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 2 225 223 43.53 1.20 2 3 225 222 43.53 1.20 3 4 202 198 125.00 1.47 4 4 204 200 119.75 1.74 5 4 205 201 119.28 1.86 6 4 225 221 54.05 0.29 7 5 184 179 130.74 1.25 8 5 185 180 130.74 1.25 9 5 202 197 125.56 1.32 10 5 203 198 125.49 1.35 11 5 204 199 125.34 1.41 12 6 9 3 885.80 0.40 13 6 201 195 134.76 0.08 14 6 202 196 130.71 1.26 15 6 222 216 98.99 0.76 16 7 194 187 147.81 3.79 17 7 195 188 148.12 3.67 18 7 201 194 144.24 2.50 19 8 194 186 148.13 3.67 20 8 195 187 148.14 3.68 21 8 199 191 148.37 3.76 22 8 200 192 147.68 3.46 23 8 201 193 147.21 3.56 24 8 222 214 99.77 0.97 25 9 222 213 99.77 0.97 26 10 200 190 148.56 3.73 27 10 221 211 101.04 0.48 28 10 222 212 100.80 0.49 29 10 223 213 100.34 0.70 30 11 200 189 150.39 3.35 31 11 220 209 101.17 0.53 32 11 221 210 101.04 0.48 33 11 223 212 100.98 0.49 34 12 177 165 211.91 14.94 35 12 200 188 151.01 3.50 36 12 219 207 108.58 3.15 37 12 220 208 101.71 0.26 38 13 177 164 215.52 16.32 39 13 217 204 118.75 1.82 40 13 218 205 117.80 1.51 41 13 219 206 108.54 3.13 42 13 243 230 31.34 1.88 43 14 157 143 216.03 16.23 44 14 177 163 215.69 16.40 45 14 217 203 118.03 1.43 46 14 218 204 117.88 1.49 47 15 156 141 216.61 16.19 48 15 157 142 216.60 16.20 49 15 215 200 120.28 1.33 50 15 216 201 120.23 1.33 51 15 217 202 118.67 1.12 52 16 157 141 216.62 16.20 53 16 159 143 216.63 16.21 54 16 212 196 146.46 3.54 55 16 214 198 123.87 1.52 56 16 215 199 120.28 1.34 57 16 216 200 119.98 1.21 58 16 218 202 117.99 1.45 59 17 149 132 217.35 16.04 60 17 152 135 217.37 16.06 61 17 156 139 217.19 16.05 62 17 157 140 217.08 16.04 63 17 158 141 216.76 16.17 64 17 159 142 216.75 16.17 65 18 159 141 217.07 16.02 66 18 209 191 149.83 3.26 67 18 212 194 148.23 3.65 68 18 213 195 142.25 1.45 69 18 214 196 123.12 1.87 70 19 149 130 217.36 16.05 71 19 158 139 217.25 16.04 72 19 159 140 217.19 16.02 73 19 160 141 217.13 16.02 74 19 163 144 217.21 16.00 75 19 167 148 217.33 16.05 76 20 147 127 218.13 15.96 77 21 139 118 218.74 16.04 78 24 135 111 218.51 15.96 79 24 138 114 219.50 15.54 80 24 139 115 218.61 15.97 81 24 142 118 220.94 16.11 82 25 142 117 221.80 16.00 83 26 102 76 220.91 16.09 84 27 99 72 230.44 13.87 85 29 99 70 365.00 18.55 86 30 97 67 370.47 15.85 87 31 35 4 759.12 2.82 88 31 36 5 714.75 6.69 89 31 39 8 616.41 5.82 90 31 93 62 380.54 12.12 91 31 97 66 380.52 12.13 92 31 98 67 371.77 16.50 93 31 99 68 367.95 18.40 94 32 35 3 851.71 1.31 95 32 36 4 759.21 2.78 96 33 36 3 851.72 3.77 97 34 38 4 859.09 1.28 98 35 38 3 852.95 1.78 99 35 39 4 852.51 1.99 100 36 39 3 858.28 0.89 101 36 40 4 852.52 1.99 102 36 93 57 440.98 4.12 103 36 94 58 440.98 4.13 104 36 97 61 440.98 4.13 105 37 40 3 867.04 0.09 106 37 41 4 852.50 1.98 107 38 41 3 859.69 1.62 108 38 42 4 852.01 2.21 109 39 42 3 855.37 0.07 110 39 43 4 839.22 4.16 111 39 93 54 441.08 4.12 112 39 100 61 441.00 4.12 113 40 43 3 850.64 1.55 114 40 44 4 850.63 1.55 115 40 90 50 441.06 4.13 116 40 93 53 441.09 4.12 117 40 94 54 441.12 4.12 118 41 44 3 847.18 3.28 119 41 45 4 831.36 0.25 120 42 45 3 851.50 1.11 121 42 46 4 832.18 1.90 122 43 46 3 847.22 3.29 123 43 47 4 829.19 0.42 124 43 89 46 441.12 4.12 125 43 100 57 441.08 4.12 126 43 104 61 441.09 4.12 127 43 137 94 411.03 15.17 128 43 141 98 409.81 15.43 129 44 47 3 857.47 4.11 130 44 48 4 857.47 4.11 131 45 48 3 857.48 4.11 132 45 49 4 857.47 4.11 133 46 49 3 863.93 1.11 134 46 50 4 857.52 4.08 135 46 140 94 410.38 15.16 136 46 141 95 409.81 15.44 137 47 50 3 862.02 1.83 138 47 51 4 845.38 4.13 139 48 51 3 853.71 0.01 140 48 52 4 856.02 1.17 141 49 52 3 863.71 5.01 142 49 53 4 848.01 2.83 143 49 140 91 411.07 15.17 144 50 53 3 853.44 1.01 145 50 54 4 836.76 2.46 146 50 140 90 411.10 15.16 147 51 54 3 877.29 2.84 148 51 55 4 853.72 0.03 149 51 81 30 443.44 3.23 150 52 55 3 876.61 3.10 151 52 56 4 848.69 2.54 152 53 56 3 852.72 3.73 153 53 57 4 848.68 2.54 154 53 140 87 411.37 15.12 155 54 57 3 849.18 1.96 156 54 58 4 847.64 2.73 157 54 77 23 444.01 3.49 158 54 80 26 444.00 3.50 159 54 136 82 412.98 14.48 160 55 58 3 853.20 4.78 161 55 59 4 852.85 4.98 162 55 77 22 446.99 2.00 163 56 59 3 855.29 4.14 164 56 60 4 852.86 4.99 165 57 60 3 855.70 3.56 166 57 61 4 852.86 4.99 167 57 73 16 447.97 1.90 168 57 136 79 413.28 14.44 169 57 169 112 393.29 23.62 170 57 170 113 393.47 23.53 171 58 61 3 855.70 3.56 172 58 62 4 852.86 4.99 173 58 70 12 449.70 2.61 174 58 73 15 447.97 1.90 175 58 77 19 447.95 1.90 176 59 62 3 862.69 0.07 177 59 63 4 852.45 5.19 178 60 63 3 866.70 2.08 179 60 64 4 838.83 0.65 180 61 64 3 861.47 0.35 181 61 65 4 835.28 0.64 182 61 66 5 835.28 0.64 183 61 70 9 471.15 4.12 184 61 73 12 449.80 2.50 185 61 169 108 393.29 23.62 186 62 65 3 847.05 1.30 187 62 66 4 647.35 8.07 188 62 70 8 480.73 0.53 189 64 173 109 394.12 23.24 190 65 69 4 786.07 26.15 191 65 168 103 394.16 23.42 192 65 169 104 394.11 23.44 193 65 173 108 394.12 23.24 194 65 193 128 224.29 18.30 195 66 69 3 859.81 1.53 196 66 70 4 835.48 1.44 197 67 70 3 839.52 0.58 198 67 71 4 835.58 1.39 199 68 72 4 857.53 1.69 200 69 72 3 861.91 0.10 201 69 73 4 850.68 1.75 202 69 189 120 252.56 4.21 203 70 73 3 863.77 4.80 204 70 74 4 850.68 1.75 205 71 74 3 863.77 4.80 206 71 75 4 849.93 2.12 207 72 75 3 862.99 0.86 208 72 76 4 849.80 2.06 209 73 76 3 852.46 4.02 210 73 77 4 845.05 0.32 211 73 165 92 393.03 23.73 212 73 166 93 393.14 23.66 213 73 169 96 393.47 23.71 214 74 77 3 850.69 4.91 215 74 78 4 843.27 1.20 216 75 78 3 847.97 3.54 217 75 79 4 839.00 0.94 218 76 79 3 850.21 0.35 219 76 80 4 838.60 0.66 220 76 129 53 413.78 14.50 221 76 133 57 413.66 14.54 222 77 80 3 848.96 1.08 223 77 81 4 838.60 0.66 224 78 81 3 845.76 0.51 225 78 82 4 838.59 0.66 226 79 82 3 845.76 0.52 227 79 85 6 722.88 7.43 228 79 130 51 413.74 14.52 229 79 133 54 413.56 14.60 230 80 85 5 830.21 3.87 231 80 108 28 441.62 4.07 232 80 133 53 413.33 14.68 233 80 137 57 411.79 15.29 234 82 85 3 853.87 2.75 235 82 86 4 844.72 1.83 236 83 86 3 863.97 4.75 237 83 87 4 845.67 2.31 238 84 87 3 865.03 0.16 239 84 88 4 843.89 3.21 240 85 88 3 845.69 2.32 241 85 89 4 843.89 3.21 242 85 107 22 444.56 4.41 243 85 108 23 444.48 4.45 244 86 89 3 863.89 0.28 245 86 90 4 843.53 3.40 246 87 90 3 859.40 4.22 247 87 91 4 843.55 3.40 248 88 91 3 850.65 0.15 249 88 92 4 853.80 1.42 250 88 107 19 444.93 4.36 251 89 92 3 877.89 5.58 252 89 93 4 853.80 1.42 253 89 104 15 447.91 2.89 254 89 107 18 444.93 4.36 255 90 93 3 853.80 1.43 256 90 94 4 843.31 3.25 257 91 94 3 851.19 2.73 258 91 95 4 826.86 1.25 259 92 95 3 847.90 1.08 260 92 96 4 721.02 6.12 261 92 97 5 721.01 6.12 262 92 98 6 630.89 10.10 263 92 103 11 488.24 1.20 264 92 107 15 461.55 3.97 265 93 97 4 660.42 1.27 266 93 98 5 625.91 12.59 267 93 100 7 559.38 19.00 268 93 103 10 507.98 2.27 269 94 97 3 839.72 5.20 270 98 103 5 631.69 10.93 271 98 106 8 677.78 12.12 272 99 102 3 849.51 0.32 273 99 103 4 786.59 15.82 274 100 103 3 836.28 6.30 275 100 104 4 765.61 27.82 276 101 105 4 834.69 3.85 277 101 138 37 410.84 15.36 278 101 141 40 410.42 15.55 279 101 142 41 410.23 15.64 280 102 105 3 851.70 3.88 281 102 106 4 854.91 2.25 282 103 106 3 862.18 5.76 283 103 107 4 860.26 4.80 284 104 107 3 863.66 6.50 285 104 108 4 855.05 2.19 286 104 137 33 411.04 15.34 287 105 108 3 874.74 0.96 288 105 109 4 829.59 2.72 289 105 138 33 410.94 15.39 290 106 109 3 844.37 0.96 291 106 110 4 825.06 3.64 292 107 110 3 840.91 2.70 293 107 111 4 840.91 2.70 294 108 111 3 855.18 2.26 295 108 112 4 850.98 2.38 296 108 130 22 413.14 14.72 297 108 131 23 411.91 15.33 298 108 134 26 411.37 15.22 299 109 112 3 852.78 3.30 300 109 113 4 828.44 1.96 301 110 113 3 852.79 3.30 302 110 114 4 839.69 3.25 303 111 114 3 856.07 4.94 304 111 115 4 855.75 4.79 305 112 115 3 859.55 4.27 306 112 116 4 850.11 7.61 307 112 131 19 412.29 15.14 308 113 116 3 864.70 6.94 309 113 117 4 850.13 7.59 310 114 117 3 862.50 1.41 311 115 118 3 858.75 0.62 312 115 127 12 413.85 14.52 313 115 130 15 413.87 14.52 314 116 127 11 413.87 14.51 315 118 123 5 816.51 0.00 316 120 123 3 858.34 3.52 317 120 124 4 829.33 2.10 318 121 124 3 829.35 2.10 319 121 125 4 838.22 6.54 320 121 187 66 255.60 2.50 321 122 125 3 867.10 7.38 322 122 126 4 867.08 7.39 323 123 126 3 860.16 3.92 324 123 127 4 838.72 6.79 325 124 127 3 846.18 6.07 326 124 128 4 842.99 4.66 327 125 128 3 852.17 0.32 328 125 129 4 851.55 0.38 329 125 187 62 254.91 2.86 330 126 129 3 862.62 2.84 331 126 130 4 842.98 4.65 332 127 130 3 871.37 3.60 333 127 131 4 865.34 6.61 334 128 131 3 865.34 6.61 335 128 132 4 845.12 3.50 336 129 132 3 860.07 2.88 337 129 133 4 851.10 6.48 338 129 165 36 392.88 23.78 339 130 133 3 871.41 0.99 340 130 134 4 863.05 1.39 341 131 134 3 871.14 2.25 342 131 135 4 843.59 4.16 343 132 135 3 855.75 1.92 344 132 136 4 843.61 4.15 345 132 164 32 392.81 23.78 346 132 166 34 392.88 23.78 347 133 136 3 868.73 3.48 348 133 137 4 853.33 0.72 349 134 137 3 853.25 0.77 350 134 138 4 853.27 0.76 351 135 138 3 865.50 4.24 352 135 139 4 854.44 1.29 353 136 139 3 854.42 1.30 354 136 140 4 847.04 2.38 355 136 166 30 392.90 23.75 356 137 140 3 873.52 8.25 357 137 141 4 847.05 2.38 358 138 141 3 859.99 1.68 359 138 142 4 847.03 2.38 360 139 142 3 844.86 6.29 361 139 143 4 827.15 7.57 362 139 144 5 667.25 0.15 363 140 143 3 839.19 1.48 364 148 151 3 872.39 3.48 365 148 170 22 394.52 23.70 366 149 152 3 886.28 2.65 367 149 158 9 393.69 23.64 368 149 167 18 394.15 23.88 369 149 170 21 394.55 23.70 370 149 171 22 394.50 23.70 371 150 170 20 420.93 10.52 372 150 172 22 446.10 18.32 373 152 156 4 859.03 3.16 374 152 175 23 806.72 1.68 375 153 175 22 808.87 0.66 376 155 175 20 808.87 0.66 377 155 177 22 808.82 0.68 378 156 175 19 809.00 0.69 379 156 176 20 808.92 0.67 380 156 177 21 808.92 0.67 381 157 177 20 808.97 0.69 382 157 180 23 808.82 0.69 383 157 218 61 117.86 1.49 384 158 163 5 846.82 6.63 385 158 171 13 809.13 0.70 386 158 176 18 809.04 0.67 387 158 178 20 808.98 0.69 388 158 179 21 808.84 0.69 389 158 180 22 808.82 0.69 390 159 180 21 808.83 0.69 391 159 208 49 192.88 23.29 392 159 209 50 191.28 24.00 393 160 163 3 918.85 9.32 394 160 180 20 809.01 0.68 395 160 181 21 808.83 0.69 396 160 182 22 808.83 0.69 397 160 209 49 190.13 21.07 398 161 181 20 809.00 0.68 399 161 182 21 808.83 0.69 400 161 183 22 808.83 0.69 401 161 209 48 196.02 19.04 402 162 181 19 809.02 0.68 403 162 183 21 808.80 0.69 404 163 167 4 857.80 3.80 405 163 181 18 809.07 0.68 406 163 190 27 223.74 18.53 407 164 167 3 863.31 1.05 408 164 168 4 858.19 3.60 409 165 168 3 861.73 1.84 410 165 169 4 859.95 2.73 411 166 169 3 863.04 1.43 412 166 170 4 848.18 3.16 413 167 170 3 844.43 1.28 414 167 171 4 829.51 6.16 415 168 171 3 820.63 1.72 416 168 190 22 223.81 18.52 417 168 193 25 223.74 18.52 418 171 176 5 809.55 0.78 419 171 179 8 809.43 0.76 420 172 175 3 862.14 8.01 421 172 176 4 809.62 0.73 422 173 176 3 863.84 7.16 423 173 179 6 809.53 0.77 424 173 197 24 222.88 18.96 425 176 179 3 924.07 1.80 426 178 200 22 219.00 17.19 427 179 194 15 222.81 19.00 428 179 197 18 222.91 18.97 429 179 199 20 222.57 18.88 430 179 200 21 219.11 17.21 431 179 201 22 218.96 17.19 432 179 202 23 218.96 17.19 433 180 202 22 218.46 16.94 434 180 205 25 217.94 17.12 435 180 220 40 101.02 0.48 436 181 202 21 218.47 16.93 437 181 203 22 218.37 16.91 438 181 204 23 217.86 16.65 439 181 205 24 217.37 16.84 440 182 203 21 217.88 16.64 441 182 204 22 217.81 16.66 442 182 205 23 217.12 16.84 443 182 206 24 216.86 16.95 444 182 207 25 216.83 16.94 445 182 209 27 215.50 16.39 446 183 203 20 217.91 16.62 447 185 188 3 860.64 6.37 448 185 191 6 686.73 3.03 449 185 203 18 217.83 16.57 450 186 191 5 686.73 3.03 451 188 191 3 869.75 4.26 452 188 192 4 842.72 0.35 453 189 192 3 855.27 2.98 454 189 193 4 842.72 0.35 455 190 193 3 845.20 1.02 456 190 194 4 847.49 2.74 457 191 194 3 871.89 5.76 458 191 195 4 846.50 2.25 459 191 203 12 218.50 16.85 460 192 195 3 856.03 2.52 461 192 196 4 843.89 3.55 462 193 196 3 867.21 8.11 463 193 197 4 843.88 3.55 464 194 197 3 848.21 1.40 465 194 198 4 813.06 0.10 466 194 199 5 811.88 0.29 467 194 201 7 484.74 7.68 468 195 198 3 815.42 1.45 469 200 220 20 101.05 0.50 470 200 222 22 99.72 0.96 471 201 220 19 101.06 0.49 472 202 205 3 890.34 1.11 473 202 220 18 100.99 0.50 474 205 208 3 854.32 1.91 475 207 210 3 855.28 1.96 476 207 211 4 855.28 1.96 477 208 211 3 849.61 0.88 478 208 212 4 792.91 27.46 479 209 212 3 849.61 0.88 480 212 216 4 829.88 8.99 481 212 218 6 524.43 0.29 482 213 216 3 855.48 0.30 483 216 229 13 99.36 1.02 484 217 229 12 99.39 1.03 485 217 230 13 99.25 0.98 486 217 231 14 99.25 0.98 487 218 227 9 99.51 1.03 488 218 228 10 99.42 1.02 489 218 229 11 99.36 1.01 490 219 227 8 99.52 1.02 491 219 228 9 99.39 1.02 492 219 231 12 99.06 0.88 493 219 236 17 50.71 0.10 494 219 239 20 33.44 1.30 495 220 227 7 99.38 1.02 496 221 224 3 864.52 3.25 497 221 225 4 554.17 0.12 498 221 226 5 472.81 4.62 499 221 228 7 367.56 40.56 500 221 239 18 30.29 1.89 501 228 231 3 867.37 0.79 502 228 235 7 628.64 10.12 503 228 239 11 486.25 0.21 504 231 235 4 768.89 23.80 505 231 236 5 729.33 15.52 506 232 235 3 838.30 5.45 507 232 236 4 838.28 5.45 508 233 236 3 838.30 5.45 509 233 237 4 838.27 5.45 510 234 237 3 844.71 2.23 511 234 238 4 838.26 5.46 512 235 238 3 859.38 4.73 513 235 239 4 838.26 5.46 514 236 239 3 837.37 5.01 515 236 240 4 837.89 5.28 516 237 240 3 842.03 7.34 517 237 241 4 842.02 7.34 518 238 241 3 859.73 11.03 519 238 242 4 847.21 4.75 520 239 242 3 847.21 4.75 521 239 243 4 847.20 4.75 522 240 243 3 847.20 4.75 523 240 244 4 847.20 4.75 524 241 244 3 848.34 0.83 525 241 245 4 843.84 3.08 526 242 245 3 853.56 3.43 527 242 246 4 837.92 5.17 528 243 246 3 859.61 0.40 529 243 247 4 836.53 5.87 530 244 247 3 853.55 2.64 531 244 248 4 837.48 5.39 532 245 248 3 846.65 6.09 533 245 249 4 815.07 0.30 534 246 249 3 837.31 11.07