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 1 126 125 197.89 0.51 2 1 127 126 197.88 0.51 3 1 158 157 43.02 0.38 4 1 159 158 34.41 0.34 5 1 160 159 34.30 0.34 6 2 127 125 197.88 0.52 7 2 128 126 197.89 0.52 8 2 158 156 43.02 0.39 9 2 159 157 34.50 0.29 10 2 165 163 33.76 0.48 11 3 121 118 197.85 0.51 12 3 124 121 197.91 0.51 13 3 127 124 197.91 0.51 14 3 128 125 197.89 0.52 15 3 130 127 197.87 0.51 16 3 157 154 46.27 0.11 17 3 158 155 44.34 0.59 18 3 160 157 37.58 0.23 19 4 42 38 336.65 5.09 20 4 43 39 336.25 4.90 21 4 45 41 336.24 4.90 22 4 128 124 197.92 0.51 23 4 129 125 197.88 0.51 24 4 130 126 197.88 0.51 25 4 156 152 51.09 0.81 26 4 157 153 48.22 0.87 27 4 166 162 33.79 0.48 28 5 130 125 197.90 0.51 29 5 132 127 197.84 0.52 30 5 136 131 146.71 0.65 31 5 137 132 138.41 0.35 32 5 140 135 121.66 0.35 33 5 155 150 51.19 0.83 34 5 156 151 51.13 0.83 35 5 158 153 50.84 0.73 36 6 38 32 337.92 5.69 37 6 42 36 337.49 5.50 38 6 58 52 336.26 4.88 39 6 129 123 197.97 0.51 40 6 130 124 197.91 0.51 41 6 131 125 197.88 0.51 42 6 132 126 197.88 0.51 43 6 154 148 65.31 0.65 44 6 155 149 51.18 0.83 45 7 14 7 551.93 5.89 46 7 132 125 197.90 0.51 47 7 134 127 195.98 0.17 48 7 137 130 146.66 0.64 49 7 150 143 82.21 0.26 50 7 151 144 80.06 0.35 51 7 152 145 78.39 0.93 52 7 153 146 76.78 1.06 53 7 154 147 67.92 0.80 54 8 20 12 371.93 1.21 55 8 54 46 335.12 4.31 56 8 55 47 335.10 4.32 57 8 58 50 337.50 5.50 58 8 132 124 197.91 0.51 59 8 133 125 197.90 0.51 60 8 152 144 78.47 0.96 61 8 153 145 77.80 0.78 62 9 27 18 365.89 3.91 63 9 31 22 362.30 3.54 64 9 34 25 362.29 3.54 65 9 58 49 339.58 6.04 66 9 152 143 78.54 0.99 67 9 153 144 78.14 0.86 68 10 14 4 564.43 0.35 69 10 15 5 567.21 1.75 70 10 27 17 366.07 3.98 71 10 28 18 366.12 3.97 72 10 30 20 366.10 3.98 73 10 31 21 363.09 3.83 74 10 34 24 363.73 2.83 75 10 152 142 78.57 1.00 76 11 14 3 580.57 0.99 77 11 20 9 390.35 6.98 78 11 25 14 366.25 3.93 79 11 26 15 366.24 3.93 80 11 27 16 366.12 3.97 81 11 28 17 366.16 3.97 82 11 54 43 366.12 3.97 83 12 15 3 586.70 0.20 84 12 16 4 560.35 2.39 85 12 28 16 366.29 3.96 86 13 16 3 564.35 4.87 87 13 17 4 558.25 3.44 88 13 18 5 520.53 9.36 89 13 19 6 520.56 9.35 90 13 20 7 495.04 3.04 91 13 23 10 374.83 0.81 92 13 25 12 367.22 3.89 93 13 82 69 275.38 0.28 94 14 17 3 568.86 2.62 95 14 152 138 82.45 0.30 96 15 28 13 367.33 3.97 97 16 84 68 274.49 0.29 98 17 84 67 273.62 0.13 99 17 85 68 273.56 0.13 100 18 82 64 275.39 0.29 101 18 83 65 275.37 0.29 102 18 84 66 273.60 0.12 103 19 77 58 334.25 6.21 104 19 80 61 290.75 4.17 105 19 81 62 278.84 1.23 106 19 82 63 275.60 0.18 107 19 83 64 275.37 0.29 108 19 85 66 273.56 0.14 109 19 88 69 272.58 0.15 110 19 96 77 257.19 6.39 111 20 23 3 601.63 1.14 112 20 25 5 532.62 7.99 113 20 54 34 377.30 4.82 114 20 74 54 336.93 6.08 115 20 77 57 334.41 6.13 116 21 52 31 377.61 4.90 117 21 54 33 377.87 4.82 118 21 74 53 336.90 6.09 119 21 75 54 336.88 6.08 120 21 77 56 334.44 6.15 121 21 81 60 281.81 0.26 122 22 52 30 377.61 4.89 123 22 73 51 337.13 6.15 124 22 74 52 337.03 6.10 125 22 75 53 336.93 6.07 126 22 76 54 335.92 5.70 127 22 81 59 302.29 10.42 128 22 108 86 253.39 7.49 129 23 54 31 378.21 4.93 130 23 81 58 281.86 0.26 131 24 52 28 377.92 4.85 132 24 53 29 377.97 4.88 133 24 54 30 378.19 4.92 134 25 54 29 378.27 4.96 135 26 53 27 378.29 4.96 136 27 31 4 550.45 1.73 137 27 32 5 553.84 3.52 138 27 54 27 378.41 4.92 139 27 57 30 378.47 4.91 140 27 58 31 378.47 4.90 141 27 61 34 378.55 4.87 142 28 31 3 562.66 1.17 143 28 32 4 564.39 2.04 144 29 32 3 576.96 1.36 145 29 33 4 576.10 1.80 146 30 33 3 576.96 1.37 147 30 34 4 576.10 1.80 148 30 37 7 564.45 3.17 149 31 34 3 577.03 1.33 150 31 35 4 574.37 0.00 151 32 35 3 577.93 1.79 152 32 36 4 574.37 0.01 153 32 57 25 378.92 4.78 154 32 61 29 379.99 5.25 155 33 36 3 574.37 0.01 156 33 37 4 574.36 0.01 157 34 37 3 587.55 0.39 158 34 38 4 574.37 0.01 159 34 152 118 78.62 0.98 160 34 153 119 78.11 0.84 161 35 38 3 587.14 0.18 162 35 39 4 572.76 0.82 163 35 58 23 379.89 5.27 164 35 61 26 380.53 5.49 165 35 62 27 380.88 5.67 166 36 39 3 587.56 0.39 167 36 61 25 380.54 5.49 168 37 41 4 580.16 3.17 169 37 170 133 33.20 0.29 170 37 171 134 33.19 0.30 171 38 41 3 574.69 5.91 172 38 42 4 566.19 1.66 173 38 58 20 381.25 5.83 174 38 62 24 381.19 5.81 175 38 153 115 77.80 0.78 176 38 170 132 33.19 0.30 177 39 61 22 381.23 5.80 178 39 62 23 381.19 5.82 179 39 63 24 381.19 5.82 180 41 168 127 33.55 0.38 181 41 170 129 33.20 0.30 182 42 62 20 491.35 2.37 183 42 64 22 491.55 2.49 184 42 129 87 198.55 0.83 185 42 131 89 198.53 0.83 186 42 155 113 56.59 0.16 187 43 64 21 491.97 2.67 188 43 129 86 198.56 0.84 189 45 64 19 492.26 2.58 190 45 127 82 198.92 0.78 191 45 128 83 198.87 0.78 192 45 129 84 198.86 0.78 193 46 127 81 198.93 0.78 194 46 128 82 198.87 0.78 195 46 129 83 198.86 0.77 196 47 64 17 492.29 2.59 197 47 66 19 492.10 2.58 198 47 67 20 492.11 2.58 199 47 129 82 198.72 0.76 200 47 131 84 198.69 0.77 201 48 66 18 492.18 2.62 202 48 67 19 492.10 2.58 203 48 69 21 491.92 2.67 204 48 72 24 485.15 1.47 205 48 120 72 220.00 2.01 206 48 124 76 199.00 0.77 207 48 128 80 198.87 0.77 208 48 129 81 198.78 0.75 209 48 130 82 198.61 0.72 210 48 131 83 198.59 0.72 211 49 55 6 502.80 2.51 212 49 56 7 492.69 2.42 213 49 59 10 492.48 2.52 214 49 66 17 492.30 2.58 215 49 67 18 492.29 2.58 216 49 68 19 492.00 2.65 217 49 69 20 491.97 2.67 218 49 72 23 485.18 1.49 219 49 131 82 198.56 0.72 220 50 55 5 542.35 4.13 221 50 56 6 503.43 2.20 222 50 68 18 492.28 2.60 223 50 69 19 492.12 2.60 224 50 72 22 485.11 1.52 225 50 73 23 482.68 0.33 226 50 131 81 198.62 0.69 227 50 132 82 198.20 0.54 228 50 133 83 198.44 0.65 229 51 56 5 542.89 3.87 230 51 68 17 492.30 2.58 231 51 70 19 492.12 2.60 232 51 73 22 487.27 2.25 233 52 55 3 582.77 3.08 234 52 56 4 566.69 0.34 235 52 73 21 490.62 2.37 236 52 133 81 198.42 0.59 237 53 56 3 579.54 4.69 238 53 57 4 568.10 1.04 239 54 57 3 581.20 3.87 240 54 58 4 568.10 1.04 241 54 74 20 488.79 1.46 242 54 133 79 198.19 0.48 243 55 58 3 572.23 0.99 244 55 59 4 568.10 1.03 245 55 131 76 198.29 0.54 246 55 133 78 197.94 0.52 247 56 59 3 583.70 6.73 248 56 60 4 566.72 0.36 249 56 68 12 492.33 2.58 250 57 60 3 569.76 1.86 251 57 61 4 558.68 0.47 252 58 61 3 587.25 0.35 253 58 62 4 559.33 0.15 254 58 131 73 198.06 0.49 255 59 62 3 569.10 0.92 256 59 63 4 559.35 0.15 257 59 64 5 510.97 3.00 258 59 66 7 492.42 2.58 259 59 131 72 197.93 0.52 260 60 63 3 567.78 1.58 261 60 64 4 558.40 0.58 262 62 131 69 197.94 0.53 263 64 129 65 198.72 0.77 264 64 131 67 198.40 0.76 265 69 72 3 588.66 0.64 266 69 120 51 220.12 2.02 267 70 73 3 568.89 1.04 268 70 116 46 223.30 1.22 269 71 116 45 223.19 1.17 270 71 120 49 220.07 2.02 271 72 120 48 220.07 2.02 272 72 130 58 198.75 0.70 273 72 132 60 198.62 0.69 274 72 133 61 198.62 0.69 275 72 136 64 146.78 0.66 276 73 113 40 223.41 1.27 277 73 116 43 223.36 1.25 278 73 133 60 198.55 0.65 279 73 136 63 155.87 1.01 280 74 113 39 223.41 1.27 281 74 116 42 223.39 1.26 282 74 133 59 198.50 0.62 283 74 134 60 198.50 0.62 284 74 135 61 197.87 0.53 285 74 136 62 177.36 1.94 286 75 102 27 254.03 7.12 287 75 108 33 253.36 7.49 288 75 109 34 253.31 7.47 289 75 110 35 252.52 7.27 290 75 113 38 223.40 1.27 291 75 116 41 223.39 1.26 292 76 81 5 530.10 16.14 293 76 104 28 254.15 7.20 294 76 106 30 253.99 7.29 295 76 107 31 253.38 7.50 296 76 108 32 253.34 7.48 297 77 80 3 580.54 2.37 298 77 81 4 530.09 16.14 299 77 96 19 270.31 0.14 300 77 102 25 254.41 7.17 301 77 104 27 254.14 7.20 302 77 107 30 253.38 7.50 303 78 81 3 593.28 3.94 304 78 105 27 254.16 7.21 305 78 106 28 253.87 7.28 306 78 107 29 253.38 7.50 307 79 105 26 254.19 7.23 308 80 83 3 575.74 5.29 309 80 88 8 343.92 34.83 310 80 92 12 272.51 0.17 311 80 102 22 254.69 7.12 312 80 104 24 254.17 7.22 313 83 88 5 470.89 25.24 314 84 87 3 574.43 0.18 315 84 88 4 558.17 2.91 316 85 88 3 569.04 2.52 317 85 93 8 464.61 18.45 318 85 96 11 422.94 1.96 319 85 97 12 416.44 1.28 320 86 93 7 552.79 1.03 321 87 93 6 553.05 1.12 322 88 92 4 560.70 1.60 323 88 93 5 553.01 1.15 324 88 96 8 549.38 0.60 325 89 92 3 577.15 0.46 326 89 93 4 567.34 4.17 327 90 93 3 569.79 2.94 328 90 94 4 560.50 0.75 329 91 94 3 576.16 0.96 330 91 95 4 560.53 0.76 331 92 95 3 569.90 3.93 332 92 96 4 566.77 2.37 333 92 102 10 254.68 7.11 334 92 104 12 254.59 7.15 335 92 105 13 254.62 7.13 336 93 96 3 578.75 0.49 337 93 97 4 560.49 0.78 338 94 97 3 571.10 4.32 339 94 98 4 560.16 0.93 340 95 98 3 586.44 3.35 341 95 99 4 554.58 1.85 342 95 100 5 443.40 5.82 343 95 101 6 409.95 3.73 344 95 102 7 254.69 7.12 345 96 99 3 549.94 2.39 346 96 102 6 389.35 2.49 347 96 138 42 198.53 0.60 348 97 138 41 198.55 0.60 349 98 142 44 146.82 0.66 350 99 110 11 253.47 7.54 351 99 114 15 252.73 7.21 352 99 138 39 198.48 0.64 353 99 139 40 194.46 2.60 354 99 142 43 146.63 0.67 355 100 110 10 253.48 7.54 356 102 109 7 253.49 7.54 357 102 110 8 253.45 7.53 358 103 107 4 562.72 2.75 359 103 109 6 253.44 7.50 360 104 107 3 573.75 4.46 361 104 108 4 547.43 2.23 362 108 116 8 540.76 4.19 363 109 112 3 562.86 0.48 364 109 113 4 556.98 0.71 365 110 113 3 573.48 3.42 366 110 114 4 559.23 0.40 367 111 114 3 562.55 2.06 368 111 115 4 560.87 1.22 369 112 115 3 568.21 2.07 370 112 116 4 559.23 0.40 371 113 116 3 564.09 1.08 372 113 117 4 560.83 1.20 373 113 135 22 198.59 0.69 374 113 136 23 190.39 4.72 375 113 139 26 146.62 0.70 376 114 117 3 568.00 1.69 377 114 118 4 562.44 2.66 378 114 139 25 143.42 1.52 379 115 118 3 570.58 0.56 380 115 119 4 562.43 2.66 381 116 119 3 571.96 1.25 382 116 120 4 562.46 2.65 383 117 120 3 576.35 0.30 384 117 121 4 562.46 2.65 385 117 136 19 173.97 12.89 386 117 140 23 127.12 0.10 387 118 121 3 567.70 0.01 388 118 122 4 558.63 0.73 389 118 139 21 140.09 1.90 390 118 140 22 127.09 0.12 391 118 143 25 119.00 0.04 392 118 160 42 40.34 1.41 393 119 122 3 570.72 0.48 394 119 123 4 564.15 2.80 395 120 123 3 571.85 1.04 396 120 124 4 564.15 2.80 397 120 130 10 198.89 0.77 398 121 124 3 581.01 2.63 399 121 130 9 198.90 0.77 400 121 140 19 122.09 0.39 401 121 160 39 35.22 0.06 402 124 130 6 424.70 32.97 403 132 136 4 552.76 1.69 404 132 137 5 550.61 2.68 405 133 136 3 586.70 4.08 406 133 137 4 551.14 2.53 407 134 137 3 579.12 0.15 408 134 138 4 551.13 2.53 409 135 138 3 561.62 1.47 410 135 139 4 553.88 3.92 411 136 139 3 572.62 3.41 412 136 140 4 563.15 0.70 413 137 140 3 577.63 0.67 414 137 141 4 561.13 0.31 415 137 150 13 82.47 0.38 416 137 156 19 51.20 0.83 417 138 141 3 573.44 5.84 418 138 142 4 558.66 0.94 419 138 148 10 82.67 0.28 420 138 149 11 82.67 0.28 421 139 142 3 574.21 5.45 422 139 143 4 559.24 1.23 423 140 143 3 578.60 3.42 424 140 144 4 566.73 2.52 425 140 158 18 50.99 0.90 426 140 160 20 48.76 0.79 427 141 144 3 578.86 8.58 428 141 145 4 558.88 1.41 429 141 146 5 507.96 4.79 430 141 147 6 473.41 12.48 431 141 148 7 82.67 0.28 432 141 150 9 189.05 52.36 433 141 156 15 51.23 0.82 434 141 158 17 51.16 0.83 435 141 164 23 40.04 0.07 436 141 167 26 35.04 0.01 437 142 145 3 578.34 8.84 438 142 146 4 529.49 15.55 439 142 148 6 87.56 0.18 440 143 160 17 49.84 0.48 441 144 158 14 51.00 0.90 442 144 160 16 50.44 0.76 443 144 161 17 49.02 0.88 444 144 162 18 46.24 0.16 445 144 163 19 46.20 0.18 446 144 164 20 46.02 0.19 447 146 164 18 46.29 0.14 448 146 167 21 43.69 1.11 449 147 167 20 43.62 0.53 450 150 154 4 541.09 0.24 451 150 156 6 285.24 4.29 452 150 167 17 35.23 0.27 453 151 154 3 571.31 3.69 454 154 168 14 33.77 0.48 455 154 169 15 33.63 0.53 456 155 167 12 33.79 0.48 457 155 168 13 33.73 0.48 458 156 166 10 33.79 0.48 459 156 167 11 33.73 0.48 460 157 164 7 34.45 0.35 461 157 165 8 33.94 0.41 462 157 166 9 33.76 0.48 463 158 163 5 169.94 38.30 464 158 164 6 33.79 0.48 465 158 165 7 33.78 0.48 466 159 162 3 594.15 2.18 467 159 163 4 406.74 5.46 468 159 165 6 59.33 12.30 469 164 167 3 707.79 3.30