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 1 192 191 32.41 0.35 2 1 193 192 32.42 0.35 3 1 194 193 32.31 0.40 4 1 195 194 29.36 0.81 5 2 193 191 33.27 0.04 6 2 195 193 32.31 0.40 7 3 195 192 32.69 0.26 8 3 196 193 32.65 0.24 9 3 197 194 32.65 0.24 10 4 197 193 34.86 0.83 11 5 188 183 33.73 0.26 12 5 197 192 35.11 0.73 13 6 10 4 706.62 5.85 14 6 11 5 651.82 1.94 15 6 186 180 33.37 0.08 16 6 197 191 36.44 0.81 17 7 10 3 721.27 1.47 18 10 197 187 59.88 1.56 19 11 184 173 59.41 1.64 20 11 186 175 59.52 1.58 21 11 197 186 59.91 1.58 22 11 199 188 59.77 1.55 23 12 183 171 59.54 1.60 24 12 184 172 59.51 1.62 25 12 199 187 59.90 1.58 26 12 201 189 59.85 1.57 27 12 202 190 59.91 1.58 28 12 203 191 59.95 1.59 29 12 204 192 61.88 0.69 30 13 16 3 739.32 3.00 31 13 17 4 732.20 0.99 32 13 183 170 59.54 1.61 33 13 184 171 59.56 1.59 34 14 17 3 734.76 1.53 35 14 21 7 600.99 1.46 36 14 180 166 59.55 1.60 37 14 182 168 59.56 1.61 38 14 183 169 59.56 1.61 39 14 201 187 59.98 1.60 40 14 237 223 51.01 0.29 41 15 183 168 59.76 1.58 42 15 237 222 53.49 0.24 43 16 204 188 141.28 0.88 44 16 205 189 150.78 0.32 45 17 21 4 761.03 2.35 46 17 202 185 140.31 1.36 47 17 203 186 142.94 0.18 48 17 204 187 147.18 0.48 49 17 205 188 152.34 1.09 50 17 207 190 152.03 0.94 51 17 208 191 149.06 1.11 52 18 205 187 161.63 0.68 53 18 206 188 159.88 1.55 54 19 206 187 163.19 0.08 55 19 207 188 159.80 1.56 56 20 23 3 760.32 3.40 57 20 177 157 177.13 0.35 58 20 178 158 177.12 0.36 59 20 207 187 174.54 0.14 60 21 24 3 743.34 2.92 61 21 25 4 734.66 4.74 62 21 175 154 176.21 0.10 63 21 176 155 177.15 0.37 64 21 177 156 177.22 0.36 65 21 178 157 177.21 0.37 66 21 179 158 177.13 0.36 67 21 180 159 177.15 0.37 68 21 201 180 176.27 0.12 69 21 202 181 176.28 0.12 70 22 25 3 743.26 2.98 71 22 26 4 740.87 1.64 72 22 176 154 178.58 0.18 73 22 177 155 178.62 0.15 74 23 26 3 755.56 0.40 75 23 27 4 752.25 0.64 76 23 207 184 178.86 0.21 77 23 208 185 178.40 0.39 78 23 210 187 176.22 0.10 79 24 27 3 755.71 1.09 80 24 28 4 752.25 0.63 81 24 175 151 178.91 0.21 82 24 200 176 178.57 0.18 83 24 201 177 178.61 0.16 84 24 202 178 178.63 0.17 85 24 208 184 178.53 0.33 86 24 213 189 178.21 0.29 87 25 28 3 753.22 0.15 88 25 29 4 738.74 0.44 89 25 175 150 178.91 0.21 90 26 29 3 735.55 1.86 91 26 210 184 179.22 0.18 92 27 87 60 178.85 0.21 93 27 88 61 178.94 0.21 94 27 162 135 178.94 0.21 95 27 208 181 190.58 0.77 96 27 210 183 179.93 0.54 97 27 213 186 179.19 0.18 98 27 214 187 179.08 0.14 99 28 162 134 178.96 0.20 100 28 165 137 178.98 0.20 101 28 166 138 179.00 0.19 102 28 169 141 190.62 0.36 103 28 175 147 191.13 0.60 104 28 213 185 184.25 1.86 105 28 217 189 179.24 0.17 106 29 162 133 179.45 0.14 107 29 166 137 188.91 0.15 108 29 170 141 192.23 1.05 109 30 162 132 191.47 0.69 110 30 166 136 191.49 0.69 111 30 170 140 192.44 1.02 112 31 162 131 192.42 0.95 113 32 61 29 193.62 0.93 114 32 85 53 192.75 1.03 115 32 86 54 192.74 1.04 116 32 88 56 192.76 1.04 117 32 162 130 192.44 0.95 118 33 53 20 193.41 0.98 119 33 61 28 193.62 0.93 120 33 64 31 193.12 1.05 121 33 84 51 192.80 1.02 122 33 85 52 192.78 1.02 123 33 86 53 192.75 1.03 124 33 88 55 192.81 1.02 125 33 112 79 193.13 1.05 126 33 114 81 192.80 1.02 127 34 84 50 192.81 1.02 128 34 85 51 192.78 1.02 129 35 38 3 788.87 0.27 130 35 53 18 193.56 0.95 131 35 83 48 192.85 1.02 132 35 84 49 192.89 1.04 133 36 83 47 192.88 1.03 134 36 121 85 192.89 1.05 135 36 125 89 192.69 1.09 136 37 81 44 193.18 0.96 137 37 82 45 193.11 1.02 138 37 83 46 193.12 1.02 139 37 121 84 192.90 1.05 140 38 51 13 194.44 0.87 141 38 53 15 194.47 0.89 142 38 80 42 193.60 0.91 143 38 81 43 193.44 0.98 144 38 82 44 193.33 0.95 145 38 84 46 193.44 0.96 146 39 51 12 194.69 0.98 147 39 79 40 194.08 0.70 148 39 80 41 193.60 0.91 149 39 81 42 193.47 0.97 150 40 49 9 194.61 0.96 151 40 50 10 195.68 1.47 152 40 51 11 195.68 1.47 153 40 78 38 195.05 0.24 154 40 79 39 195.04 0.25 155 41 50 9 203.75 1.05 156 41 51 10 203.75 1.04 157 41 52 11 203.70 0.96 158 41 63 22 207.13 0.64 159 41 106 65 208.87 0.71 160 42 49 7 207.94 0.31 161 42 50 8 207.12 0.64 162 42 78 36 208.66 0.66 163 42 105 63 208.88 0.71 164 42 106 64 208.87 0.71 165 43 46 3 806.05 1.16 166 43 48 5 631.50 0.45 167 43 49 6 208.43 0.56 168 43 50 7 208.00 0.35 169 43 74 31 208.69 0.68 170 43 78 35 208.81 0.71 171 43 104 61 209.68 0.98 172 44 48 4 712.58 10.62 173 44 50 6 596.75 9.46 174 44 94 50 208.88 0.72 175 44 95 51 208.88 0.72 176 44 96 52 208.88 0.72 177 44 104 60 209.69 0.99 178 45 48 3 757.47 3.12 179 45 65 20 209.43 0.88 180 46 71 25 209.62 0.96 181 46 74 28 209.68 0.98 182 47 65 18 210.24 0.83 183 47 67 20 209.65 0.97 184 47 68 21 209.56 0.96 185 47 70 23 209.62 0.96 186 47 71 24 209.66 0.97 187 47 74 27 209.69 0.97 188 48 65 17 210.16 0.83 189 48 66 18 209.66 0.97 190 48 67 19 209.66 0.97 191 48 74 26 210.18 0.84 192 49 65 16 210.27 0.84 193 49 66 17 210.20 0.85 194 49 68 19 210.24 0.85 195 49 74 25 210.44 0.76 196 49 77 28 210.63 0.72 197 49 78 29 210.65 0.72 198 50 63 13 211.02 0.62 199 50 64 14 210.63 0.72 200 50 65 15 210.33 0.87 201 50 95 45 210.63 0.72 202 50 107 57 211.16 0.69 203 51 63 12 211.05 0.62 204 51 64 13 210.71 0.75 205 51 66 15 210.88 0.65 206 51 82 31 210.90 0.66 207 52 62 10 211.46 0.80 208 52 63 11 211.05 0.63 209 53 61 8 211.66 0.77 210 53 62 9 211.60 0.74 211 53 63 10 211.18 0.68 212 53 64 11 211.16 0.68 213 53 84 31 210.94 0.66 214 54 61 7 211.68 0.77 215 54 62 8 211.60 0.74 216 55 58 3 762.64 0.56 217 55 59 4 582.41 16.06 218 55 60 5 602.66 5.93 219 55 61 6 211.69 0.77 220 59 110 51 281.45 0.92 221 60 110 50 282.04 1.21 222 61 64 3 823.03 1.20 223 61 110 49 282.51 1.44 224 61 112 51 259.90 0.76 225 62 109 47 283.92 1.69 226 62 110 48 283.68 1.75 227 63 95 32 284.07 1.63 228 63 106 43 284.17 1.60 229 63 107 44 284.07 1.65 230 63 108 45 284.07 1.64 231 63 109 46 284.06 1.64 232 63 110 47 283.95 1.68 233 63 111 48 283.58 1.66 234 63 112 49 283.56 1.67 235 64 112 48 283.57 1.67 236 64 114 50 283.57 1.67 237 65 94 29 284.08 1.64 238 65 95 30 284.09 1.64 239 65 112 47 284.03 1.65 240 65 113 48 283.72 1.73 241 65 114 49 283.63 1.67 242 66 114 48 283.89 1.68 243 66 116 50 283.62 1.67 244 66 118 52 283.87 1.67 245 67 114 47 284.00 1.66 246 67 115 48 283.91 1.68 247 67 116 49 283.94 1.69 248 67 218 151 283.91 1.68 249 68 73 5 702.30 4.75 250 68 74 6 681.73 5.54 251 68 77 9 657.15 4.09 252 68 116 48 283.99 1.66 253 68 118 50 284.08 1.63 254 68 218 150 283.94 1.69 255 68 220 152 284.00 1.66 256 69 73 4 734.93 4.90 257 69 218 149 284.00 1.66 258 69 219 150 284.00 1.66 259 70 73 3 756.78 2.58 260 70 74 4 734.66 5.07 261 71 74 3 738.91 6.88 262 71 75 4 734.66 5.07 263 72 75 3 756.92 2.90 264 72 76 4 734.66 5.07 265 73 76 3 740.75 2.43 266 73 77 4 735.63 4.58 267 73 218 145 284.29 1.70 268 73 219 146 284.28 1.70 269 73 220 147 284.28 1.70 270 74 77 3 754.66 1.02 271 74 78 4 737.11 3.83 272 75 78 3 749.25 3.47 273 76 80 4 746.61 3.91 274 77 80 3 737.27 2.52 275 77 82 5 688.77 7.22 276 77 118 41 284.42 1.69 277 77 120 43 285.10 1.40 278 77 220 143 284.43 1.68 279 77 222 145 284.56 1.61 280 80 120 40 353.43 0.25 281 81 120 39 353.48 0.25 282 81 121 40 353.48 0.26 283 81 122 41 353.53 0.27 284 82 118 36 353.41 0.28 285 82 119 37 353.49 0.26 286 82 120 38 353.49 0.26 287 82 121 39 353.49 0.26 288 83 118 35 353.53 0.25 289 83 119 36 353.53 0.25 290 83 121 38 353.54 0.28 291 83 125 42 353.54 0.28 292 83 152 69 353.41 0.22 293 84 114 30 591.99 7.69 294 84 117 33 353.51 0.25 295 84 118 34 353.54 0.25 296 85 114 29 599.47 9.61 297 85 117 32 353.54 0.26 298 85 152 67 353.58 0.27 299 85 159 74 352.54 0.57 300 85 162 77 352.47 0.60 301 85 163 78 352.49 0.59 302 86 114 28 599.47 9.62 303 86 158 72 353.35 0.24 304 87 114 27 615.51 1.61 305 87 158 71 353.56 0.26 306 87 214 127 353.58 0.24 307 88 112 24 658.59 3.88 308 88 113 25 616.26 1.39 309 88 114 26 615.56 1.64 310 89 92 3 808.09 1.12 311 89 93 4 724.63 4.50 312 89 112 23 698.72 0.19 313 89 113 24 651.69 0.44 314 89 114 25 616.32 1.42 315 89 115 26 634.47 7.63 316 89 210 121 353.62 0.25 317 89 211 122 353.62 0.25 318 89 214 125 353.99 0.10 319 90 93 3 743.12 3.17 320 90 111 21 775.89 4.80 321 90 112 22 711.94 1.85 322 91 210 119 354.29 0.26 323 92 209 117 354.29 0.27 324 92 210 118 354.32 0.26 325 92 211 119 354.33 0.24 326 114 117 3 896.68 5.06 327 115 158 43 355.18 0.40 328 115 211 96 354.78 0.24 329 115 214 99 354.69 0.32 330 115 215 100 354.81 0.26 331 115 217 102 355.18 0.40 332 115 218 103 355.19 0.40 333 116 158 42 355.21 0.41 334 116 217 101 355.22 0.41 335 116 218 102 355.23 0.41 336 116 220 104 355.26 0.42 337 117 156 39 355.25 0.42 338 117 158 41 355.20 0.41 339 117 220 103 355.38 0.41 340 118 156 38 355.36 0.41 341 118 220 102 355.69 0.53 342 118 222 104 355.77 0.49 343 119 124 5 705.12 2.38 344 119 154 35 355.79 0.48 345 119 222 103 355.78 0.49 346 120 124 4 710.38 0.26 347 121 124 3 750.43 3.35 348 121 125 4 732.32 4.65 349 123 153 30 378.30 1.65 350 124 152 28 375.68 0.35 351 124 153 29 375.69 0.35 352 124 154 30 375.67 0.35 353 125 151 26 387.67 2.50 354 125 152 27 387.11 2.75 355 126 130 4 740.88 1.43 356 126 151 25 401.38 0.94 357 126 152 26 419.37 2.90 358 126 153 27 422.82 2.10 359 129 149 20 482.70 1.56 360 129 150 21 482.84 1.48 361 129 151 22 482.98 1.47 362 130 149 19 483.02 1.45 363 130 150 20 483.00 1.47 364 130 153 23 483.09 1.44 365 130 225 95 483.04 1.45 366 130 226 96 483.04 1.44 367 131 147 16 483.10 1.41 368 131 148 17 483.11 1.42 369 131 149 18 483.07 1.43 370 132 147 15 483.21 1.40 371 132 148 16 483.12 1.40 372 132 150 18 483.19 1.45 373 132 160 28 483.05 1.44 374 132 225 93 483.09 1.44 375 132 228 96 483.04 1.44 376 132 229 97 483.03 1.45 377 132 230 98 483.00 1.45 378 133 146 13 483.26 1.38 379 133 147 14 483.25 1.39 380 133 229 96 483.05 1.44 381 133 230 97 483.04 1.44 382 134 145 11 483.31 1.40 383 134 146 12 483.27 1.38 384 134 148 14 483.30 1.41 385 134 164 30 483.06 1.44 386 134 230 96 483.05 1.44 387 134 232 98 483.03 1.45 388 135 142 7 564.87 6.40 389 135 144 9 515.01 14.41 390 135 145 10 483.32 1.41 391 135 229 94 483.11 1.45 392 135 230 95 483.07 1.44 393 135 231 96 483.04 1.45 394 135 232 97 483.04 1.45 395 136 142 6 599.24 10.77 396 136 143 7 564.88 6.40 397 136 144 8 515.05 14.43 398 136 146 10 515.00 14.41 399 136 168 32 483.10 1.46 400 136 232 96 483.04 1.45 401 137 140 3 748.75 3.32 402 137 141 4 654.25 15.30 403 137 142 5 599.24 10.77 404 137 231 94 483.11 1.45 405 137 232 95 483.07 1.44 406 137 233 96 483.04 1.44 407 137 234 97 483.03 1.45 408 138 141 3 731.37 3.85 409 138 143 5 614.73 4.46 410 138 172 34 483.18 1.48 411 138 182 44 483.06 1.44 412 138 234 96 483.05 1.44 413 139 234 95 483.07 1.44 414 139 235 96 483.00 1.43 415 139 236 97 483.00 1.43 416 142 145 3 820.86 0.74 417 144 167 23 483.24 1.50 418 144 168 24 483.17 1.48 419 144 172 28 483.11 1.45 420 146 164 18 483.28 1.53 421 146 167 21 483.26 1.54 422 146 168 22 483.26 1.54 423 148 160 12 483.30 1.55 424 148 163 15 483.29 1.56 425 148 164 16 483.29 1.56 426 149 163 14 483.35 1.57 427 150 155 5 657.45 2.06 428 150 159 9 592.91 8.30 429 150 225 75 487.69 0.81 430 152 155 3 758.42 1.02 431 152 159 7 701.38 1.00 432 152 225 73 522.89 0.89 433 153 224 71 522.99 0.93 434 153 225 72 522.89 0.89 435 154 223 69 523.07 0.94 436 154 224 70 523.02 0.94 437 155 159 4 738.63 4.41 438 155 160 5 727.93 0.96 439 155 222 67 523.37 1.00 440 155 223 68 523.37 1.01 441 155 225 70 523.59 0.67 442 156 159 3 751.98 2.23 443 156 160 4 738.68 4.39 444 156 221 65 523.53 0.93 445 156 222 66 523.50 0.94 446 157 160 3 743.07 2.22 447 157 161 4 727.96 0.97 448 157 189 32 523.31 1.03 449 157 196 39 523.53 0.93 450 157 198 41 523.11 0.96 451 157 221 64 523.56 0.92 452 158 161 3 735.44 3.29 453 158 162 4 727.97 0.97 454 158 217 59 523.52 0.93 455 159 162 3 746.13 3.47 456 159 163 4 727.87 1.01 457 160 163 3 744.64 8.62 458 160 164 4 744.63 8.62 459 160 189 29 525.38 0.17 460 160 223 63 528.43 0.70 461 160 228 68 527.80 0.46 462 160 230 70 524.75 0.44 463 161 164 3 754.28 3.79 464 161 165 4 732.22 0.94 465 161 187 26 524.06 0.70 466 161 189 28 527.10 0.68 467 161 198 37 524.14 0.74 468 161 217 56 529.50 0.70 469 162 165 3 754.01 3.93 470 162 166 4 732.23 0.95 471 163 166 3 740.98 0.07 472 163 167 4 736.14 0.41 473 164 167 3 743.85 0.08 474 164 168 4 736.46 0.14 475 164 187 23 528.88 1.02 476 164 230 66 528.97 0.89 477 164 232 68 528.01 0.63 478 165 168 3 738.78 1.02 479 165 169 4 736.29 0.23 480 165 174 9 625.66 0.17 481 165 175 10 625.63 0.17 482 165 198 33 529.42 1.03 483 165 199 34 529.46 1.06 484 165 200 35 529.19 1.11 485 165 213 48 530.03 0.91 486 166 169 3 750.49 2.49 487 166 170 4 736.29 0.23 488 167 170 3 745.73 3.65 489 167 171 4 722.07 3.96 490 168 172 4 692.75 0.43 491 168 173 5 679.22 7.20 492 168 174 6 631.89 3.29 493 168 200 32 529.54 1.08 494 168 232 64 529.28 0.96 495 168 234 66 529.03 0.99 496 169 173 4 674.88 9.36 497 169 174 5 636.52 5.59 498 169 175 6 631.90 3.28 499 170 173 3 738.64 1.73 500 172 181 9 559.85 0.25 501 172 182 10 559.64 0.35 502 173 176 3 763.68 0.25 503 173 181 8 559.62 0.34 504 174 180 6 591.86 15.76 505 174 182 8 559.39 0.29 506 174 200 26 530.26 0.77 507 174 201 27 530.26 0.78 508 174 234 60 529.71 0.70 509 175 179 4 697.07 7.69 510 175 200 25 530.28 0.77 511 176 179 3 710.45 1.59 512 176 181 5 685.21 7.95 513 180 201 21 537.89 0.42 514 180 237 57 530.00 0.55 515 181 236 55 530.12 0.50 516 181 237 56 530.01 0.55 517 182 201 19 538.63 0.51 518 182 234 52 530.78 0.56 519 182 235 53 530.58 0.61 520 182 236 54 530.12 0.50 521 182 237 55 530.12 0.50 522 183 235 52 530.65 0.61 523 183 236 53 530.58 0.62 524 183 237 54 530.12 0.49 525 183 238 55 530.12 0.49 526 184 201 17 539.60 0.04 527 184 234 50 531.21 0.43 528 184 235 51 530.78 0.55 529 185 200 15 542.54 1.27 530 185 233 48 532.30 0.48 531 185 234 49 531.21 0.43 532 186 197 11 544.70 0.74 533 186 198 12 544.25 0.67 534 186 199 13 543.84 0.80 535 186 200 14 543.80 0.78 536 186 232 46 533.19 0.27 537 186 233 47 532.60 0.35 538 187 197 10 544.76 0.70 539 187 198 11 544.56 0.81 540 187 200 13 544.09 0.67 541 187 230 43 534.86 0.03 542 187 231 44 534.29 0.02 543 187 232 45 533.76 0.01 544 188 195 7 546.53 1.25 545 188 196 8 546.32 1.24 546 188 197 9 544.77 0.71 547 188 230 42 534.88 0.02 548 188 231 43 534.30 0.03 549 188 233 45 534.30 0.02 550 189 195 6 546.54 1.25 551 189 196 7 546.52 1.25 552 189 198 9 546.41 1.24 553 189 228 39 535.42 0.16 554 189 229 40 535.31 0.10 555 189 230 41 534.91 0.03 556 190 194 4 704.76 2.56 557 190 195 5 568.62 11.60 558 190 227 37 535.66 0.21 559 190 228 38 535.52 0.21 560 190 229 39 535.40 0.15 561 190 231 41 535.35 0.18 562 191 194 3 746.14 8.96 563 191 223 32 535.69 0.20 564 191 224 33 535.70 0.21 565 191 227 36 535.66 0.21 566 191 228 37 535.54 0.21 567 196 221 25 537.21 0.92 568 198 216 18 537.62 0.76 569 198 217 19 537.62 0.75 570 199 213 14 537.81 0.67 571 200 213 13 537.80 0.67 572 200 232 32 533.76 0.01 573 200 234 34 532.96 0.17 574 201 234 33 532.95 0.17 575 202 208 6 538.00 0.62 576 208 213 5 718.79 2.56 577 209 212 3 739.21 4.92 578 209 213 4 722.22 4.28 579 210 213 3 735.56 0.06 580 210 214 4 724.89 5.61 581 211 214 3 738.61 5.67 582 211 215 4 722.22 4.28 583 212 215 3 746.32 0.20 584 213 216 3 765.26 0.94 585 214 217 3 760.98 1.52 586 215 218 3 741.24 2.29 587 217 220 3 754.93 4.55 588 223 228 5 651.31 1.82 589 224 227 3 733.64 1.26 590 224 228 4 688.64 4.38 591 225 228 3 750.99 1.64