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 3 599.57 3.41 2 3 7 4 598.96 3.11 3 4 7 3 614.95 0.23 4 4 8 4 603.64 1.37 5 4 42 38 47.92 0.48 6 4 43 39 47.53 0.84 7 5 8 3 603.65 1.37 8 5 9 4 603.01 1.06 9 6 9 3 603.02 1.06 10 6 10 4 601.89 1.33 11 7 10 3 610.54 1.83 12 7 11 4 597.91 3.33 13 7 28 21 59.29 2.30 14 7 32 25 59.41 2.32 15 7 34 27 59.41 2.33 16 7 39 32 54.75 2.13 17 7 43 36 50.52 0.12 18 7 49 42 49.52 0.21 19 8 11 3 610.40 1.91 20 8 12 4 598.83 4.29 21 8 43 35 50.53 0.12 22 8 49 41 49.51 0.29 23 8 52 44 48.59 0.34 24 8 53 45 48.09 0.56 25 9 12 3 612.20 0.97 26 9 13 4 603.31 2.04 27 10 13 3 601.95 0.23 28 10 14 4 596.64 2.88 29 10 28 18 59.48 2.31 30 10 31 21 59.93 2.10 31 10 32 22 59.52 2.29 32 11 14 3 603.23 0.41 33 11 15 4 601.84 0.28 34 11 28 17 59.51 2.27 35 11 49 38 51.08 0.07 36 11 53 42 49.16 0.12 37 12 15 3 608.50 1.07 38 12 16 4 603.82 1.27 39 12 53 41 48.59 0.35 40 12 57 45 48.28 0.49 41 13 16 3 612.19 2.41 42 13 17 4 603.82 1.27 43 14 17 3 607.79 0.32 44 14 18 4 593.39 1.25 45 14 23 9 181.27 44.51 46 14 27 13 80.23 0.48 47 14 28 14 71.94 2.29 48 14 31 17 66.29 0.58 49 15 18 3 614.16 1.74 50 15 19 4 568.98 8.50 51 15 20 5 451.50 3.79 52 15 23 8 350.53 6.03 53 15 46 31 59.05 2.54 54 15 50 35 51.60 0.17 55 15 53 38 51.09 0.07 56 15 95 80 48.81 0.24 57 15 98 83 50.47 0.32 58 16 94 78 48.29 0.49 59 16 95 79 50.23 0.48 60 18 22 4 566.12 17.36 61 18 23 5 481.35 15.35 62 19 22 3 595.79 4.57 63 19 23 4 590.88 4.99 64 19 101 82 52.61 0.14 65 20 23 3 629.83 5.75 66 20 46 26 59.37 2.40 67 20 47 27 59.31 2.41 68 20 50 30 57.83 2.23 69 20 98 78 51.73 0.18 70 20 101 81 53.08 0.09 71 20 102 82 56.47 1.60 72 20 105 85 58.69 2.37 73 20 106 86 58.70 2.37 74 21 46 25 59.50 2.40 75 21 101 80 56.55 1.55 76 21 105 84 58.69 2.38 77 23 27 4 601.12 0.46 78 23 46 23 59.40 2.45 79 24 27 3 612.00 1.30 80 24 28 4 603.14 1.14 81 24 46 22 58.97 2.66 82 25 28 3 603.57 0.93 83 25 29 4 601.83 0.35 84 25 46 21 58.90 2.65 85 26 29 3 622.23 1.35 86 26 30 4 601.84 0.34 87 27 30 3 622.23 1.35 88 27 31 4 601.71 0.28 89 28 31 3 619.84 6.65 90 28 32 4 601.65 0.24 91 28 49 21 58.01 2.33 92 29 32 3 623.37 4.88 93 29 33 4 601.65 0.24 94 29 34 5 470.00 1.39 95 29 35 6 440.69 10.94 96 29 36 7 337.72 2.42 97 29 39 10 296.61 12.38 98 30 33 3 593.23 3.14 99 34 38 4 606.84 2.48 100 35 38 3 619.33 3.77 101 35 39 4 627.47 0.30 102 36 39 3 631.52 1.73 103 39 43 4 330.58 6.17 104 39 44 5 300.67 10.01 105 40 43 3 596.44 3.38 106 40 44 4 365.78 32.06 107 42 48 6 516.94 32.55 108 43 49 6 319.65 1.96 109 43 52 9 368.74 20.93 110 45 48 3 610.20 4.25 111 45 49 4 603.03 0.21 112 46 49 3 603.34 0.36 113 46 50 4 603.03 0.21 114 47 50 3 603.34 0.36 115 47 51 4 595.97 3.31 116 47 102 55 192.62 0.95 117 47 106 59 199.45 0.66 118 47 111 64 195.87 0.67 119 48 51 3 603.05 0.21 120 48 52 4 600.93 0.84 121 48 115 67 196.81 1.09 122 49 52 3 602.75 0.10 123 49 53 4 600.88 0.82 124 50 53 3 606.22 2.04 125 50 54 4 600.59 0.67 126 50 98 48 200.59 0.29 127 50 99 49 201.22 0.12 128 50 102 52 203.08 0.27 129 51 54 3 602.34 0.10 130 51 55 4 600.58 0.68 131 51 102 51 203.83 0.06 132 51 111 60 205.65 0.35 133 51 115 64 203.91 0.17 134 51 116 65 202.68 0.18 135 52 55 3 601.47 0.54 136 52 56 4 592.24 4.84 137 53 56 3 596.94 6.69 138 53 57 4 591.61 5.08 139 53 95 42 253.49 1.11 140 54 58 4 596.34 2.30 141 54 95 41 253.47 1.11 142 54 99 45 248.15 0.24 143 54 116 62 211.41 0.88 144 54 119 65 207.37 1.35 145 55 58 3 597.70 2.08 146 55 59 4 601.64 0.10 147 55 119 64 210.00 0.29 148 55 122 67 223.30 7.69 149 56 59 3 604.21 1.19 150 56 60 4 601.66 0.10 151 57 60 3 601.66 0.10 152 57 61 4 595.14 3.17 153 57 91 34 254.03 1.24 154 57 92 35 254.03 1.24 155 57 95 38 254.05 1.24 156 58 61 3 603.12 0.82 157 58 62 4 595.15 3.17 158 58 92 34 254.04 1.25 159 58 119 61 235.94 1.74 160 58 122 64 237.59 0.92 161 58 123 65 225.38 6.99 162 59 62 3 609.49 0.68 163 59 63 4 595.15 3.17 164 60 63 3 601.99 1.79 165 60 64 4 599.95 0.77 166 60 91 31 254.35 1.26 167 61 64 3 601.99 1.78 168 61 65 4 598.28 0.10 169 61 82 21 256.13 1.09 170 61 85 24 255.57 1.09 171 61 86 25 255.36 1.20 172 61 89 28 254.69 1.24 173 61 91 30 254.35 1.26 174 61 92 31 254.34 1.26 175 61 93 32 254.36 1.28 176 62 65 3 602.02 1.77 177 62 66 4 600.03 0.97 178 62 122 60 238.63 0.41 179 62 126 64 238.71 0.38 180 63 66 3 602.55 1.09 181 63 67 4 600.11 0.94 182 64 67 3 604.08 0.23 183 64 68 4 604.95 4.01 184 64 89 25 255.16 1.20 185 64 90 26 255.16 1.20 186 65 68 3 607.94 2.52 187 65 69 4 599.46 1.27 188 65 78 13 258.65 2.19 189 65 81 16 258.47 2.19 190 65 82 17 256.17 1.07 191 65 85 20 255.76 1.18 192 65 126 61 238.79 0.34 193 65 130 65 242.89 1.38 194 66 69 3 616.33 1.26 195 66 70 4 609.85 1.56 196 67 70 3 656.36 4.75 197 68 71 3 630.00 0.23 198 68 81 13 258.72 2.16 199 68 85 17 258.25 2.08 200 69 72 3 625.78 1.88 201 69 78 9 258.92 2.19 202 69 81 12 258.68 2.18 203 71 81 10 359.48 34.09 204 72 77 5 546.12 6.66 205 72 78 6 418.83 4.42 206 72 81 9 392.37 17.65 207 73 77 4 589.14 1.89 208 73 78 5 589.13 1.89 209 74 77 3 597.68 0.68 210 74 78 4 589.14 1.89 211 74 139 65 252.28 1.58 212 75 78 3 589.14 1.89 213 75 79 4 590.96 1.15 214 75 130 55 243.33 1.36 215 75 133 58 249.99 1.54 216 75 134 59 247.19 0.14 217 75 137 62 252.28 1.60 218 75 139 64 252.30 1.59 219 75 140 65 252.29 1.58 220 76 79 3 610.84 4.02 221 76 80 4 596.35 1.05 222 76 139 63 252.28 1.56 223 76 140 64 252.27 1.57 224 76 183 107 230.17 0.65 225 76 184 108 230.17 0.65 226 77 80 3 606.53 0.76 227 77 81 4 596.35 1.05 228 78 81 3 604.99 0.01 229 78 82 4 596.36 1.06 230 78 130 52 243.23 1.32 231 79 82 3 606.86 0.95 232 79 83 4 601.65 3.54 233 79 127 48 242.22 1.07 234 79 130 51 243.22 1.33 235 79 131 52 243.36 1.40 236 79 152 73 240.28 0.22 237 79 178 99 234.65 0.18 238 79 179 100 233.22 0.33 239 79 182 103 230.67 0.54 240 79 183 104 230.16 0.65 241 80 83 3 606.30 1.23 242 80 84 4 596.56 0.94 243 80 176 96 234.94 0.32 244 80 179 99 233.22 0.33 245 80 180 100 233.22 0.33 246 80 183 103 230.19 0.65 247 81 84 3 601.43 1.49 248 81 85 4 601.75 1.67 249 82 85 3 612.08 3.49 250 82 86 4 596.56 4.28 251 82 93 11 362.43 11.20 252 82 126 44 242.16 1.04 253 82 127 45 242.06 0.99 254 82 130 48 243.12 1.32 255 83 86 3 611.32 3.09 256 83 87 4 602.45 1.35 257 83 127 44 242.24 1.05 258 83 156 73 238.23 0.56 259 83 175 92 234.97 0.34 260 83 179 96 233.22 0.33 261 84 87 3 623.80 2.37 262 84 88 4 602.41 1.39 263 84 172 88 235.09 0.39 264 84 175 91 234.97 0.34 265 85 88 3 602.46 1.36 266 85 89 4 596.52 4.31 267 86 89 3 611.08 5.45 268 86 93 7 362.50 11.23 269 86 156 70 238.22 0.57 270 86 160 74 237.59 0.42 271 87 160 73 237.59 0.42 272 87 168 81 235.22 0.42 273 87 171 84 235.16 0.42 274 87 172 85 235.09 0.41 275 87 175 88 235.11 0.41 276 88 172 84 235.08 0.40 277 90 94 4 573.99 1.92 278 91 94 3 626.39 2.85 279 92 95 3 611.84 1.59 280 92 96 4 600.15 0.04 281 92 99 7 569.50 4.56 282 92 123 31 238.77 0.33 283 93 96 3 606.89 0.88 284 93 157 64 237.62 0.32 285 93 160 67 237.50 0.35 286 95 98 3 607.52 0.34 287 95 99 4 594.40 5.42 288 96 99 3 602.31 1.84 289 96 100 4 594.77 5.61 290 96 157 61 237.76 0.35 291 96 161 65 237.55 0.33 292 97 100 3 607.47 0.32 293 97 101 4 602.32 1.84 294 97 161 64 237.72 0.35 295 98 101 3 607.46 0.32 296 98 102 4 597.69 4.15 297 99 102 3 598.32 4.90 298 99 103 4 592.58 6.70 299 100 103 3 597.36 3.96 300 100 104 4 595.01 2.83 301 101 104 3 608.19 0.01 302 101 105 4 595.00 2.83 303 102 106 4 575.73 1.15 304 102 112 10 336.37 8.31 305 102 116 14 270.13 10.46 306 103 107 4 549.08 14.99 307 103 112 9 289.49 15.12 308 103 116 13 268.01 9.42 309 104 107 3 610.61 2.08 310 106 109 3 642.72 1.23 311 106 112 6 419.30 15.25 312 107 112 5 419.31 15.25 313 107 113 6 419.32 15.25 314 109 112 3 627.30 2.60 315 109 113 4 609.09 2.16 316 110 114 4 574.59 5.28 317 111 115 4 407.20 21.27 318 112 116 4 513.08 4.94 319 113 117 4 478.00 22.48 320 114 117 3 568.61 2.27 321 116 119 3 606.43 1.61 322 117 120 3 627.34 3.50 323 117 121 4 609.12 1.49 324 118 121 3 605.59 0.28 325 118 122 4 609.11 1.49 326 119 122 3 619.52 0.29 327 119 123 4 609.11 1.49 328 120 123 3 600.10 6.00 329 120 124 4 599.69 6.20 330 121 124 3 608.79 1.65 331 121 125 4 585.69 5.76 332 122 125 3 601.38 2.06 333 123 127 4 618.81 0.70 334 123 153 30 296.74 6.16 335 123 154 31 296.77 6.17 336 123 157 34 296.74 6.16 337 124 127 3 618.81 0.70 338 124 128 4 597.12 0.20 339 124 149 25 296.99 6.26 340 124 150 26 296.81 6.17 341 124 153 29 296.74 6.16 342 125 128 3 597.12 0.20 343 125 129 4 598.70 0.59 344 126 129 3 616.16 0.63 345 126 130 4 598.70 0.60 346 127 130 3 606.16 4.37 347 127 131 4 598.66 0.62 348 127 149 22 297.20 6.16 349 127 152 25 297.19 6.16 350 127 153 26 297.12 6.12 351 127 156 29 297.14 6.17 352 128 131 3 612.52 3.23 353 128 132 4 597.25 0.07 354 128 145 17 297.42 6.22 355 128 146 18 297.41 6.23 356 128 149 21 297.18 6.16 357 129 132 3 611.00 3.22 358 129 133 4 584.48 6.45 359 130 134 4 584.31 6.37 360 130 140 10 379.79 4.66 361 131 134 3 599.24 1.09 362 131 135 4 596.89 0.07 363 131 140 9 379.71 4.65 364 131 145 14 297.75 6.22 365 131 148 17 297.62 6.15 366 131 149 18 297.57 6.14 367 131 152 21 297.54 6.12 368 131 182 51 232.33 0.29 369 131 186 55 174.59 4.73 370 132 135 3 604.50 3.72 371 132 136 4 582.61 0.47 372 133 136 3 596.41 0.32 373 133 137 4 577.56 3.00 374 134 137 3 588.74 2.59 375 134 138 4 577.48 2.96 376 134 139 5 499.79 6.16 377 134 140 6 487.69 11.45 378 135 138 3 577.47 2.96 379 135 140 5 499.45 5.57 380 135 141 6 417.09 12.32 381 135 142 7 381.45 5.50 382 135 145 10 335.98 1.51 383 140 183 43 230.70 0.39 384 140 187 47 150.91 1.35 385 142 145 3 609.72 6.15 386 142 148 6 533.19 10.34 387 142 186 44 194.43 14.64 388 144 147 3 617.52 0.27 389 144 148 4 577.60 3.10 390 145 148 3 614.35 1.31 391 145 149 4 577.63 3.12 392 146 149 3 591.12 3.57 393 146 150 4 589.32 2.64 394 147 150 3 596.16 1.05 395 147 151 4 590.51 3.25 396 148 151 3 590.53 3.25 397 148 152 4 577.75 3.14 398 148 182 34 230.86 0.45 399 148 186 38 150.97 1.39 400 149 152 3 603.16 2.58 401 149 153 4 581.11 1.46 402 150 153 3 589.62 1.97 403 150 154 4 591.24 3.56 404 151 154 3 609.16 4.78 405 151 155 4 581.39 1.60 406 151 182 31 230.68 0.54 407 152 155 3 599.16 6.67 408 152 156 4 591.53 3.46 409 152 182 30 230.66 0.54 410 153 156 3 606.38 1.05 411 153 157 4 592.06 3.21 412 154 157 3 592.14 3.16 413 154 158 4 592.06 3.21 414 155 158 3 596.63 0.92 415 155 159 4 592.06 3.21 416 155 178 23 234.73 0.21 417 156 159 3 608.39 4.98 418 156 160 4 592.03 3.21 419 156 175 19 235.16 0.41 420 156 178 22 234.63 0.18 421 157 160 3 608.39 4.97 422 157 161 4 592.02 3.21 423 158 161 3 611.23 3.56 424 158 162 4 587.96 1.20 425 159 163 4 581.24 4.51 426 159 175 16 235.16 0.41 427 159 178 19 234.66 0.18 428 160 164 4 579.08 2.51 429 160 171 11 235.21 0.42 430 160 175 15 235.15 0.41 431 161 164 3 612.31 0.58 432 163 166 3 625.76 0.64 433 163 171 8 324.17 5.73 434 164 171 7 543.85 13.68 435 166 171 5 581.34 4.88 436 166 174 8 569.43 1.39 437 167 170 3 610.95 7.87 438 167 171 4 581.88 4.63 439 168 171 3 589.43 2.50 440 168 172 4 595.66 0.97 441 169 172 3 603.94 4.41 442 169 173 4 598.33 0.36 443 170 173 3 608.38 1.38 444 170 174 4 591.00 4.03 445 171 174 3 602.30 4.42 446 171 175 4 589.86 4.60 447 172 175 3 602.55 4.29 448 172 176 4 593.39 2.83 449 173 176 3 605.58 1.39 450 173 177 4 582.94 3.47 451 174 177 3 599.81 4.28 452 174 178 4 583.31 3.66 453 175 178 3 600.75 5.06 454 175 179 4 600.76 5.07 455 176 179 3 605.06 2.92 456 176 180 4 600.83 5.03 457 177 180 3 604.93 2.99 458 177 181 4 600.84 5.04 459 178 181 3 600.94 4.99 460 178 182 4 600.84 5.04 461 179 182 3 596.75 1.53 462 179 183 4 586.70 2.04 463 180 183 3 602.32 4.31 464 180 184 4 600.81 5.07 465 181 184 3 603.67 3.64 466 181 185 4 600.44 5.25 467 182 185 3 604.93 3.01 468 182 186 4 604.18 3.38 469 183 186 3 599.81 1.20 470 183 187 4 584.83 1.04