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 2 6 4 788.55 2.02 2 3 6 3 793.60 0.51 3 3 7 4 779.05 6.77 4 4 7 3 795.51 0.45 5 4 8 4 789.14 1.71 6 5 8 3 795.51 0.45 7 5 9 4 785.85 3.35 8 6 9 3 793.30 1.55 9 6 10 4 789.23 0.48 10 7 10 3 799.62 4.71 11 7 11 4 793.28 1.54 12 7 117 110 29.37 0.12 13 7 120 113 29.47 0.16 14 7 121 114 29.49 0.15 15 8 11 3 804.58 2.25 16 8 117 109 29.28 0.17 17 9 166 157 91.86 1.47 18 10 166 156 92.00 1.52 19 11 116 105 38.37 0.48 20 11 120 109 39.44 0.04 21 11 166 155 92.75 1.21 22 11 169 158 92.84 1.16 23 12 163 151 92.88 1.19 24 12 164 152 92.30 1.40 25 12 165 153 92.76 1.21 26 12 166 154 92.75 1.21 27 13 126 113 39.64 0.04 28 13 127 114 39.44 0.05 29 13 164 151 93.17 1.12 30 14 17 3 912.96 3.86 31 14 125 111 49.13 0.80 32 14 126 112 45.89 0.82 33 14 127 113 41.38 0.69 34 14 160 146 92.10 1.44 35 14 162 148 92.92 1.17 36 14 164 150 93.73 0.85 37 15 69 54 68.60 0.26 38 15 127 112 64.70 2.07 39 15 162 147 93.73 0.85 40 16 72 56 92.18 1.44 41 16 160 144 93.11 1.12 42 16 161 145 93.68 0.84 43 16 162 146 93.75 0.84 44 17 69 52 92.21 1.45 45 17 72 55 92.80 1.14 46 17 73 56 92.19 1.44 47 17 125 108 92.91 1.16 48 17 126 109 92.90 1.16 49 17 127 110 92.88 1.16 50 17 156 139 92.30 1.43 51 17 157 140 92.86 1.16 52 17 158 141 92.84 1.16 53 17 159 142 92.93 1.15 54 17 161 144 95.13 0.35 55 18 159 141 94.34 0.51 56 18 160 142 98.56 0.02 57 18 161 143 103.39 1.19 58 20 74 54 103.41 1.18 59 20 159 139 104.38 1.11 60 21 74 53 104.03 0.89 61 21 159 138 105.34 0.83 62 22 26 4 763.60 1.58 63 22 27 5 745.54 2.75 64 22 30 8 743.07 1.52 65 22 74 52 104.99 0.86 66 22 75 53 104.70 0.97 67 22 124 102 105.45 0.77 68 22 157 135 105.06 0.91 69 22 158 136 105.13 0.90 70 22 159 137 105.48 0.77 71 23 26 3 796.68 0.83 72 23 27 4 796.02 0.48 73 24 27 3 796.05 0.49 74 24 28 4 796.08 0.51 75 25 28 3 802.13 2.52 76 25 29 4 796.11 0.51 77 26 29 3 810.27 7.58 78 26 30 4 796.11 0.51 79 26 122 96 116.33 0.79 80 26 159 133 124.66 1.22 81 27 30 3 810.47 7.49 82 27 31 4 783.44 6.83 83 27 50 23 110.52 1.32 84 27 75 48 114.94 0.10 85 27 77 50 111.77 1.26 86 28 31 3 802.45 3.37 87 28 32 4 785.77 0.62 88 29 32 3 818.80 4.80 89 29 33 4 789.34 1.16 90 30 33 3 804.50 2.35 91 30 34 4 799.26 4.96 92 30 77 47 124.94 1.25 93 30 115 85 116.34 0.78 94 30 118 88 120.12 1.31 95 30 119 89 120.80 1.21 96 30 122 92 125.28 1.16 97 30 124 94 125.31 1.14 98 30 157 127 125.14 1.17 99 31 34 3 796.71 0.47 100 31 35 4 791.00 0.37 101 31 48 17 120.64 1.27 102 31 77 46 125.09 1.18 103 32 35 3 791.01 0.37 104 32 36 4 791.00 0.37 105 33 36 3 791.86 0.05 106 33 37 4 791.85 0.05 107 33 114 81 125.02 1.16 108 33 118 85 125.21 1.12 109 34 37 3 820.58 1.14 110 34 48 14 125.23 1.19 111 34 111 77 124.88 1.09 112 34 114 80 124.93 1.11 113 34 115 81 125.11 1.17 114 37 110 73 125.34 1.14 115 37 111 74 125.37 1.15 116 37 114 77 125.41 1.13 117 39 42 3 770.76 5.32 118 39 43 4 748.07 6.03 119 39 44 5 448.79 0.90 120 39 107 68 125.34 1.13 121 40 43 3 818.38 4.96 122 40 103 63 125.14 1.20 123 40 107 67 125.42 1.16 124 43 83 40 135.65 2.69 125 43 86 43 135.53 2.71 126 43 103 60 135.28 2.60 127 44 85 41 135.82 2.71 128 45 81 36 135.89 2.73 129 45 82 37 135.73 2.68 130 45 83 38 135.71 2.69 131 45 85 40 135.78 2.66 132 45 86 41 135.74 2.68 133 45 103 58 135.83 2.75 134 45 104 59 135.71 2.74 135 45 107 62 135.89 2.73 136 46 80 34 136.02 2.71 137 46 82 36 135.89 2.73 138 46 85 39 136.02 2.71 139 46 108 62 135.98 2.70 140 46 111 65 136.35 2.57 141 47 79 32 136.64 2.45 142 47 80 33 136.03 2.71 143 47 82 35 136.03 2.71 144 47 85 38 136.04 2.71 145 48 77 29 137.09 2.52 146 48 78 30 137.01 2.54 147 48 79 31 136.66 2.44 148 48 111 63 136.69 2.44 149 49 77 28 137.23 2.51 150 49 78 29 137.07 2.54 151 49 80 31 137.01 2.54 152 49 143 94 137.13 2.56 153 49 145 96 137.07 2.52 154 50 75 25 138.12 2.38 155 50 77 27 137.21 2.52 156 51 56 5 757.29 3.65 157 51 57 6 620.26 31.36 158 51 60 9 703.66 10.34 159 51 76 25 137.71 2.58 160 51 78 27 137.33 2.48 161 51 143 92 137.41 2.44 162 53 56 3 791.26 7.82 163 53 57 4 779.10 3.78 164 54 57 3 786.94 0.51 165 54 58 4 779.11 3.77 166 55 58 3 793.65 3.63 167 55 59 4 790.51 2.35 168 56 59 3 804.14 1.62 169 56 60 4 790.81 2.21 170 56 142 86 199.04 0.42 171 57 60 3 801.50 1.81 172 57 61 4 790.81 2.21 173 57 70 13 429.79 6.50 174 57 71 14 315.00 45.02 175 57 73 16 313.38 41.77 176 57 74 17 313.41 41.75 177 57 75 18 310.98 42.25 178 57 76 19 305.37 41.33 179 58 61 3 801.16 1.99 180 58 62 4 795.50 4.81 181 58 71 13 322.98 46.36 182 59 62 3 797.74 1.25 183 59 63 4 790.57 2.34 184 59 142 83 225.66 0.58 185 60 63 3 798.68 3.25 186 60 64 4 781.56 2.15 187 60 70 10 435.88 3.75 188 60 76 16 311.55 40.59 189 60 132 72 225.68 0.59 190 60 139 79 225.69 0.59 191 60 142 82 225.91 0.48 192 61 64 3 810.53 2.41 193 61 65 4 787.88 1.06 194 61 66 5 703.59 7.26 195 61 67 6 566.65 6.30 196 61 68 7 476.09 10.56 197 61 70 9 435.88 3.75 198 61 71 10 435.85 3.76 199 62 65 3 798.78 0.85 200 62 66 4 750.25 4.55 201 63 131 68 229.14 0.72 202 63 134 71 229.09 0.71 203 63 135 72 228.78 0.83 204 63 138 75 228.74 0.84 205 63 139 76 228.75 0.85 206 63 142 79 228.91 0.77 207 64 67 3 825.03 1.70 208 64 70 6 595.19 29.66 209 64 129 65 229.15 0.72 210 64 131 67 229.13 0.72 211 64 132 68 229.05 0.71 212 64 134 70 229.12 0.72 213 65 134 69 229.11 0.73 214 67 70 3 825.13 1.10 215 67 129 62 229.24 0.67 216 67 131 64 229.24 0.67 217 68 71 3 810.43 0.52 218 68 72 4 769.11 2.13 219 69 72 3 797.38 2.66 220 69 73 4 769.11 2.13 221 69 127 58 266.33 17.73 222 69 129 60 337.07 17.53 223 69 156 87 229.72 0.58 224 70 76 6 386.67 23.52 225 70 129 59 337.06 17.53 226 70 156 86 229.72 0.58 227 73 156 83 304.29 1.23 228 73 157 84 304.26 1.24 229 74 157 83 326.16 12.17 230 74 158 84 325.72 12.08 231 75 156 81 349.03 20.73 232 75 157 82 337.39 17.68 233 76 129 53 374.33 29.61 234 76 132 56 377.63 30.34 235 76 154 78 374.36 29.61 236 76 155 79 362.23 26.62 237 76 156 80 351.02 21.73 238 77 115 38 377.56 30.32 239 77 154 77 374.62 29.70 240 77 155 78 371.42 31.07 241 77 157 80 371.40 31.07 242 78 132 54 377.94 30.22 243 78 143 65 378.97 30.20 244 78 151 73 378.36 30.18 245 78 153 75 377.81 30.14 246 78 154 76 377.20 30.14 247 79 108 29 378.42 30.21 248 79 111 32 378.06 30.13 249 79 112 33 377.92 30.18 250 79 115 36 377.91 30.18 251 79 151 72 378.41 30.19 252 79 152 73 378.37 30.18 253 79 153 74 378.01 30.15 254 79 155 76 377.82 30.14 255 80 108 28 378.62 30.28 256 80 145 65 380.08 30.07 257 80 149 69 379.80 30.00 258 80 150 70 378.73 30.28 259 80 151 71 378.42 30.20 260 81 104 23 378.73 30.29 261 81 105 24 378.70 30.28 262 81 108 27 378.64 30.29 263 81 149 68 379.86 30.02 264 81 150 69 378.88 30.21 265 81 152 71 378.72 30.28 266 81 237 156 296.31 1.24 267 82 85 3 836.90 3.21 268 82 86 4 813.96 0.70 269 82 148 66 380.74 30.26 270 82 149 67 379.87 30.02 271 83 86 3 813.95 0.70 272 83 87 4 801.46 0.31 273 83 95 12 381.20 30.14 274 83 100 17 380.79 30.29 275 83 103 20 380.68 30.30 276 83 104 21 380.55 30.30 277 83 148 65 380.78 30.28 278 83 237 154 296.49 1.20 279 84 87 3 809.89 2.73 280 84 88 4 801.45 0.31 281 84 146 62 381.08 30.20 282 84 147 63 381.07 30.20 283 84 148 64 380.81 30.27 284 84 149 65 380.80 30.27 285 85 88 3 817.03 6.29 286 85 89 4 799.41 1.32 287 86 89 3 790.03 3.38 288 86 90 4 789.97 3.39 289 87 90 3 789.90 3.31 290 87 91 4 760.88 0.34 291 87 93 6 448.73 3.50 292 87 95 8 444.59 1.44 293 87 148 61 381.24 30.12 294 90 93 3 811.82 3.43 295 94 100 6 786.30 0.96 296 94 240 146 296.50 1.20 297 95 100 5 786.30 0.96 298 95 148 53 568.58 7.90 299 95 240 145 296.30 1.21 300 96 100 4 798.14 1.65 301 96 236 140 296.56 1.22 302 96 238 142 296.49 1.20 303 96 239 143 296.34 1.25 304 96 240 144 296.21 1.19 305 97 100 3 806.94 2.48 306 97 101 4 798.12 1.67 307 97 240 143 295.48 1.03 308 98 101 3 798.13 1.66 309 98 102 4 794.05 0.38 310 98 238 140 295.68 0.94 311 98 240 142 295.64 0.95 312 99 102 3 802.99 0.77 313 99 103 4 790.18 0.96 314 100 103 3 794.25 1.06 315 100 104 4 787.63 2.24 316 100 237 137 296.49 1.20 317 101 104 3 796.81 2.35 318 101 105 4 787.63 2.24 319 101 150 49 617.73 3.48 320 101 232 131 298.04 1.31 321 101 237 136 296.22 1.19 322 101 238 137 295.68 0.94 323 102 105 3 818.08 4.91 324 102 106 4 787.58 2.26 325 103 106 3 799.66 4.31 326 103 107 4 785.80 0.96 327 104 108 4 785.80 0.96 328 105 108 3 790.60 0.22 329 105 109 4 782.21 0.86 330 105 150 45 642.14 2.73 331 105 152 47 641.53 2.54 332 106 109 3 790.48 1.03 333 106 110 4 785.07 0.46 334 107 110 3 805.38 1.47 335 107 111 4 782.01 1.08 336 108 111 3 798.73 4.79 337 108 112 4 783.16 1.66 338 108 152 44 645.46 2.98 339 109 112 3 792.45 1.85 340 109 113 4 787.86 4.15 341 109 153 44 649.02 1.19 342 110 113 3 801.77 1.20 343 110 114 4 785.08 2.75 344 111 114 3 797.47 0.66 345 111 115 4 794.65 2.04 346 112 115 3 803.37 3.62 347 112 116 4 797.36 0.69 348 112 128 16 650.08 1.19 349 112 153 41 650.11 1.17 350 113 116 3 797.36 0.69 351 113 117 4 797.37 0.68 352 113 128 15 650.18 1.18 353 114 117 3 802.72 2.00 354 114 118 4 797.37 0.68 355 115 118 3 791.93 2.04 356 115 119 4 791.96 2.04 357 115 155 40 650.14 1.17 358 116 119 3 791.96 2.04 359 116 120 4 791.96 2.04 360 116 126 10 650.17 1.19 361 116 128 12 650.20 1.17 362 116 155 39 650.15 1.18 363 116 157 41 649.99 1.18 364 117 120 3 799.25 0.51 365 117 121 4 791.96 2.04 366 118 121 3 793.11 2.56 367 118 122 4 793.06 2.59 368 119 122 3 808.87 5.32 369 119 123 4 792.22 3.00 370 119 124 5 760.49 1.00 371 119 157 38 650.07 1.16 372 120 123 3 802.94 2.35 373 120 124 4 761.07 1.29 374 122 159 37 650.04 1.17 375 123 159 36 650.09 1.15 376 123 160 37 650.04 1.17 377 124 158 34 650.12 1.15 378 124 159 35 650.06 1.16 379 124 160 36 650.03 1.16 380 125 157 32 650.22 1.13 381 125 158 33 650.19 1.14 382 125 160 35 650.01 1.17 383 126 156 30 650.23 1.14 384 126 157 31 650.21 1.12 385 127 155 28 650.64 1.12 386 127 156 29 650.29 1.14 387 128 153 25 650.84 1.07 388 128 154 26 650.79 1.07 389 128 155 27 650.64 1.12 390 129 132 3 825.81 5.20 391 129 153 24 650.84 1.07 392 129 154 25 650.79 1.07 393 129 156 27 650.74 1.09 394 130 133 3 820.14 2.43 395 130 153 23 650.85 1.07 396 130 225 95 299.41 1.48 397 131 134 3 797.16 5.40 398 131 225 94 299.41 1.48 399 132 136 4 759.30 6.81 400 132 139 7 651.45 1.11 401 132 151 19 651.06 1.07 402 132 153 21 650.89 1.07 403 132 154 22 650.88 1.08 404 133 136 3 741.48 15.72 405 133 152 19 651.06 1.06 406 133 225 92 299.41 1.48 407 133 227 94 299.36 1.46 408 133 228 95 298.78 1.47 409 134 225 91 299.41 1.48 410 134 227 93 299.39 1.48 411 135 138 3 791.19 2.44 412 135 139 4 775.24 4.01 413 136 139 3 789.31 3.39 414 136 140 4 775.51 4.02 415 136 150 14 651.26 1.05 416 136 151 15 651.22 1.06 417 136 227 91 299.37 1.46 418 136 228 92 299.27 1.44 419 136 231 95 297.95 1.43 420 137 140 3 785.92 1.70 421 137 141 4 775.56 4.04 422 137 231 94 297.99 1.44 423 137 234 97 296.81 1.24 424 138 141 3 791.32 3.52 425 138 142 4 776.08 3.77 426 139 142 3 788.20 3.02 427 139 143 4 776.08 3.77 428 139 151 12 651.26 1.05 429 140 143 3 810.58 9.62 430 140 144 4 776.02 3.75 431 140 145 5 737.38 0.77 432 140 151 11 651.27 1.05 433 140 231 91 298.38 1.24 434 140 235 95 296.55 1.24 435 141 144 3 778.65 5.71 436 145 149 4 793.04 13.83 437 145 151 6 651.67 1.16 438 146 149 3 832.76 4.80 439 146 235 89 296.57 1.24 440 147 234 87 297.19 1.52 441 147 235 88 296.56 1.24 442 148 235 87 296.56 1.23 443 148 236 88 296.53 1.23 444 148 237 89 296.48 1.20 445 149 235 86 296.56 1.24 446 149 237 88 296.38 1.25 447 150 231 81 298.03 1.40 448 150 232 82 297.57 1.35 449 150 237 87 296.19 1.20 450 151 231 80 298.03 1.40 451 165 203 38 325.93 1.47 452 166 199 33 326.06 1.54 453 167 196 29 326.08 1.59 454 167 199 32 326.07 1.54 455 168 192 24 326.21 1.62 456 168 195 27 326.23 1.61 457 168 196 28 326.15 1.58 458 168 199 31 326.17 1.56 459 169 192 23 326.26 1.60 460 170 174 4 783.87 3.13 461 170 192 22 326.28 1.60 462 170 212 42 326.24 1.59 463 171 174 3 808.60 4.82 464 171 175 4 783.87 3.13 465 171 192 21 326.45 1.66 466 172 175 3 806.08 7.97 467 172 176 4 760.71 8.45 468 173 188 15 327.02 1.56 469 174 177 3 864.77 2.50 470 174 184 10 327.02 1.57 471 174 188 14 327.03 1.56 472 174 189 15 327.02 1.56 473 177 180 3 826.37 0.98 474 177 181 4 594.49 58.98 475 177 182 5 430.34 7.62 476 184 189 5 759.28 5.79 477 185 188 3 802.25 0.43 478 185 189 4 788.04 6.67 479 186 189 3 809.90 1.26 480 186 190 4 803.66 1.15 481 187 190 3 806.68 0.35 482 187 191 4 803.67 1.14 483 188 191 3 817.24 0.77 484 188 192 4 792.82 6.55 485 189 192 3 806.55 0.25 486 189 193 4 770.71 4.50 487 189 212 23 348.25 1.54 488 189 213 24 348.12 1.50 489 190 193 3 806.77 0.42 490 190 194 4 779.87 3.32 491 191 194 3 797.25 0.67 492 191 195 4 779.87 3.32 493 192 195 3 800.70 0.97 494 192 196 4 780.53 2.99 495 192 212 20 348.29 1.54 496 193 196 3 803.52 0.45 497 193 197 4 777.00 1.32 498 193 211 18 348.28 1.54 499 193 212 19 348.29 1.54 500 193 213 20 348.28 1.54 501 194 197 3 799.30 2.56 502 194 198 4 782.64 1.50 503 194 209 15 350.49 1.38 504 195 198 3 799.41 0.41 505 195 199 4 782.22 1.71 506 196 199 3 785.51 0.37 507 196 200 4 791.56 3.39 508 196 212 16 349.20 1.88 509 197 200 3 806.66 3.21 510 197 201 4 791.57 3.39 511 197 209 12 350.45 1.36 512 197 210 13 350.39 1.36 513 197 211 14 349.29 1.91 514 198 201 3 811.22 5.51 515 198 202 4 803.53 9.36 516 199 202 3 820.44 3.76 517 199 203 4 807.96 7.15 518 200 203 3 804.68 8.79 519 200 204 4 791.55 3.40 520 200 210 10 350.51 1.38 521 200 211 11 350.51 1.37 522 200 212 12 350.51 1.38 523 200 215 15 350.50 1.37 524 201 204 3 791.56 3.40 525 201 207 6 388.21 20.18 526 201 208 7 361.14 6.65 527 210 214 4 785.89 4.26 528 210 218 8 744.35 5.38 529 211 214 3 785.93 4.25 530 211 215 4 786.32 4.06 531 212 215 3 786.32 4.06 532 212 216 4 786.33 4.05 533 213 216 3 799.58 3.48 534 213 217 4 786.34 4.05 535 214 217 3 793.53 0.46 536 214 218 4 793.53 0.46 537 215 218 3 813.75 0.40 538 215 219 4 791.10 0.77 539 216 219 3 792.22 0.53 540 216 220 4 778.35 0.05 541 217 220 3 809.47 2.69 542 217 221 4 781.25 1.37 543 218 221 3 821.25 2.69 544 218 222 4 809.50 2.71 545 219 222 3 809.50 2.71 546 223 226 3 820.37 3.14 547 225 228 3 820.63 0.29 548 227 230 3 808.86 2.96 549 227 231 4 764.75 5.08 550 228 231 3 794.24 5.02 551 228 232 4 786.94 0.77 552 229 232 3 801.75 1.27 553 229 233 4 789.55 2.04 554 230 233 3 796.21 1.50 555 230 234 4 789.55 2.04 556 231 234 3 796.38 1.36 557 231 235 4 789.52 2.06 558 232 235 3 796.39 0.57 559 232 236 4 789.51 2.07 560 232 237 5 688.91 13.70 561 233 236 3 781.83 1.77 562 233 237 4 762.23 5.92 563 233 238 5 727.08 11.38 564 233 239 6 571.28 50.98 565 236 239 3 831.87 0.06