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 24 405.76 0.52 2 1 95 94 265.44 0.79 3 1 96 95 265.31 0.82 4 2 23 21 405.81 0.54 5 2 27 25 405.93 0.51 6 2 95 93 266.06 0.64 7 2 97 95 265.32 0.82 8 2 99 97 265.32 0.83 9 2 134 132 235.89 0.62 10 3 22 19 405.85 0.52 11 3 23 20 405.81 0.54 12 3 93 90 271.91 1.41 13 3 95 92 266.34 0.65 14 3 97 94 265.94 0.68 15 3 98 95 265.32 0.83 16 3 99 96 265.32 0.83 17 3 134 131 235.89 0.62 18 4 21 17 405.98 0.54 19 4 22 18 405.88 0.52 20 4 99 95 265.49 0.89 21 4 134 130 235.90 0.61 22 4 135 131 235.82 0.62 23 4 138 134 235.73 0.63 24 5 19 14 406.60 0.51 25 5 20 15 406.33 0.51 26 5 21 16 406.00 0.54 27 5 86 81 281.08 1.07 28 5 89 84 279.72 0.75 29 5 90 85 277.48 0.72 30 5 98 93 266.33 0.65 31 5 99 94 266.14 0.66 32 5 100 95 265.77 0.63 33 5 101 96 265.90 0.70 34 5 135 130 235.92 0.62 35 5 138 133 235.75 0.63 36 6 19 13 406.60 0.51 37 6 20 14 406.51 0.49 38 6 86 80 282.99 0.14 39 6 101 95 265.91 0.70 40 6 129 123 236.78 0.70 41 6 135 129 236.25 0.71 42 6 138 132 235.77 0.63 43 6 139 133 235.69 0.64 44 7 10 3 588.48 0.04 45 7 17 10 407.00 0.38 46 7 18 11 406.80 0.43 47 7 19 12 406.60 0.52 48 7 82 75 283.37 0.07 49 7 86 79 283.23 0.03 50 7 142 135 219.80 0.10 51 8 17 9 407.01 0.38 52 8 18 10 406.86 0.42 53 8 142 134 226.21 1.63 54 8 143 135 219.80 0.10 55 8 146 138 203.21 0.90 56 9 12 3 534.42 3.00 57 9 17 8 407.01 0.37 58 9 146 137 213.80 2.13 59 9 164 155 119.94 1.40 60 9 188 179 57.45 0.72 61 10 17 7 407.02 0.38 62 10 78 68 283.98 0.28 63 10 79 69 283.95 0.27 64 10 82 72 283.77 0.18 65 10 103 93 269.74 0.52 66 10 188 178 57.48 0.74 67 10 191 181 42.61 0.29 68 11 164 153 119.98 1.40 69 11 191 180 42.61 0.29 70 12 146 134 224.97 1.96 71 12 163 151 120.09 1.43 72 12 164 152 119.98 1.40 73 12 188 176 57.54 0.72 74 12 191 179 42.98 0.46 75 13 163 150 120.10 1.43 76 13 164 151 120.08 1.44 77 13 165 152 120.03 1.42 78 13 170 157 119.31 1.16 79 13 174 161 101.86 1.23 80 13 187 174 57.60 0.73 81 13 188 175 57.54 0.72 82 13 191 178 42.98 0.46 83 13 193 180 38.58 2.04 84 14 153 139 181.44 1.00 85 14 160 146 120.31 1.43 86 14 163 149 120.06 1.42 87 14 170 156 119.38 1.17 88 14 174 160 101.77 1.21 89 14 177 163 96.95 0.48 90 14 186 172 57.62 0.74 91 14 187 173 57.56 0.72 92 15 66 51 405.53 0.49 93 15 150 135 196.75 0.72 94 15 153 138 174.90 1.03 95 15 186 171 57.55 0.71 96 15 188 173 57.53 0.72 97 16 64 48 405.66 0.52 98 16 65 49 405.53 0.51 99 16 66 50 405.50 0.51 100 16 149 133 197.47 0.62 101 16 188 172 57.51 0.72 102 17 63 46 405.67 0.52 103 17 64 47 405.59 0.53 104 17 69 52 338.56 0.96 105 17 78 61 284.10 0.24 106 17 81 64 284.00 0.22 107 17 85 68 283.43 0.04 108 17 188 171 57.45 0.72 109 18 61 43 405.82 0.54 110 18 62 44 405.67 0.51 111 18 63 45 405.59 0.54 112 18 142 124 219.78 0.12 113 18 145 127 216.04 0.79 114 18 146 128 203.09 0.87 115 19 61 42 405.73 0.54 116 19 62 43 405.64 0.52 117 19 82 63 283.44 0.04 118 19 85 66 283.27 0.05 119 19 86 67 283.19 0.06 120 19 89 70 283.13 0.04 121 20 60 40 405.76 0.52 122 20 61 41 405.59 0.54 123 20 89 69 283.06 0.04 124 20 138 118 235.77 0.63 125 20 141 121 222.72 1.55 126 20 142 122 219.66 0.06 127 21 59 38 405.79 0.53 128 21 60 39 405.62 0.53 129 21 89 68 281.00 0.10 130 21 93 72 280.92 0.05 131 21 138 117 235.74 0.64 132 22 53 31 715.01 0.69 133 22 57 35 563.54 5.80 134 22 58 36 468.27 20.56 135 22 59 37 405.60 0.53 136 22 93 71 278.09 0.99 137 22 134 112 236.26 0.72 138 22 137 115 235.81 0.65 139 22 138 116 235.75 0.64 140 22 141 119 222.22 0.48 141 23 57 34 624.17 2.96 142 23 58 35 539.17 0.76 143 23 93 70 274.11 2.44 144 23 134 111 236.22 0.76 145 24 134 110 236.26 0.73 146 27 134 107 236.28 0.72 147 30 133 103 236.44 0.71 148 30 134 104 236.41 0.71 149 30 137 107 236.12 0.78 150 31 133 102 236.44 0.71 151 35 133 98 236.46 0.71 152 35 136 101 236.28 0.72 153 35 137 102 236.25 0.73 154 35 140 105 235.78 0.64 155 38 140 102 236.09 0.73 156 39 129 90 249.58 5.39 157 39 130 91 237.79 0.49 158 39 143 104 235.78 0.64 159 43 147 104 219.19 0.14 160 46 140 94 236.16 0.78 161 46 143 97 235.78 0.65 162 46 144 98 227.80 2.60 163 47 144 97 232.51 2.07 164 49 140 91 236.12 0.78 165 50 140 90 236.09 0.80 166 50 141 91 235.75 0.66 167 50 144 94 218.82 0.09 168 53 137 84 236.13 0.78 169 53 140 87 235.81 0.66 170 53 141 88 235.74 0.66 171 54 141 87 235.73 0.66 172 54 145 91 217.41 0.56 173 58 92 34 281.25 0.00 174 58 93 35 279.80 0.68 175 59 141 82 231.21 0.91 176 60 89 29 281.28 0.00 177 60 92 32 281.94 0.34 178 60 93 33 281.26 0.00 179 61 89 28 283.13 0.05 180 61 92 31 282.38 0.33 181 61 141 80 227.63 0.89 182 61 145 84 203.21 0.92 183 62 85 23 283.29 0.04 184 62 88 26 283.28 0.01 185 62 89 27 283.17 0.04 186 64 68 4 529.78 3.44 187 64 69 5 526.96 2.04 188 64 72 8 450.27 19.07 189 64 85 21 283.45 0.03 190 65 68 3 531.69 2.52 191 65 69 4 529.81 3.45 192 66 69 3 529.81 3.45 193 66 70 4 529.81 3.46 194 66 185 119 57.66 0.75 195 66 186 120 57.59 0.73 196 66 187 121 57.55 0.71 197 66 188 122 57.39 0.75 198 67 70 3 541.54 0.48 199 67 71 4 529.81 3.46 200 68 71 3 541.54 0.48 201 68 72 4 531.52 4.34 202 69 72 3 544.62 1.06 203 69 73 4 531.46 4.38 204 69 78 9 285.17 0.13 205 69 81 12 284.42 0.24 206 69 188 119 57.41 0.75 207 70 73 3 541.25 1.68 208 70 188 118 57.45 0.73 209 70 189 119 57.41 0.74 210 70 190 120 48.99 0.31 211 71 74 3 559.43 0.20 212 72 75 3 559.42 0.20 213 72 76 4 522.59 1.83 214 72 81 9 286.30 0.38 215 72 84 12 286.29 0.38 216 73 76 3 528.17 0.96 217 73 78 5 418.22 3.64 218 73 81 8 297.55 0.94 219 73 190 117 51.68 1.64 220 73 191 118 49.00 0.31 221 74 190 116 55.87 0.81 222 76 80 4 528.35 0.60 223 76 81 5 526.82 2.22 224 76 84 8 504.93 0.39 225 77 80 3 541.28 0.51 226 77 81 4 529.22 1.03 227 78 81 3 538.16 4.13 228 78 82 4 532.04 2.45 229 78 191 113 42.59 0.28 230 79 82 3 532.25 2.55 231 79 83 4 532.04 2.45 232 79 103 24 269.85 0.35 233 80 83 3 534.44 6.00 234 80 84 4 529.49 3.52 235 81 84 3 536.79 4.80 236 81 85 4 526.41 2.41 237 82 85 3 550.95 4.19 238 82 86 4 526.07 2.25 239 82 103 21 269.97 0.41 240 83 86 3 537.44 7.26 241 83 87 4 534.17 3.41 242 83 110 27 278.93 0.60 243 83 113 30 280.65 0.12 244 83 114 31 279.24 0.57 245 83 117 34 286.93 0.04 246 84 87 3 550.57 1.09 247 84 88 4 535.39 2.41 248 85 88 3 544.58 0.73 249 85 89 4 540.62 0.19 250 86 89 3 554.05 0.70 251 86 90 4 542.23 1.01 252 86 100 14 270.86 0.04 253 86 101 15 270.85 0.04 254 86 110 24 283.05 1.41 255 86 114 28 286.53 0.05 256 87 90 3 542.24 1.00 257 87 91 4 542.23 1.01 258 87 114 27 286.17 0.10 259 87 117 30 296.45 4.54 260 87 118 31 301.37 2.08 261 88 91 3 542.24 0.99 262 88 92 4 542.24 1.00 263 89 92 3 544.09 0.07 264 89 93 4 533.17 5.53 265 90 93 3 548.12 2.10 266 90 94 4 526.67 2.37 267 90 95 5 526.60 2.41 268 90 98 8 286.14 2.98 269 90 100 10 283.62 1.71 270 90 114 24 430.56 3.15 271 90 118 28 431.06 3.20 272 90 120 30 447.01 0.38 273 90 122 32 355.63 29.18 274 91 94 3 535.18 1.84 275 91 118 27 431.06 3.20 276 91 120 29 447.57 0.25 277 94 120 26 489.14 2.04 278 95 98 3 557.09 0.58 279 95 120 25 489.20 2.05 280 96 121 25 489.19 2.05 281 97 121 24 489.19 2.05 282 97 122 25 489.20 2.05 283 97 123 26 489.19 2.05 284 98 121 23 489.23 2.05 285 98 122 24 489.20 2.05 286 98 123 25 489.20 2.05 287 99 123 24 489.21 2.06 288 99 132 33 236.34 0.68 289 99 135 36 235.88 0.62 290 100 110 10 489.56 2.11 291 100 114 14 489.47 2.06 292 100 122 22 489.36 2.06 293 100 123 23 489.31 2.08 294 100 124 24 489.20 2.05 295 100 125 25 489.20 2.05 296 100 128 28 395.17 11.45 297 101 110 9 489.62 2.08 298 101 125 24 489.23 2.04 299 101 127 26 488.17 1.60 300 101 128 27 417.18 1.80 301 102 107 5 489.50 2.17 302 102 110 8 489.58 2.11 303 102 124 22 489.34 2.08 304 102 125 23 489.24 2.04 305 102 126 24 489.17 2.04 306 103 110 7 489.67 2.09 307 103 126 23 489.26 2.05 308 104 126 22 489.35 2.06 309 105 126 21 489.35 2.06 310 107 110 3 549.44 1.79 311 107 111 4 541.38 8.70 312 107 124 17 489.50 2.04 313 107 125 18 489.48 2.04 314 107 126 19 489.48 2.04 315 108 111 3 552.31 3.23 316 108 112 4 527.70 9.08 317 109 112 3 553.85 2.46 318 109 113 4 518.78 0.38 319 110 113 3 548.79 0.07 320 110 114 4 525.31 3.90 321 110 124 14 489.50 2.04 322 111 114 3 537.62 2.25 323 111 115 4 528.85 2.12 324 111 122 11 489.59 2.02 325 111 124 13 489.50 2.04 326 112 115 3 542.38 3.21 327 112 116 4 521.31 1.66 328 113 116 3 537.75 5.51 329 113 117 4 521.31 1.66 330 114 117 3 544.37 2.20 331 114 118 4 516.97 3.83 332 114 122 8 489.65 2.00 333 115 118 3 531.82 3.59 334 115 119 4 497.28 0.98 335 115 120 5 490.51 2.39 336 115 121 6 489.75 2.01 337 115 122 7 489.67 2.00 338 118 122 4 562.88 0.07 339 123 132 9 236.34 0.68 340 125 128 3 522.19 1.96 341 125 131 6 236.43 0.69 342 125 132 7 236.42 0.68 343 127 130 3 570.60 6.15 344 128 131 3 538.88 2.39 345 128 132 4 495.76 1.15 346 128 135 7 236.31 0.70 347 129 135 6 236.31 0.70 348 129 136 7 236.25 0.71 349 129 139 10 235.77 0.62 350 132 135 3 528.89 2.31 351 132 136 4 516.82 1.14 352 133 136 3 520.46 2.60 353 133 137 4 523.37 0.15 354 134 137 3 540.41 0.01 355 134 138 4 532.41 3.99 356 135 138 3 532.42 4.00 357 135 139 4 526.15 0.86 358 136 139 3 536.12 1.05 359 136 140 4 531.24 1.68 360 137 140 3 535.13 1.46 361 137 141 4 533.00 2.52 362 138 141 3 550.03 2.13 363 138 142 4 527.13 0.42 364 139 142 3 547.46 0.72 365 139 143 4 527.13 0.42 366 140 143 3 541.29 1.05 367 140 144 4 538.59 0.29 368 141 144 3 541.33 1.04 369 141 145 4 532.67 2.67 370 142 145 3 539.94 0.35 371 142 146 4 531.62 2.14 372 143 146 3 534.36 4.53 373 143 147 4 530.60 2.66 374 144 147 3 541.35 0.15 375 144 148 4 527.91 4.00 376 145 148 3 543.97 0.84 377 145 149 4 533.50 4.09 378 146 149 3 541.60 0.04 379 146 150 4 534.90 3.39 380 146 162 16 120.09 1.42 381 146 164 18 120.01 1.40 382 147 150 3 537.81 1.94 383 147 151 4 530.58 2.63 384 148 151 3 538.15 4.01 385 148 152 4 532.96 4.42 386 149 152 3 534.52 3.64 387 149 153 4 532.96 4.42 388 150 153 3 537.86 2.02 389 150 154 4 537.86 2.01 390 150 160 10 120.33 1.37 391 151 154 3 539.51 1.19 392 151 155 4 538.62 2.39 393 152 155 3 544.32 0.46 394 152 156 4 540.26 1.57 395 153 156 3 540.83 1.85 396 153 157 4 534.97 4.21 397 153 160 7 309.88 93.25 398 153 186 33 57.55 0.71 399 154 157 3 539.21 2.67 400 154 158 4 435.31 50.52 401 154 159 5 133.88 1.45 402 154 160 6 127.08 1.96 403 154 161 7 120.43 1.36 404 157 177 20 98.05 0.62 405 157 184 27 57.69 0.74 406 157 186 29 57.68 0.74 407 159 169 10 119.83 1.38 408 159 173 14 118.30 0.77 409 160 163 3 571.39 2.55 410 160 169 9 119.41 1.18 411 160 170 10 119.39 1.17 412 160 173 13 109.13 2.11 413 160 177 17 99.19 0.06 414 161 167 6 119.95 1.42 415 161 169 8 119.41 1.18 416 161 170 9 119.39 1.18 417 162 167 5 119.92 1.43 418 162 170 8 119.39 1.18 419 163 170 7 119.36 1.18 420 164 167 3 555.23 3.08 421 164 170 6 119.34 1.19 422 165 171 6 120.33 1.68 423 165 193 28 39.49 1.58 424 166 171 5 526.96 0.13 425 167 170 3 536.79 2.27 426 167 171 4 538.04 2.13 427 168 171 3 541.77 3.99 428 168 172 4 534.76 3.77 429 169 172 3 538.11 2.10 430 169 173 4 534.26 3.52 431 170 173 3 548.96 3.33 432 170 174 4 534.24 3.52 433 171 174 3 537.56 1.82 434 171 175 4 531.74 2.52 435 172 175 3 546.28 2.12 436 172 176 4 543.64 3.45 437 173 176 3 546.35 2.10 438 173 177 4 543.63 3.44 439 174 177 3 543.65 3.45 440 174 178 4 543.64 3.44 441 174 187 13 57.68 0.74 442 174 193 19 57.16 0.79 443 174 197 23 34.52 0.34 444 175 178 3 551.47 0.48 445 175 179 4 528.87 0.16 446 175 197 22 34.68 0.38 447 176 179 3 530.62 2.09 448 176 180 4 527.85 0.67 449 177 180 3 532.99 2.83 450 177 181 4 526.70 0.07 451 177 182 5 521.39 1.93 452 177 183 6 59.29 1.50 453 177 184 7 61.59 0.35 454 177 187 10 57.77 0.76 455 178 181 3 539.22 5.34 456 178 183 5 240.31 44.76 457 178 194 16 57.22 0.75 458 178 197 19 36.18 0.83 459 178 198 20 34.62 0.41 460 183 187 4 526.12 2.33 461 183 189 6 60.90 0.68 462 184 187 3 551.38 3.11 463 187 194 7 93.05 15.42 464 188 191 3 532.79 0.07 465 188 194 6 336.04 10.13 466 189 194 5 337.03 9.63 467 189 198 9 93.79 14.71 468 191 194 3 542.78 4.75 469 191 195 4 521.38 0.49 470 192 195 3 531.11 2.10 471 192 196 4 521.38 0.49 472 193 196 3 540.44 5.56 473 193 197 4 521.40 0.49 474 194 197 3 533.45 0.66 475 194 198 4 528.61 3.08 476 195 198 3 531.90 1.44 477 195 199 4 524.73 2.15 478 196 199 3 540.57 4.33 479 196 200 4 521.13 0.12