 636.08 5.75 393 186 189 3 648.69 0.25 394 186 190 4 636.94 5.69 395 187 190 3 649.04 0.37 396 187 191 4 649.03 0.36 397 187 220 33 113.44 1.13 398 188 191 3 649.03 0.36 399 188 192 4 649.02 0.36 400 188 213 25 113.73 1.14 401 188 217 29 113.59 1.18 402 188 220 32 113.45 1.13 403 188 226 38 109.12 2.34 404 188 231 43 106.28 1.09 405 188 234 46 103.20 0.36 406 189 192 3 651.61 1.65 407 189 193 4 649.02 0.37 408 190 193 3 648.61 0.58 409 190 194 4 634.69 6.38 410 191 194 3 656.56 2.58 411 191 195 4 631.41 4.75 412 191 213 22 113.66 1.18 413 191 217 26 113.59 1.18 414 192 195 3 647.00 2.20 415 192 196 4 646.41 2.10 416 192 234 42 100.27 0.00 417 192 238 46 99.12 0.38 418 192 243 51 54.20 0.27 419 193 196 3 654.45 5.62 420 193 197 4 646.82 2.29 421 193 243 50 53.63 0.07 422 194 197 3 654.00 5.84 423 194 198 4 653.97 5.86 424 195 198 3 659.79 2.94 425 195 199 4 636.89 2.69 426 195 208 13 126.59 2.43 427 195 213 18 113.73 1.14 428 195 235 40 101.20 0.46 429 195 238 43 100.14 0.05 430 196 199 3 659.79 2.94 431 196 200 4 629.74 6.25 432 196 238 42 99.72 0.18 433 196 242 46 54.66 0.04 434 196 243 47 54.20 0.27 435 197 200 3 657.04 1.57 436 197 201 4 571.90 15.96 437 197 204 7 159.13 0.06 438 198 204 6 151.77 0.89 439 198 207 9 134.05 1.22 440 198 208 10 126.75 2.42 441 199 207 8 134.07 1.23 442 199 208 9 134.07 1.23 443 199 235 36 106.50 1.18 444 199 238 39 100.47 0.10 445 199 239 40 100.12 0.07 446 200 238 38 100.45 0.11 447 200 239 39 100.22 0.04 448 200 242 42 91.06 1.40 449 201 204 3 659.50 4.00 450 201 207 6 225.65 21.93 451 202 207 5 624.51 2.58 452 204 207 3 698.36 2.90 453 208 212 4 591.23 4.46 454 208 235 27 107.73 1.70 455 209 212 3 668.35 2.14 456 209 213 4 640.78 2.85 457 209 235 26 107.84 1.75 458 210 213 3 655.94 4.07 459 210 214 4 640.75 2.88 460 210 231 21 109.08 2.35 461 210 232 22 108.98 2.35 462 210 235 25 107.74 1.69 463 211 214 3 644.93 1.23 464 211 215 4 641.20 3.08 465 211 218 7 634.44 0.29 466 212 215 3 644.54 2.46 467 212 216 4 640.79 2.87 468 213 216 3 645.98 1.80 469 213 217 4 644.46 1.04 470 213 231 18 109.08 2.35 471 213 235 22 107.70 1.70 472 214 217 3 665.08 1.84 473 214 218 4 644.46 1.04 474 214 228 14 109.11 2.35 475 214 231 17 109.09 2.34 476 215 218 3 653.93 2.02 477 217 220 3 656.71 1.79 478 217 231 14 109.09 2.34 479 218 225 7 140.28 2.49 480 219 223 4 156.56 2.06 481 219 224 5 145.97 2.85 482 219 225 6 142.78 1.28 483 220 224 4 501.49 36.51 484 220 226 6 148.60 1.55 485 221 224 3 574.31 4.23 486 221 225 4 164.35 0.62 487 221 226 5 152.94 0.27 488 226 230 4 652.79 4.49 489 226 231 5 608.17 3.14 490 227 230 3 657.35 2.21 491 227 231 4 652.79 4.49 492 228 231 3 655.98 2.89 493 228 232 4 631.14 6.33 494 229 232 3 656.35 6.28 495 229 233 4 631.15 6.32 496 230 233 3 643.66 0.33 497 230 234 4 633.85 3.93 498 231 234 3 643.67 0.33 499 231 235 4 626.05 1.47 500 232 235 3 645.02 0.24 501 232 236 4 633.70 5.29 502 233 236 3 652.22 3.96 503 233 237 4 630.35 6.98 504 234 237 3 638.30 3.01 505 234 238 4 625.39 9.46 506 235 238 3 648.28 1.99 507 235 239 4 621.20 11.55 508 236 239 3 636.84 3.71 509 236 240 4 606.80 4.36 510 237 240 3 638.63 2.81 511 237 241 4 606.38 6.13 512 238 241 3 645.20 1.15 513 238 243 5 573.54 7.87