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 49.28 0.26 2 12 132 120 49.82 0.40 3 12 133 121 49.83 0.41 4 12 134 122 49.81 0.40 5 12 135 123 49.48 0.34 6 12 136 124 49.32 0.26 7 13 17 4 645.13 6.46 8 13 131 118 49.70 0.45 9 14 17 3 697.31 0.12 10 14 133 119 55.58 1.66 11 15 133 118 56.87 1.02 12 16 19 3 702.60 0.33 13 17 20 3 698.13 4.25 14 17 21 4 676.58 0.81 15 17 67 50 74.53 0.70 16 18 21 3 676.38 0.91 17 18 22 4 640.72 0.89 18 18 23 5 637.76 0.54 19 18 25 7 625.08 4.17 20 18 26 8 608.68 9.70 21 18 65 47 78.01 0.51 22 18 66 48 77.85 0.57 23 18 96 78 78.06 0.57 24 18 99 81 79.68 0.58 25 19 23 4 637.75 0.54 26 19 26 7 612.01 10.71 27 19 28 9 608.09 9.38 28 20 23 3 725.09 1.85 29 21 67 46 78.00 0.61 30 21 94 73 78.03 0.59 31 22 25 3 682.93 4.08 32 22 26 4 667.36 3.05 33 22 36 14 78.74 0.91 34 22 96 74 78.08 0.57 35 23 26 3 681.18 4.83 36 23 27 4 663.72 1.21 37 23 28 5 639.39 1.10 38 23 29 6 637.56 2.00 39 23 30 7 608.00 9.57 40 23 31 8 611.50 9.96 41 23 34 11 333.81 121.34 42 24 27 3 681.29 4.89 43 24 28 4 656.39 4.86 44 24 30 6 630.27 0.59 45 25 99 74 79.70 0.59 46 30 34 4 674.24 0.03 47 31 34 3 717.73 2.44 48 33 85 52 206.36 0.28 49 34 85 51 206.47 0.24 50 35 83 48 206.45 0.24 51 35 92 57 194.99 3.23 52 35 93 58 194.97 3.22 53 35 94 59 194.94 3.21 54 36 93 57 194.99 3.23 55 36 94 58 194.97 3.23 56 36 95 59 194.95 3.21 57 36 96 60 194.98 3.22 58 37 94 57 194.99 3.22 59 37 95 58 194.98 3.22 60 37 105 68 194.96 3.21 61 37 106 69 194.96 3.21 62 37 107 70 196.31 2.56 63 38 107 69 202.76 0.51 64 39 70 31 206.61 0.18 65 39 72 33 206.65 0.19 66 39 89 50 206.75 0.20 67 39 90 51 206.70 0.20 68 39 91 52 206.69 0.20 69 39 92 53 206.63 0.18 70 39 93 54 206.59 0.18 71 39 106 67 206.63 0.18 72 39 107 68 206.64 0.18 73 39 108 69 206.62 0.18 74 40 44 4 653.07 4.88 75 40 48 8 206.71 0.18 76 40 88 48 209.09 0.73 77 40 89 49 206.77 0.20 78 40 107 67 206.69 0.18 79 40 108 68 206.69 0.18 80 40 109 69 206.70 0.18 81 41 44 3 672.66 4.46 82 41 48 7 434.39 68.84 83 41 85 44 230.01 4.62 84 41 86 45 230.03 4.61 85 41 87 46 229.97 4.59 86 41 88 47 209.09 0.73 87 42 48 6 441.89 73.35 88 43 88 45 232.03 5.30 89 44 48 4 677.15 5.78 90 44 88 44 235.10 3.77 91 44 89 45 231.99 5.32 92 44 109 65 235.47 1.77 93 45 75 30 257.85 0.28 94 45 109 64 266.23 2.01 95 46 75 29 257.85 0.28 96 46 109 63 276.06 0.98 97 47 109 62 286.56 1.99 98 47 110 63 285.47 1.78 99 48 108 60 286.70 2.00 100 48 109 61 286.60 1.96 101 48 180 132 286.65 1.99 102 49 107 58 286.76 1.99 103 49 108 59 286.72 1.99 104 49 109 60 286.72 1.99 105 49 110 61 286.71 1.99 106 49 145 96 286.67 1.98 107 49 180 131 286.67 1.99 108 49 181 132 286.58 1.99 109 49 183 134 286.56 1.99 110 50 105 55 286.95 1.99 111 50 106 56 286.87 1.96 112 50 107 57 286.84 1.95 113 50 177 127 286.70 1.99 114 50 180 130 286.70 1.98 115 50 181 131 286.66 1.99 116 50 182 132 286.60 2.00 117 50 183 133 286.60 2.00 118 51 104 53 287.02 1.98 119 51 105 54 286.99 1.99 120 51 106 55 286.95 1.99 121 51 108 57 286.88 1.96 122 51 126 75 286.74 1.98 123 51 143 92 286.69 1.99 124 51 145 94 286.73 1.98 125 51 183 132 286.62 1.99 126 52 103 51 287.20 1.93 127 52 104 52 287.02 1.98 128 52 105 53 287.00 1.99 129 52 177 125 286.77 1.98 130 52 182 130 286.70 1.98 131 52 183 131 286.65 1.99 132 52 184 132 286.60 2.00 133 52 185 133 286.60 2.00 134 53 103 50 287.25 1.91 135 53 104 51 287.20 1.93 136 53 184 131 286.63 1.99 137 53 185 132 286.61 2.00 138 53 186 133 286.58 1.99 139 54 62 8 432.84 69.95 140 54 101 47 289.38 1.42 141 54 102 48 288.61 1.41 142 54 103 49 287.54 1.82 143 54 104 50 287.31 1.94 144 54 184 130 286.70 1.98 145 54 186 132 286.60 2.00 146 54 187 133 286.59 1.99 147 55 62 7 432.86 69.94 148 55 63 8 432.51 70.10 149 55 66 11 288.81 1.25 150 55 97 42 289.19 1.42 151 55 104 49 288.91 1.55 152 55 130 75 286.98 1.97 153 55 187 132 286.60 2.00 154 55 189 134 286.58 1.99 155 56 60 4 628.39 3.47 156 56 61 5 453.06 76.66 157 56 62 6 432.88 69.93 158 56 63 7 432.86 69.94 159 56 186 130 286.70 1.97 160 56 187 131 286.64 1.99 161 56 188 132 286.59 1.99 162 56 189 133 286.58 1.99 163 57 60 3 691.56 3.25 164 57 61 4 617.34 8.99 165 57 63 6 432.92 69.94 166 58 190 132 286.56 2.00 167 62 101 39 563.83 2.75 168 62 102 40 560.08 1.55 169 63 66 3 706.13 0.04 170 63 97 34 565.82 1.95 171 63 132 69 465.18 1.27 172 63 189 126 286.58 1.99 173 64 97 33 565.82 1.95 174 64 98 34 565.82 1.96 175 64 99 35 564.28 2.73 176 64 100 36 564.39 2.73 177 64 102 38 563.44 2.55 178 65 97 32 566.04 2.02 179 65 133 68 466.06 1.70 180 66 96 30 566.11 2.02 181 66 97 31 566.06 2.01 182 66 130 64 466.49 1.65 183 66 131 65 466.10 1.70 184 66 132 66 466.06 1.70 185 67 94 27 566.45 2.06 186 67 95 28 566.36 2.06 187 67 96 29 566.14 2.00 188 67 130 63 466.57 1.63 189 67 131 64 466.10 1.70 190 68 94 26 566.45 2.06 191 68 95 27 566.37 2.04 192 68 96 28 566.31 2.03 193 68 104 36 566.09 2.14 194 68 128 60 466.76 1.66 195 68 129 61 466.73 1.67 196 68 130 62 466.60 1.64 197 68 187 119 286.64 1.98 198 69 92 23 566.70 2.04 199 69 93 24 566.57 2.04 200 69 94 25 566.48 2.08 201 69 128 59 466.79 1.66 202 69 129 60 466.74 1.67 203 69 131 62 466.73 1.67 204 70 92 22 566.70 2.04 205 70 93 23 566.64 2.06 206 70 106 36 566.09 2.14 207 70 126 56 467.20 1.76 208 70 127 57 467.01 1.78 209 70 128 58 466.80 1.67 210 71 79 8 569.33 2.00 211 71 81 10 569.07 2.06 212 71 91 20 566.77 2.06 213 71 92 21 566.73 2.04 214 71 126 55 467.33 1.72 215 71 127 56 467.11 1.73 216 72 79 7 569.34 1.99 217 72 89 17 567.47 2.00 218 72 91 19 566.80 2.06 219 72 108 36 566.09 2.14 220 72 109 37 566.06 2.14 221 72 111 39 561.46 1.80 222 72 126 54 467.36 1.71 223 73 77 4 610.08 5.84 224 73 78 5 581.88 8.26 225 73 79 6 569.33 2.00 226 73 89 16 567.48 2.00 227 73 111 38 561.47 1.80 228 73 112 39 561.47 1.80 229 73 114 41 561.28 1.87 230 74 77 3 676.58 4.08 231 74 78 4 610.08 5.84 232 74 80 6 575.73 5.17 233 74 89 15 567.48 2.00 234 74 111 37 563.77 2.94 235 74 112 38 563.52 2.83 236 75 109 34 566.09 2.13 237 75 110 35 565.96 2.19 238 75 112 37 563.20 2.67 239 77 112 35 561.48 1.81 240 77 113 36 561.47 1.80 241 77 114 37 561.45 1.80 242 79 91 12 567.06 2.18 243 79 114 35 561.35 1.84 244 79 125 46 467.89 1.78 245 79 127 48 467.81 1.77 246 80 89 9 567.51 1.99 247 80 91 11 567.06 2.19 248 82 87 5 664.59 4.58 249 83 87 4 672.61 2.29 250 83 90 7 567.72 2.10 251 83 92 9 567.43 2.08 252 84 87 3 677.33 4.66 253 84 90 6 587.78 6.61 254 87 90 3 713.93 4.96 255 89 108 19 566.16 2.10 256 89 109 20 566.09 2.13 257 95 104 9 565.99 2.19 258 95 105 10 565.96 2.19 259 95 106 11 565.60 2.12 260 96 104 8 566.33 2.38 261 97 102 5 566.40 2.38 262 97 103 6 566.38 2.38 263 97 104 7 566.25 2.43 264 98 101 3 676.09 2.77 265 98 102 4 566.39 2.38 266 98 103 5 568.31 1.42 267 103 184 81 286.70 1.98 268 104 185 81 286.62 1.99 269 108 126 18 467.35 1.72 270 110 145 35 465.86 1.79 271 110 147 37 461.88 2.02 272 110 148 38 439.50 3.67 273 110 183 73 286.70 1.97 274 111 124 13 467.79 1.74 275 111 125 14 467.78 1.74 276 111 126 15 467.76 1.75 277 111 145 34 465.95 1.78 278 113 121 8 469.95 2.00 279 113 122 9 469.80 2.00 280 113 124 11 467.92 1.77 281 114 121 7 470.26 2.16 282 114 122 8 469.91 2.01 283 114 125 11 468.48 1.74 284 115 119 4 642.52 3.73 285 115 120 5 470.56 2.17 286 115 121 6 470.26 2.16 287 115 122 7 470.26 2.16 288 116 119 3 670.68 2.52 289 116 120 4 645.89 2.02 290 116 122 6 470.42 2.15 291 116 156 40 398.90 0.12 292 120 156 36 398.93 0.12 293 121 156 35 398.94 0.12 294 122 125 3 800.89 5.01 295 122 142 20 466.35 1.76 296 122 155 33 398.83 0.10 297 122 156 34 398.82 0.10 298 122 157 35 398.64 0.17 299 123 144 21 466.19 1.77 300 123 151 28 399.31 0.04 301 123 152 29 399.18 0.03 302 123 155 32 398.70 0.14 303 124 144 20 466.17 1.76 304 124 145 21 466.15 1.76 305 124 148 24 441.00 2.93 306 124 151 27 402.79 1.70 307 125 142 17 466.19 1.76 308 125 143 18 466.17 1.76 309 125 144 19 465.93 1.76 310 125 145 20 465.94 1.76 311 126 142 16 466.16 1.76 312 126 143 17 465.95 1.75 313 126 145 19 465.93 1.76 314 127 141 14 466.18 1.75 315 127 142 15 465.94 1.75 316 128 140 12 466.18 1.75 317 128 141 13 466.04 1.79 318 128 143 15 465.88 1.74 319 128 185 57 286.78 1.95 320 128 187 59 286.63 1.99 321 129 138 9 466.25 1.74 322 129 139 10 466.19 1.76 323 129 140 11 466.04 1.77 324 130 135 5 653.75 4.79 325 130 138 8 466.19 1.77 326 130 139 9 466.17 1.77 327 130 187 57 286.69 1.97 328 130 189 59 286.59 1.99 329 131 138 7 466.18 1.78 330 132 135 3 690.99 0.84 331 135 138 3 715.63 2.80 332 135 139 4 697.97 0.45 333 135 189 54 286.70 1.97 334 139 189 50 286.62 1.98 335 139 197 58 150.77 0.98 336 140 197 57 147.28 0.49 337 140 198 58 144.97 1.62 338 140 200 60 144.66 1.52 339 141 170 29 340.44 2.99 340 141 185 44 286.85 1.95 341 141 187 46 286.63 1.99 342 141 195 54 165.02 0.33 343 141 196 55 163.07 0.05 344 141 197 56 146.00 1.14 345 141 198 57 144.96 1.64 346 142 157 15 394.56 0.07 347 142 170 28 340.47 2.98 348 142 185 43 286.80 1.95 349 142 198 56 144.96 1.64 350 143 170 27 340.56 3.00 351 143 172 29 340.40 3.00 352 143 185 42 286.70 1.97 353 144 152 8 398.81 0.10 354 144 155 11 398.74 0.16 355 144 157 13 398.46 0.25 356 144 158 14 398.00 0.41 357 144 170 26 340.61 3.00 358 144 171 27 340.50 3.00 359 144 172 28 340.44 2.99 360 145 148 3 686.35 1.43 361 145 152 7 607.57 0.24 362 145 171 26 340.57 3.00 363 145 172 27 340.47 3.00 364 145 183 38 287.13 1.79 365 146 171 25 340.61 3.00 366 146 172 26 340.58 3.00 367 146 173 27 340.49 3.01 368 146 174 28 340.45 3.00 369 146 183 37 287.22 1.78 370 147 174 27 340.47 3.01 371 147 183 36 287.22 1.78 372 148 151 3 680.78 0.47 373 148 152 4 676.01 0.39 374 149 152 3 677.54 1.15 375 149 153 4 677.22 0.99 376 150 153 3 685.56 1.06 377 150 154 4 685.56 1.06 378 151 154 3 695.62 3.57 379 151 155 4 681.31 1.05 380 152 155 3 693.22 4.71 381 152 158 6 649.16 2.18 382 152 171 19 340.84 2.96 383 153 159 6 661.35 3.90 384 154 159 5 663.35 2.94 385 155 158 3 682.07 0.09 386 155 159 4 667.07 1.08 387 156 159 3 677.06 2.93 388 156 160 4 670.23 0.49 389 157 160 3 688.40 6.05 390 157 198 41 162.68 0.26 391 158 161 3 692.67 3.93 392 158 167 9 341.11 2.95 393 158 170 12 341.10 2.94 394 159 167 8 345.18 1.68 395 161 166 5 663.25 1.50 396 161 167 6 606.44 1.98 397 161 170 9 600.73 3.65 398 161 196 35 166.13 0.16 399 161 198 37 165.16 0.29 400 163 166 3 684.01 3.58 401 163 167 4 678.05 0.40 402 164 167 3 685.84 0.72 403 164 168 4 681.82 2.28 404 165 168 3 706.68 6.88 405 166 169 3 687.54 1.48 406 166 194 28 169.41 0.30 407 166 195 29 168.16 0.27 408 166 196 30 165.88 0.13 409 167 170 3 688.06 2.06 410 167 171 4 677.89 0.33 411 168 171 3 680.12 1.24 412 169 185 16 287.11 1.83 413 169 193 24 168.10 0.33 414 169 194 25 167.00 0.16 415 169 195 26 165.53 0.11 416 169 196 27 165.53 0.11 417 170 185 15 286.83 1.96 418 170 195 25 165.53 0.11 419 170 196 26 165.46 0.11 420 170 198 28 165.31 0.18 421 172 183 11 287.22 1.78 422 172 184 12 287.06 1.81 423 172 185 13 286.62 1.98 424 173 183 10 287.22 1.78 425 173 184 11 287.07 1.81 426 174 181 7 288.43 1.30 427 174 182 8 287.75 1.55 428 174 183 9 287.17 1.75 429 175 181 6 440.76 76.25 430 175 182 7 287.79 1.56 431 176 179 3 687.95 3.23 432 176 180 4 603.20 0.49 433 176 181 5 440.79 76.27 434 176 182 6 289.63 0.70 435 177 180 3 664.31 3.12 436 177 182 5 446.15 78.95 437 185 195 10 165.54 0.11 438 187 195 8 165.44 0.07 439 187 197 10 165.26 0.15 440 188 192 4 689.69 1.47 441 188 193 5 479.18 65.85 442 188 194 6 252.11 43.39 443 188 195 7 165.46 0.07 444 188 197 9 165.44 0.07 445 189 194 5 470.25 61.39 446 189 197 8 165.00 0.29 447 190 194 4 539.75 35.95 448 191 194 3 659.96 0.20