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 11 42 31 329.31 0.60 2 11 43 32 329.31 0.60 3 11 44 33 329.45 0.53 4 11 142 131 329.47 0.53 5 11 143 132 329.25 0.62 6 11 144 133 329.10 0.57 7 12 141 129 331.88 0.17 8 12 142 130 331.38 0.01 9 12 143 131 330.95 0.22 10 12 171 159 246.30 0.43 11 13 45 32 332.03 0.11 12 13 47 34 333.44 0.57 13 13 140 127 333.17 0.49 14 13 141 128 331.88 0.17 15 13 142 129 331.60 0.07 16 13 171 158 246.73 0.33 17 13 172 159 246.29 0.43 18 13 174 161 246.24 0.45 19 13 177 164 246.00 0.36 20 14 140 126 333.43 0.57 21 14 141 127 331.98 0.14 22 14 143 129 331.88 0.17 23 14 145 131 331.70 0.13 24 14 169 155 247.08 0.33 25 14 170 156 247.02 0.33 26 14 171 157 246.81 0.30 27 14 172 158 246.66 0.28 28 15 138 123 334.37 0.74 29 15 139 124 333.52 0.57 30 15 140 125 333.43 0.57 31 15 162 147 281.97 2.99 32 15 163 148 274.00 0.27 33 15 172 157 246.96 0.36 34 16 30 14 332.60 0.15 35 16 138 122 334.81 0.94 36 16 139 123 333.65 0.53 37 16 141 125 333.51 0.57 38 16 153 137 329.34 0.55 39 16 159 143 310.69 0.88 40 16 161 145 296.83 1.10 41 16 162 146 285.62 1.17 42 17 137 120 334.94 0.94 43 17 138 121 334.89 0.94 44 17 159 142 319.28 1.28 45 17 160 143 308.41 1.00 46 17 161 144 302.69 1.82 47 17 163 146 294.25 2.39 48 18 23 5 511.81 0.91 49 18 26 8 334.88 0.94 50 18 137 119 335.16 0.82 51 18 138 120 334.94 0.94 52 18 139 121 334.92 0.94 53 18 158 140 328.12 0.57 54 18 159 141 319.03 1.40 55 18 160 142 310.69 0.88 56 19 22 3 673.97 2.54 57 19 158 139 328.59 0.36 58 19 160 141 328.12 0.57 59 20 23 3 721.87 0.66 60 20 137 117 374.69 3.32 61 20 160 140 328.74 0.45 62 22 25 3 675.35 4.60 63 22 26 4 669.66 3.17 64 22 158 136 328.79 0.45 65 23 26 3 677.45 0.73 66 23 27 4 669.66 3.17 67 23 48 25 501.45 4.36 68 23 132 109 409.64 1.28 69 23 136 113 409.99 1.04 70 23 137 114 409.68 0.92 71 23 138 115 408.70 1.38 72 23 139 116 408.53 1.44 73 24 27 3 672.06 4.16 74 24 28 4 873.63 0.03 75 24 48 24 502.62 3.80 76 24 130 106 409.83 1.67 77 25 158 133 328.99 0.55 78 26 139 113 410.89 1.34 79 26 156 130 329.05 0.56 80 26 158 132 328.12 0.58 81 26 159 133 327.00 0.90 82 27 48 21 724.72 6.83 83 27 139 112 410.93 1.35 84 29 156 127 329.06 0.56 85 29 157 128 329.04 0.56 86 29 158 129 329.00 0.55 87 30 139 109 410.98 1.36 88 30 141 111 410.87 1.33 89 30 153 123 330.97 0.60 90 30 156 126 329.03 0.56 91 33 152 119 332.64 0.54 92 33 156 123 329.04 0.55 93 33 157 124 329.05 0.56 94 34 149 115 385.87 1.34 95 37 152 115 366.04 3.83 96 39 148 109 389.19 0.31 97 39 149 110 386.23 1.17 98 39 152 113 380.84 1.68 99 42 143 101 410.72 1.38 100 42 144 102 410.63 1.36 101 42 146 104 410.40 1.25 102 42 149 107 388.51 0.12 103 43 142 99 410.85 1.33 104 43 143 100 410.65 1.35 105 43 149 106 388.50 0.11 106 44 142 98 410.89 1.34 107 45 141 96 410.90 1.35 108 45 142 97 410.84 1.32 109 46 139 93 410.98 1.36 110 46 140 94 410.92 1.35 111 46 141 95 410.75 1.34 112 47 139 92 410.98 1.36 113 47 140 93 410.93 1.34 114 47 181 134 245.78 0.36 115 48 130 82 413.83 0.51 116 48 132 84 412.73 0.86 117 48 139 91 410.98 1.36 118 48 185 137 244.79 0.10 119 49 135 86 411.14 1.32 120 49 138 89 411.09 1.34 121 49 139 90 411.05 1.35 122 49 140 91 411.05 1.35 123 49 181 132 245.86 0.40 124 49 184 135 245.62 0.41 125 50 130 80 414.71 0.32 126 50 131 81 413.39 0.72 127 50 132 82 413.10 0.69 128 50 184 134 245.73 0.38 129 50 185 135 245.62 0.42 130 51 67 16 498.50 4.25 131 51 69 18 498.45 4.26 132 51 130 79 420.59 1.41 133 51 131 80 414.70 0.49 134 51 184 133 245.66 0.42 135 52 67 15 498.51 4.25 136 52 68 16 498.47 4.25 137 52 113 61 475.16 1.31 138 52 128 76 475.04 1.36 139 52 129 77 468.97 0.63 140 52 130 78 427.34 0.53 141 52 185 133 245.66 0.42 142 53 65 12 498.67 4.21 143 53 66 13 498.54 4.24 144 53 67 14 498.50 4.25 145 53 68 15 498.50 4.25 146 53 128 75 475.68 1.59 147 53 129 76 468.98 0.62 148 53 131 78 439.66 2.23 149 54 65 11 498.67 4.21 150 54 66 12 498.62 4.20 151 54 68 14 498.53 4.25 152 54 88 34 478.85 1.53 153 54 93 39 477.99 1.32 154 54 127 73 476.97 1.20 155 54 128 74 475.70 1.58 156 55 62 7 500.41 4.41 157 55 64 9 499.71 4.49 158 55 65 10 498.68 4.21 159 55 126 71 477.53 1.17 160 55 127 72 477.36 1.19 161 55 129 74 475.73 1.60 162 56 62 6 500.69 4.55 163 56 63 7 500.38 4.42 164 56 64 8 500.13 4.37 165 56 75 19 498.10 4.12 166 56 77 21 497.62 4.14 167 56 86 30 490.38 3.78 168 56 125 69 478.68 1.46 169 56 126 70 477.54 1.16 170 57 61 4 512.57 1.38 171 57 62 5 500.70 4.55 172 57 124 67 479.21 1.52 173 57 125 68 478.86 1.39 174 58 61 3 656.92 10.63 175 58 63 5 505.84 1.99 176 58 77 19 497.91 4.09 177 58 78 20 497.69 4.17 178 58 79 21 496.48 4.18 179 58 123 65 488.48 3.06 180 58 124 66 479.28 1.54 181 59 79 20 497.60 4.21 182 59 80 21 497.57 4.22 183 59 123 64 487.47 2.56 184 62 65 3 772.14 2.98 185 63 77 14 497.77 4.13 186 64 75 11 498.20 4.16 187 64 77 13 497.76 4.13 188 65 129 64 475.70 1.58 189 66 73 7 500.10 4.64 190 66 75 9 498.17 4.17 191 66 88 22 482.17 0.04 192 67 73 6 657.16 3.31 193 67 189 122 242.66 0.97 194 68 73 5 689.06 0.01 195 68 88 20 479.26 0.94 196 68 91 23 477.62 1.17 197 68 92 24 477.78 1.23 198 68 93 25 477.79 1.23 199 68 111 43 477.53 1.19 200 68 128 60 476.43 1.22 201 69 73 4 782.00 0.68 202 69 183 114 246.74 0.32 203 69 184 115 246.33 0.45 204 69 185 116 246.00 0.38 205 69 186 117 245.86 0.35 206 69 187 118 245.85 0.35 207 70 73 3 875.62 1.01 208 72 88 16 490.37 3.75 209 72 89 17 486.04 3.29 210 73 87 14 491.53 3.50 211 73 88 15 491.23 3.36 212 74 85 11 493.11 4.09 213 74 86 12 492.72 4.09 214 74 87 13 491.53 3.50 215 75 85 10 493.11 4.10 216 75 86 11 492.63 4.04 217 75 88 13 492.72 4.07 218 76 83 7 501.45 0.06 219 76 84 8 493.16 4.08 220 76 85 9 493.12 4.10 221 77 83 6 501.47 0.06 222 77 84 7 493.34 4.04 223 77 86 9 493.24 4.05 224 77 124 47 493.05 4.06 225 78 82 4 583.49 23.16 226 78 83 5 512.27 5.34 227 79 82 3 676.37 6.34 228 79 122 43 537.20 5.90 229 79 124 45 512.12 5.41 230 80 122 42 582.51 8.20 231 80 123 43 560.45 1.09 232 81 99 18 631.88 1.88 233 81 121 40 612.41 2.11 234 81 122 41 602.49 0.52 235 82 99 17 632.10 1.94 236 82 122 40 622.29 2.79 237 83 98 15 632.24 1.94 238 83 99 16 632.24 1.94 239 83 122 39 631.92 1.88 240 84 95 11 632.36 1.94 241 84 97 13 632.37 1.94 242 84 98 14 632.24 1.94 243 84 119 35 631.81 1.82 244 84 122 38 632.16 1.95 245 84 124 40 626.20 0.32 246 85 95 10 632.38 1.94 247 85 96 11 632.38 1.94 248 85 97 12 632.38 1.95 249 86 93 7 632.63 1.82 250 86 94 8 632.50 1.89 251 86 95 9 632.38 1.94 252 86 124 38 632.25 1.94 253 86 125 39 632.14 1.97 254 86 126 40 631.25 2.00 255 87 93 6 632.69 1.81 256 87 94 7 632.59 1.85 257 87 96 9 632.44 1.93 258 88 92 4 632.75 1.78 259 88 93 5 632.69 1.81 260 89 92 3 680.38 8.15 261 89 94 5 632.88 1.84 262 91 111 20 650.49 11.10 263 92 109 17 650.51 11.12 264 92 110 18 650.50 11.11 265 92 111 19 650.48 11.11 266 93 109 16 650.51 11.12 267 93 110 17 650.50 11.12 268 93 117 24 650.53 11.08 269 93 126 33 632.39 2.04 270 93 128 35 631.97 1.88 271 94 109 15 650.52 11.13 272 94 117 23 650.50 11.11 273 95 98 3 757.44 0.80 274 95 104 9 650.65 11.04 275 95 105 10 650.68 11.05 276 95 117 22 650.48 11.14 277 95 119 24 650.64 11.04 278 96 105 9 650.71 11.04 279 97 105 8 650.77 11.03 280 98 102 4 653.22 9.87 281 98 104 6 651.22 10.84 282 98 122 24 652.59 9.61 283 99 102 3 691.68 2.53 284 99 121 22 669.29 1.74 285 99 122 23 658.95 6.73 286 101 121 20 682.87 5.04 287 102 119 17 682.80 4.95 288 102 120 18 683.23 5.18 289 102 121 19 682.81 5.07 290 102 122 20 682.79 5.08 291 110 126 16 665.19 14.27 292 110 128 18 664.82 14.34 293 111 128 17 664.86 14.35 294 112 128 16 665.08 14.31 295 113 128 15 664.97 14.36 296 113 129 16 664.85 14.36 297 113 130 17 664.85 14.36 298 114 128 14 665.10 14.30 299 115 127 12 665.19 14.26 300 115 128 13 665.07 14.29 301 116 125 9 665.29 14.24 302 116 126 10 665.21 14.26 303 116 127 11 664.75 14.12 304 117 125 8 665.29 14.24 305 117 126 9 665.23 14.25 306 118 124 6 665.34 14.22 307 118 125 7 664.88 14.04 308 119 122 3 693.49 0.19 309 119 123 4 665.38 14.20 310 119 124 5 665.27 14.19 311 120 123 3 684.86 4.48 312 130 185 55 245.66 0.41 313 133 136 3 686.14 8.59 314 134 184 50 245.94 0.36 315 135 138 3 703.92 0.29 316 135 180 45 246.44 0.48 317 135 184 49 245.94 0.39 318 138 163 25 295.91 1.56 319 140 172 32 246.99 0.34 320 140 177 37 246.26 0.42 321 140 181 41 245.89 0.38 322 141 145 4 745.69 1.21 323 141 153 12 329.22 0.60 324 142 174 32 246.25 0.46 325 143 149 6 620.72 15.52 326 144 149 5 644.76 3.53 327 145 149 4 644.92 3.46 328 145 150 5 620.75 15.51 329 145 153 8 611.00 16.82 330 145 162 17 279.79 1.36 331 145 169 24 246.83 0.30 332 146 149 3 682.27 5.16 333 146 150 4 645.12 3.36 334 147 150 3 679.78 7.06 335 147 151 4 662.48 5.32 336 148 151 3 676.80 8.55 337 148 152 4 662.48 5.32 338 149 152 3 675.76 8.04 339 149 153 4 643.98 3.06 340 150 153 3 669.84 9.85 341 150 154 4 643.99 3.07 342 150 162 12 288.72 0.36 343 150 164 14 285.25 1.36 344 150 169 19 246.83 0.30 345 151 154 3 647.18 4.67 346 151 155 4 643.83 3.15 347 152 155 3 674.63 7.75 348 152 156 4 643.83 3.15 349 153 156 3 672.61 10.79 350 153 159 6 308.50 0.95 351 153 162 9 299.94 0.46 352 154 160 6 303.13 1.66 353 154 161 7 302.74 1.80 354 154 162 8 302.87 1.79 355 154 164 10 302.77 1.74 356 156 159 3 692.84 3.00 357 161 164 3 816.32 0.41 358 162 169 7 247.27 0.37 359 163 169 6 247.28 0.36 360 163 170 7 247.27 0.36 361 164 167 3 703.71 2.79 362 164 168 4 596.79 26.10 363 164 169 5 247.30 0.35 364 164 170 6 247.27 0.36 365 165 168 3 677.43 2.77 366 165 170 5 247.29 0.35 367 172 177 5 608.60 19.84 368 173 176 3 678.59 5.25 369 173 177 4 647.93 0.23 370 174 177 3 668.42 6.06 371 174 178 4 647.89 0.20 372 175 178 3 679.49 3.83 373 175 179 4 647.93 0.21 374 176 179 3 682.12 1.09 375 176 180 4 657.93 5.21 376 177 180 3 679.06 3.62 377 177 181 4 614.14 17.00 378 178 181 3 670.14 8.07 379 178 182 4 614.11 16.97 380 179 182 3 667.17 9.56 381 179 183 4 614.11 16.96 382 180 183 3 683.95 5.96 383 180 184 4 614.12 16.96 384 181 184 3 676.49 9.69 385 181 185 4 614.09 16.95 386 182 185 3 678.92 8.47 387 182 186 4 603.32 18.02 388 182 187 5 591.72 21.94 389 183 187 4 582.65 26.30 390 193 218 25 62.68 0.84 391 193 220 27 56.47 0.31 392 193 242 49 56.33 0.34 393 194 242 48 56.35 0.35 394 194 247 53 44.60 2.14 395 195 199 4 610.23 17.32 396 195 201 6 514.54 8.58 397 195 215 20 69.21 1.34 398 195 218 23 67.18 0.86 399 195 225 30 64.92 0.48 400 195 242 47 56.84 0.15 401 195 245 50 56.24 0.35 402 195 247 52 48.42 0.24 403 196 199 3 700.34 0.90 404 196 215 19 70.02 0.95 405 196 218 22 67.78 0.82 406 197 215 18 70.02 0.94 407 197 216 19 70.11 0.90 408 197 218 21 68.38 0.90 409 198 214 16 72.14 0.06 410 198 215 17 70.77 0.62 411 199 214 15 72.61 0.06 412 199 215 16 70.92 0.55 413 199 247 48 57.18 0.12 414 200 213 13 73.42 0.03 415 200 214 14 72.65 0.07 416 200 247 47 57.97 0.27 417 200 248 48 57.12 0.14 418 201 212 11 78.31 0.26 419 201 213 12 74.87 0.74 420 201 215 14 73.42 0.03 421 201 227 26 73.42 0.03 422 201 245 44 66.92 0.63 423 201 246 45 65.41 1.18 424 201 247 46 57.97 0.27 425 201 248 47 57.16 0.12 426 202 210 8 85.61 0.61 427 202 211 9 82.09 1.00 428 202 212 10 78.30 0.27 429 202 245 43 67.61 0.33 430 202 246 44 66.62 0.59 431 202 248 46 60.51 0.05 432 203 208 5 172.31 3.05 433 203 209 6 129.22 18.52 434 203 210 7 89.52 1.33 435 203 211 8 85.59 0.61 436 203 229 26 82.92 0.64 437 203 240 37 71.40 0.33 438 203 244 41 69.18 0.15 439 203 245 42 67.76 0.40 440 204 209 5 163.08 1.61 441 204 243 39 69.56 0.33 442 204 244 40 69.20 0.15 443 204 245 41 69.18 0.15 444 204 246 42 69.14 0.17 445 205 209 4 178.28 0.07 446 205 244 39 69.53 0.33 447 206 209 3 675.73 4.61 448 208 211 3 670.89 4.40 449 208 229 21 127.87 0.34 450 208 231 23 143.68 0.25 451 208 238 30 83.70 1.47 452 211 229 18 150.13 1.58 453 211 231 20 150.19 1.61 454 212 229 17 150.18 1.60 455 212 248 36 59.51 0.47 456 213 227 14 150.49 1.38 457 213 228 15 150.52 1.42 458 213 229 16 150.19 1.61 459 214 227 13 150.60 1.40 460 214 228 14 150.62 1.41 461 215 218 3 743.75 3.15 462 215 225 10 150.61 1.41 463 215 226 11 150.63 1.41 464 215 227 12 150.63 1.41 465 216 226 10 150.72 1.39 466 216 227 11 150.74 1.39 467 216 228 12 150.75 1.39 468 217 225 8 150.78 1.39 469 217 226 9 150.74 1.39 470 218 225 7 151.18 1.20 471 218 242 24 150.76 1.37 472 219 222 3 679.27 4.79 473 219 223 4 565.74 34.27 474 219 224 5 177.21 0.87 475 219 225 6 151.36 1.28 476 219 226 7 164.69 5.38 477 219 239 20 151.31 1.26 478 220 223 3 605.96 16.06 479 220 242 22 150.95 1.39 480 223 241 18 151.09 1.31 481 223 242 19 150.91 1.41 482 224 240 16 151.25 1.26 483 224 241 17 150.96 1.38 484 224 242 18 150.96 1.38 485 225 238 13 156.50 0.35 486 225 239 14 155.47 0.49 487 225 240 15 151.23 1.26 488 225 242 17 150.96 1.38 489 225 245 20 131.72 1.45 490 226 237 11 157.89 0.76 491 226 238 12 156.49 0.33 492 226 239 13 155.69 0.60 493 227 236 9 164.82 2.07 494 227 237 10 158.72 0.47 495 227 238 11 156.51 0.33 496 227 240 13 156.46 0.34 497 228 235 7 174.94 2.99 498 228 236 8 164.83 2.07 499 228 237 9 164.78 2.08 500 229 234 5 419.05 71.61 501 229 235 6 176.19 2.85 502 229 236 7 174.96 2.98 503 229 238 9 164.80 2.07 504 229 240 11 164.80 2.07 505 230 233 3 612.47 12.72 506 230 234 4 347.02 75.42 507 230 235 5 178.12 1.89 508 231 234 3 662.51 10.06 509 231 236 5 178.87 1.64 510 240 244 4 641.88 1.76 511 240 245 5 600.66 18.84 512 241 244 3 658.21 6.41 513 241 245 4 661.35 7.04 514 242 245 3 694.21 4.00