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 3 616.52 2.75 2 3 7 4 608.14 1.43 3 3 34 31 54.20 0.81 4 3 38 35 56.00 0.96 5 4 7 3 605.62 3.54 6 4 8 4 603.07 3.97 7 4 42 38 50.66 1.59 8 4 43 39 50.72 1.62 9 5 8 3 621.04 0.76 10 6 9 3 592.93 1.06 11 6 10 4 583.36 3.72 12 6 32 26 61.04 0.71 13 7 10 3 602.32 0.95 14 7 11 4 572.39 0.14 15 7 28 21 59.84 0.15 16 7 32 25 61.79 0.35 17 7 34 27 61.79 0.35 18 7 39 32 60.02 0.20 19 7 43 36 59.87 0.18 20 8 11 3 590.84 2.07 21 8 12 4 566.15 2.37 22 8 43 35 60.05 0.21 23 8 49 41 55.94 0.38 24 8 52 44 55.91 0.40 25 8 53 45 51.27 1.90 26 10 13 3 626.56 2.84 27 10 14 4 582.37 3.33 28 10 31 21 62.29 0.32 29 10 32 22 62.26 0.33 30 11 14 3 593.25 2.00 31 11 15 4 582.50 3.37 32 11 28 17 62.14 0.26 33 11 49 38 60.13 0.26 34 11 53 42 60.06 0.28 35 12 15 3 610.66 2.15 36 12 16 4 599.27 2.73 37 12 53 41 60.07 0.28 38 12 57 45 60.04 0.28 39 12 90 78 60.02 0.29 40 12 91 79 59.97 0.26 41 12 95 83 60.01 0.27 42 13 16 3 603.28 0.73 43 13 17 4 582.44 3.33 44 14 17 3 600.04 0.89 45 14 18 4 576.70 6.19 46 14 19 5 576.67 6.20 47 14 23 9 100.06 3.50 48 14 27 13 73.74 1.08 49 14 28 14 69.88 0.59 50 14 31 17 71.21 0.10 51 15 19 4 530.74 5.60 52 15 20 5 526.88 3.67 53 15 23 8 101.23 2.08 54 15 46 31 63.00 0.71 55 15 49 34 61.86 0.17 56 15 50 35 60.92 0.07 57 15 53 38 60.90 0.07 58 15 98 83 60.12 0.27 59 16 19 3 595.28 4.49 60 16 94 78 60.02 0.27 61 16 95 79 60.02 0.27 62 18 22 4 546.48 8.85 63 18 23 5 497.16 8.64 64 19 22 3 605.15 0.32 65 19 23 4 590.13 1.52 66 19 101 82 61.66 0.28 67 20 23 3 627.33 3.34 68 20 46 26 63.13 0.70 69 20 47 27 63.02 0.69 70 20 50 30 61.87 0.20 71 20 98 78 60.94 0.05 72 20 101 81 61.67 0.28 73 20 102 82 61.80 0.23 74 20 105 85 62.76 0.58 75 20 106 86 62.92 0.68 76 21 101 80 62.14 0.42 77 21 105 84 62.77 0.58 78 22 27 5 599.11 2.68 79 23 27 4 599.10 2.68 80 23 46 23 63.10 0.73 81 24 27 3 599.10 2.68 82 24 28 4 599.11 2.68 83 24 46 22 63.07 0.76 84 25 28 3 612.37 0.12 85 25 29 4 601.77 1.35 86 25 46 21 63.07 0.76 87 26 29 3 601.75 1.34 88 26 30 4 598.84 2.79 89 27 30 3 602.38 1.09 90 27 31 4 598.62 0.78 91 28 31 3 618.74 0.96 92 28 32 4 591.31 2.73 93 28 49 21 62.94 0.76 94 29 32 3 599.28 0.59 95 29 33 4 587.79 5.54 96 29 34 5 498.81 18.28 97 29 35 6 489.77 22.80 98 29 36 7 279.11 79.92 99 29 39 10 92.81 5.49 100 30 33 3 602.37 1.09 101 34 38 4 592.93 2.87 102 35 38 3 603.19 1.80 103 35 39 4 612.32 5.84 104 36 39 3 632.86 3.81 105 37 40 3 623.71 0.15 106 38 42 4 594.09 3.27 107 39 42 3 601.63 0.75 108 39 43 4 549.26 1.73 109 40 43 3 593.42 1.83 110 40 44 4 478.19 24.03 111 43 48 5 581.62 7.50 112 43 49 6 445.91 0.26 113 44 48 4 592.20 2.24 114 45 48 3 602.71 1.36 115 45 49 4 598.04 0.97 116 46 49 3 598.05 0.97 117 46 50 4 598.04 0.97 118 47 50 3 598.03 0.97 119 47 51 4 596.38 0.14 120 47 102 55 378.12 0.01 121 47 106 59 378.20 0.04 122 48 51 3 596.38 0.14 123 48 52 4 602.72 2.46 124 49 52 3 602.75 2.48 125 49 53 4 602.75 2.47 126 50 53 3 622.78 1.27 127 50 54 4 609.00 0.66 128 50 98 48 384.47 0.45 129 50 99 49 384.45 0.43 130 50 102 52 384.41 0.45 131 51 54 3 617.41 1.42 132 51 55 4 609.02 0.67 133 51 102 51 384.46 0.43 134 51 115 64 382.46 0.23 135 51 116 65 380.52 0.59 136 52 55 3 609.44 0.47 137 52 56 4 603.66 3.35 138 53 56 3 603.67 3.35 139 53 57 4 603.36 3.50 140 53 95 42 384.94 0.58 141 54 57 3 604.22 3.06 142 54 58 4 594.47 0.86 143 54 95 41 384.95 0.58 144 54 99 45 384.63 0.45 145 54 116 62 384.30 0.42 146 54 119 65 384.19 0.40 147 55 58 3 605.00 2.68 148 55 59 4 590.38 1.51 149 55 118 63 384.28 0.42 150 55 119 64 384.14 0.41 151 55 122 67 384.19 0.42 152 56 59 3 597.91 0.80 153 56 60 4 590.38 1.51 154 57 60 3 597.87 0.82 155 57 61 4 590.38 1.51 156 57 91 34 385.11 0.59 157 57 92 35 385.05 0.58 158 57 95 38 385.05 0.58 159 58 62 4 597.59 5.96 160 58 92 34 385.09 0.60 161 58 119 61 384.28 0.42 162 58 122 64 384.25 0.42 163 58 123 65 384.17 0.40 164 59 62 3 609.04 0.24 165 59 63 4 604.27 2.62 166 59 122 63 384.26 0.42 167 60 63 3 609.16 0.18 168 60 64 4 600.97 0.97 169 60 91 31 385.76 0.39 170 61 64 3 609.03 0.24 171 61 65 4 603.49 3.01 172 61 82 21 386.37 0.26 173 61 85 24 386.30 0.29 174 61 86 25 386.25 0.31 175 61 89 28 386.00 0.39 176 61 91 30 385.76 0.39 177 61 93 32 385.76 0.39 178 62 65 3 606.84 0.85 179 62 66 4 597.85 1.09 180 62 126 64 383.44 0.42 181 63 66 3 598.97 0.54 182 63 67 4 597.87 1.08 183 64 67 3 612.26 4.78 184 64 68 4 597.88 1.08 185 64 89 25 386.23 0.31 186 64 90 26 386.19 0.29 187 65 68 3 606.02 1.68 188 65 69 4 597.38 0.84 189 65 78 13 386.70 0.27 190 65 81 16 386.54 0.29 191 65 82 17 386.39 0.24 192 65 85 20 386.35 0.28 193 65 130 65 383.32 0.41 194 66 69 3 607.35 4.13 195 66 70 4 598.08 0.51 196 68 71 3 625.75 9.18 197 68 85 17 386.51 0.29 198 69 72 3 610.20 1.53 199 69 78 9 386.70 0.28 200 69 81 12 386.66 0.28 201 71 81 10 412.57 13.14 202 72 77 5 528.70 1.07 203 72 78 6 516.24 0.82 204 72 81 9 412.57 13.14 205 73 77 4 583.53 1.27 206 73 78 5 581.01 1.74 207 74 77 3 600.34 1.27 208 74 78 4 581.62 1.44 209 74 139 65 343.73 0.66 210 75 78 3 591.94 5.46 211 75 79 4 583.73 0.70 212 75 130 55 383.44 0.45 213 75 133 58 383.17 0.40 214 75 134 59 372.48 3.50 215 75 137 62 345.47 0.81 216 75 139 64 340.00 1.21 217 75 140 65 343.70 0.65 218 76 79 3 602.18 0.35 219 76 80 4 600.11 0.69 220 76 139 63 339.99 1.21 221 76 140 64 339.97 1.20 222 76 183 107 208.94 1.39 223 77 80 3 602.57 1.92 224 77 81 4 600.10 0.70 225 78 81 3 606.71 3.58 226 78 82 4 600.10 0.70 227 78 130 52 383.42 0.45 228 79 82 3 607.10 1.16 229 79 83 4 607.08 1.16 230 79 127 48 384.36 0.48 231 79 130 51 383.42 0.45 232 79 131 52 383.34 0.41 233 79 152 73 222.79 0.48 234 79 179 100 212.33 1.91 235 79 182 103 209.07 1.43 236 79 183 104 208.81 1.42 237 80 83 3 626.18 2.48 238 80 84 4 599.46 1.01 239 80 176 96 218.28 0.68 240 80 179 99 212.33 1.91 241 80 180 100 212.33 1.91 242 80 183 103 208.84 1.44 243 81 84 3 601.11 1.83 244 81 85 4 596.42 0.47 245 82 85 3 622.52 4.38 246 82 86 4 615.70 7.78 247 82 126 44 384.34 0.47 248 82 127 45 384.32 0.47 249 83 86 3 622.52 4.38 250 83 87 4 618.94 6.16 251 83 127 44 384.37 0.48 252 83 156 73 221.74 0.66 253 83 175 92 218.38 0.66 254 83 179 96 212.33 1.91 255 84 87 3 624.53 3.38 256 84 175 91 218.41 0.67 257 84 176 92 218.36 0.67 258 85 88 3 606.09 1.67 259 85 89 4 587.45 2.50 260 86 89 3 625.16 5.36 261 86 93 7 386.31 0.33 262 86 160 74 219.40 0.58 263 87 160 73 219.40 0.57 264 87 171 84 218.49 0.67 265 87 172 85 218.44 0.67 266 87 175 88 218.43 0.67 267 88 168 80 218.52 0.69 268 90 94 4 596.13 1.22 269 91 94 3 629.20 0.26 270 92 95 3 623.00 2.15 271 92 96 4 602.82 0.61 272 92 123 31 384.24 0.41 273 93 96 3 612.12 4.30 274 93 160 67 218.99 0.57 275 95 98 3 613.07 5.84 276 95 99 4 588.33 1.31 277 96 99 3 600.19 0.58 278 96 100 4 588.34 1.31 279 96 157 61 219.03 0.59 280 96 161 65 218.95 0.56 281 97 100 3 593.54 3.91 282 97 101 4 604.57 6.80 283 97 161 64 218.94 0.56 284 98 101 3 609.77 4.21 285 98 102 4 604.57 6.81 286 99 102 3 610.12 4.04 287 99 103 4 604.53 6.83 288 100 103 3 615.77 1.21 289 100 104 4 604.47 6.86 290 101 104 3 608.94 4.86 291 101 105 4 594.90 2.12 292 102 105 3 595.36 1.95 293 102 106 4 592.92 3.12 294 102 112 10 385.66 0.10 295 102 116 14 384.91 0.46 296 103 107 4 584.84 7.14 297 103 112 9 384.94 0.42 298 103 113 10 385.64 0.09 299 104 107 3 604.67 2.71 300 106 109 3 614.25 2.08 301 106 112 6 386.06 0.10 302 107 112 5 455.18 0.55 303 109 112 3 626.08 2.75 304 110 114 4 575.58 5.21 305 111 114 3 595.86 2.64 306 111 115 4 571.85 0.64 307 112 115 3 618.59 0.23 308 112 116 4 554.59 9.26 309 113 116 3 588.89 14.62 310 113 117 4 556.20 10.06 311 115 118 3 606.23 3.45 312 116 119 3 601.43 1.07 313 116 120 4 586.13 1.54 314 117 120 3 586.12 1.54 315 117 121 4 593.51 2.15 316 118 121 3 611.78 5.32 317 118 122 4 587.72 5.05 318 119 122 3 594.90 1.46 319 119 123 4 587.72 5.05 320 120 123 3 600.24 5.68 321 120 124 4 587.71 5.05 322 120 150 30 222.50 0.48 323 121 124 3 611.64 3.23 324 121 125 4 586.34 2.63 325 122 125 3 614.90 0.67 326 123 126 3 632.44 0.20 327 123 153 30 222.03 0.57 328 123 154 31 222.03 0.57 329 123 157 34 221.59 0.79 330 124 127 3 613.00 2.54 331 124 128 4 598.45 3.25 332 124 146 22 222.81 0.52 333 124 149 25 222.55 0.46 334 124 150 26 222.52 0.47 335 124 153 29 222.03 0.58 336 125 128 3 598.54 3.30 337 125 129 4 597.65 1.79 338 126 129 3 620.14 1.04 339 126 130 4 598.89 2.41 340 127 130 3 611.49 3.29 341 127 131 4 598.89 2.42 342 127 149 22 222.66 0.47 343 127 152 25 222.65 0.47 344 127 153 26 222.54 0.48 345 127 156 29 222.58 0.49 346 128 131 3 610.57 1.32 347 128 132 4 598.89 2.42 348 128 145 17 222.94 0.57 349 128 146 18 222.94 0.57 350 128 149 21 222.66 0.48 351 129 132 3 602.09 1.42 352 129 133 4 583.43 2.98 353 130 133 3 614.05 0.03 354 130 134 4 586.00 3.29 355 130 140 10 437.70 2.38 356 131 134 3 591.74 3.77 357 131 135 4 586.02 3.31 358 131 140 9 421.18 5.89 359 131 142 11 229.45 2.58 360 131 145 14 223.02 0.56 361 131 148 17 222.99 0.56 362 131 149 18 222.96 0.57 363 131 152 21 222.96 0.56 364 131 182 51 208.99 1.38 365 131 186 55 177.16 1.52 366 132 135 3 598.57 1.47 367 132 136 4 599.45 1.92 368 132 145 13 223.01 0.57 369 133 136 3 599.82 0.84 370 133 137 4 585.08 3.77 371 134 137 3 590.83 5.07 372 134 138 4 585.06 3.78 373 134 139 5 498.58 11.76 374 134 140 6 450.56 4.05 375 135 138 3 586.09 2.27 376 135 140 5 476.42 9.39 377 135 141 6 373.23 18.08 378 135 142 7 339.50 1.35 379 135 145 10 267.76 14.41 380 140 183 43 208.97 1.38 381 142 145 3 588.62 6.02 382 142 148 6 535.53 14.13 383 142 186 44 177.89 0.91 384 144 147 3 614.53 6.12 385 144 148 4 604.28 0.98 386 145 148 3 604.29 0.98 387 145 149 4 604.28 0.98 388 146 149 3 604.29 0.98 389 146 150 4 604.29 0.98 390 147 150 3 620.29 3.23 391 147 151 4 602.59 0.12 392 148 151 3 602.59 0.12 393 148 152 4 602.59 0.12 394 148 182 34 208.95 1.38 395 148 186 38 174.05 2.83 396 149 152 3 602.60 0.12 397 149 153 4 602.59 0.12 398 150 153 3 602.59 0.12 399 150 154 4 602.13 0.11 400 151 154 3 614.58 6.11 401 151 155 4 591.10 0.60 402 151 182 31 208.88 1.36 403 152 155 3 606.40 2.02 404 152 156 4 591.32 0.70 405 152 182 30 208.78 1.41 406 153 156 3 605.44 2.26 407 153 157 4 591.33 0.71 408 154 157 3 591.35 0.70 409 154 158 4 591.32 0.71 410 155 158 3 599.95 5.00 411 155 159 4 591.34 0.72 412 155 178 23 212.38 1.92 413 156 159 3 592.86 1.52 414 156 160 4 591.23 0.70 415 156 175 19 218.38 0.64 416 156 178 22 212.39 1.91 417 157 160 3 601.76 2.79 418 157 161 4 586.93 1.38 419 158 161 3 600.40 2.11 420 158 162 4 569.08 3.95 421 159 163 4 581.78 10.30 422 159 175 16 218.38 0.64 423 159 178 19 212.81 2.12 424 160 163 3 627.27 1.27 425 160 164 4 598.18 3.31 426 160 171 11 218.50 0.67 427 160 175 15 218.41 0.66 428 161 164 3 627.26 1.27 429 163 166 3 632.88 3.15 430 163 171 8 222.12 1.09 431 163 174 11 218.48 0.67 432 164 171 7 470.42 3.03 433 166 171 5 564.67 0.39 434 167 170 3 615.71 5.83 435 167 171 4 599.74 2.76 436 168 171 3 608.64 0.35 437 168 172 4 599.74 2.75 438 169 172 3 612.25 1.45 439 169 173 4 588.60 6.45 440 170 173 3 588.61 6.45 441 170 174 4 588.70 6.50 442 171 174 3 603.03 0.67 443 171 175 4 583.66 9.02 444 172 175 3 597.63 10.81 445 172 176 4 594.74 3.50 446 173 176 3 600.02 0.86 447 173 177 4 594.75 3.50 448 174 177 3 602.66 0.39 449 174 178 4 598.47 1.67 450 175 178 3 606.11 4.34 451 175 179 4 604.97 4.92 452 176 179 3 601.33 6.74 453 176 180 4 594.83 3.48 454 177 180 3 596.86 2.47 455 177 181 4 594.83 3.48 456 178 181 3 611.50 5.66 457 178 182 4 591.43 1.81 458 179 182 3 612.14 5.33 459 179 183 4 591.44 1.81 460 180 183 3 606.10 2.10 461 180 184 4 591.43 1.81 462 181 184 3 605.78 2.26 463 181 185 4 605.76 2.27 464 182 185 3 617.41 2.06 465 182 186 4 606.41 0.90 466 183 186 3 617.40 2.06 467 183 187 4 608.92 2.18 468 184 187 3 617.56 2.73