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 4 7 3 710.38 0.34 2 4 8 4 710.71 0.36 3 4 51 47 253.15 1.37 4 4 52 48 254.80 2.20 5 5 8 3 712.85 0.62 6 5 9 4 711.31 0.13 7 6 9 3 712.82 0.88 8 6 10 4 712.08 0.25 9 7 10 3 713.74 1.08 10 7 11 4 712.08 0.26 11 7 51 44 259.58 0.14 12 7 52 45 261.89 0.36 13 8 11 3 712.09 0.25 14 8 12 4 712.08 0.26 15 8 52 44 265.03 0.39 16 8 75 67 198.97 1.92 17 9 12 3 712.09 0.25 18 9 13 4 708.05 2.26 19 10 13 3 711.45 0.56 20 10 14 4 710.59 0.12 21 10 44 34 266.14 0.82 22 10 48 38 265.06 0.38 23 11 14 3 710.58 0.12 24 11 15 4 710.59 0.12 25 11 49 38 265.15 0.34 26 11 52 41 268.62 0.74 27 11 71 60 204.17 1.27 28 11 74 63 202.59 0.96 29 11 75 64 201.03 1.70 30 12 15 3 729.52 9.59 31 12 16 4 710.58 0.12 32 12 75 63 202.25 0.82 33 13 16 3 715.38 1.75 34 13 17 4 710.50 0.15 35 13 38 25 270.58 1.23 36 14 17 3 708.47 0.86 37 14 18 4 700.64 3.08 38 14 38 24 270.61 1.22 39 14 40 26 270.61 1.22 40 14 45 31 269.79 1.26 41 14 48 34 269.80 1.26 42 14 49 35 269.77 1.26 43 14 71 57 204.98 0.89 44 15 18 3 700.65 3.08 45 15 19 4 700.75 3.12 46 15 68 53 206.15 0.90 47 15 71 56 205.74 0.82 48 15 72 57 205.50 0.90 49 15 75 60 202.72 0.95 50 15 77 62 202.52 0.96 51 16 19 3 701.71 3.60 52 16 20 4 700.75 3.12 53 16 77 61 202.53 0.96 54 17 20 3 721.44 2.54 55 17 21 4 700.76 3.12 56 17 34 17 270.65 1.21 57 17 37 20 270.66 1.21 58 17 38 21 270.66 1.21 59 18 21 3 717.72 1.54 60 18 22 4 710.82 1.91 61 18 29 11 270.76 1.18 62 18 34 16 270.68 1.22 63 18 64 46 252.09 0.19 64 18 67 49 224.97 0.21 65 18 68 50 206.28 0.93 66 18 71 53 206.84 1.21 67 19 22 3 722.76 1.17 68 19 23 4 710.76 1.92 69 19 68 49 208.09 0.04 70 20 23 3 718.29 1.83 71 20 24 4 699.71 2.56 72 21 24 3 718.29 1.83 73 21 25 4 699.71 2.56 74 21 26 5 628.30 26.77 75 21 29 8 284.04 0.86 76 21 33 12 271.50 1.46 77 21 34 13 270.94 1.18 78 21 37 16 271.51 1.46 79 21 64 43 268.41 1.50 80 22 25 3 709.75 2.45 81 22 26 4 693.04 5.60 82 22 64 42 269.27 1.20 83 22 65 43 266.18 0.43 84 22 68 46 237.17 2.15 85 26 29 3 769.48 1.72 86 26 33 7 634.89 25.07 87 26 64 38 269.52 1.17 88 27 63 36 269.67 1.18 89 27 64 37 269.52 1.17 90 27 65 38 269.52 1.17 91 28 60 32 269.89 1.25 92 28 62 34 269.85 1.24 93 28 63 35 269.70 1.20 94 28 64 36 269.60 1.20 95 29 33 4 707.40 7.13 96 29 34 5 684.70 2.31 97 29 61 32 269.87 1.24 98 29 62 33 269.83 1.23 99 29 64 35 269.58 1.20 100 30 33 3 713.66 4.00 101 30 34 4 707.40 7.13 102 30 61 31 269.85 1.22 103 31 34 3 705.51 8.09 104 31 35 4 705.50 8.09 105 31 42 11 274.66 0.99 106 31 45 14 274.56 1.00 107 31 46 15 274.50 1.01 108 31 62 31 269.88 1.23 109 32 35 3 724.98 1.66 110 32 36 4 705.49 8.09 111 32 42 10 274.68 0.99 112 33 36 3 716.88 2.39 113 33 37 4 715.98 2.83 114 34 37 3 716.86 2.38 115 34 38 4 687.37 0.92 116 34 45 11 274.62 1.02 117 34 49 15 274.61 1.02 118 34 62 28 269.87 1.24 119 34 67 33 226.63 0.95 120 35 38 3 707.40 1.79 121 35 39 4 683.02 2.18 122 35 40 5 320.54 3.72 123 35 42 7 274.71 0.98 124 35 45 10 274.63 1.01 125 36 39 3 691.22 4.54 126 40 44 4 709.47 2.21 127 40 45 5 697.43 3.78 128 41 44 3 709.47 2.21 129 41 45 4 709.49 2.20 130 42 45 3 709.50 2.19 131 42 46 4 709.49 2.19 132 43 46 3 715.46 3.98 133 43 47 4 709.49 2.19 134 44 47 3 709.49 2.19 135 44 48 4 708.16 1.54 136 45 48 3 714.96 1.48 137 45 49 4 702.48 4.79 138 46 49 3 723.37 0.89 139 46 50 4 702.48 4.78 140 46 58 12 270.05 1.24 141 46 62 16 269.89 1.23 142 47 50 3 711.62 0.22 143 47 51 4 702.48 4.78 144 48 51 3 711.62 0.22 145 48 52 4 702.48 4.79 146 49 52 3 706.02 3.02 147 49 53 4 698.28 3.66 148 49 54 5 481.76 44.05 149 49 62 13 269.94 1.22 150 49 67 18 206.27 0.93 151 49 71 22 203.27 0.83 152 50 53 3 698.25 3.65 153 50 54 4 633.82 27.42 154 50 55 5 629.20 29.66 155 52 74 22 200.13 2.19 156 54 67 13 206.27 0.93 157 54 70 16 205.28 1.04 158 55 62 7 270.05 1.25 159 56 62 6 270.02 1.25 160 57 60 3 706.27 2.83 161 57 61 4 302.00 12.43 162 62 67 5 632.52 26.91 163 63 66 3 713.02 6.22 164 63 67 4 703.61 5.86 165 64 67 3 720.40 2.54 166 64 68 4 704.89 5.22 167 65 68 3 704.90 5.21 168 65 69 4 706.65 4.33 169 66 69 3 712.23 4.78 170 66 70 4 695.71 1.15 171 67 70 3 709.90 5.94 172 67 71 4 695.70 1.16 173 68 71 3 708.93 3.18 174 68 72 4 706.65 4.32 175 69 72 3 710.23 2.53 176 69 73 4 708.96 3.12 177 70 73 3 712.15 1.56 178 70 74 4 710.22 2.52 179 71 74 3 713.73 0.78 180 71 75 4 710.22 2.52 181 72 75 3 714.77 0.24 182 72 76 4 700.92 7.17 183 72 77 5 483.56 42.80 184 72 78 6 331.65 5.16 185 73 76 3 709.07 5.36 186 73 78 5 466.15 51.52 187 76 79 3 726.16 4.59 188 76 81 5 642.91 20.70 189 77 104 27 622.65 3.24 190 77 105 28 637.63 1.18 191 79 104 25 671.87 0.34 192 80 103 23 671.97 0.35 193 80 104 24 671.87 0.34 194 80 106 26 671.88 0.34 195 80 108 28 671.82 0.35 196 81 104 23 671.97 0.35 197 81 105 24 671.91 0.35 198 81 106 25 671.89 0.33 199 81 142 61 557.75 0.29 200 81 143 62 557.72 0.28 201 82 106 24 671.92 0.35 202 82 108 26 671.83 0.35 203 82 140 58 557.87 0.28 204 82 141 59 557.82 0.28 205 82 142 60 557.79 0.28 206 82 143 61 557.77 0.28 207 83 101 18 672.09 0.35 208 83 105 22 672.05 0.35 209 83 106 23 672.00 0.35 210 83 107 24 671.91 0.34 211 83 108 25 671.91 0.34 212 83 109 26 671.88 0.34 213 83 141 58 557.86 0.29 214 83 143 60 557.78 0.29 215 83 145 62 557.73 0.28 216 84 107 23 671.98 0.35 217 84 109 25 671.85 0.33 218 84 111 27 671.78 0.33 219 84 141 57 557.88 0.28 220 84 143 59 557.84 0.28 221 84 144 60 557.75 0.29 222 84 145 61 557.73 0.28 223 84 160 76 461.99 0.01 224 85 88 3 758.48 4.43 225 85 92 7 672.30 0.33 226 85 95 10 672.27 0.34 227 85 96 11 672.10 0.39 228 85 107 22 672.06 0.35 229 85 109 24 671.94 0.33 230 85 110 25 671.84 0.34 231 85 111 26 671.84 0.34 232 85 145 60 557.76 0.28 233 85 147 62 557.72 0.28 234 86 111 25 671.87 0.32 235 86 130 44 562.19 0.04 236 86 133 47 559.38 0.20 237 86 144 58 557.87 0.28 238 86 145 59 557.82 0.27 239 86 146 60 557.76 0.28 240 86 147 61 557.73 0.28 241 86 148 62 557.66 0.26 242 86 156 70 462.10 0.04 243 86 160 74 462.06 0.03 244 87 92 5 672.65 0.41 245 87 111 24 671.93 0.33 246 87 112 25 671.84 0.35 247 87 147 60 557.73 0.27 248 87 148 61 557.65 0.26 249 88 92 4 672.65 0.41 250 88 93 5 672.65 0.41 251 88 96 8 672.65 0.41 252 88 110 22 672.03 0.34 253 88 111 23 671.94 0.33 254 88 112 24 671.88 0.32 255 88 117 29 564.36 0.21 256 88 120 32 563.71 0.03 257 88 122 34 563.57 0.07 258 88 127 39 562.75 0.10 259 89 92 3 707.35 0.91 260 89 93 4 699.70 2.63 261 89 117 28 593.82 14.51 262 90 93 3 720.67 0.35 263 90 94 4 702.13 1.71 264 91 94 3 710.89 1.36 265 91 95 4 708.98 1.95 266 91 147 56 557.79 0.28 267 91 171 80 461.03 0.01 268 92 95 3 713.25 0.18 269 92 96 4 708.99 1.96 270 92 147 55 557.74 0.27 271 93 96 3 709.29 1.81 272 93 97 4 709.00 1.96 273 93 120 27 563.69 0.03 274 94 97 3 713.20 0.14 275 94 98 4 708.99 1.96 276 95 98 3 708.86 1.94 277 95 101 6 677.68 1.62 278 95 145 50 557.82 0.29 279 95 147 52 557.75 0.28 280 95 171 76 460.99 0.01 281 96 107 11 672.14 0.33 282 96 110 14 672.03 0.34 283 96 123 27 563.10 0.02 284 97 123 26 563.10 0.03 285 98 101 3 783.61 0.90 286 101 105 4 672.43 0.35 287 101 107 6 672.31 0.37 288 101 145 44 557.74 0.28 289 102 105 3 730.57 5.23 290 105 143 38 557.77 0.28 291 107 110 3 852.10 1.85 292 108 140 32 557.88 0.28 293 108 141 33 557.86 0.29 294 109 141 32 557.87 0.28 295 110 122 12 563.08 0.03 296 110 123 13 563.32 0.08 297 110 125 15 562.76 0.10 298 110 127 17 562.56 0.09 299 110 128 18 562.56 0.09 300 111 127 16 562.65 0.09 301 111 128 17 562.56 0.09 302 111 129 18 562.55 0.09 303 111 130 19 562.19 0.03 304 111 133 22 559.38 0.20 305 111 136 25 558.31 0.34 306 111 141 30 558.00 0.27 307 112 117 5 564.38 0.18 308 112 118 6 564.16 0.16 309 112 127 15 562.95 0.09 310 112 128 16 562.75 0.10 311 112 129 17 562.57 0.09 312 112 130 18 562.51 0.09 313 113 129 16 562.62 0.09 314 113 130 17 562.56 0.09 315 114 117 3 705.57 0.80 316 114 118 4 682.03 4.11 317 115 118 3 687.71 6.95 318 117 120 3 719.42 0.28 319 117 127 10 563.57 0.07 320 118 127 9 563.49 0.10 321 118 128 10 563.43 0.08 322 118 129 11 563.02 0.09 323 119 126 7 563.68 0.10 324 119 127 8 563.50 0.10 325 120 126 6 563.71 0.09 326 120 127 7 563.63 0.10 327 121 125 4 634.75 30.59 328 121 126 5 563.71 0.09 329 122 125 3 714.86 3.34 330 122 126 4 563.95 0.01 331 122 127 5 563.94 0.01 332 128 132 4 716.42 0.40 333 128 136 8 562.48 1.48 334 129 132 3 735.64 4.62 335 130 133 3 736.78 2.67 336 130 159 29 462.08 0.04 337 131 134 3 790.21 0.69 338 131 135 4 740.71 2.08 339 132 135 3 721.47 0.65 340 132 136 4 717.74 2.52 341 133 136 3 717.01 0.11 342 133 137 4 701.75 1.16 343 133 138 5 708.39 2.16 344 133 159 26 461.95 0.09 345 133 160 27 462.03 0.04 346 133 163 30 461.56 0.08 347 134 138 4 702.39 5.17 348 134 163 29 461.56 0.08 349 136 140 4 690.19 0.11 350 136 141 5 574.56 8.30 351 137 140 3 706.04 4.91 352 137 141 4 561.65 1.92 353 137 163 26 461.51 0.06 354 137 164 27 461.50 0.06 355 137 165 28 461.36 0.04 356 138 163 25 461.53 0.05 357 141 165 24 461.27 0.01 358 142 165 23 461.20 0.01 359 142 166 24 461.18 0.01 360 142 167 25 461.12 0.02 361 143 165 22 461.29 0.03 362 143 167 24 460.99 0.02 363 144 160 16 461.82 0.01 364 144 165 21 461.35 0.01 365 144 167 23 461.20 0.01 366 144 168 24 460.98 0.02 367 144 169 25 460.97 0.02 368 145 169 24 460.98 0.03 369 145 171 26 460.95 0.01 370 146 153 7 462.17 0.06 371 146 156 10 462.11 0.04 372 146 157 11 462.09 0.04 373 146 160 14 462.06 0.04 374 146 168 22 461.23 0.01 375 146 169 23 461.15 0.01 376 146 170 24 461.05 0.01 377 146 171 25 460.97 0.03 378 146 172 26 460.94 0.01 379 146 176 30 394.29 6.87 380 147 171 24 461.00 0.01 381 148 152 4 692.12 3.69 382 148 153 5 527.63 32.05 383 148 156 8 462.22 0.07 384 148 172 24 461.01 0.01 385 149 152 3 719.96 2.75 386 149 153 4 684.63 0.82 387 150 153 3 705.15 1.00 388 150 172 22 461.10 0.01 389 150 173 23 461.08 0.01 390 150 174 24 460.98 0.01 391 152 155 3 709.98 2.38 392 152 156 4 699.72 1.82 393 153 156 3 709.98 2.38 394 153 157 4 699.72 1.82 395 153 172 19 461.09 0.01 396 153 174 21 460.89 0.04 397 153 176 23 409.16 0.68 398 154 157 3 700.55 1.41 399 154 158 4 700.55 1.41 400 154 176 22 407.91 0.06 401 154 177 23 407.90 0.06 402 155 158 3 703.44 2.44 403 155 159 4 696.37 1.09 404 156 159 3 707.82 0.74 405 156 160 4 696.35 1.10 406 157 160 3 703.94 2.69 407 157 161 4 687.23 2.57 408 157 168 11 461.47 0.02 409 157 176 19 393.35 6.41 410 157 178 21 215.57 33.59 411 158 161 3 696.94 6.19 412 158 162 4 687.24 2.58 413 159 162 3 693.86 0.71 414 159 163 4 687.24 2.59 415 160 163 3 703.07 3.10 416 160 164 4 687.22 2.60 417 160 165 5 579.54 6.28 418 160 168 8 461.47 0.01 419 161 164 3 706.25 6.92 420 161 165 4 582.18 4.98 421 161 178 17 139.18 4.58 422 161 179 18 139.16 4.57 423 161 182 21 138.78 4.65 424 165 168 3 801.30 1.54 425 165 182 17 138.72 4.62 426 166 182 16 138.72 4.62 427 166 183 17 138.70 4.62 428 167 182 15 138.72 4.62 429 167 183 16 138.63 4.62 430 168 176 8 324.22 5.26 431 168 178 10 141.22 3.58 432 168 182 14 138.80 4.63 433 168 183 15 138.68 4.62 434 168 184 16 138.60 4.63 435 168 185 17 138.31 4.72 436 169 185 16 138.22 4.75 437 169 187 18 137.69 4.56 438 170 174 4 721.72 0.32 439 170 176 6 356.22 12.16 440 170 184 14 138.62 4.63 441 170 185 15 138.38 4.75 442 170 186 16 137.97 4.62 443 170 187 17 137.77 4.53 444 171 187 16 137.56 4.63 445 176 184 8 138.88 4.64 446 178 182 4 629.94 32.20 447 178 184 6 139.03 4.57 448 179 182 3 715.96 8.14 449 188 191 3 770.24 0.59 450 189 192 3 702.85 0.22 451 189 193 4 699.97 0.16 452 190 193 3 701.21 0.46 453 190 194 4 699.97 0.16 454 191 194 3 695.87 2.00 455 191 195 4 689.58 3.14 456 192 195 3 705.32 4.83 457 192 196 4 689.48 3.08 458 193 196 3 705.31 4.83 459 193 197 4 689.50 3.08 460 194 197 3 695.82 0.79 461 194 198 4 695.82 0.78 462 195 198 3 709.89 2.10 463 195 199 4 704.19 4.96 464 196 199 3 715.49 0.70 465 196 200 4 704.19 4.95 466 197 200 3 715.48 0.70 467 197 201 4 708.81 4.03 468 198 201 3 715.48 0.70 469 198 202 4 700.93 0.09 470 198 205 7 523.14 23.71 471 199 202 3 700.23 0.43 472 199 203 4 656.47 20.45 473 200 203 3 698.54 1.95 474 202 205 3 702.36 0.15 475 205 209 4 710.14 1.96 476 205 210 5 710.58 2.25 477 206 209 3 727.64 0.20 478 207 210 3 721.56 3.24 479 208 211 3 712.98 3.40