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 8 11 3 681.82 2.44 2 8 12 4 662.25 1.80 3 8 115 107 311.47 0.03 4 9 12 3 678.41 0.73 5 9 13 4 662.24 1.80 6 10 13 3 670.58 1.09 7 10 14 4 662.25 1.80 8 10 109 99 316.38 0.95 9 10 111 101 315.03 1.60 10 10 112 102 312.88 0.53 11 10 115 105 312.86 0.53 12 11 14 3 682.00 4.62 13 11 15 4 670.48 2.10 14 11 41 30 312.88 0.53 15 11 112 101 312.89 0.53 16 11 115 104 312.88 0.54 17 12 15 3 672.64 1.04 18 12 16 4 670.51 2.10 19 13 16 3 683.44 1.17 20 13 17 4 675.12 2.29 21 13 105 92 335.25 0.30 22 13 108 95 335.24 0.31 23 13 109 96 335.22 0.30 24 13 112 99 334.27 0.52 25 14 17 3 691.15 1.77 26 14 18 4 676.76 1.01 27 14 41 27 334.99 0.24 28 14 69 55 334.79 0.34 29 14 97 83 335.81 0.56 30 14 102 88 335.75 0.55 31 14 105 91 335.25 0.30 32 14 112 98 334.35 0.48 33 15 18 3 676.76 1.01 34 15 41 26 335.05 0.26 35 15 43 28 335.00 0.24 36 15 95 80 335.43 0.42 37 17 97 80 336.17 0.39 38 17 105 88 335.73 0.21 39 18 95 77 336.20 0.40 40 18 96 78 336.17 0.39 41 18 97 79 336.19 0.38 42 19 95 76 336.59 0.49 43 19 96 77 336.39 0.41 44 20 43 23 338.03 0.89 45 20 93 73 338.04 0.89 46 20 94 74 337.71 0.84 47 20 95 75 336.82 0.60 48 21 93 72 338.05 0.89 49 21 94 73 338.00 0.87 50 21 96 75 337.76 0.74 51 22 92 70 343.12 3.40 52 22 93 71 338.08 0.90 53 23 27 4 574.12 7.51 54 23 29 6 504.61 5.49 55 23 88 65 452.42 0.78 56 23 91 68 455.76 0.89 57 23 92 69 346.10 1.91 58 23 94 71 345.24 2.35 59 24 27 3 674.07 4.42 60 24 88 64 468.18 2.60 61 24 91 67 456.22 0.87 62 25 88 63 469.06 2.89 63 25 89 64 469.94 3.33 64 25 90 65 460.37 1.46 65 25 91 66 460.03 1.43 66 26 87 61 473.77 1.66 67 26 88 62 471.09 2.89 68 27 87 60 477.11 1.05 69 27 88 61 475.50 0.81 70 28 31 3 725.72 3.31 71 28 86 58 477.48 1.02 72 28 87 59 477.35 1.07 73 29 47 18 477.50 1.03 74 29 70 41 475.50 2.00 75 29 86 57 477.59 1.06 76 29 87 58 477.50 1.03 77 29 88 59 477.49 1.03 78 29 94 65 473.61 1.65 79 30 34 4 680.95 0.04 80 30 40 10 474.97 2.26 81 30 70 40 477.19 1.15 82 30 71 41 473.91 2.79 83 30 82 52 479.13 0.96 84 30 84 54 478.54 1.12 85 30 85 55 478.12 0.99 86 30 86 56 477.60 1.06 87 31 34 3 684.49 1.73 88 31 82 51 479.27 0.91 89 31 85 54 478.44 1.11 90 32 51 19 479.09 0.95 91 32 82 50 479.31 0.93 92 32 83 51 479.16 0.95 93 32 84 52 478.68 1.10 94 32 85 53 478.62 1.08 95 33 81 48 480.67 0.43 96 33 82 49 479.37 0.96 97 34 81 47 481.63 0.15 98 34 82 48 481.47 0.12 99 35 80 45 483.55 0.96 100 35 81 46 483.38 1.02 101 36 74 38 485.81 0.26 102 36 80 44 485.02 0.69 103 36 81 45 484.54 0.45 104 36 82 46 483.44 1.00 105 36 99 63 476.51 0.82 106 37 82 45 485.22 0.59 107 37 98 61 476.57 0.82 108 37 99 62 476.51 0.82 109 38 71 33 487.66 0.39 110 38 82 44 485.53 0.60 111 38 96 58 477.02 0.82 112 38 97 59 476.81 0.81 113 38 98 60 476.58 0.83 114 38 99 61 476.53 0.82 115 39 69 30 487.90 0.31 116 39 70 31 487.70 0.38 117 39 71 32 487.67 0.39 118 39 72 33 487.42 0.30 119 39 96 57 477.03 0.82 120 39 97 58 476.90 0.85 121 39 99 60 476.55 0.84 122 39 102 63 471.08 1.68 123 40 69 29 487.94 0.29 124 40 70 30 487.84 0.32 125 40 71 31 487.70 0.38 126 40 82 42 486.74 0.24 127 40 94 54 478.06 0.93 128 40 95 55 477.69 0.78 129 40 96 56 477.03 0.82 130 41 67 26 488.91 0.43 131 41 68 27 488.38 0.50 132 41 69 28 487.94 0.29 133 41 94 53 478.06 0.93 134 41 95 54 477.97 0.91 135 42 45 3 727.22 5.90 136 42 47 5 645.18 0.25 137 42 64 22 489.65 0.58 138 42 65 23 489.55 0.62 139 42 66 24 489.26 0.49 140 42 67 25 489.08 0.52 141 42 68 26 488.68 0.39 142 42 70 28 488.06 0.35 143 42 93 51 478.86 1.05 144 42 94 52 478.12 0.96 145 43 66 23 489.30 0.51 146 43 93 50 478.92 1.04 147 43 95 52 478.80 1.02 148 44 66 22 489.68 0.57 149 44 92 48 480.14 0.78 150 44 93 49 480.10 0.76 151 45 65 20 489.84 0.50 152 45 66 21 489.73 0.54 153 45 90 45 484.91 0.70 154 45 91 46 484.49 0.49 155 45 92 47 480.14 0.78 156 46 64 18 490.04 0.53 157 46 65 19 489.84 0.50 158 46 88 42 485.30 0.58 159 46 89 43 485.26 0.57 160 46 90 44 485.23 0.57 161 46 92 46 483.82 0.82 162 47 63 16 490.34 0.48 163 47 64 17 490.13 0.58 164 47 70 23 489.56 0.62 165 47 86 39 486.17 0.38 166 47 87 40 485.93 0.29 167 47 88 41 485.30 0.58 168 47 89 42 485.26 0.57 169 47 92 45 484.02 0.71 170 48 62 14 490.42 0.48 171 48 63 15 490.35 0.48 172 48 86 38 486.19 0.40 173 48 87 39 486.12 0.38 174 49 60 11 490.75 0.55 175 49 61 12 490.66 0.58 176 49 62 13 490.62 0.58 177 49 64 15 490.41 0.49 178 49 84 35 487.10 0.21 179 49 85 36 486.80 0.24 180 49 86 37 486.20 0.40 181 50 58 8 491.31 0.72 182 50 59 9 491.16 0.68 183 50 60 10 490.79 0.56 184 50 84 34 487.10 0.21 185 50 85 35 486.91 0.24 186 50 87 37 486.78 0.23 187 50 174 124 68.41 0.79 188 51 58 7 491.34 0.73 189 51 59 8 491.25 0.70 190 51 61 10 491.13 0.64 191 51 83 32 487.44 0.28 192 51 84 33 487.12 0.21 193 51 85 34 487.12 0.21 194 52 57 5 492.19 0.36 195 52 58 6 491.35 0.73 196 52 85 33 487.44 0.29 197 53 56 3 680.95 9.35 198 53 57 4 513.79 3.06 199 58 87 29 487.26 0.20 200 58 174 116 68.41 0.79 201 59 174 115 68.41 0.79 202 59 175 116 68.41 0.79 203 59 176 117 68.47 0.78 204 59 177 118 68.48 0.77 205 60 63 3 773.73 2.07 206 60 174 114 68.33 0.75 207 60 175 115 68.33 0.75 208 61 84 23 487.14 0.22 209 61 130 69 297.53 1.91 210 63 89 26 485.31 0.57 211 63 153 90 34.46 1.34 212 63 175 112 68.11 0.81 213 64 68 4 620.57 12.59 214 64 70 6 498.10 2.03 215 64 123 59 339.01 1.04 216 65 68 3 686.72 0.50 217 65 153 88 34.38 1.31 218 65 154 89 32.52 2.25 219 67 119 52 339.21 0.98 220 68 119 51 339.21 0.98 221 68 123 55 339.04 1.05 222 69 112 43 339.53 0.96 223 69 116 47 339.25 0.99 224 69 119 50 339.21 0.98 225 69 123 54 338.99 1.09 226 70 86 16 485.26 0.57 227 70 94 24 478.06 0.93 228 71 82 11 485.66 0.55 229 71 99 28 476.64 0.88 230 72 75 3 683.59 1.51 231 72 116 44 339.35 0.99 232 72 120 48 339.23 0.99 233 72 123 51 339.07 1.05 234 73 83 10 485.60 0.57 235 73 120 47 339.26 1.00 236 74 77 3 691.29 1.50 237 74 80 6 486.69 0.19 238 74 99 25 476.54 0.83 239 75 99 24 476.51 0.82 240 75 102 27 476.34 0.77 241 75 103 28 471.81 0.18 242 75 106 31 464.42 1.11 243 75 116 41 339.68 0.92 244 76 113 37 339.89 0.90 245 76 120 44 339.57 0.96 246 77 80 3 722.51 0.27 247 78 103 25 476.11 0.96 248 82 99 17 476.52 0.82 249 88 92 4 596.01 4.55 250 97 101 4 671.35 4.86 251 97 102 5 658.25 1.68 252 97 105 8 639.27 6.54 253 98 101 3 677.37 1.85 254 98 102 4 671.86 5.07 255 99 102 3 690.27 4.14 256 99 103 4 671.89 5.05 257 100 103 3 696.31 1.12 258 100 104 4 673.50 4.25 259 101 104 3 673.50 4.25 260 101 105 4 673.48 4.25 261 102 105 3 681.18 1.84 262 102 106 4 666.90 0.97 263 102 112 10 503.62 2.04 264 102 116 14 339.67 0.92 265 103 106 3 677.49 0.61 266 103 107 4 673.66 2.52 267 104 107 3 689.56 1.52 268 104 108 4 673.66 2.52 269 105 108 3 677.72 4.40 270 105 109 4 668.19 0.18 271 106 109 3 689.19 1.33 272 106 110 4 649.61 2.95 273 106 112 6 607.15 8.43 274 106 113 7 521.28 3.66 275 109 112 3 721.84 2.73 276 110 113 3 677.00 2.60 277 110 114 4 659.12 0.97 278 111 114 3 673.49 6.20 279 111 115 4 659.66 0.71 280 112 115 3 678.88 0.03 281 112 116 4 667.07 3.04 282 113 116 3 676.05 1.45 283 113 117 4 668.23 2.46 284 114 117 3 672.74 2.90 285 114 118 4 670.30 3.50 286 115 118 3 686.07 0.81 287 115 119 4 671.70 2.81 288 116 119 3 692.38 3.97 289 116 120 4 680.41 3.62 290 117 120 3 672.24 2.53 291 117 121 4 659.57 1.84 292 118 121 3 696.14 2.08 293 118 122 4 660.96 2.55 294 119 122 3 680.14 5.92 295 119 123 4 661.79 2.97 296 120 123 3 680.60 5.69 297 120 124 4 660.82 3.74 298 121 124 3 676.35 2.18 299 121 125 4 670.89 4.91 300 122 125 3 675.12 2.79 301 122 126 4 669.10 5.80 302 123 126 3 675.13 2.79 303 123 127 4 677.65 1.54 304 124 127 3 677.66 1.54 305 124 128 4 677.65 1.54 306 125 128 3 677.68 1.54 307 125 129 4 677.66 1.53 308 126 129 3 684.22 4.80 309 126 130 4 669.78 2.41 310 127 130 3 684.22 4.80 311 127 131 4 669.78 2.41 312 128 131 3 684.17 4.83 313 128 132 4 663.62 4.67 314 129 132 3 679.12 2.50 315 129 133 4 663.10 4.42 316 130 133 3 672.56 0.21 317 130 134 4 662.97 4.42 318 131 134 3 682.77 1.76 319 131 135 4 662.92 4.40 320 132 135 3 674.45 0.73 321 132 136 4 654.37 1.76 322 133 136 3 684.77 7.50 323 133 137 4 652.62 0.87 324 133 142 9 195.09 3.41 325 133 145 12 187.50 0.39 326 134 142 8 500.09 0.45 327 134 176 42 76.00 0.91 328 137 141 4 640.24 3.20 329 137 142 5 631.77 1.04 330 137 145 8 610.35 2.60 331 138 141 3 672.62 2.68 332 138 142 4 662.75 0.88 333 139 142 3 672.39 2.79 334 139 143 4 662.75 0.89 335 139 176 37 103.37 4.23 336 139 178 39 103.37 4.22 337 139 186 47 101.78 4.71 338 140 143 3 671.09 0.66 339 140 144 4 662.76 0.89 340 140 186 46 102.00 4.64 341 140 190 50 101.71 4.74 342 141 144 3 664.91 1.97 343 141 145 4 662.86 0.94 344 142 145 3 671.36 5.21 345 142 146 4 669.46 1.42 346 142 176 34 104.00 4.11 347 143 146 3 677.51 2.13 348 143 147 4 669.49 1.41 349 143 172 29 103.69 4.06 350 143 176 33 104.04 4.09 351 143 183 40 103.46 4.18 352 143 186 43 103.44 4.18 353 143 187 44 103.34 4.13 354 143 190 47 102.43 4.59 355 144 147 3 683.37 4.65 356 144 148 4 675.35 1.05 357 145 148 3 695.11 0.01 358 145 149 4 673.26 3.29 359 146 149 3 682.52 1.34 360 146 150 4 669.48 1.42 361 146 175 29 104.10 4.10 362 146 176 30 104.10 4.10 363 147 150 3 696.21 0.06 364 147 172 25 104.08 4.11 365 147 187 40 103.62 4.21 366 147 190 43 103.52 4.16 367 147 196 49 103.09 4.09 368 147 203 56 101.58 4.69 369 147 205 58 92.84 4.94 370 148 151 3 692.49 1.80 371 148 152 4 678.15 3.54 372 148 205 57 95.69 4.78 373 149 152 3 682.85 1.20 374 150 153 3 690.52 2.62 375 150 156 6 193.09 3.59 376 150 165 15 103.89 4.12 377 150 167 17 104.07 4.10 378 150 175 25 105.61 4.05 379 151 156 5 198.94 0.66 380 151 163 12 103.67 4.01 381 151 165 14 103.92 4.12 382 153 156 3 656.28 0.35 383 155 166 11 134.32 0.84 384 157 163 6 179.94 3.45 385 157 164 7 167.18 0.39 386 158 163 5 179.94 3.45 387 158 164 6 179.94 3.45 388 159 162 3 675.38 2.78 389 159 163 4 192.37 0.06 390 159 164 5 185.94 0.47 391 159 204 45 106.62 3.23 392 161 204 43 106.67 3.25 393 161 205 44 106.64 3.25 394 161 206 45 106.36 3.27 395 162 205 43 106.61 3.27 396 163 205 42 106.62 3.28 397 164 202 38 111.48 1.15 398 164 203 39 111.37 1.19 399 165 202 37 111.48 1.15 400 165 203 38 111.48 1.15 401 165 205 40 111.39 1.15 402 166 201 35 120.57 0.43 403 167 171 4 660.48 3.52 404 167 172 5 651.02 8.26 405 167 201 34 120.76 0.47 406 167 203 36 120.77 0.49 407 168 171 3 673.13 0.83 408 168 172 4 657.54 5.00 409 168 201 33 122.90 0.66 410 169 172 3 673.13 0.83 411 169 173 4 671.23 0.07 412 169 180 11 129.49 1.53 413 169 183 14 129.02 1.37 414 169 184 15 129.04 1.36 415 169 187 18 128.95 1.40 416 169 201 32 127.59 1.06 417 170 173 3 673.13 0.83 418 170 174 4 671.23 0.07 419 170 180 10 134.09 3.82 420 171 174 3 671.86 0.18 421 171 175 4 671.22 0.07 422 172 175 3 673.63 1.14 423 172 176 4 669.10 1.12 424 172 183 11 140.97 4.25 425 172 187 15 129.27 1.46 426 172 203 31 128.84 1.35 427 173 176 3 671.09 0.12 428 173 177 4 633.19 0.18 429 173 178 5 202.94 3.05 430 173 183 10 141.08 4.21 431 178 182 4 668.74 0.82 432 178 183 5 655.22 3.79 433 179 182 3 678.84 3.82 434 179 183 4 666.74 0.21 435 180 183 3 668.76 0.81 436 180 184 4 666.74 0.20 437 181 184 3 670.47 0.18 438 181 185 4 666.75 0.20 439 182 185 3 668.27 0.92 440 182 186 4 666.74 0.20 441 183 186 3 678.14 3.93 442 183 187 4 653.47 6.78 443 184 187 3 679.94 3.02 444 184 188 4 670.76 1.56 445 185 188 3 679.46 0.72 446 185 189 4 675.06 0.59 447 186 189 3 676.29 1.21 448 186 190 4 675.06 0.59 449 187 190 3 679.48 1.61 450 187 191 4 671.15 2.54 451 187 196 9 349.97 78.28 452 187 203 16 161.79 0.54 453 188 191 3 682.19 4.17 454 188 192 4 671.15 2.54 455 189 192 3 669.44 1.69 456 189 193 4 667.00 0.47 457 190 193 3 672.45 3.20 458 190 194 4 663.82 1.12 459 190 195 5 583.66 16.05 460 190 196 6 522.55 4.66 461 191 194 3 648.81 8.26 462 191 196 5 372.49 67.02 463 191 198 7 207.05 6.82 464 194 206 12 161.96 0.66 465 195 206 11 161.96 0.66 466 196 203 7 169.65 2.89 467 196 204 8 169.42 2.90 468 196 205 9 162.44 0.53 469 196 206 10 162.10 0.60 470 197 203 6 169.65 2.89 471 197 204 7 169.52 2.92 472 197 206 9 169.38 2.92 473 198 202 4 529.28 2.07 474 198 203 5 169.66 2.89 475 199 202 3 653.25 3.46