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 5 30 25 613.40 1.64 2 5 49 44 547.12 0.30 3 5 120 115 268.64 5.63 4 6 30 24 613.40 1.64 5 6 31 25 613.40 1.64 6 6 49 43 547.18 0.30 7 6 50 44 547.10 0.32 8 6 51 45 547.10 0.32 9 7 24 17 613.71 1.54 10 7 29 22 613.74 1.54 11 7 30 23 613.72 1.54 12 7 31 24 613.45 1.61 13 7 32 25 613.41 1.64 14 7 51 44 547.14 0.29 15 7 53 46 547.08 0.32 16 7 116 109 283.21 7.11 17 7 120 113 273.80 5.38 18 8 32 24 613.45 1.61 19 8 34 26 613.41 1.64 20 8 40 32 547.79 0.17 21 8 44 36 547.55 0.26 22 8 51 43 547.19 0.30 23 8 52 44 547.11 0.31 24 8 53 45 547.11 0.31 25 8 77 69 456.89 1.19 26 9 16 7 615.84 2.23 27 9 17 8 614.33 1.70 28 9 20 11 613.96 1.58 29 9 24 15 613.96 1.58 30 9 31 22 613.74 1.53 31 9 32 23 613.69 1.55 32 9 33 24 613.60 1.54 33 9 34 25 613.41 1.64 34 9 53 44 547.14 0.29 35 10 34 24 613.44 1.64 36 10 36 26 613.35 1.60 37 10 37 27 602.78 1.20 38 10 40 30 551.27 1.31 39 10 52 42 547.26 0.29 40 10 53 43 547.20 0.30 41 10 54 44 547.10 0.32 42 10 55 45 547.10 0.32 43 10 58 48 543.32 0.55 44 10 66 56 461.26 2.07 45 11 16 5 620.01 4.05 46 11 17 6 619.09 3.80 47 11 34 23 613.67 1.55 48 11 35 24 613.48 1.60 49 11 55 44 547.12 0.31 50 11 58 47 545.41 0.26 51 11 82 71 455.59 1.54 52 11 105 94 363.19 2.28 53 12 17 5 630.94 4.35 54 12 35 23 613.49 1.59 55 12 55 43 547.18 0.30 56 12 57 45 547.14 0.29 57 12 58 46 545.17 0.38 58 12 59 47 543.32 0.55 59 13 16 3 659.67 1.45 60 13 17 4 650.10 6.23 61 14 17 3 660.60 1.91 62 14 18 4 634.16 5.96 63 15 19 4 630.84 6.40 64 16 19 3 653.99 0.40 65 16 20 4 630.84 6.40 66 16 82 66 455.51 1.58 67 16 105 89 362.10 1.84 68 17 21 4 633.62 7.37 69 17 33 16 613.85 1.55 70 17 34 17 613.84 1.54 71 17 35 18 613.78 1.53 72 18 21 3 653.56 9.55 73 18 22 4 653.60 9.53 74 19 22 3 672.32 0.18 75 19 23 4 653.61 9.53 76 20 23 3 671.48 0.59 77 20 24 4 648.74 7.10 78 20 53 33 547.21 0.30 79 20 107 87 346.84 0.21 80 20 112 92 284.06 7.00 81 21 25 4 654.62 4.14 82 21 31 10 614.00 1.61 83 22 25 3 668.71 0.80 84 22 26 4 666.54 1.83 85 23 26 3 670.77 0.60 86 23 27 4 667.43 2.28 87 23 109 86 284.35 6.89 88 24 27 3 669.97 1.02 89 24 28 4 665.27 2.48 90 24 29 5 622.75 2.10 91 24 31 7 615.50 2.12 92 24 113 89 283.94 6.97 93 24 116 92 283.58 6.98 94 25 28 3 681.25 0.88 95 25 29 4 638.60 3.69 96 25 30 5 622.89 2.18 97 25 31 6 622.72 2.08 98 27 113 86 283.94 6.97 99 29 113 84 283.96 6.99 100 29 120 91 273.81 5.38 101 34 39 5 627.14 1.01 102 34 40 6 547.95 0.25 103 34 43 9 547.84 0.20 104 36 39 3 692.22 4.38 105 36 40 4 661.15 1.45 106 36 58 22 545.78 0.56 107 37 40 3 663.21 0.42 108 37 41 4 663.70 3.48 109 37 58 21 545.89 0.61 110 37 61 24 461.67 2.12 111 37 66 29 461.28 2.07 112 38 41 3 666.52 2.08 113 38 42 4 666.10 4.69 114 38 61 23 473.41 5.48 115 39 42 3 675.13 4.46 116 39 43 4 665.90 4.79 117 40 43 3 665.90 4.79 118 40 44 4 661.09 7.20 119 40 52 12 547.28 0.28 120 40 66 26 461.28 2.06 121 40 70 30 460.13 1.88 122 41 44 3 662.88 6.29 123 41 61 20 484.92 0.29 124 41 66 25 461.28 2.06 125 41 69 28 460.38 1.85 126 41 70 29 460.13 1.88 127 41 73 32 459.31 1.84 128 44 48 4 682.08 0.60 129 44 70 26 459.83 2.02 130 44 75 31 457.16 1.10 131 44 77 33 457.01 1.12 132 45 48 3 669.23 0.14 133 46 75 29 457.00 1.14 134 49 120 71 273.79 5.39 135 49 123 74 268.08 7.47 136 49 124 75 267.48 7.18 137 49 127 78 200.63 6.96 138 50 77 27 456.78 1.20 139 50 78 28 456.54 1.11 140 50 120 70 273.79 5.39 141 50 123 73 268.10 7.48 142 51 77 26 456.81 1.16 143 51 80 29 455.53 1.51 144 51 116 65 283.32 7.11 145 51 119 68 273.84 5.37 146 51 120 69 273.80 5.39 147 52 70 18 459.66 2.02 148 52 77 25 456.89 1.19 149 52 78 26 456.82 1.19 150 52 79 27 455.53 1.51 151 52 80 28 455.53 1.51 152 53 80 27 455.52 1.52 153 53 82 29 455.42 1.55 154 53 112 59 284.30 6.88 155 53 116 63 283.51 7.08 156 54 58 4 722.44 2.75 157 54 63 9 461.31 2.10 158 54 66 12 461.26 2.06 159 54 79 25 456.88 1.19 160 54 80 26 456.55 1.12 161 54 81 27 455.42 1.55 162 54 82 28 455.42 1.55 163 55 58 3 719.66 4.14 164 55 63 8 461.39 2.09 165 55 82 27 455.42 1.55 166 55 105 50 363.20 2.28 167 56 62 6 462.00 1.80 168 56 63 7 461.39 2.09 169 56 64 8 461.39 2.10 170 56 81 25 456.86 1.20 171 56 82 26 456.68 1.20 172 56 83 27 455.44 1.55 173 56 90 34 365.10 2.03 174 56 102 46 364.48 2.06 175 57 85 28 455.64 1.44 176 57 88 31 420.64 0.28 177 58 61 3 698.53 2.69 178 58 63 5 508.65 21.18 179 60 65 5 660.82 3.48 180 61 65 4 648.50 2.68 181 61 66 5 645.13 1.01 182 61 69 8 642.02 0.14 183 62 65 3 667.32 4.03 184 62 66 4 660.83 3.48 185 63 66 3 667.59 0.14 186 63 67 4 669.21 0.67 187 63 81 18 456.88 1.21 188 64 67 3 671.01 0.22 189 64 68 4 669.23 0.68 190 64 81 17 457.08 1.14 191 64 94 30 364.83 2.13 192 65 68 3 675.08 3.62 193 65 69 4 669.22 0.70 194 66 69 3 671.79 0.58 195 66 70 4 669.22 0.70 196 67 70 3 672.76 0.90 197 67 71 4 668.65 0.99 198 67 79 12 457.15 1.10 199 67 81 14 457.03 1.13 200 67 94 27 364.72 2.10 201 67 97 30 364.56 2.04 202 68 71 3 670.49 1.93 203 68 72 4 668.59 1.02 204 68 93 25 364.91 2.12 205 69 72 3 670.75 2.26 206 69 73 4 666.38 0.08 207 70 73 3 671.25 2.02 208 70 74 4 666.38 0.07 209 70 75 5 585.50 17.79 210 70 77 7 457.18 1.10 211 70 79 9 457.16 1.10 212 71 74 3 666.38 0.07 213 78 98 20 364.48 2.06 214 78 100 22 364.39 2.05 215 78 119 41 279.94 6.37 216 78 123 45 272.20 5.50 217 79 98 19 364.49 2.06 218 79 99 20 364.42 2.06 219 79 100 21 364.42 2.06 220 80 100 20 364.41 2.06 221 80 101 21 364.36 2.06 222 80 103 23 363.89 1.96 223 80 112 32 284.42 6.85 224 80 115 35 283.98 6.96 225 80 116 36 284.03 6.92 226 81 99 18 364.53 2.06 227 81 101 20 364.43 2.05 228 81 102 21 364.24 2.12 229 81 103 22 363.89 1.96 230 82 103 21 363.63 2.07 231 82 105 23 363.23 2.27 232 82 107 25 362.04 1.84 233 82 112 30 284.70 6.74 234 83 103 20 364.40 2.06 235 83 104 21 363.26 2.26 236 83 105 22 363.25 2.27 237 84 105 21 363.36 2.22 238 85 88 3 694.50 2.38 239 90 94 4 637.95 12.38 240 90 95 5 554.50 29.35 241 90 102 12 364.60 2.05 242 91 94 3 647.45 7.66 243 91 95 4 653.57 0.44 244 92 95 3 654.35 0.83 245 92 96 4 653.58 0.43 246 93 96 3 659.51 3.41 247 93 97 4 633.83 10.31 248 94 97 3 648.78 2.83 249 94 99 5 410.99 25.03 250 95 99 4 410.98 25.03 251 95 102 7 365.31 2.30 252 99 102 3 767.66 0.99 253 100 115 15 284.32 6.86 254 100 118 18 283.97 6.86 255 100 119 19 283.20 7.11 256 100 122 22 280.29 6.30 257 101 115 14 284.35 6.85 258 103 107 4 655.18 5.29 259 103 111 8 284.75 6.74 260 103 112 9 284.74 6.74 261 103 115 12 284.72 6.75 262 104 107 3 693.78 4.82 263 107 112 5 638.76 2.98 264 108 111 3 668.56 0.85 265 108 112 4 659.74 4.29 266 109 112 3 667.82 1.22 267 109 113 4 657.36 0.98 268 110 113 3 667.80 1.23 269 110 114 4 657.36 0.98 270 111 114 3 655.60 4.25 271 111 115 4 657.21 3.79 272 112 115 3 675.86 5.54 273 112 116 4 655.95 4.42 274 113 116 3 671.31 3.27 275 113 117 4 665.44 0.34 276 114 117 3 687.75 2.81 277 114 118 4 665.84 0.14 278 115 118 3 669.74 2.06 279 115 119 4 665.86 0.14 280 116 119 3 665.87 0.14 281 116 120 4 665.87 0.14 282 117 120 3 665.87 0.14 283 117 121 4 665.86 0.14 284 118 121 3 667.25 0.85 285 118 122 4 676.98 1.52 286 119 122 3 676.98 1.52 287 119 123 4 669.69 2.12 288 120 123 3 669.81 2.06 289 120 124 4 669.83 2.06 290 121 124 3 669.99 2.14 291 121 125 4 669.98 2.14 292 122 125 3 669.98 2.14 293 122 126 4 657.09 0.69 294 123 126 3 679.78 1.54 295 123 127 4 663.25 6.72 296 124 127 3 679.78 1.54 297 124 128 4 666.25 5.22 298 125 128 3 679.78 1.54 299 125 129 4 663.23 6.73 300 126 130 4 665.46 5.61 301 127 130 3 675.30 0.28 302 127 131 4 661.07 0.10 303 128 131 3 677.23 0.69 304 128 132 4 656.36 1.04 305 129 132 3 672.41 2.11 306 129 133 4 661.96 0.53 307 130 133 3 679.12 1.25 308 130 134 4 659.40 1.81 309 131 134 3 671.82 2.40 310 131 135 4 659.42 1.80 311 132 135 3 672.88 2.23 312 132 136 4 663.49 3.24 313 132 199 67 24.59 0.56 314 133 136 3 665.89 2.04 315 133 137 4 663.51 3.24 316 134 137 3 667.07 5.01 317 134 138 4 662.90 3.56 318 135 138 3 663.00 3.51 319 135 139 4 660.86 4.58 320 136 140 4 663.58 3.21 321 136 196 60 38.79 2.23 322 136 199 63 31.43 1.42 323 136 200 64 29.94 2.13 324 137 140 3 666.50 2.66 325 137 141 4 646.24 4.50 326 138 141 3 673.91 3.03 327 138 142 4 659.15 0.98 328 139 142 3 677.93 1.02 329 139 184 45 66.95 0.75 330 139 185 46 59.70 0.35 331 139 186 47 62.32 0.68 332 139 196 57 56.31 0.42 333 140 143 3 682.12 1.05 334 140 151 11 137.97 4.49 335 140 185 45 66.76 0.86 336 140 196 56 57.27 0.86 337 140 197 57 56.30 0.42 338 142 184 42 72.81 1.92 339 143 147 4 655.54 2.04 340 143 151 8 389.59 1.19 341 143 181 38 74.28 2.62 342 143 184 41 72.89 1.94 343 143 185 42 72.89 1.94 344 144 147 3 669.99 0.04 345 144 148 4 664.77 2.57 346 144 184 40 96.00 9.86 347 145 148 3 669.99 0.03 348 145 149 4 664.78 2.57 349 146 149 3 679.96 4.95 350 146 150 4 667.41 1.26 351 146 177 31 113.95 3.21 352 147 150 3 667.42 1.26 353 147 151 4 667.41 1.26 354 147 177 30 113.95 3.21 355 147 180 33 113.95 3.21 356 147 181 34 113.94 3.21 357 147 184 37 113.27 3.03 358 148 151 3 663.15 0.88 359 148 152 4 663.06 0.92 360 149 152 3 673.65 1.33 361 149 153 4 659.49 0.89 362 149 167 18 117.53 3.23 363 150 153 3 676.72 6.91 364 150 154 4 657.94 1.66 365 150 163 13 117.67 3.30 366 150 167 17 117.89 3.39 367 150 169 19 117.53 3.23 368 150 174 24 114.11 3.21 369 150 177 27 114.09 3.21 370 150 178 28 114.06 3.23 371 150 181 31 114.02 3.22 372 151 154 3 664.96 0.90 373 151 155 4 657.96 1.66 374 151 181 30 113.99 3.23 375 151 185 34 113.14 2.96 376 151 193 42 94.30 1.73 377 151 197 46 92.67 1.26 378 152 155 3 691.25 0.81 379 152 156 4 666.18 1.75 380 153 156 3 671.34 0.83 381 153 157 4 664.79 2.44 382 153 158 5 637.51 2.25 383 153 163 10 121.48 1.71 384 153 166 13 121.53 1.73 385 153 167 14 121.42 1.76 386 154 157 3 666.45 2.47 387 154 163 9 153.13 0.82 388 154 178 24 114.14 3.22 389 154 190 36 100.19 4.17 390 154 193 39 96.82 2.90 391 155 193 38 94.40 1.69 392 155 194 39 94.20 1.68 393 155 197 42 93.06 1.15 394 158 162 4 660.04 1.26 395 158 163 5 651.98 1.95 396 158 166 8 434.83 93.52 397 159 162 3 662.97 0.21 398 159 163 4 659.91 1.32 399 160 163 3 680.69 7.74 400 160 164 4 660.04 1.26 401 160 171 11 131.30 10.01 402 160 174 14 118.06 3.41 403 160 175 15 118.05 3.41 404 160 178 18 118.01 3.42 405 161 164 3 679.71 8.22 406 161 165 4 658.50 2.02 407 161 171 10 131.31 10.02 408 162 165 3 659.13 1.18 409 162 166 4 652.28 1.84 410 163 166 3 655.40 2.21 411 163 167 4 652.11 1.76 412 163 174 11 118.05 3.41 413 163 178 15 117.91 3.47 414 164 167 3 671.16 2.96 415 164 168 4 518.36 64.69 416 164 169 5 186.82 11.54 417 164 171 7 137.27 7.05 418 164 174 10 118.05 3.41 419 169 173 4 660.45 1.64 420 169 174 5 657.76 2.98 421 169 177 8 631.64 2.35 422 170 173 3 667.01 1.65 423 170 174 4 667.01 1.65 424 171 174 3 664.07 0.18 425 171 175 4 660.56 1.59 426 172 175 3 662.35 0.70 427 172 176 4 660.44 1.65 428 173 176 3 670.20 4.63 429 173 177 4 660.38 1.62 430 174 177 3 660.39 1.50 431 174 178 4 657.74 2.82 432 175 178 3 668.71 3.56 433 175 179 4 655.62 1.77 434 176 179 3 656.97 1.09 435 176 180 4 655.60 1.76 436 177 180 3 666.45 4.79 437 177 181 4 655.36 1.61 438 178 181 3 666.45 4.79 439 178 182 4 657.86 0.52 440 178 190 12 151.62 1.54 441 179 182 3 675.59 0.95 442 179 183 4 657.90 0.50 443 180 183 3 666.04 1.38 444 180 184 4 657.85 0.48 445 181 184 3 657.89 0.49 446 181 185 4 657.90 0.50 447 181 193 12 151.59 1.56 448 182 185 3 658.50 0.81 449 182 186 4 657.83 0.48 450 182 187 5 250.69 10.34 451 182 188 6 255.89 12.93 452 182 189 7 182.41 11.47 453 182 190 8 153.94 1.22 454 182 193 11 151.59 1.55 455 183 186 3 650.72 4.03 456 185 193 8 152.59 1.08 457 185 196 11 151.62 1.55 458 185 197 12 151.51 1.60 459 187 192 5 383.24 45.87 460 187 193 6 252.93 19.28 461 187 196 9 175.99 8.29 462 188 192 4 662.53 0.18 463 189 192 3 665.86 1.84 464 189 193 4 657.66 2.62 465 190 193 3 663.24 0.17 466 190 194 4 657.66 2.62 467 191 194 3 684.32 4.83 468 191 195 4 657.82 2.69 469 192 195 3 665.01 2.93 470 192 196 4 655.10 1.16 471 193 196 3 682.38 5.62 472 193 197 4 654.68 0.96 473 194 197 3 666.13 2.35 474 194 198 4 654.68 0.96 475 195 198 3 654.69 0.96 476 195 199 4 653.73 1.43 477 196 199 3 659.38 1.03 478 196 200 4 650.77 0.06 479 197 200 3 648.36 2.73