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 1 499 241 242 27.05 0.07 2 500 92 92 343.50 1.78 3 500 95 95 343.58 1.75 4 500 96 96 343.61 1.73 5 500 241 241 27.05 0.08 6 1 96 95 343.64 1.72 7 1 97 96 343.61 1.73 8 1 98 97 343.58 1.74 9 1 237 236 39.84 1.05 10 1 238 237 38.80 0.56 11 1 241 240 27.05 0.08 12 2 92 90 343.66 1.73 13 2 98 96 343.58 1.74 14 2 100 98 343.56 1.74 15 2 122 120 243.91 0.36 16 2 123 121 243.88 0.35 17 2 125 123 243.21 0.32 18 2 126 124 243.21 0.32 19 3 97 94 343.71 1.73 20 3 98 95 343.64 1.73 21 3 99 96 343.58 1.74 22 3 100 97 343.58 1.74 23 3 126 123 243.22 0.32 24 3 128 125 243.19 0.32 25 4 100 96 343.60 1.74 26 4 102 98 343.50 1.74 27 4 109 105 252.35 2.48 28 4 119 115 244.52 0.20 29 4 125 121 243.81 0.36 30 4 126 122 243.27 0.30 31 4 127 123 243.21 0.32 32 4 128 124 243.20 0.32 33 5 13 8 343.64 1.73 34 5 16 11 343.67 1.73 35 5 17 12 343.64 1.72 36 5 20 15 343.76 1.71 37 5 99 94 343.70 1.73 38 5 100 95 343.63 1.73 39 5 102 97 343.55 1.72 40 5 128 123 243.22 0.32 41 5 130 125 243.17 0.32 42 5 233 228 58.31 0.04 43 6 13 7 343.69 1.74 44 6 102 96 343.61 1.73 45 6 106 100 263.19 1.60 46 6 110 104 252.49 2.41 47 6 127 121 243.80 0.36 48 6 128 122 243.27 0.30 49 6 129 123 243.19 0.32 50 6 130 124 243.19 0.32 51 6 152 146 232.15 0.10 52 7 11 4 537.77 1.27 53 7 13 6 343.70 1.73 54 7 106 99 295.18 9.19 55 7 129 122 243.27 0.30 56 7 130 123 243.20 0.32 57 8 11 3 636.07 6.73 58 8 104 96 343.57 1.71 59 8 106 98 320.11 0.86 60 9 104 95 343.59 1.70 61 9 105 96 343.58 1.71 62 10 166 156 237.61 1.66 63 11 130 119 243.38 0.26 64 11 132 121 242.92 0.43 65 11 165 154 236.83 1.72 66 11 166 155 237.24 1.81 67 12 16 4 590.72 4.04 68 12 165 153 236.81 1.73 69 13 16 3 591.73 3.54 70 13 17 4 593.74 2.53 71 13 101 88 345.70 1.50 72 13 102 89 345.69 1.50 73 13 103 90 345.42 1.53 74 13 104 91 343.90 1.75 75 13 130 117 243.19 0.32 76 14 17 3 604.82 3.00 77 14 18 4 593.93 2.44 78 14 42 28 346.95 2.06 79 14 43 29 347.31 2.23 80 14 101 87 345.72 1.49 81 15 18 3 606.69 1.70 82 15 19 4 581.94 4.74 83 15 43 28 347.32 2.19 84 15 224 209 102.81 2.03 85 16 19 3 598.77 5.65 86 16 20 4 581.04 5.19 87 16 130 114 243.19 0.32 88 16 165 149 236.72 1.71 89 16 222 206 119.87 1.23 90 16 224 208 91.65 0.74 91 16 230 214 91.22 0.86 92 17 21 4 607.39 1.41 93 17 32 15 346.98 1.67 94 17 44 27 347.81 2.11 95 17 99 82 346.30 1.32 96 17 101 84 345.78 1.57 97 18 21 3 624.89 5.14 98 18 22 4 601.03 4.58 99 18 32 14 347.79 2.08 100 18 43 25 347.49 2.23 101 18 44 26 347.45 2.25 102 19 22 3 640.88 3.18 103 19 23 4 612.40 1.10 104 19 224 205 91.65 0.74 105 19 227 208 91.52 0.73 106 19 230 211 91.28 0.83 107 20 23 3 651.63 1.53 108 20 24 4 612.39 1.10 109 20 99 79 347.95 2.10 110 20 230 210 69.73 0.97 111 20 233 213 70.33 1.28 112 21 24 3 612.55 1.02 113 21 25 4 594.09 8.04 114 21 30 9 348.55 1.82 115 21 32 11 347.97 2.10 116 21 99 78 347.97 2.10 117 22 25 3 607.10 1.31 118 22 26 4 598.90 5.07 119 22 32 10 348.70 1.90 120 22 43 21 348.17 2.21 121 22 44 22 348.16 2.21 122 22 227 205 91.54 0.74 123 23 26 3 649.46 3.53 124 23 227 204 91.49 0.72 125 23 230 207 82.52 0.08 126 23 231 208 78.73 0.10 127 23 234 211 71.20 0.24 128 24 27 3 654.27 1.12 129 24 28 4 566.37 4.30 130 24 30 6 529.49 5.82 131 24 97 73 351.81 2.47 132 24 99 75 350.57 1.86 133 24 234 210 58.41 0.02 134 25 28 3 618.90 7.28 135 25 30 5 529.49 5.81 136 25 32 7 536.45 2.33 137 28 96 68 453.12 1.55 138 28 97 69 453.07 1.53 139 28 234 206 58.10 0.06 140 29 95 66 453.14 1.54 141 29 96 67 453.12 1.55 142 29 97 68 453.13 1.54 143 30 95 65 453.19 1.54 144 30 97 67 453.13 1.55 145 30 99 69 453.12 1.54 146 31 47 16 526.04 1.45 147 31 91 60 453.32 1.52 148 31 95 64 453.26 1.54 149 31 97 66 453.19 1.54 150 31 98 67 453.14 1.54 151 31 99 68 453.13 1.54 152 32 44 12 526.08 1.47 153 32 45 13 526.10 1.46 154 32 46 14 526.06 1.45 155 32 47 15 526.06 1.44 156 32 48 16 526.04 1.45 157 32 99 67 453.14 1.54 158 33 48 15 526.04 1.45 159 33 88 55 453.50 1.53 160 33 98 65 453.26 1.54 161 33 99 66 453.19 1.54 162 33 100 67 453.14 1.54 163 33 101 68 453.13 1.54 164 34 42 8 526.46 1.48 165 34 44 10 526.50 1.48 166 34 46 12 526.35 1.44 167 34 48 14 526.23 1.41 168 34 49 15 526.11 1.42 169 34 50 16 526.11 1.42 170 34 101 67 453.16 1.54 171 35 50 15 526.25 1.48 172 35 74 39 460.09 3.02 173 35 100 65 453.27 1.54 174 35 101 66 453.18 1.54 175 35 102 67 453.16 1.54 176 35 103 68 453.12 1.55 177 35 109 74 300.12 26.36 178 35 114 79 246.55 0.59 179 35 118 83 244.72 0.28 180 36 39 3 667.54 3.37 181 36 50 14 526.35 1.46 182 36 51 15 526.33 1.45 183 36 74 38 460.10 3.01 184 36 101 65 453.26 1.53 185 36 103 67 453.12 1.55 186 36 104 68 453.16 1.54 187 37 50 13 526.35 1.45 188 37 51 14 526.33 1.46 189 37 54 17 525.07 1.03 190 37 55 18 502.13 4.94 191 37 56 19 502.11 4.93 192 37 73 36 460.10 3.01 193 37 74 37 460.10 3.01 194 37 77 40 459.97 3.01 195 38 56 18 494.71 1.24 196 39 42 3 734.94 2.62 197 39 51 12 526.41 1.46 198 40 51 11 526.45 1.45 199 42 46 4 629.96 6.14 200 42 51 9 526.46 1.44 201 44 101 57 453.16 1.54 202 46 49 3 646.13 6.59 203 47 91 44 453.39 1.53 204 48 84 36 453.78 1.46 205 48 87 39 453.55 1.53 206 48 88 40 453.54 1.54 207 49 52 3 641.62 6.84 208 49 84 35 453.86 1.48 209 50 53 3 627.44 10.03 210 50 54 4 581.23 5.33 211 50 77 27 457.77 2.94 212 50 84 34 453.86 1.48 213 51 54 3 579.18 2.70 214 51 55 4 537.96 0.39 215 53 76 23 460.09 3.02 216 53 77 24 460.04 3.04 217 53 80 27 454.10 1.41 218 53 84 31 453.91 1.50 219 54 59 5 586.24 0.74 220 54 73 19 460.17 3.04 221 54 76 22 460.10 3.02 222 54 77 23 460.07 3.02 223 55 58 3 611.90 12.07 224 55 59 4 598.68 2.26 225 56 59 3 615.33 0.39 226 56 60 4 598.68 2.26 227 56 69 13 460.41 2.93 228 56 70 14 460.40 2.93 229 56 73 17 460.38 2.94 230 57 60 3 608.88 2.85 231 57 61 4 592.53 0.83 232 58 61 3 600.63 0.12 233 58 62 4 600.82 3.31 234 59 62 3 600.83 3.31 235 59 63 4 600.82 3.32 236 59 64 5 573.72 4.13 237 59 69 10 460.60 2.85 238 59 72 13 460.60 2.85 239 59 73 14 460.60 2.85 240 59 76 17 460.59 2.85 241 60 63 3 610.12 3.00 242 60 64 4 600.76 3.35 243 60 65 5 572.26 4.86 244 60 66 6 546.92 1.42 245 60 69 9 460.81 2.95 246 64 68 4 566.01 5.21 247 64 69 5 563.79 5.19 248 64 72 8 507.89 0.94 249 65 68 3 595.13 1.19 250 65 69 4 593.41 2.04 251 66 69 3 605.78 2.90 252 66 70 4 598.76 0.62 253 67 70 3 653.08 0.68 254 67 71 4 598.76 0.62 255 68 71 3 642.38 4.67 256 68 72 4 607.10 3.54 257 69 72 3 618.04 1.93 258 69 73 4 607.10 3.54 259 70 73 3 627.21 5.30 260 70 74 4 607.05 3.57 261 70 105 35 453.25 1.51 262 70 108 38 451.71 1.91 263 71 74 3 619.53 1.42 264 71 75 4 602.84 5.67 265 72 75 3 601.95 6.12 266 72 76 4 587.31 1.20 267 73 76 3 599.37 0.99 268 73 77 4 588.53 0.58 269 74 77 3 598.36 4.56 270 74 78 4 586.53 1.35 271 74 103 29 453.31 1.53 272 74 108 34 432.49 2.35 273 74 114 40 247.58 0.91 274 75 79 4 611.55 1.69 275 76 79 3 631.09 11.45 276 77 80 3 605.63 4.65 277 77 81 4 581.88 0.69 278 77 84 7 558.79 3.78 279 77 114 37 247.18 0.71 280 78 81 3 598.08 8.42 281 78 113 35 247.19 0.71 282 78 114 36 247.16 0.71 283 78 117 39 247.07 0.66 284 80 83 3 620.37 1.31 285 80 84 4 595.34 1.16 286 81 84 3 599.91 1.30 287 81 85 4 595.34 1.16 288 81 114 33 247.12 0.70 289 81 117 36 245.88 0.33 290 81 118 37 245.01 0.16 291 82 85 3 615.62 1.06 292 82 86 4 600.43 3.70 293 83 86 3 619.91 6.54 294 83 87 4 602.02 4.51 295 84 87 3 618.88 7.05 296 84 88 4 607.93 1.57 297 85 88 3 634.59 8.28 298 85 89 4 607.92 1.57 299 85 118 33 244.36 0.26 300 85 121 36 244.00 0.35 301 85 122 37 244.01 0.35 302 86 89 3 607.90 1.56 303 86 90 4 605.45 2.79 304 87 90 3 627.04 4.50 305 87 91 4 606.11 2.44 306 88 91 3 632.50 10.75 307 88 92 4 606.10 2.44 308 88 98 10 453.34 1.53 309 88 100 12 453.28 1.52 310 88 118 30 244.37 0.27 311 89 92 3 610.57 0.20 312 89 93 4 618.73 8.02 313 89 121 32 243.98 0.36 314 89 122 33 243.91 0.36 315 90 93 3 659.41 1.65 316 90 94 4 644.38 4.81 317 91 94 3 652.49 0.76 318 91 95 4 605.87 2.54 319 91 98 7 453.31 1.53 320 92 95 3 650.32 0.33 321 92 98 6 453.29 1.52 322 92 123 31 243.47 0.35 323 95 98 3 669.80 2.42 324 97 234 137 57.90 0.10 325 97 237 140 41.72 0.12 326 100 122 22 244.30 0.27 327 102 109 7 351.79 52.20 328 103 106 3 657.60 0.26 329 103 108 5 536.02 12.59 330 103 109 6 506.06 20.23 331 105 108 3 612.20 9.67 332 105 109 4 600.57 3.85 333 106 109 3 645.15 3.81 334 106 110 4 585.10 3.62 335 106 129 23 243.93 0.35 336 106 148 42 229.34 0.21 337 107 110 3 588.99 4.83 338 107 111 4 581.65 2.58 339 107 112 5 581.65 2.58 340 108 111 3 626.30 9.08 341 108 112 4 584.41 3.96 342 109 115 6 245.03 0.17 343 109 118 9 245.27 0.24 344 109 119 10 245.03 0.17 345 109 156 47 233.56 0.67 346 110 116 6 245.08 0.16 347 110 152 42 233.06 0.64 348 110 155 45 233.55 0.67 349 110 156 46 233.56 0.66 350 112 115 3 655.18 2.16 351 113 116 3 613.22 5.28 352 113 117 4 569.34 8.64 353 114 118 4 582.87 1.88 354 115 118 3 639.33 11.62 355 115 119 4 592.63 0.93 356 115 156 41 233.37 0.74 357 116 119 3 604.06 0.50 358 116 120 4 597.83 1.67 359 116 155 39 233.25 0.70 360 116 156 40 233.25 0.70 361 117 120 3 608.10 5.47 362 117 121 4 606.77 6.14 363 118 121 3 617.81 7.38 364 118 122 4 606.77 6.14 365 119 122 3 617.90 7.34 366 119 125 6 486.20 2.69 367 119 127 8 243.83 0.37 368 119 156 37 233.19 0.68 369 119 158 39 233.38 0.74 370 122 125 3 650.58 11.60 371 124 240 116 38.36 0.30 372 124 244 120 17.37 3.63 373 125 158 33 630.64 1.49 374 125 240 115 38.65 0.45 375 126 159 33 632.58 1.99 376 126 161 35 634.83 1.36 377 126 236 110 50.20 3.06 378 126 237 111 44.84 0.50 379 126 240 114 39.90 0.35 380 127 152 25 630.71 1.29 381 127 156 29 632.38 1.93 382 127 158 31 632.61 2.00 383 127 159 32 632.77 1.94 384 127 160 33 633.74 1.46 385 127 161 34 634.83 1.36 386 128 161 33 634.86 1.37 387 128 163 35 635.08 1.34 388 128 222 94 125.53 0.75 389 128 233 105 58.25 0.07 390 129 145 16 624.19 0.42 391 129 148 19 630.91 1.21 392 129 149 20 630.51 1.39 393 129 152 23 633.67 1.21 394 129 160 31 634.89 1.39 395 129 161 32 634.90 1.39 396 129 162 33 635.06 1.33 397 129 163 34 635.15 1.38 398 130 163 33 635.16 1.38 399 130 165 35 635.56 1.35 400 130 222 92 126.33 0.96 401 131 135 4 661.62 0.82 402 131 145 14 629.58 1.72 403 131 163 32 635.54 1.35 404 131 164 33 635.57 1.33 405 131 165 34 640.42 0.32 406 132 135 3 672.96 2.40 407 132 166 34 645.17 0.66 408 133 136 3 655.35 2.32 409 133 164 31 642.29 0.12 410 133 165 32 645.10 0.64 411 133 166 33 645.24 0.64 412 133 170 37 645.72 0.60 413 133 178 45 642.85 0.27 414 134 137 3 700.44 0.05 415 135 141 6 645.06 0.70 416 135 145 10 645.08 0.71 417 136 141 5 645.53 0.47 418 136 142 6 645.06 0.70 419 136 145 9 645.47 0.91 420 136 164 28 768.87 19.87 421 136 178 42 646.73 1.10 422 136 182 46 646.63 1.06 423 137 141 4 652.43 0.67 424 138 141 3 652.47 0.66 425 138 142 4 652.44 0.68 426 139 142 3 652.69 0.55 427 139 143 4 652.44 0.67 428 139 188 49 647.62 0.84 429 139 191 52 647.62 0.83 430 139 192 53 647.58 0.84 431 140 143 3 652.44 0.68 432 140 144 4 747.96 4.12 433 140 192 52 740.38 25.70 434 140 203 63 647.50 0.79 435 141 144 3 823.50 0.00 436 146 149 3 823.50 0.00 437 146 209 63 823.32 0.09 438 146 216 70 128.41 0.50 439 146 217 71 128.37 0.48 440 146 219 73 127.08 0.76 441 147 209 62 823.40 0.02 442 150 214 64 128.28 0.54 443 152 156 4 823.50 0.00 444 159 240 81 41.55 0.21 445 161 218 57 127.02 0.75 446 161 220 59 126.33 0.96 447 161 236 75 50.65 3.24 448 162 217 55 127.52 0.65 449 162 218 56 127.08 0.75 450 162 219 57 126.95 0.72 451 162 220 58 126.89 0.70 452 163 219 56 127.02 0.76 453 163 220 57 126.92 0.71 454 163 222 59 126.33 0.96 455 164 167 3 823.50 0.00 456 164 220 56 127.03 0.74 457 164 221 57 126.83 0.73 458 164 222 58 126.44 0.91 459 165 222 57 126.43 0.91 460 166 222 56 127.00 0.74 461 166 223 57 126.23 0.94 462 167 170 3 823.50 0.00 463 167 221 54 127.06 0.76 464 167 222 55 127.03 0.75 465 167 223 56 126.92 0.71 466 167 228 61 96.25 0.21 467 168 223 55 127.03 0.75 468 168 226 58 126.21 1.00 469 172 175 3 823.50 0.00 470 177 180 3 823.50 0.00 471 178 221 43 128.18 0.60 472 179 221 42 128.28 0.62 473 182 219 37 128.49 0.55 474 182 221 39 128.50 0.55 475 183 218 35 128.55 0.56 476 183 219 36 128.54 0.56 477 183 221 38 128.55 0.54 478 185 209 24 823.46 0.02 479 185 210 25 815.23 1.26 480 186 189 3 823.50 0.00 481 187 190 3 823.50 0.00 482 189 193 4 823.50 0.00 483 198 201 3 823.50 0.00 484 199 202 3 823.50 0.00 485 199 203 4 823.50 0.00 486 203 206 3 823.50 0.00 487 208 211 3 550.32 6.60 488 208 212 4 480.44 7.29 489 209 213 4 480.30 7.34 490 209 214 5 132.64 0.09 491 210 213 3 579.00 7.20 492 210 215 5 130.91 0.78 493 210 216 6 130.10 1.15 494 220 232 12 76.89 0.82 495 220 233 13 73.64 0.15 496 220 236 16 63.40 2.22 497 221 228 7 131.26 0.17 498 221 229 8 131.06 0.20 499 222 228 6 131.28 0.16 500 222 229 7 131.15 0.17 501 222 230 8 131.12 0.18 502 222 233 11 130.97 0.14 503 223 226 3 604.49 2.12 504 223 227 4 133.59 0.92 505 223 228 5 131.34 0.16 506 223 230 7 131.62 0.03 507 224 227 3 622.68 6.98 508 224 230 6 143.12 0.34 509 227 230 3 602.34 0.31 510 227 231 4 619.38 0.84 511 229 232 3 612.02 4.53 512 229 233 4 602.91 0.03 513 230 233 3 610.35 0.63 514 230 234 4 602.92 0.03 515 231 234 3 606.73 1.88 516 231 235 4 598.82 2.07 517 232 235 3 602.89 0.03 518 232 236 4 593.32 0.67 519 233 236 3 619.52 8.35 520 233 237 4 595.84 3.34 521 234 237 3 578.10 5.53 522 234 238 4 565.82 0.61 523 235 238 3 592.34 1.59 524 235 239 4 563.40 0.57 525 236 239 3 595.59 1.71 526 236 240 4 574.82 5.00 527 237 240 3 633.58 17.20 528 237 241 4 595.20 1.90 529 238 241 3 595.20 1.90 530 238 242 4 595.20 1.90 531 239 242 3 595.20 1.89 532 239 243 4 588.11 1.66 533 240 243 3 588.10 1.67 534 240 244 4 574.84 4.96 535 241 244 3 624.24 12.80