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 5 3 604.16 1.98 2 2 19 17 44.68 0.86 3 2 20 18 44.56 0.92 4 2 23 21 45.57 1.24 5 2 70 68 34.34 0.62 6 3 20 17 45.47 1.25 7 3 23 20 45.70 1.23 8 3 57 54 45.45 1.30 9 3 70 67 35.71 0.48 10 3 71 68 37.24 1.12 11 3 72 69 44.26 1.43 12 4 57 53 45.45 1.30 13 4 58 54 45.44 1.30 14 4 60 56 45.27 1.26 15 4 70 66 45.47 1.26 16 5 60 55 45.51 1.27 17 5 69 64 45.50 1.27 18 5 70 65 45.51 1.27 19 6 60 54 45.52 1.27 20 6 62 56 45.52 1.28 21 6 63 57 45.51 1.27 22 6 64 58 45.51 1.27 23 6 68 62 45.51 1.27 24 6 69 63 45.52 1.27 25 7 11 4 580.42 0.63 26 7 12 5 559.27 5.21 27 7 16 9 528.22 3.38 28 7 67 60 45.52 1.28 29 7 68 61 45.59 1.25 30 7 70 63 45.73 1.23 31 8 11 3 584.96 1.58 32 8 12 4 591.02 4.66 33 8 67 59 45.59 1.25 34 9 12 3 596.56 1.90 35 9 36 27 45.59 1.24 36 9 66 57 45.66 1.22 37 9 67 58 45.70 1.24 38 9 68 59 45.70 1.24 39 11 16 5 575.62 0.74 40 12 17 5 575.63 0.75 41 12 34 22 46.58 0.90 42 12 35 23 46.50 0.94 43 12 36 24 46.45 0.96 44 12 68 56 46.51 0.93 45 12 70 58 47.30 0.98 46 12 170 158 47.84 0.26 47 13 16 3 588.48 3.02 48 13 17 4 579.00 0.01 49 13 170 157 55.79 0.98 50 14 17 3 580.83 0.80 51 14 18 4 578.09 0.47 52 14 160 146 62.73 1.10 53 14 162 148 67.16 0.22 54 14 168 154 66.31 0.61 55 14 170 156 57.26 0.27 56 15 18 3 592.42 3.62 57 15 19 4 579.68 0.32 58 16 19 3 590.00 4.83 59 16 20 4 579.69 0.33 60 16 70 54 67.14 0.23 61 17 20 3 579.69 0.33 62 17 21 4 579.69 0.33 63 17 32 15 67.20 0.21 64 17 33 16 67.20 0.21 65 17 34 17 67.16 0.22 66 17 70 53 67.19 0.21 67 17 168 151 67.24 0.24 68 17 169 152 67.20 0.21 69 17 170 153 67.18 0.21 70 18 21 3 586.57 3.12 71 18 22 4 578.18 0.41 72 18 168 150 68.46 0.35 73 19 22 3 581.79 1.27 74 19 23 4 581.78 1.27 75 20 23 3 598.38 1.31 76 20 24 4 584.20 1.88 77 20 32 12 68.98 0.58 78 20 70 50 68.86 0.58 79 20 71 51 68.88 0.58 80 20 72 52 68.88 0.59 81 21 24 3 598.38 1.31 82 21 30 9 69.36 0.55 83 21 31 10 69.27 0.55 84 21 32 11 69.09 0.59 85 21 166 145 69.39 0.56 86 21 167 146 69.35 0.55 87 21 168 147 69.20 0.56 88 22 25 3 601.82 1.02 89 24 27 3 639.23 1.99 90 24 30 6 70.23 0.89 91 24 31 7 69.50 0.56 92 24 72 48 69.48 0.56 93 24 73 49 69.53 0.54 94 25 30 5 574.71 0.01 95 27 30 3 629.84 1.89 96 27 74 47 146.68 0.36 97 27 75 48 176.02 0.48 98 28 75 47 176.21 0.43 99 29 74 45 176.25 0.46 100 29 75 46 176.21 0.43 101 29 83 54 176.18 0.43 102 29 104 75 176.09 0.45 103 29 105 76 176.19 0.45 104 29 106 77 176.22 0.45 105 29 108 79 176.23 0.45 106 29 165 136 176.03 0.47 107 30 73 43 176.22 0.42 108 30 74 44 176.25 0.46 109 30 165 135 176.12 0.46 110 30 166 136 176.10 0.44 111 30 167 137 176.09 0.45 112 31 72 41 176.41 0.48 113 31 73 42 176.38 0.47 114 31 84 53 176.31 0.48 115 31 102 71 176.12 0.46 116 31 104 73 176.24 0.45 117 31 161 130 176.09 0.45 118 31 167 136 176.09 0.45 119 31 169 138 176.09 0.45 120 32 71 39 176.56 0.48 121 32 72 40 176.44 0.49 122 32 167 135 176.15 0.45 123 32 168 136 176.11 0.45 124 32 169 137 176.10 0.45 125 33 70 37 176.79 0.45 126 33 71 38 176.61 0.48 127 33 88 55 176.39 0.49 128 33 102 69 176.33 0.48 129 33 169 136 176.10 0.45 130 34 69 35 177.18 0.54 131 34 70 36 176.80 0.44 132 34 169 135 176.15 0.45 133 34 170 136 176.11 0.45 134 34 171 137 176.10 0.45 135 35 43 8 500.30 2.46 136 35 68 33 177.59 0.53 137 35 69 34 177.40 0.58 138 35 88 53 176.73 0.47 139 35 98 63 176.37 0.50 140 35 100 65 176.41 0.50 141 35 171 136 176.10 0.45 142 35 173 138 176.09 0.45 143 36 67 31 367.91 2.93 144 36 68 32 177.58 0.54 145 36 171 135 176.15 0.45 146 36 172 136 176.10 0.45 147 36 173 137 176.10 0.45 148 37 41 4 591.52 3.26 149 37 42 5 554.70 6.87 150 37 43 6 508.91 5.29 151 37 63 26 455.87 5.84 152 37 64 27 466.95 0.42 153 37 65 28 465.62 1.06 154 37 66 29 456.03 5.84 155 37 67 30 368.51 2.96 156 38 65 27 480.73 1.44 157 38 66 28 459.45 4.13 158 38 172 134 176.18 0.44 159 38 173 135 176.12 0.45 160 38 174 136 176.10 0.45 161 38 175 137 176.11 0.45 162 39 43 4 616.24 1.58 163 39 65 26 498.32 2.25 164 39 155 116 176.36 0.48 165 39 173 134 176.16 0.45 166 39 174 135 176.12 0.45 167 39 175 136 176.11 0.45 168 40 65 25 498.51 2.35 169 40 175 135 176.12 0.45 170 41 65 24 498.57 2.33 171 41 93 52 439.27 1.06 172 42 63 21 498.66 2.35 173 42 64 22 498.58 2.33 174 42 65 23 498.59 2.32 175 42 92 50 439.56 0.96 176 42 93 51 439.35 1.06 177 43 62 19 498.87 2.38 178 43 63 20 498.78 2.33 179 43 69 26 498.66 2.37 180 43 90 47 440.01 1.18 181 43 91 48 439.61 0.97 182 43 92 49 439.56 0.96 183 43 98 55 439.32 1.07 184 43 173 130 176.16 0.45 185 44 61 17 498.90 2.37 186 44 62 18 498.88 2.38 187 44 90 46 440.51 1.12 188 44 91 47 440.18 1.23 189 45 59 14 498.84 2.34 190 45 60 15 498.94 2.37 191 45 61 16 498.94 2.37 192 45 89 44 440.85 1.25 193 45 90 45 440.56 1.14 194 46 89 43 440.87 1.25 195 46 90 44 440.64 1.17 196 46 91 45 440.62 1.16 197 46 97 51 440.35 1.15 198 46 123 77 333.78 1.33 199 46 124 78 333.73 1.34 200 46 125 79 333.38 1.28 201 47 59 12 499.15 2.41 202 47 88 41 440.93 1.25 203 47 89 42 440.90 1.26 204 47 125 78 333.55 1.32 205 47 126 79 333.31 1.33 206 48 59 11 499.17 2.42 207 48 71 23 499.09 2.40 208 48 87 39 441.03 1.28 209 48 88 40 440.93 1.25 210 48 126 78 333.41 1.38 211 49 86 37 441.15 1.29 212 49 87 38 441.09 1.31 213 49 126 77 333.44 1.40 214 49 127 78 333.32 1.34 215 49 128 79 333.31 1.33 216 49 131 82 326.41 2.23 217 50 53 3 613.31 0.56 218 50 54 4 558.22 1.10 219 50 55 5 563.30 1.44 220 50 71 21 499.26 2.41 221 50 73 23 498.96 2.46 222 50 85 35 441.59 1.33 223 50 86 36 441.15 1.29 224 50 102 52 440.26 1.16 225 51 85 34 441.76 1.26 226 51 86 35 441.59 1.33 227 51 128 77 333.49 1.43 228 51 131 80 331.81 1.27 229 52 82 30 442.09 1.22 230 52 83 31 442.02 1.22 231 52 84 32 441.95 1.22 232 52 85 33 441.90 1.20 233 53 74 21 498.92 2.46 234 53 75 22 498.73 2.42 235 53 76 23 498.50 2.31 236 53 83 30 442.00 1.22 237 53 84 31 441.90 1.20 238 54 73 19 499.13 2.39 239 54 74 20 498.95 2.46 240 55 71 16 499.50 2.43 241 55 72 17 499.25 2.41 242 55 73 18 499.07 2.42 243 56 74 18 499.25 2.41 244 57 71 14 499.53 2.43 245 57 72 15 499.42 2.38 246 58 71 13 499.56 2.42 247 59 71 12 499.56 2.42 248 59 88 29 440.92 1.25 249 59 90 31 440.87 1.24 250 60 63 3 623.05 0.96 251 60 69 9 499.62 2.43 252 60 70 10 499.62 2.43 253 60 90 30 440.86 1.25 254 63 67 4 562.34 6.25 255 63 69 6 499.67 2.44 256 63 90 27 440.56 1.14 257 64 67 3 581.70 2.71 258 69 90 21 440.87 1.25 259 71 88 17 440.94 1.26 260 73 84 11 441.59 1.34 261 74 77 3 713.67 3.78 262 74 84 10 441.62 1.32 263 75 80 5 555.18 6.19 264 75 82 7 442.05 1.22 265 75 83 8 441.96 1.22 266 75 84 9 441.91 1.19 267 75 106 31 438.64 0.90 268 76 80 4 581.50 2.96 269 76 82 6 468.28 14.30 270 77 80 3 637.97 3.41 271 81 106 25 439.26 0.99 272 82 106 24 439.16 0.99 273 83 104 21 439.40 1.02 274 83 105 22 439.23 1.01 275 83 106 23 438.81 0.97 276 84 102 18 440.25 1.16 277 84 103 19 439.47 1.02 278 84 104 20 439.41 0.99 279 85 102 17 440.25 1.16 280 85 103 18 439.45 1.02 281 85 104 19 439.45 1.02 282 85 131 46 329.87 2.21 283 86 101 15 440.27 1.17 284 86 102 16 440.09 1.08 285 87 100 13 440.31 1.17 286 87 101 14 439.54 0.98 287 87 126 39 333.45 1.41 288 87 130 43 326.42 2.23 289 87 131 44 326.28 2.27 290 88 99 11 440.31 1.17 291 88 100 12 440.17 1.16 292 88 102 14 439.72 1.01 293 88 126 38 333.31 1.33 294 89 97 8 440.41 1.12 295 89 98 9 440.31 1.17 296 89 99 10 440.10 1.09 297 89 124 35 333.75 1.33 298 89 126 37 333.12 1.32 299 89 130 41 326.40 2.23 300 90 97 7 441.30 0.67 301 90 98 8 440.25 1.14 302 91 95 4 559.42 10.04 303 91 96 5 510.01 1.39 304 91 97 6 441.31 0.67 305 91 122 31 333.78 1.32 306 91 123 32 333.59 1.32 307 92 95 3 583.95 0.62 308 92 96 4 532.91 5.17 309 92 98 6 441.31 0.69 310 92 119 27 334.23 1.35 311 92 155 63 240.20 0.81 312 95 122 27 333.73 1.34 313 96 119 23 334.24 1.35 314 96 120 24 333.98 1.36 315 96 121 25 333.79 1.33 316 96 122 26 333.73 1.35 317 96 153 57 240.61 0.62 318 97 119 22 334.23 1.35 319 97 120 23 334.08 1.41 320 97 122 25 333.80 1.33 321 97 123 26 333.68 1.35 322 97 124 27 333.58 1.31 323 97 130 33 326.38 2.25 324 98 117 19 334.35 1.38 325 98 118 20 334.30 1.36 326 98 119 21 334.24 1.35 327 98 151 53 240.75 0.57 328 98 173 75 176.13 0.45 329 99 117 18 334.35 1.38 330 99 118 19 334.30 1.38 331 99 120 21 334.25 1.36 332 99 130 31 326.24 2.30 333 99 134 35 317.50 0.13 334 100 116 16 334.44 1.36 335 100 117 17 334.36 1.38 336 100 134 34 317.52 0.14 337 100 169 69 176.22 0.45 338 100 171 71 176.16 0.44 339 101 114 13 334.67 1.33 340 101 115 14 334.45 1.37 341 101 116 15 334.44 1.36 342 101 131 30 326.34 2.25 343 101 134 33 317.50 0.13 344 101 135 34 317.50 0.12 345 101 139 38 286.61 0.82 346 102 114 12 334.67 1.33 347 102 115 13 334.48 1.37 348 102 161 59 231.47 0.97 349 102 169 67 176.16 0.45 350 103 113 10 334.77 1.31 351 103 114 11 334.71 1.33 352 103 135 32 317.61 0.10 353 103 161 58 231.62 0.98 354 104 108 4 608.75 2.02 355 104 113 9 334.86 1.35 356 104 161 57 231.62 0.98 357 104 165 61 176.20 0.45 358 104 167 63 176.18 0.44 359 105 108 3 633.06 0.56 360 105 111 6 511.59 0.81 361 105 112 7 421.12 44.42 362 105 113 8 334.94 1.38 363 107 111 4 544.81 2.20 364 108 111 3 537.82 5.70 365 108 112 4 517.63 3.77 366 108 113 5 544.88 2.16 367 108 164 56 230.41 0.74 368 108 165 57 228.69 0.10 369 112 141 29 286.62 0.82 370 113 141 28 286.52 0.78 371 113 142 29 285.84 0.79 372 113 161 48 231.66 0.99 373 113 162 49 231.59 1.00 374 113 163 50 228.68 1.41 375 113 164 51 225.91 0.23 376 113 167 54 176.21 0.45 377 114 135 21 320.51 1.32 378 114 139 25 286.65 0.81 379 114 140 26 286.61 0.81 380 114 141 27 286.22 0.83 381 114 142 28 285.84 0.79 382 114 161 47 231.65 0.99 383 115 139 24 286.62 0.82 384 115 140 25 286.51 0.77 385 115 141 26 286.22 0.83 386 115 142 27 285.84 0.78 387 115 147 32 241.15 0.43 388 115 157 42 240.79 0.58 389 115 159 44 238.19 0.66 390 115 160 45 231.68 0.99 391 115 161 46 231.59 0.97 392 115 169 54 176.18 0.44 393 115 171 56 176.15 0.44 394 116 134 18 317.57 0.14 395 116 138 22 286.63 0.81 396 116 139 23 286.36 0.85 397 116 140 24 286.31 0.87 398 116 149 33 240.84 0.57 399 117 134 17 317.57 0.15 400 117 149 32 240.78 0.55 401 117 151 34 240.80 0.58 402 117 157 40 240.07 0.78 403 117 171 54 176.16 0.44 404 117 173 56 176.13 0.44 405 118 133 15 323.35 1.44 406 118 134 16 317.51 0.12 407 118 151 33 240.78 0.58 408 119 151 32 240.72 0.56 409 119 152 33 240.80 0.58 410 119 153 34 240.81 0.58 411 119 155 36 240.68 0.61 412 120 124 4 567.34 4.72 413 120 130 10 326.38 2.25 414 120 133 13 321.39 1.77 415 120 134 14 317.53 0.14 416 121 124 3 678.74 6.83 417 121 153 32 240.80 0.58 418 124 130 6 564.66 3.12 419 125 130 5 569.50 4.71 420 126 130 4 574.38 2.27 421 127 130 3 591.13 2.73 422 127 131 4 574.42 2.25 423 128 131 3 574.65 2.31 424 128 132 4 574.42 2.25 425 129 132 3 587.59 1.08 426 129 133 4 576.60 1.15 427 130 133 3 576.77 1.23 428 130 134 4 576.77 1.24 429 131 134 3 582.08 1.61 430 131 135 4 574.68 2.09 431 131 136 5 574.67 2.09 432 132 135 3 582.79 4.24 433 132 136 4 564.31 2.69 434 133 137 4 558.30 0.23 435 134 139 5 508.98 4.88 436 135 139 4 540.33 10.80 437 140 147 7 241.16 0.43 438 140 149 9 241.22 0.47 439 140 157 17 240.97 0.59 440 142 161 19 231.66 0.98 441 142 162 20 231.65 0.99 442 142 163 21 231.06 0.86 443 143 147 4 648.59 8.25 444 143 161 18 237.22 1.13 445 143 163 20 231.59 1.02 446 144 160 16 239.47 1.09 447 144 161 17 238.31 0.60 448 144 162 18 233.12 0.27 449 144 163 19 232.08 0.80 450 145 160 15 239.61 1.16 451 146 158 12 240.85 0.70 452 146 159 13 240.69 0.63 453 146 160 14 240.67 0.62 454 146 170 24 176.22 0.45 455 147 157 10 242.00 0.55 456 147 158 11 240.86 0.71 457 147 159 12 240.83 0.70 458 148 156 8 242.50 0.61 459 148 157 9 241.74 0.42 460 148 158 10 240.94 0.71 461 149 156 7 242.50 0.61 462 149 157 8 242.34 0.67 463 150 155 5 371.29 63.68 464 150 156 6 242.50 0.62 465 151 155 4 420.09 39.30 466 151 156 5 242.55 0.63 467 151 157 6 242.54 0.62 468 151 173 22 176.18 0.43 469 152 155 3 585.75 1.05 470 154 175 21 176.12 0.44 471 155 173 18 176.19 0.45 472 155 174 19 176.15 0.45 473 155 175 20 176.10 0.45 474 156 173 17 176.18 0.43 475 156 174 18 176.15 0.44 476 157 171 14 176.23 0.44 477 157 172 15 176.18 0.44 478 157 173 16 176.13 0.44 479 158 171 13 176.21 0.44 480 158 172 14 176.18 0.44 481 159 170 11 176.21 0.44 482 159 171 12 176.15 0.45 483 160 169 9 176.22 0.45 484 160 170 10 176.18 0.44 485 161 167 6 176.24 0.45 486 161 168 7 176.22 0.45 487 161 169 8 176.17 0.45 488 162 167 5 176.23 0.45 489 162 168 6 176.22 0.45 490 164 167 3 587.50 0.60