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 7 48 41 82.67 13.10 2 7 49 42 82.74 13.12 3 8 41 33 82.47 13.00 4 8 44 36 82.56 13.04 5 8 45 37 82.71 13.12 6 8 48 40 82.73 13.12 7 8 74 66 82.25 13.11 8 8 77 69 82.14 13.12 9 9 41 32 82.73 12.98 10 9 77 68 82.52 13.01 11 10 33 23 82.99 12.76 12 10 34 24 83.06 12.73 13 10 37 27 82.84 12.84 14 10 38 28 83.08 12.80 15 10 41 31 82.87 13.04 16 11 33 22 83.23 12.81 17 11 37 26 83.28 12.84 18 11 77 66 82.88 13.05 19 11 81 70 82.51 13.01 20 13 17 4 678.44 1.81 21 13 29 16 84.06 12.44 22 13 33 20 83.51 12.79 23 13 84 71 82.95 12.80 24 14 84 70 83.25 12.85 25 14 85 71 83.07 12.82 26 15 19 4 636.97 2.36 27 15 20 5 637.22 2.48 28 15 29 14 87.99 10.97 29 15 84 69 83.31 12.87 30 15 87 72 83.21 12.82 31 15 88 73 82.98 12.71 32 15 89 74 84.30 12.04 33 16 19 3 660.36 4.62 34 17 26 9 90.12 9.90 35 17 29 12 87.98 10.97 36 17 30 13 88.09 11.03 37 17 33 16 88.20 11.09 38 17 34 17 88.50 11.22 39 18 21 3 675.93 3.15 40 18 26 8 90.15 9.90 41 19 89 70 87.56 10.40 42 20 23 3 704.96 0.36 43 20 24 4 640.96 0.61 44 20 29 9 158.40 1.20 45 20 87 67 88.09 10.65 46 20 88 68 88.03 10.64 47 20 89 69 87.94 10.56 48 20 190 170 79.56 6.40 49 21 24 3 675.43 0.39 50 21 25 4 610.17 12.10 51 21 26 5 602.51 15.93 52 23 90 67 95.97 6.64 53 23 176 153 104.44 5.40 54 23 186 163 95.83 6.63 55 23 189 166 95.17 6.27 56 23 190 167 92.55 4.95 57 24 28 4 649.69 0.32 58 24 29 5 637.52 5.69 59 24 87 63 96.19 6.75 60 24 175 151 107.89 3.68 61 24 183 159 96.20 6.71 62 24 190 166 92.28 4.79 63 25 28 3 661.76 0.16 64 25 29 4 656.08 1.91 65 25 175 150 116.56 0.12 66 26 29 3 673.73 0.89 67 26 30 4 667.72 3.91 68 27 30 3 679.73 1.06 69 27 31 4 672.05 1.74 70 27 174 147 125.08 1.07 71 28 31 3 682.35 0.25 72 28 32 4 672.06 1.74 73 28 170 142 125.20 1.12 74 28 171 143 124.98 1.04 75 28 172 144 124.14 0.61 76 28 173 145 125.24 0.99 77 28 174 146 125.24 0.99 78 28 175 147 125.06 1.06 79 29 32 3 675.45 3.44 80 29 33 4 672.06 1.74 81 29 84 55 123.58 0.62 82 30 33 3 674.44 0.52 83 30 34 4 655.40 0.01 84 31 34 3 666.03 0.51 85 31 35 4 639.44 4.07 86 31 36 5 643.84 1.87 87 31 174 143 128.28 0.18 88 32 36 4 636.40 5.58 89 32 37 5 636.39 5.58 90 32 80 48 127.95 0.14 91 32 83 51 127.95 0.14 92 32 84 52 127.85 0.09 93 32 166 134 127.98 0.15 94 32 170 138 128.03 0.16 95 32 171 139 127.97 0.14 96 33 37 4 628.00 1.38 97 33 38 5 639.61 1.39 98 33 84 51 127.84 0.10 99 34 38 4 651.01 4.29 100 35 38 3 674.88 0.51 101 35 39 4 661.06 0.69 102 36 39 3 673.46 0.88 103 36 40 4 663.03 1.64 104 36 170 134 132.46 0.44 105 37 40 3 677.42 0.89 106 37 41 4 666.27 2.75 107 37 77 40 131.71 0.82 108 37 80 43 131.52 0.88 109 37 81 44 131.69 0.82 110 37 84 47 131.69 0.82 111 38 41 3 675.66 0.01 112 38 42 4 657.63 1.57 113 39 42 3 672.71 1.49 114 39 43 4 665.25 2.23 115 40 43 3 665.60 2.08 116 40 44 4 662.66 3.54 117 40 72 32 133.15 0.62 118 40 73 33 133.03 0.58 119 40 76 36 132.91 0.55 120 40 77 37 132.95 0.57 121 40 80 40 132.99 0.58 122 40 151 111 133.05 0.58 123 40 168 128 133.25 0.59 124 40 170 130 133.28 0.58 125 41 44 3 677.91 1.12 126 41 45 4 669.06 0.34 127 41 77 36 132.96 0.57 128 42 45 3 680.43 2.74 129 42 46 4 667.32 0.57 130 43 46 3 685.60 0.15 131 43 47 4 670.92 2.36 132 43 73 30 133.18 0.66 133 44 47 3 685.60 0.15 134 44 48 4 674.98 0.34 135 44 73 29 133.23 0.63 136 44 74 30 133.18 0.66 137 45 48 3 674.98 0.34 138 45 49 4 672.75 0.78 139 46 49 3 676.65 0.32 140 46 50 4 668.73 1.24 141 47 50 3 668.74 1.24 142 47 51 4 668.72 1.24 143 47 66 19 133.33 0.60 144 47 69 22 133.36 0.58 145 47 70 23 133.31 0.59 146 48 51 3 681.25 7.50 147 48 52 4 668.69 1.26 148 48 70 22 133.33 0.58 149 49 52 3 673.83 1.13 150 49 53 4 668.52 1.32 151 50 53 3 684.87 4.95 152 50 54 4 668.68 1.20 153 51 54 3 676.95 0.99 154 51 55 4 667.38 0.22 155 51 61 10 133.81 0.67 156 51 66 15 133.47 0.61 157 52 55 3 679.91 2.46 158 52 56 4 667.38 0.22 159 53 56 3 675.01 0.01 160 53 57 4 656.21 5.37 161 54 57 3 671.56 1.72 162 54 58 4 646.79 2.64 163 54 59 5 600.23 1.62 164 54 61 7 135.26 0.06 165 55 58 3 656.72 2.33 166 62 65 3 687.09 1.28 167 62 66 4 657.87 4.28 168 63 66 3 672.62 0.67 169 63 67 4 657.17 4.12 170 64 67 3 675.08 0.56 171 64 68 4 666.81 0.68 172 65 68 3 673.20 2.89 173 65 69 4 670.60 1.59 174 66 69 3 682.27 2.20 175 66 70 4 667.80 0.18 176 67 70 3 674.73 0.46 177 67 71 4 670.62 1.59 178 68 71 3 688.74 4.50 179 68 72 4 682.23 4.21 180 69 72 3 682.25 4.20 181 69 73 4 670.62 1.60 182 70 73 3 684.00 3.33 183 70 74 4 667.20 0.02 184 71 75 4 644.48 1.91 185 71 152 81 263.86 0.80 186 72 75 3 677.34 1.75 187 72 76 4 652.12 0.08 188 72 150 78 270.12 0.57 189 72 151 79 265.28 0.09 190 72 152 80 264.00 0.73 191 72 168 96 285.38 0.40 192 73 76 3 667.93 5.90 193 73 77 4 655.32 1.52 194 74 77 3 658.77 3.25 195 74 78 4 655.32 1.53 196 75 78 3 675.21 2.25 197 75 79 4 660.18 0.88 198 75 151 76 280.58 0.98 199 76 79 3 679.65 0.03 200 76 80 4 660.21 0.89 201 76 151 75 286.19 0.68 202 77 80 3 683.14 1.77 203 77 81 4 663.55 0.80 204 78 81 3 674.77 0.52 205 78 82 4 663.59 0.78 206 78 161 83 292.85 1.19 207 79 82 3 674.81 0.53 208 79 83 4 660.24 0.86 209 79 131 52 297.02 0.30 210 79 133 54 295.60 0.49 211 79 148 69 297.01 0.30 212 79 151 72 297.06 0.32 213 79 161 82 293.00 1.12 214 79 164 85 295.48 0.55 215 80 83 3 664.37 2.93 216 80 84 4 661.54 1.52 217 80 131 51 297.24 0.27 218 80 151 71 297.31 0.25 219 80 166 86 297.23 0.27 220 80 170 90 299.77 0.40 221 81 84 3 684.98 2.66 222 81 85 4 660.61 2.00 223 82 85 3 660.61 2.00 224 82 86 4 660.60 1.99 225 82 161 79 297.04 0.30 226 82 164 82 297.25 0.29 227 82 199 117 296.70 0.21 228 83 86 3 685.76 1.54 229 83 87 4 660.52 2.02 230 83 131 48 299.69 0.41 231 83 164 81 297.66 0.39 232 83 165 82 299.12 0.60 233 83 166 83 299.69 0.41 234 83 183 100 300.10 0.41 235 83 187 104 299.69 0.39 236 84 87 3 686.43 3.44 237 85 195 110 299.56 0.40 238 85 199 114 299.54 0.41 239 86 163 77 299.69 0.39 240 86 164 78 299.74 0.40 241 86 187 101 299.95 0.41 242 86 191 105 299.70 0.38 243 86 192 106 299.67 0.38 244 86 195 109 299.60 0.38 245 86 196 110 299.57 0.39 246 86 199 113 299.62 0.36 247 87 187 100 299.94 0.41 248 87 190 103 299.89 0.42 249 87 191 104 299.72 0.39 250 87 192 105 299.70 0.38 251 88 93 5 299.92 0.41 252 88 190 102 299.94 0.41 253 88 192 104 299.76 0.39 254 89 92 3 668.56 0.66 255 89 93 4 619.21 7.62 256 90 93 3 653.62 7.92 257 90 189 99 311.32 0.50 258 90 190 100 300.08 0.40 259 93 190 97 332.07 1.98 260 93 191 98 331.81 1.93 261 93 192 99 317.63 0.78 262 94 188 94 332.25 1.93 263 94 189 95 332.26 1.94 264 94 190 96 332.24 1.92 265 94 191 97 332.06 1.98 266 94 193 99 331.08 1.56 267 95 193 98 335.00 0.64 268 96 112 16 341.12 3.35 269 96 193 97 335.00 0.64 270 97 101 4 661.62 3.98 271 97 102 5 628.46 11.28 272 97 105 8 596.93 4.53 273 97 112 15 351.13 1.55 274 97 193 96 335.00 0.65 275 97 197 100 334.99 0.65 276 98 101 3 697.78 2.48 277 98 102 4 661.62 3.98 278 98 197 99 335.24 0.68 279 99 102 3 680.95 0.72 280 99 103 4 661.65 3.97 281 100 103 3 673.70 2.05 282 100 104 4 670.98 0.69 283 100 200 100 335.41 0.76 284 101 104 3 673.26 0.45 285 101 105 4 670.96 0.69 286 101 134 33 430.36 1.61 287 101 143 42 461.43 0.46 288 101 193 92 335.82 0.71 289 101 196 95 335.64 0.66 290 101 197 96 335.41 0.76 291 101 200 99 335.41 0.76 292 102 105 3 673.26 0.45 293 102 106 4 667.57 2.39 294 103 106 3 675.34 1.49 295 103 107 4 667.61 2.38 296 104 107 3 669.13 1.62 297 104 108 4 662.91 0.04 298 104 136 32 483.19 5.37 299 104 141 37 483.57 5.22 300 104 143 39 483.17 5.36 301 104 200 96 335.49 0.79 302 105 108 3 675.97 1.78 303 105 109 4 656.94 2.95 304 105 110 5 643.90 3.46 305 105 111 6 615.11 8.84 306 105 112 7 520.27 1.15 307 105 115 10 483.23 5.34 308 105 143 38 483.45 5.26 309 106 109 3 669.21 0.88 310 106 110 4 620.26 6.27 311 106 111 5 615.11 8.84 312 107 141 34 484.43 4.84 313 107 142 35 484.39 4.86 314 108 142 34 484.36 4.86 315 108 143 35 484.34 4.86 316 109 114 5 537.39 1.61 317 109 115 6 520.33 1.14 318 109 118 9 520.34 1.14 319 109 143 34 484.40 4.84 320 109 145 36 484.38 4.84 321 111 114 3 668.18 1.34 322 111 115 4 661.05 1.56 323 112 115 3 668.18 1.34 324 112 116 4 661.06 1.56 325 112 193 81 337.20 0.60 326 113 116 3 664.38 3.23 327 113 117 4 661.06 1.57 328 114 117 3 675.69 2.73 329 114 118 4 661.06 1.57 330 115 118 3 675.49 0.29 331 115 119 4 659.15 0.66 332 115 134 19 507.97 0.60 333 115 145 30 508.13 0.68 334 115 163 48 508.37 0.40 335 115 188 73 341.41 0.42 336 115 193 78 338.06 0.55 337 116 119 3 675.83 1.21 338 116 120 4 659.15 0.66 339 116 185 69 341.88 0.54 340 116 188 72 341.41 0.42 341 117 120 3 669.59 4.33 342 117 121 4 659.16 0.66 343 118 121 3 677.78 0.41 344 118 122 4 663.93 3.67 345 118 145 27 509.35 0.21 346 119 122 3 664.88 4.14 347 119 123 4 669.49 0.89 348 119 132 13 508.90 0.06 349 119 133 14 509.28 0.20 350 119 134 15 509.31 0.20 351 119 145 26 509.32 0.20 352 119 163 44 509.29 0.21 353 119 165 46 509.22 0.24 354 119 188 69 341.60 0.51 355 120 123 3 679.84 6.06 356 120 124 4 660.56 1.98 357 120 184 64 341.92 0.53 358 120 188 68 341.69 0.46 359 121 124 3 665.20 3.04 360 121 125 4 646.57 0.32 361 122 126 4 648.05 5.55 362 122 132 10 508.98 0.07 363 122 145 23 509.59 0.30 364 122 147 25 509.31 0.21 365 123 126 3 675.87 2.33 366 123 132 9 509.25 0.18 367 123 165 42 509.00 0.08 368 123 167 44 507.85 0.39 369 123 180 57 343.65 0.04 370 123 184 61 342.95 0.04 371 124 180 56 343.42 0.04 372 124 181 57 343.28 0.02 373 124 184 60 343.19 0.14 374 125 147 22 509.99 0.28 375 126 147 21 509.98 0.29 376 126 167 41 509.19 0.20 377 126 180 54 344.44 0.12 378 127 149 22 515.67 0.25 379 128 180 52 344.97 0.32 380 129 149 20 516.49 0.37 381 129 150 21 516.48 0.36 382 129 168 39 509.20 0.21 383 130 148 18 516.53 0.36 384 130 149 19 516.49 0.37 385 130 150 20 516.48 0.36 386 130 167 37 509.64 0.23 387 130 168 38 509.56 0.23 388 131 147 16 516.68 0.40 389 131 148 17 516.60 0.36 390 131 150 19 516.71 0.38 391 131 151 20 516.68 0.39 392 131 164 33 509.84 0.21 393 131 165 34 509.79 0.23 394 131 166 35 509.73 0.25 395 131 167 36 509.71 0.26 396 131 168 37 509.68 0.24 397 132 146 14 516.97 0.29 398 132 164 32 509.84 0.21 399 132 165 33 509.82 0.22 400 133 145 12 517.20 0.34 401 133 146 13 516.99 0.29 402 133 148 15 516.97 0.29 403 133 161 28 511.90 1.06 404 133 163 30 509.99 0.25 405 133 164 31 509.84 0.22 406 134 143 9 517.88 0.37 407 134 144 10 517.75 0.35 408 134 145 11 517.23 0.33 409 134 161 27 512.17 0.94 410 134 162 28 510.23 0.24 411 134 163 29 510.07 0.29 412 135 143 8 517.88 0.36 413 135 144 9 517.75 0.35 414 135 146 11 517.73 0.35 415 135 159 24 516.02 0.30 416 135 160 25 515.88 0.33 417 135 162 27 511.90 1.07 418 136 141 5 548.22 14.73 419 136 142 6 518.03 0.34 420 136 143 7 517.91 0.35 421 136 159 23 516.02 0.30 422 136 162 26 515.60 0.18 423 136 200 64 336.66 0.79 424 136 203 67 335.40 0.73 425 137 140 3 678.63 3.04 426 137 141 4 550.44 13.63 427 137 142 5 518.06 0.35 428 137 144 7 517.94 0.36 429 137 159 22 516.01 0.30 430 138 141 3 656.60 6.23 431 140 144 4 743.71 2.67 432 143 162 19 515.79 0.24 433 143 200 57 336.22 0.95 434 144 156 12 516.67 0.43 435 144 159 15 516.24 0.35 436 146 155 9 516.66 0.42 437 146 156 10 516.65 0.42 438 146 159 13 516.15 0.29 439 147 154 7 517.62 0.06 440 148 151 3 702.11 3.83 441 148 152 4 651.92 4.56 442 148 153 5 525.23 1.94 443 148 155 7 516.86 0.36 444 149 152 3 709.12 0.33 445 149 153 4 584.12 7.77 446 149 154 5 562.93 1.27 447 150 153 3 694.01 2.53 448 150 168 18 509.66 0.22 449 151 168 17 509.74 0.21 450 152 155 3 694.68 5.01 451 156 159 3 683.66 3.35 452 160 203 43 336.94 0.73 453 161 164 3 743.00 0.18 454 161 199 38 337.20 0.66 455 162 196 34 337.25 0.65 456 162 199 37 337.12 0.69 457 162 200 38 336.98 0.76 458 162 203 41 337.10 0.68 459 163 187 24 341.95 0.54 460 163 191 28 338.76 0.55 461 163 193 30 338.38 0.65 462 163 196 33 337.50 0.53 463 163 199 36 337.25 0.64 464 164 187 23 342.91 0.07 465 165 183 18 343.16 0.04 466 165 184 19 343.16 0.04 467 165 187 22 341.95 0.55 468 166 170 4 703.75 0.15 469 166 171 5 612.72 13.67 470 166 183 17 343.42 0.06 471 167 172 5 652.85 5.29 472 167 180 13 344.14 0.27 473 167 184 17 343.38 0.07 474 168 171 3 682.53 3.18 475 168 172 4 676.85 6.02 476 169 172 3 694.17 2.64 477 169 173 4 651.75 5.83 478 171 183 12 344.69 0.21 479 172 175 3 688.56 4.34 480 172 176 4 631.12 4.38 481 172 177 5 555.34 7.02 482 172 180 8 345.18 0.45 483 172 183 11 344.68 0.21 484 173 176 3 654.89 0.68 485 173 177 4 546.41 11.46 486 173 178 5 546.41 11.46 487 174 177 3 675.07 0.83 488 176 179 3 659.61 2.62 489 176 182 6 457.33 55.98 490 176 183 7 345.78 0.21 491 176 186 10 347.58 1.11 492 179 182 3 690.23 3.55 493 179 183 4 659.02 1.67 494 180 183 3 658.43 1.96 495 180 184 4 649.41 1.28 496 181 184 3 660.93 0.83 497 181 185 4 649.84 1.50 498 182 185 3 661.84 3.70 499 182 186 4 649.77 1.54 500 183 186 3 667.67 2.54 501 183 187 4 656.98 2.21 502 184 187 3 665.66 3.43 503 184 188 4 665.85 3.33 504 185 188 3 692.08 2.45 505 186 189 3 685.50 1.83 506 186 190 4 675.00 2.49 507 187 190 3 685.12 1.69 508 187 191 4 661.36 1.10 509 188 191 3 676.56 3.27 510 188 193 5 661.34 1.08 511 191 196 5 660.57 1.39 512 192 195 3 680.76 6.15 513 192 196 4 660.57 1.39 514 193 196 3 662.23 0.66 515 193 197 4 655.28 1.26 516 194 197 3 666.66 1.67 517 194 198 4 661.42 4.29 518 195 198 3 666.32 1.84 519 195 199 4 661.44 4.29 520 196 199 3 667.06 1.48 521 196 200 4 657.02 0.91 522 197 200 3 661.48 1.31 523 197 201 4 661.70 1.43 524 198 201 3 669.62 0.37 525 198 202 4 667.49 1.44 526 199 202 3 686.75 0.90 527 199 203 4 675.52 1.78 528 200 203 3 689.21 2.13 529 200 204 4 668.28 1.84 530 201 204 3 669.44 4.82