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 3 606.34 2.37 2 3 7 4 598.71 2.98 3 4 7 3 611.32 1.58 4 4 8 4 602.49 0.80 5 4 42 38 42.04 2.03 6 4 43 39 41.13 2.58 7 5 8 3 607.77 0.18 8 5 9 4 598.41 2.84 9 6 9 3 612.31 2.45 10 6 10 4 604.83 2.80 11 7 10 3 611.32 2.95 12 7 11 4 600.87 4.78 13 7 28 21 56.22 0.78 14 7 32 25 56.14 0.79 15 7 34 27 56.26 0.72 16 7 39 32 51.48 0.35 17 7 43 36 51.27 0.45 18 7 49 42 51.00 0.47 19 8 11 3 609.26 3.98 20 8 12 4 594.24 1.47 21 8 43 35 51.27 0.45 22 8 49 41 50.98 0.48 23 8 52 44 50.52 0.26 24 8 53 45 50.45 0.24 25 8 56 48 50.45 0.24 26 9 12 3 611.86 2.64 27 9 13 4 595.47 2.44 28 10 13 3 595.71 2.33 29 10 14 4 595.63 2.36 30 10 31 21 56.66 0.57 31 10 32 22 56.52 0.64 32 11 14 3 592.58 0.74 33 11 15 4 590.83 5.22 34 11 28 17 58.02 1.25 35 11 49 38 51.15 0.44 36 11 53 42 50.95 0.48 37 12 15 3 607.85 1.91 38 12 16 4 590.84 5.22 39 12 53 41 50.95 0.48 40 12 57 45 50.60 0.31 41 13 16 3 614.34 1.33 42 13 17 4 597.86 1.72 43 14 17 3 600.10 0.60 44 14 18 4 590.86 5.21 45 14 19 5 581.77 0.67 46 14 23 9 84.59 3.29 47 14 27 13 81.63 4.75 48 14 28 14 71.48 3.00 49 15 19 4 507.40 20.50 50 15 20 5 490.03 29.18 51 15 23 8 95.67 1.51 52 15 46 31 56.29 0.65 53 15 50 35 51.38 0.36 54 15 53 38 51.26 0.42 55 15 95 80 51.02 0.46 56 15 98 83 51.09 0.43 57 16 94 78 50.61 0.31 58 16 95 79 50.96 0.49 59 18 22 4 546.13 15.54 60 18 23 5 428.11 11.29 61 19 22 3 592.97 3.94 62 19 23 4 592.96 3.94 63 19 98 79 51.34 0.43 64 19 101 82 53.22 0.30 65 20 23 3 620.90 5.01 66 20 46 26 56.37 0.67 67 20 47 27 56.32 0.66 68 20 50 30 55.65 0.80 69 20 98 78 51.70 0.42 70 20 101 81 53.23 0.29 71 20 102 82 53.23 0.30 72 20 105 85 56.10 0.57 73 20 106 86 56.30 0.66 74 21 46 25 56.37 0.68 75 21 101 80 54.27 0.23 76 21 105 84 56.11 0.58 77 22 27 5 609.12 2.74 78 23 27 4 597.74 1.25 79 23 46 23 56.35 0.68 80 24 27 3 609.12 2.75 81 24 28 4 598.21 1.47 82 24 46 22 56.25 0.64 83 25 28 3 602.84 0.30 84 25 29 4 598.22 1.47 85 26 29 3 621.27 3.33 86 26 30 4 609.32 2.65 87 27 30 3 609.32 2.65 88 27 31 4 609.32 2.65 89 28 31 3 631.51 0.82 90 28 32 4 596.94 2.11 91 29 32 3 603.66 5.48 92 29 33 4 581.14 0.75 93 29 34 5 541.48 4.52 94 29 36 7 225.35 58.84 95 30 33 3 619.62 1.52 96 34 38 4 605.75 3.02 97 35 38 3 611.78 0.01 98 35 39 4 608.45 1.67 99 36 39 3 633.95 2.01 100 37 40 3 611.78 0.01 101 38 41 3 627.40 1.09 102 39 43 4 570.54 5.12 103 40 43 3 598.69 2.29 104 40 44 4 522.80 30.09 105 43 48 5 428.19 10.13 106 43 49 6 347.94 28.81 107 43 52 9 347.94 28.81 108 44 48 4 580.49 4.44 109 45 48 3 580.49 4.44 110 45 49 4 585.54 1.91 111 46 49 3 598.08 2.70 112 46 50 4 580.53 4.40 113 47 50 3 600.93 1.28 114 47 51 4 583.15 3.09 115 47 102 55 284.16 49.79 116 47 106 59 289.74 46.12 117 48 51 3 603.99 0.26 118 48 52 4 587.32 1.01 119 48 115 67 290.02 46.07 120 49 52 3 605.41 3.08 121 49 53 4 602.48 1.62 122 50 53 3 602.48 1.61 123 50 54 4 602.47 1.61 124 50 98 48 294.76 45.34 125 50 99 49 292.56 46.44 126 50 102 52 294.95 45.16 127 51 54 3 602.47 1.62 128 51 55 4 602.46 1.61 129 51 102 51 296.07 44.68 130 51 115 64 294.42 45.12 131 51 119 68 291.67 46.06 132 52 55 3 603.05 1.32 133 52 56 4 594.65 5.51 134 53 56 3 604.29 0.67 135 53 57 4 603.93 0.83 136 53 95 42 296.43 44.92 137 54 57 3 604.00 0.86 138 54 58 4 598.51 1.89 139 54 95 41 296.55 44.86 140 54 99 45 296.15 44.66 141 54 119 65 295.88 44.62 142 55 58 3 610.04 3.88 143 55 59 4 603.13 0.62 144 55 118 63 296.80 44.19 145 55 119 64 296.60 44.24 146 55 122 67 296.65 44.26 147 56 59 3 603.13 0.62 148 56 60 4 602.65 0.86 149 57 60 3 607.61 2.85 150 57 61 4 591.68 6.57 151 57 91 34 297.64 44.56 152 57 92 35 297.48 44.48 153 58 62 4 590.51 7.16 154 58 92 34 297.54 44.51 155 58 119 61 301.36 41.91 156 58 122 64 296.85 44.16 157 58 123 65 296.80 44.15 158 59 62 3 603.50 0.80 159 59 63 4 590.63 7.22 160 59 122 63 302.14 41.52 161 60 63 3 599.27 2.90 162 60 64 4 598.79 3.14 163 60 91 31 304.00 41.55 164 61 64 3 603.71 0.70 165 61 65 4 598.79 3.14 166 61 82 21 304.54 41.88 167 61 85 24 304.54 41.85 168 61 86 25 304.28 41.74 169 61 89 28 304.29 41.70 170 61 91 30 304.00 41.55 171 61 92 31 304.00 41.55 172 61 93 32 304.05 41.58 173 62 65 3 604.90 0.09 174 62 66 4 600.96 2.05 175 62 126 64 302.75 41.02 176 63 66 3 604.89 0.07 177 63 67 4 604.77 0.14 178 64 67 3 604.78 0.13 179 64 68 4 604.77 0.14 180 64 89 25 306.80 40.45 181 64 90 26 306.82 40.44 182 65 68 3 604.89 0.04 183 65 69 4 603.46 0.76 184 65 78 13 307.61 40.90 185 65 81 16 307.59 40.88 186 65 82 17 307.10 40.63 187 65 85 20 307.07 40.62 188 65 126 61 305.40 39.84 189 65 130 65 304.91 39.55 190 66 69 3 617.83 0.51 191 66 70 4 609.77 0.03 192 67 70 3 638.25 0.24 193 68 71 3 620.96 0.61 194 68 81 13 307.98 40.70 195 68 85 17 307.65 40.54 196 69 72 3 605.76 1.21 197 69 78 9 307.95 40.73 198 69 81 12 307.99 40.70 199 72 77 5 547.56 3.83 200 72 78 6 408.52 4.87 201 72 81 9 367.49 10.98 202 73 77 4 584.19 3.62 203 73 78 5 576.07 0.42 204 74 77 3 595.57 1.88 205 74 78 4 584.18 3.63 206 74 139 65 313.55 7.79 207 75 78 3 591.38 0.02 208 75 79 4 587.76 1.83 209 75 130 55 341.20 21.78 210 75 133 58 340.89 21.56 211 75 134 59 323.41 12.83 212 75 139 64 313.53 7.78 213 75 140 65 313.55 7.79 214 76 79 3 609.08 4.90 215 76 80 4 594.70 0.90 216 76 139 63 313.54 7.78 217 76 140 64 311.12 6.57 218 76 183 107 239.00 6.13 219 77 80 3 602.27 2.89 220 77 81 4 592.27 0.32 221 78 81 3 595.55 0.46 222 78 82 4 592.34 0.35 223 78 130 52 340.86 21.58 224 79 82 3 608.35 1.70 225 79 83 4 592.35 0.35 226 79 127 48 341.48 21.91 227 79 130 51 340.91 21.55 228 79 131 52 340.86 21.50 229 79 152 73 266.80 14.49 230 79 179 100 240.78 5.95 231 79 182 103 239.28 6.07 232 79 183 104 238.97 6.16 233 80 83 3 608.44 2.06 234 80 84 4 593.43 0.89 235 80 176 96 244.27 4.99 236 80 179 99 240.77 5.95 237 80 180 100 240.77 5.95 238 80 183 103 239.02 6.13 239 81 84 3 596.91 2.62 240 81 85 4 592.88 1.16 241 82 85 3 605.75 0.37 242 82 86 4 597.85 3.62 243 82 93 11 375.36 6.70 244 82 126 44 341.46 21.89 245 82 127 45 341.44 21.89 246 82 130 48 340.88 21.48 247 83 86 3 603.87 0.62 248 83 87 4 609.89 3.63 249 83 127 44 341.57 21.86 250 83 156 73 266.18 14.43 251 83 175 92 244.38 5.04 252 83 179 96 241.53 6.32 253 84 87 3 625.30 1.61 254 84 88 4 609.90 3.63 255 84 172 88 244.47 5.07 256 84 175 91 244.38 5.04 257 84 176 92 244.38 5.05 258 85 88 3 609.89 3.62 259 85 89 4 597.87 3.64 260 86 89 3 617.40 2.29 261 86 93 7 375.35 6.70 262 86 156 70 266.37 14.55 263 86 160 74 265.82 14.52 264 87 160 73 265.83 14.52 265 87 168 81 244.98 5.30 266 87 171 84 244.86 5.27 267 87 172 85 244.78 5.25 268 87 175 88 244.78 5.24 269 90 94 4 590.98 0.30 270 91 94 3 627.37 2.37 271 92 95 3 626.17 2.96 272 92 96 4 592.22 0.92 273 92 99 7 520.46 1.94 274 92 123 31 341.33 21.92 275 93 96 3 601.65 0.71 276 93 157 64 266.32 14.68 277 93 160 67 266.01 14.61 278 95 98 3 603.38 0.93 279 95 99 4 579.32 2.48 280 96 99 3 595.90 4.67 281 96 100 4 598.03 3.60 282 96 157 61 266.83 14.88 283 96 161 65 266.06 14.63 284 97 100 3 599.50 4.34 285 97 101 4 588.69 1.07 286 98 101 3 598.32 3.75 287 98 102 4 588.68 1.06 288 99 102 3 598.32 3.75 289 99 103 4 588.68 1.06 290 99 116 17 342.00 21.68 291 100 103 3 600.28 3.96 292 100 104 4 595.71 2.47 293 101 104 3 608.72 0.26 294 101 105 4 589.41 4.21 295 102 105 3 594.02 1.91 296 102 106 4 589.39 4.20 297 102 112 10 354.35 15.81 298 102 116 14 342.01 21.68 299 103 106 3 617.85 0.68 300 103 107 4 561.22 2.35 301 103 112 9 354.35 15.81 302 103 116 13 342.01 21.68 303 104 107 3 612.11 2.83 304 106 109 3 612.18 2.87 305 106 112 6 366.23 9.89 306 107 112 5 379.38 3.33 307 109 112 3 628.80 1.84 308 110 113 3 628.80 1.84 309 111 114 3 613.02 0.20 310 111 115 4 612.47 0.48 311 112 115 3 614.31 0.45 312 112 116 4 564.12 12.02 313 113 117 4 577.61 5.28 314 114 117 3 591.85 5.25 315 114 118 4 577.66 5.30 316 115 118 3 577.89 5.19 317 115 119 4 577.68 5.31 318 116 120 4 579.83 4.29 319 117 120 3 595.79 3.69 320 117 121 4 609.12 2.98 321 118 121 3 626.53 2.29 322 119 122 3 610.61 2.24 323 119 123 4 579.27 4.59 324 120 123 3 612.56 4.70 325 120 124 4 588.75 0.14 326 121 124 3 599.83 2.83 327 121 125 4 572.53 4.77 328 122 125 3 594.64 2.77 329 123 153 30 268.72 15.64 330 123 154 31 268.72 15.64 331 123 157 34 268.49 15.67 332 124 127 3 611.29 4.45 333 124 128 4 591.88 2.39 334 124 149 25 268.92 15.61 335 124 150 26 268.92 15.60 336 124 153 29 268.71 15.66 337 125 128 3 591.88 2.39 338 125 129 4 583.31 6.67 339 126 129 3 617.66 1.38 340 126 130 4 577.11 3.56 341 127 130 3 579.69 1.26 342 127 131 4 567.14 6.74 343 127 149 22 269.20 15.71 344 127 152 25 269.00 15.63 345 127 153 26 268.99 15.63 346 127 156 29 268.98 15.63 347 128 131 3 601.65 0.81 348 128 132 4 567.14 6.74 349 128 145 17 269.53 15.77 350 128 146 18 269.44 15.72 351 128 149 21 269.00 15.62 352 129 132 3 585.69 6.67 353 129 133 4 576.19 11.34 354 130 134 4 581.35 8.76 355 130 140 10 381.22 3.91 356 131 134 3 600.23 0.60 357 131 135 4 586.08 6.46 358 131 140 9 372.81 8.09 359 131 145 14 269.68 15.72 360 131 148 17 269.63 15.73 361 131 149 18 269.51 15.77 362 131 152 21 269.47 15.74 363 131 182 51 240.66 6.75 364 131 183 52 239.12 6.11 365 131 186 55 228.57 8.18 366 132 135 3 605.49 3.23 367 132 136 4 586.05 6.45 368 132 145 13 269.67 15.72 369 133 136 3 598.72 0.81 370 133 137 4 586.05 6.45 371 134 137 3 589.02 4.97 372 134 138 4 586.03 6.46 373 134 139 5 529.08 15.52 374 134 140 6 501.72 5.20 375 135 138 3 594.90 2.00 376 135 140 5 505.06 3.52 377 135 141 6 373.61 7.70 378 135 142 7 340.26 8.17 379 135 145 10 276.33 18.70 380 140 183 43 239.24 6.04 381 140 186 46 226.22 0.07 382 140 187 47 218.41 3.88 383 142 145 3 611.22 5.40 384 142 148 6 563.35 4.85 385 142 186 44 235.73 4.84 386 144 147 3 619.02 1.02 387 144 148 4 596.32 0.21 388 145 148 3 606.88 5.05 389 145 149 4 596.32 0.21 390 146 149 3 599.28 1.27 391 146 150 4 596.32 0.21 392 147 150 3 597.67 0.30 393 147 151 4 592.00 2.51 394 148 151 3 594.38 1.32 395 148 152 4 582.73 2.28 396 148 182 34 240.70 6.75 397 148 186 38 230.80 9.78 398 149 152 3 592.15 2.43 399 149 153 4 582.74 2.28 400 150 153 3 594.71 0.76 401 150 154 4 582.75 2.28 402 151 154 3 607.75 5.48 403 151 155 4 582.88 2.35 404 151 182 31 241.31 6.50 405 152 155 3 604.64 3.94 406 152 156 4 592.18 1.79 407 152 182 30 240.57 6.81 408 153 156 3 597.24 0.68 409 153 157 4 583.69 2.44 410 154 157 3 587.49 0.57 411 154 158 4 583.69 2.44 412 155 158 3 590.69 1.05 413 155 159 4 589.78 0.60 414 155 178 23 243.68 5.88 415 156 159 3 609.88 5.73 416 156 160 4 589.43 0.43 417 156 175 19 244.89 5.29 418 156 178 22 243.66 5.87 419 157 160 3 593.47 2.48 420 157 161 4 583.01 2.25 421 158 161 3 612.73 4.30 422 158 162 4 581.72 1.71 423 159 163 4 567.03 9.04 424 159 175 16 244.92 5.29 425 159 178 19 244.53 5.45 426 160 171 11 245.02 5.32 427 160 175 15 244.92 5.29 428 161 164 3 615.78 0.82 429 162 165 3 737.47 1.01 430 163 166 3 625.19 0.20 431 163 171 8 268.53 17.06 432 163 174 11 245.20 5.40 433 164 171 7 548.20 0.14 434 166 170 4 589.26 0.93 435 166 171 5 569.38 0.26 436 166 174 8 568.63 0.20 437 167 170 3 597.41 0.48 438 167 171 4 589.28 0.92 439 168 171 3 606.00 3.82 440 168 172 4 590.59 1.57 441 169 172 3 597.16 1.72 442 169 173 4 590.58 1.57 443 170 173 3 605.87 2.63 444 170 174 4 589.64 5.49 445 171 174 3 604.06 3.53 446 171 175 4 584.70 6.15 447 172 175 3 604.06 3.53 448 172 176 4 584.70 6.15 449 173 176 3 596.19 0.40 450 173 177 4 577.43 1.63 451 174 177 3 601.03 9.39 452 174 178 4 579.93 2.88 453 175 178 3 604.92 4.48 454 175 179 4 592.70 2.80 455 176 179 3 595.59 2.49 456 176 180 4 592.27 3.02 457 177 180 3 600.83 0.94 458 177 181 4 592.47 2.92 459 178 181 3 606.23 7.62 460 178 182 4 594.52 1.88 461 179 182 3 609.36 6.06 462 179 183 4 593.20 0.12 463 180 183 3 620.88 0.31 464 180 184 4 588.11 1.33 465 181 184 3 599.53 1.57 466 181 185 4 588.19 1.28 467 182 185 3 606.41 3.75 468 182 186 4 591.57 2.92 469 183 186 3 599.07 0.83