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 26 42 16 575.70 3.84 2 26 43 17 593.79 1.94 3 26 53 27 568.50 0.40 4 26 54 28 547.63 1.06 5 26 55 29 506.82 18.73 6 28 43 15 612.33 2.46 7 28 44 16 612.39 2.44 8 28 45 17 612.84 2.43 9 29 41 12 611.96 2.29 10 29 42 13 612.47 2.51 11 29 43 14 612.37 2.46 12 29 44 15 612.98 2.41 13 30 40 10 613.18 2.44 14 30 41 11 613.11 2.42 15 30 42 12 612.99 2.40 16 30 44 14 613.12 2.42 17 31 39 8 613.61 2.51 18 31 40 9 613.19 2.44 19 31 41 10 613.15 2.43 20 32 39 7 613.69 2.54 21 32 40 8 613.47 2.58 22 32 42 10 613.68 2.54 23 32 71 39 613.73 2.54 24 32 72 40 613.70 2.54 25 32 94 62 613.79 2.56 26 33 38 5 679.83 28.78 27 33 39 6 677.74 29.47 28 34 38 4 679.83 28.78 29 34 39 5 677.81 29.45 30 34 40 6 677.82 29.44 31 34 90 56 613.74 2.54 32 34 94 60 613.88 2.58 33 34 97 63 613.70 2.55 34 35 38 3 811.37 2.09 35 35 94 59 614.29 2.64 36 35 95 60 614.14 2.68 37 35 96 61 613.74 2.53 38 35 97 62 613.71 2.54 39 35 115 80 70.51 0.53 40 36 115 79 71.12 0.78 41 38 58 20 614.46 2.67 42 38 88 50 614.31 2.64 43 38 97 59 614.43 2.69 44 39 56 17 614.91 2.65 45 40 54 14 615.06 2.64 46 40 55 15 614.99 2.63 47 40 56 16 614.93 2.65 48 40 72 32 615.15 2.68 49 40 76 36 614.94 2.65 50 40 90 50 614.98 2.66 51 41 54 13 615.21 2.71 52 41 55 14 615.06 2.64 53 42 52 10 615.84 2.79 54 42 53 11 615.66 2.85 55 42 54 12 615.27 2.67 56 42 70 28 615.82 2.79 57 42 72 30 615.54 2.83 58 43 52 9 615.85 2.79 59 43 53 10 615.81 2.79 60 44 52 8 678.78 28.38 61 45 52 7 678.82 28.39 62 46 50 4 746.00 4.40 63 46 51 5 711.39 12.11 64 46 52 6 678.79 28.37 65 47 50 3 766.01 1.95 66 47 51 4 745.99 4.40 67 51 66 15 708.43 12.27 68 51 67 16 708.14 12.21 69 52 66 14 708.82 12.09 70 52 67 15 708.32 12.20 71 52 69 17 708.27 12.14 72 52 70 18 708.27 12.14 73 53 65 12 709.49 11.92 74 53 66 13 709.24 12.01 75 54 64 10 709.87 12.03 76 54 65 11 709.55 11.90 77 54 66 12 709.49 11.92 78 54 67 13 709.46 11.93 79 54 72 18 708.86 11.84 80 54 73 19 708.91 11.81 81 54 74 20 708.91 11.72 82 54 76 22 708.96 11.61 83 55 62 7 744.45 4.21 84 55 63 8 710.40 12.28 85 55 64 9 709.60 11.89 86 55 76 21 709.00 11.60 87 56 62 6 745.09 4.53 88 56 63 7 743.90 4.46 89 56 76 20 709.03 11.60 90 56 88 32 677.25 4.29 91 57 60 3 824.88 3.29 92 57 61 4 769.57 3.33 93 57 62 5 745.08 4.54 94 58 61 3 805.72 1.19 95 58 63 5 759.41 1.75 96 58 88 30 677.60 4.45 97 58 99 41 674.57 4.58 98 61 79 18 742.02 4.94 99 61 80 19 741.99 4.96 100 61 86 25 710.47 20.68 101 62 78 16 742.00 4.93 102 63 76 13 741.92 4.89 103 63 77 14 741.97 4.94 104 63 78 15 741.93 4.98 105 63 86 23 710.48 20.73 106 63 88 25 710.16 20.74 107 63 99 36 674.66 4.65 108 64 76 12 741.97 4.93 109 64 77 13 741.96 4.97 110 65 75 10 742.01 4.94 111 65 76 11 741.94 4.98 112 67 73 6 742.07 4.92 113 67 74 7 741.96 4.99 114 69 73 4 757.47 4.67 115 69 92 23 709.34 21.23 116 71 92 21 709.45 21.26 117 71 94 23 709.26 21.18 118 72 90 18 709.66 21.21 119 72 94 22 709.39 21.28 120 73 90 17 709.58 21.25 121 73 91 18 709.57 21.25 122 73 92 19 709.46 21.27 123 73 94 21 694.75 14.09 124 74 89 15 710.33 20.91 125 74 90 16 709.68 21.21 126 75 87 12 710.50 20.91 127 75 88 13 710.39 20.93 128 75 89 14 710.11 21.04 129 76 87 11 710.50 20.91 130 76 88 12 710.31 20.98 131 76 90 14 710.31 20.98 132 77 86 9 710.70 20.84 133 77 87 10 710.50 20.91 134 78 85 7 711.14 21.00 135 78 86 8 710.74 20.86 136 79 84 5 711.27 20.99 137 79 85 6 711.15 21.01 138 80 83 3 775.44 4.65 139 80 84 4 711.28 20.99 140 80 86 6 711.27 21.00 141 80 101 21 674.56 4.63 142 83 104 21 673.27 4.58 143 84 101 17 674.55 4.63 144 84 102 18 674.50 4.62 145 85 101 16 674.55 4.64 146 85 102 17 674.48 4.62 147 85 103 18 674.43 4.62 148 85 104 19 666.89 1.68 149 85 106 21 531.66 0.81 150 86 99 13 674.69 4.66 151 86 100 14 674.56 4.63 152 86 101 15 674.47 4.62 153 87 99 12 674.67 4.66 154 87 100 13 674.52 4.62 155 87 102 15 674.47 4.62 156 88 97 9 674.74 4.63 157 88 98 10 674.69 4.66 158 88 99 11 674.60 4.62 159 89 97 8 674.74 4.63 160 89 98 9 674.69 4.66 161 90 94 4 761.29 2.47 162 90 96 6 675.11 4.54 163 90 97 7 674.69 4.66 164 91 94 3 794.41 7.36 165 91 95 4 772.96 3.37 166 91 96 5 684.27 6.05 167 95 116 21 70.05 0.68 168 96 114 18 72.42 0.39 169 96 115 19 71.16 0.77 170 96 116 20 70.06 0.67 171 97 114 17 72.39 0.39 172 97 115 18 71.14 0.77 173 98 112 14 75.62 1.12 174 98 113 15 72.46 0.40 175 98 114 16 72.41 0.38 176 99 112 13 75.61 1.11 177 99 113 14 72.50 0.41 178 100 109 9 392.31 44.19 179 100 111 11 285.36 97.44 180 100 112 12 73.52 0.07 181 101 109 8 392.31 44.20 182 101 110 9 391.96 44.36 183 101 111 10 319.42 80.42 184 102 106 4 763.22 3.98 185 102 107 5 697.49 36.84 186 102 108 6 518.46 7.36 187 102 109 7 392.31 44.20 188 102 110 8 392.00 44.35 189 103 106 3 816.18 1.95 190 103 108 5 523.81 5.25 191 103 110 7 397.00 46.54 192 105 108 3 840.52 5.30 193 109 112 3 919.16 2.89 194 109 126 17 45.22 0.68 195 110 125 15 45.44 0.65 196 110 126 16 45.23 0.66 197 111 124 13 47.72 0.48 198 111 125 14 45.35 0.61 199 112 123 11 49.50 0.04 200 112 124 12 47.40 0.33 201 113 121 8 65.59 5.17 202 113 122 9 52.30 1.26 203 113 123 10 48.68 0.01 204 114 121 7 75.05 9.89 205 114 122 8 62.68 6.59 206 115 119 4 789.79 6.98 207 115 120 5 637.38 62.55 208 115 121 6 75.05 9.89 209 116 119 3 805.32 0.78 210 116 120 4 788.48 7.63 211 117 120 3 831.88 3.91 212 118 139 21 37.17 0.47 213 119 139 20 37.16 0.47 214 120 137 17 37.20 0.48 215 120 138 18 37.20 0.48 216 121 136 15 37.42 0.49 217 121 137 16 37.25 0.49 218 122 134 12 37.50 0.51 219 122 135 13 37.43 0.49 220 122 136 14 37.34 0.53 221 123 134 11 66.42 13.96 222 123 135 12 37.47 0.52 223 124 131 7 396.83 44.30 224 124 133 9 66.47 13.96 225 124 134 10 66.43 13.96 226 125 131 6 396.84 44.31 227 125 132 7 396.82 44.30 228 125 133 8 313.19 79.70 229 126 129 3 844.01 1.92 230 126 130 4 785.25 5.02 231 126 131 5 404.47 48.12 232 126 132 6 396.83 44.30 233 127 130 3 823.98 6.13 234 127 132 5 634.61 52.16 235 130 150 20 146.08 0.66 236 130 151 21 146.01 0.69 237 131 134 3 905.19 5.08 238 131 149 18 146.22 0.58 239 132 148 16 146.93 0.41 240 132 149 17 146.22 0.58 241 133 146 13 146.93 0.42 242 133 147 14 147.02 0.43 243 133 149 16 147.22 0.53 244 134 145 11 147.44 0.48 245 134 146 12 147.31 0.53 246 134 149 15 147.72 0.60 247 135 143 8 316.22 83.62 248 135 144 9 147.72 0.59 249 135 145 10 147.46 0.48 250 135 146 11 147.71 0.59 251 136 143 7 316.24 83.62 252 136 144 8 147.78 0.60 253 136 146 10 148.13 0.43 254 137 141 4 766.55 1.17 255 137 142 5 470.02 36.47 256 137 143 6 317.49 83.85 257 138 141 3 784.02 2.67 258 138 142 4 580.65 91.78 259 138 144 6 470.02 36.47 260 138 159 21 149.14 0.40 261 138 190 52 149.10 0.43 262 138 240 102 149.00 0.40 263 140 239 99 149.12 0.40 264 140 240 100 149.10 0.40 265 142 160 18 150.09 0.69 266 142 161 19 150.02 0.72 267 142 240 98 149.29 0.45 268 143 159 16 150.23 0.65 269 143 160 17 150.18 0.67 270 144 158 14 150.40 0.62 271 144 159 15 150.25 0.65 272 144 190 46 150.73 0.49 273 145 157 12 150.92 0.49 274 145 158 13 150.71 0.52 275 145 160 15 150.81 0.56 276 146 149 3 864.49 4.25 277 146 156 10 151.16 0.42 278 146 157 11 151.09 0.42 279 146 170 24 151.16 0.42 280 146 175 29 151.15 0.42 281 147 155 8 226.68 38.04 282 147 156 9 151.32 0.38 283 148 155 7 226.69 38.04 284 149 153 4 768.86 4.90 285 149 154 5 404.18 44.75 286 149 155 6 226.78 38.03 287 149 170 21 272.85 15.04 288 150 153 3 807.26 3.31 289 150 154 4 634.70 54.35 290 153 170 17 413.98 21.36 291 153 171 18 412.87 21.11 292 154 170 16 413.98 21.36 293 154 171 17 412.87 21.11 294 155 169 14 415.25 21.82 295 155 170 15 415.05 21.89 296 156 168 12 415.44 21.78 297 156 169 13 415.30 21.84 298 157 167 10 415.82 21.91 299 157 168 11 415.61 21.87 300 157 169 12 415.44 21.79 301 157 170 13 415.43 21.79 302 157 175 18 415.13 21.93 303 157 177 20 415.19 22.00 304 158 165 7 416.35 21.80 305 158 166 8 416.11 21.87 306 158 167 9 415.82 21.91 307 158 177 19 415.44 22.11 308 159 165 6 416.34 21.80 309 159 166 7 416.12 21.87 310 159 177 18 415.53 22.16 311 159 188 29 415.57 22.14 312 160 165 5 416.34 21.79 313 161 164 3 795.60 4.00 314 161 166 5 758.44 3.65 315 161 240 79 231.61 1.84 316 163 262 99 231.16 1.92 317 164 242 78 231.61 1.84 318 164 261 97 231.19 1.92 319 164 262 98 231.15 1.92 320 164 263 99 231.12 1.92 321 164 264 100 231.05 1.96 322 164 267 103 231.12 1.93 323 166 177 11 418.68 23.79 324 166 179 13 418.52 23.77 325 166 188 22 418.17 23.44 326 166 264 98 231.03 1.96 327 166 267 101 231.03 1.96 328 167 177 10 418.63 23.82 329 167 178 11 418.63 23.82 330 168 176 8 418.78 23.87 331 168 177 9 418.51 23.88 332 169 175 6 418.83 23.90 333 169 176 7 418.76 23.90 334 170 174 4 709.91 0.48 335 170 175 5 418.82 23.91 336 171 174 3 797.68 2.85 337 172 192 20 457.49 3.89 338 173 192 19 457.51 3.88 339 174 189 15 457.89 3.84 340 174 190 16 457.84 3.85 341 174 191 17 457.66 3.79 342 175 189 14 457.92 3.83 343 175 190 15 457.72 3.77 344 176 187 11 458.03 3.78 345 176 188 12 458.00 3.79 346 176 189 13 457.76 3.75 347 177 187 10 458.04 3.77 348 177 188 11 457.86 3.70 349 177 190 13 457.84 3.71 350 178 185 7 458.32 3.83 351 178 186 8 458.26 3.83 352 178 187 9 458.04 3.78 353 179 185 6 458.34 3.82 354 179 186 7 458.30 3.82 355 179 264 85 231.09 1.94 356 179 267 88 231.04 1.96 357 179 268 89 230.97 1.94 358 179 271 92 228.68 1.99 359 180 184 4 653.21 67.77 360 180 185 5 458.35 3.82 361 180 268 88 231.05 1.96 362 181 184 3 782.44 3.29 363 181 268 87 231.02 1.97 364 181 271 90 228.78 2.03 365 181 272 91 228.22 1.78 366 183 202 19 452.86 1.79 367 183 203 20 452.44 1.58 368 183 204 21 452.38 1.58 369 184 200 16 453.53 1.78 370 184 201 17 453.22 1.91 371 184 202 18 452.44 1.57 372 184 211 27 235.19 1.06 373 184 271 87 229.05 2.08 374 185 200 15 453.25 1.89 375 185 201 16 453.06 1.85 376 186 198 12 453.98 1.99 377 186 199 13 453.46 1.79 378 186 200 14 453.05 1.86 379 186 222 36 234.57 1.10 380 186 234 48 233.52 1.48 381 186 267 81 231.05 1.97 382 186 271 85 228.68 1.99 383 187 198 11 453.50 1.79 384 187 199 12 453.15 1.83 385 188 196 8 460.13 4.71 386 188 197 9 459.00 4.54 387 188 198 10 458.50 4.51 388 188 236 48 231.91 1.96 389 189 195 6 465.81 7.32 390 189 196 7 460.14 4.71 391 189 197 8 459.12 4.22 392 189 199 10 458.52 4.52 393 190 194 4 517.50 2.96 394 190 195 5 465.81 7.32 395 190 196 6 460.18 4.70 396 191 194 3 770.13 0.55 397 191 195 4 639.83 64.60 398 196 215 19 234.59 1.13 399 196 236 40 233.83 1.01 400 197 215 18 234.56 1.12 401 198 215 17 234.56 1.12 402 198 222 24 234.50 1.11 403 198 236 38 233.84 1.02 404 200 211 11 235.20 1.06 405 200 212 12 235.01 1.09 406 200 213 13 234.86 1.17 407 200 222 22 234.69 1.14 408 200 224 24 234.83 1.18 409 200 271 71 228.98 2.12 410 202 210 8 235.30 1.08 411 202 211 9 235.22 1.05 412 204 209 5 625.41 57.80 413 204 210 6 236.36 1.60 414 206 209 3 822.58 0.14 415 206 210 4 717.26 11.86 416 207 227 20 276.55 3.56 417 208 226 18 283.83 3.10 418 209 226 17 284.06 2.98 419 210 226 16 284.35 2.93 420 211 224 13 284.44 2.92 421 211 225 14 284.42 2.91 422 211 226 15 284.42 2.91 423 211 271 60 229.66 2.06 424 211 272 61 229.65 2.06 425 212 224 12 284.44 2.93 426 212 225 13 284.44 2.92 427 213 222 9 284.65 2.92 428 213 223 10 284.55 2.88 429 213 224 11 284.45 2.92 430 214 222 8 285.12 2.69 431 214 223 9 284.66 2.91 432 215 220 5 643.10 57.47 433 215 221 6 403.04 52.72 434 215 222 7 288.44 4.35 435 215 236 21 422.40 35.98 436 216 219 3 828.44 6.04 437 216 220 4 762.88 2.39 438 216 221 5 514.54 3.01 439 217 220 3 791.23 3.92 440 220 235 15 449.97 33.04 441 220 236 16 449.95 33.05 442 221 233 12 450.10 33.03 443 221 234 13 450.09 33.03 444 221 235 14 450.00 33.02 445 222 233 11 450.12 33.03 446 222 234 12 450.11 33.04 447 222 236 14 450.11 33.03 448 223 230 7 496.38 9.96 449 223 232 9 450.19 33.01 450 223 233 10 450.13 33.04 451 223 247 24 450.00 33.09 452 224 230 6 497.16 10.33 453 224 231 7 450.30 32.98 454 224 232 8 450.24 32.98 455 224 234 10 450.31 33.02 456 224 270 46 231.00 1.93 457 224 271 47 230.15 2.06 458 225 228 3 818.03 0.95 459 225 229 4 602.45 35.26 460 225 230 5 497.16 10.33 461 226 229 3 802.73 0.21 462 226 231 5 513.13 2.45 463 229 249 20 449.97 33.09 464 229 250 21 449.56 33.05 465 229 251 22 330.55 6.41 466 230 247 17 450.19 33.12 467 230 251 21 359.79 8.22 468 231 246 15 450.25 33.11 469 231 247 16 450.13 33.16 470 232 244 12 450.79 33.08 471 232 245 13 450.44 33.20 472 232 246 14 450.22 33.12 473 232 247 15 450.14 33.16 474 232 270 38 231.08 1.93 475 233 243 10 451.07 33.12 476 233 244 11 450.81 33.09 477 233 245 12 450.51 33.21 478 233 247 14 450.32 33.26 479 233 254 21 294.96 0.01 480 234 242 8 451.10 33.11 481 234 243 9 451.08 33.11 482 234 244 10 450.81 33.08 483 234 270 36 231.06 1.93 484 235 242 7 451.11 33.11 485 235 243 8 451.09 33.11 486 236 241 5 586.01 44.97 487 236 242 6 451.17 33.13 488 237 240 3 802.78 4.01 489 237 241 4 592.03 41.97 490 237 243 6 585.78 45.08 491 241 260 19 278.37 3.62 492 242 260 18 278.29 3.64 493 242 261 19 278.23 3.63 494 242 267 25 247.96 3.42 495 243 258 15 280.47 4.60 496 243 259 16 278.32 3.62 497 243 260 17 278.26 3.63 498 243 261 18 278.11 3.69 499 244 258 14 280.56 4.71 500 244 259 15 278.32 3.62 501 244 261 17 278.11 3.69 502 244 270 26 231.12 1.95 503 245 254 9 294.95 0.01 504 245 255 10 294.92 0.03 505 245 256 11 294.71 0.05 506 245 257 12 291.69 0.83 507 245 258 13 278.35 3.60 508 246 254 8 295.13 0.07 509 246 255 9 294.92 0.01 510 247 251 4 446.38 35.05 511 247 253 6 302.24 2.91 512 247 254 7 295.18 0.05 513 247 255 8 295.13 0.07 514 248 251 3 788.63 3.23 515 248 252 4 670.10 16.70 516 248 253 5 441.88 32.81 517 248 255 7 297.11 0.36 518 261 266 5 784.19 1.98 519 261 267 6 642.65 55.01 520 262 266 4 792.89 1.76 521 263 266 3 804.82 2.06 522 263 267 4 797.59 1.55 523 264 267 3 807.27 0.07 524 264 268 4 795.45 0.48 525 265 268 3 800.73 0.01 526 265 269 4 793.08 1.67 527 266 269 3 799.49 0.79 528 266 270 4 792.48 1.37 529 267 270 3 820.00 2.41 530 267 271 4 795.12 2.69 531 268 271 3 803.76 1.54 532 268 272 4 795.16 2.68 533 269 272 3 812.82 3.00