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 83 81 376.20 0.95 2 2 150 148 94.20 0.45 3 3 83 80 376.56 0.77 4 3 84 81 376.58 0.76 5 3 150 147 94.39 0.45 6 4 84 80 376.59 0.76 7 4 85 81 376.58 0.76 8 4 150 146 94.43 0.46 9 4 153 149 94.37 0.45 10 4 154 150 94.23 0.47 11 5 83 78 376.72 0.73 12 5 85 80 376.61 0.75 13 5 87 82 376.58 0.75 14 5 143 138 95.67 0.50 15 5 146 141 95.33 0.44 16 5 147 142 95.23 0.42 17 5 150 145 94.64 0.57 18 5 161 156 93.91 0.45 19 6 61 55 378.17 0.69 20 6 82 76 377.56 0.69 21 6 83 77 377.26 0.77 22 6 85 79 376.91 0.62 23 6 86 80 376.60 0.74 24 6 87 81 376.60 0.74 25 6 147 141 95.25 0.42 26 7 87 80 376.60 0.74 27 7 140 133 95.91 0.49 28 7 143 136 95.67 0.50 29 7 144 137 95.67 0.50 30 7 147 140 95.33 0.43 31 8 13 5 616.95 1.53 32 8 14 6 594.68 9.58 33 8 17 9 496.56 7.04 34 8 62 54 378.17 0.69 35 8 86 78 377.30 0.76 36 8 87 79 376.71 0.70 37 8 88 80 376.58 0.75 38 8 89 81 376.58 0.75 39 9 14 5 617.22 1.68 40 9 89 80 376.58 0.74 41 9 92 83 353.23 4.12 42 10 13 3 641.27 0.62 43 10 14 4 621.68 0.58 44 11 14 3 632.68 4.92 45 11 15 4 621.68 0.58 46 11 94 83 323.13 2.18 47 11 97 86 254.62 22.87 48 12 15 3 634.15 0.12 49 12 16 4 621.68 0.58 50 13 16 3 624.36 0.77 51 13 17 4 621.65 0.59 52 13 60 47 379.86 1.42 53 14 17 3 627.20 3.36 54 14 18 4 620.35 0.07 55 14 88 74 377.61 0.67 56 14 89 75 377.60 0.67 57 14 97 83 254.62 22.86 58 15 18 3 631.97 1.22 59 15 94 79 351.75 2.81 60 15 96 81 254.63 22.84 61 15 97 82 254.62 22.86 62 15 100 85 252.88 22.59 63 16 19 3 637.13 1.36 64 16 22 6 512.37 0.47 65 16 56 40 381.40 1.32 66 16 57 41 381.39 1.32 67 16 60 44 381.31 1.36 68 17 23 6 494.29 6.33 69 17 26 9 478.65 1.49 70 17 62 45 381.20 1.39 71 17 86 69 378.07 0.67 72 17 88 71 377.78 0.68 73 18 23 5 572.78 0.95 74 18 97 79 254.63 22.84 75 18 100 82 252.85 22.59 76 19 22 3 629.24 2.00 77 19 23 4 613.04 3.51 78 19 53 34 452.59 0.04 79 20 23 3 638.06 0.75 80 20 24 4 617.84 1.12 81 21 24 3 619.29 1.84 82 21 25 4 613.06 3.52 83 21 43 22 465.33 1.77 84 21 45 24 465.18 1.77 85 21 53 32 456.34 1.76 86 22 25 3 629.19 5.36 87 22 26 4 611.58 4.25 88 22 53 31 460.98 0.57 89 22 56 34 456.34 1.76 90 22 57 35 452.85 0.01 91 23 26 3 623.52 2.63 92 23 27 4 610.99 3.95 93 24 27 3 622.63 1.43 94 24 28 4 619.11 0.10 95 24 43 19 465.88 1.70 96 25 28 3 629.24 0.25 97 25 29 4 619.85 0.26 98 25 39 14 466.02 1.62 99 25 43 18 466.38 1.80 100 25 50 25 465.61 1.83 101 25 53 28 465.47 1.77 102 25 54 29 465.41 1.75 103 25 57 32 465.37 1.77 104 26 29 3 629.24 0.25 105 26 30 4 625.06 2.35 106 26 57 31 465.36 1.77 107 26 62 36 464.85 1.58 108 26 63 37 465.26 1.79 109 26 81 55 464.16 1.50 110 26 86 60 378.68 0.84 111 27 30 3 647.94 1.20 112 27 81 54 464.69 1.59 113 28 31 3 642.88 1.33 114 28 39 11 466.43 1.77 115 28 42 14 466.47 1.78 116 28 43 15 466.47 1.78 117 29 32 3 622.41 0.23 118 29 33 4 583.10 5.88 119 29 34 5 567.15 1.66 120 29 39 10 466.47 1.78 121 29 63 34 465.38 1.79 122 29 79 50 465.39 1.78 123 29 80 51 465.15 1.84 124 29 81 52 464.63 1.62 125 30 81 51 465.26 1.79 126 30 84 54 436.80 0.10 127 30 162 132 93.88 0.48 128 32 38 6 613.73 2.70 129 33 66 33 465.73 1.80 130 33 67 34 465.81 1.77 131 33 78 45 465.76 1.79 132 33 79 46 465.50 1.79 133 33 80 47 465.30 1.85 134 34 38 4 618.92 0.10 135 34 39 5 606.17 1.06 136 34 78 44 465.78 1.79 137 34 79 45 465.51 1.79 138 35 38 3 630.08 2.68 139 35 39 4 621.11 0.99 140 35 71 36 466.81 1.71 141 35 76 41 466.01 1.83 142 35 77 42 466.00 1.84 143 35 78 43 465.84 1.79 144 36 39 3 634.79 3.76 145 36 40 4 619.65 0.97 146 36 47 11 466.89 1.76 147 36 50 14 466.66 1.75 148 36 51 15 466.39 1.88 149 36 79 43 466.00 1.83 150 37 40 3 633.27 5.09 151 37 41 4 621.12 0.98 152 37 76 39 466.32 1.86 153 38 41 3 646.60 1.56 154 38 42 4 620.46 1.31 155 38 71 33 466.84 1.73 156 38 78 40 466.06 1.80 157 39 42 3 635.18 4.15 158 39 43 4 606.06 1.05 159 39 50 11 466.88 1.76 160 39 54 15 466.36 1.88 161 40 44 4 569.27 2.62 162 40 45 5 467.49 1.50 163 40 46 6 467.49 1.50 164 40 47 7 467.00 1.73 165 40 50 10 466.80 1.72 166 43 50 7 546.56 13.92 167 45 49 4 625.61 0.14 168 45 50 5 614.35 5.37 169 46 49 3 637.96 4.47 170 46 50 4 625.66 0.17 171 47 50 3 640.14 3.38 172 47 51 4 625.66 0.17 173 48 51 3 640.14 3.39 174 48 52 4 637.06 4.92 175 49 52 3 635.01 0.26 176 49 53 4 625.71 0.21 177 50 53 3 628.43 0.43 178 50 54 4 625.68 0.23 179 51 54 3 642.89 2.96 180 51 55 4 625.65 0.24 181 52 55 3 631.56 2.70 182 52 56 4 619.38 3.39 183 53 56 3 627.05 0.18 184 53 57 4 618.23 3.96 185 54 57 3 618.27 3.94 186 54 58 4 604.36 3.12 187 54 63 9 468.10 1.91 188 54 79 25 467.47 1.77 189 55 58 3 622.05 0.54 190 55 59 4 613.19 1.30 191 56 59 3 639.94 4.17 192 56 60 4 615.77 2.60 193 57 60 3 634.62 6.83 194 57 61 4 615.77 2.60 195 57 62 5 526.54 1.73 196 57 63 6 526.53 1.73 197 58 61 3 607.18 1.70 198 58 63 5 470.71 3.21 199 58 65 7 470.69 3.20 200 58 77 19 468.45 2.08 201 58 79 21 468.06 1.89 202 61 82 21 467.79 1.91 203 62 81 19 467.81 1.92 204 62 82 20 467.78 1.91 205 62 86 24 466.93 1.77 206 63 79 16 468.56 2.05 207 63 80 17 467.83 1.93 208 63 81 18 467.81 1.92 209 63 82 19 467.81 1.92 210 64 79 15 468.64 2.02 211 64 80 16 468.40 1.97 212 64 82 18 468.10 2.06 213 65 68 3 691.86 3.85 214 65 77 12 468.79 1.99 215 65 78 13 468.69 2.02 216 65 79 14 468.64 2.02 217 66 78 12 468.75 2.02 218 66 79 13 468.69 2.02 219 66 80 14 468.67 2.01 220 66 81 15 468.69 2.02 221 67 77 10 469.01 1.98 222 67 78 11 468.81 2.00 223 68 75 7 469.46 1.95 224 68 76 8 469.25 2.02 225 68 77 9 469.00 1.98 226 69 75 6 469.49 1.94 227 69 76 7 469.29 2.02 228 69 78 9 469.21 2.00 229 70 73 3 688.03 2.19 230 70 74 4 546.97 14.05 231 70 75 5 469.49 1.94 232 71 74 3 630.22 1.11 233 71 76 5 496.12 11.38 234 71 78 7 496.16 11.36 235 81 84 3 662.15 0.74 236 81 85 4 654.16 0.14 237 81 86 5 643.38 3.00 238 82 86 4 661.12 2.20 239 83 86 3 663.48 1.02 240 84 158 74 93.86 0.48 241 85 158 73 93.97 0.46 242 85 162 77 93.86 0.48 243 87 139 52 95.92 0.48 244 87 143 56 95.70 0.51 245 87 162 75 93.94 0.45 246 87 165 78 93.93 0.45 247 88 136 48 96.61 0.34 248 88 140 52 95.94 0.48 249 89 92 3 647.36 1.22 250 89 97 8 254.60 22.86 251 89 140 51 95.94 0.48 252 90 97 7 254.59 22.86 253 90 101 11 252.69 22.66 254 90 104 14 252.70 22.66 255 90 136 46 96.87 0.22 256 91 98 7 253.98 23.16 257 91 101 10 252.89 22.62 258 91 105 14 252.89 22.62 259 91 129 38 126.00 0.15 260 91 132 41 109.98 2.85 261 91 133 42 97.30 0.10 262 91 136 45 97.24 0.09 263 94 97 3 619.32 0.42 264 94 98 4 610.72 3.88 265 95 98 3 622.69 2.11 266 95 99 4 619.86 1.60 267 96 99 3 635.34 2.19 268 96 100 4 614.56 4.26 269 97 100 3 628.19 5.76 270 97 101 4 614.57 4.26 271 98 101 3 627.18 0.14 272 98 102 4 614.56 4.26 273 98 129 31 130.06 0.36 274 99 102 3 614.56 4.26 275 99 103 4 614.56 4.26 276 100 103 3 636.23 4.41 277 100 104 4 606.60 0.29 278 101 104 3 633.57 5.75 279 101 105 4 606.60 0.30 280 102 105 3 623.45 0.23 281 102 106 4 614.34 4.20 282 102 125 23 130.93 0.52 283 102 126 24 130.91 0.53 284 102 129 27 130.15 0.33 285 103 106 3 619.39 4.11 286 103 107 4 616.31 5.65 287 104 107 3 644.78 5.39 288 104 108 4 622.14 2.73 289 104 136 32 129.95 0.39 290 105 108 3 624.38 1.60 291 105 109 4 622.02 0.36 292 105 125 20 131.16 0.41 293 105 128 23 130.81 0.52 294 105 129 24 130.68 0.56 295 105 132 27 130.53 0.57 296 106 109 3 622.12 0.40 297 106 110 4 622.00 0.35 298 106 125 19 131.28 0.43 299 107 110 3 629.12 2.39 300 107 111 4 624.17 1.42 301 108 111 3 629.49 1.24 302 108 112 4 624.16 1.42 303 108 128 20 131.66 0.28 304 109 112 3 632.89 0.46 305 109 113 4 627.57 3.12 306 109 119 10 324.97 73.58 307 109 121 12 137.20 2.14 308 109 124 15 137.00 2.22 309 109 125 16 131.85 0.34 310 109 128 19 131.65 0.27 311 110 113 3 640.90 0.80 312 110 114 4 607.92 0.23 313 111 114 3 626.73 1.95 314 111 115 4 607.91 0.22 315 112 115 3 614.68 2.00 316 112 116 4 604.73 1.36 317 112 117 5 572.84 6.92 318 112 119 7 560.29 0.66 319 112 124 12 157.71 3.08 320 112 128 16 151.63 0.98 321 112 190 78 44.40 1.01 322 113 116 3 604.73 1.36 323 113 117 4 578.10 4.30 324 113 119 6 567.63 9.53 325 113 121 8 324.97 73.56 326 116 192 76 44.26 0.97 327 117 190 73 44.86 1.02 328 117 191 74 44.59 0.95 329 117 192 75 43.30 0.51 330 118 191 73 44.87 1.03 331 119 124 5 610.35 1.58 332 119 189 70 45.12 0.94 333 119 190 71 44.95 1.02 334 120 123 3 638.93 1.57 335 120 124 4 612.52 0.51 336 121 124 3 623.10 3.68 337 121 125 4 612.51 0.51 338 122 125 3 624.74 2.86 339 122 126 4 610.37 1.59 340 123 126 3 623.82 0.07 341 123 127 4 615.58 4.19 342 123 185 62 50.48 0.60 343 123 189 66 45.09 0.96 344 124 127 3 626.07 3.77 345 124 128 4 613.12 5.42 346 124 186 62 47.77 0.55 347 124 189 65 44.66 0.92 348 124 190 66 44.26 0.98 349 125 128 3 620.64 1.69 350 125 129 4 613.08 5.45 351 126 129 3 617.79 3.12 352 126 130 4 613.07 5.45 353 127 130 3 631.76 4.98 354 127 131 4 597.73 1.22 355 127 182 55 50.77 0.59 356 127 185 58 48.73 0.27 357 127 186 59 47.48 0.35 358 127 189 62 44.92 1.01 359 128 131 3 631.74 4.99 360 128 132 4 606.88 7.43 361 129 132 3 616.64 2.56 362 129 133 4 596.14 2.06 363 130 133 3 620.45 2.98 364 130 134 4 618.97 3.73 365 130 182 52 50.90 0.66 366 131 134 3 630.78 0.77 367 131 135 4 609.86 8.28 368 131 179 48 56.62 0.07 369 131 182 51 50.48 0.46 370 131 183 52 50.47 0.45 371 131 186 55 45.30 0.87 372 132 135 3 628.06 6.13 373 132 136 4 596.91 1.82 374 133 136 3 627.85 0.70 375 133 137 4 627.72 0.78 376 134 137 3 632.31 3.01 377 134 138 4 627.72 0.78 378 134 173 39 80.73 0.34 379 134 176 42 77.14 0.39 380 134 178 44 62.41 1.81 381 134 179 45 54.06 1.34 382 135 138 3 637.47 2.60 383 135 139 4 612.09 7.05 384 135 173 38 80.59 0.33 385 135 179 44 54.06 1.34 386 136 139 3 634.18 0.97 387 136 140 4 616.37 4.92 388 137 140 3 618.33 3.94 389 137 141 4 620.07 3.08 390 138 141 3 620.08 3.08 391 138 142 4 622.38 1.93 392 138 169 31 83.89 0.29 393 138 172 34 80.59 0.34 394 138 173 35 80.58 0.34 395 139 142 3 644.63 5.11 396 139 143 4 620.08 3.08 397 139 165 26 93.95 0.45 398 139 169 30 83.84 0.32 399 140 143 3 641.51 5.36 400 140 144 4 622.39 1.93 401 141 144 3 633.02 1.08 402 141 145 4 626.98 1.45 403 141 172 31 80.60 0.35 404 142 145 3 632.36 1.42 405 142 146 4 624.07 2.74 406 142 165 23 93.94 0.45 407 142 168 26 85.39 1.05 408 142 169 27 82.31 0.45 409 142 172 30 80.58 0.35 410 143 146 3 624.22 2.82 411 143 147 4 624.21 2.82 412 143 165 22 93.64 0.34 413 144 147 3 630.31 0.24 414 144 148 4 624.20 2.82 415 145 148 3 625.99 1.79 416 145 149 4 616.65 0.56 417 146 149 3 616.62 0.57 418 146 150 4 616.61 0.56 419 146 153 7 568.94 5.54 420 146 161 15 93.97 0.46 421 146 165 19 93.63 0.34 422 147 150 3 639.90 0.17 423 149 152 3 634.37 0.51 424 149 153 4 612.59 1.39 425 150 153 3 634.04 0.35 426 150 154 4 610.58 2.40 427 151 154 3 638.73 0.41 428 152 155 3 697.76 0.90 429 153 156 3 641.23 0.80 430 153 161 8 152.00 2.08 431 156 161 5 601.59 4.50 432 157 160 3 614.97 0.21 433 157 161 4 608.42 2.56 434 158 161 3 616.70 0.65 435 158 162 4 608.43 2.56 436 159 162 3 627.20 0.38 437 159 163 4 614.07 0.26 438 160 163 3 615.42 0.42 439 160 164 4 614.07 0.26 440 161 164 3 625.37 0.58 441 161 165 4 614.56 4.81 442 162 165 3 625.37 0.58 443 162 166 4 625.37 0.58 444 163 166 3 625.37 0.58 445 163 167 4 625.37 0.58 446 164 167 3 639.56 1.51 447 164 168 4 625.34 0.58 448 165 168 3 628.16 0.81 449 165 169 4 607.65 2.83 450 166 169 3 613.21 5.46 451 166 170 4 603.64 4.45 452 167 170 3 625.34 0.60 453 167 171 4 603.64 4.45 454 168 171 3 612.93 8.05 455 168 172 4 603.27 4.61 456 169 172 3 605.09 1.91 457 169 173 4 601.88 4.19 458 170 173 3 619.30 1.98 459 170 174 4 602.65 3.79 460 171 174 3 604.39 3.14 461 171 175 4 607.77 1.24 462 172 175 3 639.38 1.46 463 173 176 3 631.81 2.69 464 173 179 6 228.97 5.18 465 173 180 7 396.87 78.77 466 174 180 6 396.87 78.77 467 176 179 3 616.76 1.09 468 176 180 4 624.43 6.09 469 177 180 3 627.78 4.42 470 177 181 4 627.77 4.42 471 178 181 3 627.78 4.42 472 178 182 4 610.54 2.13 473 179 182 3 610.56 2.12 474 179 183 4 610.56 2.13 475 180 183 3 615.47 4.58 476 180 184 4 610.56 2.13 477 181 184 3 628.22 1.79 478 181 185 4 608.93 1.31 479 182 185 3 631.00 4.17 480 182 186 4 614.29 4.19 481 183 186 3 614.30 4.19 482 183 187 4 613.14 4.76 483 184 187 3 614.30 4.19 484 184 188 4 614.61 4.03 485 185 188 3 614.61 4.03 486 185 189 4 604.25 5.40 487 186 189 3 607.70 3.68 488 186 190 4 604.25 5.40