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 3 877.19 1.24 2 5 11 6 580.96 1.75 3 5 13 8 580.99 1.73 4 6 11 5 697.70 57.04 5 8 11 3 858.26 1.56 6 9 15 6 817.66 5.87 7 11 14 3 856.24 3.27 8 11 15 4 849.01 0.34 9 12 15 3 852.83 2.79 10 12 16 4 840.74 3.81 11 13 16 3 849.06 0.33 12 13 17 4 849.05 0.33 13 14 17 3 851.69 0.98 14 14 18 4 849.06 0.33 15 14 248 234 35.52 1.80 16 15 18 3 863.24 3.66 17 15 19 4 848.86 0.23 18 16 19 3 849.14 0.37 19 16 20 4 848.78 0.26 20 17 20 3 854.60 2.36 21 17 21 4 848.77 0.26 22 17 248 231 38.23 2.87 23 18 21 3 862.81 1.74 24 18 22 4 838.23 0.04 25 18 246 228 47.48 0.03 26 18 247 229 39.91 3.62 27 18 248 230 37.94 3.02 28 19 22 3 843.82 2.75 29 19 23 4 836.93 0.61 30 20 23 3 855.81 2.85 31 20 24 4 842.74 3.52 32 21 24 3 851.48 1.51 33 21 25 4 842.74 3.52 34 21 244 223 53.41 2.89 35 21 247 226 51.36 1.80 36 21 248 227 45.83 0.80 37 22 25 3 849.82 0.88 38 22 26 4 842.71 3.53 39 22 244 222 55.12 2.60 40 22 245 223 52.88 2.54 41 22 246 224 52.77 2.48 42 23 26 3 859.26 1.66 43 23 27 4 842.70 3.53 44 24 27 3 859.03 4.60 45 24 28 4 839.72 4.42 46 24 244 220 57.12 2.48 47 25 28 3 855.18 1.81 48 25 29 4 849.35 0.24 49 25 115 90 199.41 64.85 50 25 158 133 199.80 65.08 51 25 159 134 199.79 65.08 52 25 244 219 57.11 2.50 53 25 245 220 55.69 2.69 54 26 29 3 849.02 0.41 55 26 30 4 847.84 0.51 56 27 30 3 847.84 0.51 57 27 32 5 809.08 2.52 58 27 33 6 658.37 0.87 59 28 33 5 644.12 9.27 60 28 34 6 641.40 9.31 61 28 116 88 274.77 27.46 62 28 183 155 285.94 21.77 63 29 116 87 281.32 24.18 64 29 183 154 288.60 20.53 65 29 184 155 299.92 14.67 66 30 33 3 839.83 3.77 67 30 183 153 308.75 10.59 68 31 56 25 785.20 2.73 69 31 57 26 774.98 0.47 70 31 183 152 308.81 10.56 71 31 184 153 308.75 10.60 72 31 185 154 308.12 10.48 73 31 191 160 286.91 0.23 74 32 56 24 785.94 2.66 75 33 56 23 786.00 2.67 76 33 183 150 342.01 1.17 77 34 54 20 786.19 2.61 78 34 55 21 786.18 2.62 79 34 116 82 455.21 1.39 80 34 183 149 343.32 1.65 81 35 54 19 786.23 2.62 82 35 55 20 786.21 2.62 83 35 57 22 786.20 2.62 84 35 58 23 786.12 2.65 85 35 59 24 785.99 2.63 86 35 114 79 455.28 1.33 87 35 116 81 455.23 1.38 88 35 117 82 455.20 1.39 89 35 183 148 343.32 1.66 90 36 53 17 786.30 2.65 91 36 54 18 786.23 2.62 92 36 59 23 786.16 2.62 93 36 113 77 455.46 1.30 94 36 114 78 455.30 1.32 95 37 52 15 786.38 2.67 96 37 53 16 786.34 2.64 97 37 59 22 786.23 2.62 98 37 60 23 786.17 2.63 99 37 61 24 785.99 2.64 100 37 111 74 457.95 0.10 101 37 112 75 457.92 0.10 102 37 113 76 455.47 1.30 103 37 179 142 369.37 0.19 104 38 50 12 786.65 2.60 105 38 51 13 786.53 2.62 106 38 52 14 786.39 2.66 107 38 61 23 786.19 2.64 108 38 111 73 457.98 0.10 109 38 112 74 457.93 0.10 110 38 113 75 457.92 0.10 111 38 114 76 457.99 0.14 112 38 224 186 201.95 0.79 113 38 230 192 201.12 0.98 114 38 231 193 201.08 0.97 115 39 50 11 786.66 2.60 116 39 51 12 786.57 2.62 117 39 61 22 786.25 2.62 118 39 68 29 757.18 4.55 119 39 109 70 499.25 0.22 120 39 110 71 489.00 4.89 121 39 111 72 468.61 5.21 122 39 177 138 377.41 1.26 123 39 179 140 371.22 0.64 124 40 48 8 786.88 2.64 125 40 49 9 786.78 2.60 126 40 50 10 786.66 2.60 127 40 109 69 504.67 1.69 128 40 110 70 488.99 4.90 129 40 112 72 488.98 4.89 130 40 220 180 202.19 0.88 131 40 224 184 202.19 0.88 132 40 225 185 202.16 0.86 133 40 232 192 201.09 0.98 134 41 48 7 786.90 2.64 135 41 49 8 786.79 2.60 136 41 106 65 564.74 5.85 137 41 108 67 560.61 5.98 138 41 109 68 528.42 9.04 139 42 47 5 786.99 2.65 140 42 48 6 786.93 2.65 141 42 106 64 564.79 5.86 142 42 107 65 564.76 5.86 143 42 108 66 563.15 5.74 144 42 109 67 561.08 5.96 145 42 110 68 560.83 6.08 146 42 165 123 455.63 1.31 147 42 232 190 202.13 0.89 148 43 46 3 855.97 0.10 149 43 47 4 787.06 2.62 150 43 49 6 786.97 2.64 151 43 68 25 779.66 0.73 152 43 69 26 762.16 6.73 153 43 70 27 757.11 4.42 154 43 104 61 564.93 5.83 155 43 105 62 564.91 5.83 156 43 106 63 564.81 5.85 157 43 107 64 564.79 5.85 158 43 213 170 286.80 0.29 159 44 103 59 564.96 5.83 160 44 107 63 564.87 5.84 161 45 70 25 778.19 1.26 162 46 215 169 285.73 0.74 163 46 216 170 285.45 0.82 164 47 70 23 757.22 4.55 165 47 213 166 286.74 0.26 166 47 214 167 285.75 0.72 167 47 215 168 285.50 0.74 168 47 216 169 285.07 0.70 169 48 213 165 285.75 0.72 170 48 214 166 285.67 0.71 171 48 217 169 248.14 1.14 172 48 220 172 205.00 0.03 173 49 68 19 757.22 4.55 174 49 211 162 286.80 0.28 175 49 212 163 285.82 0.70 176 49 213 164 285.66 0.71 177 50 210 160 286.81 0.28 178 50 211 161 285.81 0.69 179 50 212 162 285.79 0.69 180 50 214 164 285.60 0.70 181 50 220 170 202.09 0.86 182 50 224 174 202.12 0.88 183 51 61 10 786.32 2.58 184 51 63 12 786.22 2.61 185 51 68 17 756.99 4.46 186 51 209 158 286.81 0.28 187 51 210 159 285.83 0.68 188 51 211 160 285.73 0.69 189 52 61 9 786.34 2.56 190 52 209 157 285.83 0.69 191 52 210 158 285.80 0.69 192 52 224 172 201.50 0.97 193 52 230 178 201.11 0.97 194 53 59 6 786.37 2.56 195 53 60 7 786.36 2.56 196 53 61 8 786.30 2.53 197 53 207 154 286.78 0.26 198 53 208 155 285.87 0.68 199 53 209 156 285.73 0.70 200 54 59 5 786.39 2.56 201 54 207 153 285.81 0.69 202 54 208 154 285.80 0.68 203 55 58 3 892.98 3.69 204 55 59 4 790.10 1.17 205 55 203 148 286.95 0.26 206 55 207 152 285.75 0.70 207 56 203 147 286.89 0.26 208 57 182 125 365.26 1.01 209 57 183 126 363.99 0.51 210 57 191 134 287.32 0.17 211 57 196 139 287.32 0.17 212 57 199 142 287.00 0.24 213 57 200 143 286.97 0.24 214 57 203 146 286.91 0.27 215 58 181 123 365.35 1.04 216 58 182 124 365.13 1.07 217 58 183 125 364.00 0.51 218 58 200 142 287.01 0.23 219 58 204 146 286.90 0.28 220 59 113 54 457.64 0.24 221 59 180 121 368.51 0.03 222 59 181 122 365.35 1.04 223 60 179 119 369.38 0.21 224 60 180 120 368.56 0.01 225 61 178 117 371.95 0.97 226 61 179 118 371.18 0.65 227 62 177 115 377.28 1.28 228 62 178 116 371.95 0.97 229 63 67 4 835.13 0.79 230 63 68 5 828.73 0.82 231 63 176 113 380.31 0.73 232 63 177 114 377.50 1.30 233 63 209 146 286.95 0.26 234 64 67 3 850.09 1.04 235 64 68 4 838.38 0.96 236 64 176 112 380.32 0.73 237 65 68 3 850.09 1.04 238 65 69 4 840.06 1.81 239 65 86 21 568.08 5.26 240 65 89 24 568.21 5.21 241 65 90 25 568.29 5.24 242 65 105 40 564.81 5.85 243 65 129 64 456.28 1.37 244 65 174 109 381.22 0.58 245 65 175 110 380.49 0.71 246 65 176 111 380.44 0.73 247 66 69 3 850.09 1.04 248 66 86 20 567.86 5.39 249 66 90 24 568.31 5.24 250 68 106 38 564.78 5.86 251 68 109 41 562.90 5.24 252 68 175 107 380.62 0.65 253 68 176 108 380.33 0.74 254 68 177 109 380.25 0.72 255 69 82 13 568.04 5.26 256 69 86 17 568.22 5.28 257 69 104 35 564.84 5.87 258 69 105 36 564.80 5.86 259 69 106 37 564.79 5.86 260 70 104 34 564.84 5.86 261 70 213 143 286.81 0.28 262 71 77 6 577.86 2.85 263 71 213 142 286.89 0.27 264 72 75 3 855.50 2.18 265 72 76 4 836.51 3.25 266 72 77 5 625.39 14.97 267 72 213 141 286.88 0.24 268 75 213 138 287.31 0.28 269 77 82 5 838.05 2.96 270 78 81 3 856.56 3.11 271 78 82 4 838.48 2.75 272 78 99 21 571.66 5.48 273 79 82 3 856.43 3.17 274 79 83 4 839.98 2.00 275 80 83 3 856.52 3.12 276 80 84 4 853.89 4.42 277 81 84 3 853.90 4.43 278 81 85 4 853.89 4.43 279 81 97 16 571.75 5.48 280 81 98 17 571.74 5.49 281 81 99 18 571.73 5.49 282 82 85 3 844.53 0.26 283 82 86 4 846.26 0.61 284 82 99 17 571.73 5.48 285 82 102 20 569.44 5.55 286 82 104 22 565.23 5.86 287 83 86 3 851.50 1.98 288 83 87 4 851.49 1.99 289 84 87 3 860.04 2.28 290 84 88 4 853.60 1.51 291 84 95 11 571.95 5.50 292 84 96 12 571.93 5.50 293 84 97 13 571.80 5.46 294 85 88 3 853.60 1.51 295 85 89 4 853.60 1.51 296 85 97 12 571.78 5.47 297 85 99 14 571.75 5.46 298 85 102 17 570.71 5.13 299 86 89 3 853.60 1.51 300 86 90 4 843.23 0.04 301 87 90 3 854.18 1.23 302 87 91 4 841.63 0.85 303 87 94 7 572.61 5.23 304 87 95 8 572.06 5.47 305 88 91 3 842.31 1.18 306 88 92 4 832.36 3.77 307 88 93 5 720.96 3.62 308 88 94 6 572.22 5.46 309 88 95 7 572.15 5.44 310 89 105 16 571.25 5.38 311 89 129 40 457.01 1.59 312 89 174 85 381.87 0.51 313 90 129 39 457.00 1.59 314 90 130 40 457.00 1.59 315 91 94 3 835.02 5.24 316 99 102 3 895.13 1.53 317 100 171 71 453.72 1.47 318 101 105 4 864.52 1.40 319 101 107 6 835.22 4.20 320 101 171 70 453.74 1.49 321 102 105 3 864.44 1.45 322 105 171 66 453.44 1.35 323 105 173 68 406.79 4.94 324 105 174 69 381.50 0.48 325 106 109 3 919.03 3.94 326 106 168 62 454.25 1.37 327 107 167 60 455.16 1.32 328 107 168 61 454.33 1.33 329 107 169 62 454.23 1.37 330 108 165 57 455.63 1.31 331 108 166 58 455.26 1.34 332 108 167 59 454.81 1.33 333 108 168 60 454.53 1.44 334 109 165 56 455.44 1.43 335 109 166 57 455.21 1.34 336 109 168 59 454.56 1.44 337 109 175 66 381.23 0.56 338 109 177 68 378.37 1.73 339 110 163 53 456.10 1.45 340 110 164 54 455.75 1.37 341 110 165 55 455.16 1.33 342 110 232 122 201.10 0.98 343 110 233 123 201.03 1.01 344 111 124 13 457.12 1.76 345 111 150 39 456.12 1.45 346 111 163 52 456.11 1.45 347 111 164 53 455.79 1.36 348 111 166 55 455.50 1.50 349 111 177 66 377.48 1.29 350 111 179 68 371.21 0.64 351 112 153 41 457.05 1.79 352 112 162 50 456.25 1.50 353 112 163 51 456.12 1.45 354 112 231 119 201.08 0.97 355 112 232 120 200.91 0.98 356 112 233 121 200.68 1.01 357 113 117 4 822.84 8.30 358 113 122 9 458.80 1.90 359 113 150 37 457.00 1.84 360 113 161 48 457.14 1.77 361 113 162 49 456.60 1.67 362 113 179 66 370.60 0.34 363 113 180 67 368.95 0.01 364 113 181 68 367.74 0.37 365 114 117 3 878.72 4.55 366 114 161 47 457.17 1.76 367 114 162 48 457.17 1.76 368 115 159 44 457.26 1.71 369 115 160 45 457.22 1.74 370 115 161 46 457.21 1.74 371 115 162 47 457.22 1.74 372 115 184 69 365.08 1.24 373 116 183 67 365.08 1.24 374 116 184 68 365.08 1.24 375 117 121 4 860.94 2.54 376 117 122 5 816.39 0.47 377 117 162 45 457.48 1.65 378 117 181 64 367.74 0.37 379 117 182 65 365.48 1.16 380 117 183 66 365.09 1.24 381 117 184 67 365.08 1.24 382 118 121 3 860.94 2.54 383 118 182 64 367.72 0.38 384 118 184 66 365.09 1.24 385 119 122 3 858.22 3.90 386 119 147 28 457.91 1.74 387 119 150 31 457.63 1.60 388 119 162 43 457.58 1.63 389 121 181 60 368.87 0.19 390 121 182 61 368.75 0.16 391 122 145 23 459.13 1.49 392 122 146 24 459.06 1.47 393 122 147 25 458.75 1.50 394 122 150 28 458.20 1.76 395 122 179 57 372.45 0.83 396 122 180 58 370.64 0.45 397 122 181 59 368.76 0.15 398 123 143 20 459.39 1.42 399 123 144 21 459.37 1.43 400 123 145 22 459.14 1.49 401 123 179 56 372.45 0.83 402 123 180 57 371.56 0.48 403 124 143 19 459.41 1.41 404 124 144 20 459.39 1.42 405 124 146 22 459.31 1.40 406 124 164 40 456.87 1.21 407 124 166 42 456.62 1.19 408 124 177 53 379.96 0.94 409 124 178 54 374.96 0.12 410 124 179 55 372.94 0.62 411 125 142 17 459.45 1.40 412 125 143 18 459.41 1.42 413 125 177 52 380.17 0.83 414 125 178 53 378.29 1.72 415 126 133 7 459.75 1.47 416 126 166 40 455.92 1.38 417 126 175 49 381.30 0.58 418 126 176 50 381.22 0.60 419 126 177 51 380.38 0.73 420 127 132 5 459.81 1.44 421 127 133 6 459.75 1.47 422 127 175 48 381.31 0.58 423 127 176 49 381.26 0.59 424 128 131 3 847.98 6.45 425 128 132 4 635.00 7.83 426 128 174 46 381.71 0.43 427 128 176 48 381.31 0.58 428 129 174 45 381.70 0.43 429 131 176 45 381.38 0.55 430 132 135 3 876.48 1.72 431 132 136 4 763.64 11.72 432 132 137 5 639.78 2.29 433 132 140 8 604.08 6.71 434 133 137 4 839.01 2.52 435 133 140 7 604.03 6.67 436 133 141 8 604.02 6.67 437 133 142 9 536.11 27.18 438 134 139 5 681.27 0.34 439 134 140 6 604.02 6.67 440 135 139 4 857.66 6.17 441 136 139 3 866.72 1.65 442 136 140 4 838.61 2.56 443 137 140 3 839.80 1.96 444 146 149 3 859.27 8.63 445 146 150 4 840.72 1.15 446 146 164 18 458.81 2.18 447 147 150 3 850.38 2.16 448 149 164 15 458.82 2.18 449 150 162 12 460.32 1.54 450 150 163 13 458.97 2.21 451 150 164 14 458.83 2.18 452 150 179 29 373.07 0.52 453 151 162 11 461.64 1.85 454 151 163 12 460.67 1.37 455 151 233 82 201.03 0.98 456 151 237 86 154.69 8.40 457 152 159 7 462.53 1.88 458 152 161 9 462.12 2.06 459 152 162 10 461.70 1.87 460 153 159 6 462.56 1.89 461 153 160 7 462.51 1.90 462 153 161 8 462.14 2.06 463 153 162 9 462.02 2.00 464 153 163 10 462.00 2.00 465 153 231 78 201.06 1.00 466 153 232 79 200.99 0.98 467 153 233 80 200.74 0.90 468 153 239 86 134.25 0.88 469 153 240 87 134.25 0.88 470 154 158 4 608.38 7.16 471 154 159 5 462.56 1.89 472 154 160 6 462.56 1.89 473 154 239 85 134.36 0.84 474 155 158 3 837.05 2.76 475 155 160 5 604.64 4.96 476 155 239 84 134.50 0.80 477 155 240 85 134.35 0.84 478 155 241 86 133.96 0.75 479 155 243 88 130.19 1.52 480 156 243 87 131.47 0.88 481 156 247 91 112.41 3.71 482 158 243 85 116.50 5.76 483 158 244 86 116.52 5.76 484 158 245 87 112.20 3.81 485 158 247 89 111.81 3.73 486 159 162 3 946.00 0.12 487 160 231 71 200.74 0.94 488 160 240 80 134.12 0.86 489 160 241 81 120.43 4.72 490 160 242 82 117.51 6.18 491 160 243 83 116.16 5.61 492 161 231 70 200.75 0.94 493 163 233 70 200.69 0.88 494 166 175 9 430.44 24.00 495 166 177 11 381.07 0.59 496 168 173 5 492.73 55.13 497 168 175 7 492.72 55.13 498 169 173 4 853.06 6.18 499 170 173 3 853.08 6.17 500 185 189 4 841.79 2.81 501 185 191 6 635.98 18.36 502 189 195 6 639.39 8.73 503 189 196 7 613.04 4.44 504 190 193 3 843.56 5.45 505 191 196 5 613.05 4.44 506 191 197 6 613.03 4.43 507 191 200 9 602.94 0.56 508 192 197 5 603.00 0.58 509 192 200 8 602.94 0.56 510 193 196 3 856.68 8.10 511 193 197 4 684.01 12.58 512 194 197 3 835.29 0.55 513 196 199 3 848.71 0.73 514 196 200 4 843.25 3.46 515 197 200 3 846.00 2.66 516 197 201 4 843.25 3.46 517 198 201 3 843.25 3.46 518 198 202 4 843.25 3.46 519 199 202 3 832.04 1.83 520 199 203 4 832.03 1.83 521 200 203 3 839.93 0.06 522 200 204 4 832.06 1.82 523 201 204 3 855.50 3.84 524 201 205 4 841.28 6.43 525 202 205 3 850.99 1.58 526 202 206 4 829.45 1.51 527 203 206 3 829.31 1.55 528 203 207 4 829.29 1.56 529 204 207 3 858.05 0.56 530 210 224 14 201.35 0.91 531 214 219 5 714.52 3.02 532 214 220 6 639.79 0.45 533 214 224 10 628.33 2.52 534 215 219 4 848.38 5.55 535 216 219 3 851.86 3.82 536 216 220 4 848.37 5.56 537 217 220 3 848.39 5.55 538 217 221 4 842.94 2.83 539 217 232 15 478.86 3.08 540 217 234 17 200.86 1.05 541 217 235 18 200.85 1.05 542 218 221 3 857.47 0.04 543 218 222 4 838.96 0.86 544 219 222 3 841.95 3.31 545 219 223 4 810.23 3.94 546 219 224 5 809.84 3.76 547 220 223 3 849.69 0.57 548 220 224 4 750.99 22.71 549 220 225 5 705.33 0.12 550 220 232 12 543.81 35.56 551 221 225 4 720.75 6.27 552 221 226 5 762.98 27.39 553 221 232 11 543.82 35.55 554 221 234 13 201.09 0.98 555 221 240 19 134.47 0.74 556 222 227 5 813.04 2.36 557 223 227 4 817.21 0.38 558 224 227 3 877.90 3.47 559 224 228 4 850.28 6.15 560 224 230 6 698.54 3.29 561 225 228 3 874.32 5.25 562 225 229 4 836.28 0.83 563 225 230 5 674.26 6.57 564 225 231 6 666.75 4.30 565 225 232 7 650.28 1.58 566 225 240 15 134.09 0.85 567 226 229 3 850.30 6.14 568 229 242 13 129.71 0.07 569 230 241 11 132.38 0.88 570 231 240 9 133.60 0.61 571 231 241 10 126.87 1.50 572 232 239 7 134.49 0.76 573 232 240 8 134.12 0.87 574 233 237 4 660.64 17.54 575 233 238 5 527.25 27.12 576 233 239 6 328.21 97.62 577 234 237 3 839.97 1.12 578 234 238 4 628.47 12.19 579 234 240 6 538.35 21.57 580 243 247 4 850.30 5.79 581 244 247 3 861.13 0.36