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 12 16 4 715.58 6.11 2 14 18 4 650.44 3.53 3 15 18 3 778.29 7.09 4 17 97 80 141.56 2.16 5 17 98 81 141.56 2.16 6 17 99 82 141.34 2.04 7 17 100 83 141.03 1.91 8 17 101 84 141.56 2.16 9 19 53 34 230.05 1.55 10 19 63 44 226.01 4.09 11 19 64 45 225.44 3.88 12 19 98 79 222.44 4.54 13 19 99 80 219.59 4.76 14 20 64 44 233.34 0.42 15 20 99 79 222.63 4.54 16 21 99 78 222.90 4.67 17 21 100 79 222.91 4.67 18 21 190 169 209.22 1.55 19 22 56 34 233.99 0.65 20 22 60 38 234.11 0.61 21 22 64 42 234.03 0.62 22 22 190 168 212.78 0.36 23 23 187 164 221.41 3.63 24 23 190 167 212.81 0.37 25 23 191 168 212.81 0.37 26 24 29 5 745.03 6.79 27 24 52 28 235.14 0.32 28 24 56 32 235.32 0.25 29 24 183 159 232.99 0.24 30 24 186 162 232.84 0.18 31 24 187 163 229.62 1.77 32 25 28 3 777.38 0.26 33 25 29 4 763.00 2.19 34 26 29 3 777.86 9.61 35 26 30 4 763.00 2.18 36 26 180 154 234.25 0.78 37 26 183 157 235.17 0.34 38 26 184 158 235.16 0.34 39 26 187 161 235.19 0.33 40 27 30 3 789.26 3.91 41 27 31 4 765.28 1.05 42 27 180 153 250.99 0.81 43 28 31 3 779.44 0.70 44 28 32 4 767.24 0.07 45 28 55 27 274.94 5.31 46 28 59 31 342.03 33.95 47 29 32 3 786.29 0.90 48 29 33 4 769.89 1.40 49 29 51 22 256.55 0.60 50 29 55 26 279.58 3.00 51 29 179 150 256.55 0.60 52 29 183 154 256.55 0.60 53 30 33 3 798.14 1.76 54 30 34 4 767.25 0.07 55 30 124 94 287.78 4.17 56 30 176 146 256.72 0.69 57 30 179 149 256.56 0.60 58 30 180 150 256.55 0.60 59 31 34 3 791.00 1.81 60 31 35 4 778.65 2.62 61 31 124 93 288.87 3.98 62 32 35 3 785.64 0.86 63 32 36 4 774.33 4.78 64 32 50 18 288.07 4.16 65 32 51 19 288.06 4.17 66 32 55 23 288.07 4.16 67 33 36 3 778.67 2.62 68 33 37 4 776.16 3.87 69 33 47 14 288.11 4.18 70 33 48 15 288.07 4.17 71 33 51 18 288.07 4.17 72 33 175 142 288.88 4.17 73 33 176 143 288.49 4.18 74 33 179 146 288.06 4.17 75 34 37 3 798.13 3.35 76 34 38 4 783.35 5.03 77 34 124 90 289.26 4.10 78 34 126 92 289.32 4.12 79 34 129 95 296.73 2.43 80 34 130 96 296.74 2.44 81 34 131 97 296.78 2.44 82 34 169 135 291.07 3.41 83 34 172 138 289.22 4.10 84 34 173 139 289.23 4.11 85 34 176 142 289.15 4.07 86 35 38 3 799.13 1.49 87 35 39 4 777.82 3.02 88 36 39 3 784.86 0.49 89 36 46 10 289.33 4.11 90 36 47 11 289.21 4.12 91 37 43 6 290.61 3.59 92 37 44 7 290.60 3.59 93 37 47 10 289.89 3.94 94 37 168 131 320.34 2.76 95 37 171 134 294.88 1.51 96 37 172 135 290.66 3.62 97 37 175 138 290.64 3.61 98 38 41 3 752.46 8.38 99 38 131 93 319.45 3.21 100 38 132 94 322.22 2.37 101 38 168 130 328.08 0.92 102 38 169 131 320.46 2.82 103 39 42 3 802.66 4.58 104 39 46 7 628.38 10.81 105 41 76 35 643.95 1.20 106 42 46 4 757.71 0.61 107 42 70 28 643.97 1.20 108 42 73 31 643.97 1.20 109 42 76 34 643.96 1.20 110 43 46 3 789.88 3.81 111 43 47 4 765.46 1.82 112 43 76 33 643.96 1.20 113 44 47 3 793.79 2.53 114 44 48 4 768.32 0.39 115 44 87 43 643.60 1.18 116 44 88 44 643.38 1.20 117 44 175 131 337.74 0.55 118 45 48 3 795.57 1.56 119 45 49 4 780.26 9.21 120 45 72 27 644.13 1.21 121 45 75 30 644.00 1.20 122 45 87 42 643.60 1.18 123 45 88 43 643.49 1.18 124 45 91 46 643.45 1.17 125 46 49 3 795.58 1.56 126 46 50 4 765.43 1.86 127 46 69 23 644.40 1.18 128 46 70 24 644.35 1.16 129 46 72 26 644.12 1.21 130 47 50 3 797.12 0.79 131 47 51 4 782.84 4.80 132 47 175 128 337.86 0.54 133 48 51 3 792.77 0.16 134 48 52 4 792.77 0.16 135 48 88 40 643.62 1.18 136 48 91 43 643.58 1.20 137 48 92 44 643.52 1.20 138 48 175 127 337.84 0.54 139 48 179 131 337.56 0.47 140 49 52 3 794.43 0.67 141 49 53 4 782.85 4.81 142 49 67 18 644.56 1.13 143 49 69 20 644.49 1.14 144 49 72 23 644.24 1.20 145 49 91 42 643.63 1.16 146 49 94 45 643.39 1.19 147 49 95 46 642.35 0.96 148 49 98 49 642.13 0.89 149 50 53 3 792.78 0.15 150 50 54 4 743.71 4.76 151 50 55 5 743.75 4.76 152 50 58 8 743.25 4.53 153 50 69 19 644.43 1.17 154 51 55 4 743.72 4.76 155 51 179 128 337.58 0.47 156 52 55 3 803.22 1.75 157 52 56 4 763.99 4.04 158 52 92 40 643.65 1.17 159 52 95 43 642.53 0.89 160 52 182 130 336.75 0.27 161 52 186 134 333.22 0.18 162 53 56 3 768.66 2.12 163 53 57 4 770.85 7.48 164 53 64 11 644.81 1.06 165 53 67 14 644.60 1.13 166 53 69 16 644.53 1.14 167 53 95 42 642.39 0.96 168 53 98 45 642.13 0.89 169 54 57 3 778.65 3.58 170 54 58 4 777.73 4.04 171 54 69 15 644.49 1.14 172 55 58 3 778.65 3.58 173 55 59 4 777.73 4.04 174 56 59 3 791.95 3.07 175 56 60 4 746.92 6.04 176 56 64 8 644.83 1.06 177 56 99 43 642.28 0.93 178 57 60 3 789.13 4.48 179 57 61 4 697.98 11.90 180 57 64 7 644.83 1.06 181 57 65 8 644.82 1.07 182 60 64 4 811.47 4.99 183 61 64 3 848.10 4.96 184 61 65 4 778.50 1.59 185 62 65 3 813.64 3.90 186 62 66 4 790.34 4.30 187 63 66 3 797.41 1.83 188 64 67 3 802.56 1.80 189 64 69 5 795.00 1.97 190 64 99 35 642.18 0.88 191 67 71 4 817.28 4.29 192 67 72 5 804.23 0.04 193 68 71 3 810.16 0.81 194 69 72 3 819.80 5.99 195 70 73 3 801.97 1.17 196 71 74 3 803.38 1.87 197 72 75 3 800.11 1.95 198 72 90 18 643.64 1.16 199 72 91 19 643.46 1.17 200 73 76 3 796.64 5.95 201 74 79 5 664.34 8.27 202 74 80 6 664.34 8.27 203 75 78 3 782.24 6.77 204 75 79 4 664.37 8.29 205 75 87 12 643.63 1.13 206 75 90 15 643.64 1.16 207 76 79 3 770.03 0.67 208 76 80 4 685.14 18.59 209 76 81 5 664.47 8.24 210 77 81 4 664.38 8.29 211 77 82 5 664.38 8.29 212 77 83 6 664.21 8.35 213 78 82 4 664.36 8.29 214 78 83 5 664.22 8.35 215 78 84 6 648.21 0.38 216 78 85 7 648.21 0.38 217 78 147 69 374.32 2.48 218 79 82 3 785.72 4.98 219 79 84 5 664.26 8.32 220 79 85 6 664.18 8.36 221 83 147 64 374.21 2.59 222 83 148 65 374.15 2.56 223 84 146 62 374.50 2.52 224 84 147 63 374.45 2.50 225 85 89 4 772.00 1.91 226 85 90 5 768.19 3.77 227 85 113 28 392.62 11.38 228 85 145 60 374.52 2.52 229 85 146 61 374.51 2.52 230 86 89 3 796.83 0.98 231 86 90 4 772.00 1.91 232 86 116 30 392.22 11.23 233 86 145 59 374.51 2.52 234 86 147 61 374.11 2.58 235 87 90 3 787.85 3.51 236 87 91 4 771.60 2.11 237 88 91 3 794.03 0.42 238 88 92 4 771.59 2.11 239 88 175 87 337.86 0.53 240 88 178 90 337.72 0.47 241 89 92 3 792.23 0.48 242 89 93 4 775.90 0.21 243 89 112 23 392.68 11.37 244 89 113 24 392.60 11.38 245 89 116 27 392.17 11.25 246 89 145 56 374.52 2.52 247 89 178 89 337.72 0.47 248 90 93 3 781.64 1.50 249 90 94 4 766.32 0.01 250 91 94 3 798.48 3.60 251 91 95 4 787.42 3.44 252 92 95 3 799.93 2.08 253 92 96 4 791.31 1.52 254 92 112 20 392.81 11.30 255 92 182 90 334.99 0.58 256 93 96 3 792.01 1.88 257 93 109 16 392.81 11.30 258 93 112 19 392.82 11.30 259 93 113 20 392.83 11.29 260 94 97 3 799.13 2.42 261 95 98 3 797.24 1.99 262 95 99 4 797.24 2.00 263 95 186 91 333.30 0.18 264 96 99 3 799.88 0.67 265 96 100 4 765.79 0.34 266 96 105 9 459.81 11.07 267 96 108 12 396.05 9.89 268 96 109 13 402.15 6.84 269 96 112 16 393.06 11.38 270 96 182 86 336.88 0.29 271 96 185 89 334.85 0.54 272 96 186 90 333.31 0.20 273 97 100 3 777.91 0.33 274 97 105 8 601.70 21.74 275 100 104 4 770.56 3.12 276 100 105 5 770.41 3.06 277 100 108 8 740.36 1.38 278 100 186 86 334.84 0.54 279 100 189 89 331.52 0.16 280 100 190 90 330.53 0.23 281 101 104 3 792.47 1.63 282 101 105 4 776.37 0.21 283 102 105 3 792.75 1.50 284 102 106 4 782.62 3.28 285 103 106 3 809.29 1.30 286 103 107 4 813.15 2.38 287 104 107 3 830.06 1.06 288 104 108 4 795.08 0.34 289 104 189 85 333.25 0.18 290 104 194 90 268.02 2.02 291 105 108 3 810.14 0.88 292 105 109 4 778.05 0.89 293 106 109 3 798.43 4.98 294 106 110 4 776.27 1.75 295 106 226 120 95.02 0.71 296 107 110 3 781.96 1.08 297 107 111 4 778.59 2.77 298 107 196 89 208.15 0.80 299 107 198 91 206.11 0.42 300 108 111 3 799.76 6.11 301 108 112 4 772.49 2.18 302 108 185 77 334.94 0.57 303 108 186 78 334.93 0.58 304 108 189 81 330.07 0.32 305 108 196 88 208.14 0.79 306 109 112 3 784.03 0.05 307 109 113 4 770.97 1.42 308 110 113 3 786.01 0.77 309 110 114 4 767.32 2.98 310 110 198 88 206.66 0.20 311 110 226 116 95.09 0.74 312 111 114 3 798.72 6.63 313 111 115 4 767.59 2.87 314 111 181 70 337.97 0.50 315 111 185 74 335.08 0.53 316 111 198 87 206.33 0.36 317 111 199 88 206.18 0.42 318 111 200 89 205.80 0.40 319 112 115 3 785.61 0.09 320 112 116 4 783.87 4.37 321 112 181 69 337.73 0.48 322 112 182 70 337.58 0.46 323 112 185 73 334.96 0.56 324 113 116 3 783.88 4.36 325 113 117 4 788.99 1.80 326 113 145 32 376.21 1.74 327 114 117 3 795.12 0.40 328 114 118 4 789.00 1.80 329 114 200 86 206.19 0.41 330 114 201 87 206.12 0.42 331 114 202 88 205.93 0.43 332 114 203 89 197.31 1.04 333 115 118 3 793.50 3.58 334 115 119 4 771.97 1.54 335 115 121 6 765.53 1.67 336 115 177 62 345.34 0.60 337 115 178 63 345.05 0.50 338 115 181 66 337.93 0.46 339 115 200 85 206.11 0.42 340 116 121 5 740.22 0.38 341 116 142 26 377.03 1.63 342 116 144 28 376.81 1.71 343 116 145 29 376.72 1.70 344 116 150 34 376.39 1.69 345 116 174 58 361.38 0.82 346 117 141 24 377.07 1.62 347 117 142 25 377.03 1.63 348 117 143 26 376.81 1.71 349 117 144 27 376.81 1.71 350 117 145 28 376.78 1.69 351 117 203 86 205.84 0.52 352 117 227 110 96.14 0.94 353 117 228 111 95.88 1.06 354 118 141 23 377.08 1.62 355 118 200 82 207.05 0.36 356 119 123 4 864.76 0.21 357 119 141 22 377.11 1.63 358 120 139 19 377.37 1.55 359 120 140 20 377.26 1.57 360 120 141 21 377.11 1.63 361 121 139 18 377.39 1.54 362 121 140 19 377.35 1.54 363 121 174 53 365.73 0.22 364 121 177 56 363.56 0.42 365 122 137 15 377.58 1.51 366 122 138 16 377.57 1.51 367 122 139 17 377.49 1.51 368 122 170 48 367.19 0.34 369 122 173 51 365.83 0.27 370 122 174 52 365.74 0.23 371 122 177 55 364.81 0.12 372 123 177 54 364.94 0.15 373 124 173 49 367.24 0.34 374 124 176 52 365.48 0.09 375 124 177 53 365.29 0.01 376 125 135 10 378.01 1.38 377 125 173 48 367.44 0.43 378 126 129 3 768.00 1.58 379 126 130 4 512.10 22.34 380 126 169 43 370.25 1.41 381 126 173 47 367.93 0.68 382 127 130 3 805.71 0.94 383 127 134 7 378.94 1.13 384 128 134 6 389.30 6.31 385 130 133 3 805.11 7.03 386 130 134 4 568.81 75.70 387 132 165 33 370.68 1.48 388 132 169 37 370.48 1.50 389 133 165 32 370.67 1.50 390 133 166 33 370.63 1.48 391 133 169 36 369.87 1.20 392 133 173 40 370.38 1.45 393 135 173 38 369.82 1.18 394 137 154 17 376.85 1.70 395 137 166 29 369.63 1.17 396 137 169 32 369.50 1.21 397 137 170 33 368.79 1.07 398 137 173 36 368.75 1.08 399 138 154 16 376.60 1.59 400 138 158 20 375.62 2.02 401 140 154 14 376.15 1.79 402 142 150 8 376.33 1.72 403 142 153 11 377.13 1.90 404 143 228 85 95.88 1.06 405 143 230 87 95.43 1.06 406 143 231 88 94.95 1.11 407 144 149 5 553.98 48.48 408 146 149 3 781.58 2.47 409 146 150 4 740.13 3.23 410 146 227 81 95.86 1.05 411 147 150 3 776.32 0.17 412 147 151 4 740.26 3.16 413 148 152 4 717.00 1.97 414 149 153 4 729.97 1.55 415 149 231 82 94.91 1.09 416 149 232 83 94.19 0.73 417 150 154 4 776.17 5.18 418 150 170 20 370.39 2.89 419 151 154 3 781.47 6.22 420 151 155 4 776.16 5.18 421 151 167 16 371.11 3.33 422 151 170 19 371.09 3.32 423 151 171 20 370.25 2.91 424 152 155 3 790.70 2.08 425 152 156 4 755.24 5.32 426 153 156 3 781.89 6.02 427 153 157 4 755.25 5.32 428 154 157 3 795.58 0.83 429 154 158 4 752.61 6.63 430 154 160 6 742.71 2.06 431 154 166 12 444.13 4.05 432 154 167 13 400.63 5.82 433 154 170 16 389.88 11.20 434 155 158 3 795.59 0.83 435 155 159 4 742.77 2.08 436 155 160 5 625.19 39.27 437 155 161 6 625.04 39.23 438 155 162 7 483.10 11.31 439 155 167 12 400.64 5.82 440 156 159 3 788.14 4.55 441 160 164 4 757.31 1.79 442 160 166 6 615.90 29.90 443 161 164 3 767.78 5.92 444 161 167 6 694.12 9.21 445 162 167 5 741.19 14.18 446 163 167 4 780.64 0.51 447 164 167 3 795.12 5.88 448 164 168 4 784.05 1.19 449 165 168 3 789.33 3.83 450 165 169 4 779.32 1.18 451 166 169 3 774.68 2.55 452 166 170 4 773.25 1.85 453 167 170 3 762.10 3.71 454 167 171 4 762.10 3.71 455 168 171 3 771.85 4.83 456 168 172 4 762.03 3.65 457 169 172 3 775.45 3.02 458 169 173 4 767.45 2.68 459 170 173 3 782.32 4.75 460 170 174 4 777.84 0.95 461 171 174 3 790.05 0.07 462 171 175 4 777.84 0.95 463 172 175 3 791.00 0.41 464 172 176 4 790.05 0.07 465 173 176 3 785.36 2.42 466 173 177 4 777.83 0.96 467 174 177 3 775.31 2.60 468 174 178 4 760.60 4.75 469 175 178 3 776.07 0.12 470 175 179 4 754.69 1.79 471 176 179 3 775.69 8.85 472 176 180 4 767.13 4.58 473 177 180 3 773.94 1.18 474 177 181 4 772.51 1.89 475 178 181 3 789.36 6.53 476 178 182 4 759.57 4.63 477 179 182 3 778.41 1.31 478 179 183 4 761.59 3.60 479 180 183 3 779.52 4.63 480 180 184 4 768.65 7.13 481 181 184 3 787.98 2.83 482 181 185 4 787.97 2.83 483 182 185 3 787.98 2.83 484 182 186 4 774.02 9.81 485 183 186 3 787.98 2.83 486 183 187 4 761.56 3.51 487 184 187 3 776.91 8.37 488 184 188 4 754.47 1.62 489 185 188 3 774.27 2.31 490 185 189 4 756.64 0.58 491 185 196 11 429.23 6.83 492 186 189 3 775.12 3.79 493 186 190 4 763.43 2.81 494 187 190 3 785.47 1.59 495 187 191 4 767.25 0.90 496 188 191 3 773.41 3.98 497 188 192 4 767.24 0.90 498 188 196 8 446.58 2.45 499 189 192 3 790.85 0.18 500 189 193 4 756.54 0.54 501 189 194 5 756.54 0.54 502 189 196 7 432.83 5.08 503 192 195 3 783.19 0.17 504 192 196 4 517.99 0.01 505 193 196 3 793.61 1.88 506 202 206 4 773.85 7.78 507 202 207 5 743.91 5.87 508 203 206 3 791.44 1.02 509 203 207 4 773.84 7.78 510 203 226 23 97.00 0.99 511 203 227 24 96.92 1.01 512 203 228 25 96.73 0.98 513 204 207 3 787.99 0.70 514 204 208 4 773.84 7.77 515 205 208 3 780.87 4.26 516 205 209 4 741.89 4.82 517 205 228 23 96.88 1.02 518 205 229 24 96.81 1.01 519 205 230 25 96.69 0.95 520 206 210 4 741.85 4.84 521 206 214 8 455.49 0.85 522 206 226 20 97.00 0.99 523 206 227 21 96.98 1.00 524 206 228 22 96.82 0.99 525 206 229 23 96.81 1.00 526 207 210 3 784.86 2.25 527 207 211 4 777.51 2.48 528 208 211 3 798.52 4.58 529 209 212 3 811.30 5.80 530 209 213 4 767.36 7.55 531 209 229 20 96.92 1.03 532 210 213 3 776.33 3.08 533 210 214 4 605.87 55.21 534 210 215 5 605.86 55.21 535 211 215 4 629.34 43.48 536 211 218 7 422.96 5.44 537 212 218 6 399.82 6.13 538 212 220 8 255.06 72.58 539 212 221 9 109.71 0.33 540 213 220 7 110.31 0.20 541 213 221 8 109.70 0.33 542 213 222 9 109.70 0.33 543 213 223 10 109.17 0.19 544 214 221 7 251.38 71.16 545 214 223 9 109.55 0.39 546 214 226 12 100.52 1.54 547 215 218 3 783.55 0.86 548 215 221 6 251.80 70.95 549 216 221 5 266.81 69.05 550 218 221 3 752.72 8.74 551 228 231 3 854.29 1.76 552 229 232 3 816.88 3.12 553 229 233 4 751.63 9.88 554 230 233 3 799.72 4.83 555 230 234 4 738.16 5.70 556 231 239 8 406.48 10.22 557 232 239 7 427.12 2.40 558 235 239 4 743.28 4.61 559 235 240 5 742.38 5.01 560 236 239 3 767.08 2.47 561 236 240 4 756.34 1.29 562 237 240 3 777.59 0.48 563 237 242 5 753.26 0.25 564 238 242 4 787.75 1.95 565 241 244 3 804.72 2.47 566 242 246 4 472.55 0.91