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 49.62 0.62 2 12 132 120 49.91 0.59 3 12 133 121 49.93 0.60 4 12 134 122 49.92 0.59 5 12 135 123 49.76 0.58 6 12 136 124 49.63 0.62 7 13 17 4 652.18 5.83 8 13 131 118 49.70 0.59 9 14 17 3 703.75 1.46 10 14 133 119 54.62 0.29 11 15 18 3 791.23 0.86 12 15 133 118 54.86 0.18 13 16 19 3 713.76 3.56 14 17 20 3 698.81 3.92 15 17 21 4 669.85 2.56 16 17 67 50 71.69 0.01 17 18 21 3 674.54 0.95 18 18 22 4 641.22 2.21 19 18 23 5 637.78 0.50 20 18 25 7 623.40 6.50 21 18 26 8 609.06 9.89 22 18 65 47 72.95 0.24 23 18 96 78 75.23 0.46 24 18 99 81 76.98 0.28 25 19 23 4 639.32 1.28 26 19 26 7 609.73 9.58 27 19 28 9 592.59 1.64 28 20 23 3 725.09 1.85 29 21 67 46 73.31 0.49 30 21 94 73 73.69 0.69 31 22 25 3 685.42 2.83 32 22 26 4 669.23 2.12 33 22 36 14 79.19 0.69 34 23 26 3 689.03 1.02 35 23 27 4 665.56 0.28 36 23 28 5 640.00 0.78 37 23 29 6 637.40 2.07 38 23 30 7 610.39 10.53 39 23 31 8 611.51 9.97 40 23 34 11 332.13 115.87 41 24 27 3 679.13 5.98 42 24 28 4 656.38 4.87 43 24 30 6 630.28 0.59 44 24 36 12 87.02 0.76 45 25 99 74 80.26 0.30 46 30 34 4 675.59 0.71 47 31 34 3 717.73 2.44 48 33 85 52 203.68 1.49 49 34 85 51 203.84 1.55 50 35 83 48 203.83 1.55 51 35 92 57 186.25 1.14 52 35 94 59 186.19 1.12 53 36 93 57 186.25 1.15 54 36 94 58 186.24 1.15 55 36 95 59 186.24 1.15 56 36 96 60 186.24 1.15 57 37 94 57 186.26 1.14 58 37 95 58 186.25 1.15 59 37 105 68 186.27 1.14 60 37 106 69 186.27 1.14 61 37 107 70 190.40 0.91 62 38 107 69 195.68 1.73 63 39 70 31 203.89 1.55 64 39 72 33 203.91 1.54 65 39 89 50 204.12 1.49 66 39 90 51 204.08 1.50 67 39 91 52 204.06 1.49 68 39 92 53 204.03 1.48 69 39 93 54 203.88 1.54 70 39 106 67 203.91 1.54 71 39 107 68 203.92 1.53 72 39 108 69 203.91 1.54 73 40 44 4 653.07 4.88 74 40 48 8 204.16 1.46 75 40 88 48 210.95 1.67 76 40 89 49 204.13 1.50 77 40 107 67 204.09 1.48 78 40 108 68 204.08 1.49 79 40 109 69 204.09 1.49 80 41 44 3 687.27 0.57 81 41 48 7 388.25 86.98 82 41 85 44 230.72 4.17 83 41 86 45 230.72 4.17 84 41 87 46 230.57 4.14 85 41 88 47 213.75 0.56 86 42 48 6 615.40 6.65 87 43 88 45 230.75 4.21 88 44 48 4 677.15 5.77 89 44 88 44 230.75 4.21 90 44 89 45 230.74 4.20 91 44 109 65 232.06 3.47 92 45 75 30 260.97 0.87 93 45 109 64 262.48 0.12 94 46 75 29 260.52 1.09 95 46 109 63 264.57 1.17 96 47 109 62 295.43 1.05 97 47 110 63 292.93 0.64 98 47 181 134 295.44 1.06 99 48 108 60 295.54 1.06 100 48 109 61 295.44 1.05 101 48 180 132 295.50 1.07 102 49 107 58 295.60 1.05 103 49 108 59 295.56 1.06 104 49 109 60 295.55 1.06 105 49 110 61 295.53 1.06 106 49 145 96 295.48 1.07 107 49 180 131 295.50 1.07 108 49 181 132 295.45 1.06 109 49 183 134 295.44 1.05 110 50 105 55 295.80 1.01 111 50 106 56 295.67 1.07 112 50 107 57 295.62 1.05 113 50 177 127 295.53 1.07 114 50 180 130 295.54 1.07 115 50 181 131 295.50 1.07 116 50 182 132 295.45 1.06 117 50 183 133 295.45 1.06 118 51 104 53 296.01 0.94 119 51 105 54 295.81 1.01 120 51 106 55 295.68 1.07 121 51 108 57 295.68 1.06 122 51 126 75 295.55 1.06 123 51 143 92 295.52 1.06 124 51 145 94 295.54 1.07 125 51 183 132 295.48 1.07 126 52 103 51 296.12 0.91 127 52 104 52 296.01 0.94 128 52 105 53 295.85 1.01 129 52 177 125 295.57 1.07 130 52 182 130 295.55 1.07 131 52 183 131 295.50 1.07 132 52 184 132 295.47 1.07 133 52 185 133 295.47 1.07 134 53 103 50 296.24 0.95 135 53 104 51 296.09 0.92 136 53 184 131 295.50 1.06 137 53 185 132 295.47 1.07 138 53 186 133 295.45 1.07 139 54 62 8 296.68 0.98 140 54 101 47 296.55 0.94 141 54 102 48 296.33 0.95 142 54 103 49 296.25 0.96 143 54 104 50 296.24 0.95 144 54 184 130 295.55 1.07 145 54 186 132 295.46 1.07 146 54 187 133 295.46 1.07 147 55 62 7 296.71 1.00 148 55 63 8 296.56 0.97 149 55 66 11 296.12 0.91 150 55 97 42 296.39 0.92 151 55 104 49 296.44 0.98 152 55 130 75 295.97 0.95 153 55 187 132 295.47 1.07 154 55 189 134 295.43 1.06 155 56 60 4 628.37 3.46 156 56 61 5 584.76 10.79 157 56 62 6 296.74 1.01 158 56 63 7 296.71 1.00 159 56 186 130 295.53 1.07 160 56 187 131 295.49 1.07 161 56 188 132 295.44 1.07 162 56 189 133 295.44 1.07 163 57 60 3 691.57 3.25 164 57 61 4 610.71 5.68 165 57 63 6 517.08 22.88 166 57 189 132 295.45 1.07 167 58 190 132 295.39 1.06 168 62 101 39 563.85 2.54 169 62 102 40 560.50 1.34 170 63 66 3 699.69 0.89 171 63 97 34 565.04 2.74 172 63 132 69 465.07 1.91 173 63 189 126 295.44 1.06 174 64 97 33 565.04 2.74 175 64 98 34 565.12 2.77 176 64 99 35 565.09 2.77 177 64 100 36 565.13 2.79 178 64 102 38 563.10 2.18 179 65 97 32 565.18 2.78 180 65 99 34 565.15 2.78 181 65 132 67 466.22 1.67 182 65 133 68 466.21 1.68 183 66 96 30 565.48 2.85 184 66 97 31 565.25 2.76 185 66 130 64 466.56 1.68 186 66 131 65 466.39 1.72 187 66 132 66 466.22 1.67 188 67 94 27 565.81 2.84 189 67 95 28 565.74 2.85 190 67 96 29 565.48 2.85 191 67 130 63 466.58 1.67 192 67 131 64 466.39 1.72 193 68 94 26 565.82 2.83 194 68 95 27 565.74 2.85 195 68 96 28 565.72 2.85 196 68 104 36 565.39 2.90 197 68 128 60 466.79 1.68 198 68 129 61 466.73 1.68 199 68 130 62 466.65 1.70 200 68 187 119 295.50 1.07 201 69 92 23 566.25 2.83 202 69 93 24 566.07 2.83 203 69 94 25 565.83 2.83 204 69 128 59 466.84 1.69 205 69 129 60 466.75 1.67 206 69 131 62 466.74 1.67 207 70 92 22 566.25 2.83 208 70 93 23 566.15 2.86 209 70 106 36 565.39 2.89 210 70 126 56 467.20 1.77 211 70 127 57 467.01 1.77 212 70 128 58 466.85 1.69 213 71 79 8 567.95 2.65 214 71 81 10 567.88 2.65 215 71 91 20 566.33 2.83 216 71 92 21 566.32 2.84 217 71 126 55 467.25 1.78 218 71 127 56 467.10 1.73 219 72 79 7 567.95 2.65 220 72 89 17 567.12 2.73 221 72 91 19 566.33 2.83 222 72 108 36 565.42 2.87 223 72 109 37 565.24 2.94 224 72 111 39 562.51 2.08 225 72 126 54 467.25 1.78 226 73 77 4 635.25 0.22 227 73 78 5 567.99 2.67 228 73 79 6 567.95 2.65 229 73 89 16 567.21 2.77 230 73 111 38 563.52 2.58 231 73 112 39 563.48 2.56 232 73 114 41 561.60 2.11 233 74 77 3 676.58 4.08 234 74 78 4 628.28 3.26 235 74 80 6 574.38 5.86 236 74 89 15 567.07 2.71 237 74 111 37 564.53 3.02 238 74 112 38 563.61 2.60 239 75 109 34 565.40 2.87 240 75 110 35 565.23 2.95 241 75 112 37 563.74 2.52 242 77 112 35 563.50 2.58 243 77 113 36 563.57 2.61 244 77 114 37 563.48 2.58 245 79 91 12 566.59 2.83 246 79 114 35 563.39 2.61 247 79 125 46 467.88 1.78 248 79 127 48 467.67 1.70 249 80 89 9 567.54 2.91 250 80 91 11 566.59 2.81 251 82 87 5 666.73 3.50 252 83 87 4 670.04 3.58 253 83 90 7 567.70 2.97 254 83 92 9 567.49 2.93 255 84 87 3 679.00 5.50 256 84 90 6 600.19 3.42 257 85 90 5 652.82 1.95 258 87 90 3 713.93 4.96 259 89 108 19 565.46 2.85 260 89 109 20 565.44 2.86 261 95 104 9 565.28 2.96 262 95 105 10 565.25 2.96 263 95 106 11 565.14 2.93 264 96 104 8 565.27 2.98 265 97 102 5 565.46 2.93 266 97 103 6 565.32 3.00 267 97 104 7 565.26 3.00 268 98 101 3 676.09 2.78 269 98 102 4 575.73 2.20 270 98 103 5 576.52 1.79 271 103 184 81 295.54 1.07 272 104 185 81 295.49 1.07 273 108 126 18 467.36 1.73 274 110 145 35 465.81 1.77 275 110 147 37 459.62 0.94 276 110 148 38 447.91 0.53 277 110 183 73 295.54 1.08 278 111 124 13 467.63 1.70 279 111 125 14 467.63 1.70 280 111 126 15 467.62 1.70 281 111 145 34 465.93 1.77 282 113 121 8 470.02 1.61 283 113 122 9 469.12 1.46 284 113 124 11 467.74 1.68 285 114 121 7 470.05 1.61 286 114 122 8 470.00 1.62 287 114 125 11 468.23 1.61 288 115 119 4 642.52 3.72 289 115 120 5 470.13 1.64 290 115 121 6 470.05 1.61 291 115 122 7 470.05 1.61 292 116 119 3 679.85 0.52 293 116 120 4 649.43 0.28 294 116 122 6 470.12 1.65 295 116 156 40 397.49 0.16 296 120 156 36 397.55 0.23 297 121 156 35 397.47 0.20 298 122 125 3 800.89 5.01 299 122 142 20 466.43 1.75 300 122 155 33 397.42 0.21 301 122 156 34 397.41 0.21 302 122 157 35 397.36 0.21 303 123 144 21 466.18 1.76 304 123 151 28 397.60 0.17 305 123 152 29 397.59 0.19 306 123 155 32 397.42 0.21 307 124 144 20 466.13 1.77 308 124 145 21 466.12 1.76 309 124 148 24 445.50 1.77 310 124 151 27 401.75 0.61 311 125 142 17 466.17 1.76 312 125 143 18 466.13 1.76 313 125 144 19 465.92 1.76 314 125 145 20 465.93 1.76 315 126 142 16 466.15 1.75 316 126 143 17 465.98 1.78 317 126 145 19 465.92 1.76 318 127 141 14 466.22 1.72 319 127 142 15 465.93 1.75 320 128 140 12 466.25 1.70 321 128 141 13 466.04 1.70 322 128 143 15 465.87 1.75 323 128 185 57 295.56 1.07 324 128 187 59 295.48 1.07 325 129 138 9 466.30 1.71 326 129 139 10 466.26 1.71 327 129 140 11 466.14 1.74 328 130 135 5 651.31 0.99 329 130 138 8 466.25 1.69 330 130 139 9 466.24 1.70 331 130 187 57 295.51 1.08 332 130 189 59 295.45 1.07 333 131 138 7 466.25 1.72 334 132 135 3 688.19 2.25 335 135 138 3 715.63 2.80 336 135 139 4 690.25 4.31 337 135 189 54 295.52 1.07 338 139 189 50 295.48 1.07 339 139 197 58 151.98 0.81 340 140 197 57 148.41 0.97 341 140 198 58 144.67 1.52 342 140 200 60 144.37 1.37 343 141 170 29 340.46 2.98 344 141 185 44 295.60 1.07 345 141 187 46 295.50 1.07 346 141 195 54 165.03 0.18 347 141 196 55 163.88 0.17 348 141 197 56 146.84 0.44 349 141 198 57 146.59 0.32 350 142 157 15 395.64 0.39 351 142 170 28 340.47 2.98 352 142 185 43 295.56 1.07 353 142 198 56 146.83 0.43 354 143 170 27 340.56 3.01 355 143 172 29 340.38 3.00 356 143 185 42 295.53 1.08 357 144 152 8 520.67 26.37 358 144 155 11 397.41 0.21 359 144 157 13 397.06 0.36 360 144 158 14 396.70 0.20 361 144 170 26 340.60 3.01 362 144 171 27 340.46 2.98 363 144 172 28 340.44 2.99 364 145 148 3 685.99 1.60 365 145 152 7 620.76 4.83 366 145 171 26 340.58 3.02 367 145 172 27 340.44 3.00 368 145 183 38 295.60 1.07 369 146 149 3 699.26 0.58 370 146 171 25 340.60 3.01 371 146 172 26 340.58 3.01 372 146 173 27 340.50 3.02 373 146 174 28 340.45 3.00 374 147 174 27 340.45 3.00 375 147 183 36 295.63 1.07 376 148 151 3 684.88 1.57 377 148 152 4 671.33 0.99 378 149 152 3 679.50 2.14 379 149 153 4 676.23 1.48 380 150 153 3 681.63 3.20 381 150 154 4 685.55 1.06 382 151 154 3 688.50 0.01 383 151 155 4 683.59 0.09 384 152 155 3 683.62 0.10 385 152 158 6 660.24 4.50 386 152 171 19 340.79 2.99 387 153 159 6 663.26 2.94 388 154 159 5 664.71 2.25 389 155 158 3 682.07 0.09 390 155 159 4 670.07 0.42 391 156 159 3 676.93 3.00 392 156 160 4 670.08 0.42 393 157 160 3 677.52 2.71 394 157 198 41 162.53 0.12 395 158 161 3 689.39 1.98 396 158 167 9 341.19 2.89 397 158 170 12 341.19 2.88 398 159 167 8 463.48 57.62 399 161 166 5 662.86 4.17 400 161 167 6 603.51 5.56 401 161 170 9 541.35 30.71 402 161 196 35 165.16 0.26 403 161 198 37 165.01 0.20 404 163 166 3 688.08 2.46 405 163 167 4 675.34 1.76 406 164 167 3 685.84 0.72 407 164 168 4 675.20 1.68 408 165 168 3 692.45 0.30 409 166 169 3 683.87 3.31 410 166 194 28 168.18 0.28 411 166 195 29 167.02 0.16 412 166 196 30 165.42 0.10 413 167 170 3 688.10 2.04 414 167 171 4 677.37 0.59 415 168 171 3 680.57 1.01 416 169 185 16 295.61 1.08 417 169 193 24 167.71 0.51 418 169 194 25 166.62 0.04 419 169 195 26 165.30 0.14 420 169 196 27 165.22 0.10 421 170 185 15 295.56 1.08 422 170 195 25 165.22 0.10 423 170 196 26 165.17 0.11 424 170 198 28 165.00 0.00 425 171 185 14 295.54 1.08 426 172 183 11 295.62 1.07 427 172 184 12 295.58 1.07 428 172 185 13 295.51 1.05 429 173 183 10 295.64 1.07 430 173 184 11 295.60 1.07 431 174 181 7 471.37 61.14 432 174 182 8 295.72 1.09 433 174 183 9 295.62 1.06 434 175 181 6 471.38 61.14 435 175 182 7 323.49 12.79 436 176 179 3 687.95 3.23 437 176 180 4 473.01 61.02 438 176 181 5 471.38 61.15 439 176 182 6 471.36 61.14 440 177 180 3 664.31 3.12 441 177 182 5 472.69 60.86 442 187 195 8 164.99 0.01 443 187 197 10 164.98 0.01 444 188 192 4 685.11 3.76 445 188 193 5 479.21 65.80 446 188 194 6 230.84 32.73 447 188 195 7 165.20 0.09 448 188 197 9 165.21 0.09 449 189 194 5 479.25 65.81 450 189 197 8 164.97 0.21 451 190 194 4 549.63 40.89 452 191 194 3 663.56 1.60