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 1 100 99 355.93 21.70 2 1 101 100 355.93 21.70 3 2 24 22 495.61 23.16 4 2 25 23 495.61 23.16 5 2 26 24 495.54 23.12 6 2 61 59 494.38 22.57 7 2 97 95 356.86 21.54 8 2 98 96 356.63 21.59 9 2 99 97 355.95 21.70 10 2 100 98 355.94 21.71 11 2 101 99 355.94 21.70 12 3 24 21 495.63 23.16 13 3 25 22 495.61 23.16 14 3 27 24 495.59 23.14 15 3 30 27 495.61 23.15 16 3 99 96 356.24 21.77 17 3 101 98 355.94 21.70 18 3 103 100 355.93 21.70 19 3 140 137 268.20 0.44 20 4 23 19 495.87 23.25 21 4 24 20 495.64 23.16 22 4 99 95 356.67 21.57 23 4 101 97 356.02 21.73 24 4 102 98 355.93 21.70 25 4 103 99 355.93 21.70 26 4 140 136 268.24 0.43 27 5 22 17 496.68 22.89 28 5 23 18 496.62 22.91 29 5 103 98 355.94 21.70 30 5 140 135 268.25 0.43 31 5 141 136 268.06 0.39 32 5 144 139 267.55 0.42 33 6 20 14 497.96 22.66 34 6 21 15 497.51 22.48 35 6 22 16 496.68 22.89 36 6 88 82 359.04 21.38 37 6 91 85 359.38 21.20 38 6 92 86 358.67 21.19 39 6 102 96 356.79 21.51 40 6 103 97 356.16 21.64 41 6 104 98 355.93 21.70 42 6 105 99 355.94 21.70 43 6 141 135 268.25 0.42 44 6 144 138 267.64 0.39 45 7 20 13 497.97 22.66 46 7 21 14 497.92 22.64 47 7 88 81 359.78 21.07 48 7 105 98 355.94 21.70 49 7 135 128 270.61 0.21 50 7 141 134 268.33 0.43 51 7 144 137 267.85 0.43 52 7 145 138 267.50 0.44 53 8 11 3 786.16 1.22 54 8 18 10 498.37 22.48 55 8 19 11 498.32 22.48 56 8 20 12 497.96 22.66 57 8 84 76 359.94 21.09 58 8 88 80 359.84 21.06 59 8 148 140 262.86 1.45 60 9 18 9 498.37 22.48 61 9 19 10 498.34 22.46 62 9 148 139 266.74 0.65 63 9 149 140 262.86 1.44 64 9 152 143 243.74 0.74 65 10 13 3 726.98 1.45 66 10 18 8 498.35 22.46 67 10 152 142 253.63 1.36 68 10 195 185 86.20 0.01 69 11 18 7 498.36 22.47 70 11 80 69 361.18 20.88 71 11 84 73 360.81 20.89 72 11 107 96 357.30 21.25 73 11 195 184 86.21 0.01 74 12 170 158 152.09 2.38 75 12 171 159 152.09 2.38 76 13 152 139 266.62 0.82 77 13 169 156 152.13 2.38 78 13 170 157 152.09 2.38 79 13 171 158 152.09 2.38 80 13 195 182 86.25 0.01 81 13 198 185 82.52 0.09 82 14 169 155 152.19 2.40 83 14 171 157 152.13 2.40 84 14 176 162 150.77 2.83 85 14 180 166 139.55 0.60 86 14 194 180 86.33 0.01 87 14 195 181 86.25 0.01 88 14 198 184 82.35 0.05 89 14 200 186 68.39 0.30 90 14 201 187 67.15 0.90 91 15 152 137 267.05 0.62 92 15 159 144 218.11 0.93 93 15 166 151 153.37 1.93 94 15 169 154 152.18 2.40 95 15 176 161 150.75 2.86 96 15 179 164 145.53 0.41 97 15 180 165 139.47 0.62 98 15 193 178 86.35 0.01 99 15 194 179 86.25 0.01 100 16 70 54 493.83 22.72 101 16 152 136 263.17 1.28 102 16 159 143 216.81 0.35 103 16 193 177 86.33 0.02 104 16 195 179 86.22 0.02 105 17 67 50 494.47 22.57 106 17 68 51 494.26 22.64 107 17 69 52 493.89 22.68 108 17 70 53 493.73 22.77 109 17 73 56 450.69 23.88 110 17 152 135 259.98 0.08 111 17 155 138 237.92 0.69 112 17 195 178 86.19 0.01 113 18 67 49 494.37 22.59 114 18 68 50 494.14 22.67 115 18 73 55 445.36 21.39 116 18 80 62 361.27 20.84 117 18 83 65 361.12 20.86 118 18 84 66 360.81 20.89 119 18 195 177 86.14 0.02 120 19 65 46 494.51 22.59 121 19 66 47 494.39 22.59 122 19 67 48 493.96 22.66 123 19 148 129 264.85 0.70 124 19 151 132 256.86 1.56 125 19 152 133 243.69 0.72 126 20 65 45 494.43 22.58 127 20 66 46 494.21 22.65 128 20 68 48 493.94 22.68 129 20 87 67 359.82 21.05 130 20 88 68 359.79 21.07 131 20 91 71 359.66 21.05 132 21 64 43 494.44 22.57 133 21 65 44 494.06 22.71 134 21 144 123 267.69 0.38 135 21 147 126 264.88 0.72 136 21 148 127 261.20 0.66 137 22 63 41 494.45 22.56 138 22 64 42 494.13 22.59 139 22 91 69 359.06 21.12 140 22 92 70 358.65 21.20 141 22 95 73 358.28 21.06 142 23 60 37 494.69 22.52 143 23 62 39 494.60 22.48 144 23 63 40 493.98 22.66 145 23 140 117 268.26 0.43 146 23 143 120 267.83 0.41 147 23 144 121 267.52 0.43 148 23 147 124 264.58 0.58 149 24 60 36 494.69 22.51 150 24 61 37 494.63 22.49 151 24 62 38 494.49 22.50 152 24 95 71 357.91 21.11 153 24 97 73 356.95 21.54 154 24 99 75 356.67 21.57 155 25 29 4 701.45 0.48 156 25 30 5 685.72 5.08 157 25 33 8 577.56 29.73 158 25 59 34 494.75 22.48 159 25 60 35 494.63 22.48 160 25 61 36 494.61 22.47 161 25 140 115 268.23 0.43 162 26 29 3 723.67 4.72 163 26 30 4 707.52 3.52 164 26 61 35 494.62 22.46 165 27 30 3 732.18 0.47 166 27 31 4 734.33 0.47 167 28 31 3 775.72 4.36 168 29 32 3 734.33 0.47 169 29 33 4 723.98 4.71 170 30 33 3 729.69 2.79 171 30 34 4 708.61 1.96 172 30 140 110 268.24 0.42 173 31 34 3 710.73 2.18 174 31 35 4 701.13 1.11 175 32 35 3 702.10 3.22 176 32 36 4 697.26 0.83 177 32 59 27 494.97 22.38 178 33 36 3 697.19 0.89 179 33 37 4 697.14 0.87 180 33 38 5 679.54 5.67 181 33 56 23 495.00 22.37 182 33 59 26 495.00 22.37 183 33 139 106 268.31 0.42 184 33 140 107 268.31 0.42 185 33 143 110 267.84 0.41 186 34 37 3 696.99 0.95 187 34 139 105 268.31 0.43 188 36 52 16 495.70 22.16 189 36 55 19 495.67 22.17 190 36 56 20 495.65 22.17 191 36 59 23 495.60 22.16 192 37 40 3 720.31 3.23 193 38 41 3 717.54 2.58 194 38 52 14 495.74 22.18 195 38 56 18 495.70 22.16 196 38 139 101 268.39 0.43 197 38 142 104 268.31 0.43 198 38 146 108 267.75 0.41 199 39 136 97 269.51 0.25 200 39 137 98 269.51 0.25 201 39 139 100 268.44 0.42 202 39 142 103 268.33 0.42 203 41 44 3 679.43 4.93 204 41 49 8 497.80 23.07 205 41 52 11 495.92 22.14 206 41 146 105 268.19 0.45 207 42 135 93 306.08 1.32 208 42 136 94 303.80 0.29 209 44 48 4 688.40 0.03 210 44 49 5 604.03 31.38 211 44 52 8 599.29 27.91 212 45 48 3 703.14 1.04 213 45 49 4 688.41 0.04 214 46 49 3 701.65 0.14 215 46 50 4 686.37 1.39 216 47 50 3 694.43 2.29 217 47 51 4 686.45 1.38 218 48 51 3 690.21 0.50 219 48 52 4 686.46 1.38 220 49 52 3 694.81 2.41 221 49 53 4 686.84 1.24 222 49 146 97 267.94 0.43 223 49 149 100 267.70 0.38 224 49 150 101 263.38 1.76 225 50 53 3 686.84 1.24 226 50 54 4 695.69 1.24 227 50 150 100 264.18 1.35 228 50 154 104 240.19 0.99 229 51 54 3 705.28 4.92 230 51 55 4 692.45 3.91 231 52 55 3 704.52 5.65 232 52 56 4 693.11 3.58 233 52 146 94 267.85 0.42 234 53 56 3 709.33 3.25 235 53 57 4 709.84 2.99 236 53 65 12 494.79 22.46 237 53 146 93 267.82 0.42 238 53 147 94 267.68 0.39 239 53 150 97 259.79 0.04 240 53 154 101 240.18 1.00 241 54 57 3 710.98 2.43 242 54 58 4 709.85 2.98 243 55 58 3 709.85 2.98 244 55 59 4 709.85 2.98 245 56 59 3 718.01 1.10 246 56 60 4 709.84 2.98 247 56 143 87 267.90 0.41 248 56 146 90 267.74 0.39 249 56 147 91 267.55 0.45 250 57 60 3 712.62 1.58 251 57 63 6 613.50 33.26 252 57 147 90 267.55 0.45 253 60 63 3 776.19 2.90 254 60 147 87 267.30 0.46 255 61 97 36 356.83 21.59 256 62 95 33 357.87 21.10 257 62 96 34 357.68 21.18 258 62 97 35 356.91 21.55 259 63 95 32 358.13 21.00 260 63 147 84 262.86 1.44 261 64 91 27 358.68 21.18 262 64 94 30 358.34 21.03 263 64 95 31 358.18 21.01 264 65 147 82 264.58 0.60 265 65 151 86 244.19 0.70 266 66 87 21 359.86 21.04 267 66 90 24 359.83 21.04 268 66 91 25 359.76 21.02 269 67 151 84 258.89 0.55 270 67 155 88 220.47 0.57 271 68 73 5 685.99 2.48 272 68 83 15 361.12 20.85 273 68 87 19 360.37 20.93 274 69 72 3 725.01 1.46 275 69 73 4 689.34 0.82 276 70 73 3 712.23 0.42 277 70 74 4 689.35 0.83 278 70 193 123 86.34 0.01 279 70 194 124 86.23 0.01 280 70 195 125 86.11 0.03 281 71 74 3 709.50 5.03 282 71 75 4 689.34 0.83 283 72 75 3 690.50 2.54 284 72 76 4 688.18 1.41 285 72 83 11 428.30 12.39 286 73 76 3 696.83 0.43 287 73 83 10 427.94 12.48 288 73 195 122 86.13 0.01 289 73 198 125 82.25 0.84 290 74 196 122 85.64 0.21 291 74 198 124 80.09 0.46 292 76 79 3 786.02 3.03 293 76 80 4 714.69 1.11 294 76 83 7 428.94 12.68 295 78 82 4 682.89 1.34 296 79 82 3 701.49 1.15 297 79 83 4 692.77 3.57 298 80 83 3 693.55 3.96 299 80 84 4 692.77 3.57 300 81 84 3 696.70 1.61 301 81 85 4 694.36 2.78 302 81 109 28 357.33 21.04 303 82 85 3 703.16 4.83 304 82 86 4 688.92 0.06 305 83 86 3 712.69 2.12 306 83 87 4 688.91 0.07 307 84 87 3 717.32 2.81 308 84 88 4 685.16 0.84 309 85 88 3 704.39 1.66 310 85 89 4 691.03 2.10 311 85 114 29 313.35 1.05 312 85 117 32 314.64 1.74 313 85 118 33 315.45 2.39 314 85 121 36 315.68 2.50 315 86 89 3 706.94 3.04 316 86 90 4 686.85 0.01 317 86 121 35 315.68 2.49 318 87 90 3 686.95 0.04 319 87 91 4 693.28 3.26 320 88 91 3 705.75 2.91 321 88 92 4 705.70 2.94 322 88 104 16 357.32 21.30 323 88 114 26 315.75 2.26 324 88 118 30 315.47 2.41 325 89 92 3 715.54 1.99 326 89 93 4 698.90 0.46 327 89 118 29 315.47 2.42 328 89 121 32 315.43 2.63 329 89 122 33 315.37 2.66 330 90 93 3 706.38 2.61 331 90 94 4 698.90 0.46 332 91 94 3 717.89 2.48 333 91 95 4 706.37 2.61 334 92 95 3 713.54 4.70 335 92 102 10 360.21 19.88 336 92 118 26 383.66 36.57 337 92 122 30 383.74 36.87 338 92 124 32 415.07 52.69 339 93 98 5 654.21 3.98 340 93 121 28 383.86 36.84 341 93 122 29 383.75 36.88 342 93 123 30 415.17 52.61 343 93 124 31 415.14 52.65 344 95 98 3 729.98 0.15 345 95 99 4 729.98 0.15 346 98 123 25 485.53 88.06 347 98 124 26 485.31 88.17 348 99 102 3 742.45 1.79 349 99 124 25 485.31 88.19 350 99 126 27 484.99 88.30 351 100 126 26 484.99 88.31 352 100 127 27 484.99 88.31 353 101 127 26 484.91 88.35 354 101 129 28 484.88 88.34 355 102 122 20 485.85 88.00 356 102 124 22 485.64 88.12 357 102 126 24 485.08 88.33 358 102 127 25 485.04 88.33 359 102 128 26 484.88 88.36 360 102 129 27 484.88 88.36 361 103 129 26 484.91 88.36 362 103 138 35 268.33 0.42 363 103 140 37 268.27 0.43 364 103 141 38 268.10 0.40 365 104 114 10 486.13 87.80 366 104 118 14 486.20 87.84 367 104 128 24 485.09 88.33 368 104 129 25 484.95 88.37 369 104 130 26 484.83 88.38 370 104 131 27 484.83 88.38 371 104 134 30 432.42 80.67 372 105 131 26 484.79 88.42 373 105 133 28 482.14 89.50 374 105 134 29 432.42 80.67 375 105 135 30 432.42 80.67 376 105 141 36 268.35 0.43 377 106 109 3 711.48 5.97 378 106 111 5 615.11 23.32 379 106 114 8 486.44 87.72 380 106 130 24 484.99 88.38 381 106 131 25 484.90 88.38 382 106 132 26 484.57 88.50 383 108 132 24 484.93 88.38 384 109 114 5 697.33 6.66 385 109 132 23 485.32 88.25 386 110 113 3 701.94 4.36 387 110 114 4 697.35 6.67 388 111 114 3 711.50 3.93 389 111 115 4 701.97 4.38 390 111 130 19 485.45 88.24 391 111 131 20 485.43 88.25 392 111 132 21 485.43 88.25 393 112 115 3 709.55 4.90 394 112 116 4 701.97 4.38 395 113 116 3 709.33 0.70 396 113 117 4 696.01 7.36 397 114 117 3 716.86 4.46 398 114 118 4 702.38 4.16 399 114 130 16 485.49 88.25 400 115 118 3 723.11 1.34 401 115 119 4 699.25 2.60 402 115 128 13 485.63 88.20 403 115 129 14 485.61 88.22 404 115 130 15 485.46 88.27 405 116 119 3 703.52 0.46 406 116 120 4 702.05 1.19 407 117 120 3 714.66 1.57 408 117 121 4 707.98 1.77 409 118 121 3 711.37 0.08 410 118 122 4 702.10 4.71 411 118 128 10 485.66 88.23 412 119 122 3 716.12 3.10 413 119 128 9 485.66 88.23 414 122 126 4 700.21 5.50 415 122 128 6 485.80 88.19 416 131 134 3 703.66 0.14 417 131 137 6 644.88 8.76 418 131 138 7 554.99 0.21 419 132 137 5 696.23 4.01 420 133 136 3 725.81 1.66 421 133 137 4 700.18 2.04 422 134 137 3 700.19 2.04 423 134 138 4 672.74 7.71 424 134 141 7 268.39 0.43 425 135 141 6 268.39 0.43 426 135 142 7 268.31 0.45 427 135 145 10 267.69 0.36 428 138 141 3 687.86 0.02 429 138 142 4 685.05 1.13 430 139 142 3 685.68 0.89 431 139 143 4 694.51 3.27 432 140 143 3 695.43 3.73 433 140 144 4 694.52 3.27 434 141 144 3 701.41 0.18 435 141 145 4 694.56 3.25 436 142 145 3 701.41 0.18 437 142 146 4 694.54 3.24 438 143 146 3 700.77 0.14 439 143 147 4 691.72 1.48 440 144 147 3 706.44 0.83 441 144 148 4 688.39 0.18 442 145 148 3 698.98 4.56 443 145 149 4 686.49 0.53 444 146 149 3 695.12 2.63 445 146 150 4 684.77 1.40 446 147 150 3 695.77 0.07 447 147 151 4 687.69 1.09 448 148 151 3 690.95 2.34 449 148 152 4 697.60 0.99 450 149 152 3 697.61 1.00 451 149 153 4 689.56 5.03 452 150 153 3 696.73 1.44 453 150 154 4 689.54 5.03 454 151 154 3 709.03 4.71 455 151 155 4 690.91 4.34 456 152 155 3 697.48 1.82 457 152 156 4 689.34 5.13 458 152 168 16 152.13 2.39 459 153 156 3 689.95 0.07 460 153 157 4 674.90 2.08 461 154 157 3 695.78 2.85 462 154 158 4 686.78 1.52 463 155 158 3 696.32 2.58 464 155 159 4 683.42 0.62 465 156 159 3 721.28 2.65 466 156 160 4 686.99 1.15 467 156 166 10 153.34 1.91 468 156 167 11 152.47 2.27 469 157 160 3 695.35 2.60 470 157 161 4 687.00 1.15 471 158 161 3 696.04 2.27 472 158 162 4 687.00 1.15 473 159 162 3 694.94 2.82 474 159 163 4 686.99 1.15 475 159 166 7 309.64 76.20 476 159 193 34 86.34 0.03 477 160 163 3 699.58 5.16 478 160 164 4 598.46 21.68 479 160 165 5 593.97 19.43 480 160 166 6 330.89 86.83 481 160 167 7 309.64 76.20 482 163 166 3 766.13 4.44 483 163 179 16 147.05 1.87 484 163 183 20 131.91 0.49 485 163 191 28 86.53 0.01 486 163 192 29 86.53 0.01 487 163 193 30 86.44 0.03 488 165 175 10 150.89 2.89 489 165 179 14 149.97 2.63 490 166 176 10 150.75 2.88 491 166 179 13 142.53 0.16 492 166 193 27 86.39 0.01 493 167 173 6 151.80 2.47 494 167 175 8 150.78 2.87 495 167 176 9 150.75 2.87 496 168 173 5 152.88 1.95 497 168 176 8 150.75 2.87 498 169 176 7 150.72 2.87 499 170 173 3 697.65 1.57 500 170 176 6 150.77 2.85 501 171 177 6 152.67 1.83 502 171 200 29 70.50 0.84 503 173 176 3 682.11 1.61 504 173 177 4 682.11 1.60 505 174 177 3 694.19 2.02 506 174 178 4 682.11 1.60 507 175 178 3 687.82 0.96 508 175 179 4 684.65 0.32 509 176 179 3 700.99 7.84 510 176 180 4 684.66 0.32 511 177 180 3 704.23 0.90 512 177 181 4 692.18 6.89 513 177 200 23 83.79 0.10 514 177 204 27 64.69 0.06 515 178 181 3 699.81 3.36 516 178 182 4 692.21 6.88 517 179 182 3 711.96 4.57 518 179 183 4 699.16 10.97 519 179 191 12 86.70 0.04 520 179 193 14 86.58 0.04 521 180 183 3 730.44 4.67 522 180 184 4 699.16 10.97 523 180 190 10 86.64 0.07 524 180 191 11 86.70 0.04 525 180 194 14 86.44 0.03 526 180 200 20 86.06 0.01 527 180 201 21 76.63 0.94 528 180 204 24 66.03 0.35 529 181 184 3 715.07 3.02 530 181 185 4 673.64 2.46 531 181 204 23 66.06 0.35 532 181 207 26 64.19 0.03 533 181 208 27 53.95 0.31 534 182 185 3 713.94 3.58 535 182 186 4 687.71 9.48 536 183 186 3 707.45 0.56 537 183 187 4 672.36 2.46 538 183 189 6 556.54 30.00 539 183 190 7 86.75 0.02 540 183 191 8 86.73 0.01 541 184 187 3 692.81 7.87 542 184 188 4 651.42 11.46 543 184 189 5 215.72 63.12 544 184 190 6 86.77 0.03 545 184 205 21 66.05 0.35 546 184 208 24 58.01 0.23 547 184 209 25 55.38 0.98 548 185 208 23 59.94 0.27 549 185 211 26 53.68 0.30 550 190 194 4 684.90 5.53 551 190 201 11 82.28 0.34 552 190 204 14 67.11 0.72 553 190 205 15 65.62 0.29 554 191 194 3 739.49 5.09 555 194 201 7 67.81 0.57 556 195 198 3 719.54 6.50 557 195 201 6 543.66 16.57 558 196 201 5 600.48 12.36 559 198 201 3 728.53 3.68 560 199 202 3 689.60 8.50 561 199 203 4 689.60 8.50 562 200 203 3 703.96 2.18 563 200 204 4 694.16 6.21 564 201 204 3 707.71 0.31 565 201 205 4 685.36 1.80 566 202 205 3 701.11 2.99 567 202 206 4 685.35 1.80 568 203 206 3 694.79 1.59 569 203 207 4 687.38 2.83 570 204 207 3 691.62 3.79 571 204 208 4 687.37 2.83 572 205 208 3 705.50 1.81 573 205 209 4 678.21 3.00 574 206 209 3 684.91 6.34 575 206 210 4 678.20 3.00 576 207 210 3 714.63 2.27 577 207 211 4 685.14 6.46 578 208 211 3 712.78 3.19 579 209 212 3 714.95 2.11 580 213 216 3 765.11 1.19 581 216 219 3 743.82 2.56 582 217 220 3 797.32 9.08