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 3 6 3 613.52 0.94 2 3 7 4 601.14 1.99 3 3 34 31 196.60 67.95 4 3 38 35 196.09 67.71 5 4 7 3 622.75 1.00 6 4 8 4 609.81 2.35 7 4 42 38 192.47 69.50 8 4 43 39 192.31 69.58 9 5 8 3 608.25 3.58 10 5 9 4 602.74 0.92 11 6 9 3 602.75 0.92 12 6 10 4 603.33 2.06 13 6 32 26 199.71 68.11 14 7 10 3 611.25 2.19 15 7 11 4 599.38 4.03 16 7 28 21 199.48 68.20 17 7 32 25 199.72 68.11 18 7 34 27 199.69 68.09 19 7 39 32 197.57 67.47 20 7 43 36 196.27 67.62 21 7 49 42 194.59 68.39 22 8 11 3 607.86 3.18 23 8 12 4 599.38 4.03 24 8 43 35 196.27 67.61 25 8 49 41 194.59 68.39 26 8 52 44 192.95 69.14 27 8 53 45 192.81 69.08 28 9 12 3 611.78 1.18 29 9 13 4 603.33 2.06 30 10 13 3 605.91 1.76 31 10 14 4 596.73 2.83 32 10 31 21 200.28 68.27 33 10 32 22 199.84 68.16 34 11 14 3 603.22 0.41 35 11 15 4 596.73 2.83 36 11 28 17 199.86 68.06 37 11 49 38 196.59 67.46 38 11 53 42 196.00 67.50 39 12 15 3 611.78 1.56 40 12 16 4 601.81 0.28 41 12 53 41 196.00 67.49 42 12 57 45 195.96 67.47 43 12 90 78 182.05 60.52 44 12 91 79 182.00 60.50 45 12 95 83 181.88 60.41 46 13 16 3 607.38 0.53 47 13 17 4 596.41 2.94 48 14 17 3 605.38 1.53 49 14 18 4 593.36 4.32 50 14 23 9 201.84 68.36 51 14 27 13 201.34 68.63 52 14 28 14 201.30 68.63 53 14 31 17 201.35 68.63 54 15 18 3 609.44 4.10 55 15 19 4 551.59 3.12 56 15 20 5 417.11 3.33 57 15 23 8 214.66 63.73 58 15 46 31 200.15 68.31 59 15 50 35 196.59 67.45 60 15 53 38 196.54 67.42 61 15 95 80 181.94 60.40 62 15 98 83 181.06 59.94 63 16 94 78 181.99 60.42 64 16 95 79 181.96 60.41 65 18 22 4 549.31 14.11 66 18 23 5 473.24 11.27 67 19 22 3 589.32 5.89 68 19 23 4 579.22 0.84 69 19 101 82 181.52 59.62 70 20 23 3 629.83 5.75 71 20 46 26 200.51 68.20 72 20 47 27 200.46 68.20 73 20 50 30 199.43 67.97 74 20 98 78 181.61 59.67 75 20 101 81 181.58 59.58 76 20 102 82 181.33 59.45 77 20 105 85 181.73 58.96 78 20 106 86 181.73 58.95 79 21 46 25 200.53 68.20 80 21 101 80 181.58 59.58 81 21 105 84 181.72 58.95 82 22 27 5 600.73 0.05 83 23 27 4 599.35 0.40 84 23 46 23 200.56 68.20 85 24 27 3 607.82 3.39 86 24 28 4 599.40 0.40 87 24 46 22 200.56 68.20 88 25 28 3 599.40 0.40 89 25 29 4 599.41 0.41 90 26 29 3 619.77 2.58 91 26 30 4 599.42 0.41 92 27 30 3 607.82 3.40 93 27 31 4 595.34 2.90 94 28 31 3 630.01 1.56 95 28 32 4 583.95 0.66 96 28 39 11 210.05 65.83 97 28 49 21 198.88 67.44 98 29 33 4 548.51 5.50 99 29 34 5 489.25 35.12 100 29 35 6 429.82 16.38 101 29 36 7 222.69 61.96 102 29 39 10 218.83 61.45 103 30 33 3 595.10 3.02 104 34 38 4 604.21 3.79 105 34 39 5 590.08 4.71 106 35 38 3 628.14 0.43 107 35 39 4 609.26 1.27 108 36 39 3 626.45 0.42 109 37 40 3 608.23 1.78 110 38 41 3 631.53 1.73 111 39 43 4 567.73 7.18 112 40 43 3 601.14 1.02 113 40 44 4 557.92 12.09 114 41 44 3 624.69 1.01 115 42 48 6 567.03 4.41 116 42 52 10 427.81 12.50 117 43 48 5 562.49 6.65 118 43 49 6 442.31 5.26 119 43 52 9 442.31 5.26 120 44 48 4 572.25 1.82 121 45 48 3 585.78 1.84 122 45 49 4 581.00 2.53 123 46 49 3 596.58 3.45 124 46 50 4 589.29 6.67 125 47 50 3 605.13 1.25 126 47 51 4 589.27 6.68 127 47 102 55 339.64 19.71 128 47 106 59 331.00 26.63 129 48 51 3 603.06 0.21 130 48 52 4 589.23 6.73 131 48 115 67 309.70 34.70 132 49 52 3 604.47 2.06 133 49 53 4 601.01 0.88 134 50 53 3 601.58 0.61 135 50 54 4 601.01 0.88 136 50 98 48 346.38 22.72 137 50 99 49 346.36 22.75 138 50 102 52 346.06 22.91 139 51 54 3 605.53 1.02 140 51 102 51 346.43 23.07 141 51 115 64 315.06 37.32 142 52 55 3 602.88 0.04 143 52 56 4 593.20 4.79 144 53 56 3 602.85 0.06 145 53 57 4 593.08 4.74 146 53 95 42 348.06 22.64 147 54 57 3 606.04 0.27 148 54 58 4 601.66 0.10 149 54 95 41 348.06 22.64 150 54 99 45 346.78 22.93 151 54 119 65 315.31 37.52 152 55 58 3 602.36 0.07 153 55 59 4 601.79 0.04 154 55 122 67 315.89 37.82 155 56 59 3 609.28 1.34 156 56 60 4 601.80 0.04 157 57 60 3 604.35 1.11 158 57 61 4 602.01 0.08 159 57 91 34 348.49 22.73 160 57 92 35 348.31 22.69 161 57 95 38 348.29 22.71 162 58 61 3 603.84 0.74 163 58 62 4 602.11 0.12 164 58 92 34 348.37 22.67 165 58 119 61 316.66 38.11 166 58 122 64 316.40 38.06 167 58 123 65 316.38 38.11 168 59 62 3 602.11 0.12 169 59 63 4 602.12 0.12 170 59 122 63 316.48 38.06 171 60 63 3 609.98 3.32 172 60 64 4 602.11 0.12 173 60 91 31 348.69 22.68 174 61 64 3 603.95 0.81 175 61 65 4 602.10 0.12 176 61 82 21 349.44 22.68 177 61 85 24 349.28 22.77 178 61 86 25 349.29 22.75 179 61 89 28 348.92 22.71 180 61 91 30 348.70 22.68 181 61 92 31 348.70 22.68 182 61 93 32 348.70 22.68 183 62 65 3 603.94 0.81 184 62 66 4 603.31 0.71 185 62 122 60 316.67 38.09 186 62 125 63 316.43 38.13 187 62 126 64 316.10 38.16 188 63 66 3 603.16 0.79 189 63 67 4 603.38 0.69 190 64 67 3 604.22 0.29 191 64 68 4 603.42 0.70 192 64 89 25 349.11 22.70 193 64 90 26 349.11 22.70 194 64 91 27 348.90 22.72 195 65 68 3 604.10 0.36 196 65 69 4 603.40 0.69 197 65 78 13 350.10 22.65 198 65 81 16 349.74 22.64 199 65 82 17 349.48 22.70 200 65 85 20 349.43 22.71 201 65 126 61 316.23 38.23 202 65 130 65 315.47 37.98 203 66 69 3 616.33 1.26 204 66 70 4 616.33 1.26 205 67 70 3 662.72 1.57 206 68 71 3 631.57 1.16 207 68 81 13 350.05 22.66 208 68 85 17 349.45 22.70 209 69 72 3 625.59 1.98 210 69 78 9 350.21 22.59 211 69 81 12 350.06 22.66 212 71 81 10 350.58 22.47 213 72 77 5 499.32 13.37 214 72 78 6 390.03 18.80 215 72 81 9 370.39 12.56 216 73 77 4 590.38 0.88 217 74 77 3 590.39 0.87 218 74 78 4 589.74 1.20 219 74 139 65 248.83 37.92 220 75 78 3 588.63 1.75 221 75 79 4 586.61 2.76 222 75 130 55 316.11 38.18 223 75 133 58 311.62 39.87 224 75 139 64 248.81 37.92 225 75 140 65 248.81 37.92 226 76 79 3 610.91 3.98 227 76 80 4 591.43 1.40 228 76 139 63 248.81 37.92 229 76 140 64 248.81 37.92 230 76 183 107 141.13 42.44 231 77 80 3 606.53 0.76 232 77 81 4 590.76 1.08 233 78 81 3 606.86 0.96 234 78 82 4 590.75 1.08 235 78 130 52 315.81 38.06 236 79 82 3 606.89 0.94 237 79 83 4 590.75 1.08 238 79 127 48 316.50 38.16 239 79 130 51 315.82 38.06 240 79 131 52 315.81 38.06 241 79 152 73 160.74 39.87 242 79 179 100 144.80 42.72 243 79 182 103 141.87 42.12 244 79 183 104 141.12 42.44 245 80 83 3 602.47 3.15 246 80 84 4 590.28 1.30 247 80 176 96 151.12 41.00 248 80 179 99 144.85 42.68 249 80 180 100 144.78 42.71 250 80 183 103 141.13 42.44 251 81 84 3 590.29 1.30 252 81 85 4 590.27 1.30 253 82 85 3 596.16 1.73 254 82 86 4 590.20 1.28 255 82 93 11 349.69 22.41 256 82 126 44 316.53 38.14 257 82 127 45 316.44 38.14 258 82 130 48 315.53 37.97 259 83 86 3 596.25 1.75 260 83 87 4 602.34 1.35 261 83 127 44 316.51 38.13 262 83 156 73 159.55 39.90 263 83 175 92 151.15 41.01 264 83 179 96 144.78 42.71 265 84 87 3 623.80 2.37 266 84 172 88 151.16 41.02 267 84 175 91 151.15 41.01 268 84 176 92 151.14 41.01 269 85 88 3 602.39 1.33 270 85 89 4 590.18 1.30 271 86 93 7 348.92 22.73 272 86 156 70 159.06 40.13 273 86 160 74 153.93 42.22 274 87 160 73 153.88 42.19 275 87 168 81 151.27 41.05 276 87 171 84 151.18 41.02 277 87 172 85 151.16 41.02 278 87 175 88 151.15 41.01 279 88 168 80 151.25 41.05 280 90 94 4 593.82 6.10 281 91 94 3 633.13 0.21 282 92 95 3 623.56 4.27 283 92 96 4 604.37 2.15 284 92 119 27 316.72 38.11 285 92 123 31 316.46 38.12 286 93 96 3 606.90 0.88 287 93 157 64 154.28 42.17 288 93 160 67 153.84 42.20 289 95 98 3 601.90 1.67 290 95 99 4 589.38 2.91 291 96 99 3 607.75 0.89 292 96 100 4 594.77 5.61 293 96 157 61 154.33 42.20 294 96 161 65 153.81 42.24 295 97 100 3 602.46 2.87 296 97 101 4 596.91 4.54 297 98 101 3 606.37 0.18 298 98 102 4 596.90 4.54 299 99 102 3 596.89 4.54 300 99 103 4 594.23 3.21 301 100 103 3 617.14 4.45 302 100 104 4 594.24 3.21 303 100 161 61 153.99 42.30 304 100 162 62 153.96 42.31 305 101 104 3 609.20 1.48 306 101 105 4 596.75 4.47 307 102 105 3 604.90 3.63 308 102 106 4 596.75 7.71 309 102 112 10 316.92 38.09 310 103 107 4 572.61 3.09 311 103 112 9 316.91 38.09 312 103 113 10 316.91 38.08 313 103 116 13 316.76 38.11 314 104 107 3 613.63 0.57 315 106 109 3 601.81 2.32 316 106 112 6 316.89 38.11 317 107 112 5 316.91 38.11 318 109 112 3 621.06 5.71 319 110 113 3 634.31 2.27 320 111 114 3 581.12 2.02 321 111 115 4 581.12 2.02 322 112 116 4 578.65 2.52 323 113 116 3 600.12 1.52 324 114 117 3 610.32 0.34 325 115 118 3 617.38 3.19 326 115 119 4 601.43 0.96 327 116 119 3 606.50 1.57 328 116 120 4 594.33 4.50 329 117 120 3 605.58 0.27 330 117 121 4 607.74 2.19 331 118 121 3 609.13 1.50 332 118 122 4 609.13 1.50 333 119 122 3 612.54 3.21 334 119 123 4 607.69 2.21 335 120 123 3 612.35 0.11 336 120 124 4 607.68 2.21 337 120 150 30 160.47 39.83 338 121 124 3 609.65 1.22 339 121 125 4 600.36 1.45 340 122 125 3 604.53 0.62 341 123 153 30 160.09 39.97 342 123 154 31 160.10 39.97 343 123 157 34 160.04 39.97 344 124 127 3 609.79 5.20 345 124 128 4 594.02 4.63 346 124 149 25 160.53 39.81 347 124 150 26 160.50 39.81 348 124 153 29 160.10 39.96 349 125 128 3 595.19 0.77 350 125 129 4 595.19 0.77 351 126 129 3 607.16 3.88 352 126 130 4 585.70 0.47 353 127 130 3 596.81 3.34 354 127 131 4 582.95 6.52 355 127 149 22 160.56 39.81 356 127 152 25 160.50 39.81 357 127 153 26 160.42 39.84 358 127 156 29 160.45 39.83 359 128 131 3 608.85 5.07 360 128 132 4 574.85 10.59 361 128 145 17 160.90 39.88 362 128 146 18 160.75 39.84 363 128 149 21 160.56 39.81 364 129 132 3 608.55 1.99 365 129 133 4 574.84 10.59 366 130 134 4 596.74 0.18 367 130 140 10 358.12 16.84 368 131 134 3 596.88 0.12 369 131 135 4 596.77 0.20 370 131 140 9 358.01 16.86 371 131 142 11 195.01 22.92 372 131 145 14 160.95 39.88 373 131 148 17 160.87 39.91 374 131 149 18 160.76 39.86 375 131 152 21 160.83 39.90 376 131 182 51 142.25 42.72 377 131 186 55 125.71 41.41 378 132 135 3 604.30 3.83 379 132 136 4 596.78 0.19 380 133 136 3 598.91 1.26 381 133 137 4 596.77 0.19 382 134 137 3 596.74 0.21 383 134 138 4 596.74 0.21 384 134 139 5 516.32 13.98 385 134 140 6 466.57 10.88 386 135 138 3 584.66 5.79 387 135 140 5 478.03 16.60 388 135 141 6 377.03 26.92 389 135 142 7 377.02 26.93 390 135 145 10 211.62 39.54 391 140 183 43 141.42 42.30 392 140 186 46 125.88 41.38 393 142 145 3 609.90 6.05 394 142 148 6 556.10 5.69 395 142 186 44 130.27 43.62 396 144 147 3 617.52 0.27 397 144 148 4 596.02 1.13 398 145 148 3 617.52 0.27 399 145 149 4 594.82 0.54 400 146 149 3 596.01 1.14 401 146 150 4 596.01 1.14 402 147 150 3 607.12 6.53 403 147 151 4 594.82 0.54 404 148 151 3 593.71 1.56 405 148 152 4 585.24 0.47 406 148 182 34 142.25 42.72 407 148 186 38 107.58 32.37 408 149 152 3 602.67 2.83 409 149 153 4 585.21 0.48 410 150 153 3 597.45 0.46 411 150 154 4 590.35 2.73 412 151 154 3 609.15 4.78 413 151 155 4 590.34 2.73 414 151 182 31 141.97 42.87 415 152 155 3 603.14 4.69 416 152 156 4 591.73 3.43 417 152 182 30 141.18 42.47 418 153 156 3 605.31 0.52 419 153 157 4 592.01 3.23 420 154 157 3 592.01 3.23 421 154 158 4 592.02 3.23 422 155 158 3 592.02 3.23 423 155 159 4 592.05 3.22 424 155 178 23 145.78 43.12 425 156 159 3 608.41 4.96 426 156 160 4 592.06 3.22 427 156 175 19 151.16 41.02 428 156 178 22 145.75 43.11 429 157 160 3 605.23 3.37 430 157 161 4 592.06 3.22 431 158 161 3 611.23 3.56 432 158 162 4 592.03 3.21 433 159 163 4 575.40 7.42 434 159 175 16 151.16 41.02 435 159 178 19 146.27 43.36 436 160 164 4 571.08 11.36 437 160 175 15 151.16 41.02 438 161 164 3 605.50 5.96 439 163 166 3 622.53 1.52 440 163 171 8 391.01 78.83 441 164 171 7 520.78 13.94 442 166 170 4 603.25 4.75 443 166 171 5 572.75 0.07 444 166 174 8 569.97 1.30 445 167 170 3 613.02 6.84 446 167 171 4 591.89 3.73 447 168 171 3 606.04 3.35 448 168 172 4 606.04 3.35 449 169 172 3 606.04 3.35 450 169 173 4 598.47 0.43 451 170 173 3 598.48 0.43 452 170 174 4 598.47 0.43 453 171 174 3 610.46 0.34 454 171 175 4 591.88 1.78 455 172 175 3 602.56 4.29 456 172 176 4 594.71 0.36 457 173 176 3 617.16 2.29 458 173 177 4 594.71 0.36 459 174 177 3 602.46 2.95 460 174 178 4 591.28 2.00 461 175 178 3 603.42 3.73 462 175 179 4 591.28 2.00 463 176 179 3 599.00 5.95 464 176 180 4 589.31 2.98 465 177 180 3 601.03 4.93 466 177 181 4 598.28 6.31 467 178 181 3 603.70 3.60 468 178 182 4 598.87 6.02 469 179 182 3 599.38 0.21 470 179 183 4 591.13 3.91 471 180 183 3 604.97 3.00 472 180 184 4 604.96 2.99 473 181 184 3 604.96 2.99 474 181 185 4 604.96 2.99 475 182 185 3 604.96 2.99 476 182 186 4 604.96 2.99 477 183 186 3 604.96 2.99 478 183 187 4 604.96 2.99