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 1 101 100 372.90 0.00 2 2 24 22 517.26 2.05 3 2 25 23 517.14 2.02 4 2 26 24 516.98 2.00 5 2 61 59 513.57 1.80 6 2 97 95 373.43 0.01 7 2 98 96 373.30 0.01 8 2 99 97 372.94 0.01 9 2 100 98 372.96 0.00 10 2 101 99 372.91 0.00 11 3 24 21 517.26 2.05 12 3 25 22 517.23 2.06 13 3 26 23 517.15 2.02 14 3 27 24 517.13 2.02 15 3 30 27 517.14 2.02 16 3 99 96 373.22 0.01 17 3 101 98 372.91 0.00 18 3 103 100 372.90 0.00 19 3 140 137 237.06 0.12 20 4 23 19 517.32 2.05 21 4 24 20 517.26 2.06 22 4 99 95 373.35 0.02 23 4 101 97 373.11 0.04 24 4 102 98 372.90 0.00 25 4 103 99 372.90 0.00 26 4 140 136 237.11 0.14 27 5 22 17 517.63 2.07 28 5 23 18 517.54 2.08 29 5 103 98 372.91 0.00 30 5 140 135 237.12 0.14 31 5 141 136 237.00 0.12 32 5 144 139 236.69 0.21 33 6 20 14 519.92 2.06 34 6 21 15 519.65 2.15 35 6 22 16 517.69 2.10 36 6 88 82 374.87 0.05 37 6 91 85 374.81 0.09 38 6 92 86 374.51 0.06 39 6 102 96 373.30 0.00 40 6 103 97 373.05 0.01 41 6 104 98 372.91 0.00 42 6 105 99 372.90 0.00 43 6 141 135 237.12 0.14 44 6 144 138 236.71 0.21 45 7 20 13 519.94 2.05 46 7 21 14 519.81 2.08 47 7 88 81 375.25 0.05 48 7 105 98 372.90 0.01 49 7 141 134 237.31 0.19 50 7 144 137 236.77 0.21 51 7 145 138 236.69 0.21 52 8 11 3 751.69 6.53 53 8 18 10 520.59 2.19 54 8 19 11 520.29 2.12 55 8 20 12 519.94 2.05 56 8 84 76 375.26 0.04 57 8 88 80 375.25 0.05 58 8 148 140 233.22 1.10 59 9 18 9 520.61 2.19 60 9 19 10 520.40 2.10 61 9 148 139 235.98 0.07 62 9 149 140 233.22 1.10 63 9 152 143 216.40 0.79 64 10 13 3 692.00 2.36 65 10 17 7 520.63 2.19 66 10 18 8 520.61 2.19 67 10 152 142 225.61 1.20 68 10 195 185 61.54 0.83 69 11 18 7 520.62 2.19 70 11 84 73 375.61 0.04 71 11 107 96 373.14 0.04 72 11 195 184 61.54 0.83 73 12 170 158 125.23 0.14 74 12 171 159 125.23 0.14 75 13 152 139 236.01 0.05 76 13 169 156 125.23 0.14 77 13 170 157 125.23 0.14 78 13 171 158 125.24 0.14 79 13 195 182 61.70 0.90 80 14 169 155 125.31 0.15 81 14 171 157 125.27 0.15 82 14 176 162 124.95 0.31 83 14 180 166 113.72 0.60 84 14 194 180 61.73 0.89 85 14 195 181 61.66 0.89 86 14 198 184 52.40 0.66 87 14 201 187 40.16 0.72 88 15 152 137 235.97 0.09 89 15 166 151 125.67 0.23 90 15 169 154 125.28 0.16 91 15 176 161 124.91 0.34 92 15 180 165 113.62 0.65 93 15 193 178 61.77 0.90 94 15 194 179 61.66 0.88 95 16 70 54 512.97 1.96 96 16 152 136 233.14 1.08 97 16 159 143 182.71 1.09 98 16 193 177 61.73 0.88 99 16 195 179 61.60 0.85 100 17 67 50 513.52 1.78 101 17 68 51 513.47 1.78 102 17 69 52 513.01 1.97 103 17 70 53 512.97 1.96 104 17 152 135 230.26 0.49 105 17 155 138 211.48 0.61 106 17 195 178 61.54 0.83 107 18 67 49 513.50 1.78 108 18 68 50 513.06 1.96 109 18 73 55 429.62 4.65 110 18 84 66 375.63 0.05 111 18 195 177 61.52 0.83 112 19 65 46 513.70 1.79 113 19 66 47 513.50 1.77 114 19 67 48 513.07 1.97 115 19 148 129 235.00 0.23 116 19 151 132 225.46 0.53 117 19 152 133 213.53 0.65 118 20 65 45 513.53 1.77 119 20 66 46 513.46 1.78 120 20 68 48 513.04 1.96 121 20 87 67 375.26 0.04 122 20 88 68 375.25 0.05 123 20 91 71 374.94 0.06 124 21 64 43 513.58 1.77 125 21 65 44 513.10 1.94 126 21 144 123 236.73 0.22 127 21 147 126 235.06 0.20 128 21 148 127 232.80 0.96 129 22 63 41 513.61 1.78 130 22 64 42 513.49 1.75 131 22 91 69 374.50 0.07 132 22 92 70 374.45 0.08 133 22 95 73 373.82 0.08 134 23 60 37 513.73 1.78 135 23 62 39 513.66 1.79 136 23 63 40 513.42 1.78 137 23 140 117 237.24 0.17 138 23 144 121 236.66 0.19 139 23 147 124 233.29 1.08 140 24 60 36 513.71 1.78 141 24 61 37 513.69 1.78 142 24 62 38 513.49 1.75 143 24 95 71 373.55 0.01 144 24 97 73 373.47 0.03 145 24 99 75 373.34 0.01 146 25 29 4 644.72 5.25 147 25 30 5 613.50 10.46 148 25 33 8 544.82 3.90 149 25 59 34 513.75 1.79 150 25 60 35 513.67 1.79 151 25 61 36 513.61 1.78 152 25 140 115 237.09 0.14 153 26 29 3 669.31 0.35 154 26 30 4 673.74 2.56 155 26 61 35 513.58 1.79 156 27 30 3 698.24 0.63 157 28 31 3 715.14 0.54 158 29 32 3 696.34 0.32 159 29 33 4 682.39 2.32 160 29 59 30 513.73 1.77 161 30 33 3 691.13 2.05 162 30 34 4 679.38 3.83 163 31 34 3 680.64 0.03 164 31 35 4 675.27 1.79 165 32 35 3 673.94 2.73 166 32 36 4 673.88 2.71 167 32 59 27 513.76 1.78 168 33 36 3 673.95 2.68 169 33 38 5 618.80 1.49 170 33 139 106 237.31 0.18 171 33 140 107 237.30 0.19 172 33 143 110 236.81 0.23 173 34 37 3 674.73 2.29 174 36 52 16 514.12 1.84 175 36 55 19 514.03 1.80 176 36 56 20 514.00 1.82 177 36 59 23 514.01 1.80 178 37 40 3 687.25 5.25 179 38 41 3 688.08 3.62 180 38 52 14 514.19 1.81 181 38 56 18 514.11 1.84 182 38 139 101 237.41 0.16 183 38 142 104 237.38 0.16 184 38 143 105 237.22 0.20 185 39 136 97 237.41 0.14 186 39 142 103 237.40 0.16 187 40 44 4 693.28 6.58 188 41 44 3 677.47 0.93 189 41 49 8 530.39 0.20 190 41 52 11 523.36 2.53 191 41 146 105 236.86 0.21 192 42 49 7 568.50 7.70 193 42 135 93 274.06 2.27 194 42 136 94 272.50 2.38 195 44 48 4 636.39 7.26 196 44 49 5 621.06 0.39 197 44 52 8 621.07 0.39 198 45 48 3 672.18 1.76 199 45 49 4 659.84 4.41 200 46 49 3 679.38 1.86 201 46 50 4 669.99 0.67 202 47 50 3 673.61 1.02 203 47 51 4 670.50 2.01 204 48 51 3 670.50 2.01 205 48 52 4 668.01 3.27 206 49 52 3 670.97 1.80 207 49 53 4 672.85 2.67 208 49 146 97 236.81 0.24 209 49 149 100 236.69 0.21 210 49 150 101 234.62 0.40 211 50 53 3 672.85 2.67 212 50 54 4 672.85 2.67 213 50 150 100 234.22 0.59 214 50 154 104 212.17 0.27 215 51 54 3 691.53 0.99 216 51 55 4 674.03 2.11 217 52 55 3 674.08 2.12 218 52 56 4 674.06 2.13 219 52 146 94 236.77 0.24 220 53 56 3 674.08 2.12 221 53 57 4 674.07 2.13 222 53 65 12 513.83 1.81 223 53 146 93 236.73 0.22 224 53 147 94 236.66 0.24 225 53 150 97 231.57 1.72 226 53 154 101 212.18 0.27 227 54 57 3 678.12 0.10 228 54 58 4 674.21 2.06 229 55 58 3 682.43 2.04 230 55 59 4 681.36 1.73 231 56 59 3 694.87 0.33 232 56 60 4 671.07 0.49 233 56 143 87 236.81 0.23 234 56 146 90 236.69 0.21 235 56 147 91 236.53 0.22 236 57 60 3 690.81 8.10 237 57 63 6 545.67 1.04 238 57 147 90 236.22 0.30 239 60 63 3 727.46 2.79 240 60 147 87 236.14 0.34 241 61 97 36 373.38 0.01 242 62 95 33 373.52 0.01 243 62 96 34 373.49 0.01 244 62 97 35 373.39 0.01 245 63 95 32 373.55 0.01 246 63 147 84 233.28 1.08 247 64 91 27 374.47 0.09 248 64 94 30 373.84 0.14 249 64 95 31 373.55 0.01 250 65 147 82 234.94 0.27 251 65 151 86 216.34 0.76 252 66 87 21 375.25 0.04 253 66 90 24 375.10 0.01 254 66 91 25 374.93 0.06 255 67 151 84 230.25 0.49 256 67 155 88 196.84 0.29 257 68 73 5 613.41 4.42 258 68 83 15 375.84 0.10 259 68 87 19 375.31 0.06 260 69 72 3 680.69 5.40 261 69 73 4 652.35 0.92 262 70 73 3 672.32 0.07 263 70 74 4 652.35 0.92 264 70 192 122 61.80 0.91 265 70 193 123 61.73 0.89 266 70 194 124 61.65 0.85 267 70 195 125 61.43 0.84 268 71 75 4 664.87 2.21 269 72 75 3 677.74 0.97 270 72 76 4 677.52 1.42 271 72 83 11 376.13 0.10 272 73 76 3 693.64 6.98 273 73 80 7 376.13 0.14 274 73 83 10 376.00 0.09 275 73 195 122 61.45 0.83 276 74 195 121 61.45 0.83 277 74 196 122 61.43 0.84 278 76 83 7 376.18 0.11 279 79 82 3 684.71 2.43 280 79 83 4 670.04 4.84 281 80 83 3 676.24 1.74 282 80 84 4 670.04 4.84 283 81 84 3 678.27 0.72 284 81 85 4 665.17 2.14 285 82 85 3 677.81 0.80 286 82 86 4 665.17 2.14 287 82 121 39 281.53 0.38 288 83 86 3 677.82 0.80 289 83 87 4 665.16 2.13 290 84 87 3 677.79 0.82 291 84 88 4 664.81 2.23 292 84 107 23 373.04 0.10 293 85 88 3 670.00 0.36 294 85 89 4 662.43 0.89 295 85 114 29 281.59 0.35 296 85 117 32 281.39 0.43 297 85 118 33 281.38 0.43 298 85 121 36 281.12 0.42 299 86 89 3 680.85 5.07 300 86 90 4 662.52 0.84 301 86 121 35 281.07 0.43 302 87 90 3 666.51 2.83 303 87 91 4 665.91 2.54 304 88 91 3 690.48 5.25 305 88 92 4 666.19 2.40 306 88 114 26 281.56 0.37 307 88 118 30 281.35 0.42 308 89 92 3 679.99 0.01 309 89 93 4 666.18 2.40 310 89 118 29 281.27 0.45 311 89 121 32 280.89 0.51 312 90 93 3 666.18 2.40 313 90 94 4 666.18 2.40 314 91 94 3 675.11 1.53 315 91 95 4 670.83 0.07 316 92 95 3 692.33 0.83 317 92 98 6 619.02 2.60 318 92 102 10 373.40 0.01 319 92 118 26 281.23 0.47 320 92 122 30 280.13 0.55 321 92 124 32 280.08 0.55 322 93 98 5 661.13 1.01 323 93 121 28 280.87 0.52 324 93 122 29 280.13 0.56 325 93 123 30 280.08 0.55 326 93 124 31 280.05 0.54 327 94 98 4 697.62 1.45 328 95 98 3 692.22 2.06 329 95 99 4 693.98 0.01 330 98 123 25 279.97 0.55 331 98 124 26 279.30 0.71 332 99 102 3 721.42 1.28 333 99 124 25 279.28 0.71 334 99 126 27 279.01 0.75 335 100 126 26 279.00 0.75 336 100 127 27 279.00 0.75 337 101 127 26 278.99 0.74 338 101 129 28 278.87 0.80 339 102 122 20 280.10 0.55 340 102 124 22 279.96 0.58 341 102 126 24 279.19 0.70 342 102 127 25 279.06 0.75 343 102 128 26 278.97 0.74 344 102 129 27 278.87 0.80 345 103 129 26 278.86 0.81 346 103 138 35 237.31 0.18 347 103 140 37 237.29 0.20 348 103 141 38 237.05 0.12 349 104 114 10 281.38 0.43 350 104 128 24 279.20 0.70 351 104 129 25 279.04 0.76 352 104 130 26 278.85 0.81 353 104 131 27 278.79 0.78 354 104 141 37 237.10 0.13 355 105 131 26 278.83 0.81 356 105 133 28 273.77 1.57 357 105 134 29 243.66 3.26 358 105 141 36 237.31 0.18 359 106 111 5 281.40 0.45 360 106 114 8 281.40 0.44 361 106 130 24 279.05 0.76 362 106 131 25 278.91 0.80 363 106 132 26 278.72 0.75 364 107 114 7 426.27 72.59 365 107 132 25 279.04 0.75 366 108 132 24 279.04 0.75 367 109 132 23 279.17 0.69 368 110 113 3 689.77 0.30 369 110 114 4 677.66 2.53 370 111 114 3 677.67 2.53 371 111 115 4 658.38 0.65 372 111 130 19 279.49 0.71 373 111 131 20 279.38 0.69 374 111 132 21 279.35 0.68 375 112 115 3 681.16 0.79 376 112 116 4 660.90 1.79 377 113 116 3 669.10 5.25 378 113 117 4 658.50 0.59 379 114 117 3 674.84 2.37 380 114 118 4 664.14 2.24 381 114 130 16 279.36 0.68 382 115 119 4 663.98 2.38 383 115 128 13 279.88 0.65 384 115 130 15 279.36 0.68 385 116 119 3 674.09 2.68 386 116 120 4 667.75 0.49 387 117 120 3 704.31 1.16 388 117 121 4 668.36 0.80 389 118 121 3 681.86 5.96 390 118 122 4 668.35 0.80 391 118 128 10 279.88 0.58 392 119 122 3 674.33 2.19 393 122 128 6 359.55 39.30 394 129 138 9 237.32 0.18 395 131 134 3 668.91 1.45 396 131 138 7 237.41 0.17 397 134 137 3 676.88 1.90 398 134 138 4 646.93 4.20 399 134 141 7 237.46 0.19 400 136 142 6 237.47 0.18 401 138 141 3 667.09 0.48 402 138 142 4 667.18 0.53 403 139 142 3 667.18 0.53 404 139 143 4 672.86 2.31 405 140 143 3 689.85 6.19 406 140 144 4 672.88 2.31 407 141 144 3 672.88 2.31 408 141 145 4 672.87 2.32 409 142 145 3 672.86 2.33 410 142 146 4 672.86 2.33 411 143 146 3 674.74 3.13 412 143 147 4 674.59 3.21 413 144 147 3 690.64 4.82 414 144 148 4 674.40 3.30 415 145 148 3 682.66 0.83 416 145 149 4 667.09 0.29 417 146 149 3 669.28 0.82 418 146 150 4 659.04 1.03 419 147 150 3 677.14 4.74 420 147 151 4 655.98 0.34 421 148 151 3 679.14 3.43 422 148 152 4 668.13 0.53 423 149 152 3 670.01 0.42 424 149 153 4 666.00 1.59 425 150 153 3 687.68 3.62 426 150 154 4 663.59 0.03 427 151 154 3 692.70 2.06 428 151 155 4 668.00 2.22 429 152 155 3 675.00 1.28 430 152 156 4 663.12 0.29 431 152 195 43 61.66 0.86 432 153 156 3 685.86 4.30 433 153 157 4 663.96 0.14 434 154 157 3 676.68 2.11 435 154 158 4 672.27 4.00 436 155 158 3 677.83 1.54 437 155 159 4 681.16 3.79 438 156 159 3 686.38 1.18 439 156 160 4 681.17 3.78 440 156 166 10 125.63 0.23 441 157 160 3 689.69 4.62 442 157 161 4 681.19 3.77 443 158 161 3 691.52 3.70 444 158 162 4 681.19 3.77 445 159 162 3 676.27 1.31 446 159 163 4 669.23 2.21 447 159 166 7 125.80 0.27 448 159 193 34 61.74 0.89 449 160 163 3 673.32 0.16 450 160 164 4 617.64 6.64 451 160 166 6 125.76 0.29 452 163 166 3 713.03 1.79 453 163 179 16 121.59 0.30 454 163 183 20 107.24 0.47 455 163 191 28 61.84 0.93 456 163 192 29 61.84 0.93 457 163 193 30 61.83 0.93 458 165 175 10 125.29 0.20 459 165 179 14 123.99 0.35 460 166 176 10 125.02 0.32 461 166 179 13 119.31 0.86 462 166 193 27 61.80 0.91 463 167 173 6 125.40 0.22 464 167 175 8 125.29 0.20 465 167 176 9 125.19 0.24 466 168 173 5 125.76 0.39 467 168 175 7 125.39 0.23 468 168 176 8 125.25 0.28 469 169 176 7 125.09 0.38 470 170 173 3 657.25 3.93 471 170 176 6 125.51 0.59 472 171 177 6 596.36 3.48 473 171 200 29 39.22 0.26 474 172 177 5 670.62 2.08 475 173 176 3 682.43 2.44 476 173 177 4 670.66 2.10 477 174 177 3 673.98 3.71 478 174 178 4 670.69 2.06 479 175 178 3 672.72 2.97 480 175 179 4 670.79 2.01 481 176 179 3 681.79 0.20 482 176 180 4 670.82 2.00 483 177 180 3 670.69 1.92 484 177 181 4 665.03 0.90 485 177 200 23 60.14 1.24 486 178 181 3 665.06 0.89 487 178 182 4 657.75 4.54 488 179 182 3 682.12 2.37 489 179 183 4 666.28 0.27 490 179 191 12 62.38 0.93 491 179 193 14 62.22 0.90 492 180 183 3 684.84 1.01 493 180 184 4 670.60 2.19 494 180 190 10 62.38 0.93 495 180 191 11 62.27 0.88 496 180 194 14 61.88 0.92 497 180 201 21 53.62 1.28 498 181 184 3 679.84 1.49 499 181 185 4 670.62 2.19 500 181 204 23 39.85 0.28 501 181 207 26 34.63 1.28 502 181 208 27 26.47 0.10 503 182 185 3 680.89 2.79 504 182 186 4 670.63 2.18 505 183 186 3 702.60 1.65 506 183 187 4 666.01 0.11 507 183 189 6 583.48 20.16 508 183 190 7 62.38 0.93 509 183 191 8 62.37 0.93 510 184 188 4 605.36 9.22 511 184 189 5 346.55 138.62 512 184 190 6 63.44 1.46 513 184 205 21 39.23 0.68 514 185 188 3 683.73 0.99 515 185 208 23 34.63 1.28 516 185 209 24 28.82 1.28 517 190 194 4 650.79 0.17 518 190 201 11 57.87 0.24 519 190 204 14 40.63 0.49 520 190 205 15 39.08 0.76 521 191 194 3 698.43 0.85 522 194 201 7 595.00 6.11 523 195 198 3 713.03 4.40 524 195 201 6 657.23 3.20 525 196 201 5 660.06 4.20 526 197 201 4 675.39 3.24 527 198 201 3 684.14 0.49 528 199 202 3 684.52 1.36 529 199 203 4 685.19 0.11 530 200 203 3 695.07 2.83 531 200 204 4 685.19 0.11 532 201 204 3 692.95 3.22 533 201 205 4 685.19 0.11 534 202 205 3 693.54 2.92 535 202 206 4 685.17 0.10 536 203 206 3 685.50 0.46 537 203 207 4 675.09 0.56 538 204 207 3 685.98 0.70 539 204 208 4 675.69 0.26 540 205 208 3 704.89 2.09 541 205 210 5 602.04 8.19 542 206 210 4 585.72 0.34