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 1 35 34 258.95 0.91 2 1 56 55 172.42 0.69 3 1 57 56 172.33 0.69 4 1 58 57 171.87 0.79 5 1 59 58 171.78 0.83 6 2 32 30 259.07 0.89 7 2 33 31 259.04 0.90 8 2 34 32 258.99 0.90 9 2 35 33 258.98 0.90 10 2 60 58 171.77 0.83 11 2 61 59 171.50 0.96 12 2 62 60 171.50 0.96 13 2 189 187 34.58 0.07 14 2 192 190 19.71 0.63 15 3 35 32 258.99 0.90 16 3 37 34 258.98 0.90 17 3 53 50 172.44 0.68 18 3 58 55 172.33 0.69 19 3 60 57 172.09 0.70 20 3 61 58 171.53 0.96 21 3 62 59 171.50 0.96 22 4 22 18 259.18 0.83 23 4 25 21 259.14 0.85 24 4 34 30 259.08 0.89 25 4 35 31 259.05 0.90 26 4 36 32 258.99 0.90 27 4 37 33 258.98 0.90 28 4 62 58 171.56 0.94 29 4 64 60 171.50 0.96 30 4 185 181 57.91 0.18 31 4 189 185 45.48 0.36 32 5 22 17 259.20 0.83 33 5 37 32 258.98 0.90 34 5 39 34 258.97 0.90 35 5 53 48 173.41 0.73 36 5 62 57 172.19 0.69 37 5 63 58 171.80 0.83 38 5 64 59 171.51 0.96 39 6 18 12 259.45 0.87 40 6 22 16 259.20 0.83 41 6 37 31 259.05 0.90 42 6 38 32 258.99 0.90 43 6 39 33 258.99 0.90 44 6 64 58 171.81 0.82 45 7 16 9 259.98 0.88 46 7 18 11 259.58 0.82 47 7 19 12 259.59 0.82 48 7 38 31 259.02 0.90 49 7 39 32 258.99 0.90 50 7 40 33 258.99 0.90 51 7 41 34 258.94 0.90 52 7 46 39 181.88 0.57 53 7 64 57 172.24 0.69 54 7 65 58 172.11 0.71 55 7 138 131 176.08 0.32 56 7 139 132 172.38 0.70 57 7 142 135 173.57 0.82 58 8 16 8 260.01 0.86 59 8 38 30 259.08 0.88 60 8 39 31 259.05 0.90 61 8 40 32 259.00 0.90 62 8 41 33 258.99 0.90 63 8 90 82 211.66 0.18 64 9 13 4 547.81 10.78 65 9 14 5 260.32 0.87 66 9 15 6 260.17 0.93 67 9 16 7 260.02 0.87 68 9 19 10 260.01 0.86 69 9 90 81 211.69 0.19 70 10 13 3 667.63 2.12 71 10 16 6 260.20 0.93 72 10 41 31 259.04 0.90 73 10 66 56 172.40 0.69 74 10 68 58 172.35 0.68 75 10 87 77 211.55 0.14 76 10 90 80 211.66 0.18 77 10 137 127 195.62 1.87 78 11 87 76 211.52 0.12 79 11 90 79 211.77 0.15 80 15 20 5 654.40 2.52 81 15 164 149 171.56 0.85 82 15 166 151 133.16 1.93 83 15 167 152 124.92 0.51 84 16 19 3 664.11 2.24 85 16 20 4 663.46 1.83 86 16 66 50 172.18 0.70 87 17 20 3 663.46 1.83 88 17 21 4 663.29 1.92 89 17 66 49 172.17 0.70 90 17 161 144 172.16 0.70 91 17 163 146 170.97 0.83 92 17 164 147 143.99 1.11 93 17 167 150 124.92 0.51 94 17 178 161 65.29 0.65 95 17 181 164 64.96 0.77 96 18 21 3 668.92 3.79 97 18 22 4 668.92 3.79 98 18 64 46 172.18 0.70 99 18 65 47 172.16 0.70 100 18 161 143 171.99 0.69 101 19 22 3 686.32 0.76 102 19 38 19 259.07 0.89 103 20 23 3 687.63 0.89 104 20 178 158 64.78 0.85 105 21 24 3 672.03 2.35 106 21 25 4 660.37 0.38 107 21 64 43 172.18 0.70 108 21 161 140 172.02 0.70 109 21 178 157 64.78 0.85 110 21 181 160 64.73 0.87 111 21 182 161 64.48 0.96 112 21 185 164 58.09 0.20 113 22 25 3 660.45 0.34 114 22 36 14 259.19 0.89 115 22 37 15 259.18 0.88 116 22 38 16 259.17 0.89 117 22 64 42 172.15 0.71 118 24 178 154 64.77 0.84 119 24 179 155 64.77 0.84 120 24 182 158 64.49 0.96 121 25 34 9 396.25 66.66 122 25 36 11 388.65 63.62 123 25 182 157 64.39 0.92 124 25 185 160 58.12 0.18 125 25 186 161 58.07 0.19 126 25 189 164 51.59 1.49 127 26 29 3 719.31 3.42 128 26 34 8 396.27 66.67 129 26 36 10 396.25 66.66 130 26 186 160 58.09 0.20 131 27 33 6 396.44 66.69 132 27 34 7 396.36 66.70 133 27 36 9 396.34 66.70 134 28 31 3 668.83 2.21 135 28 32 4 579.46 3.15 136 28 33 5 396.44 66.69 137 28 34 6 396.42 66.68 138 29 32 3 661.46 3.42 139 29 34 5 564.45 16.21 140 29 186 157 57.30 0.11 141 29 189 160 46.37 0.38 142 29 190 161 45.69 0.10 143 30 189 159 46.66 0.24 144 30 190 160 46.29 0.41 145 34 189 155 46.06 0.29 146 35 53 18 172.49 0.70 147 35 56 21 172.41 0.69 148 37 53 16 172.63 0.71 149 39 46 7 508.20 1.05 150 39 49 10 178.09 0.90 151 39 50 11 219.78 21.78 152 39 53 14 177.93 0.90 153 39 63 24 172.38 0.70 154 39 142 103 176.98 1.05 155 40 45 5 556.56 10.38 156 40 46 6 522.32 0.95 157 40 49 9 223.04 20.28 158 40 138 98 178.53 0.69 159 41 89 48 211.50 0.13 160 41 90 49 211.65 0.18 161 41 137 96 182.80 1.20 162 41 138 97 178.52 0.70 163 42 45 3 652.97 1.01 164 42 46 4 624.45 2.96 165 42 89 47 211.65 0.18 166 42 91 49 211.75 0.15 167 42 138 96 185.10 0.71 168 43 46 3 661.24 4.83 169 43 85 42 211.53 0.13 170 43 89 46 211.78 0.16 171 43 95 52 211.49 0.14 172 43 138 95 188.09 0.12 173 43 141 98 187.43 0.46 174 44 93 49 211.87 0.12 175 45 48 3 680.85 0.62 176 45 49 4 658.08 1.28 177 46 49 3 659.79 0.50 178 46 50 4 658.08 1.28 179 46 138 92 211.55 0.03 180 46 141 95 211.58 0.04 181 46 142 96 211.31 0.09 182 46 145 99 211.59 0.03 183 47 50 3 671.77 0.35 184 47 51 4 663.27 3.90 185 47 145 98 211.61 0.03 186 47 149 102 269.80 0.64 187 48 51 3 677.22 3.07 188 48 52 4 663.27 3.90 189 49 52 3 680.51 1.42 190 49 53 4 670.78 0.14 191 50 53 3 670.28 0.10 192 50 54 4 670.28 0.10 193 50 63 13 194.88 3.81 194 50 142 92 212.01 0.09 195 50 145 95 212.09 0.11 196 50 146 96 212.06 0.11 197 51 54 3 670.29 0.09 198 51 55 4 670.28 0.10 199 51 149 98 308.07 4.49 200 52 55 3 676.06 1.87 201 52 56 4 673.15 1.33 202 53 56 3 677.08 0.62 203 53 58 5 653.35 0.23 204 54 57 3 673.43 1.20 205 54 58 4 653.18 0.14 206 54 146 92 301.25 7.89 207 54 149 95 326.22 0.08 208 54 150 96 326.22 0.09 209 58 61 3 706.55 0.74 210 59 154 95 408.01 1.43 211 59 155 96 408.01 1.43 212 60 154 94 408.01 1.43 213 60 155 95 408.01 1.43 214 60 192 132 22.43 0.27 215 61 150 89 408.17 1.43 216 61 154 93 408.11 1.44 217 61 155 94 408.05 1.43 218 61 156 95 408.01 1.43 219 61 157 96 408.01 1.43 220 62 112 50 408.03 1.43 221 62 157 95 408.01 1.43 222 62 158 96 408.00 1.43 223 62 159 97 407.98 1.43 224 62 185 123 57.93 0.18 225 62 188 126 46.38 0.38 226 62 189 127 46.27 0.42 227 62 192 130 29.05 1.31 228 63 142 79 408.11 1.41 229 63 143 80 408.07 1.42 230 63 146 83 408.18 1.42 231 63 156 93 408.12 1.44 232 63 157 94 408.05 1.44 233 63 158 95 408.00 1.43 234 63 159 96 408.00 1.43 235 64 158 94 408.05 1.43 236 64 159 95 408.02 1.43 237 64 161 97 407.94 1.44 238 64 185 121 57.95 0.17 239 65 139 74 408.12 1.42 240 65 158 93 408.12 1.44 241 65 159 94 408.06 1.44 242 65 160 95 408.00 1.43 243 65 161 96 408.00 1.44 244 66 160 94 408.05 1.44 245 66 161 95 408.00 1.44 246 66 162 96 407.98 1.43 247 66 163 97 407.88 1.47 248 66 167 101 316.66 2.21 249 67 70 3 668.33 1.96 250 67 160 93 408.09 1.44 251 67 161 94 408.05 1.44 252 67 162 95 408.00 1.43 253 67 163 96 408.00 1.43 254 68 163 95 408.01 1.43 255 68 173 105 79.12 0.98 256 70 74 4 689.89 0.90 257 70 76 6 674.43 2.08 258 70 129 59 499.36 0.22 259 70 131 61 442.26 2.53 260 70 133 63 430.93 0.54 261 70 160 90 408.23 1.43 262 70 162 92 408.10 1.44 263 70 163 93 408.10 1.44 264 71 162 91 408.13 1.44 265 71 174 103 72.48 0.29 266 71 176 105 71.34 0.83 267 72 127 55 501.28 0.90 268 72 128 56 501.25 0.90 269 72 129 57 501.25 0.90 270 72 162 90 408.18 1.43 271 72 176 104 71.28 0.82 272 73 121 48 501.62 0.95 273 73 126 53 501.55 0.94 274 73 128 55 501.28 0.90 275 73 129 56 501.28 0.90 276 73 159 86 408.38 1.41 277 73 160 87 408.29 1.42 278 73 161 88 408.24 1.42 279 73 162 89 408.24 1.43 280 73 181 108 65.36 0.68 281 73 184 111 65.06 0.78 282 74 129 55 501.28 0.91 283 74 131 57 501.15 0.86 284 74 159 85 408.41 1.41 285 74 160 86 408.31 1.42 286 75 112 37 502.44 0.91 287 75 114 39 502.32 0.95 288 75 117 42 502.31 0.95 289 75 118 43 502.18 0.88 290 75 121 46 502.16 0.89 291 75 129 54 501.53 0.96 292 75 130 55 501.29 0.91 293 75 131 56 501.28 0.91 294 75 158 83 408.63 1.40 295 75 159 84 408.29 1.45 296 76 110 34 502.68 0.94 297 76 114 38 502.40 0.93 298 76 131 55 501.29 0.91 299 76 133 57 500.87 1.01 300 76 134 58 491.27 2.25 301 76 143 67 444.94 0.17 302 76 158 82 408.66 1.40 303 76 160 84 408.60 1.39 304 77 109 32 502.75 0.93 305 77 110 33 502.69 0.95 306 77 114 37 502.43 0.92 307 77 130 53 501.59 0.96 308 77 131 54 501.51 0.94 309 77 132 55 501.29 0.91 310 78 107 29 503.03 0.89 311 78 108 30 502.81 0.92 312 78 109 31 502.75 0.93 313 78 110 32 502.74 0.93 314 78 132 54 501.51 0.94 315 78 143 65 445.51 0.21 316 79 107 28 503.09 0.92 317 79 108 29 502.98 0.88 318 79 140 61 457.75 0.71 319 79 143 64 445.51 0.21 320 79 144 65 445.75 0.04 321 79 147 68 444.67 0.09 322 80 100 20 504.20 0.59 323 80 106 26 503.19 0.89 324 80 107 27 503.10 0.92 325 80 135 55 501.50 0.95 326 80 140 60 459.69 0.57 327 80 144 64 457.76 0.65 328 81 99 18 504.23 0.59 329 81 100 19 504.17 0.60 330 81 101 20 504.16 0.60 331 81 104 23 503.26 0.88 332 81 105 24 503.24 0.89 333 81 106 25 503.19 0.90 334 81 144 63 458.77 0.37 335 82 97 15 504.97 0.68 336 82 98 16 504.74 0.71 337 82 99 17 504.24 0.58 338 82 100 18 504.22 0.59 339 82 136 54 501.50 0.95 340 82 140 58 489.56 3.10 341 83 95 12 505.06 0.69 342 83 96 13 505.06 0.70 343 83 97 14 505.04 0.70 344 83 98 15 504.85 0.66 345 83 99 16 504.49 0.58 346 83 100 17 504.46 0.57 347 83 136 53 501.50 0.95 348 83 141 58 469.75 2.10 349 84 95 11 505.10 0.70 350 84 96 12 505.06 0.70 351 84 97 13 505.06 0.70 352 84 136 52 501.56 0.97 353 85 89 4 671.14 0.79 354 85 93 8 505.50 0.73 355 85 94 9 505.12 0.71 356 85 95 10 505.12 0.70 357 85 136 51 501.93 0.86 358 85 137 52 501.55 0.97 359 86 137 51 501.99 0.89 360 87 137 50 502.03 0.90 361 88 92 4 514.41 5.16 362 88 93 5 505.56 0.76 363 88 94 6 505.50 0.76 364 88 137 49 502.05 0.90 365 89 92 3 653.11 0.09 366 89 93 4 517.16 3.77 367 89 137 48 502.03 0.89 368 89 138 49 502.00 0.88 369 95 98 3 710.63 2.49 370 99 102 3 661.37 3.35 371 100 140 40 495.57 0.39 372 100 141 41 468.12 2.83 373 100 144 44 460.21 0.26 374 100 145 45 459.76 0.18 375 101 104 3 655.50 3.83 376 101 144 43 460.25 0.26 377 101 145 44 460.15 0.29 378 101 148 47 446.15 0.16 379 104 144 40 460.23 0.27 380 104 148 44 445.81 0.25 381 105 108 3 699.38 2.75 382 105 144 39 460.16 0.29 383 105 148 43 445.78 0.24 384 108 144 36 445.79 0.04 385 108 147 39 444.45 0.02 386 108 148 40 444.37 0.05 387 109 147 38 444.44 0.02 388 110 143 33 445.48 0.20 389 110 147 37 444.29 0.07 390 110 156 46 408.95 1.41 391 111 147 36 443.77 0.33 392 111 150 39 431.78 2.16 393 111 151 40 417.85 2.47 394 111 152 41 409.34 1.46 395 111 154 43 409.20 1.43 396 111 155 44 409.04 1.43 397 111 156 45 408.96 1.41 398 112 117 5 654.28 0.59 399 112 156 44 409.09 1.45 400 112 157 45 408.84 1.47 401 112 188 76 52.38 1.83 402 112 192 80 42.62 0.83 403 113 116 3 673.77 4.55 404 113 117 4 654.28 0.59 405 113 191 78 45.94 0.59 406 114 117 3 679.39 1.74 407 114 118 4 667.97 7.45 408 114 130 16 501.54 0.95 409 115 118 3 679.38 1.74 410 115 119 4 652.21 1.62 411 116 119 3 662.54 4.75 412 116 120 4 653.14 1.16 413 116 191 75 51.01 1.17 414 117 120 3 653.54 0.26 415 117 121 4 652.41 0.80 416 117 188 71 57.30 0.42 417 117 191 74 46.32 0.41 418 118 121 3 668.47 7.19 419 118 122 4 653.18 1.18 420 118 128 10 501.63 0.97 421 118 129 11 501.63 0.97 422 118 130 12 501.62 0.97 423 119 122 3 670.04 0.70 424 119 123 4 668.23 0.21 425 120 123 3 670.05 0.70 426 120 124 4 660.96 3.43 427 120 187 67 58.26 0.11 428 120 191 71 57.45 0.41 429 121 124 3 655.88 0.17 430 121 125 4 655.88 0.17 431 121 126 5 617.18 10.67 432 121 128 7 566.70 4.83 433 121 159 38 409.19 1.47 434 121 184 63 64.58 0.92 435 121 187 66 58.37 0.17 436 121 188 67 58.38 0.18 437 122 125 3 655.88 0.18 438 122 126 4 640.52 1.23 439 124 183 59 65.30 0.65 440 124 187 63 64.78 0.81 441 126 180 54 65.42 0.66 442 126 183 57 65.39 0.66 443 126 184 58 65.36 0.66 444 126 187 61 65.06 0.71 445 134 140 6 486.84 15.25 446 134 160 26 408.31 1.52 447 135 140 5 593.42 5.12 448 136 140 4 638.95 2.58 449 137 140 3 668.11 0.06 450 137 141 4 660.76 3.72 451 138 141 3 662.51 2.86 452 138 142 4 658.11 5.05 453 139 142 3 668.05 0.09 454 139 143 4 658.12 5.04 455 139 158 19 408.50 1.43 456 139 160 21 408.19 1.51 457 140 143 3 668.03 0.08 458 140 144 4 658.99 1.70 459 141 144 3 667.07 0.41 460 141 145 4 658.98 1.69 461 142 145 3 664.08 1.08 462 142 146 4 658.98 1.70 463 143 146 3 669.74 3.92 464 143 147 4 658.97 1.69 465 143 156 13 408.67 1.40 466 143 157 14 408.61 1.40 467 143 158 15 408.31 1.44 468 144 147 3 668.03 0.07 469 144 148 4 656.60 2.84 470 145 148 3 662.63 2.76 471 145 149 4 639.54 2.96 472 146 149 3 662.78 4.29 473 146 150 4 636.54 1.46 474 146 156 10 408.61 1.38 475 147 150 3 668.51 1.14 476 147 156 9 408.62 1.39 477 150 154 4 600.81 1.47 478 150 156 6 473.37 30.98 479 151 154 3 660.68 1.88 480 155 192 37 28.52 1.39 481 159 185 26 58.05 0.21 482 159 188 29 46.38 0.39 483 161 181 20 65.00 0.75 484 161 185 24 64.72 0.83 485 162 176 14 71.28 0.82 486 162 181 19 69.48 0.97 487 163 167 4 638.81 0.65 488 163 173 10 79.12 0.98 489 163 174 11 74.98 0.96 490 163 175 12 71.30 0.82 491 163 176 13 71.29 0.82 492 163 181 18 71.12 0.88 493 164 167 3 674.38 5.64 494 164 168 4 651.43 1.51 495 164 175 11 71.31 0.82 496 164 176 12 71.28 0.82 497 164 178 14 71.14 0.79 498 164 181 17 70.99 0.81 499 165 168 3 664.30 0.64 500 165 169 4 651.42 1.51 501 165 175 10 71.39 0.81 502 165 177 12 71.28 0.82 503 165 178 13 71.27 0.82 504 166 169 3 664.17 0.57 505 166 170 4 655.54 3.56 506 167 170 3 668.91 2.93 507 167 171 4 655.54 3.56 508 168 171 3 648.06 3.17 509 168 172 4 597.82 7.63 510 168 173 5 590.93 11.08 511 168 175 7 77.05 0.06 512 176 180 4 657.15 2.23 513 176 181 5 642.33 3.16 514 177 180 3 669.74 3.32 515 177 181 4 654.02 0.66 516 178 181 3 667.84 6.24 517 178 182 4 654.03 0.67 518 179 182 3 663.24 0.81 519 179 183 4 647.01 2.83 520 180 183 3 656.67 0.38 521 180 184 4 657.38 2.37 522 181 184 3 659.08 1.52 523 181 185 4 659.01 1.55 524 182 185 3 661.00 0.56 525 182 186 4 659.60 1.83 526 183 186 3 661.93 0.67 527 183 187 4 663.58 0.15 528 184 187 3 665.85 0.97 529 184 188 4 659.60 1.83 530 185 188 3 674.62 1.17 531 185 189 4 658.99 2.13 532 186 189 3 664.67 0.71 533 186 190 4 658.97 2.12 534 187 190 3 669.20 1.54 535 187 191 4 663.43 4.38 536 188 191 3 668.08 2.06 537 189 192 3 668.58 1.81