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 24 20 50.54 0.42 2 4 92 88 50.53 0.42 3 4 93 89 50.51 0.41 4 4 94 90 50.40 0.42 5 6 95 89 50.45 0.39 6 7 21 14 50.56 0.40 7 7 22 15 50.62 0.40 8 7 60 53 50.66 0.40 9 7 94 87 50.62 0.40 10 7 95 88 50.52 0.41 11 7 96 89 50.44 0.40 12 7 97 90 50.38 0.42 13 8 97 89 50.45 0.41 14 8 99 91 50.38 0.42 15 9 13 4 682.44 1.57 16 9 66 57 50.55 0.40 17 9 97 88 50.54 0.42 18 9 98 89 50.45 0.41 19 9 99 90 50.38 0.42 20 10 13 3 696.06 0.19 21 10 99 89 50.47 0.42 22 11 66 55 50.56 0.41 23 11 67 56 50.57 0.40 24 11 68 57 50.55 0.41 25 11 69 58 50.57 0.40 26 11 98 87 50.59 0.41 27 11 99 88 50.55 0.40 28 11 100 89 50.51 0.40 29 11 101 90 50.45 0.39 30 11 103 92 50.45 0.39 31 12 65 53 50.62 0.40 32 12 66 54 50.61 0.40 33 12 101 89 50.55 0.39 34 12 103 91 50.49 0.41 35 13 17 4 726.13 3.48 36 13 19 6 646.00 0.38 37 13 65 52 50.65 0.41 38 14 19 5 694.23 3.56 39 16 19 3 783.77 0.46 40 17 62 45 61.97 0.89 41 17 63 46 59.63 0.38 42 17 64 47 59.27 0.20 43 17 65 48 59.27 0.21 44 18 61 43 65.64 0.03 45 18 62 44 61.97 0.89 46 18 63 45 59.29 0.21 47 19 61 42 65.78 0.03 48 19 62 43 65.59 0.01 49 20 59 39 73.19 0.71 50 20 60 40 65.89 0.01 51 20 61 41 65.83 0.01 52 21 51 30 65.89 0.01 53 21 60 39 68.17 1.11 54 21 61 40 65.88 0.01 55 21 62 41 65.88 0.01 56 21 96 75 65.75 0.04 57 22 59 37 82.30 1.27 58 22 60 38 76.55 0.64 59 23 57 34 85.07 0.04 60 23 58 35 82.41 1.26 61 23 59 36 82.28 1.29 62 24 36 12 87.11 0.77 63 24 53 29 82.43 1.27 64 24 58 34 82.44 1.27 65 24 60 36 82.40 1.27 66 24 78 54 82.42 1.27 67 24 92 68 82.45 1.29 68 24 94 70 82.42 1.28 69 25 36 11 93.09 0.14 70 26 29 3 683.59 0.54 71 26 34 8 257.12 5.38 72 26 36 10 93.51 0.04 73 26 80 54 93.13 0.15 74 26 88 62 104.28 0.81 75 26 89 63 98.75 1.54 76 27 30 3 703.96 3.54 77 28 31 3 669.53 2.75 78 28 32 4 666.07 1.01 79 28 34 6 615.70 7.08 80 28 88 60 108.17 0.98 81 28 89 61 108.17 0.98 82 29 32 3 666.08 1.02 83 29 34 5 615.37 6.92 84 29 36 7 616.21 6.50 85 32 82 50 186.71 0.52 86 32 88 56 186.31 0.66 87 33 56 23 248.39 2.99 88 33 82 49 186.76 0.53 89 33 83 50 186.74 0.54 90 34 80 46 186.81 0.53 91 34 81 47 186.80 0.53 92 34 82 48 186.82 0.55 93 34 88 54 186.62 0.56 94 35 55 20 248.40 2.99 95 35 56 21 248.41 3.00 96 35 80 45 186.91 0.52 97 35 81 46 186.84 0.54 98 35 83 48 186.87 0.56 99 36 53 17 248.56 3.08 100 36 55 19 248.42 2.99 101 36 58 22 248.41 3.00 102 36 79 43 186.95 0.53 103 36 80 44 186.91 0.53 104 37 53 16 248.82 2.97 105 37 78 41 187.15 0.47 106 37 79 42 187.07 0.50 107 38 43 5 623.63 1.51 108 38 51 13 258.92 2.06 109 38 52 14 248.95 2.93 110 38 53 15 248.94 2.97 111 38 60 22 248.91 2.96 112 38 76 38 187.39 0.47 113 38 77 39 187.24 0.48 114 38 78 40 187.16 0.48 115 38 79 41 187.16 0.48 116 38 94 56 186.56 0.56 117 39 43 4 629.56 1.39 118 39 44 5 623.61 1.52 119 39 45 6 623.60 1.51 120 39 76 37 187.40 0.47 121 39 77 38 187.35 0.48 122 39 79 40 187.22 0.47 123 40 43 3 667.05 0.62 124 40 44 4 629.57 1.40 125 40 45 5 623.61 1.52 126 40 76 36 187.47 0.49 127 41 45 4 623.62 1.52 128 41 46 5 623.60 1.51 129 41 74 33 187.98 0.46 130 41 76 35 187.68 0.47 131 42 45 3 696.39 5.10 132 42 47 5 623.53 1.51 133 42 49 7 521.07 48.26 134 42 50 8 516.61 47.38 135 42 51 9 513.25 49.05 136 42 74 32 187.98 0.46 137 42 76 34 187.81 0.48 138 43 48 5 520.94 48.19 139 43 49 6 519.08 48.57 140 43 51 8 441.11 85.08 141 43 76 33 187.53 0.46 142 44 48 4 636.01 1.94 143 45 48 3 670.33 2.75 144 47 50 3 712.62 2.46 145 47 71 24 200.91 5.46 146 47 74 27 189.10 0.93 147 49 52 3 680.20 2.66 148 49 63 14 249.66 2.71 149 50 62 12 249.66 2.71 150 50 63 13 249.66 2.71 151 50 64 14 249.65 2.70 152 50 66 16 249.22 2.68 153 50 74 24 188.10 0.43 154 51 60 9 249.93 2.61 155 51 61 10 249.74 2.69 156 51 62 11 249.67 2.71 157 51 66 15 249.66 2.71 158 51 74 23 187.97 0.46 159 51 76 25 187.60 0.49 160 51 96 45 186.53 0.58 161 52 60 8 249.93 2.61 162 52 61 9 249.90 2.62 163 52 63 11 249.76 2.68 164 53 58 5 252.87 1.23 165 53 59 6 250.13 2.58 166 53 60 7 249.93 2.61 167 54 57 3 677.82 3.79 168 54 58 4 443.21 1.52 169 54 59 5 250.14 2.58 170 54 61 7 250.12 2.58 171 60 94 34 186.61 0.58 172 60 96 36 186.24 0.47 173 62 66 4 694.22 0.82 174 66 74 8 348.64 34.42 175 66 98 32 186.34 0.65 176 67 70 3 674.05 2.49 177 67 71 4 661.22 0.27 178 68 71 3 674.06 2.49 179 68 72 4 602.50 5.66 180 68 98 30 186.44 0.64 181 68 99 31 186.43 0.64 182 68 100 32 185.81 0.46 183 68 135 67 156.57 0.24 184 68 136 68 160.43 1.67 185 68 137 69 165.72 0.60 186 69 100 31 186.44 0.64 187 69 103 34 169.91 1.36 188 69 104 35 160.46 1.71 189 69 135 66 156.56 0.24 190 69 136 67 160.40 1.67 191 71 74 3 743.64 1.27 192 71 98 27 186.60 0.56 193 72 97 25 186.62 0.57 194 72 98 26 186.50 0.55 195 73 95 22 186.74 0.58 196 73 96 23 186.60 0.56 197 73 98 25 186.50 0.56 198 74 94 20 186.76 0.58 199 74 95 21 186.59 0.56 200 74 96 22 186.56 0.56 201 74 98 24 186.52 0.56 202 75 93 18 186.75 0.58 203 75 94 19 186.60 0.55 204 75 95 20 186.56 0.56 205 76 93 17 186.65 0.56 206 76 94 18 186.58 0.55 207 76 96 20 186.53 0.56 208 77 91 14 186.75 0.58 209 77 92 15 186.64 0.57 210 77 93 16 186.57 0.55 211 78 91 13 186.65 0.56 212 78 92 14 186.60 0.56 213 78 94 16 186.54 0.55 214 79 91 12 186.57 0.55 215 80 87 7 229.03 19.87 216 80 88 8 190.34 0.54 217 80 89 9 188.84 0.14 218 81 85 4 627.68 2.12 219 81 86 5 339.96 35.58 220 81 87 6 229.04 19.87 221 81 88 7 229.03 19.87 222 82 85 3 658.43 1.79 223 82 86 4 608.34 2.75 224 82 88 6 259.75 4.51 225 100 136 36 364.69 0.83 226 100 137 37 370.78 1.25 227 100 141 41 384.46 2.37 228 100 143 43 377.98 3.28 229 101 136 35 387.94 0.23 230 101 143 42 383.28 2.10 231 102 136 34 398.85 0.14 232 102 143 41 383.28 2.10 233 102 195 93 377.99 3.27 234 102 196 94 389.29 0.58 235 102 201 99 374.88 0.69 236 103 136 33 400.47 0.60 237 103 201 98 398.89 0.12 238 104 134 30 399.05 0.09 239 104 135 31 399.09 0.08 240 104 136 32 401.13 0.28 241 104 195 91 399.09 0.09 242 104 201 97 398.97 0.12 243 105 201 96 398.94 0.10 244 105 202 97 398.91 0.12 245 106 132 26 399.06 0.08 246 106 133 27 400.34 0.55 247 106 134 28 400.46 0.60 248 106 146 40 401.41 0.49 249 106 193 87 398.94 0.10 250 106 194 88 400.34 0.54 251 106 195 89 403.68 0.23 252 106 201 95 404.42 0.28 253 106 202 96 399.07 0.09 254 106 203 97 398.93 0.11 255 107 132 25 400.34 0.55 256 107 133 26 401.06 0.32 257 107 203 96 401.16 0.95 258 108 113 5 661.13 1.22 259 108 130 22 400.34 0.55 260 108 131 23 400.48 0.61 261 108 132 24 400.48 0.61 262 108 148 40 404.44 0.24 263 108 191 83 401.35 0.43 264 108 192 84 404.34 0.20 265 108 193 85 404.44 0.24 266 108 203 95 404.67 0.23 267 108 204 96 404.50 0.27 268 108 205 97 399.06 0.08 269 109 113 4 700.07 1.43 270 109 131 22 404.48 0.28 271 109 132 23 404.68 0.23 272 109 133 24 404.74 0.24 273 110 113 3 700.07 1.43 274 110 205 95 404.69 0.24 275 111 205 94 404.69 0.24 276 111 206 95 404.68 0.24 277 112 206 94 404.68 0.24 278 112 208 96 404.60 0.26 279 113 128 15 404.92 0.21 280 113 129 16 404.91 0.23 281 113 130 17 404.88 0.23 282 113 131 18 404.98 0.22 283 113 205 92 404.83 0.25 284 113 206 93 404.72 0.24 285 113 207 94 404.68 0.23 286 113 208 95 404.65 0.24 287 114 128 14 404.95 0.21 288 114 208 94 404.69 0.24 289 115 128 13 404.95 0.21 290 115 208 93 404.73 0.24 291 115 209 94 404.66 0.24 292 115 210 95 404.65 0.24 293 116 127 11 405.00 0.21 294 116 209 93 404.70 0.24 295 116 210 94 404.65 0.24 296 116 212 96 404.54 0.28 297 117 121 4 655.10 3.00 298 117 127 10 405.01 0.21 299 117 163 46 404.95 0.21 300 117 174 57 404.97 0.20 301 117 179 62 404.84 0.24 302 117 209 92 404.81 0.25 303 117 210 93 404.72 0.24 304 117 211 94 404.64 0.24 305 117 212 95 404.60 0.26 306 118 121 3 666.29 2.60 307 118 179 61 404.87 0.23 308 118 212 94 404.64 0.24 309 119 179 60 404.87 0.23 310 119 180 61 404.87 0.23 311 119 181 62 404.78 0.27 312 119 211 92 404.77 0.25 313 119 212 93 404.70 0.24 314 119 213 94 404.64 0.24 315 121 125 4 632.80 2.29 316 121 174 53 405.13 0.22 317 122 125 3 678.05 0.55 318 122 174 52 405.20 0.24 319 123 174 51 405.20 0.25 320 123 175 52 405.16 0.24 321 123 176 53 405.10 0.24 322 123 177 54 405.07 0.23 323 124 174 50 405.24 0.24 324 125 173 48 405.57 0.27 325 125 174 49 405.28 0.25 326 126 171 45 405.80 0.26 327 126 172 46 405.70 0.29 328 126 173 47 405.59 0.28 329 127 172 45 405.78 0.26 330 127 173 46 405.73 0.30 331 127 174 47 405.69 0.30 332 127 209 82 405.64 0.32 333 128 171 43 406.03 0.26 334 128 172 44 405.82 0.26 335 128 207 79 405.81 0.27 336 128 209 81 405.61 0.26 337 129 169 40 406.25 0.26 338 129 170 41 406.18 0.28 339 129 171 42 406.05 0.24 340 130 148 18 406.35 0.24 341 130 170 40 406.25 0.26 342 130 172 42 406.16 0.27 343 130 191 61 406.13 0.29 344 130 207 77 405.88 0.26 345 131 148 17 406.50 0.20 346 132 146 14 406.72 0.24 347 132 148 16 406.62 0.20 348 132 193 61 406.52 0.21 349 133 146 13 406.88 0.23 350 134 143 9 407.29 0.28 351 134 144 10 406.91 0.23 352 134 146 12 406.89 0.23 353 134 195 61 406.90 0.23 354 136 143 7 407.32 0.26 355 136 144 8 407.28 0.27 356 137 140 3 679.50 4.12 357 137 141 4 612.78 6.50 358 138 141 3 674.74 1.35 359 138 144 6 407.92 0.50 360 142 145 3 653.14 0.43 361 142 196 54 483.74 0.59 362 142 197 55 512.77 6.10 363 143 195 52 503.54 0.55 364 143 196 53 517.97 1.97 365 144 195 51 525.78 0.96 366 145 195 50 533.88 0.96 367 145 196 51 534.24 1.14 368 145 197 52 534.27 1.12 369 146 193 47 533.17 1.00 370 146 194 48 534.21 1.13 371 146 195 49 534.24 1.14 372 147 167 20 586.03 0.79 373 147 193 46 534.29 1.14 374 147 194 47 534.29 1.14 375 147 197 50 534.34 1.13 376 147 198 51 534.32 1.14 377 148 165 17 586.00 0.81 378 148 166 18 586.07 0.79 379 148 167 19 586.06 0.80 380 148 168 20 586.20 0.84 381 148 169 21 586.20 0.84 382 148 170 22 586.03 0.87 383 148 192 44 534.29 1.14 384 148 193 45 534.30 1.14 385 149 165 16 586.14 0.83 386 149 191 42 534.31 1.14 387 149 192 43 534.31 1.14 388 150 163 13 586.15 0.83 389 150 164 14 586.14 0.83 390 150 165 15 586.18 0.83 391 150 189 39 534.28 1.17 392 150 190 40 534.51 1.06 393 150 191 41 534.31 1.14 394 151 190 39 534.55 1.06 395 151 192 41 534.50 1.09 396 151 204 53 534.42 1.10 397 152 189 37 534.76 1.05 398 152 190 38 534.58 1.05 399 153 156 3 702.92 2.14 400 153 157 4 722.68 0.89 401 153 159 6 656.50 0.03 402 153 160 7 592.07 0.95 403 153 161 8 591.70 0.94 404 153 162 9 590.73 1.42 405 153 187 34 536.89 0.61 406 153 188 35 536.85 0.62 407 153 189 36 534.75 1.04 408 154 187 33 536.94 0.60 409 154 188 34 536.86 0.62 410 155 184 29 539.42 0.76 411 155 186 31 539.14 0.67 412 155 187 32 537.08 0.66 413 156 159 3 670.04 0.59 414 156 160 4 640.06 6.50 415 157 184 27 539.49 0.78 416 157 187 30 539.34 0.73 417 158 162 4 680.20 3.16 418 158 178 20 585.88 0.98 419 158 184 26 539.58 0.82 420 158 187 29 539.46 0.77 421 159 162 3 703.43 0.52 422 159 176 17 587.25 0.51 423 161 175 14 587.45 0.45 424 161 176 15 587.33 0.51 425 162 174 12 587.57 0.51 426 162 175 13 587.46 0.45 427 162 176 14 587.33 0.50 428 162 177 15 587.33 0.51 429 162 178 16 587.30 0.50 430 162 179 17 586.60 0.74 431 162 187 25 536.87 0.63 432 163 172 9 587.81 0.50 433 163 173 10 587.66 0.49 434 163 174 11 587.58 0.50 435 163 175 12 587.52 0.48 436 163 179 16 587.33 0.51 437 163 187 24 536.86 0.63 438 163 189 26 535.04 1.18 439 163 209 46 533.86 0.96 440 164 172 8 587.81 0.51 441 164 173 9 587.72 0.51 442 164 175 11 587.56 0.49 443 165 170 5 588.26 0.30 444 165 171 6 588.10 0.37 445 165 172 7 587.79 0.52 446 166 169 3 674.00 9.53 447 166 170 4 602.48 1.90 448 166 171 5 588.22 0.32 449 167 197 30 534.55 1.15 450 167 198 31 534.54 1.16 451 172 189 17 534.78 1.06 452 172 191 19 534.63 1.11 453 172 207 35 533.85 0.96 454 172 209 37 532.12 1.27 455 179 187 8 539.55 0.84 456 179 211 32 533.75 0.94 457 180 183 3 665.27 2.56 458 180 184 4 607.61 5.45 459 181 184 3 658.43 0.81 460 181 185 4 599.73 3.52 461 181 211 30 534.14 1.05 462 181 212 31 534.14 1.05 463 181 213 32 533.77 0.92 464 184 187 3 757.77 1.41 465 184 211 27 534.28 1.12 466 185 210 25 534.29 1.12 467 185 211 26 534.27 1.12 468 186 208 22 534.46 1.10 469 186 209 23 534.31 1.12 470 186 210 24 534.27 1.11 471 187 207 20 534.49 1.10 472 187 208 21 534.31 1.12 473 187 209 22 534.29 1.12 474 187 211 24 534.26 1.11 475 188 206 18 534.50 1.10 476 188 207 19 534.39 1.08 477 188 208 20 534.29 1.12 478 189 206 17 534.44 1.09 479 189 207 18 534.29 1.11 480 189 209 20 534.26 1.11 481 190 204 14 534.53 1.10 482 190 205 15 534.50 1.10 483 190 206 16 534.38 1.06 484 191 204 13 534.52 1.11 485 191 205 14 534.50 1.11 486 191 207 16 534.37 1.06 487 192 202 10 535.12 1.07 488 192 203 11 534.97 1.00 489 192 204 12 534.51 1.12 490 193 202 9 535.12 1.07 491 193 203 10 535.06 1.05 492 194 198 4 599.07 2.57 493 194 201 7 535.52 0.98 494 194 202 8 535.11 1.07 495 195 198 3 656.50 2.29 496 195 199 4 631.03 4.63 497 195 200 5 566.45 12.21 498 195 201 6 538.03 1.84 499 196 199 3 656.50 2.29 500 196 200 4 599.11 2.59