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 2 208 206 87.89 1.58 2 2 225 223 48.36 1.04 3 2 226 224 37.55 0.60 4 2 227 225 36.20 0.81 5 3 204 201 132.63 0.95 6 3 225 222 50.08 0.28 7 4 202 198 132.97 0.79 8 4 204 200 130.16 0.17 9 4 205 201 127.24 0.90 10 4 225 221 61.04 1.05 11 5 184 179 133.04 0.77 12 5 185 180 133.25 0.82 13 5 186 181 134.44 1.33 14 5 202 197 133.27 0.75 15 5 203 198 133.06 0.77 16 5 204 199 132.94 0.81 17 6 201 195 134.24 1.02 18 6 202 196 133.27 0.75 19 6 222 216 73.18 2.16 20 6 225 219 70.55 3.23 21 7 194 187 134.86 1.27 22 7 201 194 134.70 1.24 23 7 202 195 134.23 1.02 24 8 199 191 136.41 0.82 25 8 200 192 135.65 0.88 26 8 201 193 135.65 0.87 27 8 222 214 79.97 0.81 28 9 200 191 136.16 0.95 29 9 222 213 80.07 0.76 30 10 200 190 136.22 0.93 31 10 221 211 81.52 0.32 32 10 222 212 80.36 0.88 33 11 220 209 99.79 3.78 34 11 221 210 81.52 0.32 35 11 223 212 85.73 1.80 36 11 239 228 27.81 1.27 37 11 243 232 20.35 0.24 38 12 177 165 165.27 2.74 39 12 219 207 113.17 4.88 40 12 220 208 101.05 4.03 41 13 177 164 165.58 2.59 42 13 217 204 119.23 2.45 43 13 218 205 118.66 2.56 44 13 219 206 116.81 3.06 45 13 240 227 33.88 1.81 46 13 243 230 31.26 0.59 47 14 157 143 168.33 2.92 48 14 177 163 166.08 2.35 49 14 218 204 118.69 2.55 50 15 156 141 171.51 3.91 51 15 157 142 171.51 3.91 52 15 215 200 119.39 2.46 53 15 216 201 119.36 2.45 54 15 217 202 119.23 2.45 55 16 159 143 171.59 3.90 56 16 212 196 133.98 0.43 57 16 213 197 132.16 1.28 58 16 214 198 121.71 3.20 59 16 215 199 119.55 2.39 60 16 216 200 119.39 2.46 61 16 218 202 118.78 2.60 62 17 156 139 171.94 3.97 63 17 157 140 171.93 3.97 64 17 158 141 171.63 3.90 65 17 159 142 171.63 3.89 66 18 159 141 171.86 3.98 67 18 209 191 151.14 1.57 68 18 212 194 137.47 0.21 69 18 213 195 132.07 1.23 70 18 214 196 121.88 3.52 71 19 149 130 173.00 3.73 72 19 158 139 172.16 3.98 73 19 159 140 172.03 4.01 74 19 160 141 172.00 4.01 75 19 163 144 172.06 4.00 76 21 139 118 196.30 0.48 77 22 139 117 196.36 0.46 78 24 135 111 196.34 0.47 79 24 138 114 196.49 0.41 80 24 139 115 196.38 0.46 81 24 142 118 198.36 0.62 82 24 144 120 196.71 0.61 83 26 101 75 203.40 1.88 84 26 102 76 203.41 1.90 85 26 105 79 203.41 1.90 86 27 99 72 204.91 2.46 87 28 102 74 204.84 2.52 88 28 105 77 214.25 2.19 89 29 99 70 419.95 3.96 90 30 97 67 443.72 6.73 91 31 35 4 820.84 1.22 92 31 36 5 811.19 3.56 93 31 39 8 788.62 3.08 94 31 97 66 450.14 3.58 95 31 98 67 450.14 3.58 96 31 99 68 450.14 3.57 97 32 35 3 853.10 3.45 98 32 36 4 825.93 3.77 99 33 36 3 844.21 2.87 100 33 37 4 838.53 5.85 101 34 38 4 854.94 2.33 102 35 38 3 871.62 6.00 103 35 39 4 844.37 2.95 104 36 39 3 855.45 2.17 105 36 40 4 844.74 2.77 106 36 93 57 459.81 2.36 107 36 94 58 459.81 2.35 108 37 40 3 864.24 2.31 109 37 41 4 844.71 2.74 110 38 41 3 862.70 0.84 111 38 42 4 842.01 3.48 112 39 42 3 846.04 1.98 113 39 43 4 836.72 4.89 114 39 93 54 462.08 1.98 115 39 99 60 461.30 1.70 116 39 100 61 461.25 1.69 117 40 43 3 843.53 1.47 118 40 44 4 825.89 0.43 119 40 94 54 462.29 1.93 120 41 44 3 844.78 2.10 121 41 45 4 822.92 1.91 122 41 46 5 822.34 1.78 123 42 46 4 816.07 1.32 124 43 46 3 847.53 1.77 125 43 47 4 827.93 2.74 126 43 86 43 462.68 1.92 127 43 89 46 462.49 1.94 128 43 90 47 462.56 1.90 129 43 93 50 462.49 1.94 130 43 100 57 461.88 1.90 131 44 47 3 871.42 4.82 132 44 48 4 835.58 6.15 133 44 86 42 462.75 1.94 134 45 48 3 845.59 2.08 135 45 49 4 845.59 2.08 136 46 49 3 866.37 2.08 137 46 50 4 850.09 0.17 138 47 50 3 855.03 2.31 139 47 51 4 841.88 4.27 140 47 80 33 463.74 1.68 141 47 81 34 463.69 1.77 142 47 86 39 463.11 2.00 143 48 51 3 862.77 6.17 144 48 52 4 836.81 1.73 145 49 52 3 861.55 6.79 146 49 53 4 836.81 1.73 147 50 53 3 861.55 6.79 148 50 54 4 824.33 1.79 149 50 80 30 464.32 1.82 150 50 137 87 407.14 4.22 151 50 140 90 406.87 4.17 152 51 55 4 825.51 2.22 153 51 81 30 464.31 1.83 154 52 55 3 830.89 0.46 155 52 56 4 825.59 2.19 156 53 56 3 855.13 1.98 157 53 57 4 843.66 3.64 158 53 140 87 407.25 4.17 159 53 146 93 406.76 4.16 160 54 57 3 855.39 2.11 161 54 58 4 843.97 3.48 162 54 80 26 464.57 1.75 163 54 136 82 407.44 4.13 164 55 58 3 855.53 2.18 165 55 59 4 855.39 2.11 166 55 77 22 464.76 1.84 167 56 59 3 886.56 3.06 168 56 60 4 849.35 4.44 169 57 60 3 858.30 0.82 170 57 61 4 845.83 4.42 171 57 169 112 400.13 5.39 172 57 170 113 399.92 5.38 173 58 61 3 858.83 1.08 174 58 62 4 847.62 5.29 175 58 70 12 469.56 0.23 176 58 73 15 465.19 1.89 177 58 77 19 465.20 1.89 178 59 62 3 848.68 5.83 179 59 63 4 831.69 2.39 180 60 63 3 848.38 0.33 181 60 64 4 824.97 0.79 182 60 150 90 406.20 4.31 183 60 169 109 400.17 5.37 184 60 170 110 400.12 5.38 185 61 64 3 847.58 0.96 186 61 65 4 821.24 2.63 187 61 66 5 821.16 2.62 188 61 73 12 472.47 1.53 189 61 169 108 400.34 5.45 190 62 66 4 748.18 8.67 191 62 67 5 604.57 3.50 192 62 70 8 519.10 8.24 193 64 173 109 400.11 5.39 194 65 69 4 837.35 2.08 195 65 168 103 400.49 5.45 196 65 169 104 400.47 5.45 197 65 193 128 307.22 4.66 198 66 69 3 871.25 0.34 199 67 70 3 839.07 5.21 200 69 72 3 857.06 3.71 201 69 73 4 858.84 2.26 202 70 73 3 858.85 2.26 203 70 74 4 846.03 1.79 204 71 74 3 852.83 0.74 205 71 75 4 851.47 1.73 206 72 75 3 866.32 2.51 207 72 76 4 856.71 0.90 208 73 76 3 856.71 0.90 209 73 77 4 856.71 0.90 210 73 165 92 400.43 5.44 211 73 166 93 400.40 5.43 212 73 169 96 400.41 5.44 213 74 77 3 873.96 0.79 214 74 78 4 857.45 1.27 215 75 78 3 857.44 1.28 216 75 79 4 856.70 0.91 217 76 79 3 855.68 3.02 218 76 80 4 853.59 4.05 219 76 133 57 407.77 4.07 220 77 80 3 854.38 2.82 221 77 81 4 846.40 0.47 222 78 81 3 852.74 3.64 223 78 82 4 821.00 2.48 224 79 82 3 822.17 1.89 225 79 85 6 769.44 0.91 226 79 111 32 461.49 1.50 227 79 126 47 408.31 4.11 228 79 130 51 407.82 4.07 229 80 133 53 407.37 4.18 230 80 137 57 407.25 4.17 231 82 85 3 848.20 2.79 232 82 86 4 838.18 4.51 233 83 86 3 850.14 1.80 234 83 87 4 847.10 0.24 235 84 87 3 856.79 1.71 236 84 88 4 847.06 0.09 237 85 88 3 860.15 3.39 238 85 89 4 850.81 1.97 239 85 107 22 490.10 7.20 240 86 89 3 859.52 3.71 241 86 90 4 838.77 4.05 242 87 90 3 859.15 1.16 243 87 91 4 841.85 5.75 244 88 91 3 870.32 0.84 245 88 92 4 849.34 3.75 246 89 92 3 870.33 0.84 247 89 93 4 847.59 2.88 248 89 103 14 512.81 2.75 249 89 104 15 511.12 3.54 250 89 107 18 503.96 7.12 251 90 93 3 870.32 0.84 252 90 94 4 841.95 0.06 253 91 94 3 836.19 2.91 254 91 95 4 830.16 5.92 255 92 95 3 841.73 0.13 256 92 96 4 821.58 10.19 257 92 97 5 821.58 10.19 258 92 98 6 709.11 4.96 259 92 103 11 566.34 2.53 260 92 106 14 544.48 4.57 261 92 107 15 542.48 5.55 262 93 97 4 787.63 18.73 263 93 98 5 649.47 1.69 264 93 100 7 661.86 27.68 265 93 103 10 571.82 4.50 266 94 97 3 838.00 4.78 267 98 102 4 782.23 29.98 268 98 103 5 714.36 3.95 269 98 106 8 714.31 3.97 270 99 102 3 849.78 3.77 271 99 103 4 823.89 9.17 272 100 104 4 831.17 5.53 273 100 141 41 406.54 4.04 274 101 105 4 841.27 1.21 275 101 138 37 406.62 4.01 276 101 141 40 406.55 4.04 277 101 142 41 406.55 4.04 278 102 105 3 859.61 0.07 279 102 106 4 845.43 0.83 280 103 106 3 872.23 6.38 281 103 107 4 876.30 4.35 282 104 107 3 876.30 4.35 283 104 108 4 845.45 0.85 284 105 108 3 857.94 4.83 285 105 109 4 845.45 0.85 286 106 109 3 849.44 0.38 287 106 110 4 846.18 1.25 288 107 110 3 864.57 3.38 289 107 111 4 846.16 1.27 290 108 111 3 850.16 3.33 291 108 112 4 846.09 1.30 292 108 134 26 406.81 4.08 293 109 113 4 830.45 6.52 294 110 113 3 835.10 4.30 295 110 114 4 822.98 3.10 296 111 114 3 852.17 1.00 297 111 115 4 836.14 1.50 298 111 130 19 407.81 3.98 299 112 115 3 851.22 1.48 300 112 116 4 848.05 0.12 301 112 127 15 408.14 4.11 302 113 116 3 850.24 0.88 303 113 117 4 848.05 0.12 304 114 117 3 850.26 0.86 305 114 118 4 852.29 2.23 306 115 118 3 854.30 1.23 307 115 123 8 454.70 27.16 308 115 127 12 408.33 4.16 309 115 130 15 408.36 4.15 310 116 124 8 502.18 11.15 311 118 123 5 770.09 11.44 312 120 123 3 853.41 2.64 313 120 124 4 840.67 0.33 314 121 124 3 850.01 4.34 315 121 125 4 850.22 4.24 316 122 125 3 858.04 0.33 317 122 126 4 850.22 4.24 318 123 126 3 851.21 3.75 319 123 127 4 845.11 1.66 320 124 127 3 850.24 4.22 321 124 128 4 853.37 2.67 322 125 128 3 848.23 0.10 323 125 129 4 845.90 1.07 324 126 129 3 845.90 1.07 325 126 130 4 842.76 1.50 326 127 130 3 852.12 2.04 327 127 131 4 846.00 1.01 328 128 131 3 862.98 0.37 329 128 132 4 846.06 0.98 330 129 132 3 862.90 0.34 331 129 133 4 846.07 0.98 332 129 165 36 400.41 5.44 333 130 133 3 852.00 1.99 334 130 134 4 847.19 1.55 335 131 134 3 847.20 1.55 336 131 135 4 847.18 1.55 337 132 135 3 850.71 3.38 338 132 136 4 847.12 1.58 339 132 166 34 400.14 5.39 340 133 136 3 849.24 4.11 341 133 137 4 844.55 1.70 342 134 137 3 849.31 4.08 343 134 138 4 844.56 1.70 344 135 138 3 857.48 8.12 345 135 139 4 844.79 1.59 346 136 139 3 849.45 2.91 347 136 140 4 844.80 1.59 348 136 166 30 400.17 5.38 349 137 140 3 869.20 2.27 350 137 141 4 844.67 1.53 351 138 141 3 850.16 4.27 352 138 142 4 841.56 0.03 353 139 143 4 804.50 17.32 354 139 144 5 643.89 3.28 355 139 146 7 584.07 6.11 356 140 143 3 795.98 13.15 357 140 146 6 731.57 10.79 358 148 151 3 871.97 1.67 359 148 152 4 850.78 0.69 360 149 152 3 876.26 3.81 361 149 170 21 399.82 5.52 362 150 170 20 399.79 5.51 363 150 172 22 399.25 5.63 364 152 175 23 397.37 5.76 365 155 175 20 397.62 5.88 366 156 177 21 397.61 5.87 367 157 177 20 392.69 3.63 368 157 180 23 392.61 3.66 369 157 218 61 118.76 2.61 370 158 163 5 854.99 0.36 371 158 171 13 400.50 5.48 372 158 178 20 392.66 3.63 373 158 179 21 385.17 0.16 374 158 180 22 379.85 2.50 375 159 180 21 379.75 2.50 376 159 208 49 273.57 2.14 377 159 209 50 260.31 4.20 378 159 218 59 118.75 2.62 379 160 163 3 893.61 4.11 380 160 180 20 379.43 2.66 381 160 181 21 370.50 6.71 382 160 182 22 370.50 6.71 383 160 209 49 260.29 4.20 384 161 182 21 327.32 1.65 385 161 209 48 260.23 4.17 386 162 181 19 333.54 4.76 387 163 167 4 814.96 9.48 388 163 168 5 814.95 9.47 389 163 181 18 330.12 6.48 390 164 167 3 837.85 1.18 391 164 168 4 837.85 1.18 392 165 168 3 837.86 1.18 393 165 169 4 833.91 0.80 394 165 189 24 306.92 4.71 395 166 169 3 837.86 1.18 396 166 170 4 837.86 1.18 397 167 170 3 861.90 2.88 398 167 171 4 833.91 0.79 399 168 171 3 833.93 0.79 400 168 189 21 306.97 4.71 401 168 193 25 307.08 4.69 402 171 176 5 838.01 1.00 403 171 179 8 597.20 0.79 404 172 175 3 896.71 3.46 405 172 176 4 840.65 2.31 406 173 176 3 864.78 6.04 407 173 179 6 817.36 9.33 408 173 197 24 307.88 4.29 409 176 179 3 1009.09 3.72 410 179 190 11 308.31 4.30 411 179 197 18 308.09 4.25 412 179 199 20 307.76 4.28 413 179 201 22 307.69 4.25 414 179 202 23 307.69 4.25 415 180 202 22 307.67 4.27 416 180 205 25 307.28 4.33 417 181 190 9 308.32 4.29 418 181 202 21 307.71 4.25 419 181 203 22 307.54 4.24 420 181 205 24 307.47 4.25 421 182 203 21 307.70 4.25 422 182 205 23 307.47 4.25 423 182 206 24 307.17 4.38 424 182 207 25 307.16 4.38 425 182 208 26 305.49 3.55 426 182 209 27 305.47 3.54 427 183 188 5 553.02 7.62 428 183 203 20 307.72 4.25 429 183 204 21 307.68 4.24 430 184 203 19 307.75 4.26 431 184 204 20 307.62 4.20 432 185 188 3 730.90 3.10 433 186 195 9 646.93 8.31 434 188 191 3 844.98 3.79 435 188 192 4 844.88 3.83 436 189 192 3 844.88 3.83 437 189 193 4 838.90 0.84 438 190 193 3 851.75 0.39 439 190 194 4 838.90 0.84 440 190 203 13 307.70 4.20 441 191 194 3 839.53 0.53 442 191 195 4 817.16 1.46 443 191 203 12 307.74 4.24 444 192 195 3 845.11 4.09 445 192 196 4 820.20 0.06 446 193 196 3 850.91 4.00 447 193 197 4 788.75 2.05 448 194 198 4 738.02 2.50 449 194 199 5 632.72 5.88 450 194 201 7 494.62 2.79 451 195 198 3 815.53 10.18 452 200 222 22 79.94 0.83 453 201 220 19 81.27 0.41 454 202 205 3 906.95 2.15 455 202 220 18 81.25 0.41 456 202 225 23 71.31 3.06 457 202 227 25 71.10 3.10 458 205 208 3 860.82 5.97 459 207 210 3 837.62 2.38 460 207 211 4 832.53 4.92 461 208 211 3 837.67 2.40 462 208 212 4 787.08 5.46 463 212 216 4 803.66 13.74 464 212 218 6 591.18 2.21 465 212 229 17 71.16 3.12 466 213 216 3 845.25 0.21 467 216 229 13 71.44 3.10 468 217 229 12 71.45 3.10 469 217 230 13 71.28 3.02 470 218 227 9 71.64 3.02 471 218 228 10 71.45 3.10 472 218 229 11 71.28 3.03 473 219 228 9 71.29 3.03 474 219 231 12 71.12 2.95 475 219 236 17 46.58 0.73 476 221 224 3 889.47 4.89 477 221 225 4 823.38 5.95 478 221 226 5 569.94 9.37 479 221 228 7 511.85 10.17 480 221 239 18 26.71 0.74 481 228 231 3 868.62 2.71 482 231 235 4 801.32 12.70 483 231 236 5 723.12 9.31 484 232 235 3 865.58 12.43 485 232 236 4 824.73 0.98 486 233 236 3 833.12 0.90 487 233 237 4 806.98 4.65 488 234 238 4 838.20 2.73 489 235 238 3 863.46 9.87 490 235 239 4 838.01 2.82 491 236 239 3 854.60 5.47 492 236 240 4 838.01 2.82 493 237 240 3 865.66 0.07 494 237 241 4 837.48 4.17 495 238 241 3 855.33 4.68 496 238 242 4 854.09 5.29 497 239 242 3 855.50 4.59 498 239 243 4 836.11 4.86 499 240 243 3 860.52 2.08 500 240 244 4 842.70 1.56 501 241 244 3 848.98 0.90 502 241 245 4 837.69 0.96 503 242 245 3 838.55 0.55 504 242 246 4 838.55 0.55 505 243 246 3 845.96 3.88 506 243 247 4 838.55 0.54 507 244 247 3 850.92 2.49 508 244 248 4 836.53 1.52 509 245 248 3 835.83 5.05 510 245 249 4 829.18 1.73 511 246 249 3 836.24 4.84