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 9 13 4 624.46 2.23 2 10 13 3 632.19 6.09 3 10 14 4 624.47 2.23 4 10 52 42 478.25 1.21 5 11 14 3 632.88 6.42 6 11 15 4 624.48 2.23 7 12 15 3 627.81 3.90 8 12 16 4 626.36 3.18 9 13 16 3 627.68 2.52 10 13 17 4 629.81 0.50 11 13 44 31 492.38 5.24 12 13 52 39 488.24 3.73 13 14 17 3 640.10 4.64 14 14 18 4 618.49 5.16 15 14 52 38 488.20 3.75 16 14 53 39 488.23 3.75 17 15 18 3 632.11 6.90 18 15 19 4 616.46 6.15 19 16 19 3 643.48 1.21 20 16 20 4 620.08 4.27 21 16 42 26 493.62 5.07 22 16 44 28 493.42 4.99 23 17 20 3 633.48 0.02 24 17 21 4 620.07 4.26 25 17 38 21 493.37 4.96 26 17 42 25 493.62 5.09 27 17 44 27 493.44 5.00 28 17 49 32 491.19 5.17 29 17 52 35 491.19 5.17 30 17 53 36 491.18 5.17 31 17 59 42 489.62 5.71 32 18 21 3 627.72 2.86 33 18 22 4 620.06 4.23 34 18 53 35 491.20 5.17 35 18 59 41 489.62 5.71 36 18 62 44 466.50 1.17 37 18 63 45 466.36 1.20 38 18 66 48 456.26 0.73 39 19 22 3 633.06 0.21 40 19 23 4 622.11 5.26 41 19 66 47 462.68 0.55 42 20 23 3 628.77 0.13 43 20 24 4 620.04 4.22 44 20 38 18 493.75 5.15 45 20 41 21 493.76 5.14 46 20 42 22 493.76 5.14 47 21 24 3 629.78 0.75 48 21 25 4 619.93 4.17 49 21 33 12 493.72 5.15 50 21 38 17 493.74 5.15 51 21 59 38 489.74 5.73 52 21 63 42 466.53 1.17 53 22 25 3 635.33 1.03 54 22 26 4 619.98 4.14 55 22 63 41 470.10 0.60 56 22 66 44 465.04 1.58 57 22 67 45 456.28 0.73 58 22 105 83 338.62 0.75 59 22 110 88 337.75 0.88 60 23 26 3 635.03 1.19 61 23 105 82 338.37 0.79 62 23 106 83 338.30 0.81 63 24 27 3 650.27 7.48 64 24 28 4 604.75 1.60 65 24 37 13 493.94 5.17 66 24 38 14 493.89 5.17 67 24 41 17 493.91 5.17 68 25 28 3 623.64 4.50 69 25 29 4 525.04 4.55 70 25 30 5 494.03 5.20 71 25 33 8 493.93 5.17 72 25 110 85 337.77 0.87 73 26 105 79 338.71 0.74 74 26 106 80 338.70 0.74 75 26 107 81 338.17 0.79 76 26 108 82 338.17 0.79 77 26 110 84 337.77 0.88 78 27 106 79 338.70 0.74 79 27 107 80 338.25 0.82 80 28 37 9 495.01 5.38 81 29 32 3 625.85 2.82 82 29 117 88 306.33 2.87 83 30 33 3 639.76 6.55 84 30 60 30 490.81 5.29 85 30 63 33 489.66 5.70 86 30 64 34 484.04 2.96 87 30 110 80 337.76 0.86 88 30 114 84 306.83 2.66 89 30 117 87 306.32 2.87 90 30 118 88 306.31 2.85 91 30 125 95 267.67 0.55 92 31 60 29 490.96 5.28 93 31 117 86 306.33 2.87 94 31 118 87 306.30 2.86 95 31 121 90 288.61 0.72 96 32 37 5 614.65 0.20 97 33 38 5 612.89 1.09 98 33 56 23 491.31 5.24 99 33 59 26 491.10 5.34 100 33 60 27 490.81 5.28 101 33 63 30 484.04 2.95 102 34 37 3 623.84 1.10 103 34 38 4 617.95 1.84 104 34 56 22 491.31 5.24 105 34 59 25 491.10 5.34 106 35 38 3 624.01 1.19 107 35 39 4 614.69 0.21 108 35 46 11 495.07 5.26 109 35 49 14 495.04 5.26 110 35 50 15 495.03 5.27 111 35 53 18 491.95 4.98 112 35 55 20 491.35 5.23 113 35 56 21 491.31 5.24 114 35 59 24 491.09 5.33 115 36 39 3 622.12 2.31 116 36 40 4 618.00 1.88 117 36 46 10 495.10 5.25 118 37 40 3 624.08 1.16 119 37 41 4 616.25 2.75 120 38 41 3 617.07 2.35 121 38 42 4 616.25 2.76 122 38 49 11 495.06 5.26 123 38 59 21 490.98 5.29 124 39 42 3 636.24 4.20 125 39 43 4 604.03 3.29 126 39 44 5 497.53 4.06 127 39 45 6 495.18 5.24 128 39 46 7 495.14 5.24 129 39 49 10 495.10 5.24 130 40 43 3 616.14 2.82 131 44 48 4 610.48 2.44 132 44 49 5 607.96 1.19 133 45 48 3 622.72 1.96 134 45 49 4 615.91 0.34 135 46 49 3 622.89 2.08 136 46 50 4 622.41 3.58 137 47 50 3 634.12 1.56 138 47 51 4 630.76 0.59 139 48 51 3 641.76 1.45 140 48 52 4 633.74 0.81 141 49 52 3 639.93 0.12 142 49 53 4 625.77 1.91 143 50 53 3 624.37 3.88 144 50 54 4 593.45 3.08 145 53 58 5 501.25 7.82 146 53 59 6 489.97 5.88 147 53 62 9 489.63 6.04 148 55 58 3 629.12 0.46 149 55 59 4 616.45 2.29 150 56 59 3 625.72 2.35 151 56 60 4 614.05 3.48 152 57 60 3 622.97 0.97 153 57 61 4 622.95 0.97 154 57 124 67 267.71 0.57 155 57 125 68 267.66 0.55 156 58 61 3 625.72 2.35 157 58 62 4 622.90 0.99 158 58 124 66 267.71 0.57 159 59 62 3 628.08 6.32 160 59 63 4 616.82 0.69 161 60 63 3 632.62 1.15 162 60 64 4 616.83 0.68 163 60 118 58 306.28 2.85 164 60 125 65 267.66 0.55 165 61 64 3 630.38 0.03 166 61 65 4 623.16 3.58 167 61 124 63 267.71 0.58 168 61 125 64 267.66 0.55 169 61 128 67 267.41 0.55 170 62 65 3 631.09 1.55 171 62 66 4 623.20 3.58 172 63 66 3 637.46 1.63 173 63 67 4 623.41 3.48 174 63 110 47 337.75 0.87 175 64 67 3 636.94 1.37 176 64 68 4 629.33 2.44 177 64 110 46 337.74 0.88 178 64 111 47 337.69 0.88 179 64 114 50 312.80 0.31 180 64 128 64 267.43 0.54 181 64 129 65 267.38 0.55 182 64 132 68 264.81 0.24 183 65 68 3 632.98 0.61 184 65 69 4 625.33 4.44 185 66 69 3 632.57 1.17 186 66 70 4 623.24 1.75 187 67 70 3 628.93 4.59 188 67 71 4 623.23 1.74 189 67 105 38 338.72 0.74 190 67 110 43 337.76 0.88 191 67 111 44 337.74 0.88 192 68 71 3 623.31 2.58 193 68 72 4 625.46 0.63 194 68 111 43 337.74 0.88 195 68 132 64 264.71 0.28 196 68 135 67 263.14 0.38 197 68 136 68 262.82 0.51 198 69 72 3 633.90 3.39 199 69 73 4 625.46 0.62 200 70 73 3 630.94 0.54 201 70 74 4 625.46 0.62 202 70 104 34 338.75 0.72 203 71 74 3 643.41 4.28 204 71 75 4 618.62 4.02 205 71 99 28 339.44 0.88 206 71 111 40 337.80 0.88 207 71 136 65 262.95 0.48 208 72 75 3 622.75 3.93 209 72 76 4 601.25 2.35 210 72 77 5 596.89 6.54 211 72 136 64 262.96 0.47 212 72 139 67 260.05 0.65 213 73 77 4 610.32 0.17 214 73 78 5 610.32 0.17 215 74 78 4 629.68 1.01 216 74 95 21 340.44 0.92 217 74 98 24 340.38 0.93 218 74 99 25 340.22 0.84 219 74 102 28 339.96 0.90 220 74 104 30 338.84 0.74 221 75 78 3 664.93 1.64 222 75 79 4 637.74 2.91 223 75 92 17 340.44 0.92 224 75 95 20 340.44 0.92 225 75 96 21 340.37 0.89 226 75 99 24 340.33 0.90 227 75 136 61 264.02 0.28 228 76 79 3 642.27 0.65 229 76 80 4 637.49 1.75 230 76 92 16 340.45 0.92 231 76 136 60 264.05 0.29 232 76 139 63 261.56 0.07 233 77 80 3 639.25 0.86 234 78 81 3 664.26 2.48 235 78 95 17 340.50 0.91 236 79 82 3 637.86 2.71 237 79 88 9 340.65 0.91 238 79 91 12 340.57 0.91 239 79 92 13 340.58 0.91 240 79 95 16 340.54 0.91 241 80 88 8 340.87 0.83 242 82 87 5 424.50 42.42 243 82 88 6 340.88 0.84 244 82 91 9 340.87 0.83 245 83 87 4 577.12 15.15 246 83 88 5 562.27 17.28 247 83 150 67 231.47 0.89 248 84 88 4 587.82 4.54 249 84 143 59 258.45 1.33 250 84 146 62 239.18 1.02 251 84 150 66 229.13 0.28 252 85 88 3 643.13 1.33 253 85 89 4 623.65 1.59 254 85 143 58 258.47 1.33 255 85 146 61 238.29 0.58 256 85 147 62 234.30 1.35 257 85 152 67 194.21 0.88 258 86 89 3 633.74 3.37 259 86 90 4 623.74 1.55 260 86 147 61 236.88 0.07 261 86 152 66 194.19 0.88 262 86 153 67 194.18 0.88 263 86 197 111 63.84 1.02 264 87 90 3 646.86 3.20 265 87 91 4 624.43 1.21 266 88 91 3 629.46 3.71 267 88 92 4 622.69 1.03 268 88 139 51 262.86 0.53 269 88 143 55 258.43 1.32 270 89 92 3 631.97 2.46 271 89 93 4 617.54 1.63 272 89 140 51 262.44 0.49 273 89 143 54 256.38 0.32 274 89 144 55 255.99 0.50 275 89 166 77 84.76 1.94 276 89 197 108 59.55 1.90 277 90 93 3 636.16 0.36 278 90 94 4 617.45 1.68 279 90 194 104 66.08 0.77 280 90 197 107 59.55 1.90 281 91 94 3 631.23 1.79 282 91 95 4 624.23 1.28 283 92 95 3 631.78 0.93 284 92 96 4 629.69 1.03 285 92 136 44 264.17 0.26 286 92 139 47 262.54 0.54 287 92 140 48 261.58 0.09 288 93 96 3 629.70 1.02 289 93 97 4 624.66 1.48 290 93 140 47 261.61 0.09 291 93 166 73 84.44 1.82 292 93 193 100 66.14 0.76 293 94 97 3 634.37 1.30 294 94 98 4 624.72 1.46 295 95 98 3 628.94 0.65 296 95 99 4 624.85 1.52 297 96 99 3 629.94 1.02 298 96 100 4 629.94 1.02 299 96 136 40 263.80 0.14 300 97 100 3 633.42 0.71 301 97 101 4 629.94 1.02 302 97 173 76 77.89 2.82 303 97 186 89 67.47 0.69 304 97 189 92 67.41 0.68 305 97 190 93 67.39 0.67 306 97 193 96 66.22 0.75 307 98 101 3 638.58 1.04 308 98 102 4 624.65 1.41 309 99 102 3 637.89 1.39 310 99 103 4 623.12 1.26 311 99 104 5 607.64 6.48 312 99 109 10 338.74 0.72 313 100 103 3 623.91 0.85 314 100 109 9 338.74 0.72 315 100 170 70 81.72 0.90 316 100 173 73 77.86 2.81 317 100 174 74 77.61 2.70 318 100 177 77 76.39 3.23 319 101 177 76 76.34 3.21 320 101 183 82 67.60 0.62 321 101 186 85 67.45 0.70 322 101 190 89 67.41 0.68 323 103 108 5 338.66 0.69 324 103 178 75 74.64 3.33 325 105 108 3 626.31 4.13 326 105 110 5 382.49 21.07 327 107 178 71 68.30 0.69 328 108 174 66 77.60 2.70 329 108 178 70 68.33 0.70 330 109 112 3 637.19 1.70 331 109 113 4 621.11 5.06 332 109 174 65 77.59 2.71 333 110 113 3 631.25 0.32 334 110 114 4 617.11 0.17 335 111 114 3 645.63 3.88 336 111 115 4 618.49 0.83 337 111 132 21 264.95 0.32 338 111 133 22 264.71 0.28 339 112 115 3 631.68 3.10 340 112 116 4 630.97 2.75 341 112 133 21 265.10 0.39 342 112 171 59 77.97 2.75 343 112 174 62 77.64 2.71 344 113 116 3 641.75 1.66 345 113 117 4 618.36 0.77 346 114 117 3 637.46 0.50 347 114 118 4 618.31 0.79 348 114 129 15 267.50 0.51 349 115 118 3 649.71 4.57 350 115 119 4 614.77 2.68 351 115 129 14 267.55 0.49 352 115 133 18 265.19 0.39 353 115 171 56 78.72 2.40 354 116 119 3 645.53 3.60 355 117 121 4 628.29 0.27 356 118 121 3 623.81 2.51 357 118 125 7 267.81 0.56 358 118 126 8 267.71 0.53 359 118 129 11 267.58 0.50 360 119 126 7 267.85 0.54 361 121 126 5 527.57 31.10 362 122 126 4 606.90 0.46 363 123 126 3 649.24 3.37 364 123 127 4 613.17 3.58 365 124 127 3 641.65 0.42 366 124 128 4 615.46 4.73 367 125 128 3 624.88 1.45 368 125 129 4 620.12 7.59 369 126 129 3 632.81 1.25 370 126 130 4 620.12 7.59 371 127 130 3 630.06 4.06 372 127 131 4 620.12 7.59 373 128 131 3 630.47 3.85 374 128 132 4 629.07 3.12 375 129 132 3 631.07 2.08 376 129 133 4 623.86 0.51 377 130 133 3 632.45 0.77 378 130 134 4 623.84 0.50 379 131 134 3 626.77 1.06 380 131 135 4 623.74 0.45 381 132 135 3 627.82 0.62 382 132 136 4 623.78 0.49 383 133 136 3 624.48 1.04 384 133 137 4 622.26 1.26 385 133 167 34 82.27 1.02 386 133 171 38 81.91 0.99 387 134 137 3 638.50 1.54 388 134 138 4 622.22 1.28 389 135 138 3 630.70 2.35 390 135 139 4 627.49 3.95 391 136 139 3 647.64 0.92 392 136 140 4 627.50 3.95 393 137 140 3 642.44 3.52 394 137 141 4 627.49 3.96 395 137 163 26 85.33 1.40 396 137 167 30 82.29 1.02 397 138 141 3 627.49 3.96 398 138 142 4 620.10 0.31 399 139 142 3 633.35 1.01 400 139 143 4 629.38 2.98 401 140 143 3 651.79 0.24 402 140 144 4 618.61 1.06 403 140 163 23 85.45 1.47 404 140 166 26 84.95 1.62 405 140 167 27 84.38 1.89 406 141 144 3 641.07 5.12 407 141 145 4 623.16 1.20 408 141 159 18 87.50 1.21 409 141 160 19 87.49 1.21 410 141 163 22 86.13 1.25 411 142 145 3 627.07 1.88 412 142 146 4 622.14 0.66 413 143 146 3 630.24 4.70 414 143 147 4 624.61 0.48 415 144 147 3 626.47 1.40 416 144 148 4 625.70 1.02 417 144 153 9 194.16 0.89 418 144 157 13 107.75 0.12 419 144 159 15 87.51 1.21 420 144 162 18 87.05 1.44 421 144 163 19 86.90 1.39 422 144 166 22 86.86 1.41 423 144 197 53 59.55 1.90 424 145 148 3 637.58 4.32 425 145 149 4 624.60 0.48 426 145 159 14 94.74 1.95 427 146 149 3 624.61 0.48 428 146 150 4 623.57 0.04 429 147 150 3 617.22 3.21 430 147 151 4 614.15 4.73 431 147 152 5 536.92 10.39 432 147 153 6 194.16 0.89 433 148 151 3 613.91 4.85 434 148 153 5 194.20 0.88 435 148 154 6 194.19 0.88 436 148 155 7 193.97 0.91 437 148 157 9 135.75 9.87 438 148 159 11 106.60 0.75 439 153 157 4 555.83 6.94 440 153 197 44 65.09 1.20 441 154 157 3 626.10 1.75 442 157 162 5 624.06 2.65 443 157 196 39 66.03 0.80 444 157 197 40 65.95 0.78 445 157 199 42 59.54 1.91 446 157 200 43 58.91 2.20 447 158 161 3 641.78 1.56 448 158 162 4 626.36 3.79 449 158 200 42 41.90 2.00 450 159 162 3 634.02 2.33 451 159 163 4 624.31 2.52 452 160 163 3 624.32 2.52 453 160 164 4 624.30 2.52 454 161 164 3 631.25 0.96 455 161 165 4 624.30 2.52 456 161 200 39 25.46 0.65 457 162 165 3 624.29 2.52 458 162 166 4 624.09 2.62 459 162 196 34 59.79 1.79 460 162 200 38 25.46 0.65 461 163 166 3 631.54 3.84 462 163 167 4 621.34 1.25 463 164 167 3 640.54 0.39 464 164 168 4 621.23 1.31 465 165 168 3 634.02 2.60 466 165 169 4 618.57 0.03 467 165 196 31 59.91 1.72 468 165 200 35 26.75 0.00 469 166 169 3 628.81 5.15 470 166 170 4 634.14 1.02 471 166 193 27 66.20 0.75 472 166 196 30 59.57 1.89 473 166 197 31 59.57 1.89 474 167 170 3 634.14 1.02 475 167 171 4 634.14 1.02 476 168 171 3 634.14 1.02 477 168 172 4 617.61 0.42 478 169 172 3 634.14 1.02 479 169 173 4 621.41 2.34 480 169 189 20 67.46 0.68 481 169 192 23 66.27 0.72 482 169 193 24 66.25 0.73 483 170 173 3 628.56 1.23 484 170 174 4 621.41 2.34 485 171 174 3 637.06 3.75 486 171 175 4 625.95 1.80 487 172 175 3 643.28 0.67 488 172 176 4 612.77 4.79 489 173 176 3 643.29 0.67 490 173 177 4 623.88 2.84 491 173 185 12 67.52 0.68 492 173 186 13 67.50 0.68 493 173 189 16 67.43 0.68 494 174 177 3 643.29 0.66 495 174 178 4 610.62 3.79 496 175 178 3 633.08 4.45 497 175 179 4 601.90 0.55 498 176 180 4 383.44 1.55 499 176 181 5 264.94 60.79 500 176 182 6 108.00 2.48 501 176 185 9 89.84 1.46 502 177 181 4 116.69 1.16 503 177 182 5 115.14 1.08 504 177 183 6 108.01 2.48 505 182 185 3 646.35 0.09 506 183 186 3 658.89 3.96 507 184 187 3 658.89 3.96 508 184 188 4 622.95 5.54 509 185 188 3 623.93 3.41 510 185 189 4 603.08 4.39 511 186 189 3 624.27 4.00 512 186 190 4 603.15 4.43 513 187 190 3 612.47 1.90 514 187 191 4 610.32 0.81 515 188 191 3 629.25 7.49 516 188 192 4 624.16 6.12 517 189 192 3 640.31 1.96 518 189 193 4 627.54 4.42 519 190 193 3 641.78 1.22 520 190 194 4 640.31 1.95 521 191 194 3 643.74 0.35 522 191 195 4 640.27 1.93 523 192 195 3 641.75 1.20 524 192 196 4 625.86 9.14 525 193 196 3 640.28 1.94 526 193 197 4 626.45 8.85 527 194 197 3 637.35 3.40 528 194 198 4 624.26 9.94 529 195 198 3 613.04 0.32 530 196 200 4 400.13 8.81