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 11 136 125 48.55 1.25 2 12 132 120 49.79 0.69 3 12 133 121 49.79 0.69 4 12 134 122 49.79 0.69 5 12 135 123 48.84 1.12 6 12 136 124 48.56 1.26 7 13 17 4 645.13 6.46 8 13 131 118 49.59 0.77 9 14 17 3 692.67 0.05 10 14 133 119 51.16 1.29 11 15 133 118 53.61 0.81 12 16 19 3 700.26 0.84 13 17 20 3 698.13 4.25 14 17 21 4 669.52 2.73 15 17 67 50 71.00 0.04 16 18 21 3 676.38 0.91 17 18 22 4 641.39 2.16 18 18 23 5 636.60 0.01 19 18 25 7 618.94 4.16 20 18 26 8 618.27 3.84 21 18 65 47 77.44 0.36 22 18 96 78 77.59 0.40 23 18 99 81 78.45 0.06 24 19 23 4 636.76 0.10 25 19 26 7 618.50 3.95 26 19 28 9 617.64 3.52 27 20 23 3 725.09 1.85 28 21 67 46 77.58 0.41 29 21 94 73 77.66 0.41 30 22 25 3 696.38 2.53 31 22 26 4 682.15 4.34 32 22 36 14 78.16 0.21 33 22 96 74 77.66 0.37 34 23 26 3 681.94 4.46 35 23 27 4 669.85 1.33 36 23 28 5 639.59 1.01 37 23 29 6 639.56 0.99 38 23 30 7 610.31 10.58 39 23 31 8 621.12 5.17 40 23 34 11 96.12 2.18 41 24 27 3 681.79 4.64 42 24 28 4 668.40 2.04 43 24 30 6 624.62 3.42 44 25 99 74 78.34 0.01 45 30 34 4 674.24 0.03 46 31 34 3 717.73 2.44 47 33 85 52 206.16 0.17 48 34 85 51 206.63 0.20 49 35 83 48 206.58 0.18 50 35 92 57 194.19 1.27 51 35 94 59 194.13 1.27 52 36 93 57 194.18 1.27 53 36 94 58 194.15 1.27 54 36 95 59 194.15 1.27 55 36 96 60 194.15 1.27 56 37 94 57 194.18 1.27 57 37 95 58 194.16 1.27 58 37 105 68 194.16 1.28 59 37 106 69 194.16 1.28 60 37 107 70 194.47 1.13 61 38 107 69 200.25 1.77 62 39 70 31 206.62 0.18 63 39 72 33 206.66 0.20 64 39 89 50 206.75 0.20 65 39 90 51 206.71 0.19 66 39 91 52 206.70 0.20 67 39 92 53 206.65 0.19 68 39 93 54 206.61 0.19 69 39 106 67 206.62 0.19 70 39 107 68 206.66 0.20 71 39 108 69 206.62 0.18 72 40 44 4 653.50 4.66 73 40 48 8 206.74 0.20 74 40 88 48 207.45 0.52 75 40 89 49 206.76 0.20 76 40 107 67 206.69 0.20 77 40 108 68 206.69 0.19 78 40 109 69 206.71 0.18 79 41 44 3 672.66 4.46 80 41 48 7 592.94 1.91 81 41 85 44 221.00 0.68 82 41 86 45 221.08 0.64 83 41 87 46 221.08 0.64 84 41 88 47 213.44 0.41 85 42 48 6 613.02 7.84 86 44 48 4 677.15 5.77 87 44 88 44 226.37 2.96 88 44 89 45 229.50 4.52 89 44 109 65 232.22 0.15 90 45 75 30 260.66 1.16 91 45 109 64 264.12 0.95 92 46 75 29 260.66 1.16 93 46 109 63 278.50 1.77 94 47 109 62 292.16 1.04 95 47 110 63 291.63 1.28 96 47 181 134 292.43 0.94 97 48 108 60 292.55 0.91 98 48 109 61 292.44 0.94 99 48 180 132 292.50 0.93 100 49 107 58 292.62 0.91 101 49 108 59 292.58 0.92 102 49 109 60 292.55 0.92 103 49 110 61 292.53 0.92 104 49 145 96 292.50 0.93 105 49 180 131 292.50 0.93 106 49 181 132 292.47 0.93 107 49 183 134 292.43 0.94 108 50 105 55 292.72 0.89 109 50 106 56 292.69 0.89 110 50 107 57 292.63 0.91 111 50 177 127 292.53 0.92 112 50 180 130 292.54 0.92 113 50 181 131 292.52 0.92 114 50 182 132 292.44 0.94 115 50 183 133 292.45 0.94 116 51 104 53 292.81 0.89 117 51 105 54 292.75 0.91 118 51 106 55 292.71 0.89 119 51 108 57 292.72 0.90 120 51 126 75 292.57 0.92 121 51 143 92 292.53 0.93 122 51 145 94 292.54 0.93 123 51 183 132 292.48 0.93 124 52 103 51 293.00 0.97 125 52 104 52 292.78 0.90 126 52 105 53 292.75 0.91 127 52 177 125 292.61 0.92 128 52 182 130 292.54 0.92 129 52 183 131 292.51 0.93 130 52 184 132 292.48 0.94 131 52 185 133 292.46 0.94 132 53 103 50 293.05 0.99 133 53 104 51 292.93 0.94 134 53 184 131 292.48 0.93 135 53 185 132 292.47 0.94 136 53 186 133 292.44 0.94 137 54 62 8 436.08 71.77 138 54 101 47 293.89 0.80 139 54 102 48 293.38 0.96 140 54 103 49 293.20 0.93 141 54 104 50 293.14 0.95 142 54 184 130 292.56 0.92 143 54 186 132 292.46 0.93 144 54 187 133 292.46 0.93 145 55 62 7 436.17 71.73 146 55 63 8 436.06 71.78 147 55 66 11 435.41 72.02 148 55 97 42 293.69 0.82 149 55 104 49 293.69 0.83 150 55 130 75 292.72 0.92 151 55 187 132 292.47 0.93 152 55 189 134 292.43 0.94 153 56 60 4 628.42 3.48 154 56 61 5 617.36 9.01 155 56 62 6 436.28 71.68 156 56 63 7 436.18 71.73 157 56 186 130 292.54 0.93 158 56 187 131 292.49 0.94 159 56 188 132 292.46 0.94 160 56 189 133 292.44 0.94 161 57 60 3 691.57 3.25 162 57 61 4 617.38 9.01 163 57 63 6 436.29 71.67 164 57 189 132 292.47 0.93 165 58 190 132 292.44 0.94 166 62 101 39 573.02 0.16 167 62 102 40 565.15 1.68 168 63 66 3 703.83 1.19 169 63 97 34 573.26 0.48 170 63 132 69 473.49 0.85 171 63 189 126 292.46 0.93 172 64 97 33 573.27 0.48 173 64 98 34 574.33 0.10 174 64 99 35 574.22 0.14 175 64 100 36 574.35 0.15 176 64 102 38 572.54 0.14 177 65 97 32 574.42 0.14 178 65 99 34 574.40 0.14 179 65 132 67 473.88 0.67 180 65 133 68 473.85 0.68 181 66 96 30 574.67 0.21 182 66 97 31 574.59 0.20 183 66 130 64 474.19 0.68 184 66 131 65 473.96 0.69 185 66 132 66 473.89 0.68 186 67 94 27 575.28 0.22 187 67 95 28 575.12 0.23 188 67 96 29 574.99 0.21 189 67 130 63 474.23 0.67 190 67 131 64 473.96 0.69 191 68 94 26 575.28 0.22 192 68 95 27 575.25 0.21 193 68 96 28 575.12 0.23 194 68 104 36 574.75 0.24 195 68 128 60 474.56 0.67 196 68 129 61 474.39 0.68 197 68 130 62 474.25 0.67 198 68 187 119 292.50 0.93 199 69 92 23 575.76 0.21 200 69 93 24 575.48 0.14 201 69 94 25 575.28 0.22 202 69 128 59 474.59 0.68 203 69 129 60 474.55 0.68 204 69 131 62 474.42 0.70 205 70 92 22 575.76 0.21 206 70 93 23 575.51 0.14 207 70 106 36 574.72 0.23 208 70 126 56 474.91 0.71 209 70 127 57 474.72 0.73 210 70 128 58 474.60 0.68 211 71 79 8 578.77 0.07 212 71 81 10 578.48 0.04 213 71 91 20 575.84 0.24 214 71 92 21 575.78 0.21 215 71 126 55 474.92 0.70 216 71 127 56 474.73 0.74 217 72 79 7 578.77 0.07 218 72 89 17 576.84 0.24 219 72 91 19 575.86 0.23 220 72 108 36 574.66 0.26 221 72 109 37 574.52 0.33 222 72 111 39 570.27 1.50 223 72 126 54 474.93 0.70 224 73 77 4 617.03 9.33 225 73 78 5 592.72 2.58 226 73 79 6 578.78 0.07 227 73 89 16 576.85 0.23 228 73 111 38 570.27 1.50 229 73 112 39 570.27 1.51 230 73 114 41 568.68 0.82 231 74 77 3 676.59 4.08 232 74 78 4 592.75 2.58 233 74 80 6 592.71 2.60 234 74 89 15 576.79 0.25 235 74 111 37 571.53 1.22 236 74 112 38 571.14 1.07 237 75 109 34 574.42 0.39 238 75 110 35 574.32 0.40 239 75 112 37 570.32 1.48 240 77 112 35 570.28 1.52 241 77 113 36 570.26 1.51 242 77 114 37 570.22 1.50 243 79 91 12 576.02 0.14 244 79 114 35 570.12 1.53 245 79 125 46 475.24 0.66 246 79 127 48 475.11 0.69 247 80 89 9 576.89 0.24 248 80 91 11 576.05 0.13 249 82 87 5 664.60 4.58 250 83 87 4 672.60 2.29 251 83 90 7 577.04 0.18 252 83 92 9 576.92 0.23 253 84 87 3 677.33 4.66 254 84 90 6 602.89 2.07 255 85 90 5 652.77 1.92 256 87 90 3 713.93 4.96 257 89 108 19 574.78 0.23 258 89 109 20 574.76 0.23 259 95 104 9 574.80 0.21 260 95 105 10 574.78 0.21 261 95 106 11 574.72 0.23 262 96 104 8 574.81 0.21 263 97 102 5 574.88 0.21 264 97 103 6 574.85 0.21 265 97 104 7 574.81 0.21 266 98 101 3 676.15 2.75 267 98 102 4 577.73 1.20 268 98 103 5 574.89 0.22 269 103 184 81 292.54 0.92 270 104 185 81 292.48 0.94 271 108 126 18 475.04 0.65 272 110 145 35 472.47 0.26 273 110 147 37 467.54 0.29 274 110 148 38 435.93 0.29 275 110 183 73 292.54 0.93 276 111 124 13 475.17 0.67 277 111 125 14 475.17 0.67 278 111 126 15 475.13 0.66 279 111 145 34 473.55 0.73 280 113 121 8 477.58 1.20 281 113 122 9 477.31 1.10 282 113 124 11 475.31 0.69 283 114 121 7 477.60 1.20 284 114 122 8 477.53 1.22 285 114 125 11 476.52 0.82 286 115 119 4 642.53 3.73 287 115 120 5 555.18 39.95 288 115 121 6 477.60 1.19 289 115 122 7 477.60 1.19 290 116 119 3 668.08 1.07 291 116 120 4 642.53 3.73 292 116 122 6 564.95 42.49 293 116 156 40 404.68 0.26 294 120 156 36 404.78 0.26 295 121 156 35 404.78 0.27 296 122 125 3 800.89 5.01 297 122 142 20 474.07 0.65 298 122 155 33 404.43 0.12 299 122 156 34 404.44 0.12 300 122 157 35 404.37 0.10 301 123 144 21 473.77 0.71 302 123 151 28 405.14 0.36 303 123 152 29 405.10 0.37 304 123 155 32 404.69 0.26 305 124 144 20 473.75 0.72 306 124 145 21 473.65 0.76 307 124 148 24 436.78 1.53 308 124 151 27 405.31 0.44 309 125 142 17 473.78 0.71 310 125 143 18 473.75 0.71 311 125 144 19 473.34 0.61 312 125 145 20 473.34 0.61 313 126 142 16 473.75 0.71 314 126 143 17 473.35 0.61 315 126 145 19 473.25 0.57 316 127 141 14 473.76 0.71 317 127 142 15 473.25 0.57 318 128 140 12 473.76 0.71 319 128 141 13 473.69 0.70 320 128 143 15 473.22 0.56 321 128 185 57 292.56 0.92 322 128 187 59 292.49 0.94 323 129 138 9 473.84 0.68 324 129 139 10 473.77 0.71 325 129 140 11 473.62 0.74 326 130 135 5 653.61 0.17 327 130 138 8 473.74 0.72 328 130 139 9 473.72 0.71 329 130 187 57 292.53 0.93 330 130 189 59 292.44 0.94 331 131 138 7 473.73 0.71 332 132 135 3 690.99 0.84 333 135 138 3 715.63 2.80 334 135 139 4 690.25 4.30 335 135 189 54 292.55 0.93 336 139 189 50 292.48 0.94 337 139 197 58 150.38 0.78 338 140 197 57 147.77 0.53 339 140 198 58 145.28 1.77 340 140 200 60 145.08 1.68 341 141 170 29 348.93 1.25 342 141 185 44 292.60 0.93 343 141 187 46 292.48 0.94 344 141 195 54 161.14 0.41 345 141 196 55 160.43 0.20 346 141 197 56 147.66 0.58 347 141 198 57 145.56 1.62 348 142 157 15 401.44 0.27 349 142 170 28 348.93 1.25 350 142 185 43 292.57 0.92 351 142 198 56 147.65 0.58 352 143 170 27 349.00 1.22 353 143 172 29 348.88 1.25 354 143 185 42 292.55 0.92 355 144 152 8 404.94 0.30 356 144 155 11 404.67 0.24 357 144 157 13 403.91 0.06 358 144 158 14 401.79 0.29 359 144 170 26 349.06 1.23 360 144 171 27 348.94 1.25 361 144 172 28 348.91 1.25 362 145 148 3 686.03 1.58 363 145 152 7 603.44 4.80 364 145 171 26 349.05 1.23 365 145 172 27 348.97 1.23 366 145 183 38 292.61 0.93 367 146 171 25 349.07 1.23 368 146 172 26 349.05 1.23 369 146 173 27 348.96 1.24 370 146 174 28 348.92 1.24 371 147 174 27 348.97 1.24 372 147 183 36 292.62 0.94 373 148 151 3 680.45 0.64 374 148 152 4 675.98 0.37 375 149 152 3 677.54 1.15 376 149 153 4 675.97 0.37 377 150 153 3 685.56 1.06 378 150 154 4 685.55 1.06 379 151 154 3 687.39 0.56 380 151 155 4 685.54 1.06 381 152 155 3 693.24 4.70 382 152 158 6 644.26 1.02 383 152 171 19 349.22 1.22 384 153 159 6 661.34 3.90 385 154 159 5 670.19 0.53 386 155 158 3 682.07 0.09 387 155 159 4 670.20 0.53 388 156 159 3 677.11 2.91 389 156 160 4 670.21 0.53 390 157 160 3 689.41 5.55 391 157 198 41 159.69 0.64 392 158 161 3 696.93 1.79 393 158 167 9 349.33 1.17 394 158 170 12 349.49 1.27 395 159 167 8 350.38 0.98 396 161 166 5 649.38 2.71 397 161 167 6 477.18 63.25 398 161 170 9 351.64 0.48 399 161 196 35 164.11 0.06 400 161 198 37 163.52 0.11 401 163 166 3 686.88 2.15 402 163 167 4 671.00 0.14 403 164 167 3 685.84 0.72 404 165 168 3 706.68 6.88 405 166 169 3 689.97 2.77 406 166 194 28 166.06 0.64 407 166 195 29 164.63 0.17 408 166 196 30 163.98 0.12 409 167 170 3 698.07 5.25 410 167 171 4 678.93 0.38 411 168 171 3 675.09 1.73 412 169 185 16 292.62 0.92 413 169 193 24 164.85 0.25 414 169 194 25 164.59 0.14 415 169 195 26 163.34 0.18 416 169 196 27 162.85 0.43 417 170 185 15 292.60 0.92 418 170 195 25 163.34 0.17 419 170 196 26 161.40 0.29 420 170 198 28 160.71 0.20 421 172 183 11 292.63 0.94 422 172 184 12 292.57 0.92 423 172 185 13 292.49 0.92 424 173 183 10 292.64 0.94 425 173 184 11 292.58 0.92 426 174 181 7 319.99 14.48 427 174 182 8 292.75 0.89 428 174 183 9 292.60 0.94 429 175 181 6 320.00 14.48 430 175 182 7 292.80 0.89 431 176 179 3 688.19 3.11 432 176 180 4 606.24 2.83 433 176 181 5 321.79 13.59 434 176 182 6 319.99 14.48 435 177 180 3 664.31 3.12 436 177 182 5 476.50 63.77 437 187 195 8 160.93 0.10 438 187 197 10 160.93 0.10 439 188 192 4 691.53 0.55 440 188 193 5 479.43 65.72 441 188 194 6 229.72 33.28 442 188 195 7 161.88 0.57 443 189 194 5 470.50 61.27 444 189 197 8 160.91 0.09 445 190 194 4 489.69 70.86 446 191 194 3 657.55 1.40