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 3 6 3 609.39 1.12 2 3 7 4 599.94 3.60 3 3 34 31 53.90 0.36 4 3 38 35 53.35 0.43 5 4 7 3 617.41 3.67 6 4 8 4 604.02 1.56 7 4 42 38 52.15 0.69 8 4 43 39 50.38 1.57 9 5 8 3 604.01 1.55 10 5 9 4 604.01 1.55 11 6 9 3 605.16 2.12 12 6 10 4 598.49 1.21 13 6 32 26 65.08 0.21 14 7 10 3 610.81 2.70 15 7 11 4 596.78 3.14 16 7 28 21 65.13 0.36 17 7 32 25 65.20 0.28 18 7 34 27 65.08 0.21 19 7 39 32 58.25 1.15 20 7 43 36 57.90 1.28 21 7 49 42 53.40 0.43 22 8 11 3 610.80 2.71 23 8 12 4 599.96 4.72 24 8 43 35 57.90 1.28 25 8 49 41 53.40 0.43 26 8 52 44 53.36 0.42 27 8 53 45 53.05 0.27 28 9 12 3 611.36 2.39 29 9 13 4 604.32 2.54 30 10 13 3 601.83 1.29 31 10 14 4 597.47 3.46 32 10 28 18 66.17 0.01 33 10 31 21 66.30 0.00 34 10 32 22 66.28 0.00 35 11 14 3 597.66 3.38 36 11 15 4 597.46 3.46 37 11 28 17 66.20 0.02 38 11 49 38 54.25 0.29 39 11 53 42 53.65 0.48 40 12 15 3 612.78 1.06 41 12 16 4 597.46 3.46 42 12 53 41 53.64 0.46 43 12 57 45 53.61 0.46 44 12 91 79 53.61 0.46 45 13 16 3 613.84 1.58 46 13 17 4 591.09 2.56 47 14 17 3 606.37 1.03 48 14 18 4 572.75 6.61 49 14 23 9 201.44 60.10 50 14 27 13 72.09 2.34 51 14 28 14 66.86 0.27 52 15 19 4 506.95 4.11 53 15 20 5 244.47 75.09 54 15 23 8 198.66 54.93 55 15 46 31 66.21 0.03 56 15 50 35 54.33 0.32 57 15 95 80 53.66 0.47 58 15 98 83 53.63 0.46 59 16 94 78 53.63 0.46 60 16 95 79 53.64 0.46 61 18 22 4 528.86 4.55 62 18 23 5 469.52 10.47 63 18 27 9 432.61 9.04 64 19 22 3 604.68 0.12 65 19 23 4 579.85 10.49 66 19 101 82 54.65 0.37 67 20 23 3 630.83 6.25 68 20 46 26 66.52 0.09 69 20 47 27 66.41 0.14 70 20 50 30 65.44 0.15 71 20 98 78 54.52 0.42 72 20 101 81 59.24 2.66 73 20 102 82 54.66 0.37 74 20 105 85 66.26 0.21 75 20 106 86 66.39 0.14 76 21 46 25 66.55 0.07 77 21 101 80 63.02 0.98 78 21 105 84 66.25 0.21 79 22 27 5 608.61 2.99 80 23 27 4 598.25 0.98 81 23 46 23 66.58 0.09 82 24 27 3 608.62 3.00 83 24 28 4 598.26 0.99 84 24 46 22 66.58 0.09 85 25 28 3 600.72 0.08 86 25 29 4 598.25 0.99 87 25 46 21 66.58 0.10 88 26 29 3 602.70 0.16 89 26 30 4 598.25 0.99 90 27 30 3 608.82 2.90 91 27 31 4 590.55 0.73 92 28 31 3 631.01 1.06 93 28 32 4 584.85 0.10 94 28 39 11 192.75 58.42 95 28 49 21 66.40 0.24 96 29 32 3 599.62 7.50 97 29 33 4 582.52 1.05 98 29 34 5 534.40 7.08 99 29 39 10 232.89 73.92 100 30 33 3 614.15 0.72 101 34 38 4 607.96 1.92 102 34 39 5 602.66 0.65 103 35 38 3 619.71 3.95 104 35 39 4 608.02 1.89 105 36 39 3 619.71 3.95 106 36 40 4 608.02 1.89 107 37 40 3 608.02 1.89 108 37 41 4 608.02 1.89 109 38 41 3 626.13 0.96 110 39 43 4 577.18 2.72 111 40 43 3 604.58 0.98 112 40 44 4 532.50 19.91 113 41 44 3 619.75 1.46 114 42 48 6 572.69 4.94 115 43 48 5 555.42 3.23 116 43 49 6 479.17 6.77 117 43 52 9 461.59 4.13 118 44 48 4 591.67 1.16 119 45 48 3 591.68 1.16 120 45 49 4 599.50 2.00 121 46 49 3 604.04 0.28 122 46 50 4 604.07 0.29 123 47 50 3 604.08 0.29 124 47 51 4 597.00 3.82 125 47 102 55 186.65 0.62 126 47 106 59 195.94 0.64 127 47 112 65 195.40 0.55 128 48 51 3 604.10 0.29 129 48 52 4 597.03 3.81 130 49 52 3 603.40 0.64 131 49 53 4 601.96 1.35 132 50 53 3 603.40 0.64 133 50 54 4 602.84 0.92 134 50 98 48 196.50 0.93 135 50 99 49 196.50 0.91 136 50 102 52 200.32 0.14 137 51 54 3 606.40 1.58 138 51 55 4 602.85 0.92 139 51 102 51 202.11 0.57 140 51 115 64 200.33 0.15 141 51 119 68 199.54 0.55 142 52 55 3 607.65 2.33 143 52 56 4 603.43 0.57 144 53 56 3 607.66 2.33 145 53 57 4 603.41 0.56 146 53 95 42 239.09 17.92 147 54 57 3 603.76 0.38 148 54 58 4 602.93 0.32 149 54 95 41 239.06 17.90 150 54 99 45 239.52 17.02 151 54 119 65 203.61 0.15 152 55 58 3 609.54 3.62 153 55 59 4 598.38 1.94 154 55 119 64 204.49 0.28 155 55 122 67 204.81 0.12 156 56 59 3 607.84 2.23 157 56 60 4 602.15 0.60 158 57 60 3 607.07 2.61 159 57 61 4 588.50 0.01 160 57 91 34 247.59 19.51 161 57 92 35 246.66 19.05 162 57 95 38 247.37 19.37 163 58 61 3 598.34 1.67 164 58 62 4 594.32 2.87 165 58 92 34 247.57 19.50 166 58 119 61 224.67 6.71 167 58 122 64 223.45 7.41 168 58 123 65 223.31 7.39 169 59 62 3 602.25 0.56 170 59 63 4 594.34 2.87 171 59 122 63 231.35 5.05 172 60 63 3 610.46 4.08 173 60 64 4 599.18 0.45 174 60 91 31 255.79 15.43 175 61 64 3 601.07 0.48 176 61 65 4 601.06 0.48 177 61 82 21 256.24 15.68 178 61 85 24 256.18 15.63 179 61 86 25 256.17 15.62 180 61 89 28 255.98 15.53 181 61 91 30 255.79 15.43 182 61 92 31 255.79 15.43 183 61 93 32 255.97 15.52 184 62 65 3 606.17 3.04 185 62 66 4 601.05 0.48 186 62 126 64 233.63 4.46 187 63 66 3 602.40 1.17 188 63 67 4 601.05 0.48 189 64 67 3 604.88 0.25 190 64 68 4 598.35 1.83 191 64 89 25 258.74 14.29 192 64 90 26 258.79 14.28 193 64 91 27 258.54 14.18 194 65 68 3 595.39 3.26 195 65 69 4 575.20 6.83 196 65 78 13 259.00 14.46 197 65 81 16 258.93 14.42 198 65 82 17 258.83 14.38 199 65 85 20 258.85 14.38 200 65 126 61 236.36 3.23 201 65 130 65 238.56 4.31 202 66 69 3 603.10 0.67 203 68 71 3 627.81 4.04 204 68 81 13 258.98 14.42 205 68 85 17 258.93 14.37 206 69 72 3 605.26 1.46 207 69 78 9 267.93 18.89 208 69 81 12 258.98 14.42 209 71 81 10 330.52 12.40 210 72 77 5 549.90 6.79 211 72 78 6 314.66 25.21 212 72 81 9 381.43 15.24 213 73 77 4 598.74 0.18 214 74 77 3 598.75 0.18 215 74 78 4 595.52 1.45 216 74 139 65 321.62 17.66 217 75 78 3 595.63 1.39 218 75 79 4 595.63 1.39 219 75 130 55 301.64 27.14 220 75 133 58 309.81 23.14 221 75 134 59 301.94 27.26 222 75 137 62 321.70 17.69 223 75 139 64 321.71 17.71 224 75 140 65 321.71 17.71 225 76 79 3 608.69 5.09 226 76 80 4 598.76 0.17 227 76 139 63 321.69 17.70 228 76 140 64 321.70 17.71 229 76 183 107 238.58 5.84 230 77 80 3 606.43 0.81 231 77 81 4 595.65 1.36 232 78 81 3 596.56 0.97 233 78 82 4 589.41 1.75 234 78 130 52 301.73 27.18 235 79 82 3 614.19 1.73 236 79 83 4 595.74 1.38 237 79 127 48 301.58 27.19 238 79 130 51 302.05 27.34 239 79 131 52 302.16 27.39 240 79 152 73 301.44 27.18 241 79 179 100 240.25 5.71 242 79 182 103 239.63 6.01 243 79 183 104 238.95 6.18 244 80 83 3 607.63 1.56 245 80 84 4 595.72 1.39 246 80 176 96 243.50 4.60 247 80 179 99 240.26 5.71 248 80 180 100 240.25 5.72 249 80 183 103 239.28 6.19 250 81 84 3 601.38 1.47 251 81 85 4 595.70 1.38 252 82 85 3 601.88 0.14 253 82 86 4 585.65 3.65 254 82 93 11 331.79 12.92 255 82 126 44 301.64 27.24 256 82 127 45 301.88 27.37 257 82 130 48 302.25 27.44 258 83 86 3 596.82 2.40 259 83 127 44 302.12 27.48 260 83 156 73 292.01 24.72 261 83 175 92 243.50 4.60 262 83 179 96 240.26 5.71 263 84 87 3 624.80 1.86 264 84 172 88 243.97 4.82 265 84 175 91 243.50 4.61 266 84 176 92 243.73 4.72 267 85 88 3 605.18 3.83 268 85 89 4 575.19 4.33 269 86 93 7 331.78 12.91 270 86 156 70 296.50 26.97 271 86 160 74 288.51 24.00 272 87 160 73 288.72 24.14 273 87 168 81 244.61 5.11 274 87 171 84 244.50 5.08 275 87 172 85 244.47 5.09 276 87 175 88 244.46 5.08 277 88 168 80 244.61 5.11 278 90 94 4 592.81 0.67 279 91 94 3 637.82 1.55 280 92 95 3 621.48 5.32 281 92 96 4 601.16 0.46 282 92 99 7 551.10 3.47 283 92 119 27 300.04 28.62 284 92 123 31 300.02 28.64 285 93 96 3 607.89 0.38 286 93 157 64 297.53 27.70 287 93 160 67 289.68 24.66 288 95 98 3 602.88 1.18 289 95 99 4 590.37 2.41 290 96 99 3 590.38 2.41 291 96 100 4 590.37 2.41 292 96 157 61 297.76 27.61 293 96 161 65 289.71 24.64 294 97 100 3 603.46 2.37 295 97 101 4 594.98 4.71 296 97 161 64 292.39 24.98 297 98 101 3 598.62 3.60 298 98 102 4 591.02 0.62 299 99 102 3 597.81 4.01 300 99 103 4 595.23 2.72 301 99 116 17 317.50 19.98 302 100 103 3 598.52 3.58 303 100 104 4 599.07 2.65 304 100 161 61 297.70 27.60 305 101 104 3 610.20 0.98 306 101 105 4 599.73 2.98 307 102 105 3 622.39 2.81 308 102 106 4 599.40 3.15 309 102 112 10 405.01 7.09 310 103 106 3 621.46 2.48 311 103 107 4 579.27 2.27 312 103 112 9 404.95 7.07 313 103 113 10 346.19 5.94 314 103 116 13 328.80 14.48 315 104 107 3 623.01 1.70 316 106 109 3 623.32 4.90 317 106 112 6 410.84 10.00 318 107 112 5 517.37 14.28 319 109 112 3 621.38 5.55 320 109 113 4 612.57 1.16 321 110 113 3 622.06 5.21 322 111 115 4 582.38 3.65 323 112 115 3 612.51 0.45 324 112 116 4 582.38 3.65 325 113 116 3 596.99 1.06 326 113 117 4 575.63 6.96 327 114 117 3 603.69 1.17 328 114 118 4 583.95 1.74 329 115 118 3 588.81 0.37 330 115 119 4 583.96 1.72 331 116 120 4 588.24 2.58 332 117 120 3 588.24 2.58 333 117 121 4 610.13 2.00 334 118 121 3 610.14 2.00 335 118 122 4 610.13 2.00 336 119 122 3 610.13 2.00 337 119 123 4 608.63 2.73 338 120 123 3 613.33 0.38 339 120 124 4 608.63 2.73 340 120 150 30 327.47 15.88 341 121 124 3 606.81 0.48 342 121 125 4 588.08 0.52 343 122 125 3 596.25 1.48 344 123 153 30 327.44 15.89 345 123 154 31 327.45 15.89 346 123 157 34 327.38 15.87 347 124 127 3 604.38 1.49 348 124 128 4 599.46 1.91 349 124 146 22 328.25 16.05 350 124 149 25 327.91 16.09 351 124 150 26 327.93 16.09 352 124 153 29 327.45 15.89 353 125 128 3 601.36 0.96 354 125 129 4 599.49 1.92 355 126 129 3 611.45 3.98 356 126 130 4 596.44 3.46 357 127 130 3 597.75 2.81 358 127 131 4 597.75 2.81 359 127 149 22 328.11 16.14 360 127 152 25 328.10 16.14 361 127 153 26 328.10 16.14 362 127 156 29 328.10 16.14 363 128 131 3 601.37 1.00 364 128 132 4 578.68 5.41 365 128 145 17 328.50 16.10 366 128 146 18 328.48 16.09 367 128 149 21 328.14 16.14 368 129 132 3 609.55 2.49 369 129 133 4 579.51 3.58 370 130 133 3 612.01 3.72 371 130 134 4 577.00 4.45 372 130 140 10 379.43 9.05 373 131 134 3 598.07 0.48 374 131 135 4 585.01 6.34 375 131 140 9 366.54 2.64 376 131 142 11 342.06 9.39 377 131 145 14 328.61 16.05 378 131 148 17 328.59 16.05 379 131 149 18 328.45 16.07 380 131 152 21 328.46 16.05 381 131 182 51 239.64 6.01 382 131 183 52 238.61 5.85 383 131 186 55 214.22 14.88 384 132 135 3 604.83 3.56 385 132 136 4 584.62 6.54 386 132 145 13 328.63 16.06 387 133 136 3 580.50 3.70 388 133 137 4 584.62 6.54 389 134 137 3 587.86 4.92 390 134 138 4 584.62 6.54 391 134 139 5 542.29 14.89 392 134 140 6 451.19 22.14 393 135 138 3 582.53 1.73 394 135 140 5 450.13 29.71 395 135 141 6 363.00 0.87 396 135 142 7 362.98 0.88 397 135 145 10 342.14 9.42 398 140 183 43 238.74 5.79 399 142 145 3 610.72 5.65 400 142 148 6 556.01 6.48 401 142 186 44 235.81 6.05 402 144 147 3 618.52 0.77 403 144 148 4 595.82 0.04 404 145 148 3 615.35 0.82 405 145 149 4 595.82 0.04 406 146 149 3 598.78 1.52 407 146 150 4 590.94 2.48 408 147 150 3 597.16 0.55 409 147 151 4 588.29 3.16 410 148 151 3 594.70 1.06 411 148 152 4 590.45 2.07 412 148 182 34 239.50 6.14 413 148 186 38 216.88 16.23 414 149 152 3 594.79 1.11 415 149 153 4 582.25 2.03 416 150 153 3 591.72 2.66 417 150 154 4 586.99 4.40 418 151 154 3 607.25 5.73 419 151 155 4 582.18 2.00 420 151 182 31 239.59 6.19 421 152 155 3 604.15 4.18 422 152 156 4 590.98 2.39 423 152 182 30 239.37 6.21 424 153 156 3 598.24 0.18 425 153 157 4 582.26 1.99 426 154 157 3 591.01 2.39 427 154 158 4 591.01 2.39 428 155 158 3 591.65 2.07 429 155 159 4 593.01 2.71 430 155 178 23 242.86 5.86 431 156 159 3 609.38 5.48 432 156 160 4 591.72 2.06 433 156 175 19 244.47 5.08 434 156 178 22 242.81 5.83 435 157 160 3 615.55 0.80 436 157 161 4 591.71 2.05 437 158 161 3 612.23 4.05 438 158 162 4 583.58 2.02 439 159 162 3 615.69 0.87 440 159 163 4 588.94 0.66 441 159 175 16 244.50 5.08 442 159 178 19 244.38 5.13 443 160 171 11 244.62 5.12 444 160 175 15 244.49 5.08 445 161 164 3 609.98 3.73 446 163 166 3 623.53 1.02 447 163 171 8 494.75 26.96 448 164 171 7 547.80 0.44 449 166 170 4 595.41 2.14 450 166 171 5 578.99 3.75 451 166 174 8 569.37 0.99 452 167 170 3 615.34 6.68 453 167 171 4 595.41 2.14 454 168 171 3 608.37 3.19 455 168 172 4 595.39 2.12 456 169 172 3 607.02 3.86 457 169 173 4 595.37 2.12 458 170 173 3 599.48 0.09 459 170 174 4 597.53 1.05 460 171 174 3 608.77 1.18 461 171 175 4 595.72 0.14 462 172 175 3 605.37 2.88 463 172 176 4 597.56 1.03 464 173 176 3 611.12 0.39 465 173 177 4 590.40 2.51 466 174 177 3 593.03 0.92 467 174 178 4 588.28 1.02 468 175 178 3 601.35 5.76 469 175 179 4 593.64 1.81 470 176 179 3 595.09 2.24 471 176 180 4 593.64 1.81 472 177 180 3 596.16 2.77 473 177 181 4 593.64 1.81 474 178 181 3 601.76 5.40 475 178 182 4 587.38 1.32 476 179 182 3 603.34 4.81 477 179 183 4 587.35 1.30 478 180 183 3 619.41 0.54 479 180 184 4 601.85 5.54 480 181 184 3 605.95 3.50 481 181 185 4 605.95 3.50 482 182 185 3 605.94 3.50 483 182 186 4 605.94 3.50 484 183 186 3 601.56 1.32 485 183 187 4 599.32 0.20 486 184 187 3 621.66 0.12