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 1 126 125 200.16 2.44 2 1 127 126 200.16 2.43 3 1 158 157 39.49 0.66 4 1 159 158 36.20 0.38 5 1 160 159 34.09 0.31 6 2 127 125 200.16 2.43 7 2 128 126 200.16 2.43 8 2 158 156 39.58 0.61 9 2 165 163 33.76 0.48 10 3 121 118 200.12 2.43 11 3 124 121 200.20 2.43 12 3 127 124 200.22 2.43 13 3 128 125 200.16 2.43 14 3 130 127 200.13 2.43 15 3 157 154 45.31 1.06 16 3 158 155 44.18 0.68 17 3 160 157 37.73 0.16 18 4 42 38 327.66 8.44 19 4 43 39 327.27 8.25 20 4 45 41 327.27 8.25 21 4 128 124 200.22 2.43 22 4 129 125 200.16 2.43 23 4 130 126 200.13 2.44 24 4 156 152 50.70 0.66 25 4 157 153 46.82 1.56 26 4 166 162 33.81 0.48 27 4 168 164 33.75 0.48 28 5 130 125 200.16 2.43 29 5 132 127 200.13 2.44 30 5 136 131 146.66 0.63 31 5 137 132 138.07 0.18 32 5 140 135 120.70 0.28 33 5 155 150 51.97 1.24 34 5 156 151 50.77 0.65 35 5 158 153 50.63 0.63 36 6 38 32 329.41 9.09 37 6 42 36 328.61 8.69 38 6 58 52 328.28 8.59 39 6 129 123 200.28 2.42 40 6 130 124 200.21 2.44 41 6 131 125 200.14 2.44 42 6 132 126 200.13 2.44 43 6 154 148 63.59 1.52 44 6 155 149 51.97 1.24 45 7 14 7 565.37 0.02 46 7 132 125 200.18 2.44 47 7 134 127 189.00 0.01 48 7 137 130 146.68 0.64 49 7 150 143 80.06 0.46 50 7 151 144 78.90 0.93 51 7 152 145 78.21 0.97 52 7 153 146 77.61 0.70 53 7 154 147 69.17 0.24 54 8 14 6 567.19 0.92 55 8 20 12 369.12 3.62 56 8 54 46 328.38 8.58 57 8 55 47 327.32 8.21 58 8 58 50 328.58 8.69 59 8 132 124 200.23 2.43 60 8 133 125 200.17 2.43 61 8 152 144 78.36 1.01 62 8 153 145 78.08 0.92 63 9 27 18 366.54 3.57 64 9 31 22 365.57 3.15 65 9 34 25 364.29 3.77 66 9 58 49 354.06 3.37 67 9 152 143 78.45 1.03 68 9 153 144 78.09 0.92 69 10 14 4 566.39 0.53 70 10 15 5 566.39 0.52 71 10 27 17 367.02 3.60 72 10 28 18 367.06 3.61 73 10 30 20 367.06 3.61 74 10 31 21 366.39 3.51 75 10 34 24 366.72 3.67 76 10 152 142 78.52 1.03 77 11 14 3 579.63 1.47 78 11 15 4 571.70 1.33 79 11 20 9 467.81 11.82 80 11 25 14 367.02 3.60 81 11 26 15 367.06 3.61 82 11 27 16 367.02 3.60 83 11 28 17 367.08 3.62 84 11 54 43 367.02 3.60 85 12 15 3 572.35 1.23 86 12 16 4 568.37 0.46 87 12 28 16 367.23 3.62 88 13 16 3 569.06 0.81 89 13 17 4 568.37 0.46 90 13 18 5 553.25 6.04 91 13 19 6 540.78 0.20 92 13 20 7 497.97 1.58 93 13 23 10 376.05 0.96 94 13 25 12 368.49 3.64 95 13 82 69 274.01 0.65 96 14 17 3 570.77 1.66 97 14 20 6 498.88 1.97 98 15 28 13 368.40 3.44 99 16 84 68 272.72 0.02 100 17 84 67 272.67 0.01 101 17 85 68 272.67 0.01 102 18 82 64 277.15 2.21 103 18 83 65 274.00 0.65 104 18 84 66 272.96 0.17 105 19 77 58 322.55 10.40 106 19 80 61 292.68 5.78 107 19 81 62 278.14 2.15 108 19 82 63 277.46 2.35 109 19 83 64 274.01 0.65 110 19 85 66 272.43 0.12 111 19 88 69 272.45 0.12 112 19 96 77 247.36 4.16 113 20 23 3 608.01 2.05 114 20 25 5 500.02 5.75 115 20 54 34 418.44 10.30 116 20 74 54 326.32 8.89 117 20 77 57 322.56 10.39 118 21 52 31 418.91 10.52 119 21 54 33 418.92 10.52 120 21 74 53 326.29 8.90 121 21 75 54 326.16 8.88 122 21 77 56 324.97 9.19 123 21 81 60 281.69 0.37 124 22 52 30 418.99 10.55 125 22 73 51 326.91 8.90 126 22 74 52 326.64 9.02 127 22 75 53 326.55 8.97 128 22 76 54 326.06 8.90 129 22 81 59 281.80 0.35 130 23 54 31 419.57 10.65 131 23 81 58 281.74 0.35 132 24 52 28 419.26 10.56 133 24 53 29 419.50 10.62 134 24 54 30 419.56 10.65 135 25 54 29 419.59 10.65 136 26 53 27 419.79 10.67 137 27 31 4 552.57 0.68 138 27 32 5 553.06 0.43 139 27 54 27 419.84 10.66 140 27 57 30 419.91 10.64 141 27 58 31 419.91 10.64 142 27 61 34 420.02 10.63 143 28 31 3 569.85 2.19 144 28 32 4 565.61 2.65 145 29 32 3 577.56 2.00 146 29 33 4 571.71 0.40 147 30 33 3 572.58 0.83 148 30 34 4 571.71 0.40 149 30 37 7 560.68 1.28 150 31 34 3 573.54 0.42 151 31 35 4 574.37 0.01 152 32 35 3 577.93 1.79 153 32 36 4 574.37 0.01 154 32 57 25 420.07 10.69 155 32 61 29 420.79 10.98 156 33 36 3 577.93 1.79 157 33 37 4 574.37 0.01 158 34 37 3 587.55 0.39 159 34 38 4 574.38 0.01 160 34 152 118 78.51 1.03 161 34 153 119 78.09 0.92 162 35 38 3 580.96 2.92 163 35 39 4 577.07 1.62 164 35 58 23 420.15 10.71 165 35 61 26 421.44 11.05 166 35 62 27 421.44 11.05 167 36 39 3 586.72 0.80 168 36 61 25 421.43 11.04 169 37 41 4 580.16 3.17 170 37 170 133 33.21 0.30 171 37 171 134 33.20 0.31 172 38 41 3 574.62 5.94 173 38 42 4 563.35 3.19 174 38 58 20 421.69 11.03 175 38 62 24 421.68 11.02 176 38 153 115 77.98 0.88 177 38 170 132 33.20 0.31 178 39 61 22 421.73 11.04 179 39 62 23 421.68 11.03 180 39 63 24 421.68 11.02 181 41 168 127 33.74 0.48 182 41 170 129 33.21 0.31 183 42 62 20 486.12 1.11 184 42 64 22 486.18 1.15 185 42 129 87 200.43 2.33 186 42 131 89 200.22 2.43 187 42 155 113 56.27 0.20 188 43 64 21 486.38 1.09 189 43 129 86 200.69 2.19 190 45 64 19 486.50 1.09 191 45 127 82 200.81 2.23 192 45 128 83 200.77 2.22 193 45 129 84 200.75 2.22 194 46 127 81 200.82 2.23 195 46 128 82 200.77 2.22 196 46 129 83 200.76 2.23 197 47 64 17 486.50 1.09 198 47 66 19 486.44 1.10 199 47 67 20 486.43 1.10 200 47 129 82 200.70 2.25 201 47 131 84 200.62 2.25 202 48 66 18 486.46 1.11 203 48 67 19 486.43 1.10 204 48 69 21 486.42 1.11 205 48 72 24 482.08 0.09 206 48 120 72 209.86 2.19 207 48 124 76 200.90 2.23 208 48 128 80 200.79 2.23 209 48 129 81 200.72 2.25 210 48 130 82 200.59 2.24 211 48 131 83 200.57 2.25 212 49 55 6 487.03 0.99 213 49 56 7 487.00 0.99 214 49 59 10 486.66 1.07 215 49 66 17 486.48 1.10 216 49 67 18 486.48 1.10 217 49 68 19 486.43 1.10 218 49 69 20 486.43 1.10 219 49 72 23 482.09 0.10 220 49 131 82 200.55 2.27 221 50 55 5 509.56 12.26 222 50 56 6 487.59 1.27 223 50 68 18 486.48 1.10 224 50 69 19 486.45 1.10 225 50 72 22 482.09 0.09 226 50 73 23 473.00 1.21 227 50 131 81 200.65 2.29 228 50 132 82 200.44 2.35 229 50 133 83 200.55 2.30 230 51 56 5 519.29 7.41 231 51 68 17 486.48 1.10 232 51 70 19 486.44 1.10 233 51 73 22 485.85 1.33 234 52 55 3 582.77 3.08 235 52 56 4 563.12 3.52 236 52 73 21 486.31 1.10 237 52 133 81 200.46 2.36 238 53 56 3 570.30 0.06 239 53 57 4 537.08 1.00 240 54 58 4 545.47 0.60 241 54 74 20 484.02 0.93 242 54 133 79 200.39 2.38 243 55 58 3 566.48 0.40 244 55 59 4 566.54 0.35 245 55 131 76 200.49 2.35 246 55 133 78 200.36 2.37 247 56 59 3 585.31 5.92 248 56 60 4 562.75 1.56 249 56 68 12 486.53 1.08 250 57 60 3 569.68 1.90 251 57 61 4 569.67 1.90 252 58 61 3 587.25 0.35 253 58 62 4 562.74 1.56 254 58 131 73 200.31 2.41 255 59 62 3 570.29 0.69 256 59 63 4 562.71 1.57 257 59 64 5 519.49 7.58 258 59 66 7 486.61 1.07 259 59 131 72 200.22 2.43 260 60 63 3 565.25 2.85 261 60 64 4 535.31 0.06 262 62 131 69 200.23 2.43 263 64 129 65 200.68 2.25 264 64 131 67 200.22 2.43 265 69 72 3 583.25 2.07 266 69 120 51 210.00 2.23 267 70 73 3 567.14 1.43 268 70 116 46 213.48 3.69 269 71 116 45 213.44 3.69 270 71 120 49 209.93 2.17 271 72 120 48 209.93 2.17 272 72 130 58 200.77 2.26 273 72 132 60 200.61 2.27 274 72 133 61 200.61 2.27 275 72 136 64 146.75 0.64 276 73 113 40 213.56 3.66 277 73 116 43 213.49 3.68 278 73 133 60 200.61 2.29 279 73 136 63 158.44 0.28 280 74 113 39 213.56 3.66 281 74 116 42 213.56 3.66 282 74 133 59 200.62 2.30 283 74 134 60 200.62 2.30 284 74 135 61 200.13 2.44 285 74 136 62 169.13 5.54 286 75 108 33 218.96 5.99 287 75 110 35 218.34 5.81 288 75 113 38 213.56 3.66 289 75 116 41 213.56 3.65 290 76 81 5 513.41 7.81 291 76 104 28 219.88 5.69 292 76 106 30 219.81 5.66 293 76 107 31 219.06 5.95 294 76 108 32 218.97 5.99 295 77 80 3 580.55 2.37 296 77 81 4 393.08 3.85 297 77 96 19 270.22 0.18 298 77 102 25 219.99 5.74 299 77 104 27 219.88 5.69 300 77 107 30 219.08 5.94 301 78 81 3 593.23 3.97 302 78 105 27 219.91 5.68 303 78 106 28 219.81 5.66 304 78 107 29 219.08 5.93 305 79 105 26 219.95 5.67 306 80 83 3 580.62 2.85 307 80 88 8 302.26 10.81 308 80 92 12 272.52 0.14 309 80 102 22 223.75 4.21 310 80 104 24 219.96 5.67 311 80 105 25 219.99 5.66 312 83 88 5 476.99 7.37 313 84 87 3 569.03 2.52 314 84 88 4 560.72 1.63 315 85 88 3 569.03 2.52 316 85 93 8 457.61 15.35 317 85 96 11 457.60 15.35 318 85 97 12 457.60 15.35 319 86 93 7 519.79 2.55 320 87 93 6 525.94 0.49 321 88 92 4 555.94 3.25 322 88 93 5 525.92 0.49 323 88 96 8 501.61 6.46 324 89 92 3 573.78 1.23 325 89 93 4 562.27 0.13 326 90 93 3 576.50 0.41 327 90 94 4 562.27 0.13 328 91 95 4 562.27 0.14 329 92 95 3 569.89 3.94 330 92 96 4 566.75 2.38 331 92 102 10 255.62 11.70 332 93 96 3 575.12 0.85 333 93 97 4 559.93 1.27 334 94 97 3 571.11 4.32 335 94 98 4 559.91 1.27 336 95 98 3 575.62 2.06 337 95 99 4 557.83 0.24 338 95 100 5 511.50 1.31 339 95 101 6 440.42 24.54 340 95 102 7 264.56 10.12 341 96 99 3 557.59 2.38 342 96 102 6 285.70 0.45 343 96 138 42 200.65 2.31 344 97 138 41 200.68 2.31 345 98 142 44 146.77 0.62 346 99 110 11 221.67 4.70 347 99 114 15 221.17 4.45 348 99 138 39 199.46 1.68 349 99 139 40 198.22 1.11 350 99 142 43 146.64 0.68 351 100 110 10 221.69 4.71 352 101 110 9 221.69 4.71 353 102 109 7 221.70 4.71 354 102 110 8 221.65 4.70 355 103 107 4 564.20 9.25 356 103 108 5 253.52 11.12 357 103 109 6 221.66 4.68 358 104 107 3 573.76 4.46 359 104 108 4 569.14 6.78 360 108 116 8 549.14 2.05 361 109 112 3 572.02 0.18 362 109 113 4 556.64 0.56 363 110 113 3 573.48 3.42 364 110 114 4 560.53 1.39 365 111 114 3 573.31 3.33 366 111 115 4 567.83 2.27 367 112 115 3 572.38 3.79 368 112 116 4 566.11 3.12 369 113 116 3 578.39 3.01 370 113 117 4 566.12 3.12 371 113 135 22 200.66 2.25 372 113 136 23 200.25 2.11 373 113 139 26 146.53 0.65 374 114 117 3 573.55 1.09 375 114 118 4 558.45 0.72 376 114 139 25 145.30 0.58 377 115 118 3 572.60 1.57 378 115 119 4 562.42 2.67 379 116 119 3 572.60 1.57 380 116 120 4 571.75 2.00 381 117 120 3 576.36 0.30 382 117 121 4 562.47 2.65 383 117 136 19 146.77 0.65 384 117 140 23 127.66 0.17 385 118 121 3 571.75 2.00 386 118 122 4 562.45 2.65 387 118 139 21 143.50 0.19 388 118 140 22 125.91 0.71 389 118 143 25 118.71 0.24 390 118 160 42 41.34 0.27 391 119 122 3 572.62 1.56 392 119 123 4 571.73 2.01 393 120 123 3 571.85 1.04 394 120 124 4 562.35 3.70 395 120 130 10 200.84 2.21 396 121 124 3 575.92 0.99 397 121 130 9 200.85 2.21 398 121 140 19 122.17 0.39 399 121 160 39 36.95 0.21 400 124 130 6 499.75 16.59 401 132 136 4 560.42 2.15 402 132 137 5 555.94 0.03 403 133 136 3 569.41 3.33 404 133 137 4 560.43 2.14 405 134 137 3 579.12 0.15 406 134 138 4 560.45 2.12 407 135 138 3 571.75 3.52 408 135 139 4 560.46 2.12 409 136 139 3 572.62 3.41 410 136 140 4 563.14 0.71 411 137 140 3 577.63 0.67 412 137 141 4 561.13 0.29 413 137 150 13 81.31 0.73 414 137 156 19 50.81 0.66 415 138 141 3 574.21 5.45 416 138 142 4 558.56 0.89 417 138 148 10 82.53 0.35 418 138 149 11 82.54 0.36 419 139 142 3 574.38 5.53 420 139 143 4 558.96 1.36 421 140 143 3 590.72 2.65 422 140 144 4 559.85 0.92 423 140 160 20 48.84 0.95 424 141 144 3 578.86 8.58 425 141 145 4 558.88 1.41 426 141 146 5 459.32 18.11 427 141 147 6 425.32 17.57 428 141 148 7 82.52 0.35 429 141 150 9 151.69 33.47 430 141 156 15 50.86 0.68 431 141 164 23 39.09 0.54 432 141 167 26 36.79 0.65 433 142 145 3 578.19 8.92 434 142 146 4 537.36 5.22 435 142 148 6 156.43 35.19 436 143 160 17 49.05 0.96 437 144 158 14 50.45 0.75 438 144 160 16 49.05 0.96 439 144 161 17 48.87 0.96 440 144 162 18 47.02 0.24 441 144 163 19 43.29 1.18 442 144 164 20 43.21 1.22 443 146 164 18 44.95 0.89 444 146 167 21 41.76 0.36 445 147 167 20 42.23 0.47 446 149 167 18 40.95 0.09 447 150 154 4 524.29 8.17 448 150 156 6 285.24 4.29 449 150 167 17 37.37 0.35 450 151 154 3 567.54 5.58 451 151 169 18 34.06 0.36 452 154 168 14 33.79 0.48 453 154 169 15 33.69 0.50 454 155 167 12 33.80 0.48 455 155 168 13 33.76 0.48 456 156 166 10 34.06 0.36 457 156 167 11 33.76 0.48 458 157 164 7 37.35 0.36 459 157 165 8 37.34 0.36 460 157 166 9 33.78 0.48 461 158 163 5 255.50 81.07 462 158 164 6 37.36 0.35 463 158 165 7 37.35 0.36 464 159 162 3 594.15 2.18 465 159 163 4 487.11 34.73 466 159 165 6 60.30 11.82 467 164 167 3 678.46 0.79