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 1 104 103 18.85 0.51 2 1 107 106 18.84 0.51 3 1 108 107 18.86 0.51 4 2 6 4 535.53 0.55 5 2 7 5 530.14 0.03 6 2 101 99 19.12 0.39 7 2 102 100 19.04 0.42 8 2 103 101 18.86 0.51 9 3 6 3 543.95 3.65 10 3 7 4 541.23 2.08 11 3 99 96 24.70 0.08 12 3 100 97 23.28 0.56 13 3 101 98 20.41 0.21 14 4 7 3 548.41 1.75 15 4 8 4 545.26 0.18 16 4 26 22 41.74 0.98 17 4 27 23 41.55 1.05 18 4 30 26 41.21 1.03 19 4 100 96 24.82 0.14 20 5 8 3 555.01 0.72 21 5 9 4 544.98 4.16 22 5 30 25 41.45 0.95 23 5 31 26 41.61 1.02 24 6 9 3 549.11 2.10 25 6 10 4 543.73 4.88 26 7 10 3 549.58 2.03 27 7 11 4 545.24 4.12 28 8 11 3 549.18 2.16 29 8 12 4 545.25 4.12 30 8 23 15 45.29 0.82 31 8 26 18 42.23 0.73 32 9 12 3 545.30 4.09 33 9 13 4 548.80 2.34 34 9 19 10 65.73 0.26 35 10 13 3 555.36 0.93 36 10 14 4 545.42 0.65 37 11 14 3 554.31 0.42 38 11 15 4 545.44 0.65 39 11 17 6 533.31 1.74 40 12 15 3 550.87 0.75 41 12 16 4 545.44 0.65 42 12 17 5 493.76 2.47 43 12 19 7 318.23 13.64 44 13 16 3 536.92 3.62 45 17 23 6 533.86 0.50 46 19 23 4 530.94 0.96 47 19 24 5 530.93 0.96 48 20 23 3 556.21 2.60 49 20 24 4 536.10 0.87 50 21 24 3 539.03 1.86 51 21 25 4 536.10 0.87 52 22 25 3 547.68 1.53 53 22 26 4 539.96 2.33 54 23 26 3 547.23 1.97 55 23 27 4 539.98 2.35 56 24 27 3 549.01 2.17 57 24 28 4 539.88 2.40 58 25 28 3 553.85 4.58 59 25 29 4 548.97 2.14 60 26 29 3 552.82 0.21 61 26 30 4 548.99 2.12 62 27 30 3 545.56 1.12 63 27 31 4 539.39 2.68 64 28 31 3 544.03 0.36 65 28 32 4 539.38 2.68 66 29 32 3 539.41 2.67 67 29 33 4 539.38 2.68 68 30 33 3 553.36 6.04 69 30 34 4 539.27 1.00 70 30 98 68 114.89 3.50 71 30 99 69 110.56 5.66 72 30 100 70 96.28 5.58 73 31 34 3 537.31 0.03 74 33 36 3 561.32 0.29 75 33 37 4 539.52 0.48 76 33 145 112 148.72 0.67 77 33 148 115 148.65 0.63 78 33 149 116 144.66 0.78 79 34 37 3 550.51 3.52 80 34 38 4 547.44 3.48 81 35 38 3 555.31 1.11 82 35 39 4 547.44 3.48 83 36 39 3 551.71 1.34 84 36 40 4 544.52 4.94 85 36 145 109 148.93 0.76 86 36 146 110 148.87 0.72 87 36 149 113 148.86 0.72 88 37 40 3 551.49 1.24 89 37 41 4 545.15 3.90 90 37 97 60 148.83 0.72 91 37 149 112 148.91 0.75 92 38 41 3 545.15 3.90 93 38 42 4 545.15 3.90 94 39 42 3 547.37 2.79 95 39 43 4 543.12 4.92 96 39 142 103 165.05 0.85 97 39 146 107 164.97 0.85 98 40 43 3 554.03 0.55 99 40 44 4 534.22 0.47 100 40 97 57 165.01 0.84 101 40 142 102 165.06 0.85 102 40 146 106 165.02 0.85 103 40 149 109 165.00 0.84 104 40 150 110 164.94 0.82 105 41 44 3 552.36 0.04 106 41 45 4 536.38 0.62 107 41 97 56 165.01 0.84 108 41 98 57 165.06 0.86 109 42 45 3 540.80 3.24 110 42 46 4 538.61 2.15 111 43 46 3 557.60 1.24 112 43 47 4 526.66 5.49 113 43 142 99 165.81 0.86 114 44 48 4 510.11 5.39 115 44 51 7 438.96 12.41 116 44 90 46 165.75 0.87 117 44 93 49 165.73 0.85 118 44 94 50 165.72 0.86 119 44 97 53 165.75 0.84 120 44 138 94 165.80 0.85 121 44 142 98 166.08 0.76 122 44 150 106 165.75 0.87 123 45 48 3 547.53 0.05 124 47 50 3 555.07 1.17 125 47 51 4 536.50 4.08 126 47 141 94 195.97 0.83 127 48 51 3 549.67 1.03 128 48 52 4 535.22 1.18 129 48 90 42 172.95 2.37 130 49 52 3 552.22 0.17 131 49 53 4 550.74 0.91 132 50 53 3 550.75 0.91 133 50 54 4 535.19 1.21 134 51 54 3 550.76 0.92 135 51 55 4 535.19 1.21 136 51 90 39 207.15 2.56 137 51 134 83 207.15 2.56 138 51 137 86 208.81 1.79 139 51 138 87 208.79 1.78 140 51 141 90 208.86 1.76 141 52 55 3 556.96 2.90 142 52 56 4 535.17 1.22 143 52 83 31 208.93 1.79 144 52 86 34 207.21 2.58 145 52 87 35 207.21 2.58 146 53 56 3 552.83 4.96 147 53 57 4 543.64 4.49 148 53 83 30 209.42 2.02 149 54 57 3 553.39 0.37 150 54 58 4 549.67 1.49 151 54 133 79 209.52 2.04 152 55 58 3 550.85 0.90 153 55 59 4 549.68 1.48 154 55 86 31 209.59 2.04 155 55 130 75 209.49 2.02 156 55 133 78 209.53 2.04 157 55 134 79 209.53 2.04 158 56 59 3 558.29 0.70 159 56 60 4 551.72 0.47 160 56 82 26 209.73 1.97 161 56 83 27 209.74 1.98 162 56 86 30 209.72 1.98 163 57 60 3 562.94 4.40 164 57 61 4 537.55 2.79 165 58 61 3 543.61 2.34 166 58 62 4 533.23 0.64 167 58 133 75 209.59 2.04 168 59 62 3 555.05 0.94 169 59 63 4 530.16 0.90 170 59 66 7 470.93 11.09 171 59 126 67 209.56 2.06 172 59 130 71 209.59 2.04 173 60 63 3 543.19 2.14 174 60 64 4 526.14 2.89 175 60 66 6 458.41 17.34 176 60 67 7 385.94 0.81 177 60 73 13 210.55 1.91 178 60 79 19 210.38 2.00 179 60 82 22 210.37 2.00 180 61 64 3 555.10 3.82 181 62 129 67 210.09 2.00 182 63 66 3 566.58 1.49 183 63 125 62 210.18 2.04 184 63 126 63 210.16 2.02 185 63 129 66 210.16 2.02 186 64 67 3 569.52 0.01 187 65 68 3 556.73 0.29 188 65 71 6 304.78 3.33 189 66 71 5 255.11 19.28 190 66 73 7 211.84 2.27 191 66 74 8 211.92 2.31 192 66 126 60 210.20 2.02 193 67 73 6 211.87 2.28 194 67 74 7 211.87 2.28 195 67 79 12 211.84 2.30 196 68 71 3 554.21 1.43 197 68 74 6 309.31 1.51 198 69 74 5 321.56 4.50 199 71 74 3 549.23 2.85 200 71 78 7 435.81 11.69 201 72 78 6 407.47 25.86 202 72 120 48 210.77 2.17 203 72 121 49 210.70 2.13 204 72 122 50 210.61 2.07 205 72 126 54 210.61 2.06 206 73 78 5 477.19 3.90 207 73 79 6 424.16 17.52 208 74 78 4 536.53 4.61 209 75 78 3 558.95 0.96 210 75 79 4 544.84 0.47 211 76 79 3 548.14 1.11 212 76 80 4 544.90 0.50 213 77 80 3 548.13 1.11 214 77 81 4 544.90 0.50 215 78 81 3 544.95 0.71 216 78 82 4 544.94 0.71 217 79 82 3 546.90 0.27 218 79 83 4 543.77 1.31 219 80 83 3 559.82 6.19 220 80 84 4 547.44 3.17 221 81 84 3 547.40 3.18 222 81 85 4 547.40 3.18 223 82 85 3 549.25 2.26 224 82 86 4 543.77 1.38 225 83 86 3 549.19 1.29 226 83 87 4 543.65 1.46 227 84 87 3 549.18 1.29 228 84 88 4 543.65 1.47 229 85 88 3 542.25 2.17 230 85 89 4 541.40 2.59 231 85 127 42 281.80 6.46 232 86 89 3 541.40 2.58 233 86 90 4 541.38 2.59 234 86 130 44 282.96 7.03 235 86 134 48 286.13 8.16 236 87 90 3 548.09 4.39 237 87 91 4 537.75 0.78 238 88 91 3 549.16 4.92 239 88 92 4 549.13 4.94 240 88 109 21 288.87 8.98 241 89 92 3 552.65 3.18 242 89 93 4 537.73 0.77 243 89 109 20 288.94 8.95 244 89 113 24 288.48 8.78 245 89 127 38 286.65 7.92 246 89 131 42 286.73 7.95 247 89 157 68 286.66 7.92 248 89 161 72 286.63 7.91 249 90 93 3 542.97 2.45 250 90 94 4 538.48 0.21 251 90 134 44 286.82 7.97 252 91 94 3 541.47 1.06 253 91 95 4 531.88 3.50 254 92 95 3 531.86 3.48 255 92 96 4 534.09 4.60 256 92 104 12 290.20 8.55 257 92 105 13 289.93 8.63 258 92 108 16 290.19 8.54 259 92 109 17 289.96 8.62 260 93 96 3 547.85 0.05 261 93 97 4 534.89 6.43 262 93 105 12 290.36 8.62 263 93 131 38 288.20 8.09 264 93 153 60 288.20 8.09 265 93 154 61 288.20 8.09 266 93 157 64 287.84 7.91 267 94 97 3 544.75 1.51 268 94 98 4 534.89 6.42 269 95 98 3 541.46 0.99 270 95 99 4 509.85 2.50 271 95 104 9 290.45 8.60 272 96 99 3 521.76 0.14 273 96 100 4 518.45 1.80 274 96 101 5 467.85 7.81 275 96 102 6 344.98 17.59 276 96 104 8 290.49 8.62 277 96 105 9 290.48 8.62 278 96 153 57 289.07 8.21 279 97 100 3 553.18 0.35 280 97 149 52 289.49 8.21 281 97 150 53 289.49 8.20 282 97 153 56 289.20 8.19 283 99 104 5 457.93 3.16 284 101 104 3 640.25 0.56 285 101 153 52 289.64 8.12 286 102 105 3 553.94 2.06 287 102 106 4 513.05 8.06 288 102 153 51 289.63 8.07 289 102 156 54 289.53 8.12 290 103 106 3 543.98 0.15 291 103 107 4 513.06 8.06 292 104 107 3 553.74 3.32 293 104 108 4 508.40 6.69 294 105 108 3 557.73 2.49 295 105 109 4 489.57 2.71 296 105 110 5 461.45 4.54 297 105 153 48 289.72 7.96 298 105 156 51 289.71 7.96 299 105 157 52 289.23 7.81 300 106 110 4 399.31 2.79 301 106 111 5 368.57 18.15 302 106 156 50 289.72 7.96 303 109 113 4 529.71 8.21 304 110 113 3 546.76 0.32 305 110 156 46 290.06 7.79 306 110 160 50 289.04 7.75 307 112 115 3 555.84 0.86 308 112 116 4 538.52 4.44 309 113 116 3 549.27 2.43 310 113 117 4 528.95 0.35 311 113 160 47 289.83 7.87 312 113 161 48 289.82 7.87 313 114 117 3 548.42 0.82 314 114 118 4 526.07 1.79 315 115 118 3 545.47 1.08 316 115 119 4 527.50 2.50 317 116 119 3 553.51 0.54 318 116 120 4 527.50 2.50 319 117 120 3 545.36 3.64 320 117 121 4 517.81 2.27 321 117 122 5 422.81 13.64 322 117 161 44 290.17 7.77 323 118 121 3 530.61 0.93 324 121 126 5 578.74 2.75 325 122 126 4 564.74 2.10 326 122 127 5 560.79 0.13 327 123 126 3 572.42 0.41 328 123 127 4 560.79 0.12 329 124 127 3 560.77 0.12 330 124 128 4 560.75 0.11 331 124 161 37 290.41 7.66 332 125 128 3 560.74 0.12 333 125 129 4 555.95 2.27 334 126 129 3 554.52 2.96 335 126 130 4 552.30 4.07 336 127 130 3 543.10 0.53 337 127 131 4 542.16 0.05 338 127 161 34 291.69 7.42 339 128 131 3 546.76 2.35 340 128 132 4 542.16 0.04 341 128 158 30 291.82 7.37 342 128 161 33 291.69 7.42 343 128 162 34 291.69 7.42 344 129 132 3 546.77 2.34 345 129 133 4 542.07 0.02 346 130 133 3 553.28 0.01 347 130 134 4 542.08 0.03 348 131 134 3 550.98 4.48 349 131 135 4 538.60 1.77 350 131 154 23 293.53 7.17 351 131 157 26 293.38 7.20 352 131 158 27 293.25 7.21 353 131 161 30 293.32 7.20 354 132 135 3 553.28 3.33 355 132 136 4 542.14 0.01 356 132 158 26 293.41 7.23 357 133 136 3 552.52 3.71 358 133 137 4 537.31 6.68 359 134 137 3 553.54 1.75 360 134 138 4 543.47 3.60 361 134 154 20 294.87 6.95 362 135 138 3 547.13 1.77 363 135 139 4 550.56 0.06 364 135 151 16 295.36 7.19 365 135 154 19 294.87 6.95 366 135 155 20 294.87 6.95 367 136 139 3 559.22 4.27 368 137 140 3 568.13 0.18 369 137 141 4 544.20 3.13 370 138 141 3 548.25 1.10 371 138 142 4 539.40 1.12 372 138 147 9 301.89 6.27 373 138 150 12 296.43 7.08 374 138 154 16 295.56 7.08 375 139 142 3 565.13 1.69 376 139 147 8 304.13 7.38 377 142 146 4 530.85 4.51 378 142 147 5 432.21 13.62 379 142 150 8 432.19 13.63 380 143 146 3 566.44 0.47 381 143 147 4 504.99 0.48 382 144 147 3 561.67 2.85 383 144 148 4 547.92 4.02 384 145 148 3 547.92 4.02 385 145 149 4 547.91 4.02 386 146 149 3 548.03 4.08 387 146 150 4 547.91 4.03 388 147 150 3 546.25 3.26 389 147 151 4 541.14 0.71 390 148 151 3 539.37 1.60 391 148 152 4 530.49 6.03 392 149 152 3 539.36 1.60 393 149 153 4 525.45 4.54 394 150 153 3 548.62 3.77 395 150 154 4 538.12 9.02 396 151 154 3 542.36 6.90 397 151 155 4 536.25 9.94 398 152 155 3 555.27 0.43 399 152 156 4 536.22 9.96 400 153 156 3 542.44 6.85 401 153 157 4 541.68 7.23 402 154 157 3 549.11 3.51 403 154 158 4 532.38 2.58 404 155 158 3 539.81 1.14 405 155 159 4 540.95 6.87 406 156 159 3 542.73 7.75 407 156 160 4 540.61 7.04 408 157 160 3 542.23 6.88 409 157 161 4 536.18 9.26 410 158 161 3 547.03 3.83 411 158 162 4 540.56 7.07 412 159 162 3 535.70 4.64