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 15 18 3 659.75 2.06 2 15 19 4 632.34 1.50 3 15 57 42 492.37 3.27 4 16 19 3 659.76 2.06 5 16 20 4 632.62 1.35 6 17 20 3 657.44 3.23 7 17 21 4 627.49 1.20 8 18 21 3 630.93 2.92 9 18 22 4 627.03 0.97 10 18 49 31 507.17 0.94 11 18 53 35 507.06 0.89 12 18 57 39 506.97 0.86 13 19 22 3 658.58 2.66 14 19 23 4 633.84 8.53 15 19 57 38 506.91 0.83 16 19 58 39 506.94 0.84 17 20 23 3 655.03 0.71 18 20 24 4 643.28 3.80 19 21 24 3 646.63 5.58 20 21 25 4 629.29 0.17 21 21 47 26 507.72 0.87 22 22 25 3 632.22 1.63 23 22 26 4 619.64 4.66 24 22 43 21 507.78 0.83 25 22 47 25 507.79 0.83 26 22 49 27 507.73 0.86 27 22 54 32 507.20 0.93 28 22 57 35 507.34 0.78 29 22 58 36 507.12 0.89 30 22 64 42 492.55 1.11 31 23 26 3 627.90 0.60 32 23 27 4 619.66 4.73 33 23 58 35 507.12 0.88 34 23 64 41 487.80 3.49 35 23 67 44 411.88 14.81 36 23 68 45 411.25 14.87 37 23 71 48 411.18 14.87 38 24 27 3 638.45 1.39 39 24 28 4 622.03 3.56 40 25 28 3 644.87 4.30 41 25 29 4 632.69 1.77 42 25 43 18 507.97 0.90 43 25 46 21 507.99 0.91 44 25 47 22 507.94 0.88 45 26 29 3 640.00 1.88 46 26 30 4 633.50 5.12 47 26 43 17 507.98 0.91 48 26 64 38 492.73 1.17 49 26 68 42 411.99 14.73 50 27 30 3 640.00 1.88 51 27 31 4 633.50 5.09 52 27 68 41 411.98 14.73 53 27 109 82 353.56 0.80 54 27 110 83 353.49 0.78 55 27 113 86 353.33 0.70 56 28 31 3 646.83 1.54 57 28 32 4 634.86 4.42 58 28 109 81 353.56 0.80 59 29 32 3 634.87 4.42 60 29 33 4 634.86 4.42 61 29 38 9 509.11 0.74 62 29 42 13 508.17 0.89 63 29 43 14 508.15 0.89 64 29 46 17 508.19 0.90 65 30 33 3 639.96 1.91 66 30 34 4 611.86 5.67 67 30 35 5 600.85 11.18 68 30 38 8 509.14 0.76 69 30 43 13 508.17 0.89 70 30 61 31 507.25 0.79 71 30 64 34 505.34 1.32 72 30 65 35 495.92 0.17 73 30 113 83 353.36 0.67 74 31 109 78 353.70 0.80 75 31 113 82 353.29 0.67 76 31 116 85 348.91 2.40 77 33 37 4 509.47 0.76 78 33 38 5 509.47 0.76 79 33 42 9 509.48 0.77 80 34 37 3 608.02 1.66 81 34 38 4 598.39 5.39 82 35 38 3 642.52 3.42 83 35 61 26 507.39 0.74 84 35 62 27 507.37 0.74 85 35 65 30 505.32 1.33 86 35 124 89 273.42 3.69 87 36 61 25 507.41 0.74 88 38 42 4 642.02 3.40 89 38 61 23 507.31 0.79 90 39 42 3 645.29 1.77 91 39 43 4 642.02 3.40 92 40 43 3 660.77 1.63 93 40 44 4 630.75 3.84 94 40 54 14 508.69 0.95 95 40 55 15 508.65 0.94 96 40 60 20 507.35 0.77 97 40 61 21 506.88 0.82 98 40 64 24 505.62 1.17 99 41 44 3 637.07 0.68 100 41 45 4 630.74 3.83 101 41 51 10 508.74 0.96 102 42 45 3 646.96 2.59 103 42 46 4 636.71 0.85 104 43 46 3 637.98 0.96 105 43 47 4 634.57 1.85 106 43 54 11 508.70 0.95 107 43 64 21 505.23 1.31 108 44 47 3 636.76 0.86 109 44 48 4 631.01 2.01 110 44 49 5 523.61 5.67 111 44 50 6 508.82 0.96 112 44 51 7 508.78 0.97 113 44 54 10 508.69 0.95 114 45 48 3 627.93 3.56 115 49 53 4 625.89 4.22 116 49 54 5 621.78 2.17 117 50 53 3 629.66 2.34 118 50 54 4 622.03 2.26 119 51 54 3 630.36 2.02 120 51 55 4 623.78 3.14 121 52 55 3 651.38 8.26 122 52 56 4 626.85 3.77 123 53 56 3 656.66 4.21 124 53 57 4 637.65 6.43 125 54 57 3 657.36 3.42 126 54 58 4 623.77 3.12 127 54 64 10 501.62 0.22 128 55 58 3 622.98 2.83 129 55 59 4 589.14 6.32 130 55 60 5 569.19 3.66 131 58 64 6 501.88 0.10 132 58 67 9 430.50 11.61 133 59 63 4 630.31 2.06 134 60 63 3 630.33 2.06 135 60 64 4 630.37 2.04 136 61 64 3 636.72 2.93 137 61 65 4 630.37 2.02 138 62 65 3 633.53 0.45 139 62 66 4 633.43 0.49 140 62 124 62 273.24 3.76 141 63 66 3 650.38 1.21 142 63 67 4 633.43 0.48 143 64 67 3 633.34 0.36 144 64 68 4 626.99 2.74 145 65 68 3 644.33 4.24 146 65 69 4 633.43 0.47 147 65 113 48 353.62 0.77 148 65 117 52 329.29 1.99 149 65 124 59 273.39 3.70 150 66 69 3 638.95 2.29 151 66 70 4 633.43 0.47 152 66 124 58 273.39 3.70 153 67 70 3 643.33 4.48 154 67 71 4 635.12 0.38 155 68 71 3 647.93 2.18 156 68 72 4 635.13 0.38 157 68 113 45 353.69 0.80 158 69 72 3 655.57 1.52 159 69 73 4 635.06 0.37 160 69 113 44 353.70 0.80 161 69 114 45 353.32 0.65 162 69 117 48 336.98 1.85 163 69 125 56 273.41 3.69 164 70 73 3 634.39 0.72 165 70 74 4 628.12 3.83 166 70 77 7 625.13 3.69 167 70 128 58 272.20 4.12 168 71 74 3 636.19 1.61 169 71 75 4 631.00 0.80 170 72 75 3 634.41 2.50 171 72 76 4 630.94 0.78 172 72 110 38 353.77 0.78 173 72 111 39 353.72 0.80 174 72 114 42 353.71 0.79 175 73 76 3 644.31 3.73 176 73 77 4 644.29 3.73 177 73 114 41 353.72 0.80 178 73 125 52 273.45 3.70 179 74 77 3 646.16 2.81 180 74 78 4 644.38 3.69 181 75 78 3 652.08 0.14 182 75 79 4 664.06 3.20 183 75 103 28 353.91 0.80 184 75 107 32 353.85 0.80 185 76 79 3 710.19 0.21 186 76 100 24 353.98 0.81 187 76 103 27 353.94 0.79 188 76 104 28 353.95 0.79 189 76 111 35 353.79 0.79 190 76 114 38 353.78 0.78 191 76 170 94 118.41 1.09 192 77 80 3 655.36 0.25 193 77 81 4 637.34 0.20 194 77 133 56 268.93 3.68 195 77 136 59 268.84 3.68 196 77 166 89 119.41 0.96 197 78 81 3 658.14 1.61 198 78 82 4 641.63 0.32 199 79 82 3 656.12 0.88 200 79 83 4 655.11 0.38 201 79 96 17 354.10 0.83 202 79 99 20 354.12 0.80 203 80 83 3 656.44 1.06 204 80 96 16 354.18 0.83 205 80 136 56 268.89 3.67 206 80 137 57 268.88 3.67 207 80 140 60 268.38 3.59 208 81 136 55 268.89 3.67 209 81 140 59 268.38 3.58 210 82 87 5 636.16 1.55 211 83 87 4 629.41 4.93 212 83 92 9 354.48 0.88 213 83 93 10 354.48 0.88 214 83 96 13 354.44 0.86 215 83 140 57 268.51 3.64 216 83 143 60 266.05 2.54 217 83 144 61 265.93 2.48 218 84 87 3 641.32 0.72 219 84 140 56 268.79 3.69 220 84 143 59 267.75 3.39 221 84 147 63 264.80 2.83 222 85 143 58 267.93 3.30 223 85 147 62 265.39 2.42 224 87 92 5 592.75 3.19 225 88 91 3 652.46 1.80 226 88 92 4 619.10 0.95 227 89 92 3 630.53 5.45 228 89 93 4 619.13 0.94 229 89 147 58 260.02 1.55 230 89 152 63 141.34 1.74 231 89 153 64 141.31 1.74 232 90 93 3 650.87 0.48 233 90 94 4 626.18 4.47 234 90 153 63 141.30 1.73 235 90 205 115 67.00 0.48 236 90 208 118 65.78 0.88 237 90 209 119 60.88 1.06 238 90 210 120 60.89 1.06 239 91 94 3 651.93 6.87 240 91 95 4 626.19 4.47 241 92 95 3 658.45 3.62 242 92 96 4 627.82 3.63 243 93 96 3 657.23 4.22 244 93 97 4 626.87 4.09 245 93 153 60 141.30 1.73 246 93 161 68 119.88 1.01 247 93 165 72 119.62 0.99 248 93 204 111 67.21 0.56 249 93 205 112 66.97 0.45 250 93 208 115 61.28 1.07 251 94 97 3 647.27 1.96 252 94 98 4 639.64 2.29 253 94 201 107 69.42 0.34 254 94 205 111 67.02 0.47 255 95 98 3 639.61 2.31 256 95 99 4 634.00 0.49 257 96 99 3 650.40 3.07 258 96 100 4 634.00 0.49 259 96 165 69 119.48 0.95 260 96 166 70 119.52 0.95 261 97 100 3 645.09 0.42 262 97 101 4 634.00 0.49 263 97 165 68 119.47 0.95 264 97 169 72 119.19 0.92 265 97 200 103 69.47 0.33 266 97 201 104 69.41 0.34 267 97 204 107 67.03 0.47 268 97 205 108 66.98 0.45 269 98 101 3 644.48 3.56 270 98 102 4 626.85 4.07 271 98 197 99 71.37 0.71 272 98 201 103 69.44 0.33 273 99 102 3 642.90 0.29 274 99 103 4 637.37 2.48 275 100 103 3 647.21 2.19 276 100 104 4 633.68 0.64 277 100 165 65 119.45 0.95 278 100 166 66 119.45 0.95 279 100 169 69 118.95 0.86 280 100 170 70 118.93 0.86 281 101 104 3 633.68 0.64 282 101 105 4 626.90 4.03 283 101 169 68 118.95 0.87 284 101 172 71 118.40 1.10 285 101 187 86 72.67 0.15 286 101 193 92 72.23 0.34 287 101 196 95 71.81 0.50 288 101 197 96 71.38 0.70 289 101 200 99 69.45 0.33 290 102 105 3 626.89 4.02 291 102 106 4 626.89 4.02 292 102 193 91 72.23 0.34 293 103 106 3 617.07 0.89 294 103 107 4 609.01 4.91 295 104 108 4 547.26 4.54 296 104 169 65 118.92 0.86 297 104 170 66 118.42 1.10 298 104 173 69 97.37 0.97 299 104 187 83 72.61 0.18 300 105 108 3 662.55 1.89 301 105 187 82 72.51 0.23 302 105 193 88 72.23 0.34 303 107 110 3 654.58 3.91 304 107 111 4 632.02 0.63 305 108 111 3 634.39 1.06 306 108 112 4 632.59 0.43 307 108 173 65 95.92 1.50 308 109 112 3 634.43 1.08 309 109 113 4 632.68 0.40 310 110 113 3 645.57 0.58 311 110 114 4 637.73 2.13 312 111 114 3 655.37 5.48 313 111 115 4 640.33 0.83 314 111 173 62 95.92 1.50 315 111 174 63 95.78 1.54 316 112 115 3 654.15 6.08 317 112 116 4 640.25 0.87 318 112 173 61 95.82 1.55 319 112 174 62 95.77 1.54 320 113 116 3 653.22 5.62 321 113 117 4 640.34 0.82 322 114 117 3 647.00 0.31 323 114 118 4 635.52 2.75 324 114 125 11 273.45 3.70 325 114 129 15 273.33 3.69 326 115 118 3 646.54 0.09 327 115 119 4 637.32 1.85 328 115 174 59 95.80 1.54 329 116 119 3 643.71 1.34 330 116 120 4 643.71 1.34 331 117 120 3 649.73 2.10 332 117 121 4 643.63 1.30 333 117 122 5 629.78 0.83 334 117 123 6 629.78 0.83 335 117 124 7 574.64 11.84 336 117 125 8 482.66 57.26 337 118 121 3 645.88 0.18 338 118 122 4 629.77 0.83 339 118 125 7 566.08 15.56 340 118 129 11 324.70 21.66 341 120 123 3 675.90 4.90 342 121 126 5 593.25 12.58 343 122 125 3 640.35 4.12 344 122 126 4 485.54 28.92 345 122 129 7 376.61 4.28 346 125 128 3 650.98 2.28 347 125 129 4 629.62 4.46 348 126 129 3 648.59 1.95 349 126 130 4 635.47 8.52 350 127 130 3 651.53 0.48 351 127 131 4 635.47 8.52 352 128 131 3 651.53 0.48 353 128 132 4 635.47 8.52 354 128 133 5 573.29 0.06 355 129 133 4 569.94 24.62 356 129 134 5 547.05 13.16 357 130 134 4 601.56 1.35 358 131 134 3 658.38 5.29 359 131 135 4 614.98 3.58 360 132 135 3 640.61 1.74 361 132 136 4 620.09 1.03 362 133 136 3 642.45 2.65 363 133 137 4 633.50 1.83 364 133 166 33 119.42 0.96 365 134 137 3 643.96 3.32 366 134 138 4 631.88 2.65 367 135 138 3 646.76 1.92 368 135 139 4 640.06 1.44 369 136 139 3 640.07 1.44 370 136 140 4 640.06 1.44 371 137 140 3 655.63 6.36 372 137 141 4 623.45 2.08 373 137 162 25 119.52 0.95 374 137 166 29 119.50 0.95 375 138 141 3 627.96 4.00 376 138 142 4 624.11 2.23 377 139 142 3 642.85 3.44 378 139 143 4 630.11 1.75 379 140 143 3 630.11 1.75 380 140 144 4 624.16 2.25 381 141 144 3 647.38 2.54 382 141 145 4 623.99 2.30 383 141 158 17 119.84 0.95 384 141 159 18 119.86 0.95 385 141 162 21 119.75 0.98 386 142 145 3 628.42 1.63 387 142 146 4 632.38 0.72 388 143 146 3 633.76 0.04 389 143 147 4 633.82 0.04 390 144 147 3 636.84 1.55 391 144 148 4 633.85 0.04 392 144 153 9 147.41 1.30 393 144 158 14 120.00 0.95 394 144 161 17 120.00 0.95 395 144 162 18 119.99 0.95 396 145 148 3 641.48 0.86 397 145 149 4 633.85 0.03 398 145 158 13 120.01 0.95 399 146 149 3 633.85 0.03 400 146 150 4 633.84 0.03 401 147 150 3 636.39 1.32 402 147 151 4 633.75 0.02 403 147 152 5 285.20 67.59 404 147 153 6 147.41 1.30 405 148 151 3 632.04 0.85 406 148 153 5 147.41 1.30 407 148 154 6 147.41 1.30 408 148 156 8 141.12 1.65 409 151 210 59 61.20 1.12 410 152 210 58 61.06 1.06 411 153 208 55 65.47 0.91 412 153 210 57 60.85 1.06 413 154 208 54 65.36 0.79 414 154 209 55 61.41 1.07 415 154 210 56 60.88 1.04 416 156 161 5 618.46 12.66 417 156 208 52 62.33 0.54 418 157 160 3 645.71 0.93 419 157 161 4 630.19 6.82 420 158 161 3 645.02 2.75 421 158 162 4 642.32 4.09 422 159 162 3 647.12 1.70 423 159 163 4 638.97 2.42 424 160 163 3 646.10 2.20 425 160 164 4 630.18 6.82 426 161 164 3 642.75 0.53 427 161 165 4 638.96 2.43 428 161 204 43 67.14 0.52 429 161 208 47 60.89 1.06 430 162 165 3 634.10 3.80 431 162 166 4 616.83 4.82 432 163 166 3 620.75 2.85 433 163 167 4 616.79 4.79 434 164 167 3 644.97 1.31 435 164 168 4 620.84 1.85 436 164 204 40 67.00 0.45 437 165 168 3 649.33 1.40 438 165 169 4 638.59 0.58 439 165 204 39 67.00 0.45 440 166 169 3 656.97 2.43 441 166 170 4 633.72 9.20 442 167 170 3 660.97 0.52 443 167 171 4 626.41 5.52 444 168 171 3 657.05 2.48 445 168 172 4 657.07 2.46 446 168 200 32 69.42 0.34 447 168 204 36 67.00 0.45 448 169 172 3 673.79 2.15 449 169 200 31 69.44 0.33 450 170 173 3 658.33 1.83 451 170 174 4 626.81 5.33 452 171 174 3 644.75 1.47 453 171 175 4 606.46 15.51 454 171 179 8 177.49 4.56 455 172 176 4 561.12 7.09 456 172 179 7 175.08 5.75 457 172 187 15 72.67 0.15 458 172 192 20 72.62 0.17 459 172 196 24 72.17 0.33 460 172 200 28 69.43 0.33 461 173 176 3 643.07 6.25 462 175 178 3 649.76 2.90 463 175 179 4 615.64 3.49 464 176 179 3 638.96 0.73 465 176 180 4 629.27 3.33 466 177 180 3 644.95 2.26 467 177 181 4 629.27 3.34 468 178 181 3 629.28 3.34 469 178 182 4 629.27 3.35 470 179 182 3 664.06 3.41 471 179 183 4 621.36 7.29 472 179 192 13 97.92 12.71 473 180 183 3 621.36 7.30 474 180 184 4 358.01 98.50 475 180 185 5 143.64 2.54 476 180 186 6 143.63 2.54 477 183 192 9 136.03 6.33 478 185 189 4 575.44 3.50 479 185 192 7 145.79 1.46 480 186 189 3 638.83 4.92 481 186 192 6 233.26 21.33 482 187 192 5 420.56 72.31 483 187 193 6 136.68 6.01 484 187 196 9 144.00 0.56 485 189 192 3 635.00 5.49 486 189 193 4 618.18 12.56 487 190 193 3 643.00 0.15 488 190 194 4 639.35 1.98 489 191 194 3 644.15 2.88 490 191 195 4 639.37 1.98 491 192 195 3 640.25 2.40 492 192 196 4 639.41 1.95 493 193 196 3 639.43 1.95 494 193 197 4 642.54 3.51 495 194 197 3 643.82 3.46 496 194 198 4 642.54 3.51 497 195 198 3 650.46 0.13 498 195 199 4 643.25 3.17 499 196 199 3 652.63 1.51 500 196 200 4 636.23 6.67 501 197 200 3 647.62 4.21 502 197 201 4 643.43 3.06 503 198 201 3 643.75 2.95 504 198 202 4 637.56 0.13 505 199 202 3 643.72 2.97 506 199 203 4 643.48 3.08 507 200 203 3 643.94 2.96 508 200 204 4 643.47 3.08 509 201 204 3 643.83 2.91 510 201 205 4 600.34 3.06 511 202 205 3 643.04 2.52 512 202 206 4 597.95 4.25 513 203 207 4 579.98 0.29 514 204 207 3 630.99 8.25 515 204 208 4 630.99 8.25 516 205 208 3 646.29 0.59 517 205 209 4 598.93 6.00 518 206 209 3 647.20 3.01