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 2 19 17 44.20 0.18 2 2 20 18 43.92 0.29 3 2 23 21 46.44 0.11 4 2 70 68 34.10 0.16 5 3 20 17 46.03 0.03 6 3 23 20 46.52 0.14 7 3 57 54 46.66 0.24 8 3 70 67 37.20 0.85 9 3 71 68 42.95 0.03 10 3 72 69 45.27 0.47 11 4 57 53 46.66 0.24 12 4 58 54 46.66 0.24 13 4 60 56 46.56 0.23 14 4 70 66 46.54 0.19 15 5 60 55 47.62 0.53 16 5 69 64 47.23 0.48 17 5 70 65 46.70 0.21 18 6 60 54 47.72 0.55 19 6 62 56 47.73 0.56 20 6 63 57 47.68 0.56 21 6 64 58 47.68 0.57 22 6 67 61 47.66 0.58 23 6 68 62 47.51 0.54 24 6 69 63 47.31 0.47 25 7 11 4 580.31 0.31 26 7 12 5 559.68 0.66 27 7 16 9 522.45 4.04 28 7 67 60 47.70 0.56 29 7 68 61 47.68 0.56 30 7 70 63 47.86 0.59 31 8 11 3 604.73 9.95 32 8 12 4 586.08 0.62 33 8 66 58 47.79 0.60 34 8 67 59 47.79 0.60 35 9 12 3 612.39 6.11 36 9 36 27 47.79 0.61 37 9 66 57 47.81 0.59 38 9 67 58 47.84 0.60 39 9 68 59 47.86 0.59 40 11 16 5 567.09 3.48 41 12 17 5 568.38 4.12 42 12 34 22 48.15 0.60 43 12 35 23 48.14 0.60 44 12 36 24 48.10 0.62 45 12 68 56 48.20 0.62 46 12 70 58 49.81 0.60 47 12 170 158 48.09 0.61 48 13 16 3 588.16 1.48 49 13 17 4 586.00 0.40 50 14 17 3 589.71 1.46 51 14 18 4 579.12 1.25 52 14 160 146 63.67 0.28 53 14 162 148 69.44 0.23 54 14 168 154 68.82 0.03 55 14 170 156 57.94 0.93 56 15 18 3 588.47 1.15 57 15 19 4 581.37 1.23 58 16 19 3 584.69 1.16 59 16 20 4 584.30 1.34 60 16 70 54 69.60 0.30 61 17 20 3 582.44 2.28 62 17 21 4 582.45 2.27 63 17 32 15 69.84 0.24 64 17 33 16 69.74 0.29 65 17 34 17 69.62 0.30 66 17 70 53 69.71 0.29 67 17 168 151 69.95 0.20 68 17 169 152 69.94 0.20 69 17 170 153 69.74 0.29 70 18 21 3 586.10 0.46 71 18 22 4 586.09 0.46 72 18 168 150 70.08 0.23 73 19 22 3 589.43 2.12 74 19 23 4 581.60 1.82 75 20 23 3 585.86 3.11 76 20 24 4 585.02 3.53 77 20 32 12 70.44 0.38 78 20 70 50 70.43 0.39 79 20 71 51 70.44 0.38 80 20 72 52 70.44 0.38 81 21 24 3 595.25 5.07 82 21 25 4 589.02 1.53 83 21 30 9 70.89 0.30 84 21 31 10 70.84 0.32 85 21 32 11 70.67 0.39 86 21 166 145 70.86 0.31 87 21 167 146 70.85 0.31 88 21 168 147 70.84 0.32 89 22 25 3 591.36 2.53 90 24 30 6 279.44 103.42 91 24 31 7 279.43 103.42 92 24 72 48 71.25 0.14 93 24 73 49 71.33 0.17 94 24 74 50 75.24 0.55 95 25 30 5 568.03 3.89 96 27 30 3 639.91 0.74 97 27 74 47 153.63 0.18 98 27 75 48 174.94 0.72 99 27 77 50 175.09 0.80 100 28 75 47 175.13 0.79 101 28 165 137 174.95 0.77 102 29 74 45 175.15 0.79 103 29 75 46 175.13 0.79 104 29 83 54 175.12 0.78 105 29 104 75 175.05 0.76 106 29 105 76 175.13 0.78 107 29 106 77 175.13 0.78 108 29 108 79 175.19 0.78 109 29 165 136 174.96 0.77 110 30 73 43 175.18 0.78 111 30 74 44 175.15 0.79 112 30 165 135 175.10 0.78 113 30 166 136 175.08 0.78 114 30 167 137 175.07 0.78 115 31 72 41 175.27 0.81 116 31 73 42 175.22 0.78 117 31 84 53 175.19 0.78 118 31 102 71 175.11 0.79 119 31 104 73 175.16 0.78 120 31 161 130 175.09 0.78 121 31 167 136 175.07 0.78 122 31 169 138 175.07 0.78 123 32 71 39 175.50 0.86 124 32 72 40 175.38 0.82 125 32 167 135 175.14 0.78 126 32 168 136 175.09 0.78 127 32 169 137 175.09 0.78 128 33 70 37 175.57 0.87 129 33 71 38 175.51 0.85 130 33 88 55 175.23 0.79 131 33 102 69 175.22 0.78 132 33 169 136 175.09 0.78 133 34 69 35 175.84 0.90 134 34 70 36 175.60 0.86 135 34 169 135 175.14 0.78 136 34 170 136 175.10 0.78 137 34 171 137 175.08 0.78 138 35 43 8 461.79 11.72 139 35 68 33 176.12 0.78 140 35 69 34 175.93 0.86 141 35 88 53 175.50 0.84 142 35 100 65 175.24 0.79 143 35 171 136 175.10 0.79 144 35 173 138 175.07 0.78 145 36 67 31 416.16 21.66 146 36 68 32 176.13 0.77 147 36 171 135 175.13 0.78 148 36 172 136 175.08 0.78 149 36 173 137 175.07 0.78 150 37 41 4 588.11 1.71 151 37 42 5 554.30 0.65 152 37 43 6 519.38 2.71 153 37 63 26 449.56 5.58 154 37 64 27 462.81 0.98 155 37 65 28 451.22 4.79 156 37 66 29 451.20 4.79 157 37 67 30 449.39 5.58 158 38 65 27 473.08 2.60 159 38 66 28 454.64 3.08 160 38 172 134 175.16 0.78 161 38 173 135 175.10 0.78 162 38 174 136 175.08 0.78 163 38 175 137 175.08 0.78 164 39 43 4 619.74 2.04 165 39 65 26 493.12 5.80 166 39 92 53 407.67 0.74 167 39 155 116 175.18 0.76 168 39 173 134 175.16 0.78 169 39 175 136 175.09 0.79 170 40 65 25 493.18 5.81 171 40 175 135 175.09 0.79 172 41 65 24 493.62 5.69 173 41 93 52 432.78 0.55 174 42 63 21 494.39 5.63 175 42 64 22 494.33 5.63 176 42 92 50 432.91 0.59 177 42 93 51 432.91 0.59 178 43 62 19 494.77 5.79 179 43 63 20 494.65 5.76 180 43 69 26 494.57 5.71 181 43 90 47 432.95 0.65 182 43 91 48 432.94 0.57 183 43 92 49 432.91 0.59 184 43 173 130 175.16 0.79 185 44 61 17 494.91 5.73 186 44 62 18 494.77 5.79 187 44 90 46 433.60 0.77 188 44 91 47 433.03 0.57 189 45 59 14 494.88 5.72 190 45 60 15 494.92 5.73 191 45 61 16 494.91 5.74 192 45 90 45 433.82 0.69 193 46 89 43 434.25 0.56 194 46 90 44 434.06 0.64 195 46 91 45 433.96 0.67 196 46 97 51 433.82 0.64 197 46 123 77 340.15 1.08 198 46 124 78 340.13 1.09 199 46 125 79 339.88 1.09 200 47 59 12 495.13 5.70 201 47 88 41 434.38 0.55 202 47 89 42 434.32 0.55 203 47 125 78 340.06 1.08 204 47 126 79 339.89 1.10 205 48 59 11 495.19 5.70 206 48 71 23 495.12 5.69 207 48 87 39 434.53 0.58 208 48 88 40 434.37 0.54 209 48 126 78 340.00 1.08 210 49 86 37 434.57 0.58 211 49 87 38 434.53 0.58 212 49 126 77 340.06 1.08 213 49 127 78 339.96 1.07 214 49 128 79 339.89 1.10 215 49 131 82 325.20 1.08 216 50 53 3 618.54 2.09 217 50 54 4 576.28 2.77 218 50 55 5 576.27 2.77 219 50 71 21 495.25 5.68 220 50 73 23 495.13 5.70 221 50 85 35 434.85 0.62 222 50 86 36 434.61 0.57 223 50 102 52 433.81 0.64 224 51 85 34 435.14 0.74 225 51 86 35 434.81 0.58 226 51 128 77 340.00 1.08 227 51 131 80 339.34 1.22 228 52 83 31 435.26 0.77 229 52 84 32 435.25 0.77 230 52 85 33 435.14 0.73 231 53 74 21 494.98 5.73 232 53 75 22 494.68 5.70 233 53 76 23 494.75 5.66 234 53 83 30 435.26 0.77 235 53 84 31 435.23 0.78 236 54 73 19 495.16 5.70 237 54 74 20 495.12 5.69 238 54 76 22 494.99 5.71 239 55 71 16 495.33 5.68 240 55 72 17 495.23 5.67 241 55 73 18 495.16 5.70 242 56 74 18 495.26 5.66 243 57 71 14 495.42 5.67 244 57 72 15 495.37 5.65 245 58 71 13 495.54 5.63 246 59 71 12 495.57 5.65 247 59 88 29 434.43 0.57 248 59 90 31 434.32 0.52 249 60 63 3 636.43 0.88 250 60 69 9 495.75 5.71 251 60 70 10 495.75 5.71 252 60 71 11 495.74 5.71 253 60 90 30 434.32 0.52 254 63 67 4 549.78 4.06 255 63 69 6 495.85 5.70 256 63 90 27 433.73 0.73 257 64 67 3 589.10 1.40 258 69 90 21 434.31 0.52 259 71 88 17 434.41 0.53 260 74 84 10 435.15 0.73 261 75 80 5 558.78 0.33 262 75 82 7 435.30 0.77 263 75 83 8 435.28 0.77 264 75 84 9 435.23 0.77 265 76 80 4 585.53 0.64 266 81 106 25 431.37 0.06 267 82 106 24 431.35 0.06 268 83 104 21 432.37 0.31 269 83 105 22 431.37 0.08 270 83 106 23 431.33 0.07 271 84 102 18 433.80 0.66 272 84 103 19 433.14 0.49 273 84 104 20 432.30 0.28 274 85 102 17 433.73 0.62 275 85 103 18 432.36 0.30 276 85 104 19 432.31 0.28 277 85 131 46 332.41 3.54 278 86 101 15 433.75 0.61 279 86 102 16 433.64 0.62 280 87 100 13 433.76 0.62 281 87 101 14 433.32 0.78 282 87 126 39 340.00 1.08 283 87 131 44 325.10 1.08 284 88 99 11 433.78 0.62 285 88 100 12 433.67 0.63 286 88 102 14 433.56 0.65 287 88 126 38 339.86 1.08 288 89 97 8 433.88 0.61 289 89 98 9 433.80 0.61 290 89 99 10 433.67 0.64 291 89 124 35 340.13 1.08 292 89 126 37 339.69 1.06 293 89 130 41 325.16 1.08 294 90 97 7 433.82 0.59 295 90 98 8 433.79 0.60 296 91 95 4 566.55 5.84 297 91 96 5 467.67 16.27 298 91 123 32 340.12 1.09 299 92 95 3 580.59 2.44 300 92 96 4 518.96 2.88 301 92 98 6 466.75 15.80 302 92 119 27 341.03 1.28 303 92 155 63 237.38 0.40 304 95 122 27 340.23 1.14 305 96 119 23 341.06 1.30 306 96 120 24 340.91 1.31 307 96 121 25 340.29 1.13 308 96 122 26 340.22 1.14 309 96 153 57 237.60 0.37 310 97 119 22 341.02 1.28 311 97 120 23 340.67 1.12 312 97 122 25 340.28 1.12 313 97 123 26 340.23 1.12 314 97 124 27 340.08 1.08 315 97 130 33 325.16 1.08 316 98 117 19 341.26 1.32 317 98 118 20 341.13 1.27 318 98 119 21 341.00 1.28 319 98 151 53 237.61 0.36 320 98 173 75 175.13 0.80 321 99 117 18 341.27 1.32 322 99 118 19 341.14 1.27 323 99 120 21 341.12 1.26 324 99 130 31 325.14 1.09 325 99 134 35 319.45 0.26 326 100 116 16 341.31 1.31 327 100 117 17 341.27 1.32 328 100 134 34 319.48 0.25 329 100 169 69 175.35 0.77 330 100 171 71 175.18 0.78 331 101 114 13 341.50 1.29 332 101 115 14 341.38 1.31 333 101 116 15 341.33 1.31 334 101 131 30 325.17 1.12 335 101 134 33 319.48 0.24 336 101 135 34 319.47 0.25 337 101 139 38 275.10 4.73 338 102 114 12 341.51 1.29 339 102 115 13 341.39 1.31 340 102 161 59 232.29 0.04 341 102 169 67 175.15 0.79 342 103 113 10 341.63 1.25 343 103 114 11 341.53 1.29 344 103 135 32 319.47 0.24 345 103 161 58 232.44 0.01 346 104 108 4 617.75 1.28 347 104 113 9 341.63 1.25 348 104 161 57 232.43 0.01 349 104 165 61 175.73 0.58 350 104 167 63 175.30 0.74 351 105 108 3 637.29 4.92 352 105 111 6 518.00 3.31 353 105 112 7 432.24 43.91 354 105 113 8 341.77 1.28 355 107 110 3 613.26 0.19 356 107 111 4 588.35 0.75 357 108 111 3 584.15 1.34 358 108 112 4 568.37 1.26 359 108 113 5 579.19 3.83 360 108 164 56 231.15 0.15 361 108 165 57 226.35 2.24 362 112 141 29 275.07 4.75 363 113 141 28 275.05 4.75 364 113 142 29 274.73 4.65 365 113 161 48 232.69 0.09 366 113 162 49 232.41 0.01 367 113 163 50 229.81 0.50 368 113 164 51 223.13 1.06 369 113 167 54 176.27 0.27 370 114 135 21 319.55 0.27 371 114 139 25 275.11 4.74 372 114 140 26 275.08 4.74 373 114 141 27 274.79 4.62 374 114 142 28 274.70 4.62 375 114 161 47 232.44 0.01 376 115 139 24 275.09 4.73 377 115 140 25 275.03 4.71 378 115 141 26 274.79 4.62 379 115 142 27 274.70 4.62 380 115 147 32 238.38 0.68 381 115 157 42 237.80 0.43 382 115 159 44 234.60 0.29 383 115 160 45 232.83 0.09 384 115 161 46 232.42 0.01 385 115 169 54 175.21 0.79 386 115 171 56 175.18 0.78 387 116 134 18 319.52 0.26 388 116 138 22 275.13 4.73 389 116 139 23 275.07 4.73 390 116 149 33 237.76 0.42 391 117 134 17 319.54 0.28 392 117 149 32 237.66 0.36 393 117 151 34 237.66 0.37 394 117 157 40 237.31 0.38 395 117 171 54 175.19 0.78 396 117 173 56 175.13 0.79 397 118 133 15 320.90 0.13 398 118 134 16 319.48 0.26 399 118 151 33 237.62 0.35 400 119 151 32 237.59 0.35 401 119 153 34 237.68 0.38 402 119 155 36 237.58 0.37 403 120 124 4 572.89 0.42 404 120 130 10 325.16 1.08 405 120 133 13 320.13 0.00 406 120 134 14 319.56 0.29 407 121 124 3 658.82 0.03 408 121 153 32 237.62 0.36 409 124 130 6 569.79 0.69 410 125 130 5 570.74 1.10 411 126 130 4 570.74 1.10 412 127 130 3 586.39 0.39 413 127 131 4 576.91 1.99 414 128 131 3 583.77 1.94 415 128 132 4 576.88 1.98 416 129 132 3 591.38 2.88 417 129 133 4 576.88 1.98 418 130 133 3 579.33 0.76 419 130 134 4 576.88 1.99 420 131 134 3 587.84 3.55 421 131 135 4 576.31 2.26 422 132 136 4 552.27 7.81 423 133 137 4 532.20 1.06 424 134 139 5 275.09 4.74 425 135 139 4 410.77 72.56 426 140 147 7 238.34 0.66 427 140 148 8 238.41 0.67 428 140 149 9 238.41 0.67 429 140 157 17 237.91 0.40 430 142 161 19 232.68 0.09 431 142 162 20 232.42 0.01 432 142 163 21 231.86 0.18 433 143 147 4 645.74 1.98 434 143 161 18 234.25 0.39 435 143 163 20 232.41 0.01 436 144 160 16 237.44 0.29 437 144 161 17 234.80 0.38 438 144 162 18 232.83 0.07 439 144 163 19 232.81 0.07 440 145 160 15 237.46 0.29 441 146 158 12 238.02 0.34 442 146 159 13 237.69 0.30 443 146 160 14 237.61 0.34 444 146 170 24 175.65 0.61 445 147 158 11 238.00 0.33 446 147 159 12 237.80 0.27 447 148 156 8 239.40 0.29 448 148 157 9 238.75 0.14 449 148 158 10 237.99 0.33 450 149 156 7 239.41 0.29 451 149 157 8 239.30 0.34 452 150 155 5 501.06 4.70 453 150 156 6 239.41 0.29 454 151 155 4 509.79 2.67 455 151 156 5 239.49 0.27 456 151 157 6 239.50 0.28 457 151 173 22 175.21 0.79 458 152 155 3 598.02 0.25 459 154 175 21 175.15 0.79 460 155 173 18 175.25 0.79 461 155 174 19 175.16 0.79 462 155 175 20 175.10 0.78 463 156 173 17 175.21 0.79 464 156 174 18 175.14 0.79 465 157 171 14 175.40 0.74 466 157 172 15 175.21 0.79 467 157 173 16 175.14 0.79 468 158 171 13 175.38 0.71 469 158 172 14 175.21 0.79 470 159 170 11 175.52 0.65 471 159 171 12 175.18 0.78 472 160 169 9 175.60 0.60 473 160 170 10 175.46 0.67 474 161 167 6 175.81 0.58 475 161 168 7 175.66 0.57 476 161 169 8 175.18 0.78 477 162 167 5 175.81 0.58 478 162 168 6 175.72 0.55 479 164 167 3 594.40 2.22