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 1 187 182 27.80 0.36 2 1 225 220 27.79 0.36 3 1 227 222 25.70 0.10 4 1 229 224 25.70 0.10 5 2 7 5 742.39 4.39 6 2 229 223 26.48 0.18 7 3 6 3 764.70 1.80 8 3 7 4 757.86 3.29 9 4 7 3 757.86 3.29 10 4 8 4 751.89 0.27 11 4 130 122 27.14 0.52 12 4 133 125 25.94 0.12 13 4 229 221 27.16 0.51 14 4 231 223 26.45 0.17 15 5 8 3 767.01 0.97 16 5 9 4 758.22 3.43 17 6 9 3 768.49 1.72 18 7 10 3 767.83 0.99 19 7 12 5 751.89 0.26 20 7 183 172 36.59 1.36 21 7 229 218 28.82 0.01 22 7 231 220 28.82 0.00 23 8 181 169 31.78 0.11 24 8 231 219 28.30 0.25 25 10 183 169 61.57 0.82 26 10 195 181 65.51 0.60 27 12 181 165 64.72 0.60 28 12 183 167 65.20 0.47 29 12 197 181 65.67 0.68 30 12 231 215 58.56 0.05 31 13 17 4 751.82 0.22 32 13 181 164 65.64 0.67 33 13 197 180 65.75 0.69 34 13 199 182 65.73 0.69 35 13 200 183 65.75 0.69 36 13 202 185 66.20 0.54 37 14 17 3 778.92 4.59 38 14 180 162 65.70 0.69 39 14 181 163 65.67 0.66 40 15 18 3 769.59 0.07 41 15 23 8 618.46 8.51 42 15 171 152 65.77 0.69 43 15 172 153 65.75 0.70 44 15 173 154 65.75 0.70 45 15 177 158 65.73 0.69 46 15 179 160 65.71 0.69 47 15 180 161 65.70 0.69 48 15 199 180 65.81 0.68 49 18 22 4 693.19 2.38 50 18 23 5 675.59 6.41 51 18 26 8 684.25 4.17 52 18 199 177 66.37 0.47 53 19 204 181 150.88 0.38 54 20 204 180 152.52 1.03 55 21 24 3 754.96 2.83 56 21 25 4 750.62 2.89 57 21 204 179 152.61 0.99 58 22 25 3 756.12 4.09 59 22 26 4 741.96 3.90 60 22 203 177 153.62 0.53 61 22 204 178 152.62 0.99 62 23 26 3 756.64 0.12 63 23 27 4 752.32 0.80 64 23 170 143 169.03 0.09 65 23 171 144 177.22 0.07 66 23 172 145 181.25 1.33 67 23 199 172 166.19 1.50 68 24 27 3 778.48 0.37 69 24 28 4 751.29 0.29 70 25 28 3 762.21 5.74 71 25 29 4 751.68 0.96 72 25 204 175 176.75 0.24 73 25 205 176 170.89 0.65 74 25 209 180 170.82 0.69 75 26 29 3 760.96 6.37 76 26 30 4 750.90 1.34 77 26 170 140 181.60 1.26 78 26 201 171 181.19 1.37 79 26 209 179 170.92 0.64 80 27 30 3 759.56 0.78 81 27 31 4 738.09 3.41 82 27 32 5 734.71 1.73 83 27 164 133 181.66 1.25 84 27 170 139 181.61 1.26 85 27 171 140 181.74 1.24 86 28 31 3 767.78 6.00 87 28 32 4 715.93 6.11 88 28 33 5 715.88 6.08 89 29 33 4 696.50 3.56 90 29 90 57 181.52 1.25 91 29 157 124 181.65 1.23 92 29 206 173 181.77 1.25 93 29 209 176 181.75 1.25 94 29 210 177 181.68 1.24 95 30 157 123 181.65 1.23 96 30 160 126 181.69 1.25 97 30 161 127 181.72 1.24 98 30 170 136 183.33 1.22 99 30 213 179 181.77 1.25 100 31 161 126 181.77 1.25 101 31 164 129 182.71 1.44 102 31 165 130 185.34 0.20 103 33 90 53 203.41 1.39 104 33 91 54 203.74 1.25 105 34 91 53 203.88 1.30 106 35 88 49 203.88 1.30 107 35 89 50 203.83 1.29 108 35 90 51 203.82 1.29 109 35 91 52 203.90 1.30 110 35 157 118 203.75 1.27 111 35 161 122 203.88 1.31 112 36 57 21 204.62 1.38 113 36 67 27 204.20 1.34 114 36 87 47 203.89 1.30 115 36 88 48 203.88 1.30 116 36 89 49 203.84 1.28 117 36 91 51 203.99 1.33 118 36 107 67 203.98 1.34 119 37 87 46 203.90 1.30 120 37 88 47 203.90 1.30 121 38 41 3 865.94 2.60 122 38 57 19 205.09 1.17 123 38 86 44 204.01 1.25 124 38 87 45 204.06 1.27 125 39 86 43 204.01 1.25 126 39 118 75 203.12 1.18 127 40 84 40 204.34 1.38 128 40 85 41 204.24 1.33 129 40 86 42 204.31 1.30 130 40 114 70 204.05 1.24 131 41 54 13 206.30 0.79 132 41 57 16 206.22 0.80 133 41 83 38 204.65 1.32 134 41 84 39 204.62 1.32 135 41 85 40 204.50 1.35 136 41 87 42 204.59 1.31 137 42 54 12 206.67 0.95 138 42 83 37 204.65 1.32 139 42 84 38 204.65 1.32 140 42 85 39 204.63 1.32 141 43 52 9 206.65 0.95 142 43 53 10 207.13 1.00 143 43 54 11 206.86 0.85 144 43 81 34 206.71 0.43 145 43 82 35 206.72 0.43 146 44 81 33 206.71 0.43 147 44 82 34 206.75 0.43 148 45 52 7 391.59 89.56 149 45 53 8 211.57 0.45 150 45 55 10 211.61 0.45 151 46 49 3 792.22 3.65 152 46 51 5 622.62 4.92 153 46 52 6 211.62 0.45 154 46 53 7 391.61 89.56 155 46 77 27 217.41 0.91 156 46 81 31 220.03 0.99 157 47 51 4 741.43 4.16 158 47 68 17 212.35 0.42 159 47 97 46 214.08 1.28 160 47 98 47 212.09 0.57 161 48 51 3 772.49 1.76 162 49 74 21 225.46 0.37 163 49 77 24 225.46 0.37 164 50 70 16 225.41 0.35 165 50 71 17 225.33 0.31 166 50 73 19 225.45 0.37 167 50 74 20 225.46 0.37 168 50 77 23 225.47 0.37 169 50 214 160 225.33 0.31 170 51 68 13 225.56 0.39 171 51 69 14 225.45 0.36 172 51 70 15 225.42 0.35 173 51 77 22 226.34 0.07 174 52 68 12 226.61 0.17 175 52 69 13 225.93 0.20 176 52 71 15 226.28 0.12 177 52 77 21 226.50 0.14 178 52 80 24 226.72 0.14 179 52 81 25 226.91 0.23 180 53 66 9 227.12 0.20 181 53 67 10 226.94 0.22 182 53 68 11 226.88 0.24 183 53 98 41 227.03 0.21 184 53 99 42 227.09 0.18 185 54 57 3 755.92 1.03 186 54 66 8 227.26 0.27 187 54 67 9 227.02 0.21 188 54 69 11 227.05 0.21 189 54 85 27 227.19 0.21 190 54 87 29 226.97 0.24 191 55 66 7 227.30 0.28 192 56 65 5 229.19 0.82 193 56 66 6 227.49 0.23 194 57 65 4 230.18 0.64 195 57 66 5 229.75 0.57 196 57 67 6 229.02 0.88 197 57 87 26 228.47 0.62 198 58 65 3 230.18 0.64 199 58 66 4 230.21 0.66 200 58 67 5 230.18 0.64 201 58 91 29 230.05 0.70 202 58 105 43 230.18 0.64 203 64 91 27 255.55 0.76 204 64 93 29 252.05 0.35 205 64 103 39 278.94 3.35 206 64 104 40 270.58 1.55 207 64 105 41 254.91 1.08 208 65 100 35 296.01 0.33 209 65 103 38 295.70 0.30 210 66 99 33 295.99 0.35 211 66 100 34 296.02 0.33 212 66 103 37 295.94 0.33 213 66 104 38 295.66 0.28 214 66 105 39 295.65 0.28 215 67 87 20 295.69 0.25 216 67 91 24 295.64 0.29 217 67 105 38 295.66 0.28 218 67 107 40 295.66 0.28 219 68 97 29 296.03 0.33 220 68 98 30 296.03 0.33 221 68 104 36 296.00 0.33 222 68 105 37 295.94 0.33 223 68 106 38 295.82 0.32 224 68 107 39 295.82 0.32 225 69 87 18 295.86 0.34 226 69 107 38 295.83 0.31 227 69 109 40 295.85 0.33 228 69 111 42 295.88 0.33 229 70 107 37 295.96 0.34 230 70 108 38 295.92 0.34 231 70 109 39 295.92 0.34 232 70 214 144 295.88 0.32 233 71 76 5 732.53 0.20 234 71 77 6 717.39 3.77 235 71 80 9 698.78 13.07 236 71 109 38 295.94 0.34 237 71 111 40 296.01 0.32 238 71 214 143 295.93 0.34 239 71 216 145 295.91 0.33 240 72 76 4 756.62 0.42 241 72 214 142 295.94 0.33 242 72 215 143 295.94 0.33 243 73 76 3 775.06 1.01 244 73 77 4 756.58 0.40 245 74 77 3 756.59 0.40 246 74 78 4 756.61 0.41 247 75 78 3 776.98 0.04 248 75 79 4 765.45 1.33 249 76 79 3 772.35 0.96 250 76 80 4 765.47 1.35 251 76 215 139 296.12 0.33 252 76 216 140 296.12 0.34 253 77 80 3 769.56 0.43 254 77 81 4 754.05 0.77 255 78 81 3 762.57 2.76 256 79 83 4 765.71 1.22 257 79 113 34 296.85 0.35 258 80 83 3 756.90 1.05 259 80 85 5 724.22 7.00 260 80 111 31 296.78 0.37 261 80 112 32 296.83 0.35 262 80 113 33 298.63 0.54 263 80 216 136 296.80 0.36 264 83 113 30 360.45 0.49 265 84 113 29 360.51 0.49 266 84 114 30 360.51 0.49 267 85 111 26 360.48 0.48 268 85 112 27 360.50 0.49 269 85 113 28 360.51 0.49 270 85 114 29 360.52 0.49 271 86 111 25 360.56 0.48 272 86 112 26 360.56 0.48 273 86 114 28 360.57 0.48 274 86 147 61 360.50 0.49 275 87 107 20 360.65 0.49 276 87 110 23 360.56 0.47 277 87 111 24 360.57 0.47 278 88 110 22 360.58 0.48 279 88 153 65 360.52 0.47 280 88 154 66 360.48 0.48 281 88 157 69 360.48 0.48 282 88 158 70 360.49 0.48 283 89 107 18 360.74 0.49 284 89 153 64 360.53 0.46 285 89 157 68 360.49 0.48 286 90 107 17 360.75 0.49 287 90 153 63 360.63 0.49 288 90 157 67 360.54 0.46 289 90 210 120 360.59 0.48 290 91 105 14 606.19 10.69 291 91 106 15 604.42 11.54 292 91 107 16 360.76 0.50 293 92 96 4 739.69 0.19 294 92 105 13 611.37 8.11 295 92 106 14 606.14 10.68 296 92 108 16 606.14 10.68 297 92 206 114 360.79 0.50 298 92 207 115 360.73 0.53 299 92 210 118 360.81 0.51 300 93 96 3 757.33 1.65 301 93 105 12 641.14 6.77 302 94 205 111 360.85 0.51 303 94 207 113 360.87 0.51 304 95 207 112 360.88 0.51 305 107 110 3 853.48 3.05 306 108 153 45 362.03 0.61 307 108 207 99 361.50 0.53 308 108 210 102 361.48 0.52 309 108 211 103 361.35 0.46 310 108 213 105 361.49 0.53 311 108 214 106 361.75 0.67 312 109 153 44 362.13 0.61 313 109 213 104 362.05 0.61 314 109 214 105 362.06 0.61 315 109 216 107 362.12 0.61 316 110 151 41 362.19 0.62 317 110 153 43 362.14 0.61 318 110 216 106 362.21 0.62 319 111 151 40 362.30 0.63 320 111 216 105 362.33 0.62 321 112 117 5 727.56 1.44 322 112 147 35 362.50 0.63 323 112 149 37 362.47 0.65 324 112 150 38 362.41 0.65 325 112 151 39 362.35 0.63 326 112 218 106 362.43 0.66 327 113 117 4 745.02 2.83 328 114 117 3 767.41 3.68 329 117 146 29 403.77 1.33 330 117 147 30 403.09 1.31 331 117 148 31 403.09 1.33 332 117 149 32 403.07 1.32 333 118 146 28 403.84 1.36 334 119 123 4 746.66 2.38 335 119 145 26 404.36 1.12 336 119 146 27 403.98 1.30 337 119 147 28 403.85 1.37 338 119 148 29 421.18 1.49 339 119 221 102 424.03 0.07 340 122 144 22 491.59 2.41 341 122 145 23 491.55 2.40 342 122 146 24 491.51 2.42 343 123 144 21 491.62 2.41 344 123 145 22 491.57 2.40 345 123 221 98 491.53 2.41 346 123 222 99 491.55 2.42 347 124 140 16 491.73 2.42 348 124 141 17 491.72 2.42 349 124 143 19 491.68 2.42 350 124 144 20 491.64 2.42 351 125 143 18 491.69 2.41 352 125 144 19 491.68 2.42 353 125 145 20 491.68 2.42 354 125 155 30 491.55 2.42 355 125 224 99 491.55 2.42 356 125 225 100 491.54 2.42 357 125 226 101 491.51 2.42 358 126 140 14 491.79 2.41 359 126 224 98 491.57 2.42 360 126 225 99 491.55 2.42 361 126 226 100 491.54 2.42 362 127 138 11 491.85 2.40 363 127 142 15 491.79 2.41 364 127 143 16 491.78 2.41 365 127 226 99 491.55 2.42 366 127 228 101 491.53 2.42 367 128 225 97 491.61 2.42 368 128 226 98 491.56 2.42 369 128 227 99 491.54 2.43 370 128 228 100 491.54 2.42 371 129 135 6 583.12 0.39 372 129 136 7 529.87 21.34 373 129 138 9 491.94 2.40 374 129 163 34 491.59 2.43 375 129 167 38 491.56 2.43 376 129 228 99 491.54 2.42 377 129 230 101 491.53 2.42 378 130 133 3 751.14 0.12 379 130 134 4 642.01 0.48 380 130 135 5 583.13 0.38 381 130 227 97 491.61 2.42 382 130 228 98 491.56 2.42 383 130 229 99 491.54 2.42 384 130 230 100 491.53 2.42 385 131 134 3 745.26 3.06 386 131 136 5 649.82 7.35 387 131 167 36 491.61 2.42 388 131 179 48 491.56 2.43 389 131 230 99 491.54 2.42 390 131 232 101 491.50 2.43 391 132 230 98 491.55 2.42 392 132 231 99 491.50 2.43 393 132 232 100 491.50 2.43 394 136 167 31 491.60 2.42 395 138 142 4 756.06 5.66 396 138 162 24 491.59 2.43 397 139 142 3 766.05 6.26 398 139 162 23 491.58 2.43 399 141 144 3 790.24 0.45 400 142 162 20 491.50 2.43 401 143 155 12 491.56 2.42 402 143 158 15 491.51 2.44 403 143 159 16 491.51 2.44 404 143 226 83 491.55 2.42 405 144 158 14 491.51 2.44 406 145 150 5 687.11 9.05 407 145 154 9 598.52 5.48 408 145 155 10 491.52 2.44 409 145 221 76 492.96 2.43 410 147 150 3 759.28 2.92 411 147 154 7 714.38 1.91 412 147 221 74 540.27 1.00 413 148 220 72 540.46 0.94 414 148 221 73 540.28 0.99 415 149 218 69 541.29 1.27 416 149 219 70 540.53 0.97 417 149 220 71 540.49 0.95 418 150 154 4 748.19 6.02 419 150 155 5 741.95 9.12 420 150 218 68 541.55 1.16 421 150 219 69 541.28 1.28 422 150 221 71 540.55 0.96 423 151 154 3 763.89 1.83 424 151 155 4 744.66 7.79 425 151 216 65 541.57 1.16 426 151 217 66 541.58 1.16 427 151 218 67 541.56 1.16 428 152 155 3 762.11 0.94 429 152 156 4 741.95 9.13 430 152 186 34 540.54 0.97 431 152 194 42 540.62 0.99 432 152 196 44 540.53 0.96 433 152 217 65 541.65 1.19 434 152 219 67 541.67 1.19 435 153 156 3 759.23 0.51 436 153 157 4 747.70 6.24 437 153 213 60 541.53 1.18 438 154 157 3 769.22 0.10 439 154 158 4 763.74 1.76 440 155 158 3 762.34 2.46 441 155 159 4 742.39 1.72 442 155 186 31 541.98 1.22 443 155 219 64 542.43 1.15 444 155 224 69 542.78 0.96 445 155 226 71 541.83 1.14 446 156 159 3 758.21 4.53 447 156 160 4 736.13 6.52 448 156 184 28 541.63 1.17 449 156 186 30 542.24 1.10 450 156 196 40 541.69 1.21 451 156 213 57 542.14 1.28 452 157 161 4 741.53 2.14 453 158 161 3 770.39 0.30 454 158 162 4 760.73 3.40 455 159 162 3 770.40 0.30 456 159 163 4 760.73 3.40 457 159 184 25 542.45 1.14 458 159 226 67 542.96 0.89 459 159 228 69 542.62 1.04 460 160 163 3 764.11 1.71 461 160 164 4 752.18 7.67 462 160 170 10 654.42 5.35 463 160 196 36 543.17 1.13 464 160 198 38 542.40 1.16 465 160 212 52 543.77 1.09 466 161 164 3 769.25 0.86 467 161 165 4 746.48 4.83 468 162 165 3 759.62 8.97 469 162 166 4 737.11 0.14 470 162 167 5 737.06 0.16 471 163 167 4 717.82 0.87 472 163 168 5 714.47 2.54 473 163 169 6 678.90 1.72 474 163 198 35 543.53 0.95 475 163 228 65 543.02 0.92 476 163 230 67 542.90 0.96 477 164 168 4 706.67 0.59 478 164 169 5 678.96 1.69 479 164 170 6 678.91 1.71 480 164 171 7 678.90 1.71 481 167 179 12 562.89 1.80 482 167 230 63 543.01 0.91 483 168 171 3 749.86 5.05 484 168 176 8 585.57 2.88 485 168 177 9 566.86 0.18 486 169 179 10 544.26 0.88 487 169 198 29 544.22 0.85 488 169 199 30 544.23 0.85 489 169 230 61 543.01 0.91 490 170 198 28 544.24 0.85 491 170 199 29 544.24 0.84 492 171 175 4 698.49 7.50 493 171 177 6 595.79 5.03 494 172 175 3 740.77 2.25 495 172 176 4 733.88 0.56 496 172 177 5 649.86 11.11 497 173 176 3 751.30 5.45 498 173 177 4 675.81 1.86 499 173 180 7 623.56 0.48 500 178 232 54 543.12 0.79 501 179 199 20 556.02 0.58 502 179 230 51 543.48 0.87 503 179 231 52 543.24 0.81 504 179 232 53 543.13 0.79 505 180 199 19 556.02 0.58 506 180 231 51 543.44 0.89 507 180 232 52 543.19 0.83 508 180 233 53 543.08 0.77 509 181 199 18 555.97 0.61 510 181 230 49 543.60 0.93 511 181 231 50 543.27 0.82 512 181 233 52 543.19 0.83 513 182 197 15 556.44 0.59 514 182 198 16 556.16 0.55 515 182 199 17 556.26 0.60 516 182 229 47 544.52 0.67 517 182 230 48 543.59 0.93 518 183 195 12 556.67 0.61 519 183 196 13 556.56 0.59 520 183 197 14 556.44 0.59 521 183 198 15 556.41 0.60 522 183 228 45 545.04 0.78 523 183 229 46 544.56 0.65 524 184 195 11 556.68 0.61 525 184 196 12 556.63 0.63 526 184 198 14 556.50 0.60 527 184 226 42 546.23 0.82 528 184 227 43 546.16 0.81 529 184 228 44 545.75 0.74 530 185 193 8 557.50 0.35 531 185 194 9 557.46 0.35 532 185 195 10 556.68 0.61 533 185 226 41 546.25 0.81 534 185 227 42 546.16 0.80 535 185 229 44 546.15 0.81 536 186 193 7 557.51 0.35 537 186 194 8 557.50 0.35 538 186 196 10 557.46 0.35 539 186 219 33 548.07 0.62 540 186 225 39 546.82 0.91 541 186 226 40 546.49 0.93 542 187 193 6 557.51 0.35 543 187 224 37 547.10 0.86 544 187 225 38 546.83 0.92 545 187 227 40 546.57 0.96 546 188 191 3 774.22 1.14 547 188 192 4 746.50 1.41 548 188 193 5 562.12 0.98 549 188 219 31 548.12 0.59 550 188 224 36 547.12 0.86 551 189 223 34 547.33 0.96 552 191 219 28 548.40 0.70 553 191 220 29 548.40 0.70 554 194 217 23 548.38 0.71 555 196 212 16 549.37 0.36 556 196 213 17 549.37 0.36 557 197 200 3 729.05 10.57 558 198 228 30 545.77 0.75 559 198 230 32 544.54 0.66 560 201 209 8 570.25 4.47 561 202 208 6 620.89 5.03 562 202 209 7 619.25 4.74 563 203 208 5 649.79 3.54 564 203 209 6 646.10 5.36 565 204 209 5 727.17 4.07 566 205 208 3 778.83 2.98 567 205 209 4 729.74 2.80 568 206 209 3 756.95 5.67 569 206 210 4 729.75 2.79 570 207 211 4 754.91 2.37 571 208 211 3 773.15 0.21 572 209 212 3 821.78 5.69 573 210 213 3 785.89 0.52 574 211 214 3 772.10 6.36 575 213 216 3 774.80 4.24 576 219 224 5 743.90 0.04 577 220 224 4 762.75 1.04 578 221 224 3 775.75 6.10