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 4 9 5 623.61 11.01 2 4 34 30 414.41 0.26 3 4 36 32 414.40 0.26 4 4 40 36 414.22 0.19 5 4 44 40 413.70 0.06 6 5 8 3 675.15 0.80 7 5 9 4 651.78 7.33 8 6 9 3 678.91 2.68 9 6 10 4 665.50 0.47 10 6 54 48 412.11 0.15 11 7 10 3 687.59 5.92 12 7 11 4 665.50 0.46 13 8 11 3 682.01 8.71 14 8 12 4 665.50 0.46 15 9 12 3 687.03 6.20 16 9 13 4 654.54 5.88 17 9 30 21 417.79 0.08 18 9 34 25 417.60 0.17 19 9 45 36 414.25 0.17 20 9 51 42 413.10 0.24 21 10 13 3 671.17 2.35 22 10 14 4 667.50 4.18 23 10 54 44 412.21 0.15 24 10 55 45 413.00 0.27 25 10 58 48 411.36 0.17 26 10 62 52 409.81 0.80 27 11 14 3 680.80 3.08 28 11 15 4 671.02 2.43 29 11 62 51 409.80 0.80 30 12 15 3 672.73 1.57 31 12 16 4 671.04 2.42 32 12 30 18 418.32 0.04 33 12 33 21 418.04 0.20 34 12 34 22 418.01 0.21 35 13 16 3 672.73 1.57 36 13 17 4 671.01 2.41 37 13 30 17 418.05 0.19 38 13 51 38 414.03 0.23 39 13 55 42 413.01 0.27 40 14 17 3 672.69 1.55 41 14 18 4 665.36 5.21 42 14 55 41 413.04 0.26 43 14 62 48 411.03 0.21 44 14 93 79 398.91 0.12 45 15 18 3 672.73 1.59 46 15 19 4 656.32 3.73 47 15 33 18 418.84 0.14 48 16 19 3 669.24 2.73 49 16 20 4 651.53 1.69 50 16 25 9 422.38 0.88 51 16 29 13 419.00 0.20 52 16 30 14 418.94 0.18 53 16 33 17 418.84 0.14 54 17 20 3 670.28 2.21 55 17 21 4 611.38 2.49 56 17 22 5 573.40 16.50 57 17 25 8 421.50 1.17 58 17 55 38 414.16 0.17 59 17 59 42 412.26 0.14 60 17 93 76 398.97 0.14 61 17 94 77 398.93 0.13 62 17 99 82 378.14 1.60 63 18 93 75 398.97 0.14 64 18 94 76 398.93 0.13 65 19 33 14 420.05 0.43 66 19 94 75 398.94 0.13 67 20 24 4 514.93 16.82 68 20 25 5 453.85 13.75 69 20 29 9 422.79 0.67 70 20 94 74 398.94 0.13 71 21 24 3 673.94 0.62 72 21 25 4 653.88 0.78 73 21 94 73 398.93 0.13 74 21 95 74 398.84 0.17 75 22 25 3 667.96 2.83 76 22 48 26 417.34 0.12 77 22 52 30 417.04 0.12 78 22 95 73 398.70 0.21 79 22 98 76 378.70 1.40 80 22 99 77 378.57 1.40 81 23 48 25 417.38 0.12 82 24 29 5 647.43 5.96 83 25 48 23 417.28 0.12 84 25 51 26 417.17 0.14 85 25 52 27 417.12 0.11 86 25 55 30 417.04 0.14 87 26 29 3 673.84 0.58 88 26 30 4 655.73 1.82 89 27 30 3 661.94 0.95 90 27 31 4 662.23 5.07 91 27 41 14 418.17 0.35 92 27 47 20 417.30 0.14 93 27 48 21 417.28 0.12 94 28 31 3 679.56 0.81 95 28 32 4 674.00 0.82 96 28 38 10 420.47 1.29 97 29 32 3 678.53 1.65 98 29 33 4 674.00 0.82 99 30 33 3 674.02 0.82 100 30 34 4 674.01 0.82 101 30 41 11 422.65 0.21 102 30 51 21 417.01 0.11 103 31 34 3 674.01 0.82 104 31 35 4 648.44 5.51 105 31 36 5 551.01 12.54 106 31 38 7 427.75 2.33 107 31 41 10 421.00 1.03 108 32 35 3 648.34 5.46 109 34 41 7 624.15 0.61 110 36 40 4 662.16 0.55 111 36 41 5 663.19 0.04 112 37 40 3 675.51 1.00 113 37 41 4 673.09 0.18 114 38 41 3 673.09 0.18 115 38 42 4 669.79 1.82 116 39 42 3 675.14 0.12 117 39 43 4 673.09 0.18 118 40 43 3 695.48 1.30 119 40 44 4 679.53 2.31 120 41 44 3 683.22 4.83 121 41 45 4 663.89 4.17 122 42 45 3 674.15 0.30 123 42 46 4 642.58 3.37 124 43 46 3 708.44 2.12 125 45 51 6 535.88 2.96 126 46 50 4 648.00 1.45 127 47 50 3 670.48 2.33 128 47 51 4 654.91 1.96 129 48 51 3 661.22 1.20 130 48 52 4 655.04 1.93 131 49 52 3 675.77 1.36 132 49 53 4 658.25 0.32 133 50 53 3 684.69 6.45 134 50 54 4 658.26 0.32 135 51 54 3 676.38 2.30 136 51 55 4 658.25 0.31 137 52 55 3 677.18 1.90 138 52 56 4 651.17 3.22 139 52 99 47 372.11 4.38 140 53 56 3 673.12 1.22 141 53 57 4 656.55 2.94 142 53 103 50 338.99 0.53 143 54 57 3 673.65 0.31 144 54 58 4 659.50 6.79 145 55 58 3 666.11 3.48 146 55 59 4 654.03 4.05 147 55 99 44 377.26 2.02 148 56 59 3 684.13 4.31 149 56 60 4 674.00 0.47 150 56 99 43 377.26 2.02 151 56 100 44 372.11 4.39 152 56 103 47 339.21 0.41 153 57 60 3 684.75 0.51 154 57 61 4 648.78 1.28 155 57 106 49 338.85 0.29 156 57 109 52 338.06 0.27 157 58 61 3 670.19 2.37 158 58 62 4 645.49 0.36 159 59 62 3 684.41 1.70 160 59 63 4 652.98 4.21 161 59 89 30 399.20 0.20 162 59 93 34 399.00 0.15 163 59 99 40 377.38 2.06 164 60 63 3 666.18 3.49 165 60 64 4 622.78 5.02 166 60 86 26 399.51 0.28 167 60 89 29 399.31 0.23 168 60 100 40 377.37 2.07 169 60 109 49 339.07 0.37 170 63 89 26 399.43 0.28 171 63 92 29 399.06 0.13 172 63 93 30 399.07 0.13 173 64 67 3 704.02 4.94 174 64 82 18 399.81 0.23 175 64 85 21 399.50 0.27 176 64 86 22 399.53 0.27 177 64 89 25 399.44 0.28 178 65 85 20 399.69 0.21 179 66 70 4 686.15 0.86 180 66 73 7 616.03 1.51 181 66 78 12 400.10 0.10 182 66 81 15 399.86 0.21 183 66 82 16 399.81 0.23 184 66 85 19 399.73 0.20 185 67 78 11 400.25 0.08 186 67 82 15 399.84 0.23 187 67 112 45 339.14 0.41 188 67 116 49 339.01 0.41 189 68 78 10 400.25 0.07 190 68 112 44 339.16 0.41 191 68 115 47 339.10 0.39 192 69 73 4 652.87 1.14 193 69 78 9 400.23 0.07 194 69 115 46 339.14 0.41 195 69 119 50 338.34 0.68 196 70 73 3 652.87 1.14 197 73 77 4 658.39 0.57 198 73 78 5 649.99 0.55 199 73 81 8 631.21 0.22 200 73 119 46 339.16 0.43 201 74 77 3 658.40 0.57 202 74 78 4 658.10 0.71 203 75 78 3 671.99 5.44 204 75 79 4 658.16 0.68 205 75 119 44 339.12 0.46 206 75 120 45 338.83 0.56 207 75 123 48 328.14 0.54 208 75 125 50 324.94 0.07 209 75 194 119 80.50 0.32 210 75 197 122 79.93 0.26 211 75 198 123 72.36 1.06 212 75 201 126 59.00 0.96 213 76 79 3 674.28 4.29 214 76 80 4 674.28 4.29 215 76 194 118 80.48 0.33 216 76 198 122 72.36 1.06 217 77 80 3 683.93 0.54 218 77 81 4 670.45 6.20 219 78 81 3 683.93 0.54 220 78 82 4 663.83 3.54 221 78 116 38 339.19 0.41 222 78 119 41 339.01 0.47 223 79 82 3 677.96 3.52 224 79 83 4 672.66 0.89 225 79 120 41 338.77 0.39 226 79 137 58 216.42 0.54 227 79 194 115 80.47 0.33 228 79 197 118 76.13 0.61 229 80 83 3 681.19 3.37 230 80 84 4 674.49 0.02 231 80 190 110 86.03 0.26 232 80 191 111 86.03 0.26 233 80 194 114 80.47 0.32 234 81 84 3 674.81 0.18 235 81 85 4 665.65 4.45 236 82 85 3 674.50 0.02 237 82 86 4 667.34 3.60 238 82 116 34 339.13 0.40 239 83 86 3 666.32 4.08 240 83 87 4 658.34 0.91 241 83 137 54 216.31 0.48 242 83 141 58 216.16 0.52 243 83 186 103 87.78 0.02 244 83 190 107 86.03 0.27 245 84 87 3 662.88 2.37 246 84 88 4 659.50 1.76 247 84 186 102 87.74 0.04 248 84 187 103 87.58 0.10 249 84 190 106 86.03 0.26 250 85 88 3 659.86 1.59 251 85 89 4 658.08 1.04 252 86 89 3 670.98 1.79 253 86 90 4 658.07 1.04 254 86 100 14 389.05 0.67 255 86 138 52 216.20 0.49 256 86 141 55 216.13 0.50 257 87 90 3 666.41 3.27 258 87 91 4 658.88 1.46 259 87 141 54 216.13 0.50 260 87 145 58 215.81 0.45 261 87 148 61 215.81 0.43 262 87 181 94 87.84 0.03 263 87 183 96 87.80 0.02 264 87 186 99 87.72 0.05 265 88 91 3 668.26 0.42 266 88 92 4 658.88 1.47 267 89 92 3 674.75 0.37 268 90 96 6 394.05 1.83 269 90 97 7 389.09 0.65 270 90 100 10 378.67 1.59 271 90 142 52 216.13 0.51 272 90 145 55 215.81 0.43 273 90 149 59 208.33 1.98 274 91 145 54 215.81 0.43 275 91 149 58 208.32 1.98 276 91 181 90 87.80 0.02 277 93 96 3 655.94 0.74 278 93 149 56 208.01 2.12 279 95 98 3 664.25 3.81 280 95 99 4 660.74 1.22 281 95 149 54 208.00 2.12 282 96 99 3 674.87 3.82 283 96 100 4 660.74 1.23 284 96 149 53 208.03 2.13 285 97 100 3 665.37 1.75 286 97 101 4 663.57 2.65 287 97 142 45 216.11 0.51 288 97 145 48 215.82 0.43 289 97 146 49 215.71 0.47 290 97 149 52 208.03 2.13 291 98 101 3 676.34 0.26 292 98 102 4 667.86 0.51 293 98 146 48 215.64 0.50 294 98 150 52 207.97 2.14 295 99 102 3 682.52 2.32 296 100 103 3 677.29 0.22 297 100 142 42 216.10 0.52 298 101 142 41 216.11 0.52 299 101 146 45 215.81 0.42 300 105 109 4 603.58 5.71 301 105 110 5 603.57 5.71 302 106 109 3 644.81 6.64 303 106 110 4 652.21 2.94 304 107 110 3 674.64 3.77 305 109 112 3 683.84 1.70 306 109 113 4 659.38 2.91 307 110 113 3 685.85 3.86 308 110 114 4 659.38 2.91 309 111 114 3 678.39 5.64 310 111 115 4 663.41 0.89 311 112 115 3 665.60 0.20 312 112 116 4 660.16 0.74 313 113 116 3 670.46 6.07 314 113 117 4 652.88 2.62 315 114 117 3 671.68 1.90 316 114 118 4 651.93 2.10 317 115 118 3 671.66 1.90 318 115 119 4 651.50 1.88 319 116 119 3 678.63 1.59 320 116 120 4 663.72 3.25 321 116 134 18 216.62 0.45 322 117 120 3 668.63 3.42 323 117 121 4 663.72 3.25 324 117 131 14 216.66 0.46 325 117 134 17 216.63 0.45 326 118 121 3 679.52 2.14 327 118 122 4 661.31 4.44 328 119 122 3 679.52 2.13 329 119 123 4 661.34 4.42 330 120 123 3 666.99 4.12 331 120 124 4 659.75 3.64 332 120 125 5 602.75 16.62 333 120 130 10 216.88 0.52 334 120 133 13 217.55 0.18 335 120 134 14 216.87 0.52 336 121 124 3 663.86 5.69 337 121 125 4 615.51 10.23 338 121 126 5 599.41 18.29 339 121 127 6 512.75 2.03 340 124 201 77 59.56 0.23 341 125 129 4 644.61 2.68 342 125 130 5 592.90 14.85 343 125 201 76 58.50 0.71 344 126 129 3 672.90 2.58 345 126 130 4 659.96 3.88 346 127 130 3 672.90 2.58 347 127 131 4 659.96 3.88 348 128 131 3 669.25 0.77 349 128 132 4 659.96 3.88 350 129 132 3 671.84 2.42 351 129 133 4 653.83 6.58 352 130 133 3 666.28 7.21 353 130 134 4 653.84 6.58 354 131 134 3 674.24 1.23 355 131 135 4 651.49 5.41 356 132 135 3 667.52 2.12 357 132 136 4 660.40 1.03 358 133 136 3 672.13 2.62 359 133 137 4 662.52 0.02 360 133 197 64 72.36 1.06 361 134 137 3 674.61 3.76 362 134 138 4 662.52 0.02 363 135 138 3 669.84 3.63 364 135 139 4 656.52 2.96 365 136 139 3 677.23 0.07 366 136 140 4 656.34 2.87 367 136 193 57 80.50 0.33 368 136 197 61 72.36 1.06 369 137 140 3 673.10 1.17 370 137 141 4 656.33 2.86 371 137 190 53 86.16 0.23 372 137 193 56 80.50 0.33 373 137 197 60 72.36 1.06 374 138 141 3 669.11 1.54 375 138 142 4 655.11 2.44 376 139 142 3 661.84 0.47 377 139 143 4 644.99 2.67 378 140 143 3 670.48 0.61 379 140 144 4 652.95 1.28 380 140 186 46 87.79 0.02 381 140 189 49 86.65 0.01 382 140 190 50 86.08 0.27 383 140 193 53 80.50 0.33 384 141 144 3 663.27 0.55 385 141 145 4 657.94 1.73 386 141 186 45 87.73 0.05 387 142 145 3 664.92 1.37 388 142 146 4 652.97 0.76 389 143 146 3 670.78 3.21 390 143 147 4 658.09 1.80 391 144 147 3 672.65 2.29 392 144 148 4 658.11 1.82 393 144 186 42 87.64 0.09 394 145 148 3 672.64 2.27 395 145 149 4 656.09 2.83 396 146 149 3 657.50 2.12 397 146 150 4 653.13 1.78 398 147 151 4 658.24 1.77 399 148 151 3 670.75 1.45 400 148 152 4 661.38 0.36 401 148 181 33 87.79 0.03 402 149 152 3 689.63 1.13 403 149 153 4 666.76 1.66 404 150 153 3 666.76 1.66 405 150 154 4 662.02 0.06 406 151 154 3 670.54 1.54 407 151 155 4 661.44 0.24 408 152 155 3 664.27 1.18 409 152 156 4 662.02 0.05 410 153 156 3 687.38 0.27 411 154 157 3 670.43 6.37 412 154 158 4 658.76 0.56 413 155 158 3 673.24 4.96 414 162 165 3 708.98 0.80 415 163 166 3 663.14 0.83 416 163 171 8 116.05 3.70 417 166 170 4 652.43 2.71 418 166 171 5 593.25 14.10 419 166 174 8 589.97 21.64 420 167 170 3 680.63 1.21 421 167 171 4 656.62 0.60 422 168 171 3 669.76 1.93 423 168 172 4 656.62 0.60 424 169 172 3 661.87 2.02 425 169 173 4 646.24 1.64 426 170 173 3 653.41 1.01 427 170 174 4 646.21 1.63 428 171 174 3 697.20 1.83 429 171 175 4 657.46 4.00 430 172 175 3 669.37 3.87 431 172 176 4 662.45 1.50 432 173 176 3 667.49 1.02 433 173 177 4 662.45 1.50 434 174 177 3 665.60 0.07 435 174 178 4 662.00 1.71 436 175 178 3 668.15 0.64 437 175 179 4 650.68 3.95 438 176 179 3 668.72 1.19 439 177 180 3 723.51 1.57 440 177 185 8 111.67 6.37 441 180 183 3 698.97 0.60 442 180 184 4 677.39 0.47 443 182 185 3 690.86 2.10 444 182 186 4 659.64 0.56 445 183 186 3 666.92 1.37 446 183 187 4 659.75 0.61 447 184 187 3 684.80 0.35 448 184 188 4 656.82 2.09 449 185 188 3 679.63 6.19 450 185 189 4 656.84 2.09 451 186 189 3 675.48 5.01 452 186 190 4 670.08 4.53 453 187 190 3 670.08 4.53 454 187 191 4 670.11 4.54 455 188 191 3 672.28 3.51 456 188 192 4 670.12 4.54 457 189 192 3 676.94 1.14 458 189 193 4 667.65 5.78 459 190 193 3 667.64 5.79 460 190 194 4 669.94 4.63 461 191 194 3 667.44 0.86 462 191 195 4 664.12 1.73 463 192 195 3 677.18 6.10 464 192 196 4 664.12 1.73 465 193 196 3 671.94 2.17 466 193 197 4 651.61 3.50 467 194 197 3 672.10 2.08 468 194 198 4 653.97 2.33 469 195 198 3 667.46 4.41 470 195 199 4 660.20 0.78 471 196 199 3 672.10 2.09 472 196 200 4 660.20 0.78 473 197 200 3 667.34 4.34 474 197 201 4 667.33 4.34 475 198 201 3 666.56 4.74 476 198 202 4 666.54 4.74 477 199 202 3 685.43 3.77 478 199 203 4 657.35 2.27 479 199 208 9 18.86 0.04 480 200 203 3 685.43 3.77 481 200 204 4 673.50 2.19 482 200 208 8 18.84 0.02 483 201 204 3 682.64 2.17 484 203 206 3 645.79 3.66 485 203 208 5 98.18 0.03