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 47.90 0.43 2 12 132 120 50.69 0.83 3 12 133 121 50.69 0.83 4 12 134 122 50.55 0.82 5 12 135 123 49.72 0.46 6 12 136 124 49.26 0.24 7 13 17 4 637.78 2.81 8 13 131 118 50.59 0.87 9 13 132 119 50.90 0.93 10 14 17 3 701.86 2.40 11 14 133 119 53.38 0.29 12 15 133 118 60.84 3.31 13 16 19 3 702.60 0.33 14 17 20 3 698.13 4.26 15 17 21 4 676.58 0.80 16 17 65 48 84.67 0.60 17 17 67 50 83.09 1.28 18 18 21 3 676.59 0.80 19 18 22 4 641.24 2.26 20 18 23 5 637.84 0.57 21 18 25 7 621.37 5.44 22 18 26 8 607.81 8.85 23 18 65 47 84.84 0.53 24 18 66 48 84.75 0.57 25 18 96 78 84.86 0.53 26 18 99 81 85.38 0.32 27 19 23 4 637.83 0.57 28 19 26 7 609.65 9.66 29 19 28 9 607.61 8.76 30 20 23 3 725.09 1.85 31 21 67 46 84.81 0.54 32 21 94 73 84.83 0.54 33 22 25 3 675.03 0.12 34 22 26 4 667.38 3.04 35 22 36 14 85.33 0.29 36 22 96 74 85.33 0.29 37 23 26 3 681.64 4.59 38 23 27 4 663.73 1.21 39 23 28 5 632.69 0.61 40 23 29 6 621.15 5.16 41 23 30 7 591.69 1.17 42 23 31 8 610.75 10.35 43 23 34 11 332.91 120.53 44 24 27 3 681.76 4.66 45 24 30 6 621.11 5.18 46 24 36 12 89.10 0.68 47 25 36 11 88.86 1.47 48 25 99 74 85.36 0.33 49 26 99 73 85.36 0.33 50 30 34 4 680.36 3.03 51 31 34 3 722.84 0.11 52 33 85 52 207.14 0.12 53 34 85 51 207.56 0.31 54 35 83 48 207.56 0.31 55 35 92 57 195.01 3.23 56 35 93 58 194.98 3.23 57 35 94 59 194.94 3.21 58 36 93 57 195.02 3.24 59 36 94 58 194.97 3.21 60 36 95 59 194.99 3.23 61 36 96 60 194.99 3.23 62 37 94 57 195.03 3.23 63 37 95 58 195.01 3.23 64 37 105 68 195.01 3.22 65 37 106 69 195.00 3.22 66 37 107 70 195.24 3.12 67 38 107 69 203.16 0.83 68 39 70 31 207.59 0.30 69 39 72 33 207.59 0.30 70 39 89 50 207.71 0.29 71 39 90 51 207.67 0.29 72 39 91 52 207.65 0.29 73 39 92 53 207.59 0.30 74 39 93 54 207.58 0.30 75 39 106 67 207.59 0.30 76 39 107 68 207.62 0.32 77 39 108 69 207.59 0.30 78 40 44 4 653.07 4.88 79 40 48 8 207.68 0.30 80 40 88 48 208.15 0.26 81 40 89 49 207.71 0.29 82 40 107 67 207.66 0.30 83 40 108 68 207.66 0.29 84 40 109 69 207.67 0.30 85 41 44 3 664.24 0.67 86 41 48 7 401.36 96.42 87 41 85 44 224.50 1.86 88 41 86 45 229.80 4.50 89 41 87 46 224.31 1.83 90 41 88 47 213.75 0.56 91 42 48 6 611.45 8.62 92 43 88 45 229.96 4.32 93 44 48 4 677.15 5.78 94 44 88 44 229.96 4.32 95 44 89 45 230.03 4.35 96 44 109 65 235.62 1.69 97 45 75 30 260.50 1.10 98 45 109 64 262.47 0.12 99 46 75 29 261.12 0.80 100 46 109 63 275.92 2.02 101 47 109 62 289.26 2.04 102 47 110 63 288.52 1.79 103 47 181 134 289.22 2.04 104 48 108 60 289.36 2.03 105 48 109 61 289.26 2.04 106 48 180 132 289.31 2.04 107 49 107 58 289.43 2.04 108 49 108 59 289.38 2.02 109 49 109 60 289.38 2.02 110 49 110 61 289.35 2.03 111 49 145 96 289.31 2.04 112 49 180 131 289.31 2.04 113 49 181 132 289.25 2.04 114 49 183 134 289.22 2.04 115 50 105 55 289.88 1.94 116 50 106 56 289.75 1.89 117 50 107 57 289.44 2.04 118 50 177 127 289.32 2.05 119 50 180 130 289.33 2.04 120 50 181 131 289.31 2.04 121 50 182 132 289.27 2.04 122 50 183 133 289.27 2.04 123 51 104 53 290.95 1.65 124 51 105 54 289.98 1.96 125 51 106 55 289.78 1.89 126 51 108 57 289.76 1.89 127 51 126 75 289.32 2.05 128 51 143 92 289.31 2.04 129 51 145 94 289.36 2.03 130 51 183 132 289.28 2.04 131 52 103 51 291.82 1.26 132 52 104 52 290.95 1.65 133 52 105 53 290.03 1.98 134 52 177 125 289.38 2.03 135 52 182 130 289.35 2.04 136 52 183 131 289.31 2.04 137 52 184 132 289.28 2.04 138 52 185 133 289.28 2.04 139 53 103 50 291.84 1.27 140 53 104 51 291.44 1.43 141 53 184 131 289.30 2.04 142 53 185 132 289.28 2.04 143 53 186 133 289.24 2.06 144 54 62 8 295.06 0.07 145 54 101 47 294.79 0.00 146 54 102 48 294.39 0.12 147 54 103 49 291.86 1.27 148 54 104 50 291.86 1.27 149 54 184 130 289.35 2.04 150 54 186 132 289.25 2.06 151 54 187 133 289.25 2.06 152 55 62 7 295.12 0.04 153 55 63 8 294.95 0.10 154 55 66 11 294.20 0.04 155 55 97 42 294.83 0.10 156 55 104 49 294.43 0.10 157 55 130 75 291.31 1.42 158 55 187 132 289.25 2.06 159 55 189 134 289.20 2.04 160 56 60 4 628.39 3.46 161 56 61 5 450.82 77.77 162 56 62 6 295.19 0.04 163 56 63 7 295.12 0.04 164 56 186 130 289.34 2.04 165 56 187 131 289.28 2.04 166 56 188 132 289.21 2.04 167 56 189 133 289.21 2.04 168 57 60 3 691.56 3.25 169 57 61 4 617.32 9.00 170 57 63 6 295.24 0.01 171 58 190 132 288.99 2.08 172 62 101 39 561.97 1.57 173 62 102 40 556.72 0.48 174 63 66 3 703.83 1.19 175 63 97 34 562.29 1.73 176 63 132 69 471.12 1.71 177 63 189 126 289.25 2.06 178 64 97 33 562.29 1.73 179 64 98 34 562.36 1.71 180 64 99 35 562.36 1.71 181 64 100 36 562.44 1.75 182 64 101 37 562.37 1.71 183 64 102 38 561.36 1.31 184 65 97 32 564.28 1.14 185 65 132 67 472.09 1.32 186 65 133 68 472.09 1.33 187 66 96 30 564.34 1.13 188 66 97 31 564.31 1.14 189 66 130 64 472.26 1.35 190 66 131 65 472.13 1.32 191 66 132 66 472.09 1.32 192 67 94 27 564.51 1.09 193 67 95 28 564.41 1.10 194 67 96 29 564.35 1.12 195 67 130 63 472.31 1.36 196 67 131 64 472.13 1.32 197 68 94 26 564.52 1.10 198 68 95 27 564.43 1.11 199 68 96 28 564.43 1.11 200 68 104 36 564.19 1.23 201 68 128 60 472.49 1.33 202 68 129 61 472.43 1.35 203 68 130 62 472.32 1.36 204 68 187 119 289.30 2.05 205 69 92 23 564.88 1.12 206 69 93 24 564.66 1.13 207 69 94 25 564.52 1.10 208 69 128 59 472.51 1.33 209 69 129 60 472.44 1.35 210 69 131 62 472.44 1.34 211 70 92 22 564.88 1.12 212 70 93 23 564.85 1.13 213 70 106 36 564.23 1.22 214 70 126 56 472.94 1.35 215 70 127 57 472.81 1.36 216 70 128 58 472.60 1.29 217 71 79 8 570.32 1.48 218 71 80 9 570.26 1.50 219 71 81 10 570.00 1.61 220 71 91 20 564.99 1.17 221 71 92 21 564.97 1.16 222 71 126 55 472.97 1.34 223 71 127 56 472.83 1.36 224 72 79 7 570.34 1.49 225 72 89 17 566.45 1.50 226 72 91 19 565.00 1.17 227 72 108 36 564.24 1.22 228 72 109 37 564.17 1.23 229 72 111 39 556.18 0.12 230 72 126 54 472.99 1.32 231 73 77 4 610.89 12.40 232 73 78 5 585.61 6.13 233 73 79 6 570.34 1.49 234 73 89 16 566.48 1.49 235 73 111 38 558.34 1.19 236 73 114 41 552.23 1.99 237 74 77 3 676.58 4.08 238 74 78 4 594.03 1.94 239 74 80 6 585.62 6.15 240 74 89 15 566.40 1.47 241 74 111 37 559.76 1.65 242 74 112 38 559.54 1.76 243 75 109 34 564.25 1.22 244 75 110 35 564.05 1.24 245 75 112 37 559.75 1.65 246 77 112 35 558.69 1.38 247 77 113 36 556.18 0.12 248 77 114 37 555.96 0.16 249 79 91 12 565.68 1.44 250 79 114 35 555.99 0.20 251 79 125 46 473.45 1.26 252 79 127 48 473.30 1.26 253 80 89 9 566.53 1.50 254 80 91 11 565.68 1.44 255 82 87 5 664.59 4.58 256 83 87 4 672.60 2.29 257 83 90 7 566.56 1.49 258 83 92 9 566.53 1.51 259 84 87 3 677.33 4.66 260 84 90 6 585.40 7.80 261 87 90 3 713.52 5.17 262 89 108 19 564.25 1.23 263 89 109 20 564.24 1.22 264 95 104 9 564.81 1.51 265 95 105 10 564.69 1.56 266 95 106 11 564.55 1.61 267 96 104 8 564.84 1.53 268 97 102 5 565.01 1.57 269 97 103 6 565.00 1.56 270 97 104 7 564.86 1.53 271 98 101 3 676.09 2.78 272 98 102 4 587.52 9.69 273 98 103 5 574.14 2.99 274 103 184 81 289.34 2.04 275 104 185 81 289.29 2.04 276 108 126 18 473.09 1.33 277 110 145 35 471.19 1.01 278 110 147 37 462.18 1.65 279 110 148 38 442.26 5.01 280 110 183 73 289.32 2.04 281 111 124 13 473.24 1.32 282 111 125 14 473.23 1.32 283 111 126 15 473.21 1.31 284 111 145 34 471.86 1.26 285 113 121 8 476.88 1.54 286 113 122 9 476.50 1.35 287 113 124 11 473.51 1.29 288 114 121 7 476.91 1.53 289 114 122 8 476.67 1.46 290 114 125 11 475.05 1.55 291 115 119 4 642.52 3.72 292 115 120 5 477.22 1.38 293 115 121 6 476.91 1.53 294 115 122 7 476.94 1.51 295 116 119 3 664.12 0.22 296 116 120 4 632.58 8.70 297 116 122 6 477.20 1.38 298 116 156 40 404.20 0.96 299 120 156 36 404.22 0.90 300 121 156 35 404.13 0.88 301 122 125 3 800.89 5.01 302 122 142 20 472.22 1.30 303 122 155 33 404.07 0.89 304 122 156 34 404.08 0.89 305 122 157 35 403.53 0.96 306 123 144 21 472.10 1.31 307 123 151 28 404.41 0.95 308 123 152 29 404.37 0.96 309 123 155 32 404.18 0.94 310 124 144 20 472.06 1.32 311 124 145 21 472.01 1.31 312 124 148 24 435.52 2.82 313 124 151 27 404.41 0.95 314 125 142 17 472.10 1.31 315 125 143 18 472.04 1.30 316 125 144 19 471.94 1.28 317 125 145 20 471.98 1.30 318 126 142 16 472.06 1.31 319 126 143 17 471.99 1.29 320 126 145 19 471.94 1.28 321 127 141 14 472.09 1.30 322 127 142 15 471.94 1.28 323 128 140 12 472.09 1.30 324 128 141 13 471.99 1.29 325 128 143 15 471.85 1.25 326 128 185 57 289.36 2.04 327 128 187 59 289.29 2.06 328 129 138 9 472.11 1.30 329 129 139 10 472.08 1.30 330 129 140 11 471.94 1.29 331 130 135 5 646.76 1.28 332 130 138 8 472.09 1.31 333 130 139 9 472.04 1.30 334 130 187 57 289.33 2.04 335 130 189 59 289.21 2.04 336 131 138 7 472.04 1.30 337 132 135 3 690.99 0.84 338 135 138 3 715.63 2.80 339 135 139 4 694.05 2.41 340 135 189 54 289.34 2.04 341 139 189 50 289.27 2.06 342 139 197 58 150.10 0.92 343 140 197 57 147.37 0.45 344 140 198 58 147.13 0.53 345 140 200 60 146.59 0.26 346 141 170 29 339.49 2.35 347 141 185 44 289.41 2.02 348 141 187 46 289.29 2.06 349 141 195 54 162.72 0.81 350 141 196 55 160.40 0.10 351 141 197 56 147.34 0.45 352 141 198 57 147.13 0.53 353 142 157 15 397.70 1.62 354 142 170 28 339.50 2.35 355 142 185 43 289.37 2.04 356 142 198 56 147.16 0.54 357 143 170 27 339.50 2.35 358 143 172 29 339.35 2.40 359 143 185 42 289.31 2.06 360 144 152 8 404.29 0.95 361 144 155 11 404.19 0.95 362 144 157 13 403.01 0.81 363 144 158 14 402.05 1.23 364 144 170 26 339.53 2.35 365 144 171 27 339.48 2.35 366 144 172 28 339.40 2.39 367 145 148 3 685.99 1.60 368 145 152 7 605.52 4.51 369 145 171 26 339.53 2.36 370 145 183 38 289.39 2.03 371 146 171 25 339.55 2.36 372 146 172 26 339.53 2.36 373 146 173 27 339.43 2.39 374 146 174 28 339.37 2.40 375 146 183 37 289.44 2.03 376 147 174 27 339.41 2.42 377 147 183 36 289.42 2.02 378 148 151 3 680.46 0.64 379 148 152 4 675.98 0.37 380 149 152 3 679.52 2.14 381 149 153 4 679.52 2.15 382 150 153 3 687.28 1.93 383 150 154 4 685.55 1.06 384 151 154 3 688.50 0.01 385 151 155 4 685.54 1.06 386 152 155 3 693.21 4.71 387 152 158 6 647.54 3.02 388 153 159 6 661.32 3.87 389 154 159 5 663.28 2.91 390 155 158 3 682.07 0.09 391 155 159 4 663.88 2.62 392 156 159 3 677.04 2.94 393 156 160 4 670.03 0.42 394 157 160 3 682.22 0.39 395 157 198 41 160.28 0.32 396 158 161 3 691.98 4.26 397 158 167 9 340.26 2.29 398 158 170 12 339.94 2.26 399 159 167 8 344.57 0.15 400 161 166 5 655.60 0.40 401 161 167 6 606.60 1.46 402 161 170 9 600.55 1.55 403 161 196 35 163.82 0.26 404 161 198 37 163.16 0.58 405 163 166 3 687.78 2.60 406 163 167 4 671.28 0.28 407 164 167 3 681.82 2.73 408 164 168 4 677.44 0.65 409 165 168 3 706.14 7.16 410 166 169 3 694.00 1.75 411 166 194 28 166.65 0.48 412 166 195 29 165.83 0.43 413 166 196 30 164.19 0.23 414 167 170 3 701.88 3.35 415 167 171 4 678.37 0.10 416 168 171 3 677.65 0.45 417 169 185 16 289.42 2.04 418 169 193 24 166.21 0.42 419 169 194 25 165.78 0.46 420 169 195 26 163.75 0.39 421 169 196 27 163.15 0.73 422 170 185 15 289.37 2.04 423 170 195 25 162.84 0.84 424 170 196 26 162.71 0.80 425 170 198 28 162.69 0.80 426 172 183 11 289.42 2.03 427 172 184 12 289.38 2.03 428 172 185 13 289.33 2.04 429 173 183 10 289.44 2.03 430 173 184 11 289.40 2.02 431 174 181 7 343.48 2.54 432 174 182 8 319.25 12.88 433 174 183 9 289.44 2.03 434 175 181 6 344.00 2.81 435 175 182 7 321.08 13.73 436 176 179 3 687.94 3.23 437 176 180 4 470.88 61.22 438 176 182 6 343.19 2.68 439 177 180 3 664.31 3.12 440 177 182 5 473.28 65.38 441 187 195 8 162.72 0.80 442 187 197 10 162.69 0.79 443 188 192 4 685.11 3.76 444 188 193 5 469.10 61.96 445 188 194 6 253.52 45.20 446 188 195 7 228.68 33.77 447 189 194 5 468.82 62.11 448 189 197 8 465.34 63.84 449 190 194 4 561.60 34.91 450 191 194 3 667.27 0.26