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 6 14 8 710.12 0.33 2 7 10 3 758.47 1.43 3 7 11 4 732.87 2.46 4 8 11 3 755.81 0.86 5 8 12 4 737.60 0.10 6 8 43 35 226.81 4.77 7 8 47 39 226.79 4.76 8 9 12 3 756.21 1.97 9 9 13 4 749.14 5.50 10 9 47 38 226.79 4.76 11 9 51 42 226.46 4.90 12 10 13 3 759.47 0.35 13 10 14 4 737.82 0.17 14 11 14 3 760.60 0.36 15 11 15 4 743.19 2.52 16 11 41 30 227.98 4.30 17 12 15 3 758.53 3.43 18 12 16 4 743.31 2.45 19 12 41 29 227.98 4.30 20 12 43 31 227.27 4.64 21 12 51 39 226.49 4.90 22 13 16 3 766.00 0.31 23 13 17 4 747.72 0.24 24 13 51 38 226.49 4.90 25 13 54 41 225.64 4.48 26 13 55 42 225.60 4.46 27 14 17 3 752.48 1.26 28 14 18 4 743.30 2.45 29 14 89 75 63.84 1.22 30 15 18 3 754.26 2.12 31 15 19 4 748.25 0.04 32 15 24 9 683.41 6.02 33 15 25 10 652.40 17.87 34 15 40 25 228.54 4.40 35 15 41 26 228.49 4.42 36 16 19 3 750.00 0.01 37 16 20 4 748.49 0.07 38 16 25 9 651.72 17.54 39 16 31 15 228.76 4.33 40 16 37 21 228.53 4.40 41 16 41 25 228.54 4.39 42 16 48 32 227.23 4.61 43 16 51 35 226.97 4.69 44 16 52 36 226.87 4.72 45 16 55 39 225.74 4.41 46 17 20 3 763.15 6.58 47 17 21 4 748.49 0.07 48 17 55 38 225.74 4.41 49 17 60 43 218.93 1.82 50 17 85 68 68.21 0.01 51 17 89 72 64.49 1.40 52 18 21 3 748.48 0.07 53 18 22 4 733.08 2.23 54 19 22 3 748.02 0.25 55 19 23 4 730.88 3.31 56 19 24 5 705.84 2.70 57 19 25 6 675.39 6.34 58 20 23 3 734.91 6.79 59 20 25 5 699.01 6.11 60 20 27 7 494.48 96.00 61 20 60 40 219.02 1.85 62 20 61 41 219.02 1.85 63 20 71 51 213.28 1.14 64 21 60 39 219.21 1.77 65 21 85 64 82.67 0.53 66 21 86 65 79.03 2.33 67 21 89 68 73.55 0.05 68 21 91 70 69.16 0.02 69 23 26 3 717.41 1.97 70 23 27 4 755.05 2.69 71 24 40 16 229.65 4.32 72 25 31 6 231.28 3.50 73 25 32 7 229.30 4.49 74 25 37 12 229.39 4.45 75 25 40 15 229.71 4.29 76 25 71 46 213.37 1.14 77 26 29 3 767.53 2.31 78 26 71 45 213.43 1.16 79 27 71 44 213.38 1.13 80 27 72 45 213.34 1.12 81 27 73 46 213.28 1.14 82 28 71 43 213.56 1.16 83 29 70 41 213.59 1.17 84 29 71 42 213.56 1.16 85 30 68 38 213.60 1.17 86 30 69 39 213.59 1.17 87 30 70 40 213.50 1.19 88 31 37 6 716.75 2.40 89 31 52 21 228.94 4.63 90 31 61 30 219.00 1.83 91 31 69 38 213.58 1.17 92 31 71 40 213.37 1.15 93 32 36 4 734.43 6.82 94 32 37 5 716.85 2.36 95 33 36 3 765.55 0.89 96 33 37 4 756.53 3.64 97 34 37 3 756.53 3.64 98 34 38 4 748.39 0.43 99 34 45 11 236.81 1.79 100 34 48 14 236.59 1.71 101 34 49 15 236.59 1.71 102 34 52 18 236.47 1.67 103 35 38 3 769.34 9.20 104 35 39 4 748.39 0.42 105 35 45 10 236.84 1.79 106 36 39 3 756.54 3.65 107 36 40 4 741.03 3.26 108 37 40 3 751.59 0.60 109 37 41 4 732.65 3.90 110 37 48 11 236.61 1.72 111 37 52 15 236.58 1.73 112 38 41 3 759.94 5.27 113 38 42 4 721.35 0.18 114 38 43 5 694.24 0.21 115 38 45 7 236.86 1.79 116 38 48 10 236.68 1.75 117 39 42 3 746.76 1.92 118 43 47 4 721.15 3.10 119 43 48 5 715.66 0.35 120 44 47 3 734.41 2.50 121 44 48 4 737.75 5.19 122 45 48 3 748.56 1.07 123 45 49 4 737.75 5.19 124 46 49 3 753.65 6.21 125 46 50 4 738.61 0.45 126 47 50 3 763.85 1.10 127 47 51 4 747.65 0.62 128 48 51 3 752.23 0.58 129 48 52 4 747.68 0.65 130 49 52 3 758.35 2.48 131 49 53 4 747.68 0.65 132 50 53 3 753.40 1.39 133 50 54 4 747.75 0.69 134 51 54 3 751.98 2.10 135 51 55 4 743.04 3.04 136 52 55 3 751.22 0.06 137 52 56 4 738.62 0.83 138 52 61 9 256.36 11.10 139 53 56 3 751.86 0.40 140 53 57 4 743.00 3.02 141 53 63 10 216.33 0.82 142 54 57 3 747.12 1.98 143 54 58 4 738.28 5.38 144 55 58 3 758.63 4.79 145 55 59 4 738.28 5.38 146 55 60 5 673.97 9.50 147 55 61 6 486.90 98.05 148 56 59 3 736.56 6.24 149 56 61 5 418.48 69.95 150 56 63 7 233.38 3.70 151 58 78 20 89.98 0.86 152 58 82 24 85.01 0.25 153 59 72 13 213.21 1.13 154 59 77 18 90.03 0.87 155 59 78 19 89.98 0.86 156 60 71 11 213.30 1.14 157 60 72 12 213.20 1.16 158 60 74 14 134.03 3.48 159 60 82 22 89.91 0.89 160 60 85 25 85.12 0.52 161 60 86 26 87.02 0.42 162 61 69 8 213.58 1.16 163 61 70 9 213.44 1.21 164 61 71 10 213.25 1.15 165 61 72 11 213.18 1.14 166 62 69 7 213.59 1.17 167 62 70 8 213.46 1.17 168 62 72 10 213.23 1.18 169 63 69 6 213.58 1.16 170 64 67 3 769.66 9.14 171 72 77 5 686.95 8.41 172 73 76 3 777.16 0.14 173 73 77 4 724.56 4.43 174 74 77 3 761.07 0.22 175 74 78 4 686.95 8.41 176 74 82 8 164.91 33.95 177 74 86 12 93.09 0.56 178 75 86 11 93.11 0.57 179 75 93 18 70.25 0.38 180 75 97 22 67.47 0.41 181 78 82 4 742.75 0.58 182 79 82 3 782.75 1.98 183 80 83 3 782.88 2.04 184 80 164 84 58.70 2.16 185 80 168 88 54.17 1.82 186 81 84 3 787.87 0.46 187 82 85 3 763.57 0.08 188 82 86 4 751.99 5.71 189 83 86 3 766.27 1.44 190 83 87 4 736.56 13.42 191 83 97 14 78.67 4.26 192 83 101 18 67.56 0.71 193 83 168 85 55.30 1.13 194 83 171 88 53.54 1.49 195 84 87 3 763.25 0.07 196 84 88 4 754.34 4.52 197 85 88 3 754.44 1.47 198 85 89 4 742.16 1.55 199 86 89 3 763.76 3.20 200 86 90 4 741.06 1.03 201 86 91 5 616.77 12.77 202 86 94 8 104.06 1.66 203 86 97 11 93.61 0.64 204 87 90 3 749.05 1.23 205 87 94 7 100.92 1.28 206 87 171 84 52.45 0.94 207 90 94 4 751.64 0.09 208 91 94 3 775.35 1.56 209 92 95 3 829.99 0.24 210 93 96 3 777.90 2.84 211 93 97 4 746.33 8.30 212 94 97 3 757.94 2.90 213 94 98 4 749.90 6.52 214 95 98 3 771.18 1.68 215 95 99 4 758.69 2.10 216 96 99 3 763.29 0.20 217 96 100 4 748.08 0.98 218 97 100 3 754.34 2.15 219 97 101 4 748.08 0.98 220 98 101 3 755.93 2.95 221 98 102 4 755.93 2.95 222 98 223 125 69.46 9.58 223 99 102 3 760.66 5.33 224 99 103 4 745.50 3.56 225 99 224 125 69.48 9.60 226 100 103 3 768.69 6.73 227 100 104 4 745.54 3.54 228 101 104 3 757.83 1.98 229 101 105 4 745.54 3.54 230 101 168 67 298.20 76.09 231 101 171 70 298.17 76.09 232 102 105 3 752.63 0.00 233 102 106 4 757.19 2.28 234 102 223 121 99.19 0.67 235 103 106 3 764.00 1.59 236 103 107 4 757.17 2.29 237 104 107 3 765.97 0.60 238 104 108 4 752.32 4.71 239 105 108 3 768.07 1.66 240 105 109 4 755.19 3.27 241 105 145 40 441.83 4.26 242 105 149 44 441.81 4.28 243 105 172 67 442.21 4.09 244 105 215 110 255.03 2.25 245 106 109 3 767.56 1.74 246 106 110 4 755.71 3.00 247 106 212 106 255.05 2.25 248 106 213 107 255.05 2.25 249 106 216 110 190.83 22.37 250 107 110 3 762.43 0.83 251 107 111 4 755.72 3.00 252 107 213 106 256.01 1.77 253 108 111 3 760.41 1.13 254 108 112 4 747.63 1.03 255 108 161 53 499.47 2.67 256 109 112 3 755.50 3.40 257 109 113 4 743.51 0.51 258 109 149 40 460.05 12.71 259 109 212 103 359.47 5.09 260 110 114 4 741.57 4.28 261 110 208 98 383.69 4.71 262 110 209 99 373.68 0.17 263 110 212 102 361.63 6.17 264 110 213 103 361.67 6.17 265 111 114 3 768.58 0.79 266 111 115 4 755.83 2.79 267 111 161 50 500.38 2.77 268 112 115 3 759.31 1.05 269 112 116 4 745.26 2.49 270 112 149 37 500.44 2.73 271 112 152 40 500.44 2.73 272 112 153 41 500.41 2.74 273 112 156 44 500.75 2.89 274 112 161 49 500.37 2.77 275 112 165 53 500.40 2.75 276 113 116 3 756.24 0.48 277 113 117 4 745.27 2.50 278 113 149 36 500.44 2.73 279 113 152 39 500.44 2.73 280 113 196 83 442.89 3.98 281 113 208 95 420.57 0.64 282 113 212 99 419.35 0.06 283 114 117 3 759.40 1.09 284 114 118 4 748.73 4.23 285 114 205 91 421.67 0.34 286 114 208 94 420.61 0.66 287 115 118 3 755.84 3.04 288 115 119 4 729.20 5.54 289 115 156 41 501.48 3.01 290 116 119 3 746.25 2.66 291 116 120 4 715.29 1.38 292 116 121 5 644.31 6.04 293 116 124 8 536.52 2.08 294 116 152 36 501.50 2.95 295 116 155 39 501.49 3.01 296 116 156 40 501.48 3.01 297 117 121 4 616.60 7.81 298 117 124 7 536.58 2.08 299 117 128 11 536.57 2.07 300 117 152 35 501.59 2.97 301 117 196 79 443.08 4.05 302 117 199 82 441.98 3.52 303 117 200 83 440.69 3.04 304 117 205 88 422.37 0.00 305 117 208 91 421.69 0.32 306 118 205 87 422.36 0.00 307 119 156 37 508.25 6.28 308 120 123 3 764.18 1.28 309 120 124 4 750.21 0.70 310 120 155 35 508.25 6.28 311 120 157 37 508.26 6.27 312 121 124 3 750.21 0.70 313 121 125 4 747.25 0.77 314 121 200 79 440.94 3.00 315 122 125 3 754.73 1.06 316 122 126 4 747.26 0.77 317 123 126 3 754.74 1.18 318 123 127 4 745.76 1.52 319 123 155 32 509.32 5.83 320 124 127 3 754.74 1.18 321 124 128 4 747.27 4.92 322 124 152 28 509.32 5.83 323 124 155 31 509.31 5.83 324 124 200 76 440.95 3.00 325 125 128 3 751.03 3.04 326 125 129 4 744.57 2.66 327 125 197 72 443.12 4.04 328 125 200 75 440.98 3.00 329 125 201 76 440.97 2.99 330 126 129 3 760.88 0.49 331 126 130 4 751.77 0.26 332 127 130 3 775.92 2.60 333 127 147 20 509.76 5.96 334 127 148 21 509.79 5.95 335 127 151 24 509.75 5.96 336 127 152 25 509.80 5.96 337 128 131 3 772.75 1.14 338 128 148 20 509.84 5.96 339 128 152 24 509.84 5.96 340 128 193 65 443.28 4.03 341 128 196 68 443.23 4.01 342 128 197 69 443.12 4.04 343 129 132 3 772.64 1.19 344 130 144 14 510.00 6.03 345 130 148 18 509.98 6.01 346 131 134 3 758.58 2.70 347 131 144 13 510.06 6.00 348 131 148 17 510.05 6.00 349 131 190 59 443.54 4.02 350 131 193 62 443.45 4.01 351 134 140 6 668.07 1.61 352 134 141 7 668.06 1.61 353 134 144 10 510.86 5.75 354 134 190 56 444.08 3.87 355 135 140 5 687.60 6.04 356 135 141 6 707.88 4.10 357 136 141 5 734.87 2.33 358 136 186 50 477.66 6.52 359 137 140 3 771.18 4.98 360 137 141 4 743.25 0.06 361 137 186 49 483.94 5.45 362 138 141 3 771.18 4.98 363 138 142 4 744.83 2.64 364 138 177 39 497.29 10.99 365 138 180 42 493.74 10.15 366 138 181 43 492.68 9.64 367 138 186 48 481.98 4.33 368 139 142 3 766.58 4.22 369 139 143 4 744.84 2.65 370 139 177 38 497.29 10.99 371 140 143 3 757.18 2.21 372 140 144 4 749.76 0.18 373 141 144 3 749.76 0.18 374 141 145 4 736.41 1.90 375 141 180 39 492.73 9.66 376 141 186 45 449.14 6.41 377 141 189 48 444.00 3.83 378 141 190 49 443.99 3.83 379 142 145 3 760.25 0.49 380 142 146 4 737.36 1.43 381 142 173 31 498.31 11.18 382 142 176 34 497.30 11.00 383 142 177 35 497.29 10.99 384 142 180 38 492.73 9.67 385 143 146 3 761.94 0.35 386 143 147 4 755.85 1.75 387 143 169 26 508.02 6.69 388 144 147 3 758.20 0.58 389 144 148 4 755.87 1.75 390 144 193 49 443.43 4.01 391 145 148 3 764.71 2.67 392 145 149 4 755.86 1.75 393 145 172 27 498.44 11.25 394 145 180 35 492.72 9.66 395 145 193 48 443.28 4.03 396 146 149 3 764.71 2.67 397 146 150 4 738.31 0.92 398 146 165 19 510.28 5.84 399 146 166 20 510.19 5.88 400 146 169 23 506.12 7.42 401 146 172 26 498.43 11.25 402 146 173 27 498.40 11.24 403 147 150 3 749.92 1.23 404 147 151 4 732.69 1.20 405 148 151 3 741.98 0.61 406 148 152 4 732.86 1.18 407 148 193 45 443.27 4.03 408 149 152 3 749.53 0.08 409 149 153 4 732.88 1.17 410 149 165 16 510.25 5.83 411 149 172 23 498.43 11.25 412 149 192 43 443.29 4.03 413 150 153 3 750.88 10.17 414 150 154 4 732.88 1.17 415 150 165 15 510.25 5.83 416 150 166 16 510.25 5.83 417 151 154 3 757.88 2.05 418 151 155 4 732.88 1.17 419 152 155 3 767.23 2.00 420 152 156 4 742.14 5.81 421 152 196 44 443.08 4.05 422 153 156 3 758.95 2.15 423 153 161 8 510.63 5.82 424 153 162 9 510.62 5.82 425 153 165 12 510.55 5.79 426 154 157 3 765.59 1.18 427 154 162 8 510.63 5.82 428 154 166 12 510.63 5.81 429 156 161 5 716.71 7.71 430 158 161 3 800.81 5.06 431 159 162 3 746.88 0.34 432 159 163 4 742.63 2.46 433 160 163 3 750.41 2.10 434 160 164 4 742.63 2.46 435 161 164 3 744.86 1.35 436 161 165 4 744.85 1.35 437 162 165 3 753.89 0.12 438 162 166 4 741.44 0.35 439 163 166 3 750.02 1.23 440 164 168 4 760.65 0.44 441 165 168 3 778.97 2.17 442 168 171 3 733.93 9.00 443 168 172 4 708.46 3.71 444 169 172 3 743.41 2.85 445 169 173 4 722.90 10.94 446 170 173 3 766.50 7.20 447 170 174 4 745.19 0.18 448 171 174 3 750.29 0.91 449 171 175 4 746.67 0.90 450 172 175 3 755.63 1.06 451 172 176 4 740.73 6.48 452 173 176 3 746.31 3.96 453 173 177 4 744.01 4.82 454 174 177 3 754.68 0.49 455 174 178 4 748.08 2.81 456 175 178 3 755.81 0.68 457 175 179 4 741.70 1.62 458 175 223 48 417.38 0.83 459 176 179 3 749.83 2.44 460 176 180 4 741.65 1.64 461 177 181 4 741.49 1.56 462 178 181 3 758.99 2.40 463 178 223 45 417.52 0.76 464 178 226 48 410.42 0.13 465 179 182 3 774.96 3.45 466 179 185 6 665.01 3.23 467 179 219 40 419.16 0.33 468 179 222 43 418.81 0.42 469 179 223 44 417.38 0.83 470 179 226 47 409.73 0.48 471 180 185 5 690.37 9.45 472 180 186 6 639.40 0.42 473 180 189 9 617.70 7.09 474 181 186 5 738.93 2.41 475 182 185 3 754.48 0.32 476 182 186 4 740.83 1.47 477 182 222 40 419.11 0.35 478 182 226 44 412.44 0.31 479 183 186 3 743.52 0.12 480 183 187 4 738.95 2.41 481 184 187 3 747.67 4.89 482 184 188 4 738.95 2.41 483 184 222 38 419.32 0.56 484 185 188 3 751.97 2.71 485 185 189 4 742.00 0.81 486 185 222 37 418.92 0.45 487 186 189 3 747.83 3.24 488 186 190 4 744.63 0.50 489 187 190 3 762.56 8.46 490 187 191 4 744.62 0.50 491 188 191 3 750.80 2.25 492 188 192 4 739.00 1.17 493 188 215 27 422.28 0.06 494 188 218 30 420.90 0.66 495 188 219 31 420.69 0.74 496 188 222 34 418.97 0.43 497 189 192 3 752.14 4.07 498 189 193 4 733.90 1.39 499 189 215 26 421.88 0.26 500 190 193 3 747.80 6.21 501 190 194 4 733.93 1.38 502 191 194 3 752.95 3.63 503 191 195 4 739.31 1.31 504 192 195 3 758.78 0.71 505 192 196 4 740.01 0.98 506 192 211 19 422.72 0.04 507 192 212 20 422.59 0.07 508 192 215 23 421.63 0.35 509 193 196 3 748.92 1.62 510 193 197 4 741.33 0.34 511 194 197 3 748.04 1.19 512 194 198 4 743.82 1.57 513 195 198 3 745.54 2.44 514 195 199 4 741.35 0.34 515 195 211 16 422.75 0.07 516 196 199 3 745.74 2.54 517 196 200 4 741.35 0.34 518 196 211 15 422.62 0.11 519 196 212 16 422.63 0.10 520 197 200 3 751.25 1.27 521 197 201 4 729.13 5.77 522 198 201 3 745.52 4.29 523 198 202 4 736.77 0.07 524 199 202 3 747.61 3.25 525 199 203 4 736.29 0.17 526 199 204 5 592.37 17.27 527 199 207 8 422.79 0.07 528 199 208 9 422.76 0.07 529 199 211 12 422.75 0.07 530 200 203 3 707.64 14.50 531 204 207 3 759.85 2.40 532 205 208 3 750.88 0.10 533 207 210 3 777.68 1.39 534 207 211 4 735.18 0.32 535 208 211 3 749.64 3.04 536 208 212 4 739.04 2.25 537 209 212 3 750.94 2.86 538 209 213 4 745.75 4.21 539 210 213 3 763.48 4.65 540 210 214 4 745.76 4.21 541 211 214 3 749.72 4.67 542 211 215 4 747.34 3.44 543 212 215 3 747.46 3.38 544 212 216 4 747.36 3.44 545 213 216 3 747.36 3.45 546 213 217 4 747.36 3.45 547 214 217 3 752.98 0.64 548 214 218 4 747.36 3.45 549 215 218 3 748.75 4.15 550 215 219 4 747.35 3.45 551 216 219 3 761.67 1.57 552 216 220 4 734.22 0.55 553 217 220 3 734.88 0.88 554 217 221 4 736.51 1.69 555 218 221 3 756.41 1.65 556 218 222 4 750.48 0.20 557 219 222 3 764.64 5.76 558 219 223 4 741.90 4.49 559 220 223 3 763.52 6.32 560 220 224 4 741.91 4.49 561 221 224 3 765.17 5.50 562 221 225 4 741.89 4.48 563 222 225 3 754.06 1.19 564 222 226 4 742.31 4.69 565 223 226 3 754.68 0.88 566 223 227 4 736.48 1.80 567 224 227 3 769.97 7.99