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 13 54 41 28.25 0.01 2 13 57 44 28.31 0.04 3 13 152 139 28.30 0.04 4 13 157 144 28.43 0.01 5 14 50 36 28.32 0.02 6 14 53 39 28.39 0.01 7 14 54 40 28.46 0.03 8 14 152 138 28.52 0.01 9 14 157 143 28.48 0.01 10 14 160 146 28.46 0.02 11 14 161 147 28.43 0.01 12 15 49 34 28.48 0.02 13 15 53 38 28.53 0.01 14 17 20 3 543.85 1.54 15 17 21 4 535.83 5.55 16 17 49 32 32.75 0.02 17 18 21 3 543.85 1.54 18 20 24 4 598.47 0.35 19 20 49 29 48.52 0.02 20 21 24 3 598.47 0.35 21 21 45 24 48.52 0.01 22 21 46 25 48.55 0.01 23 21 49 28 48.52 0.02 24 22 45 23 59.84 0.75 25 23 26 3 601.86 1.44 26 23 45 22 75.47 0.24 27 24 45 21 75.52 0.24 28 24 48 24 75.50 0.25 29 24 49 25 75.53 0.24 30 24 52 28 75.55 0.24 31 24 106 82 75.45 0.29 32 24 107 83 75.41 0.30 33 24 108 84 75.53 0.36 34 25 38 13 263.01 0.49 35 25 43 18 75.53 0.25 36 25 44 19 75.53 0.25 37 25 48 23 75.54 0.24 38 25 108 83 77.08 1.04 39 26 107 81 80.03 2.33 40 26 108 82 79.95 2.38 41 26 109 83 79.95 2.38 42 26 110 84 80.22 2.48 43 27 31 4 516.88 4.57 44 27 34 7 450.56 2.84 45 27 35 8 444.94 1.81 46 27 38 11 398.22 21.55 47 27 108 81 80.28 2.45 48 27 109 82 80.24 2.47 49 27 110 83 80.37 2.56 50 27 113 86 80.38 2.56 51 28 31 3 559.11 2.16 52 28 32 4 531.14 6.38 53 28 35 7 511.42 1.33 54 28 110 82 80.44 2.52 55 29 32 3 545.29 4.75 56 29 35 6 522.28 6.76 57 31 34 3 548.74 2.46 58 31 35 4 543.23 0.30 59 31 110 79 81.31 2.60 60 31 113 82 81.38 2.65 61 31 114 83 81.36 2.64 62 32 35 3 567.44 2.73 63 32 36 4 548.74 2.46 64 33 36 3 554.67 5.07 65 33 37 4 544.27 3.96 66 34 37 3 541.96 5.12 67 34 38 4 536.98 2.68 68 34 113 79 81.48 2.71 69 34 175 141 57.50 0.48 70 35 38 3 555.50 3.69 71 35 39 4 534.28 1.33 72 36 39 3 537.00 3.23 73 36 40 4 540.40 5.02 74 37 40 3 542.88 3.79 75 37 41 4 534.92 7.77 76 37 171 134 75.01 0.62 77 37 174 137 68.64 0.88 78 38 41 3 549.66 2.43 79 38 42 4 522.32 7.03 80 38 43 5 490.31 8.19 81 38 108 70 82.30 2.65 82 38 171 133 74.22 1.02 83 39 42 3 522.31 7.03 84 41 167 126 81.00 2.35 85 41 170 129 80.95 2.33 86 41 174 133 73.75 1.28 87 42 47 5 522.73 6.79 88 42 167 125 81.39 2.19 89 43 47 4 529.62 3.35 90 43 48 5 527.14 4.58 91 43 51 8 521.71 6.28 92 43 167 124 81.40 2.20 93 43 168 125 81.86 2.42 94 43 171 128 81.42 2.19 95 44 47 3 557.75 6.34 96 44 48 4 540.78 1.29 97 45 48 3 554.07 0.25 98 45 49 4 544.04 0.34 99 46 49 3 544.06 0.33 100 46 50 4 541.46 1.35 101 47 50 3 541.74 1.49 102 47 51 4 541.06 1.15 103 47 164 117 120.09 1.54 104 47 167 120 119.64 1.31 105 48 51 3 545.04 0.85 106 48 52 4 546.86 1.77 107 48 106 58 129.55 1.04 108 48 108 60 129.81 0.91 109 49 52 3 550.51 0.07 110 49 53 4 548.13 1.12 111 50 53 3 554.90 0.40 112 50 54 4 555.64 2.63 113 50 160 110 148.25 0.64 114 50 161 111 148.24 0.64 115 50 164 114 147.94 0.74 116 51 54 3 558.35 1.28 117 51 55 4 558.35 1.28 118 51 104 53 147.78 0.82 119 51 106 55 147.97 0.75 120 51 164 113 148.23 0.65 121 51 165 114 148.22 0.65 122 51 168 117 147.88 0.79 123 52 55 3 561.46 1.96 124 52 56 4 564.12 2.38 125 52 104 52 148.15 0.68 126 52 106 54 147.98 0.74 127 53 56 3 586.98 2.35 128 54 57 3 560.10 0.41 129 54 58 4 543.40 3.58 130 54 104 50 153.61 0.95 131 54 148 94 171.50 2.11 132 54 152 98 173.31 1.74 133 54 161 107 153.61 0.94 134 54 165 111 153.59 0.93 135 55 58 3 552.48 0.96 136 55 59 4 534.10 1.79 137 55 101 46 157.66 1.07 138 55 104 49 153.62 0.95 139 55 105 50 158.38 3.18 140 56 59 3 542.46 2.41 141 56 60 4 524.44 0.06 142 57 60 3 556.42 3.64 143 57 61 4 533.23 7.96 144 57 147 90 176.77 3.45 145 57 148 91 176.01 3.08 146 57 151 94 178.33 3.15 147 57 152 95 178.33 3.15 148 58 61 3 547.82 0.67 149 58 62 4 515.88 2.40 150 58 65 7 480.36 13.21 151 58 100 42 172.65 1.79 152 58 104 46 172.66 1.79 153 58 144 86 175.44 2.81 154 58 147 89 178.32 3.15 155 58 148 90 178.33 3.15 156 59 62 3 558.65 1.51 157 59 101 42 172.59 1.82 158 61 64 3 555.02 0.61 159 61 65 4 542.04 2.62 160 61 147 86 186.91 1.83 161 62 65 3 534.47 4.74 162 62 66 4 534.34 4.79 163 62 97 35 183.32 2.37 164 62 100 38 183.34 2.36 165 62 101 39 183.34 2.36 166 63 66 3 545.83 0.18 167 63 67 4 542.62 1.78 168 63 97 34 197.88 1.73 169 64 67 3 546.92 0.72 170 64 68 4 542.62 1.78 171 65 68 3 547.48 0.56 172 65 69 4 542.61 1.78 173 65 100 35 198.09 1.70 174 65 140 75 198.03 1.73 175 65 143 78 198.16 1.71 176 65 144 79 198.16 1.70 177 65 147 82 198.47 1.58 178 66 69 3 536.38 0.15 179 66 70 4 533.04 1.78 180 66 93 27 198.18 1.71 181 66 96 30 198.16 1.71 182 66 97 31 198.16 1.70 183 66 100 34 198.14 1.71 184 67 70 3 557.82 3.27 185 67 71 4 537.84 0.62 186 67 93 26 198.94 1.47 187 68 71 3 547.83 1.60 188 68 72 4 538.29 0.38 189 68 139 71 198.78 1.56 190 69 72 3 550.76 3.40 191 69 73 4 538.30 0.39 192 69 96 27 199.21 1.35 193 69 136 67 198.74 1.59 194 69 139 70 198.79 1.56 195 69 140 71 198.79 1.56 196 70 73 3 544.25 1.15 197 70 74 4 545.30 0.62 198 70 83 13 260.48 5.42 199 70 89 19 199.31 1.34 200 70 92 22 199.29 1.34 201 70 93 23 199.28 1.34 202 70 96 26 199.28 1.34 203 71 74 3 566.12 4.33 204 72 75 3 571.77 1.51 205 72 139 67 198.84 1.55 206 73 76 3 566.84 0.96 207 73 79 6 380.37 1.61 208 73 83 10 337.50 19.82 209 73 136 63 198.90 1.53 210 74 80 6 409.00 15.13 211 76 79 3 546.55 0.70 212 76 80 4 541.67 0.61 213 76 132 56 199.27 1.36 214 77 80 3 547.65 0.92 215 77 81 4 538.29 2.29 216 78 81 3 544.35 0.73 217 78 82 4 538.28 2.29 218 79 82 3 543.21 1.39 219 79 83 4 543.21 1.39 220 79 128 49 199.52 1.37 221 79 132 53 199.55 1.34 222 80 83 3 539.84 3.08 223 80 84 4 533.25 3.42 224 80 89 9 356.20 10.29 225 81 84 3 543.27 1.62 226 81 85 4 528.03 0.79 227 82 85 3 545.94 2.78 228 82 86 4 536.50 5.01 229 82 126 44 199.62 1.34 230 82 127 45 199.76 1.35 231 82 128 46 199.66 1.36 232 83 86 3 547.22 0.35 233 83 87 4 528.03 0.79 234 83 88 5 491.68 0.79 235 83 89 6 480.25 6.50 236 83 92 9 377.72 4.45 237 84 87 3 545.87 0.01 238 86 125 39 200.02 1.43 239 86 126 40 200.01 1.42 240 87 91 4 535.12 0.42 241 87 92 5 529.96 1.47 242 88 91 3 555.29 4.69 243 88 92 4 530.67 1.82 244 89 92 3 556.69 2.87 245 89 93 4 530.69 1.81 246 90 93 3 559.16 1.63 247 90 94 4 545.26 1.98 248 91 94 3 550.37 0.35 249 92 95 3 544.33 0.82 250 92 96 4 530.74 1.76 251 93 96 3 545.32 2.00 252 93 97 4 529.66 1.18 253 94 97 3 543.88 3.50 254 94 98 4 537.62 0.81 255 95 98 3 544.28 2.52 256 95 99 4 535.72 1.76 257 96 99 3 543.55 1.54 258 96 100 4 535.70 1.77 259 97 100 3 552.43 2.23 260 97 101 4 543.41 2.10 261 98 101 3 547.80 0.09 262 98 102 4 543.28 2.16 263 99 102 3 547.80 0.09 264 99 103 4 544.74 1.44 265 99 115 16 222.63 2.38 266 99 116 17 222.47 2.46 267 99 172 73 209.78 4.08 268 100 103 3 558.62 0.70 269 100 104 4 544.73 1.44 270 100 140 40 209.94 4.01 271 100 144 44 210.09 4.02 272 101 104 3 553.66 1.78 273 102 105 3 556.33 3.10 274 102 112 10 230.03 6.02 275 102 115 13 226.58 4.29 276 102 116 14 226.58 4.29 277 103 112 9 257.50 2.73 278 103 116 13 226.59 4.29 279 103 168 65 210.00 4.00 280 103 169 66 210.00 4.00 281 103 172 69 209.97 4.01 282 104 144 40 210.42 3.87 283 104 148 44 210.91 4.05 284 104 165 61 210.22 3.95 285 108 112 4 525.54 2.03 286 108 113 5 516.75 6.42 287 108 168 60 211.08 4.03 288 108 171 63 211.03 4.01 289 109 112 3 546.10 0.99 290 109 113 4 535.49 2.39 291 110 113 3 546.10 0.99 292 110 114 4 535.49 2.39 293 111 114 3 542.76 0.79 294 111 115 4 530.68 4.80 295 112 115 3 548.82 1.23 296 112 116 4 540.78 0.21 297 112 168 56 211.94 3.91 298 112 171 59 211.49 3.97 299 112 172 60 211.47 3.98 300 112 175 63 211.25 3.92 301 113 116 3 548.10 0.75 302 113 117 4 543.48 1.56 303 113 175 62 211.22 3.93 304 114 117 3 548.11 0.75 305 114 118 4 548.10 0.75 306 115 118 3 565.75 2.53 307 115 119 4 548.10 0.75 308 116 119 3 559.88 5.47 309 116 120 4 533.01 1.03 310 116 172 56 211.50 4.01 311 116 175 59 211.25 3.92 312 117 120 3 558.97 5.92 313 117 121 4 541.76 4.04 314 118 121 3 552.47 4.90 315 118 122 4 535.19 2.10 316 119 122 3 543.78 1.18 317 119 123 4 540.40 0.86 318 119 133 14 267.19 2.54 319 120 123 3 543.72 0.27 320 120 124 4 540.40 0.86 321 120 133 13 267.16 2.52 322 120 176 56 211.37 3.96 323 121 124 3 541.19 0.86 324 121 125 4 536.38 1.54 325 122 125 3 550.51 0.66 326 122 126 4 539.24 0.29 327 123 126 3 549.53 1.58 328 123 127 4 536.38 1.54 329 123 128 5 424.78 1.90 330 123 133 10 279.42 3.57 331 124 127 3 546.61 3.04 332 128 132 4 545.56 2.10 333 128 133 5 535.53 2.23 334 129 132 3 548.34 2.31 335 129 133 4 545.56 2.10 336 130 133 3 545.56 2.10 337 130 134 4 545.53 2.12 338 131 134 3 546.16 1.80 339 131 135 4 546.15 1.80 340 132 135 3 545.03 1.24 341 132 136 4 539.29 4.11 342 133 136 3 546.46 1.96 343 133 137 4 551.07 1.10 344 133 176 43 214.72 4.04 345 134 137 3 560.12 1.38 346 134 173 39 214.73 4.04 347 134 176 42 214.75 4.04 348 134 177 43 214.72 4.04 349 135 138 3 553.91 0.32 350 136 139 3 563.65 0.07 351 136 140 4 546.89 0.99 352 137 140 3 546.91 2.90 353 137 141 4 547.77 3.33 354 137 169 32 215.70 4.31 355 137 172 35 215.72 4.32 356 137 173 36 215.69 4.32 357 138 141 3 548.30 3.07 358 138 142 4 547.76 3.34 359 139 142 3 553.09 5.23 360 139 143 4 541.81 0.36 361 140 143 3 552.07 1.19 362 140 144 4 547.75 3.35 363 141 144 3 548.41 3.02 364 141 145 4 542.38 0.67 365 141 165 24 218.37 4.06 366 141 166 25 218.09 4.17 367 141 169 28 217.57 3.91 368 142 145 3 548.41 3.01 369 142 146 4 540.84 1.43 370 143 146 3 548.05 0.68 371 143 147 4 545.17 2.41 372 144 147 3 545.17 2.41 373 144 148 4 545.17 2.41 374 144 165 21 220.72 4.10 375 145 148 3 545.17 2.41 376 145 149 4 545.17 2.41 377 145 162 17 223.81 5.67 378 146 149 3 549.27 0.35 379 146 150 4 535.82 2.27 380 147 150 3 547.79 0.23 381 147 151 4 535.79 2.27 382 148 151 3 548.58 0.46 383 148 152 4 513.06 6.11 384 148 158 10 250.91 1.92 385 148 161 13 228.80 5.29 386 148 162 14 233.80 2.79 387 148 165 17 228.39 5.49 388 149 152 3 545.78 1.85 389 149 158 9 251.37 2.14 390 152 157 5 492.26 14.38 391 152 158 6 299.33 5.71 392 152 161 9 287.87 0.32 393 154 157 3 553.29 0.81 394 154 158 4 546.16 2.75 395 155 158 3 546.18 2.75 396 155 159 4 550.70 1.36 397 156 159 3 554.59 0.56 398 156 160 4 550.71 1.36 399 157 160 3 545.04 1.48 400 157 161 4 547.66 0.17 401 158 161 3 548.51 0.26 402 158 162 4 548.50 0.26 403 159 162 3 548.51 0.26 404 159 163 4 548.50 0.26 405 160 163 3 550.04 1.01 406 160 164 4 548.52 0.25 407 161 164 3 554.11 0.48 408 161 165 4 548.51 0.24 409 162 165 3 552.03 1.52 410 162 166 4 548.51 0.24 411 163 166 3 548.44 0.29 412 163 167 4 544.36 2.32 413 164 167 3 550.20 5.23 414 164 168 4 545.65 2.96 415 165 168 3 550.20 5.23 416 165 169 4 545.65 2.96 417 166 169 3 555.60 2.53 418 166 170 4 535.21 2.29 419 167 170 3 559.02 3.72 420 167 171 4 535.35 2.23 421 168 171 3 551.11 4.21 422 168 172 4 535.22 2.29 423 169 172 3 543.99 2.08 424 169 173 4 534.76 2.52 425 170 173 3 542.17 1.21 426 170 174 4 535.00 3.99 427 171 174 3 538.36 5.67 428 171 175 4 535.00 4.00 429 172 175 3 553.63 4.36 430 172 176 4 542.25 1.31 431 173 176 3 550.07 3.98 432 173 177 4 542.28 1.32 433 174 177 3 551.86 0.64