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 4 202 198 107.14 2.23 2 4 205 201 104.52 1.84 3 4 227 223 104.14 2.00 4 5 38 33 449.13 46.17 5 5 205 200 106.48 2.42 6 6 37 31 449.11 46.15 7 6 38 32 449.14 46.17 8 6 221 215 106.06 2.60 9 6 227 221 106.03 2.54 10 6 228 222 106.01 2.55 11 6 229 223 106.02 2.54 12 6 244 238 35.58 0.21 13 6 246 240 32.78 0.06 14 7 38 31 449.16 46.16 15 7 40 33 449.20 46.17 16 7 90 83 237.58 59.44 17 7 124 117 222.46 54.77 18 7 205 198 107.80 2.26 19 7 207 200 106.27 2.52 20 7 227 220 106.71 2.35 21 7 228 221 106.03 2.54 22 7 229 222 106.03 2.54 23 8 37 29 449.68 45.97 24 8 38 30 449.28 46.16 25 8 39 31 449.21 46.17 26 8 40 32 449.21 46.17 27 8 229 221 106.17 2.50 28 8 240 232 47.76 0.10 29 8 244 236 35.94 0.42 30 9 40 31 449.22 46.17 31 9 229 220 107.12 2.14 32 9 230 221 106.02 2.54 33 9 231 222 106.01 2.54 34 10 40 30 449.29 46.17 35 10 41 31 449.25 46.16 36 10 42 32 449.67 45.95 37 10 231 221 106.17 2.47 38 10 235 225 73.81 0.52 39 10 240 230 47.77 0.09 40 11 42 31 449.68 45.95 41 11 64 53 235.05 60.90 42 11 95 84 235.01 60.88 43 11 231 220 107.23 2.08 44 11 232 221 106.16 2.48 45 12 15 3 878.50 3.83 46 12 21 9 451.03 45.68 47 12 25 13 450.84 45.66 48 12 41 29 449.76 45.97 49 12 42 30 449.73 45.95 50 12 43 31 449.71 45.94 51 12 44 32 449.78 45.90 52 12 51 39 415.59 28.50 53 12 55 43 406.79 23.73 54 13 44 31 449.80 45.90 55 13 64 51 235.09 60.88 56 13 95 82 235.18 60.84 57 13 97 84 235.06 60.90 58 14 44 30 449.84 45.91 59 16 20 4 830.74 1.24 60 16 21 5 816.40 2.26 61 16 47 31 451.36 45.14 62 17 20 3 852.89 0.16 63 17 21 4 837.73 1.14 64 17 47 30 452.30 44.69 65 18 21 3 852.89 0.16 66 18 22 4 837.74 1.14 67 18 47 29 452.31 44.69 68 18 50 32 453.47 43.95 69 19 22 3 862.40 1.19 70 19 23 4 843.48 4.01 71 20 23 3 852.51 3.75 72 20 24 4 843.05 4.25 73 21 24 3 849.77 5.12 74 21 25 4 837.56 0.99 75 21 43 22 452.39 44.70 76 21 47 26 453.67 43.98 77 21 50 29 437.13 35.06 78 22 25 3 858.13 1.72 79 22 26 4 850.91 0.24 80 22 50 28 434.98 33.94 81 22 54 32 420.89 26.89 82 23 26 3 856.34 2.94 83 23 27 4 850.91 0.24 84 24 27 3 865.47 1.24 85 24 28 4 850.93 0.24 86 24 236 212 78.48 2.37 87 24 237 213 73.49 0.35 88 25 28 3 859.24 4.38 89 25 29 4 850.94 0.24 90 25 50 25 435.31 33.80 91 25 54 29 419.34 25.80 92 25 55 30 398.53 15.42 93 26 29 3 865.48 1.24 94 26 30 4 845.25 3.28 95 26 54 28 419.34 25.79 96 27 30 3 867.15 2.08 97 27 31 4 843.25 4.29 98 28 31 3 845.31 3.25 99 28 59 31 396.32 14.34 100 28 240 212 49.88 0.12 101 28 241 213 47.88 0.08 102 29 56 27 396.74 14.48 103 29 58 29 396.69 14.46 104 31 241 210 47.82 0.07 105 33 241 208 47.80 0.07 106 33 245 212 43.29 0.06 107 34 37 3 882.43 0.32 108 34 58 24 400.78 63.44 109 37 244 207 35.56 0.21 110 38 205 167 108.34 2.19 111 39 58 19 335.19 106.20 112 39 59 20 334.39 106.53 113 39 60 21 334.23 106.61 114 39 240 201 47.77 0.10 115 39 244 205 35.27 0.36 116 40 59 19 334.88 106.30 117 40 60 20 334.17 106.64 118 40 61 21 333.81 106.81 119 40 62 22 333.08 107.17 120 40 90 50 291.08 86.16 121 41 55 14 484.66 31.49 122 41 59 18 353.31 97.15 123 41 60 19 334.78 106.36 124 41 61 20 333.82 106.81 125 41 62 21 333.81 106.81 126 41 240 199 47.81 0.08 127 42 62 20 333.82 106.82 128 42 63 21 333.00 107.21 129 43 47 4 832.50 0.38 130 43 48 5 668.42 60.62 131 44 47 3 855.53 3.16 132 44 48 4 831.17 0.17 133 44 64 20 333.05 107.21 134 45 48 3 837.53 0.76 135 45 78 33 375.39 45.31 136 46 49 3 887.08 0.91 137 47 50 3 848.13 2.06 138 47 51 4 842.01 3.02 139 48 51 3 845.51 3.70 140 48 52 4 843.44 3.73 141 48 63 15 365.51 91.06 142 48 83 35 383.69 40.67 143 48 86 38 390.76 37.14 144 48 88 40 379.52 42.58 145 49 52 3 847.72 2.32 146 49 53 4 848.01 1.44 147 49 86 37 384.33 40.36 148 50 53 3 848.75 1.80 149 50 54 4 846.57 0.71 150 51 54 3 861.19 0.94 151 51 55 4 846.56 0.71 152 51 61 10 425.67 61.05 153 52 55 3 849.12 0.23 154 52 56 4 847.37 1.10 155 52 57 5 846.62 0.73 156 52 59 7 811.70 5.50 157 52 61 9 425.68 61.06 158 52 87 35 400.36 31.96 159 55 59 4 848.53 0.03 160 55 61 6 552.49 1.41 161 56 59 3 869.04 3.82 162 57 60 3 878.24 0.78 163 60 90 30 440.45 11.61 164 61 88 27 440.64 11.64 165 61 89 28 440.61 11.63 166 61 90 29 440.49 11.62 167 62 90 28 440.46 11.61 168 62 91 29 440.48 11.62 169 62 92 30 440.46 11.61 170 62 124 62 440.45 11.60 171 63 83 20 441.42 11.70 172 63 90 27 440.72 11.61 173 63 91 28 440.62 11.63 174 63 92 29 440.62 11.63 175 64 92 28 440.67 11.62 176 65 91 26 441.29 11.64 177 65 92 27 440.87 11.65 178 65 93 28 440.81 11.62 179 65 98 33 440.98 11.60 180 65 104 39 441.04 11.58 181 66 80 14 442.23 11.88 182 66 91 25 441.33 11.71 183 66 93 27 441.21 11.68 184 66 112 46 441.40 11.68 185 66 116 50 441.62 11.68 186 67 77 10 442.74 11.85 187 67 78 11 442.66 11.86 188 67 79 12 442.37 11.91 189 67 80 13 442.35 11.90 190 67 108 41 441.55 11.61 191 67 112 45 441.55 11.62 192 67 115 48 441.99 11.76 193 68 108 40 441.57 11.61 194 68 111 43 441.64 11.62 195 68 112 44 441.56 11.62 196 68 115 47 441.99 11.76 197 69 79 10 442.77 11.86 198 69 115 46 442.25 11.75 199 70 79 9 442.79 11.86 200 70 115 45 442.34 11.72 201 74 77 3 857.70 1.83 202 78 82 4 845.64 0.40 203 79 82 3 865.57 4.33 204 80 83 3 856.24 1.30 205 80 84 4 842.73 1.75 206 80 115 35 490.45 30.89 207 80 121 41 449.13 10.34 208 81 84 3 858.75 4.78 209 81 85 4 842.73 1.75 210 82 85 3 858.81 4.75 211 82 86 4 842.78 1.78 212 83 86 3 847.15 3.14 213 83 87 4 842.69 1.78 214 83 88 5 806.94 1.20 215 83 90 7 676.95 2.88 216 83 91 8 494.80 32.93 217 83 121 38 575.35 4.52 218 84 87 3 868.19 7.38 219 84 88 4 819.41 7.19 220 89 121 32 664.43 0.38 221 89 122 33 664.42 0.38 222 90 122 32 664.43 0.38 223 90 123 33 664.43 0.38 224 90 124 34 664.42 0.38 225 90 159 69 664.44 0.38 226 90 161 71 664.43 0.38 227 91 121 30 664.53 0.38 228 91 122 31 664.50 0.38 229 91 123 32 664.44 0.38 230 91 124 33 664.44 0.38 231 92 95 3 940.31 2.65 232 92 124 32 664.44 0.38 233 92 126 34 664.41 0.38 234 93 112 19 664.61 0.36 235 93 113 20 664.59 0.37 236 93 123 30 664.56 0.36 237 93 124 31 664.50 0.37 238 93 125 32 664.47 0.36 239 93 126 33 664.42 0.38 240 94 99 5 803.84 0.92 241 94 109 15 664.55 0.36 242 94 126 32 664.43 0.37 243 95 98 3 853.11 0.30 244 95 99 4 831.58 7.54 245 95 126 31 664.49 0.36 246 95 165 70 664.40 0.38 247 96 99 3 850.20 1.77 248 96 100 4 840.30 3.17 249 96 165 69 664.34 0.36 250 96 167 71 664.12 0.37 251 97 100 3 854.94 1.24 252 97 101 4 838.10 2.06 253 98 101 3 877.49 4.87 254 98 102 4 808.39 1.34 255 98 103 5 808.38 1.34 256 98 104 6 665.18 0.48 257 99 103 4 802.41 1.55 258 99 106 7 727.12 30.50 259 99 109 10 665.13 0.46 260 99 126 27 664.59 0.38 261 99 127 28 664.57 0.37 262 99 146 47 664.62 0.38 263 100 130 30 664.43 0.33 264 104 108 4 836.25 3.27 265 104 109 5 833.67 1.98 266 104 112 8 819.96 3.54 267 105 108 3 836.33 3.23 268 105 109 4 836.27 3.26 269 106 109 3 862.10 0.83 270 106 110 4 843.59 0.39 271 106 146 40 664.73 0.40 272 106 149 43 664.81 0.42 273 107 110 3 853.28 5.24 274 107 111 4 843.58 0.39 275 108 111 3 862.12 0.82 276 108 112 4 833.50 2.02 277 109 112 3 852.83 3.83 278 109 113 4 839.55 1.39 279 109 150 41 664.85 0.43 280 110 113 3 862.53 2.10 281 110 114 4 857.50 2.08 282 110 153 43 665.28 0.31 283 111 114 3 863.44 1.65 284 111 115 4 857.50 2.08 285 111 153 42 665.34 0.29 286 112 115 3 867.04 4.22 287 112 116 4 847.64 2.85 288 113 116 3 859.42 1.13 289 113 117 4 847.09 2.58 290 113 123 10 665.35 0.28 291 113 150 37 665.33 0.29 292 113 154 41 665.40 0.28 293 114 117 3 864.41 5.54 294 114 118 4 845.49 1.80 295 114 153 39 665.39 0.29 296 115 118 3 856.97 2.36 297 115 119 4 845.49 1.81 298 116 119 3 855.10 6.62 299 116 120 4 845.49 1.81 300 116 121 5 792.59 4.28 301 116 123 7 665.83 0.23 302 117 120 3 845.47 1.81 303 117 121 4 820.26 3.17 304 117 123 6 680.86 5.07 305 117 154 37 679.75 4.86 306 117 155 38 685.88 1.80 307 117 160 43 680.52 5.24 308 122 159 37 781.50 0.39 309 123 159 36 781.58 0.42 310 123 160 37 781.51 0.40 311 123 161 38 781.51 0.40 312 124 161 37 781.51 0.40 313 124 163 39 781.50 0.41 314 125 150 25 781.75 0.41 315 125 161 36 781.60 0.41 316 125 162 37 781.55 0.40 317 125 163 38 781.53 0.40 318 126 163 37 781.54 0.40 319 126 230 104 126.81 3.48 320 127 143 16 782.08 0.43 321 127 146 19 782.00 0.42 322 127 147 20 782.00 0.42 323 127 150 23 781.98 0.43 324 127 162 35 781.66 0.40 325 127 163 36 781.58 0.40 326 127 164 37 781.53 0.40 327 127 165 38 781.52 0.41 328 127 188 61 193.25 26.79 329 128 142 14 782.18 0.45 330 128 146 18 782.10 0.45 331 128 165 37 781.52 0.41 332 129 134 5 805.10 0.09 333 129 139 10 782.20 0.45 334 129 142 13 782.19 0.45 335 129 143 14 782.18 0.45 336 129 164 35 781.66 0.41 337 129 165 36 781.58 0.40 338 129 166 37 781.52 0.41 339 129 167 38 781.51 0.41 340 130 133 3 871.55 4.22 341 130 134 4 836.18 0.42 342 130 167 37 781.52 0.41 343 130 168 38 781.43 0.41 344 131 134 3 849.23 6.94 345 131 135 4 838.88 1.78 346 131 167 36 781.59 0.41 347 131 168 37 781.40 0.40 348 131 172 41 730.95 3.46 349 131 174 43 596.69 45.45 350 132 135 3 848.75 2.86 351 132 136 4 840.27 1.09 352 133 136 3 857.05 1.28 353 133 137 4 835.10 0.97 354 133 138 5 784.91 1.48 355 133 142 9 782.48 0.48 356 134 137 3 833.59 2.25 357 134 138 4 809.12 4.51 358 134 139 5 782.47 0.48 359 134 168 34 781.59 0.41 360 134 180 46 211.09 19.93 361 134 184 50 200.63 24.79 362 138 141 3 847.83 4.66 363 138 142 4 829.21 7.60 364 139 142 3 867.62 4.70 365 139 143 4 847.46 1.52 366 140 143 3 878.48 0.72 367 140 144 4 847.44 1.53 368 141 144 3 878.45 0.71 369 141 145 4 842.72 3.89 370 142 145 3 878.45 0.70 371 142 146 4 850.19 0.15 372 143 146 3 872.11 3.88 373 143 147 4 845.85 2.02 374 143 164 21 781.66 0.40 375 143 188 45 193.33 26.76 376 144 147 3 865.86 5.08 377 144 148 4 849.33 0.26 378 144 187 43 193.53 26.73 379 144 188 44 193.34 26.76 380 144 191 47 193.30 26.70 381 145 148 3 849.33 0.26 382 145 149 4 851.18 1.19 383 146 149 3 851.19 1.19 384 146 150 4 851.18 1.19 385 147 150 3 851.18 1.19 386 147 151 4 841.73 3.54 387 147 162 15 781.68 0.39 388 147 188 41 193.30 26.77 389 147 192 45 193.03 26.73 390 148 151 3 857.40 1.93 391 148 152 4 841.69 3.54 392 148 191 43 193.30 26.70 393 149 152 3 851.08 1.16 394 149 153 4 842.57 3.10 395 150 153 3 865.29 0.66 396 150 154 4 831.89 2.24 397 150 162 12 781.65 0.39 398 151 154 3 840.40 6.50 399 151 157 6 809.44 8.98 400 151 196 45 186.25 23.35 401 154 157 3 979.12 5.75 402 156 159 3 957.57 2.33 403 156 160 4 872.02 2.07 404 157 160 3 849.44 1.94 405 157 196 39 185.78 23.12 406 157 200 43 173.74 23.59 407 157 203 46 172.93 23.99 408 157 204 47 171.74 24.48 409 158 203 45 172.93 23.98 410 161 205 44 170.90 24.88 411 161 207 46 170.29 24.76 412 162 188 26 191.15 27.71 413 162 192 30 192.26 26.62 414 162 205 43 171.12 24.79 415 162 206 44 170.30 24.76 416 162 207 45 170.28 24.76 417 163 207 44 170.27 24.75 418 163 230 67 129.03 4.46 419 164 184 20 191.20 27.82 420 164 185 21 190.99 27.84 421 164 207 43 170.62 24.64 422 164 209 45 169.49 24.30 423 165 209 44 169.50 24.30 424 165 230 65 129.53 4.37 425 166 169 3 873.90 0.85 426 166 208 42 171.34 24.73 427 166 210 44 169.78 24.20 428 167 170 3 830.90 5.49 429 167 172 5 753.77 33.06 430 168 172 4 762.41 28.75 431 168 174 6 421.34 29.55 432 168 175 7 402.73 38.84 433 168 176 8 226.22 23.59 434 168 180 12 200.99 24.73 435 169 174 5 421.34 29.55 436 169 176 7 226.15 23.59 437 176 208 32 180.68 20.23 438 177 180 3 857.73 9.60 439 177 181 4 842.20 4.58 440 178 181 3 863.64 6.63 441 178 182 4 847.45 7.21 442 178 219 41 160.41 9.19 443 178 220 42 157.15 8.23 444 178 223 45 157.75 7.62 445 179 182 3 865.90 5.50 446 179 183 4 853.14 0.87 447 179 223 44 158.21 7.60 448 180 183 3 857.11 1.10 449 180 184 4 853.14 0.87 450 181 184 3 854.12 0.42 451 181 185 4 835.85 2.41 452 181 208 27 180.89 20.13 453 181 220 39 158.21 7.71 454 182 185 3 853.98 0.48 455 182 186 4 846.13 4.40 456 182 223 41 148.25 2.62 457 183 186 3 858.75 1.90 458 183 187 4 848.00 3.48 459 184 187 3 854.10 0.42 460 184 188 4 847.93 3.51 461 185 188 3 853.36 4.43 462 185 189 4 840.77 0.07 463 185 206 21 182.07 19.58 464 185 207 22 182.07 19.58 465 185 208 23 182.00 19.61 466 185 225 40 142.13 0.64 467 185 226 41 141.96 0.70 468 186 189 3 861.06 2.59 469 186 190 4 853.44 6.40 470 186 225 39 142.22 0.57 471 187 190 3 861.68 3.50 472 187 191 4 853.43 6.40 473 188 191 3 861.04 2.60 474 188 192 4 833.03 3.90 475 188 206 18 182.37 19.43 476 189 192 3 845.74 10.25 477 189 193 4 833.03 3.90 478 189 201 12 182.91 19.63 479 189 206 17 182.38 19.43 480 189 225 36 142.22 0.68 481 189 227 38 142.22 0.68 482 190 193 3 853.24 0.88 483 190 194 4 838.36 6.55 484 191 194 3 860.72 2.77 485 191 195 4 837.39 7.04 486 192 195 3 855.41 5.42 487 192 196 4 822.53 0.39 488 192 201 9 200.14 25.50 489 192 204 12 182.78 19.54 490 193 196 3 850.20 5.90 491 193 197 4 805.31 0.44 492 193 198 5 586.66 109.76 493 193 201 8 183.36 19.84 494 196 200 4 812.25 3.09 495 197 200 3 850.00 3.43 496 197 201 4 816.38 2.78 497 198 201 3 829.09 0.67 498 198 202 4 823.95 3.25 499 199 202 3 856.00 2.79 500 199 203 4 829.10 0.67 501 200 203 3 861.39 3.12 502 200 204 4 827.34 1.55 503 201 204 3 864.09 4.88 504 205 227 22 200.50 30.96 505 206 227 21 200.52 30.98 506 206 228 22 200.51 30.97 507 207 228 21 200.49 30.97 508 207 229 22 200.43 30.98 509 207 230 23 200.44 30.98 510 208 212 4 864.76 0.60 511 208 220 12 217.71 22.39 512 208 228 20 200.51 30.98 513 208 229 21 200.46 31.00 514 208 230 22 200.46 31.00 515 209 230 21 200.21 31.12 516 210 230 20 200.46 31.01 517 211 216 5 824.85 2.48 518 212 216 4 660.25 84.78 519 212 217 5 448.54 55.37 520 212 220 8 292.31 13.53 521 212 229 17 200.52 31.01 522 212 231 19 200.41 31.04 523 212 234 22 199.47 30.89 524 212 243 31 100.62 26.39 525 213 216 3 837.26 2.81 526 213 217 4 806.21 4.85 527 213 234 21 199.94 31.12 528 213 239 26 105.06 28.47 529 213 243 30 100.64 26.39 530 214 243 29 100.66 26.38 531 215 218 3 854.92 4.79 532 215 219 4 828.21 0.81 533 216 219 3 848.10 4.71 534 216 220 4 824.66 0.97 535 217 220 3 856.86 0.04 536 217 221 4 824.68 0.97 537 217 229 12 201.02 30.82 538 217 243 26 99.58 26.86 539 217 246 29 35.70 0.54 540 218 221 3 856.50 0.51 541 218 222 4 823.12 0.21 542 218 246 28 35.34 0.35 543 218 247 29 35.33 0.35 544 219 222 3 857.30 0.34 545 220 223 3 853.00 1.14 546 220 229 9 201.55 30.62 547 221 226 5 259.46 1.69 548 221 229 8 201.55 30.62 549 221 246 25 35.20 0.39 550 223 226 3 859.59 2.37 551 229 246 17 35.27 0.36 552 231 234 3 883.34 3.14 553 231 235 4 698.54 49.20 554 231 243 12 47.62 0.02 555 232 235 3 847.48 3.56 556 233 236 3 880.91 4.29 557 234 237 3 886.15 1.67 558 234 239 5 236.90 20.28 559 234 243 9 226.49 25.48 560 235 240 5 238.81 30.59 561 237 240 3 879.82 3.21 562 238 241 3 864.01 2.75 563 238 242 4 843.48 7.44 564 239 242 3 843.49 7.44 565 239 243 4 843.48 7.44 566 240 243 3 857.15 0.60 567 240 244 4 843.47 7.45 568 241 244 3 857.15 0.59 569 241 245 4 826.59 0.99 570 242 245 3 864.14 4.09 571 243 246 3 869.50 1.42