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 12 118 106 289.52 1.58 2 14 19 5 715.10 0.48 3 14 55 41 292.56 0.85 4 15 18 3 750.12 2.44 5 15 19 4 721.94 1.34 6 16 19 3 723.57 3.12 7 16 20 4 715.08 0.48 8 16 59 43 306.97 1.32 9 17 20 3 716.44 0.19 10 17 21 4 716.44 0.19 11 18 21 3 725.42 2.07 12 18 22 4 718.06 0.62 13 19 22 3 719.92 1.55 14 19 23 4 716.58 1.36 15 19 43 24 328.09 0.28 16 19 56 37 325.17 0.19 17 19 59 40 325.21 0.18 18 19 60 41 325.18 0.19 19 20 23 3 719.59 1.73 20 20 24 4 716.61 1.38 21 20 59 39 325.24 0.18 22 21 24 3 718.47 2.31 23 21 25 4 722.28 4.21 24 22 25 3 734.65 1.97 25 22 26 4 718.46 2.31 26 22 39 17 330.73 0.21 27 22 42 20 330.78 0.19 28 22 43 21 330.73 0.19 29 23 26 3 718.45 2.32 30 23 27 4 716.66 1.36 31 23 59 36 330.38 0.21 32 23 60 37 330.29 0.18 33 24 27 3 729.38 0.36 34 24 28 4 714.56 0.52 35 25 28 3 717.34 1.70 36 25 29 4 701.72 5.90 37 25 39 14 330.99 0.23 38 26 29 3 706.16 3.68 39 26 30 4 701.69 5.88 40 26 31 5 698.25 7.59 41 26 36 10 390.82 30.16 42 26 39 13 330.99 0.23 43 26 40 14 390.84 30.16 44 26 60 34 330.62 0.10 45 27 30 3 703.52 7.58 46 27 31 4 676.62 5.87 47 29 33 4 684.86 19.00 48 29 35 6 511.49 5.92 49 29 39 10 511.14 6.09 50 30 33 3 680.73 21.07 51 30 36 6 569.00 9.89 52 31 36 5 596.56 1.45 53 31 60 29 330.95 0.15 54 31 140 109 330.74 0.17 55 31 144 113 329.52 0.03 56 32 144 112 329.53 0.03 57 32 145 113 329.51 0.03 58 32 146 114 329.51 0.03 59 32 147 115 329.50 0.03 60 33 36 3 736.41 1.19 61 34 37 3 733.46 2.67 62 34 38 4 706.96 2.99 63 35 38 3 721.37 4.22 64 35 39 4 702.87 1.77 65 36 39 3 720.21 2.52 66 36 40 4 702.56 6.29 67 36 140 104 331.16 0.21 68 37 40 3 721.07 2.96 69 37 41 4 707.81 3.68 70 37 137 100 331.17 0.21 71 37 140 103 331.16 0.20 72 37 141 104 331.14 0.21 73 38 41 3 723.40 2.07 74 38 42 4 707.81 3.68 75 39 42 3 723.13 1.93 76 39 43 4 717.86 0.71 77 40 43 3 729.22 1.24 78 40 44 4 700.39 0.01 79 40 57 17 331.37 0.16 80 40 60 20 331.37 0.15 81 40 137 97 331.25 0.20 82 41 44 3 717.31 2.96 83 41 45 4 695.33 1.27 84 41 137 96 331.32 0.16 85 42 45 3 721.48 0.89 86 43 46 3 768.99 1.55 87 43 56 13 390.85 25.79 88 44 48 4 720.45 3.25 89 44 56 12 390.85 25.79 90 44 57 13 390.85 25.79 91 44 133 89 333.24 0.01 92 44 136 92 333.24 0.01 93 44 137 93 332.73 0.27 94 46 133 87 426.25 0.63 95 47 129 82 429.94 0.95 96 47 130 83 428.92 0.88 97 47 133 86 426.74 0.21 98 48 53 5 703.44 3.38 99 48 56 8 676.22 7.29 100 48 129 81 430.84 1.29 101 48 133 85 429.94 0.95 102 49 52 3 724.01 2.88 103 49 53 4 707.92 1.18 104 49 117 68 443.85 0.73 105 49 120 71 443.83 0.74 106 49 121 72 443.45 0.87 107 49 129 80 432.25 1.49 108 50 53 3 718.97 1.19 109 50 54 4 718.97 1.19 110 50 73 23 444.45 0.85 111 50 106 56 443.88 0.73 112 50 107 57 443.90 0.73 113 50 120 70 443.89 0.73 114 50 132 82 433.00 1.85 115 51 54 3 730.28 4.33 116 51 55 4 719.79 0.78 117 51 107 56 443.91 0.73 118 52 55 3 724.23 1.45 119 52 56 4 718.97 1.19 120 53 56 3 724.23 1.45 121 53 57 4 705.46 2.19 122 53 69 16 448.24 0.79 123 53 73 20 444.98 0.83 124 53 132 79 442.76 0.62 125 53 136 83 441.86 0.55 126 54 57 3 717.16 4.45 127 54 58 4 704.45 2.69 128 54 66 12 450.31 0.14 129 54 69 15 448.24 0.79 130 54 70 16 445.05 0.81 131 54 73 19 445.02 0.82 132 55 58 3 710.59 1.16 133 55 59 4 709.32 1.77 134 56 59 3 732.49 1.25 135 56 60 4 715.82 5.65 136 57 60 3 723.31 3.33 137 57 61 4 693.06 0.84 138 57 69 12 448.42 0.72 139 57 140 83 442.15 0.68 140 58 61 3 723.31 3.33 141 58 62 4 693.05 0.83 142 58 66 8 496.80 1.26 143 60 140 80 442.19 0.69 144 61 65 4 705.06 1.58 145 61 66 5 698.00 0.61 146 61 69 8 679.12 3.08 147 61 140 79 442.23 0.71 148 61 143 82 439.99 0.58 149 62 65 3 727.70 1.71 150 62 66 4 713.25 2.48 151 63 66 3 718.57 2.85 152 63 67 4 715.29 2.88 153 63 179 116 34.09 0.66 154 64 67 3 746.73 1.14 155 64 68 4 719.86 0.59 156 64 149 85 43.29 0.05 157 64 150 86 42.84 0.04 158 65 68 3 719.86 0.59 159 65 69 4 714.73 3.15 160 65 143 78 439.99 0.58 161 66 69 3 721.28 0.13 162 66 70 4 718.84 1.09 163 67 70 3 720.38 2.82 164 67 71 4 723.35 1.33 165 68 71 3 734.38 4.18 166 68 72 4 716.02 1.27 167 68 143 75 440.00 0.58 168 68 146 78 437.56 0.12 169 68 148 80 394.80 0.55 170 68 150 82 74.95 13.05 171 69 72 3 716.55 1.00 172 69 73 4 711.29 0.93 173 69 136 67 442.91 0.68 174 69 139 70 442.31 0.66 175 69 140 71 442.27 0.64 176 69 143 74 439.88 0.53 177 70 73 3 715.08 0.79 178 70 74 4 711.47 1.02 179 71 74 3 722.51 1.82 180 71 75 4 710.99 0.78 181 72 75 3 717.59 4.28 182 72 76 4 709.44 1.54 183 72 139 67 442.68 0.68 184 72 142 70 441.68 0.56 185 73 76 3 714.97 1.22 186 73 77 4 705.37 0.48 187 73 132 59 443.28 0.81 188 73 135 62 442.93 0.69 189 73 136 63 442.89 0.68 190 73 139 66 442.67 0.68 191 74 77 3 715.41 3.65 192 74 78 4 708.75 1.22 193 75 78 3 709.65 0.77 194 75 79 4 709.11 1.04 195 76 79 3 715.32 2.85 196 76 80 4 711.32 4.85 197 76 135 59 442.95 0.68 198 76 138 62 442.88 0.66 199 76 139 63 442.82 0.62 200 77 80 3 718.61 1.22 201 77 81 4 711.33 4.86 202 77 103 26 446.95 0.48 203 77 106 29 446.93 0.49 204 77 107 30 446.94 0.49 205 77 132 55 443.44 0.74 206 78 81 3 715.07 3.00 207 78 82 4 714.81 3.12 208 78 103 25 447.04 0.53 209 79 82 3 722.63 0.93 210 79 83 4 714.81 3.12 211 80 83 3 721.08 0.03 212 80 84 4 697.57 11.61 213 80 90 10 449.23 0.10 214 80 92 12 448.96 0.03 215 80 106 26 448.12 0.37 216 80 131 51 443.59 0.74 217 80 135 55 443.24 0.65 218 81 84 3 724.90 0.27 219 81 85 4 706.61 7.08 220 81 101 20 448.14 0.39 221 81 102 21 448.12 0.40 222 81 103 22 448.09 0.40 223 81 106 25 448.16 0.40 224 82 85 3 722.57 0.90 225 82 86 4 695.81 1.68 226 83 86 3 705.60 1.47 227 83 87 4 695.82 1.68 228 83 90 7 590.31 41.51 229 84 87 3 713.99 1.70 230 84 88 4 695.82 1.68 231 84 90 6 457.04 3.98 232 84 93 9 449.16 0.10 233 84 101 17 448.31 0.37 234 85 100 15 448.33 0.37 235 87 90 3 767.69 2.79 236 88 97 9 448.82 0.15 237 90 93 3 716.35 3.27 238 91 125 34 444.37 0.75 239 91 127 36 444.12 0.74 240 91 128 37 444.16 0.73 241 92 101 9 448.54 0.30 242 92 106 14 448.49 0.29 243 92 128 36 443.90 0.67 244 92 131 39 443.89 0.67 245 93 96 3 741.07 1.44 246 93 100 7 448.70 0.39 247 93 101 8 448.54 0.32 248 93 125 32 444.42 0.77 249 94 99 5 516.12 33.74 250 94 125 31 444.39 0.79 251 95 99 4 703.12 1.44 252 95 125 30 444.44 0.78 253 96 99 3 744.85 0.56 254 96 100 4 703.12 1.44 255 99 105 6 697.65 3.85 256 101 106 5 697.65 3.85 257 102 105 3 707.69 1.15 258 102 106 4 697.69 3.85 259 103 106 3 734.39 0.93 260 103 107 4 697.69 3.85 261 104 107 3 706.52 0.57 262 104 108 4 705.22 0.09 263 104 109 5 673.56 3.29 264 105 108 3 705.23 0.09 265 105 110 5 637.91 3.73 266 105 113 8 466.24 8.34 267 105 124 19 444.38 0.79 268 106 128 22 443.58 0.72 269 106 132 26 443.14 0.79 270 108 113 5 450.60 0.51 271 108 114 6 450.59 0.52 272 108 120 12 444.57 0.71 273 109 114 5 450.59 0.52 274 110 113 3 711.50 1.14 275 110 114 4 663.94 9.21 276 111 123 12 447.41 2.10 277 112 116 4 714.07 1.67 278 112 123 11 447.12 1.96 279 113 116 3 725.10 3.85 280 113 120 7 447.12 1.97 281 113 123 10 448.14 0.64 282 113 124 11 445.04 0.92 283 116 119 3 738.19 7.21 284 116 120 4 690.49 2.52 285 117 120 3 726.49 13.06 286 117 121 4 695.63 2.35 287 118 121 3 734.83 8.89 288 118 122 4 695.63 2.35 289 119 122 3 710.82 5.21 290 119 123 4 691.90 1.78 291 120 123 3 719.98 9.06 292 120 124 4 692.86 2.25 293 121 124 3 700.45 0.11 294 121 129 8 445.10 0.47 295 124 128 4 708.27 1.40 296 125 128 3 756.27 0.67 297 127 130 3 724.27 0.70 298 127 131 4 719.84 1.51 299 128 131 3 722.08 0.39 300 128 132 4 727.44 2.29 301 129 132 3 732.69 1.27 302 129 133 4 727.43 2.29 303 130 133 3 721.34 5.34 304 130 134 4 716.90 7.55 305 131 134 3 716.95 7.54 306 131 135 4 703.02 4.45 307 132 135 3 709.25 8.07 308 132 136 4 705.13 6.00 309 133 136 3 721.31 2.08 310 133 137 4 702.58 4.69 311 134 137 3 710.74 0.94 312 134 138 4 710.73 0.94 313 135 138 3 732.99 3.56 314 135 139 4 720.60 0.18 315 136 139 3 738.14 0.98 316 136 140 4 722.83 1.29 317 137 140 3 738.14 0.98 318 137 141 4 732.76 3.68 319 138 141 3 724.68 0.55 320 138 142 4 721.17 2.12 321 139 142 3 721.25 2.08 322 139 143 4 721.17 2.12 323 140 143 3 728.62 1.61 324 140 144 4 710.41 0.81 325 141 144 3 713.46 1.81 326 141 145 4 710.41 0.81 327 142 145 3 717.76 3.97 328 142 146 4 710.20 0.70 329 143 146 3 712.02 1.61 330 151 154 3 635.44 13.25 331 151 155 4 614.46 12.87 332 152 156 4 706.94 1.05 333 152 178 26 93.62 1.29 334 153 156 3 697.86 3.48 335 153 171 18 86.42 0.04 336 153 175 22 92.86 1.69 337 153 178 25 97.34 0.47 338 153 180 27 97.35 0.48 339 153 188 35 92.02 1.27 340 153 192 39 86.50 0.05 341 156 167 11 112.03 1.03 342 156 171 15 98.50 0.74 343 156 174 18 99.62 0.30 344 157 167 10 117.20 1.55 345 157 196 39 99.32 0.18 346 158 162 4 692.15 2.58 347 158 163 5 618.92 12.42 348 158 164 6 343.53 82.21 349 158 167 9 111.99 1.04 350 158 197 39 99.33 0.18 351 158 198 40 99.48 0.25 352 159 162 3 724.60 2.04 353 159 198 39 99.67 0.34 354 160 198 38 99.73 0.35 355 162 167 5 697.59 6.04 356 163 166 3 711.00 0.71 357 163 167 4 707.30 1.20 358 164 167 3 714.45 2.38 359 164 168 4 712.27 1.28 360 164 193 29 102.19 0.21 361 164 201 37 101.00 0.30 362 164 219 55 100.98 0.31 363 164 222 58 100.97 0.31 364 164 223 59 100.79 0.41 365 164 226 62 99.28 0.19 366 165 168 3 717.83 4.05 367 165 169 4 712.28 1.28 368 165 219 54 100.98 0.31 369 165 223 58 100.83 0.39 370 166 169 3 720.77 2.96 371 166 170 4 712.29 1.28 372 167 170 3 716.43 3.35 373 167 171 4 708.87 0.43 374 167 193 26 103.34 0.28 375 168 171 3 710.48 0.35 376 168 172 4 707.33 1.08 377 168 193 25 103.24 0.22 378 168 219 51 100.99 0.31 379 169 172 3 720.00 2.56 380 169 173 4 706.96 0.91 381 170 173 3 710.63 0.93 382 170 174 4 710.63 0.93 383 171 174 3 712.02 1.62 384 171 175 4 710.63 0.93 385 171 189 18 103.50 0.21 386 171 192 21 103.58 0.16 387 171 193 22 103.52 0.21 388 172 175 3 725.88 5.34 389 172 176 4 718.85 3.17 390 172 189 17 103.53 0.18 391 172 215 43 103.34 0.18 392 172 219 47 103.34 0.17 393 173 176 3 726.50 0.66 394 173 177 4 718.85 3.17 395 174 177 3 729.36 0.78 396 174 178 4 703.25 4.63 397 175 178 3 711.82 1.69 398 175 180 5 650.81 3.33 399 175 185 10 105.95 0.94 400 175 188 13 103.89 0.09 401 175 189 14 103.76 0.11 402 180 184 4 689.15 2.77 403 180 185 5 651.25 4.90 404 180 188 8 525.27 1.67 405 181 184 3 747.07 7.20 406 181 185 4 729.52 0.78 407 182 185 3 757.53 1.97 408 183 187 4 729.52 0.78 409 184 187 3 739.75 1.70 410 184 188 4 708.62 2.81 411 186 189 3 726.31 4.00 412 186 190 4 699.33 1.90 413 186 213 27 167.69 1.08 414 186 214 28 166.21 0.35 415 186 215 29 166.21 0.35 416 187 190 3 729.54 0.78 417 187 191 4 699.31 1.91 418 188 191 3 699.35 1.91 419 188 192 4 699.32 1.93 420 189 192 3 704.43 0.52 421 189 193 4 704.43 0.52 422 189 215 26 168.97 0.68 423 190 193 3 715.71 6.15 424 190 194 4 703.56 0.08 425 190 205 15 168.96 0.69 426 190 213 23 169.03 0.70 427 190 214 24 169.04 0.70 428 190 215 25 169.02 0.70 429 190 218 28 168.92 0.70 430 191 194 3 715.71 6.15 431 191 195 4 703.35 0.18 432 192 195 3 715.98 6.02 433 192 196 4 707.63 2.32 434 193 196 3 741.18 0.80 435 193 197 4 658.16 1.09 436 193 205 12 169.00 0.69 437 193 218 25 169.06 0.70 438 193 219 26 169.05 0.71 439 194 202 8 168.93 0.70 440 194 205 11 168.98 0.68 441 197 201 4 716.78 6.24 442 198 201 3 721.15 4.05 443 198 202 4 698.97 2.29 444 199 202 3 702.49 4.04 445 199 203 4 706.96 7.13 446 200 203 3 717.50 1.86 447 200 204 4 712.43 4.40 448 201 204 3 715.91 2.67 449 201 205 4 712.43 4.40 450 201 222 21 170.34 0.81 451 201 226 25 170.31 0.81 452 202 205 3 723.33 1.05 453 202 206 4 709.99 3.19 454 203 206 3 710.00 3.19 455 203 207 4 683.38 3.91 456 204 207 3 709.96 5.32 457 204 208 4 679.50 2.01 458 204 221 17 170.59 0.74 459 204 222 18 170.38 0.80 460 204 225 21 170.36 0.80 461 204 226 22 170.35 0.80 462 205 208 3 696.79 1.27 463 205 218 13 170.68 0.78 464 205 222 17 170.44 0.83 465 207 221 14 170.77 0.81 466 208 221 13 170.68 0.78 467 209 212 3 756.53 1.10 468 209 221 12 170.78 0.81 469 212 217 5 540.08 6.36 470 212 218 6 558.58 4.71 471 213 218 5 619.48 3.34 472 214 217 3 724.54 0.35 473 214 218 4 682.72 13.77 474 215 219 4 703.74 3.29 475 216 219 3 720.49 2.44 476 216 220 4 703.73 3.30 477 217 220 3 703.74 3.29 478 217 221 4 703.72 3.29 479 218 221 3 718.75 0.21 480 218 222 4 703.71 3.29 481 219 222 3 703.25 4.70 482 219 223 4 691.61 1.11 483 220 223 3 708.73 1.97 484 220 224 4 681.54 6.58 485 221 224 3 690.89 6.96 486 221 225 4 680.56 8.46 487 222 225 3 707.93 12.25 488 222 226 4 678.45 9.52 489 223 226 3 704.75 4.97 490 223 227 4 690.46 3.52 491 224 227 3 721.96 3.62