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 22 25 3 774.57 4.88 2 22 26 4 750.83 3.33 3 22 57 35 89.67 0.43 4 23 26 3 755.23 1.14 5 23 27 4 742.14 1.01 6 23 58 35 89.76 0.41 7 23 59 36 89.62 0.42 8 24 27 3 760.47 2.89 9 24 28 4 743.94 1.88 10 25 28 3 750.17 0.55 11 25 29 4 743.96 1.87 12 25 227 202 39.88 0.81 13 25 229 204 40.01 0.86 14 25 230 205 40.01 0.86 15 25 232 207 39.88 0.81 16 25 233 208 39.31 0.67 17 26 29 3 761.75 2.25 18 26 30 4 739.06 0.58 19 26 53 27 94.47 1.75 20 26 54 28 94.39 1.77 21 26 57 31 94.45 1.75 22 26 59 33 89.95 0.45 23 27 30 3 754.69 2.71 24 27 31 4 738.50 0.84 25 27 59 32 90.03 0.47 26 27 67 40 88.78 0.00 27 27 70 43 84.48 0.07 28 28 31 3 757.65 0.14 29 28 32 4 736.27 0.24 30 28 78 50 46.13 0.96 31 28 98 70 40.12 0.82 32 28 230 202 40.12 0.82 33 28 231 203 40.12 0.82 34 29 32 3 751.72 3.53 35 29 33 4 746.99 4.95 36 29 50 21 97.48 1.89 37 29 98 69 41.54 0.24 38 30 33 3 760.62 0.76 39 30 34 4 747.00 4.95 40 30 47 17 103.17 0.96 41 30 50 20 97.50 1.88 42 30 51 21 97.48 1.89 43 30 54 24 97.46 1.88 44 30 59 29 93.89 0.95 45 30 64 34 89.69 0.36 46 30 67 37 89.55 0.33 47 30 68 38 88.99 0.02 48 31 34 3 750.62 3.14 49 31 35 4 750.40 3.25 50 31 67 36 89.55 0.33 51 31 70 39 85.61 0.64 52 31 71 40 82.97 0.33 53 31 76 45 54.21 0.35 54 31 78 47 47.73 0.22 55 32 35 3 751.51 3.79 56 32 36 4 750.40 3.24 57 32 78 46 46.27 0.95 58 32 79 47 46.18 0.97 59 32 80 48 45.92 0.85 60 32 98 66 45.88 0.85 61 33 36 3 770.36 0.19 62 33 37 4 743.72 3.20 63 33 44 11 275.73 76.52 64 33 46 13 109.32 2.09 65 33 47 14 109.31 2.08 66 33 50 17 103.38 0.88 67 34 37 3 757.35 0.96 68 34 38 4 709.04 4.58 69 34 39 5 548.96 58.16 70 34 44 10 275.87 76.45 71 34 47 13 111.32 1.07 72 34 68 34 89.59 0.32 73 34 71 37 84.17 0.21 74 35 71 36 84.17 0.21 75 35 76 41 60.80 0.14 76 35 77 42 57.05 0.35 77 37 44 7 395.79 16.57 78 38 44 6 399.62 18.43 79 38 47 9 399.56 18.43 80 39 47 8 400.44 18.82 81 39 68 29 89.75 0.32 82 40 43 3 749.01 2.56 83 40 44 4 685.54 11.36 84 40 47 7 447.03 4.46 85 41 44 3 763.70 3.15 86 41 47 6 447.03 4.46 87 41 48 7 447.00 4.46 88 41 51 10 447.00 4.46 89 42 48 6 675.77 3.80 90 44 47 3 752.54 0.23 91 44 48 4 733.22 3.31 92 45 48 3 752.93 0.41 93 45 49 4 745.99 3.06 94 46 49 3 746.00 3.06 95 46 50 4 745.99 3.06 96 47 50 3 741.06 0.69 97 47 51 4 741.27 0.71 98 47 68 21 89.73 0.34 99 48 51 3 746.01 1.65 100 48 52 4 746.00 1.65 101 49 52 3 746.00 1.65 102 49 53 4 746.00 1.65 103 49 182 133 43.95 0.96 104 49 199 150 41.47 0.40 105 50 53 3 749.52 0.11 106 50 54 4 746.00 1.65 107 51 54 3 754.63 3.25 108 51 55 4 734.12 2.83 109 51 64 13 89.86 0.37 110 51 68 17 89.80 0.35 111 52 55 3 755.45 2.85 112 52 56 4 741.96 1.71 113 52 196 144 41.02 0.62 114 52 199 147 40.87 0.58 115 53 56 3 755.45 2.85 116 53 57 4 744.14 2.80 117 53 198 145 40.76 0.59 118 53 199 146 40.62 0.69 119 54 57 3 741.97 1.71 120 54 58 4 741.96 1.71 121 54 59 5 701.48 4.06 122 54 64 10 115.89 1.51 123 55 58 3 741.96 1.71 124 55 64 9 391.38 21.19 125 56 197 141 40.80 0.58 126 59 63 4 737.50 2.24 127 59 64 5 727.54 0.85 128 60 63 3 749.65 3.36 129 60 64 4 738.83 1.57 130 61 64 3 754.94 1.28 131 61 65 4 735.63 3.17 132 62 65 3 737.57 2.21 133 62 66 4 735.62 3.17 134 63 66 3 735.62 3.17 135 63 67 4 735.62 3.17 136 64 67 3 747.22 0.51 137 64 68 4 735.77 1.47 138 65 68 3 759.09 1.37 139 65 69 4 735.66 1.42 140 66 69 3 759.12 2.46 141 66 70 4 733.32 2.60 142 67 70 3 746.98 2.29 143 68 71 3 770.09 3.75 144 69 72 3 762.26 0.15 145 70 73 3 745.02 2.12 146 70 75 5 512.55 73.22 147 70 76 6 121.70 1.48 148 71 76 5 121.70 1.47 149 73 76 3 750.24 1.17 150 74 77 3 801.63 3.04 151 75 78 3 851.06 5.83 152 77 100 23 425.45 3.68 153 78 99 21 426.62 3.79 154 78 100 22 425.69 3.77 155 79 97 18 426.88 3.79 156 79 98 19 426.71 3.80 157 79 99 20 426.69 3.81 158 79 102 23 426.66 3.81 159 80 97 17 426.88 3.79 160 80 98 18 426.73 3.81 161 81 96 15 427.01 3.82 162 81 97 16 426.89 3.79 163 81 99 18 426.88 3.80 164 81 102 21 426.70 3.81 165 82 94 12 427.44 3.88 166 82 95 13 427.15 3.79 167 82 96 14 427.04 3.83 168 82 124 42 361.78 5.06 169 82 203 121 275.91 0.29 170 83 94 11 427.44 3.88 171 83 95 12 427.33 3.87 172 83 97 14 427.14 3.79 173 83 102 19 426.87 3.81 174 83 105 22 426.81 3.83 175 83 106 23 426.66 3.86 176 83 109 26 426.69 3.81 177 83 121 38 363.53 4.53 178 83 124 41 361.79 5.06 179 84 93 9 427.64 3.87 180 84 94 10 427.50 3.85 181 84 95 11 427.43 3.88 182 84 121 37 363.55 4.51 183 84 122 38 363.50 4.52 184 84 124 40 361.92 5.00 185 84 125 41 361.93 5.00 186 84 126 42 361.75 5.01 187 84 127 43 361.38 4.88 188 85 92 7 427.83 3.92 189 85 93 8 427.67 3.86 190 85 95 10 427.63 3.85 191 85 113 28 426.56 3.74 192 85 120 35 364.09 4.62 193 85 121 36 363.56 4.51 194 85 122 37 363.54 4.52 195 86 91 5 540.14 60.06 196 86 92 6 427.83 3.92 197 86 113 27 426.62 3.77 198 86 119 33 364.19 4.62 199 86 120 34 364.14 4.62 200 86 122 36 364.04 4.61 201 86 127 41 361.93 5.00 202 87 90 3 781.37 1.66 203 87 91 4 661.69 0.71 204 87 93 6 427.85 3.93 205 87 118 31 407.25 11.38 206 87 119 32 364.19 4.62 207 87 222 135 271.80 0.96 208 88 91 3 775.21 4.74 209 88 117 29 425.70 3.90 210 88 118 30 407.29 11.36 211 89 209 120 276.80 0.53 212 89 211 122 275.67 0.17 213 89 215 126 273.97 0.25 214 89 218 129 273.96 0.25 215 89 219 130 273.87 0.22 216 90 209 119 276.24 0.25 217 90 238 148 267.77 0.74 218 91 209 118 276.16 0.26 219 91 211 120 275.92 0.29 220 91 219 128 272.74 0.58 221 91 238 147 267.57 0.83 222 91 239 148 267.48 0.78 223 92 127 35 361.77 4.92 224 92 130 38 360.99 4.74 225 92 131 39 358.89 3.70 226 92 237 145 267.60 0.84 227 92 238 146 267.11 0.96 228 93 113 20 426.73 3.81 229 93 127 34 361.68 4.98 230 93 222 129 271.74 0.95 231 93 223 130 271.07 1.12 232 93 235 142 268.17 0.71 233 93 236 143 268.00 0.69 234 93 237 144 267.45 0.76 235 94 127 33 361.50 4.90 236 94 131 37 308.82 0.52 237 94 203 109 276.12 0.26 238 94 235 141 268.16 0.71 239 94 236 142 268.04 0.71 240 95 109 14 426.72 3.81 241 95 113 18 426.70 3.81 242 95 226 131 270.52 1.08 243 95 234 139 268.57 0.69 244 95 235 140 268.11 0.74 245 96 203 107 275.85 0.29 246 96 232 136 269.31 0.67 247 96 233 137 269.26 0.67 248 96 234 138 268.60 0.67 249 96 236 140 268.58 0.68 250 97 105 8 527.99 54.43 251 97 109 12 426.69 3.81 252 97 231 134 269.50 0.62 253 97 232 135 269.32 0.67 254 97 233 136 269.31 0.67 255 98 231 133 270.17 0.96 256 98 233 135 269.38 0.68 257 99 102 3 773.50 1.52 258 99 104 5 747.44 2.68 259 99 105 6 724.48 2.46 260 99 231 132 270.43 1.10 261 100 104 4 782.62 0.77 262 101 104 3 782.62 0.77 263 101 105 4 755.71 1.44 264 102 105 3 755.71 1.44 265 102 106 4 746.95 2.92 266 103 106 3 761.26 1.33 267 103 107 4 744.93 1.91 268 104 107 3 752.46 1.84 269 104 108 4 744.08 2.35 270 104 231 127 270.45 1.11 271 105 108 3 756.59 0.23 272 105 109 4 744.05 2.37 273 105 231 126 270.05 1.03 274 106 109 3 757.00 0.48 275 106 110 4 752.41 1.81 276 106 121 15 363.58 4.58 277 107 110 3 757.01 0.48 278 107 111 4 752.38 1.83 279 108 111 3 757.00 0.48 280 108 112 4 741.85 1.49 281 108 229 121 270.75 1.18 282 109 112 3 744.24 0.62 283 109 113 4 741.82 1.47 284 109 226 117 270.87 1.17 285 109 232 123 269.31 0.69 286 110 113 3 745.22 0.06 287 110 114 4 743.10 0.83 288 110 121 11 363.60 4.58 289 111 114 3 743.11 0.83 290 111 115 4 743.11 0.83 291 112 115 3 749.79 4.17 292 112 116 4 744.31 1.44 293 112 222 110 271.25 1.12 294 112 225 113 271.00 1.16 295 112 226 114 271.04 1.17 296 112 229 117 270.86 1.18 297 113 116 3 749.95 4.26 298 113 119 6 364.11 4.62 299 113 120 7 363.92 4.66 300 113 121 8 363.97 4.69 301 113 222 109 271.31 1.15 302 113 226 113 271.16 1.13 303 115 225 110 271.69 0.96 304 116 119 3 752.17 5.10 305 116 222 106 271.74 0.97 306 116 225 109 271.73 0.97 307 119 222 103 271.79 0.96 308 122 126 4 738.89 4.67 309 122 127 5 729.88 9.17 310 123 126 3 755.06 1.96 311 125 128 3 735.21 6.45 312 127 130 3 747.11 2.15 313 127 131 4 730.79 3.71 314 129 206 77 277.93 0.04 315 130 205 75 277.94 0.03 316 130 206 76 277.94 0.04 317 131 203 72 279.06 0.45 318 131 204 73 278.72 0.30 319 131 205 74 277.94 0.04 320 131 206 75 277.94 0.03 321 131 237 106 268.07 0.63 322 131 238 107 267.72 0.67 323 132 202 70 282.02 0.35 324 132 203 71 279.86 0.11 325 132 204 72 279.05 0.46 326 132 206 74 277.98 0.03 327 133 179 46 602.19 0.52 328 133 201 68 282.49 0.26 329 133 202 69 282.02 0.35 330 133 203 70 280.51 0.15 331 134 164 30 603.10 0.94 332 134 177 43 603.04 0.93 333 134 178 44 603.02 0.93 334 134 179 45 603.02 0.93 335 134 201 67 282.55 0.28 336 134 202 68 282.25 0.27 337 134 204 70 281.55 0.24 338 135 176 41 603.27 0.91 339 135 177 42 603.11 0.94 340 135 178 43 603.24 0.92 341 135 179 44 603.12 0.95 342 135 182 47 602.15 0.52 343 135 185 50 603.00 0.93 344 135 200 65 283.36 0.07 345 135 201 66 282.55 0.28 346 136 174 38 603.49 0.92 347 136 175 39 603.38 0.90 348 136 176 40 603.28 0.91 349 136 199 63 286.29 1.37 350 136 200 64 283.38 0.07 351 136 202 66 282.76 0.18 352 137 174 37 603.50 0.93 353 137 175 38 603.43 0.91 354 137 182 45 603.38 0.93 355 137 185 48 603.31 0.91 356 137 186 49 603.25 0.93 357 137 189 52 603.08 0.93 358 137 196 59 348.25 15.09 359 137 198 61 305.13 4.70 360 137 199 62 286.49 1.47 361 138 172 34 604.39 0.82 362 138 173 35 603.63 0.88 363 138 174 36 603.51 0.92 364 138 196 58 420.25 20.91 365 138 197 59 348.12 15.06 366 138 198 60 314.37 1.60 367 139 143 4 753.93 5.37 368 139 144 5 745.41 1.12 369 139 172 33 604.68 0.84 370 139 173 34 603.63 0.88 371 139 189 50 603.37 0.90 372 139 194 55 547.59 4.55 373 139 195 56 505.81 4.45 374 139 197 58 348.22 15.09 375 140 143 3 753.94 5.37 376 140 144 4 745.44 1.12 377 140 171 31 605.39 0.88 378 140 172 32 605.18 0.96 379 140 197 57 420.32 20.96 380 141 144 3 767.77 1.51 381 141 145 4 755.65 4.51 382 141 151 10 605.46 0.85 383 141 168 27 605.38 0.88 384 141 171 30 605.39 0.88 385 141 172 31 605.21 0.95 386 141 173 32 605.21 0.95 387 142 145 3 753.77 2.89 388 142 146 4 745.41 1.12 389 142 171 29 605.45 0.91 390 143 146 3 756.66 1.45 391 143 147 4 747.12 0.26 392 143 194 51 586.71 0.44 393 143 195 52 572.73 2.51 394 144 147 3 767.70 3.02 395 144 148 4 747.11 0.25 396 144 149 5 692.07 6.98 397 144 151 7 605.47 0.85 398 144 154 10 605.39 0.84 399 144 173 29 605.41 0.89 400 144 194 50 590.41 1.05 401 145 148 3 730.52 6.21 402 147 192 45 603.44 0.93 403 147 193 46 603.38 0.92 404 147 194 47 603.07 0.89 405 147 195 48 603.09 0.90 406 149 153 4 722.10 0.45 407 149 154 5 717.68 2.81 408 149 192 43 603.45 0.93 409 150 153 3 735.65 2.48 410 150 154 4 728.34 1.18 411 151 154 3 745.14 2.06 412 151 155 4 735.45 7.12 413 151 166 15 610.86 1.53 414 151 168 17 610.99 1.56 415 151 173 22 610.77 1.54 416 152 155 3 754.40 0.40 417 152 156 4 720.49 4.21 418 153 156 3 762.81 5.97 419 153 157 4 720.41 4.25 420 154 157 3 751.71 1.01 421 154 158 4 743.61 1.04 422 154 166 12 610.99 1.56 423 154 173 19 610.97 1.58 424 154 175 21 610.95 1.56 425 154 192 38 603.41 0.92 426 154 194 40 601.79 0.39 427 155 158 3 753.87 0.10 428 155 159 4 743.61 1.03 429 155 163 8 610.95 1.59 430 155 166 11 610.97 1.57 431 156 159 3 753.88 0.09 432 157 160 3 787.62 1.04 433 157 161 4 751.73 0.99 434 157 192 35 603.57 0.92 435 158 161 3 749.85 0.06 436 158 162 4 749.84 0.06 437 158 163 5 656.78 14.85 438 158 175 17 611.01 1.57 439 158 185 27 605.44 1.06 440 158 188 30 604.92 0.93 441 158 189 31 605.25 1.10 442 158 192 34 603.67 0.96 443 159 163 4 695.21 9.81 444 160 184 24 605.48 1.05 445 161 184 23 605.44 1.06 446 161 185 24 605.45 1.06 447 161 187 26 605.40 1.08 448 161 188 27 605.31 1.11 449 162 177 15 610.97 1.54 450 162 181 19 605.50 1.05 451 162 184 22 605.47 1.05 452 162 185 23 605.46 1.06 453 163 166 3 835.49 2.58 454 163 175 12 611.16 1.57 455 163 176 13 611.06 1.57 456 163 177 14 610.99 1.54 457 163 185 22 605.45 1.06 458 164 176 12 611.13 1.56 459 164 177 13 611.00 1.54 460 164 178 14 611.00 1.54 461 165 175 10 611.24 1.58 462 165 176 11 611.14 1.58 463 166 173 7 611.69 1.56 464 166 174 8 611.61 1.57 465 166 175 9 611.25 1.58 466 167 173 6 611.72 1.56 467 167 174 7 611.62 1.57 468 167 176 9 611.63 1.56 469 168 172 4 668.32 4.62 470 168 173 5 611.75 1.55 471 169 172 3 742.94 3.90 472 169 174 5 611.91 1.47 473 172 197 25 425.05 18.59 474 175 185 10 604.68 1.44 475 175 189 14 603.55 0.92 476 177 185 8 605.46 1.06 477 178 181 3 750.13 1.16 478 179 182 3 758.42 4.29 479 179 201 22 282.54 0.28 480 181 184 3 748.52 0.74 481 181 185 4 712.97 6.06 482 182 185 3 759.06 6.53 483 182 186 4 728.14 1.51 484 182 199 17 286.57 1.44 485 182 200 18 286.49 1.48 486 182 201 19 283.38 0.06 487 183 186 3 744.21 0.74 488 183 187 4 728.14 1.51 489 184 187 3 728.90 1.89 490 184 188 4 741.90 1.98 491 185 188 3 741.91 1.98 492 185 189 4 741.91 1.98 493 186 189 3 749.18 1.65 494 186 190 4 739.28 3.29 495 186 196 10 448.58 1.67 496 187 190 3 742.12 1.88 497 187 191 4 726.48 9.70 498 188 191 3 741.92 1.98 499 188 192 4 739.28 3.29 500 189 192 3 752.90 3.52 501 189 193 4 710.48 2.58 502 189 194 5 644.89 0.62 503 189 196 7 562.70 24.00 504 190 193 3 719.34 3.02 505 196 199 3 793.13 3.18 506 201 236 35 268.48 0.59 507 202 236 34 268.38 0.60 508 203 236 33 268.27 0.66 509 205 208 3 760.45 2.73 510 205 238 33 267.72 0.67 511 208 238 30 267.97 0.66 512 208 240 32 267.43 0.70 513 209 238 29 268.01 0.67 514 209 239 30 267.73 0.79 515 209 240 31 267.60 0.73 516 210 240 30 267.70 0.77 517 211 215 4 702.92 3.96 518 211 216 5 690.38 10.24 519 211 219 8 631.34 1.98 520 211 239 28 268.07 0.71 521 212 215 3 751.94 0.09 522 212 216 4 740.20 5.96 523 213 216 3 757.75 2.82 524 213 217 4 740.20 5.96 525 214 217 3 751.94 0.09 526 214 218 4 740.21 5.95 527 215 218 3 743.11 2.21 528 215 219 4 732.97 2.33 529 216 219 3 736.59 0.52 530 216 220 4 732.90 2.29 531 216 239 23 268.02 0.68 532 217 220 3 750.49 1.30 533 217 221 4 736.51 0.48 534 218 221 3 761.97 3.00 535 219 222 3 761.96 3.00 536 219 223 4 732.84 2.23 537 219 239 20 267.95 0.68 538 220 223 3 734.93 1.20 539 220 224 4 734.29 2.96 540 221 224 3 762.41 1.57 541 221 225 4 741.94 0.84 542 222 225 3 759.63 2.96 543 222 226 4 741.95 0.84 544 223 226 3 757.87 2.08 545 223 227 4 741.27 0.50 546 223 235 12 268.31 0.70 547 223 237 14 268.14 0.67 548 223 239 16 268.01 0.67 549 224 227 3 753.66 4.19 550 224 228 4 734.09 3.10 551 225 228 3 753.72 4.17 552 225 229 4 736.28 0.42 553 226 229 3 748.75 6.66 554 226 232 6 309.72 4.99 555 226 235 9 268.33 0.71 556 227 235 8 268.49 0.64 557 229 232 3 746.57 2.12 558 232 235 3 805.97 2.68