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 25 24 32.30 0.36 2 1 117 116 28.48 0.93 3 2 5 3 850.18 2.62 4 2 6 4 831.05 4.04 5 2 114 112 26.23 0.84 6 2 115 113 28.29 1.01 7 2 116 114 29.73 0.34 8 2 117 115 31.11 0.96 9 3 6 3 831.45 3.83 10 3 7 4 830.82 3.92 11 4 7 3 833.38 2.64 12 4 8 4 828.12 2.57 13 4 161 157 56.68 1.09 14 5 8 3 833.38 2.64 15 5 9 4 812.19 0.78 16 5 20 15 34.03 0.29 17 5 105 100 32.29 0.58 18 6 104 98 32.26 0.59 19 6 105 99 32.26 0.59 20 6 106 100 32.76 0.35 21 6 114 108 33.85 0.77 22 8 161 153 65.23 0.97 23 9 20 11 63.26 0.93 24 9 23 14 209.99 73.34 25 9 105 96 63.95 0.94 26 9 106 97 63.98 0.94 27 10 105 95 63.98 0.93 28 10 106 96 63.98 0.95 29 11 20 9 709.21 0.99 30 11 105 94 64.03 0.93 31 11 112 101 63.95 0.93 32 12 19 7 709.41 1.01 33 12 20 8 709.19 0.98 34 12 74 62 64.01 0.93 35 12 76 64 63.98 0.92 36 12 105 93 64.34 0.95 37 12 112 100 63.99 0.93 38 13 17 4 780.19 11.15 39 13 18 5 729.85 9.19 40 13 19 6 711.83 0.20 41 13 76 63 64.36 0.76 42 13 149 136 64.14 0.85 43 14 17 3 818.38 4.35 44 14 18 4 763.73 7.50 45 14 20 6 729.84 9.19 46 14 23 9 721.45 4.98 47 17 238 221 73.90 3.62 48 18 22 4 842.82 2.07 49 18 23 5 842.80 2.08 50 18 238 220 73.92 3.62 51 19 22 3 858.40 2.92 52 19 74 55 73.89 3.63 53 19 76 57 73.89 3.63 54 19 149 130 73.89 3.63 55 19 150 131 73.90 3.63 56 19 151 132 73.89 3.62 57 19 236 217 78.76 1.29 58 19 238 219 73.98 3.65 59 20 23 3 849.64 1.34 60 21 24 3 855.66 4.35 61 21 25 4 820.13 1.50 62 21 74 53 73.99 3.66 63 21 236 215 80.91 0.55 64 22 25 3 836.18 0.70 65 22 26 4 813.90 0.98 66 22 236 214 78.86 1.32 67 23 26 3 871.12 3.38 68 23 159 136 168.40 1.43 69 24 157 133 159.17 2.25 70 24 158 134 166.66 0.90 71 24 159 135 168.38 1.43 72 25 153 128 112.53 1.66 73 25 155 130 159.16 2.25 74 25 156 131 164.47 1.08 75 25 157 132 163.35 1.16 76 25 158 133 169.96 0.92 77 25 236 211 112.50 1.64 78 26 158 132 171.40 0.34 79 26 159 133 171.61 0.36 80 27 232 205 171.53 0.27 81 27 234 207 170.84 0.34 82 27 235 208 164.12 0.22 83 27 236 209 153.12 0.20 84 28 236 208 166.65 0.90 85 29 154 125 171.36 0.33 86 29 233 204 171.87 0.33 87 29 234 205 171.61 0.29 88 29 235 206 171.31 0.30 89 29 236 207 170.86 0.34 90 29 237 208 167.19 0.88 91 30 52 22 171.89 0.34 92 30 154 124 171.75 0.32 93 31 49 18 171.90 0.33 94 31 50 19 171.86 0.32 95 31 51 20 171.75 0.32 96 31 52 21 171.91 0.33 97 31 150 119 170.87 0.34 98 31 152 121 171.43 0.29 99 31 154 123 171.81 0.33 100 31 237 206 171.46 0.28 101 31 238 207 171.27 0.29 102 32 49 17 171.90 0.33 103 32 50 18 171.89 0.33 104 33 47 14 171.90 0.33 105 33 48 15 171.91 0.33 106 33 49 16 171.91 0.33 107 33 75 42 171.54 0.28 108 33 148 115 171.18 0.33 109 33 150 117 171.53 0.28 110 33 239 206 171.51 0.29 111 33 240 207 171.43 0.29 112 33 241 208 170.73 0.29 113 34 47 13 171.93 0.33 114 34 48 14 171.93 0.33 115 34 50 16 172.00 0.34 116 35 46 11 171.94 0.33 117 35 47 12 171.94 0.33 118 35 148 113 171.56 0.29 119 35 241 206 171.56 0.29 120 35 243 208 170.84 0.33 121 36 45 9 171.94 0.33 122 36 46 10 171.98 0.32 123 36 243 207 171.44 0.29 124 37 243 206 171.47 0.30 125 37 244 207 171.39 0.33 126 38 243 205 171.53 0.30 127 38 244 206 171.38 0.32 128 38 246 208 169.90 0.70 129 39 43 4 832.48 0.72 130 39 45 6 713.12 4.21 131 39 132 93 325.30 76.92 132 39 243 204 171.64 0.30 133 39 244 205 171.53 0.30 134 39 245 206 171.28 0.28 135 39 246 207 170.87 0.34 136 40 43 3 857.90 3.12 137 40 132 92 350.82 89.61 138 40 245 205 171.51 0.29 139 40 246 206 171.28 0.29 140 40 247 207 171.27 0.29 141 40 248 208 164.69 0.38 142 41 132 91 350.83 89.60 143 41 133 92 350.80 89.61 144 41 134 93 350.75 89.62 145 41 135 94 350.75 89.62 146 41 143 102 350.20 89.58 147 41 245 204 171.63 0.31 148 41 246 205 171.53 0.30 149 41 248 207 169.75 0.62 150 42 88 46 353.60 90.62 151 42 131 89 351.41 89.88 152 42 132 90 350.86 89.61 153 42 133 91 350.83 89.60 154 42 134 92 350.79 89.61 155 43 88 45 353.60 90.62 156 43 131 88 351.57 89.83 157 43 132 89 351.31 89.81 158 44 84 40 352.95 90.33 159 44 88 44 353.61 90.63 160 44 93 49 355.85 90.38 161 44 129 85 352.98 90.34 162 44 130 86 352.86 90.30 163 44 131 87 351.74 89.80 164 45 81 36 352.97 90.32 165 45 93 48 355.86 90.39 166 45 129 84 353.54 90.59 167 45 130 85 352.92 90.30 168 45 132 87 352.86 90.28 169 45 148 103 350.89 89.30 170 45 243 198 171.63 0.30 171 46 93 47 356.25 90.20 172 46 96 50 356.64 90.09 173 46 127 81 355.18 90.45 174 46 128 82 353.79 90.55 175 47 75 28 353.19 90.25 176 47 127 80 355.86 90.39 177 47 128 81 353.86 90.57 178 47 130 83 353.78 90.55 179 48 125 77 356.73 90.08 180 48 126 78 356.69 90.08 181 48 127 79 356.50 90.07 182 49 125 76 356.87 90.02 183 49 126 77 356.70 90.08 184 49 128 79 356.69 90.08 185 49 150 101 351.14 89.17 186 50 124 74 357.54 90.20 187 50 125 75 357.12 90.14 188 51 71 20 357.54 90.20 189 51 72 21 357.54 90.21 190 51 73 22 357.51 90.22 191 51 124 73 357.54 90.21 192 51 126 75 357.54 90.21 193 51 152 101 352.95 88.22 194 51 153 102 353.19 88.06 195 51 154 103 353.08 88.00 196 52 154 102 353.38 88.00 197 53 69 16 358.48 90.08 198 53 71 18 357.79 90.14 199 53 120 67 358.19 89.94 200 53 121 68 358.33 89.92 201 53 124 71 357.75 90.15 202 53 154 101 353.42 87.98 203 54 57 3 837.66 0.77 204 55 121 66 360.06 89.28 205 57 69 12 391.60 76.12 206 57 233 176 205.52 13.98 207 58 66 8 456.02 44.91 208 58 67 9 392.65 76.56 209 58 69 11 392.61 76.56 210 58 233 175 210.51 14.49 211 59 66 7 456.47 45.09 212 59 67 8 456.01 44.88 213 59 68 9 455.98 44.90 214 59 69 10 392.62 76.56 215 59 155 96 384.54 72.52 216 59 156 97 384.58 72.49 217 59 233 174 210.51 14.50 218 60 64 4 768.48 13.19 219 60 65 5 744.33 1.12 220 60 66 6 710.04 2.93 221 60 156 96 384.62 72.48 222 60 167 107 263.13 11.59 223 60 210 150 234.25 3.96 224 60 211 151 234.24 3.96 225 60 231 171 211.30 14.38 226 61 64 3 833.56 2.68 227 61 65 4 748.37 3.13 228 61 66 5 744.26 1.08 229 61 67 6 556.39 95.02 230 61 156 95 384.79 72.44 231 61 167 106 266.47 9.98 232 62 156 94 384.94 72.38 233 62 167 105 266.51 10.01 234 63 209 146 271.45 19.53 235 64 167 103 298.42 5.86 236 64 209 145 271.44 19.54 237 64 210 146 268.44 20.95 238 69 120 51 690.59 0.20 239 69 154 85 420.16 54.61 240 69 155 86 420.01 54.54 241 69 233 164 246.81 32.38 242 69 234 165 246.62 32.40 243 70 117 47 690.88 0.28 244 70 118 48 690.80 0.24 245 70 119 49 690.60 0.21 246 70 120 50 690.59 0.20 247 70 154 84 420.29 54.43 248 70 155 85 420.21 54.43 249 71 116 45 690.94 0.27 250 71 117 46 690.93 0.27 251 71 118 47 690.82 0.24 252 71 120 49 690.74 0.27 253 71 123 52 690.73 0.27 254 71 126 55 690.22 0.22 255 71 153 82 420.33 54.43 256 71 154 83 419.04 53.78 257 72 115 43 690.94 0.26 258 72 116 44 690.94 0.27 259 72 152 80 420.35 54.41 260 72 153 81 420.32 54.41 261 73 114 41 691.01 0.28 262 73 115 42 690.97 0.28 263 73 128 55 690.38 0.31 264 73 150 77 420.50 54.50 265 73 151 78 420.39 54.44 266 73 152 79 420.32 54.40 267 74 105 31 691.22 0.30 268 74 112 38 691.22 0.30 269 74 113 39 691.13 0.30 270 74 114 40 691.02 0.28 271 74 150 76 420.41 54.44 272 74 151 77 420.39 54.41 273 75 112 37 691.25 0.33 274 75 113 38 691.13 0.30 275 75 128 53 690.76 0.28 276 75 130 55 690.21 0.23 277 75 148 73 420.55 54.52 278 75 149 74 420.48 54.45 279 75 150 75 420.39 54.41 280 76 111 35 691.41 0.30 281 76 112 36 691.28 0.33 282 76 148 72 420.48 54.45 283 76 149 73 420.47 54.44 284 77 81 4 802.01 4.54 285 77 82 5 788.35 11.37 286 77 111 34 691.43 0.29 287 77 113 36 691.45 0.32 288 77 130 53 690.75 0.29 289 77 148 71 420.47 54.44 290 78 81 3 846.31 2.01 291 78 111 33 691.79 0.39 292 78 146 68 420.55 54.48 293 78 147 69 420.54 54.44 294 78 148 70 420.52 54.41 295 79 111 32 691.79 0.39 296 80 133 53 688.15 0.53 297 80 141 61 426.13 51.76 298 81 111 30 692.06 0.34 299 81 130 49 690.86 0.24 300 81 131 50 690.77 0.21 301 81 132 51 689.82 0.08 302 81 133 52 688.14 0.54 303 81 146 65 420.63 54.48 304 81 243 162 242.26 34.71 305 82 110 28 692.09 0.32 306 82 130 48 690.88 0.24 307 82 131 49 690.78 0.21 308 83 102 19 691.99 0.36 309 83 113 30 692.08 0.33 310 83 129 46 690.93 0.26 311 84 89 5 789.32 2.10 312 84 129 45 690.98 0.28 313 84 130 46 690.92 0.26 314 84 131 47 690.88 0.24 315 85 88 3 845.49 2.73 316 85 89 4 824.38 3.70 317 85 131 46 690.97 0.28 318 86 89 3 834.41 0.34 319 88 131 43 691.14 0.31 320 89 93 4 821.32 2.12 321 89 94 5 813.20 4.10 322 89 97 8 791.15 2.15 323 89 129 40 691.23 0.29 324 90 93 3 836.03 7.45 325 90 94 4 823.36 1.10 326 91 94 3 829.88 2.16 327 91 95 4 845.76 2.57 328 92 95 3 854.10 5.13 329 92 96 4 834.39 3.12 330 93 96 3 852.51 5.92 331 93 97 4 834.40 3.12 332 94 97 3 837.55 1.56 333 94 98 4 836.23 2.21 334 95 98 3 836.24 2.21 335 96 127 31 691.74 0.40 336 97 100 3 886.31 3.35 337 97 102 5 838.13 1.27 338 97 127 30 691.66 0.43 339 97 129 32 691.62 0.41 340 99 123 24 692.18 0.34 341 100 115 15 692.76 0.42 342 100 118 18 692.63 0.39 343 100 123 23 692.16 0.35 344 100 126 26 691.70 0.41 345 101 115 14 692.77 0.42 346 102 114 12 692.94 0.49 347 102 115 13 692.77 0.43 348 102 126 24 691.68 0.42 349 102 127 25 691.60 0.40 350 102 128 26 690.84 0.18 351 102 129 27 690.47 0.37 352 103 113 10 693.32 0.35 353 103 114 11 693.05 0.45 354 104 107 3 854.66 6.15 355 104 109 5 733.98 4.50 356 104 110 6 693.71 0.43 357 104 112 8 693.58 0.40 358 104 113 9 693.35 0.34 359 105 109 4 789.20 9.67 360 105 112 7 693.58 0.41 361 105 114 9 693.35 0.34 362 106 109 3 818.95 1.32 363 109 112 3 844.75 0.88 364 113 128 15 690.78 0.27 365 113 130 17 690.41 0.36 366 115 126 11 691.43 0.34 367 115 128 13 690.48 0.36 368 118 123 5 759.57 6.06 369 119 122 3 852.88 6.20 370 119 123 4 800.90 9.51 371 120 123 3 825.37 2.83 372 120 124 4 770.33 5.61 373 123 126 3 843.31 11.77 374 132 245 113 235.38 31.67 375 133 141 8 431.16 49.23 376 133 245 112 241.76 34.77 377 134 137 3 824.58 2.08 378 134 138 4 795.21 12.78 379 135 138 3 817.70 1.53 380 135 141 6 537.32 79.36 381 135 142 7 431.13 49.19 382 135 143 8 431.19 49.16 383 135 245 110 242.15 34.77 384 138 141 3 853.68 2.62 385 139 142 3 927.40 1.22 386 141 146 5 842.44 2.16 387 141 245 104 242.49 34.81 388 142 146 4 907.90 3.17 389 142 245 103 242.50 34.81 390 143 245 102 242.48 34.81 391 143 246 103 242.47 34.81 392 143 247 104 242.26 34.89 393 143 248 105 242.47 34.81 394 144 244 100 242.56 34.80 395 144 245 101 242.52 34.81 396 145 242 97 242.89 34.72 397 145 243 98 242.87 34.73 398 145 244 99 242.56 34.80 399 146 242 96 242.87 34.73 400 146 243 97 242.87 34.73 401 146 245 99 242.78 34.74 402 147 241 94 243.29 34.81 403 147 242 95 243.04 34.81 404 148 240 92 243.40 34.83 405 148 241 93 243.31 34.83 406 148 243 95 243.19 34.85 407 149 239 90 243.64 34.84 408 149 240 91 243.40 34.84 409 150 238 88 243.78 34.86 410 150 239 89 243.66 34.83 411 151 236 85 245.80 35.18 412 151 237 86 244.81 34.98 413 151 238 87 243.78 34.86 414 152 236 84 245.81 35.18 415 152 237 85 245.28 35.06 416 153 235 82 246.50 34.97 417 153 236 83 245.83 35.19 418 154 234 80 249.03 33.70 419 154 235 81 248.63 33.91 420 154 236 82 247.69 34.38 421 154 237 83 247.69 34.37 422 155 234 79 249.06 33.70 423 156 160 4 927.66 0.35 424 156 166 10 324.62 19.16 425 156 167 11 324.58 19.17 426 156 168 12 323.50 19.54 427 157 166 9 324.73 19.11 428 157 168 11 324.51 19.20 429 158 165 7 712.15 5.29 430 158 166 8 324.73 19.11 431 158 168 10 324.53 19.21 432 158 169 11 324.35 19.12 433 158 232 74 266.67 37.98 434 159 163 4 756.32 3.52 435 159 164 5 727.75 0.57 436 159 165 6 712.16 5.29 437 160 163 3 800.98 1.20 438 160 164 4 766.07 8.39 439 160 165 5 735.86 3.48 440 160 166 6 724.69 0.96 441 165 169 4 835.37 0.38 442 165 170 5 829.06 0.28 443 165 171 6 812.09 0.60 444 166 169 3 889.21 3.71 445 166 171 5 839.21 1.54 446 167 171 4 876.56 2.62 447 167 208 41 329.96 48.53 448 167 211 44 329.57 48.59 449 167 231 64 292.89 45.12 450 168 231 63 292.88 45.12 451 168 232 64 284.10 45.00 452 169 211 42 330.25 48.43 453 169 230 61 294.91 44.12 454 169 231 62 293.48 44.81 455 170 226 56 331.39 47.91 456 170 228 58 329.81 48.38 457 170 230 60 294.92 44.12 458 170 231 61 294.92 44.12 459 171 207 36 330.60 48.41 460 171 208 37 330.60 48.41 461 171 211 40 330.50 48.37 462 171 226 55 331.41 47.91 463 171 227 56 330.44 48.34 464 171 228 57 330.09 48.51 465 172 224 52 332.81 47.32 466 172 225 53 332.72 47.37 467 172 226 54 331.64 47.80 468 172 227 55 331.37 47.90 469 173 194 21 401.69 40.61 470 173 205 32 376.24 36.70 471 173 221 48 390.92 41.26 472 173 222 49 390.50 41.05 473 173 223 50 388.06 41.48 474 173 224 51 369.91 39.87 475 173 225 52 362.19 36.02 476 173 227 54 331.88 47.66 477 174 203 29 423.63 33.95 478 174 205 31 388.13 42.65 479 174 223 49 396.86 38.43 480 175 194 19 461.06 41.11 481 175 196 21 497.43 42.55 482 175 203 28 444.24 44.25 483 175 221 46 421.45 44.49 484 175 223 48 397.25 38.60 485 176 194 18 497.40 42.55 486 176 196 20 497.46 42.55 487 176 221 45 421.45 44.49 488 176 222 46 404.77 42.33 489 176 223 47 397.39 38.65 490 177 194 17 497.44 42.54 491 177 195 18 497.48 42.55 492 177 196 19 497.47 42.55 493 177 220 43 426.37 43.41 494 177 221 44 423.43 43.62 495 178 194 16 497.54 42.55 496 178 195 17 497.54 42.55 497 178 218 40 426.56 43.40 498 178 219 41 426.44 43.38 499 178 220 42 426.37 43.41 500 179 182 3 928.20 5.86 501 179 192 13 497.95 42.60 502 179 193 14 497.80 42.68 503 179 194 15 497.54 42.54 504 179 215 36 426.61 43.43 505 179 216 37 426.58 43.41 506 179 217 38 426.58 43.41 507 179 218 39 426.59 43.39 508 179 219 40 426.51 43.36 509 179 221 42 426.60 43.30 510 180 193 13 498.04 42.59 511 180 195 15 497.99 42.61 512 181 192 11 498.12 42.63 513 181 193 12 498.04 42.59 514 181 217 36 426.91 43.33 515 182 190 8 498.59 42.79 516 182 191 9 498.28 42.71 517 182 192 10 498.12 42.63 518 182 213 31 429.04 42.72 519 182 215 33 427.04 43.30 520 182 216 34 427.01 43.30 521 182 217 35 426.99 43.31 522 183 190 7 498.69 42.84 523 183 191 8 498.34 42.73 524 184 189 5 717.28 9.51 525 184 190 6 498.69 42.84 526 184 213 29 432.53 41.12 527 185 188 3 819.20 2.71 528 185 189 4 720.81 7.75 529 185 190 5 558.80 72.17 530 185 191 6 558.79 72.17 531 185 206 21 498.12 42.56 532 187 209 22 497.88 42.56 533 188 209 21 497.59 42.46 534 189 207 18 498.01 42.55 535 189 208 19 497.86 42.60 536 189 209 20 497.53 42.49 537 190 206 16 498.06 42.57 538 190 207 17 497.95 42.55 539 190 213 23 429.19 42.79 540 191 204 13 498.27 42.55 541 191 205 14 498.18 42.58 542 191 206 15 498.04 42.52 543 192 204 12 498.27 42.55 544 192 205 13 498.20 42.56 545 192 207 15 498.18 42.58 546 192 213 21 429.03 42.71 547 192 215 23 427.02 43.30 548 192 227 35 426.47 43.26 549 193 202 9 498.54 42.50 550 193 203 10 498.46 42.52 551 193 204 11 498.28 42.55 552 194 202 8 498.56 42.51 553 194 203 9 498.47 42.52 554 194 205 11 498.37 42.56 555 194 221 27 426.61 43.30 556 195 201 6 498.78 42.41 557 195 202 7 498.57 42.51 558 196 199 3 850.50 0.60 559 196 200 4 775.35 3.27 560 196 201 5 498.81 42.44 561 197 200 3 809.14 3.68 562 205 227 22 426.51 43.26 563 207 211 4 834.19 2.75 564 207 213 6 727.32 2.22 565 207 227 20 426.62 43.30 566 207 228 21 426.56 43.27 567 208 211 3 885.55 5.09 568 211 228 17 426.74 43.26 569 211 231 20 426.36 43.23 570 212 228 16 426.75 43.25 571 212 229 17 426.74 43.26 572 213 227 14 426.75 43.25 573 213 228 15 426.53 43.26 574 214 226 12 426.73 43.27 575 214 227 13 426.70 43.27 576 214 228 14 426.53 43.25 577 214 229 15 426.52 43.25 578 215 219 4 812.88 1.40 579 215 221 6 707.10 3.02 580 215 227 12 426.67 43.29 581 216 219 3 846.99 3.21 582 221 225 4 796.19 4.31 583 221 227 6 664.33 38.84 584 222 225 3 828.43 1.21 585 247 250 3 796.04 3.38