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 52 51 29.94 0.51 2 1 61 60 14.91 0.12 3 1 64 63 14.60 0.03 4 1 65 64 14.91 0.12 5 2 14 12 36.62 1.03 6 2 51 49 31.39 0.58 7 2 52 50 30.47 0.20 8 2 57 55 26.92 1.48 9 3 14 11 40.47 0.26 10 5 10 5 631.70 31.14 11 5 11 6 330.33 92.89 12 5 14 9 145.44 1.38 13 7 10 3 726.21 5.73 14 7 11 4 715.78 0.52 15 8 11 3 738.81 0.58 16 8 12 4 722.48 0.60 17 9 12 3 738.80 0.58 18 9 13 4 726.94 1.60 19 10 13 3 736.97 1.49 20 10 14 4 724.26 3.71 21 10 51 41 290.00 2.34 22 11 14 3 736.50 3.17 23 11 15 4 730.92 0.39 24 12 15 3 730.94 0.39 25 12 16 4 730.91 0.39 26 13 16 3 730.90 0.40 27 13 17 4 730.90 0.40 28 13 43 30 330.53 1.74 29 13 51 38 327.44 1.67 30 14 17 3 735.36 2.62 31 14 18 4 723.97 3.07 32 14 51 37 327.44 1.67 33 14 52 38 327.44 1.67 34 15 18 3 730.97 4.82 35 15 19 4 719.65 0.73 36 16 19 3 728.59 0.52 37 16 20 4 719.65 0.73 38 16 41 25 338.07 0.39 39 16 43 27 338.06 0.38 40 17 20 3 729.62 0.00 41 17 21 4 719.68 1.90 42 17 37 20 338.12 0.39 43 17 38 21 338.09 0.40 44 17 41 24 338.12 0.39 45 17 43 26 338.07 0.38 46 17 47 30 338.01 0.36 47 17 48 31 335.46 0.52 48 17 51 34 334.55 0.35 49 17 52 35 334.48 0.30 50 18 21 3 723.55 0.04 51 18 22 4 717.83 2.82 52 18 52 34 334.48 0.30 53 18 58 40 332.44 0.15 54 18 62 44 325.39 0.82 55 18 65 47 325.53 0.73 56 19 22 3 732.43 2.19 57 19 23 4 719.67 1.90 58 20 23 3 728.53 1.65 59 20 24 4 717.38 0.76 60 20 37 17 338.12 0.38 61 20 40 20 338.15 0.39 62 20 41 21 338.12 0.38 63 21 24 3 733.92 4.34 64 21 25 4 711.95 0.14 65 21 37 16 338.13 0.38 66 21 58 37 333.57 0.42 67 21 62 41 333.44 0.41 68 22 26 4 696.60 2.47 69 22 62 40 333.45 0.41 70 22 65 43 333.45 0.41 71 22 66 44 333.44 0.41 72 22 117 95 333.42 0.42 73 22 121 99 333.62 0.45 74 23 26 3 739.86 4.03 75 23 27 4 715.47 1.62 76 23 40 17 338.54 0.42 77 23 117 94 333.42 0.42 78 24 27 3 742.81 10.64 79 24 28 4 701.67 4.64 80 24 29 5 687.44 7.07 81 24 32 8 338.54 0.41 82 24 36 12 338.55 0.42 83 24 37 13 338.51 0.42 84 24 40 16 338.55 0.42 85 25 28 3 730.86 0.47 86 25 29 4 614.13 23.50 87 25 30 5 617.76 25.31 88 25 32 7 342.05 0.88 89 25 37 12 338.54 0.41 90 25 55 30 334.46 0.28 91 25 58 33 333.98 0.35 92 25 59 34 333.69 0.41 93 25 62 37 333.70 0.42 94 25 121 96 333.67 0.43 95 25 124 99 333.71 0.42 96 26 120 94 333.64 0.45 97 26 121 95 333.66 0.43 98 26 124 98 333.68 0.43 99 27 120 93 333.68 0.43 100 28 31 3 744.29 1.91 101 28 32 4 606.27 22.93 102 29 32 3 748.53 0.21 103 29 124 95 333.73 0.42 104 30 55 25 334.48 0.28 105 30 59 29 334.01 0.34 106 32 37 5 706.35 2.48 107 32 55 23 334.47 0.29 108 33 36 3 719.15 2.00 109 33 37 4 717.25 2.96 110 34 37 3 734.46 3.77 111 34 38 4 726.94 5.24 112 34 45 11 338.61 0.51 113 34 48 14 338.53 0.45 114 34 55 21 334.07 0.45 115 35 38 3 734.46 3.76 116 35 39 4 728.00 4.71 117 35 45 10 339.01 0.70 118 36 39 3 728.57 4.44 119 36 40 4 728.01 4.71 120 37 40 3 739.16 1.42 121 37 41 4 717.34 3.10 122 37 48 11 339.03 0.70 123 37 58 21 333.75 0.40 124 38 41 3 732.74 4.61 125 38 42 4 712.28 3.16 126 38 43 5 559.15 19.57 127 38 44 6 340.24 0.11 128 38 45 7 339.51 0.46 129 38 48 10 339.04 0.70 130 39 42 3 718.00 2.77 131 43 47 4 714.59 0.87 132 44 47 3 739.33 1.31 133 45 48 3 741.56 0.19 134 45 49 4 729.85 2.71 135 46 49 3 735.98 0.36 136 46 50 4 720.36 7.45 137 47 50 3 724.46 2.99 138 47 51 4 720.70 1.19 139 48 51 3 732.98 2.16 140 48 52 4 692.03 0.12 141 48 53 5 690.45 0.91 142 48 58 10 333.73 0.39 143 49 53 4 352.57 7.09 144 52 57 5 450.78 54.37 145 52 58 6 501.91 0.82 146 52 61 9 338.10 1.81 147 54 57 3 716.23 2.23 148 54 58 4 714.01 3.64 149 55 58 3 725.19 9.22 150 55 59 4 714.75 3.27 151 56 59 3 725.43 6.47 152 56 60 4 719.38 5.58 153 57 60 3 728.17 5.11 154 57 61 4 723.29 7.54 155 58 61 3 730.49 3.95 156 58 62 4 725.94 6.22 157 59 62 3 726.61 1.99 158 59 63 4 722.03 4.27 159 59 121 62 498.56 1.28 160 59 124 65 498.86 1.11 161 59 125 66 498.63 1.22 162 59 130 71 498.62 1.22 163 59 132 73 496.83 2.10 164 60 63 3 728.63 0.99 165 60 64 4 726.60 1.99 166 60 131 71 498.62 1.22 167 60 132 72 497.67 1.69 168 60 135 75 495.49 2.77 169 61 64 3 726.20 1.79 170 61 65 4 726.16 1.81 171 62 65 3 726.77 2.10 172 62 66 4 726.16 1.80 173 62 121 59 499.11 1.09 174 63 66 3 727.13 2.29 175 63 67 4 722.24 0.15 176 63 121 58 499.13 1.10 177 63 132 69 498.87 1.09 178 63 135 72 498.62 1.22 179 63 136 73 498.56 1.19 180 64 67 3 722.25 0.15 181 64 68 4 722.25 0.15 182 64 135 71 498.87 1.09 183 64 139 75 498.25 1.03 184 65 68 3 726.57 0.52 185 65 69 4 715.31 3.31 186 65 118 53 499.61 1.02 187 66 69 3 723.73 0.90 188 66 70 4 714.71 3.61 189 66 118 52 499.61 1.02 190 66 121 55 499.61 1.02 191 66 122 56 499.61 1.02 192 66 136 70 499.15 0.96 193 67 70 3 739.12 3.56 194 67 71 4 712.52 4.60 195 67 135 68 499.19 0.95 196 67 136 69 499.14 0.96 197 67 139 72 498.78 0.79 198 67 140 73 498.68 0.73 199 68 71 3 725.24 3.39 200 68 72 4 713.91 6.32 201 68 139 71 498.83 0.79 202 69 72 3 742.18 1.99 203 69 73 4 724.89 0.84 204 69 109 40 500.25 0.92 205 69 115 46 499.85 0.95 206 69 118 49 499.79 0.97 207 70 73 3 726.63 1.17 208 70 74 4 726.08 1.44 209 70 109 39 500.24 0.91 210 70 118 48 499.80 0.97 211 70 140 70 498.79 0.78 212 71 74 3 742.91 0.56 213 71 75 4 726.12 1.43 214 71 140 69 498.80 0.78 215 72 75 3 730.77 3.75 216 72 76 4 743.02 0.07 217 73 76 3 803.19 1.17 218 73 109 36 500.30 0.88 219 74 77 3 734.54 4.17 220 74 78 4 717.58 4.50 221 74 102 28 500.62 0.97 222 74 105 31 500.59 0.97 223 74 106 32 500.58 0.97 224 74 109 35 500.58 0.97 225 74 144 70 498.42 0.67 226 75 78 3 726.02 1.30 227 75 79 4 719.65 5.63 228 76 79 3 727.11 1.91 229 76 80 4 710.52 1.11 230 77 80 3 724.35 3.27 231 77 81 4 705.26 1.52 232 77 98 21 500.75 0.99 233 77 102 25 500.69 0.99 234 77 144 67 498.69 0.72 235 77 147 70 497.76 0.43 236 77 148 71 497.74 0.43 237 77 151 74 478.39 1.89 238 78 81 3 719.58 5.67 239 78 82 4 714.38 3.08 240 78 147 69 497.74 0.43 241 79 82 3 731.46 4.02 242 79 83 4 708.80 0.30 243 80 83 3 728.23 2.41 244 80 84 4 708.81 0.31 245 80 98 18 500.94 1.04 246 80 101 21 500.89 1.02 247 81 84 3 719.13 3.60 248 81 85 4 717.55 2.88 249 81 98 17 500.90 1.03 250 81 147 66 497.91 0.43 251 81 151 70 484.64 3.39 252 82 85 3 722.86 0.23 253 82 86 4 717.56 2.89 254 82 147 65 498.49 0.62 255 83 86 3 730.03 2.75 256 84 87 3 749.02 0.01 257 84 90 6 501.30 1.04 258 84 94 10 501.26 1.04 259 84 95 11 501.22 1.02 260 84 98 14 501.11 1.08 261 85 90 5 506.63 1.43 262 85 150 65 497.88 0.45 263 85 151 66 497.73 0.43 264 85 154 69 472.32 1.07 265 87 90 3 715.60 5.64 266 87 91 4 738.79 2.50 267 90 95 5 701.35 0.72 268 91 94 3 715.57 7.80 269 91 95 4 707.07 0.12 270 92 95 3 719.84 5.59 271 92 96 4 708.09 0.62 272 92 155 63 472.35 1.05 273 92 219 127 92.65 1.92 274 93 96 3 721.58 2.57 275 93 97 4 708.10 0.62 276 94 97 3 722.24 2.90 277 94 98 4 717.47 5.31 278 95 98 3 722.73 2.69 279 95 99 4 722.72 2.69 280 95 151 56 495.90 0.28 281 95 154 59 473.71 0.38 282 95 155 60 467.61 0.35 283 96 99 3 722.73 2.69 284 96 100 4 722.73 2.69 285 96 155 59 469.78 0.95 286 96 212 116 107.39 0.23 287 96 215 119 95.14 2.77 288 97 100 3 730.58 0.67 289 97 101 4 722.71 2.69 290 98 101 3 722.68 2.67 291 98 102 4 724.08 3.37 292 98 151 53 495.39 0.53 293 99 102 3 737.38 3.27 294 99 103 4 724.07 3.38 295 99 148 49 497.73 0.43 296 99 151 52 491.05 0.19 297 99 152 53 485.28 2.91 298 99 211 112 107.40 0.23 299 99 215 116 95.12 2.76 300 100 103 3 733.15 1.16 301 100 104 4 720.89 4.98 302 100 204 104 118.52 0.16 303 100 208 108 117.78 0.11 304 100 211 111 107.40 0.23 305 101 104 3 735.40 2.27 306 101 105 4 723.86 3.50 307 102 105 3 739.84 1.28 308 102 106 4 723.86 3.50 309 102 148 46 497.42 0.58 310 103 106 3 731.83 0.48 311 103 107 4 731.88 0.51 312 103 176 73 121.23 0.65 313 103 207 104 117.92 0.16 314 103 211 108 107.39 0.23 315 104 107 3 735.49 1.28 316 104 108 4 722.91 5.00 317 104 204 100 118.47 0.19 318 105 108 3 743.00 2.48 319 105 109 4 723.61 4.65 320 106 109 3 732.02 0.45 321 106 110 4 723.62 4.64 322 106 148 42 496.93 0.78 323 106 173 67 121.51 0.61 324 106 176 70 121.22 0.65 325 106 177 71 121.20 0.66 326 107 110 3 712.59 0.89 327 107 111 4 712.58 0.89 328 107 176 69 121.21 0.65 329 107 200 93 118.53 0.17 330 107 203 96 118.52 0.17 331 107 204 97 118.41 0.22 332 107 207 100 117.94 0.15 333 108 111 3 739.88 3.54 334 108 112 4 712.58 0.90 335 109 112 3 739.51 0.72 336 109 115 6 511.59 4.62 337 110 119 9 499.95 0.96 338 110 180 70 119.95 0.29 339 111 180 69 120.12 0.38 340 111 195 84 118.56 0.15 341 111 200 89 118.45 0.21 342 111 203 92 118.48 0.19 343 112 115 3 747.10 0.96 344 112 180 68 120.13 0.38 345 113 116 3 728.53 1.28 346 113 183 70 119.79 0.30 347 115 118 3 721.39 0.77 348 115 119 4 703.57 0.70 349 115 180 65 119.98 0.32 350 116 119 3 721.35 0.74 351 116 120 4 710.11 2.31 352 116 180 64 119.94 0.31 353 116 183 67 119.10 0.01 354 117 120 3 710.61 2.06 355 117 121 4 703.82 0.83 356 118 121 3 722.75 0.09 357 118 122 4 708.28 3.23 358 119 122 3 728.93 1.28 359 119 123 4 696.48 2.83 360 119 180 61 119.94 0.30 361 120 123 3 729.98 2.10 362 120 124 4 718.39 1.82 363 121 124 3 738.79 2.30 364 121 125 4 725.59 1.35 365 121 132 11 500.38 0.39 366 122 125 3 725.62 1.37 367 122 126 4 725.59 1.34 368 122 136 14 499.24 0.95 369 123 126 3 729.39 1.77 370 123 127 4 727.91 2.50 371 123 181 58 119.92 0.30 372 124 127 3 729.39 1.77 373 124 128 4 723.21 2.54 374 125 128 3 720.12 4.09 375 125 129 4 696.98 2.25 376 125 130 5 696.97 2.25 377 125 132 7 543.86 20.61 378 125 133 8 499.29 0.96 379 126 133 7 499.44 0.90 380 129 133 4 713.00 2.10 381 130 133 3 734.77 0.42 382 130 134 4 721.09 1.90 383 131 134 3 730.51 2.83 384 131 135 4 724.88 0.01 385 132 135 3 735.93 0.14 386 132 136 4 730.52 2.83 387 133 136 3 732.49 3.81 388 133 137 4 722.37 1.27 389 133 141 8 675.57 0.62 390 134 137 3 724.88 0.01 391 134 138 4 706.65 6.58 392 135 138 3 737.95 1.09 393 135 139 4 714.46 2.68 394 136 139 3 725.64 2.67 395 136 140 4 707.33 1.88 396 136 141 5 695.62 1.07 397 137 140 3 746.57 5.17 398 137 141 4 676.19 0.36 399 137 142 5 676.19 0.37 400 137 143 6 676.30 0.41 401 138 142 4 694.10 8.50 402 138 143 5 702.54 1.93 403 139 143 4 708.33 0.96 404 140 143 3 736.74 8.18 405 140 144 4 708.33 0.96 406 141 144 3 737.37 7.87 407 141 145 4 713.87 1.81 408 142 145 3 728.64 0.84 409 142 146 4 708.16 1.03 410 143 146 3 728.19 1.06 411 143 147 4 708.33 1.11 412 144 147 3 723.45 1.31 413 144 148 4 708.13 1.02 414 145 148 3 723.02 1.45 415 145 149 4 708.08 1.01 416 145 166 21 125.68 0.97 417 145 170 25 122.48 0.15 418 145 173 28 121.89 0.43 419 146 149 3 721.68 0.66 420 146 150 4 721.56 0.71 421 147 150 3 721.57 0.71 422 147 151 4 706.09 3.03 423 148 151 3 718.91 3.37 424 148 152 4 706.11 1.84 425 148 169 21 122.81 0.01 426 148 173 25 122.31 0.24 427 149 152 3 715.73 1.78 428 149 153 4 715.57 1.70 429 149 160 11 136.91 0.80 430 149 165 16 127.39 0.39 431 149 166 17 125.92 0.91 432 149 169 20 122.80 0.01 433 150 153 3 714.47 2.28 434 150 154 4 714.43 2.31 435 150 160 10 136.89 0.79 436 150 161 11 145.70 2.19 437 151 154 3 726.94 3.08 438 151 155 4 715.11 1.97 439 152 155 3 725.75 0.39 440 152 156 4 722.77 1.87 441 152 165 13 136.41 0.96 442 152 169 17 125.62 0.90 443 152 172 20 125.63 0.92 444 152 215 63 95.11 2.77 445 153 156 3 726.25 3.41 446 153 157 4 696.00 10.73 447 153 158 5 225.52 7.45 448 153 159 6 194.36 1.49 449 153 160 7 148.04 1.41 450 153 165 12 138.80 1.19 451 154 157 3 708.93 5.25 452 155 215 60 95.19 2.79 453 155 216 61 95.17 2.80 454 155 219 64 83.42 1.62 455 156 165 9 171.49 1.70 456 156 215 59 95.26 2.83 457 156 218 62 87.35 0.32 458 156 219 63 82.55 1.44 459 158 165 7 615.19 4.69 460 159 162 3 722.26 2.19 461 159 165 6 615.21 4.69 462 160 165 5 622.61 8.38 463 160 166 6 615.22 4.69 464 162 165 3 713.88 2.15 465 162 166 4 710.48 3.85 466 163 166 3 721.95 0.57 467 163 167 4 713.31 2.44 468 164 167 3 724.93 3.38 469 164 168 4 724.93 3.38 470 165 168 3 720.00 5.84 471 165 169 4 720.00 5.84 472 166 169 3 731.57 4.36 473 166 170 4 717.41 4.59 474 167 170 3 734.10 1.21 475 167 171 4 723.90 1.35 476 168 171 3 739.19 6.27 477 168 172 4 723.91 1.35 478 168 218 50 85.46 0.60 479 169 172 3 735.95 0.60 480 169 173 4 723.90 1.35 481 170 173 3 723.91 1.35 482 170 174 4 714.00 1.97 483 171 174 3 743.94 4.62 484 171 175 4 721.62 0.32 485 172 175 3 728.29 2.78 486 172 214 42 95.14 2.76 487 173 176 3 745.24 3.06 488 173 177 4 712.68 2.25 489 174 177 3 734.30 0.21 490 174 178 4 712.87 2.35 491 175 178 3 741.26 3.69 492 175 179 4 741.26 3.69 493 175 207 32 117.94 0.16 494 175 210 35 108.80 0.21 495 176 179 3 758.26 0.83 496 176 207 31 117.95 0.17 497 177 180 3 741.26 3.69 498 177 181 4 708.47 0.18 499 178 181 3 735.19 6.72 500 178 182 4 666.66 6.13 501 179 183 4 607.81 20.88 502 179 186 7 178.21 1.87 503 179 195 16 137.47 1.08 504 179 203 24 118.48 0.18 505 179 207 28 117.95 0.17 506 180 183 3 687.29 1.19 507 182 185 3 729.65 1.95 508 182 186 4 700.23 0.28 509 183 186 3 729.68 4.44 510 183 187 4 708.37 3.79 511 183 195 12 166.28 1.91 512 184 187 3 730.06 4.25 513 184 188 4 708.37 3.79 514 185 188 3 722.79 6.80 515 185 189 4 708.37 3.79 516 186 189 3 717.04 0.55 517 186 190 4 708.36 3.78 518 186 195 9 184.00 2.69 519 187 190 3 719.09 4.96 520 187 191 4 694.26 1.02 521 187 192 5 529.79 1.93 522 187 193 6 358.27 83.83 523 187 194 7 184.52 2.96 524 187 195 8 184.01 2.70 525 188 191 3 702.90 1.52 526 192 195 3 783.53 2.52 527 192 199 7 623.45 1.02 528 192 202 10 623.33 1.79 529 192 203 11 617.96 3.77 530 193 199 6 706.09 4.61 531 194 199 5 706.10 4.62 532 195 199 4 706.09 4.61 533 195 203 8 648.90 13.50 534 196 199 3 742.57 1.81 535 196 200 4 718.34 1.07 536 197 200 3 718.35 1.07 537 197 201 4 724.87 2.18 538 198 201 3 724.88 2.19 539 198 202 4 728.20 3.83 540 199 202 3 728.20 3.83 541 199 203 4 728.19 3.83 542 200 203 3 728.20 3.83 543 200 204 4 724.87 2.18 544 201 204 3 728.20 3.83 545 201 205 4 703.93 1.50 546 202 205 3 719.66 6.71 547 202 206 4 706.59 0.17 548 203 206 3 715.08 7.07 549 203 207 4 703.91 1.51 550 204 207 3 717.03 9.71 551 204 208 4 686.41 1.29 552 205 208 3 728.55 3.95 553 205 209 4 700.33 3.25 554 206 209 3 725.53 2.44 555 206 210 4 704.71 1.11 556 207 210 3 715.66 1.38 557 207 211 4 704.71 1.11 558 208 211 3 732.72 10.70 559 208 212 4 710.89 1.96 560 209 212 3 736.88 8.62 561 209 213 4 718.32 5.67 562 210 213 3 728.11 0.78 563 210 214 4 718.33 5.67 564 211 214 3 718.33 5.67 565 211 215 4 718.33 5.67 566 212 215 3 725.50 3.46 567 212 216 4 702.25 2.38 568 213 216 3 727.25 4.33 569 213 217 4 706.93 4.71 570 214 217 3 719.11 1.78 571 214 218 4 710.93 1.95 572 215 218 3 720.39 2.31 573 215 219 4 711.39 2.19 574 216 219 3 719.21 1.72 575 216 220 4 716.70 0.46 576 217 220 3 739.89 3.71