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 8 11 3 674.70 1.60 2 8 12 4 656.73 3.10 3 8 115 107 85.76 0.57 4 9 12 3 680.60 8.84 5 9 13 4 659.06 1.93 6 10 13 3 680.14 0.55 7 10 14 4 675.62 2.81 8 10 109 99 106.58 1.71 9 10 111 101 97.12 2.98 10 10 115 105 94.76 4.08 11 11 14 3 675.62 2.81 12 11 15 4 675.62 2.81 13 11 41 30 111.52 10.06 14 12 15 3 676.25 2.49 15 12 16 4 676.23 2.50 16 13 16 3 682.02 1.93 17 13 17 4 674.19 1.46 18 13 105 92 127.08 0.42 19 13 108 95 127.05 0.41 20 13 109 96 126.55 0.62 21 14 17 3 685.26 2.02 22 14 18 4 674.19 1.46 23 14 41 27 128.34 1.92 24 14 69 55 127.67 2.29 25 14 97 83 129.07 1.27 26 14 102 88 127.09 0.42 27 14 105 91 127.08 0.42 28 14 112 98 125.31 1.14 29 15 18 3 674.16 1.46 30 15 41 26 128.10 1.79 31 15 43 28 129.16 1.58 32 15 95 80 128.83 1.43 33 17 97 80 129.27 1.18 34 17 101 84 128.69 0.91 35 17 105 88 127.31 0.31 36 18 95 77 129.53 1.32 37 18 96 78 129.31 1.22 38 18 97 79 129.24 1.19 39 19 95 76 129.71 1.30 40 19 96 77 129.62 1.26 41 20 43 23 130.67 1.71 42 20 93 73 130.85 1.78 43 20 94 74 129.94 1.34 44 20 95 75 129.71 1.29 45 21 93 72 130.91 1.75 46 21 94 73 130.59 1.67 47 21 96 75 130.59 1.66 48 22 92 70 209.06 37.98 49 22 93 71 131.09 1.81 50 23 27 4 659.82 4.37 51 23 29 6 434.34 58.38 52 23 91 68 344.89 51.12 53 23 92 69 224.88 45.88 54 23 94 71 204.48 38.30 55 23 96 73 205.33 37.90 56 24 27 3 687.62 5.65 57 24 88 64 363.57 52.31 58 24 91 67 360.48 50.84 59 25 88 63 365.47 52.69 60 25 89 64 365.92 52.05 61 25 90 65 363.58 52.31 62 25 91 66 363.55 52.33 63 26 87 61 369.22 51.34 64 26 88 62 368.46 51.45 65 27 87 60 370.15 50.98 66 27 88 61 369.49 51.20 67 28 31 3 721.10 0.70 68 28 85 57 370.55 50.96 69 28 86 58 370.43 50.98 70 28 87 59 370.17 50.98 71 29 47 18 370.44 50.98 72 29 70 41 369.19 51.11 73 29 86 57 370.51 50.98 74 29 87 58 370.48 50.96 75 29 88 59 370.45 50.98 76 29 94 65 368.42 51.49 77 30 34 4 674.03 0.90 78 30 40 10 376.90 47.25 79 30 70 40 369.64 50.91 80 30 71 41 369.04 51.17 81 30 82 52 370.98 51.08 82 30 84 54 370.92 51.01 83 30 85 55 370.82 50.98 84 30 86 56 370.73 51.01 85 31 34 3 689.10 0.56 86 31 82 51 371.11 51.09 87 31 85 54 370.87 50.99 88 32 82 50 371.09 51.06 89 32 83 51 371.03 51.05 90 32 84 52 370.93 51.01 91 32 85 53 370.92 51.01 92 33 81 48 372.91 50.45 93 33 82 49 371.98 50.74 94 34 81 47 373.33 50.51 95 34 82 48 372.92 50.40 96 35 79 44 373.83 50.65 97 35 80 45 373.80 50.65 98 35 81 46 373.47 50.58 99 36 74 38 373.75 50.67 100 36 80 44 373.81 50.65 101 36 82 46 373.49 50.57 102 36 99 63 369.97 50.95 103 37 98 61 370.02 50.97 104 37 99 62 369.91 50.91 105 38 71 33 376.48 51.02 106 38 82 44 374.12 50.65 107 38 96 58 370.41 51.01 108 38 97 59 370.39 51.01 109 38 98 60 370.02 50.97 110 38 99 61 370.00 50.97 111 39 69 30 377.07 50.86 112 39 70 31 376.85 50.95 113 39 71 32 376.48 51.02 114 39 72 33 376.47 51.02 115 39 96 57 370.44 50.99 116 39 97 58 370.39 51.01 117 39 99 60 370.01 50.97 118 39 102 63 357.04 47.76 119 40 69 29 377.07 50.86 120 40 70 30 376.94 50.91 121 40 82 42 375.66 50.71 122 40 94 54 370.78 50.95 123 40 95 55 370.64 50.95 124 40 96 56 370.45 51.00 125 41 67 26 379.01 50.03 126 41 68 27 378.86 50.04 127 41 69 28 377.07 50.86 128 41 94 53 370.78 50.95 129 41 95 54 370.68 50.95 130 42 45 3 723.87 0.40 131 42 47 5 626.29 0.18 132 42 64 22 380.05 50.06 133 42 65 23 379.62 50.23 134 42 66 24 379.50 50.25 135 42 67 25 379.05 50.05 136 42 68 26 378.97 50.05 137 42 70 28 378.17 50.39 138 43 66 23 379.60 50.25 139 43 93 50 371.01 50.93 140 43 95 52 370.88 50.93 141 44 66 22 379.66 50.23 142 44 92 48 372.05 50.62 143 44 93 49 371.21 51.02 144 45 65 20 380.06 50.05 145 45 66 21 380.03 50.05 146 45 90 45 373.98 50.56 147 45 91 46 373.50 50.52 148 45 92 47 372.06 50.62 149 46 64 18 380.84 50.09 150 46 65 19 380.05 50.06 151 46 88 42 374.35 50.68 152 46 89 43 374.19 50.65 153 46 90 44 374.16 50.65 154 46 92 46 373.12 50.51 155 47 63 16 381.08 49.98 156 47 64 17 380.97 50.02 157 47 70 23 379.94 50.05 158 47 86 39 375.29 50.86 159 47 87 40 374.60 50.79 160 47 88 41 374.32 50.69 161 47 89 42 374.22 50.66 162 47 92 45 372.81 50.36 163 48 62 14 381.31 49.99 164 48 63 15 381.11 49.98 165 48 86 38 375.36 50.83 166 48 87 39 374.93 50.94 167 48 89 41 374.30 50.70 168 49 60 11 381.63 49.84 169 49 61 12 381.62 49.85 170 49 62 13 381.33 49.98 171 49 64 15 381.30 50.00 172 49 84 35 376.14 50.92 173 49 85 36 375.81 50.77 174 49 86 37 375.36 50.83 175 50 59 9 382.28 49.68 176 50 60 10 382.09 49.73 177 50 84 34 376.18 50.91 178 50 85 35 375.84 50.77 179 50 87 37 375.82 50.78 180 51 58 7 398.24 41.73 181 51 59 8 383.12 49.27 182 51 61 10 382.25 49.68 183 51 84 33 376.20 50.91 184 51 85 34 376.19 50.91 185 52 56 4 617.64 13.93 186 52 57 5 497.20 7.24 187 52 58 6 398.25 41.73 188 52 85 33 376.24 50.93 189 53 56 3 679.59 1.90 190 53 57 4 556.08 19.05 191 58 87 29 376.22 50.93 192 58 174 116 50.59 1.39 193 59 174 115 50.06 1.20 194 59 175 116 50.06 1.20 195 60 63 3 770.33 2.54 196 60 171 111 49.73 1.07 197 60 174 114 49.83 1.12 198 60 175 115 49.59 1.10 199 61 130 69 103.06 1.74 200 63 89 26 374.22 50.66 201 63 150 87 39.50 1.98 202 63 153 90 37.96 1.15 203 63 167 104 45.22 0.88 204 63 171 108 49.59 1.11 205 63 175 112 49.62 1.10 206 64 68 4 636.90 11.79 207 64 70 6 432.98 46.77 208 64 123 59 126.54 0.47 209 65 68 3 677.63 3.45 210 65 153 88 37.80 1.21 211 65 154 89 37.73 1.18 212 67 119 52 128.62 0.47 213 68 119 51 128.55 0.47 214 68 123 55 127.53 0.96 215 69 112 43 129.02 0.49 216 69 116 47 128.71 0.48 217 69 119 50 128.59 0.48 218 69 123 54 128.48 0.51 219 70 86 16 374.00 50.68 220 71 82 11 375.37 50.85 221 71 99 28 370.01 50.98 222 72 75 3 683.29 4.41 223 72 76 4 683.29 4.41 224 72 116 44 128.88 0.51 225 72 120 48 128.67 0.47 226 72 123 51 128.53 0.53 227 73 80 7 408.47 37.30 228 73 83 10 375.12 50.76 229 74 77 3 703.28 0.47 230 74 80 6 405.49 35.80 231 74 99 25 370.01 50.97 232 75 99 24 369.97 50.96 233 75 102 27 369.39 51.00 234 75 103 28 355.20 48.75 235 75 116 41 129.60 0.28 236 76 113 37 202.43 35.87 237 76 116 40 202.44 35.89 238 76 120 44 129.03 0.54 239 77 80 3 716.19 2.82 240 82 99 17 370.00 50.97 241 88 92 4 582.38 26.04 242 89 155 66 38.05 1.26 243 97 101 4 657.77 0.28 244 97 102 5 644.69 6.25 245 97 105 8 642.12 4.98 246 98 101 3 665.76 3.31 247 98 102 4 657.78 0.28 248 99 102 3 658.62 0.70 249 99 103 4 658.50 0.11 250 100 103 3 674.80 1.56 251 100 104 4 658.59 0.15 252 101 104 3 670.91 3.50 253 101 105 4 658.61 0.14 254 102 105 3 676.02 7.30 255 102 106 4 658.53 0.18 256 102 112 10 502.20 1.69 257 102 116 14 300.06 12.91 258 103 106 3 685.95 1.38 259 103 107 4 672.40 7.10 260 104 107 3 683.35 1.63 261 104 108 4 672.60 7.00 262 105 108 3 679.45 3.58 263 105 109 4 672.60 7.01 264 106 109 3 672.60 7.00 265 106 110 4 610.49 9.47 266 106 112 6 615.94 1.24 267 106 113 7 536.76 9.04 268 109 112 3 692.79 3.52 269 110 113 3 678.03 4.32 270 110 114 4 675.61 5.53 271 111 114 3 678.03 4.32 272 111 115 4 675.61 5.53 273 112 115 3 681.96 2.35 274 112 116 4 675.60 5.54 275 113 116 3 662.93 1.01 276 113 117 4 658.37 1.27 277 114 117 3 669.30 2.17 278 114 118 4 659.19 0.85 279 115 118 3 668.10 2.77 280 115 119 4 667.94 2.85 281 116 119 3 677.13 1.49 282 116 120 4 663.95 0.85 283 117 120 3 668.81 3.12 284 117 121 4 656.19 3.37 285 118 121 3 662.59 0.61 286 118 122 4 665.94 7.11 287 119 122 3 672.49 3.83 288 119 123 4 664.79 7.68 289 120 123 3 671.63 4.26 290 120 124 4 670.43 4.87 291 121 124 3 679.23 0.47 292 121 125 4 670.43 4.87 293 122 125 3 672.71 3.73 294 122 126 4 657.63 1.53 295 123 126 3 664.00 0.62 296 123 127 4 657.62 1.52 297 124 127 3 679.60 3.95 298 124 128 4 657.56 1.55 299 125 128 3 668.39 2.48 300 125 129 4 657.88 1.71 301 126 129 3 672.57 4.92 302 126 130 4 661.63 0.55 303 127 130 3 662.61 0.07 304 127 131 4 661.63 0.55 305 128 131 3 673.89 0.32 306 128 132 4 662.86 0.92 307 129 132 3 674.63 0.06 308 129 133 4 662.88 0.92 309 130 133 3 673.91 0.30 310 130 134 4 662.88 0.92 311 131 134 3 669.02 2.15 312 131 135 4 662.88 0.92 313 132 135 3 669.02 2.15 314 132 136 4 659.14 2.78 315 133 136 3 681.04 4.73 316 133 137 4 636.01 7.28 317 134 142 8 509.01 6.75 318 137 141 4 639.97 2.63 319 137 142 5 629.38 7.92 320 137 145 8 621.96 5.39 321 138 141 3 659.47 1.93 322 138 142 4 658.33 2.52 323 139 142 3 664.79 0.70 324 139 143 4 663.72 0.17 325 139 176 37 381.80 56.67 326 139 178 39 381.64 56.68 327 139 182 43 381.62 56.68 328 139 186 47 381.42 56.58 329 140 143 3 676.26 0.81 330 140 144 4 663.74 0.18 331 140 186 46 381.41 56.59 332 140 189 49 381.39 56.59 333 140 190 50 381.39 56.59 334 141 144 3 673.44 0.03 335 141 145 4 663.76 0.19 336 142 145 3 673.44 0.03 337 142 146 4 663.75 0.20 338 142 176 34 381.84 56.65 339 143 146 3 664.45 0.14 340 143 147 4 660.53 1.81 341 143 172 29 381.84 56.66 342 143 176 33 381.91 56.62 343 143 178 35 381.91 56.62 344 143 183 40 381.67 56.70 345 143 186 43 381.67 56.70 346 143 187 44 381.66 56.70 347 143 190 47 381.62 56.70 348 144 147 3 669.19 2.51 349 144 148 4 671.30 3.57 350 145 148 3 665.06 0.16 351 145 149 4 660.53 1.81 352 146 149 3 659.99 1.56 353 146 150 4 654.49 1.07 354 146 175 29 381.97 56.62 355 146 176 30 381.95 56.62 356 147 150 3 664.19 2.40 357 147 151 4 658.05 0.70 358 147 165 18 382.10 56.65 359 147 172 25 381.97 56.62 360 147 190 43 381.64 56.70 361 147 196 49 377.63 57.55 362 147 203 56 373.62 58.08 363 147 205 58 332.61 54.76 364 148 151 3 664.31 2.33 365 148 152 4 660.00 1.68 366 148 205 57 332.92 54.77 367 149 152 3 667.98 1.75 368 149 153 4 660.28 1.81 369 150 153 3 661.57 1.21 370 150 156 6 549.27 11.12 371 150 165 15 382.13 56.63 372 150 167 17 382.05 56.63 373 150 175 25 382.05 56.61 374 151 156 5 386.19 58.44 375 151 165 14 382.14 56.63 376 153 156 3 662.66 4.82 377 156 164 8 383.46 56.39 378 157 163 6 384.07 56.45 379 157 164 7 383.54 56.36 380 157 166 9 383.86 56.52 381 158 163 5 384.09 56.47 382 158 164 6 384.07 56.45 383 159 162 3 676.28 1.02 384 159 163 4 384.25 56.53 385 159 164 5 384.25 56.53 386 159 204 45 376.29 57.50 387 161 204 43 376.31 57.51 388 161 206 45 375.89 57.54 389 162 205 43 375.97 57.54 390 163 204 41 375.94 57.52 391 163 205 42 375.91 57.52 392 164 202 38 376.20 57.45 393 164 203 39 375.94 57.52 394 164 204 40 375.86 57.49 395 165 202 37 375.96 57.52 396 165 203 38 375.94 57.51 397 165 205 40 375.79 57.51 398 166 201 35 376.00 57.54 399 166 202 36 375.91 57.51 400 167 171 4 669.81 1.99 401 167 172 5 652.07 3.83 402 167 201 34 376.00 57.54 403 167 203 36 375.90 57.51 404 168 171 3 673.79 0.00 405 168 172 4 661.58 2.13 406 168 201 33 375.93 57.52 407 169 172 3 674.40 0.21 408 169 173 4 661.57 2.12 409 169 180 11 383.69 56.97 410 169 183 14 383.68 56.97 411 169 184 15 383.68 56.97 412 169 187 18 383.67 56.97 413 170 173 3 669.79 1.99 414 170 174 4 657.61 4.11 415 170 180 10 383.69 56.97 416 171 174 3 673.54 3.87 417 171 175 4 655.89 3.25 418 172 175 3 666.53 0.51 419 172 176 4 655.88 3.25 420 172 183 11 383.75 57.01 421 172 187 15 383.74 57.01 422 172 203 31 375.78 57.45 423 173 177 4 603.37 13.14 424 173 178 5 384.18 56.98 425 173 183 10 383.76 57.01 426 178 182 4 664.50 4.16 427 178 183 5 656.13 2.71 428 179 182 3 664.76 4.03 429 179 183 4 662.00 5.46 430 180 183 3 671.27 0.82 431 180 184 4 662.02 5.45 432 181 184 3 671.08 0.93 433 181 185 4 662.02 5.45 434 182 185 3 670.33 1.30 435 182 186 4 662.02 5.45 436 183 186 3 667.01 1.30 437 183 187 4 659.47 1.33 438 184 187 3 667.03 1.30 439 184 188 4 664.75 2.44 440 185 188 3 677.12 0.48 441 185 189 4 664.76 2.44 442 186 189 3 667.03 1.31 443 186 190 4 661.72 0.92 444 187 190 3 676.72 2.18 445 187 191 4 658.57 1.99 446 187 196 9 387.31 56.93 447 187 203 16 372.53 57.52 448 188 191 3 667.37 0.10 449 188 192 4 666.79 0.40 450 189 192 3 672.85 2.64 451 189 193 4 660.28 2.85 452 190 193 3 667.51 0.03 453 190 194 4 657.72 4.14 454 190 195 5 601.35 23.50 455 190 196 6 497.30 1.94 456 191 194 3 659.62 3.19 457 191 196 5 496.75 2.22 458 191 197 6 386.77 56.67 459 191 198 7 386.77 56.67 460 194 206 12 355.50 58.80 461 195 206 11 352.56 57.37 462 196 203 7 379.32 54.16 463 196 204 8 368.73 58.98 464 196 205 9 361.28 56.84 465 196 206 10 355.49 58.81 466 197 203 6 380.99 54.98 467 197 204 7 371.94 57.36 468 197 206 9 368.68 58.79 469 198 202 4 526.50 11.39 470 198 203 5 381.00 54.98 471 199 202 3 654.71 1.55