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 5 21 16 60.68 1.18 2 5 23 18 55.05 0.03 3 5 24 19 54.55 0.03 4 5 37 32 34.69 4.76 5 5 166 161 54.95 0.01 6 6 20 14 71.98 0.46 7 7 10 3 558.72 0.94 8 7 37 30 59.45 0.49 9 8 13 5 190.00 2.44 10 8 14 6 69.67 0.42 11 8 15 7 72.33 0.58 12 8 18 10 72.56 0.47 13 8 19 11 72.72 0.55 14 8 20 12 72.48 0.43 15 8 21 13 72.56 0.47 16 8 37 29 67.09 0.71 17 8 121 113 69.27 0.62 18 8 123 115 72.31 0.58 19 8 167 159 68.68 0.92 20 9 13 4 477.67 8.59 21 9 15 6 72.56 0.47 22 10 13 3 599.33 5.76 23 11 76 65 72.55 0.47 24 12 37 25 72.72 0.54 25 12 38 26 72.37 0.56 26 12 76 64 72.55 0.47 27 12 119 107 72.33 0.58 28 12 170 158 72.34 0.58 29 13 16 3 613.31 2.17 30 13 76 63 72.73 0.55 31 13 119 106 72.81 0.52 32 14 17 3 610.14 2.21 33 14 18 4 590.21 1.02 34 14 37 23 72.86 0.53 35 14 119 105 72.84 0.53 36 14 121 107 72.84 0.53 37 14 168 154 72.84 0.53 38 15 18 3 603.89 0.48 39 16 119 103 78.53 1.25 40 17 69 52 78.56 1.25 41 17 71 54 78.55 1.25 42 17 83 66 78.58 1.25 43 17 121 104 78.67 1.19 44 17 123 106 84.71 0.49 45 17 151 134 85.23 0.24 46 17 152 135 85.71 0.04 47 18 123 105 85.67 0.04 48 18 125 107 116.22 0.55 49 18 151 133 85.72 0.04 50 18 152 134 85.73 0.04 51 18 155 137 108.41 0.90 52 18 163 145 115.59 0.24 53 19 155 136 116.20 0.54 54 19 162 143 116.21 0.54 55 19 163 144 117.44 0.06 56 21 123 102 109.67 0.35 57 21 163 142 124.72 1.36 58 21 164 143 127.64 0.10 59 21 165 144 113.59 1.22 60 21 166 145 108.44 0.92 61 22 163 141 130.47 1.04 62 22 164 142 128.26 0.04 63 23 55 32 157.27 1.73 64 23 56 33 157.65 1.78 65 23 164 141 131.59 1.47 66 23 165 142 128.47 0.07 67 23 166 143 128.49 0.08 68 24 55 31 157.81 1.84 69 24 166 142 130.69 1.02 70 25 53 28 158.08 1.85 71 25 54 29 158.08 1.85 72 25 55 30 157.96 1.89 73 25 122 97 131.00 1.16 74 25 124 99 138.00 1.94 75 25 165 140 138.04 1.85 76 25 166 141 131.56 1.41 77 25 167 142 130.68 1.02 78 26 34 8 158.72 10.02 79 26 35 9 139.96 0.93 80 26 53 27 158.16 1.82 81 26 54 28 158.09 1.84 82 27 33 6 340.94 78.80 83 27 34 7 159.75 9.54 84 27 50 23 158.35 1.67 85 27 52 25 158.56 1.68 86 27 53 26 158.18 1.81 87 27 122 95 141.49 0.21 88 27 167 140 141.57 0.18 89 28 32 4 547.12 3.98 90 28 33 5 502.63 2.05 91 28 50 22 158.58 1.66 92 28 51 23 158.61 1.67 93 28 52 24 158.57 1.68 94 29 32 3 584.62 5.74 95 29 33 4 536.12 2.36 96 29 34 5 555.98 0.44 97 29 41 12 151.34 0.45 98 29 45 16 155.16 0.14 99 29 46 17 151.47 0.42 100 29 48 19 158.81 1.54 101 29 50 21 158.59 1.66 102 29 51 22 158.78 1.59 103 29 106 77 158.87 1.54 104 29 122 93 158.59 1.58 105 29 169 140 151.34 0.45 106 30 51 21 158.80 1.59 107 32 41 9 167.51 5.94 108 32 45 13 158.88 1.53 109 33 39 6 527.86 1.41 110 33 41 8 187.65 0.34 111 34 39 5 511.52 6.75 112 34 41 7 340.73 76.84 113 34 167 133 158.83 1.56 114 34 168 134 158.83 1.56 115 34 169 135 158.78 1.55 116 35 39 4 598.11 0.85 117 36 39 3 595.69 0.36 118 37 167 130 159.49 1.34 119 37 168 131 159.49 1.34 120 38 168 130 159.50 1.34 121 38 169 131 159.50 1.33 122 38 170 132 159.47 1.33 123 39 168 129 159.82 1.26 124 39 169 130 159.70 1.25 125 39 170 131 159.70 1.25 126 40 117 77 159.72 1.25 127 40 170 130 159.72 1.25 128 41 45 4 588.54 0.47 129 41 46 5 571.45 2.14 130 41 169 128 159.93 1.26 131 41 170 129 159.80 1.27 132 41 171 130 159.09 0.93 133 42 45 3 597.31 2.25 134 42 46 4 590.21 1.30 135 42 174 132 135.10 1.17 136 43 46 3 597.86 2.52 137 43 47 4 582.82 2.39 138 43 109 66 159.99 1.26 139 43 111 68 159.99 1.26 140 43 171 128 155.89 0.69 141 43 172 129 155.88 0.69 142 43 173 130 146.28 0.21 143 43 174 131 135.58 1.41 144 43 176 133 107.39 0.28 145 43 177 134 106.67 0.62 146 44 47 3 608.02 0.36 147 44 174 130 135.31 1.54 148 44 176 132 106.98 0.48 149 46 106 60 177.49 1.03 150 46 108 62 160.05 1.28 151 46 109 63 160.06 1.28 152 46 169 123 160.07 1.29 153 47 106 59 177.52 1.02 154 47 176 129 107.03 0.45 155 48 106 58 177.60 1.02 156 49 87 38 177.59 1.02 157 49 97 48 179.05 1.38 158 49 102 53 178.73 1.36 159 49 105 56 177.67 1.03 160 49 106 57 177.60 1.02 161 50 53 3 649.72 1.18 162 50 97 47 179.05 1.37 163 50 106 56 177.68 1.03 164 50 122 72 177.55 0.99 165 53 66 13 179.13 1.45 166 53 92 39 291.83 46.48 167 53 95 42 283.44 50.58 168 53 97 44 283.73 50.44 169 54 58 4 598.23 0.99 170 55 58 3 601.69 0.72 171 55 64 9 497.81 1.29 172 55 92 37 424.27 5.05 173 55 94 39 425.06 5.44 174 55 95 40 412.16 1.01 175 55 124 69 192.14 0.04 176 55 164 109 195.59 1.65 177 55 165 110 179.13 1.45 178 58 64 6 532.51 0.32 179 58 94 36 464.51 1.02 180 58 95 37 466.76 0.11 181 59 62 3 596.84 2.64 182 59 64 5 575.88 4.75 183 59 94 35 474.15 3.81 184 60 94 34 474.15 3.81 185 62 93 31 494.03 1.50 186 62 94 32 493.68 1.65 187 62 126 64 368.70 0.95 188 63 91 28 494.11 1.49 189 63 92 29 494.10 1.49 190 63 93 30 494.07 1.49 191 63 126 63 368.78 0.97 192 63 127 64 368.30 0.90 193 63 129 66 367.90 0.87 194 63 130 67 367.82 0.88 195 64 90 26 494.45 1.52 196 64 91 27 494.25 1.55 197 64 92 28 494.12 1.50 198 64 94 30 494.12 1.50 199 64 124 60 368.98 0.94 200 64 125 61 368.89 0.96 201 64 126 62 368.81 0.97 202 64 127 63 368.67 0.96 203 64 164 100 293.28 0.21 204 65 88 23 494.81 1.46 205 65 89 24 494.53 1.56 206 65 90 25 494.45 1.52 207 65 124 59 369.06 0.97 208 65 125 60 368.97 0.94 209 65 127 62 368.88 0.96 210 65 131 66 367.95 0.88 211 65 154 89 299.05 0.10 212 65 160 95 294.17 0.40 213 66 87 21 494.94 1.49 214 66 88 22 494.81 1.46 215 66 89 23 494.56 1.56 216 66 92 26 494.51 1.57 217 66 97 31 494.04 1.50 218 66 122 56 370.16 0.94 219 66 123 57 369.44 1.01 220 66 124 58 369.06 0.97 221 67 87 20 494.94 1.49 222 67 88 21 494.81 1.46 223 67 122 55 370.17 0.94 224 67 123 56 369.58 1.06 225 67 125 58 369.45 1.01 226 67 149 82 325.31 1.02 227 67 151 84 299.29 0.12 228 68 85 17 495.44 1.52 229 68 86 18 495.18 1.59 230 68 87 19 495.00 1.51 231 68 106 38 492.76 1.53 232 68 120 52 371.17 0.71 233 68 121 53 370.46 0.93 234 68 122 54 370.20 0.94 235 68 169 101 293.04 0.24 236 69 83 14 495.99 1.59 237 69 84 15 495.90 1.65 238 69 85 16 495.44 1.52 239 69 120 51 371.25 0.70 240 69 121 52 370.91 0.71 241 69 123 54 370.89 0.71 242 69 151 82 299.45 0.19 243 70 73 3 624.10 5.63 244 70 83 13 496.03 1.59 245 70 84 14 495.92 1.63 246 70 86 16 495.88 1.64 247 70 118 48 372.21 0.51 248 70 119 49 371.80 0.68 249 70 120 50 371.34 0.66 250 71 79 8 521.95 3.98 251 71 82 11 496.08 1.59 252 71 83 12 496.06 1.60 253 71 119 48 372.18 0.53 254 71 121 50 371.79 0.66 255 72 75 3 601.95 0.77 256 72 76 4 522.02 3.99 257 72 79 7 521.95 3.98 258 72 82 10 502.14 1.17 259 72 118 46 372.53 0.62 260 72 119 47 372.25 0.49 261 73 79 6 522.05 4.00 262 73 80 7 522.04 4.00 263 73 81 8 521.76 3.98 264 73 82 9 503.95 0.29 265 73 84 11 496.28 1.50 266 73 118 45 373.10 0.48 267 74 78 4 585.25 1.81 268 74 79 5 524.08 3.00 269 74 80 6 522.08 4.00 270 74 81 7 521.95 3.99 271 74 112 38 440.48 3.27 272 74 115 41 373.54 0.52 273 74 118 44 373.20 0.52 274 75 78 3 593.35 5.87 275 75 79 4 564.20 3.73 276 75 115 40 373.55 0.52 277 75 118 43 373.20 0.52 278 76 79 3 606.70 0.81 279 76 119 43 373.19 0.52 280 79 82 3 589.81 3.18 281 80 148 68 363.47 0.79 282 81 84 3 640.28 3.13 283 81 147 66 363.45 0.79 284 81 148 67 363.38 0.77 285 82 119 37 372.48 0.60 286 82 148 66 363.13 0.72 287 82 149 67 363.13 0.72 288 82 150 68 363.10 0.72 289 83 146 63 363.52 0.81 290 83 147 64 363.18 0.73 291 83 148 65 363.13 0.72 292 83 149 66 362.87 0.66 293 83 150 67 359.62 1.99 294 83 151 68 348.72 0.89 295 84 107 23 493.17 1.73 296 84 143 59 363.68 0.79 297 84 146 62 363.38 0.78 298 84 147 63 363.14 0.72 299 84 184 100 25.32 2.66 300 85 88 3 680.43 5.29 301 85 104 19 493.43 1.61 302 85 138 53 366.06 0.81 303 85 145 60 363.53 0.81 304 85 146 61 363.26 0.77 305 85 149 64 335.86 1.46 306 86 105 19 493.40 1.61 307 86 106 20 492.99 1.64 308 86 107 21 481.38 1.87 309 86 108 22 479.36 0.85 310 86 109 23 479.30 0.89 311 86 120 34 371.31 0.66 312 86 146 60 363.29 0.79 313 87 97 10 494.67 1.65 314 87 102 15 493.64 1.65 315 87 104 17 493.38 1.61 316 87 106 19 492.48 1.46 317 87 122 35 370.60 0.86 318 88 102 14 493.61 1.64 319 88 103 15 493.43 1.60 320 88 104 16 493.31 1.58 321 88 149 61 328.37 0.15 322 88 154 66 299.28 0.11 323 89 92 3 639.44 1.00 324 89 100 11 493.70 1.67 325 89 101 12 493.65 1.65 326 89 102 13 493.40 1.62 327 90 100 10 493.69 1.66 328 90 101 11 493.61 1.65 329 90 103 13 493.40 1.62 330 90 127 37 368.94 0.95 331 90 131 41 367.87 0.86 332 90 133 43 367.57 0.97 333 90 154 64 299.09 0.09 334 91 100 9 493.66 1.67 335 91 127 36 368.85 0.97 336 91 130 39 367.87 0.86 337 91 131 40 367.85 0.85 338 92 95 3 640.76 2.45 339 92 96 4 576.52 2.88 340 92 97 5 545.49 3.31 341 92 99 7 493.66 1.67 342 92 100 8 493.44 1.59 343 93 96 3 611.63 1.97 344 93 99 6 510.73 2.96 345 96 99 3 601.33 0.83 346 96 100 4 597.78 0.48 347 97 100 3 623.51 3.98 348 102 105 3 613.39 2.97 349 103 133 30 367.83 0.86 350 103 135 32 366.40 0.62 351 103 137 34 364.05 0.75 352 103 138 35 364.04 0.74 353 103 154 51 299.60 0.26 354 104 138 34 364.01 0.74 355 104 146 42 363.17 0.73 356 105 138 33 364.40 0.94 357 105 139 34 363.92 0.74 358 105 140 35 363.80 0.73 359 105 146 41 363.39 0.77 360 106 122 16 371.16 0.70 361 106 140 34 363.69 0.81 362 107 140 33 363.69 0.81 363 107 146 39 363.45 0.80 364 107 180 73 39.59 2.73 365 107 184 77 25.34 2.66 366 108 180 72 39.59 2.73 367 109 120 11 371.51 0.62 368 109 169 60 293.30 0.23 369 109 171 62 292.10 0.10 370 109 180 71 39.59 2.73 371 110 177 67 197.03 3.79 372 110 180 70 39.59 2.73 373 110 181 71 39.59 2.73 374 111 118 7 373.11 0.85 375 111 120 9 372.81 0.73 376 111 171 60 293.12 0.21 377 111 172 61 291.66 0.41 378 111 173 62 291.35 0.46 379 111 177 66 239.64 0.41 380 112 115 3 598.90 2.94 381 112 118 6 521.39 0.75 382 112 173 61 291.64 0.40 383 112 181 69 220.91 0.52 384 113 173 60 292.73 0.14 385 115 118 3 714.12 0.01 386 116 172 56 293.28 0.21 387 117 170 53 293.36 0.23 388 117 171 54 293.28 0.21 389 117 172 55 292.82 0.15 390 118 170 52 293.35 0.23 391 118 171 53 293.27 0.21 392 119 168 49 293.38 0.23 393 119 169 50 293.36 0.23 394 119 170 51 292.91 0.18 395 120 168 48 293.32 0.21 396 120 169 49 293.20 0.24 397 120 171 51 292.29 0.12 398 121 167 46 293.35 0.22 399 121 168 47 292.87 0.17 400 122 166 44 293.35 0.22 401 122 167 45 293.19 0.25 402 122 169 47 292.36 0.10 403 123 151 28 299.28 0.12 404 123 163 40 293.58 0.29 405 123 165 42 293.35 0.22 406 123 166 43 293.04 0.26 407 124 163 39 293.38 0.22 408 124 164 40 293.37 0.23 409 124 165 41 292.52 0.01 410 125 151 26 299.21 0.15 411 125 155 30 295.34 0.80 412 125 160 35 294.18 0.40 413 125 161 36 294.16 0.41 414 125 162 37 293.58 0.27 415 125 163 38 293.33 0.21 416 125 164 39 293.28 0.21 417 126 160 34 294.17 0.40 418 126 164 38 292.43 0.05 419 127 130 3 649.96 1.86 420 127 131 4 607.50 0.15 421 127 160 33 294.03 0.41 422 128 161 33 294.11 0.42 423 131 158 27 294.47 0.35 424 131 160 29 294.33 0.32 425 132 158 26 296.47 0.23 426 133 154 21 299.56 0.27 427 133 158 25 297.19 0.14 428 134 157 23 299.46 0.26 429 134 158 24 299.15 0.24 430 135 154 19 299.59 0.27 431 135 157 22 299.50 0.24 432 135 158 23 299.44 0.24 433 138 144 6 363.55 0.82 434 138 145 7 363.52 0.81 435 138 146 8 363.31 0.76 436 139 146 7 363.54 0.81 437 140 146 6 531.87 13.85 438 140 183 43 30.84 0.56 439 140 184 44 25.34 2.66 440 141 183 42 30.84 0.56 441 141 184 43 25.34 2.66 442 142 184 42 30.19 0.24 443 143 146 3 598.46 1.51 444 143 184 41 25.33 2.67 445 146 149 3 627.74 0.97 446 149 154 5 594.57 1.33 447 150 153 3 603.12 0.80 448 150 154 4 595.10 1.07 449 151 154 3 603.93 3.34 450 151 155 4 595.11 1.07 451 152 155 3 609.92 0.35 452 152 156 4 595.11 1.07 453 153 156 3 609.92 0.35 454 153 157 4 589.30 1.80 455 154 157 3 602.36 3.43 456 154 158 4 594.81 0.96 457 155 158 3 607.55 0.83 458 155 159 4 581.75 0.40 459 155 160 5 559.87 1.39 460 155 161 6 559.88 1.39 461 155 162 7 552.90 4.86 462 156 159 3 586.58 2.11 463 173 177 4 603.88 1.15 464 173 178 5 603.88 1.15 465 174 177 3 621.38 0.29 466 174 178 4 621.63 0.42 467 175 178 3 633.09 3.85 468 176 179 3 612.00 0.59 469 176 180 4 603.46 1.31 470 177 180 3 603.79 1.44 471 177 181 4 598.56 1.11 472 178 181 3 594.23 1.02 473 178 182 4 594.21 1.02 474 179 182 3 597.06 2.44 475 179 183 4 589.42 1.38 476 180 183 3 593.28 0.17 477 180 184 4 590.14 1.74 478 181 184 3 585.05 3.95