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 1 500 92 92 341.00 1.72 2 500 93 93 341.06 1.70 3 500 95 95 341.06 1.70 4 500 96 96 341.06 1.70 5 1 92 91 341.08 1.70 6 1 96 95 341.07 1.69 7 1 97 96 341.06 1.70 8 1 98 97 341.06 1.70 9 1 237 236 41.80 0.20 10 1 238 237 38.95 0.12 11 1 241 240 26.87 0.51 12 2 88 86 341.08 1.70 13 2 92 90 341.11 1.70 14 2 98 96 341.06 1.70 15 2 100 98 341.06 1.70 16 2 122 120 240.91 0.84 17 2 123 121 240.88 0.84 18 2 125 123 239.76 1.07 19 2 126 124 239.75 1.07 20 3 97 94 341.12 1.70 21 3 98 95 341.09 1.70 22 3 99 96 341.07 1.70 23 3 100 97 341.06 1.70 24 3 126 123 239.78 1.06 25 3 128 125 239.75 1.07 26 4 100 96 341.06 1.70 27 4 102 98 341.04 1.71 28 4 109 105 254.24 0.97 29 4 119 115 241.22 0.92 30 4 125 121 240.75 0.90 31 4 126 122 239.87 1.08 32 4 127 123 239.77 1.07 33 4 128 124 239.77 1.07 34 5 13 8 341.08 1.70 35 5 16 11 341.10 1.70 36 5 17 12 341.10 1.70 37 5 20 15 341.20 1.67 38 5 99 94 341.18 1.67 39 5 100 95 341.08 1.70 40 5 102 97 341.06 1.70 41 5 128 123 239.77 1.07 42 5 130 125 239.75 1.07 43 5 233 228 59.79 0.30 44 6 13 7 341.13 1.70 45 6 102 96 341.05 1.71 46 6 106 100 284.03 2.12 47 6 109 103 254.61 1.15 48 6 127 121 240.74 0.90 49 6 128 122 239.84 1.07 50 6 129 123 239.77 1.07 51 6 130 124 239.76 1.07 52 6 152 146 224.95 0.09 53 6 156 150 226.90 0.09 54 7 11 4 430.46 42.35 55 7 13 6 341.14 1.69 56 7 106 99 294.23 2.85 57 7 129 122 239.84 1.08 58 7 130 123 239.77 1.06 59 8 11 3 636.20 3.44 60 8 104 96 341.04 1.71 61 8 106 98 320.41 4.71 62 9 104 95 341.05 1.71 63 10 166 156 229.61 0.38 64 11 130 119 239.83 1.08 65 11 165 154 229.12 0.34 66 11 166 155 229.48 0.39 67 12 15 3 628.77 0.15 68 12 16 4 580.53 2.45 69 12 130 118 239.83 1.08 70 12 165 153 228.83 0.28 71 13 16 3 591.31 2.93 72 13 17 4 580.54 2.44 73 13 101 88 341.98 1.57 74 13 102 89 341.96 1.58 75 13 104 91 341.30 1.71 76 13 130 117 239.74 1.08 77 14 17 3 616.63 15.38 78 14 18 4 580.55 2.45 79 14 42 28 344.05 1.78 80 14 43 29 344.27 1.69 81 14 44 30 344.33 1.68 82 14 101 87 341.99 1.58 83 15 18 3 612.94 9.46 84 15 19 4 581.72 1.86 85 15 43 28 344.26 1.67 86 15 224 209 99.31 2.79 87 16 19 3 624.25 2.74 88 16 20 4 595.39 0.92 89 16 130 114 239.72 1.08 90 16 165 149 228.35 0.23 91 16 222 206 122.90 1.01 92 16 224 208 85.79 3.97 93 16 230 214 72.39 1.57 94 17 20 3 619.26 5.24 95 17 21 4 605.59 1.58 96 17 32 15 345.32 0.90 97 17 44 27 345.72 1.02 98 17 99 82 343.44 1.91 99 17 101 84 341.76 1.65 100 18 21 3 628.91 3.37 101 18 22 4 613.16 4.51 102 18 32 14 345.66 1.02 103 18 43 25 345.66 1.02 104 18 44 26 345.66 1.02 105 19 22 3 628.92 3.36 106 19 23 4 598.48 1.97 107 19 224 205 85.78 3.97 108 19 227 208 72.47 1.58 109 19 230 211 72.39 1.56 110 20 23 3 613.16 4.51 111 20 24 4 595.63 0.55 112 20 99 79 345.75 1.01 113 20 230 210 60.48 0.41 114 20 233 213 59.90 0.29 115 20 234 214 59.70 0.28 116 21 24 3 609.64 6.27 117 21 25 4 595.77 0.63 118 21 30 9 345.94 1.08 119 21 32 11 345.93 1.08 120 21 99 78 345.76 1.01 121 22 25 3 595.19 0.93 122 22 26 4 616.01 7.71 123 22 32 10 346.40 1.15 124 22 43 21 346.30 1.09 125 22 44 22 346.27 1.08 126 22 227 205 73.61 2.16 127 23 26 3 655.59 1.14 128 23 227 204 72.45 1.59 129 23 230 207 60.97 0.17 130 23 231 208 64.85 2.59 131 23 234 211 59.80 0.27 132 24 27 3 648.06 2.62 133 24 28 4 587.00 4.99 134 24 30 6 491.38 16.45 135 24 97 73 350.19 0.70 136 24 99 75 346.47 1.15 137 24 234 210 55.52 1.27 138 25 28 3 642.18 1.28 139 25 30 5 436.55 43.88 140 25 32 7 491.40 16.47 141 25 45 20 528.88 1.17 142 28 96 68 451.03 1.09 143 28 97 69 450.97 1.10 144 29 94 65 451.17 1.10 145 29 95 66 451.09 1.09 146 29 96 67 451.06 1.09 147 29 97 68 451.05 1.08 148 30 97 67 451.05 1.08 149 30 99 69 451.04 1.09 150 31 47 16 558.38 5.03 151 31 91 60 451.19 1.12 152 31 95 64 451.22 1.11 153 31 97 66 451.10 1.09 154 31 98 67 451.05 1.09 155 31 99 68 451.06 1.08 156 32 44 12 558.41 5.03 157 32 45 13 558.42 5.02 158 32 46 14 558.41 5.01 159 32 47 15 558.41 5.02 160 32 48 16 558.40 5.02 161 32 99 67 451.07 1.08 162 33 48 15 558.40 5.03 163 33 88 55 451.56 1.11 164 33 91 58 451.55 1.12 165 33 98 65 451.20 1.09 166 33 99 66 451.11 1.09 167 33 100 67 451.06 1.09 168 33 101 68 451.06 1.09 169 34 39 5 572.53 2.92 170 34 42 8 558.66 5.07 171 34 44 10 558.65 5.09 172 34 48 14 558.50 5.03 173 34 49 15 558.40 5.03 174 34 50 16 558.41 5.03 175 34 51 17 558.40 5.03 176 34 101 67 451.07 1.08 177 35 50 15 558.41 5.03 178 35 74 39 461.54 2.39 179 35 100 65 451.21 1.09 180 35 101 66 451.11 1.09 181 35 102 67 451.06 1.08 182 35 103 68 451.03 1.09 183 35 109 74 254.25 0.97 184 35 114 79 242.24 0.70 185 35 118 83 241.46 0.96 186 36 39 3 645.59 0.68 187 36 50 14 558.63 5.07 188 36 51 15 558.57 5.07 189 36 74 38 461.56 2.40 190 36 102 66 451.11 1.08 191 36 103 67 451.01 1.09 192 36 104 68 451.03 1.08 193 37 50 13 558.66 5.06 194 37 51 14 558.57 5.07 195 37 54 17 553.45 3.08 196 37 55 18 475.55 6.96 197 37 56 19 475.52 6.96 198 37 73 36 461.57 2.40 199 37 74 37 461.57 2.40 200 37 77 40 461.51 2.37 201 38 56 18 475.54 6.96 202 39 42 3 701.02 3.27 203 39 51 12 558.69 5.05 204 40 51 11 558.72 5.07 205 41 51 10 558.77 5.06 206 42 46 4 645.34 3.82 207 42 49 7 558.80 5.06 208 42 51 9 558.78 5.06 209 44 101 57 451.07 1.08 210 46 49 3 653.16 7.11 211 47 91 44 451.25 1.11 212 48 84 36 451.62 1.12 213 48 87 39 451.56 1.11 214 48 88 40 451.56 1.11 215 48 91 43 451.55 1.12 216 49 52 3 640.84 3.93 217 50 53 3 632.57 0.96 218 50 54 4 585.21 0.56 219 50 77 27 460.90 2.16 220 50 84 34 451.76 1.07 221 51 54 3 600.82 7.24 222 51 55 4 522.83 16.67 223 53 76 23 461.53 2.39 224 53 77 24 461.51 2.38 225 53 80 27 452.17 1.15 226 53 84 31 452.00 1.14 227 54 59 5 597.47 1.96 228 54 73 19 461.55 2.39 229 54 76 22 461.54 2.39 230 54 77 23 461.50 2.37 231 55 58 3 634.33 1.97 232 55 59 4 614.14 6.67 233 56 59 3 626.00 1.72 234 56 60 4 601.11 0.14 235 56 69 13 461.66 2.39 236 56 70 14 461.66 2.39 237 56 73 17 461.61 2.38 238 57 60 3 601.12 0.14 239 57 61 4 601.13 0.14 240 58 61 3 611.48 5.04 241 58 62 4 610.90 5.33 242 59 62 3 610.91 5.32 243 59 63 4 610.90 5.33 244 59 64 5 589.06 2.12 245 59 69 10 461.78 2.41 246 59 72 13 461.75 2.40 247 59 73 14 461.69 2.39 248 59 76 17 461.69 2.39 249 60 63 3 614.42 3.56 250 60 64 4 583.45 0.69 251 60 66 6 462.53 2.22 252 60 69 9 461.78 2.39 253 62 76 14 462.50 2.19 254 64 68 4 595.31 1.72 255 64 69 5 547.21 15.97 256 64 72 8 501.40 4.50 257 64 76 12 506.45 3.53 258 65 68 3 630.10 0.88 259 65 69 4 615.31 6.52 260 66 69 3 628.19 7.92 261 66 70 4 615.34 6.52 262 67 70 3 643.12 0.45 263 67 71 4 630.12 0.87 264 68 71 3 643.12 0.45 265 68 72 4 618.17 5.09 266 69 72 3 618.17 5.09 267 69 73 4 604.37 1.80 268 70 73 3 604.75 2.93 269 70 74 4 629.75 2.29 270 70 105 35 451.17 1.08 271 70 108 38 449.01 0.72 272 71 74 3 632.95 0.70 273 71 75 4 629.75 2.29 274 71 108 37 448.99 0.73 275 72 75 3 629.75 2.29 276 72 76 4 616.69 8.83 277 73 76 3 630.50 1.93 278 73 77 4 616.70 8.83 279 74 77 3 631.16 1.59 280 74 78 4 604.42 2.68 281 74 103 29 451.25 1.09 282 74 108 34 422.56 0.14 283 74 112 38 254.16 0.95 284 75 78 3 639.02 2.33 285 75 79 4 631.15 1.59 286 75 112 37 254.19 0.96 287 76 79 3 636.53 0.98 288 77 80 3 631.07 6.46 289 77 81 4 622.21 10.89 290 77 84 7 508.94 1.62 291 77 114 37 242.38 0.65 292 78 81 3 577.23 1.18 293 78 112 34 254.12 0.96 294 78 113 35 249.83 0.44 295 78 114 36 242.38 0.65 296 78 117 39 242.34 0.64 297 80 83 3 620.15 8.57 298 80 84 4 598.71 0.01 299 81 84 3 635.95 4.45 300 81 85 4 599.01 0.17 301 81 114 33 242.35 0.64 302 81 117 36 242.06 0.76 303 81 118 37 241.72 0.86 304 82 85 3 625.21 6.04 305 82 86 4 598.70 0.01 306 83 86 3 627.57 8.63 307 83 87 4 601.11 1.22 308 84 87 3 617.44 6.95 309 84 88 4 613.87 5.17 310 84 114 30 242.35 0.64 311 84 118 34 241.46 0.95 312 85 88 3 631.47 0.07 313 85 89 4 601.09 1.22 314 85 118 33 241.33 0.89 315 85 121 36 241.02 0.84 316 85 122 37 240.92 0.83 317 86 89 3 599.94 1.79 318 86 90 4 596.32 3.60 319 87 90 3 634.29 1.35 320 87 91 4 605.49 0.80 321 88 91 3 638.55 0.77 322 88 92 4 620.44 8.29 323 88 100 12 451.22 1.07 324 88 118 30 241.31 0.88 325 88 122 34 240.91 0.83 326 89 92 3 627.72 8.01 327 89 93 4 634.81 1.59 328 89 122 33 240.91 0.83 329 89 123 34 240.90 0.83 330 90 93 3 659.35 3.77 331 90 94 4 615.43 9.38 332 91 94 3 637.89 2.93 333 91 95 4 615.43 9.38 334 91 98 7 451.22 1.06 335 92 95 3 644.27 6.13 336 92 98 6 451.23 1.06 337 92 123 31 240.75 0.90 338 95 98 3 670.53 1.46 339 97 234 137 55.08 1.04 340 97 237 140 41.93 0.14 341 100 122 22 241.07 0.86 342 102 109 7 254.24 0.97 343 103 106 3 613.56 9.05 344 103 108 5 263.93 1.92 345 103 109 6 254.61 1.15 346 105 108 3 648.86 3.73 347 106 109 3 617.19 9.04 348 106 110 4 583.18 5.21 349 106 129 23 240.90 0.84 350 106 148 42 224.34 0.20 351 107 110 3 578.17 2.71 352 107 111 4 572.56 5.50 353 108 112 4 254.12 0.96 354 109 115 6 241.68 0.86 355 109 116 7 241.68 0.86 356 109 119 10 241.68 0.86 357 109 156 47 226.88 0.08 358 110 116 6 241.72 0.87 359 110 148 38 224.41 0.13 360 110 152 42 225.05 0.09 361 110 155 45 226.87 0.08 362 110 156 46 226.88 0.08 363 112 116 4 609.90 10.56 364 113 116 3 638.19 1.48 365 113 117 4 593.22 2.22 366 114 117 3 639.27 3.52 367 114 118 4 595.62 3.42 368 115 118 3 632.41 0.24 369 115 119 4 603.59 0.56 370 116 119 3 630.44 0.74 371 116 120 4 605.11 1.31 372 116 155 39 225.67 0.39 373 116 156 40 225.05 0.08 374 117 120 3 635.92 0.96 375 117 121 4 611.32 8.23 376 118 121 3 633.42 2.21 377 118 122 4 611.33 8.22 378 119 122 3 632.84 0.58 379 119 125 6 361.88 59.65 380 119 127 8 240.90 0.83 381 119 156 37 225.03 0.07 382 119 158 39 226.87 0.09 383 122 125 3 655.45 1.08 384 124 240 116 36.61 1.02 385 124 244 120 19.91 1.56 386 125 158 33 622.38 0.71 387 126 159 33 622.41 0.73 388 126 233 107 58.80 0.80 389 126 236 110 51.62 0.63 390 126 237 111 44.04 0.35 391 126 240 114 37.34 0.65 392 127 152 25 622.50 0.68 393 127 156 29 622.70 0.61 394 127 158 31 622.54 0.79 395 127 159 32 622.56 0.78 396 127 160 33 622.56 0.78 397 127 161 34 622.91 0.73 398 128 161 33 622.93 0.73 399 128 163 35 623.34 0.82 400 128 222 94 124.31 1.57 401 128 233 105 58.80 0.80 402 129 148 19 622.65 0.59 403 129 149 20 622.38 0.71 404 129 152 23 622.93 0.73 405 129 160 31 623.02 0.77 406 129 161 32 623.09 0.73 407 129 162 33 623.09 0.73 408 129 163 34 623.37 0.82 409 130 163 33 623.45 0.78 410 130 165 35 623.93 0.82 411 130 222 92 124.67 1.50 412 131 135 4 633.45 4.46 413 131 145 14 622.15 0.68 414 131 163 32 623.78 0.90 415 131 164 33 623.78 0.90 416 131 165 34 623.98 0.82 417 132 135 3 653.39 3.89 418 133 136 3 638.16 3.61 419 133 164 31 625.25 0.35 420 133 165 32 632.70 2.69 421 133 170 37 660.35 3.06 422 133 178 45 631.86 0.01 423 134 137 3 676.19 3.83 424 135 141 6 634.87 0.65 425 135 145 10 632.96 0.32 426 136 141 5 640.24 1.97 427 136 142 6 634.87 0.64 428 136 145 9 643.24 0.61 429 136 164 28 813.95 0.75 430 136 178 42 660.15 3.15 431 136 182 46 651.78 2.58 432 137 141 4 645.76 0.43 433 138 141 3 646.83 0.02 434 138 142 4 646.19 0.24 435 139 142 3 650.53 1.55 436 139 143 4 647.01 0.12 437 139 181 42 818.24 0.75 438 139 188 49 804.63 7.44 439 139 191 52 797.25 4.37 440 139 192 53 796.88 4.44 441 140 143 3 650.98 1.33 442 140 144 4 817.45 0.48 443 146 216 70 125.64 1.54 444 146 217 71 125.62 1.53 445 146 218 72 125.53 1.49 446 146 219 73 125.03 1.43 447 147 210 63 661.67 2.48 448 150 210 60 803.28 6.12 449 159 240 81 41.99 1.16 450 161 217 56 125.07 1.43 451 161 218 57 124.81 1.52 452 161 220 59 124.75 1.52 453 161 236 75 52.13 0.74 454 162 217 55 125.17 1.44 455 162 219 57 124.76 1.53 456 162 220 58 124.76 1.52 457 163 219 56 124.80 1.53 458 163 220 57 124.75 1.52 459 163 222 59 124.73 1.52 460 164 219 55 125.17 1.44 461 164 220 56 124.91 1.48 462 164 221 57 124.75 1.52 463 164 222 58 124.74 1.52 464 165 222 57 124.67 1.51 465 165 223 58 124.48 1.58 466 165 224 59 124.48 1.59 467 166 222 56 124.78 1.53 468 166 223 57 124.39 1.54 469 167 221 54 125.15 1.43 470 167 222 55 124.91 1.51 471 167 223 56 124.75 1.53 472 167 228 61 100.89 2.22 473 168 223 55 124.91 1.51 474 168 225 57 124.73 1.53 475 168 226 58 124.46 1.57 476 179 221 42 125.55 1.48 477 182 218 36 125.77 1.55 478 182 219 37 125.58 1.50 479 182 221 39 125.61 1.52 480 183 218 35 125.77 1.55 481 185 211 26 803.19 0.92 482 185 216 31 126.53 1.47 483 207 210 3 643.79 5.37 484 207 211 4 585.27 0.64 485 208 211 3 633.60 3.38 486 208 212 4 607.69 9.96 487 209 212 3 630.09 1.62 488 209 213 4 607.84 9.89 489 210 213 3 641.94 4.00 490 211 216 5 134.44 2.79 491 220 229 9 72.34 1.62 492 220 232 12 69.02 1.59 493 220 233 13 68.31 1.43 494 221 228 7 72.45 1.59 495 221 229 8 72.36 1.62 496 222 228 6 72.45 1.58 497 222 229 7 72.36 1.62 498 222 233 11 69.76 1.91 499 223 226 3 608.77 10.50 500 223 227 4 97.91 13.21 501 223 228 5 96.81 13.75 502 224 230 6 104.51 17.46 503 227 230 3 633.82 0.51 504 227 231 4 637.28 2.24 505 229 232 3 608.16 9.79 506 229 233 4 599.52 9.44 507 230 233 3 633.00 7.29 508 230 234 4 544.88 21.79 509 231 234 3 586.53 0.98 510 231 235 4 553.12 17.71 511 232 235 3 637.79 5.82 512 232 236 4 591.28 1.36 513 233 236 3 596.45 3.95 514 233 237 4 599.38 5.42 515 234 237 3 619.19 4.46 516 234 238 4 599.39 5.42 517 235 238 3 599.32 5.47 518 235 239 4 583.18 13.52 519 236 239 3 597.89 6.17 520 236 240 4 595.38 7.42 521 237 240 3 629.04 9.42 522 237 241 4 607.49 1.36 523 238 241 3 607.49 1.35 524 238 242 4 607.48 1.35 525 239 242 3 620.12 7.67 526 239 243 4 595.37 7.41 527 240 243 3 611.83 11.81 528 240 244 4 611.82 11.81