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 50.36 0.96 2 12 132 120 51.41 1.34 3 12 133 121 51.41 1.34 4 12 134 122 51.40 1.34 5 12 135 123 51.36 1.36 6 12 136 124 51.30 1.34 7 13 17 4 641.88 2.54 8 13 131 118 51.41 1.34 9 13 132 119 51.41 1.34 10 14 17 3 703.75 1.46 11 14 133 119 51.74 1.51 12 15 18 3 792.88 1.70 13 15 133 118 56.44 1.21 14 16 19 3 713.76 3.56 15 17 20 3 713.76 3.56 16 17 21 4 669.53 2.72 17 17 67 50 73.14 1.11 18 18 21 3 676.83 0.20 19 18 22 4 636.81 0.02 20 18 23 5 636.62 0.12 21 18 25 7 621.24 5.28 22 18 26 8 621.15 5.30 23 18 65 47 77.52 0.41 24 18 96 78 77.59 0.40 25 18 99 81 78.47 0.07 26 19 23 4 639.00 0.10 27 19 26 7 621.22 5.27 28 19 28 9 618.33 3.83 29 20 23 3 725.09 1.85 30 21 67 46 77.57 0.40 31 21 94 73 77.67 0.45 32 22 25 3 685.41 2.83 33 22 26 4 668.90 2.29 34 22 36 14 78.26 0.27 35 22 96 74 77.75 0.41 36 23 26 3 682.27 4.40 37 23 27 4 665.23 0.45 38 23 28 5 637.22 0.62 39 23 29 6 634.76 0.61 40 23 30 7 606.98 8.81 41 23 31 8 606.98 8.81 42 23 34 11 329.07 117.75 43 24 27 3 682.84 4.12 44 24 28 4 656.40 4.86 45 24 30 6 630.27 0.59 46 25 99 74 78.57 0.03 47 30 34 4 674.24 0.03 48 31 34 3 722.84 0.11 49 33 85 52 205.39 0.64 50 34 85 51 205.66 0.65 51 35 83 48 205.65 0.64 52 35 92 57 199.18 1.00 53 35 93 58 199.16 1.00 54 35 94 59 199.09 0.99 55 36 93 57 199.18 1.00 56 36 94 58 199.12 1.01 57 36 95 59 199.18 0.99 58 36 96 60 199.19 0.99 59 37 94 57 199.19 0.99 60 37 95 58 199.19 0.99 61 37 105 68 199.19 0.99 62 37 106 69 199.18 0.99 63 37 107 70 199.22 0.99 64 38 107 69 201.47 0.13 65 39 70 31 205.68 0.66 66 39 72 33 205.74 0.62 67 39 89 50 205.87 0.61 68 39 90 51 205.84 0.61 69 39 91 52 205.78 0.65 70 39 92 53 205.76 0.64 71 39 93 54 205.68 0.66 72 39 106 67 205.73 0.63 73 39 107 68 205.75 0.64 74 39 108 69 205.72 0.63 75 40 44 4 653.07 4.88 76 40 48 8 205.85 0.61 77 40 88 48 206.59 0.46 78 40 89 49 205.88 0.62 79 40 107 67 205.84 0.61 80 40 108 68 205.83 0.62 81 40 109 69 205.84 0.61 82 41 44 3 673.58 4.00 83 41 48 7 573.79 5.80 84 41 85 44 232.38 3.22 85 41 86 45 232.40 3.21 86 41 87 46 229.00 1.54 87 41 88 47 209.03 0.72 88 42 48 6 582.14 9.97 89 43 88 45 232.41 3.09 90 44 48 4 677.15 5.77 91 44 88 44 232.72 3.01 92 44 89 45 232.42 3.09 93 45 75 30 260.41 1.28 94 45 109 64 260.43 1.15 95 46 75 29 260.32 1.25 96 46 109 63 281.65 3.58 97 47 109 62 292.71 1.03 98 47 110 63 291.60 1.28 99 47 181 134 293.06 1.15 100 48 108 60 293.18 1.12 101 48 109 61 292.87 1.08 102 48 180 132 293.12 1.15 103 49 107 58 293.22 1.13 104 49 108 59 293.19 1.13 105 49 109 60 293.18 1.12 106 49 110 61 293.15 1.13 107 49 145 96 293.09 1.14 108 49 180 131 293.13 1.15 109 49 181 132 293.09 1.15 110 49 183 134 293.06 1.15 111 50 105 55 293.32 1.13 112 50 106 56 293.26 1.11 113 50 107 57 293.22 1.13 114 50 177 127 293.12 1.14 115 50 180 130 293.16 1.15 116 50 181 131 293.12 1.15 117 50 182 132 293.08 1.14 118 50 183 133 293.08 1.14 119 51 104 53 293.43 1.12 120 51 105 54 293.33 1.13 121 51 106 55 293.30 1.12 122 51 108 57 293.25 1.13 123 51 126 75 293.18 1.12 124 51 143 92 293.12 1.14 125 51 145 94 293.17 1.14 126 51 183 132 293.10 1.14 127 52 103 51 293.47 1.14 128 52 104 52 293.43 1.12 129 52 105 53 293.34 1.13 130 52 177 125 293.22 1.14 131 52 182 130 293.18 1.14 132 52 183 131 293.13 1.15 133 52 184 132 293.10 1.14 134 52 185 133 293.09 1.14 135 53 103 50 293.49 1.13 136 53 104 51 293.45 1.14 137 53 184 131 293.12 1.14 138 53 185 132 293.09 1.15 139 53 186 133 293.06 1.15 140 54 62 8 294.85 1.16 141 54 101 47 294.55 1.16 142 54 102 48 293.91 1.17 143 54 103 49 293.58 1.12 144 54 184 130 293.18 1.14 145 54 186 132 293.07 1.14 146 54 187 133 293.07 1.14 147 55 62 7 429.38 66.08 148 55 63 8 294.62 1.16 149 55 66 11 293.76 1.24 150 55 97 42 294.34 1.16 151 55 104 49 294.15 1.06 152 55 130 75 293.31 1.18 153 55 187 132 293.07 1.15 154 55 189 134 293.04 1.16 155 56 60 4 617.32 8.98 156 56 61 5 584.05 11.15 157 56 62 6 294.89 1.18 158 56 63 7 294.88 1.17 159 56 186 130 293.16 1.15 160 56 187 131 293.11 1.15 161 56 188 132 293.06 1.15 162 56 189 133 293.06 1.15 163 57 60 3 673.61 5.72 164 57 61 4 611.48 5.30 165 57 63 6 294.98 1.13 166 57 189 132 293.06 1.15 167 58 190 132 293.01 1.15 168 62 101 39 564.51 4.08 169 62 102 40 563.56 3.93 170 63 66 3 703.83 1.19 171 63 97 34 564.90 4.12 172 63 132 69 473.00 0.40 173 63 189 126 293.05 1.16 174 64 97 33 564.90 4.12 175 64 98 34 565.19 4.21 176 64 99 35 565.19 4.21 177 64 100 36 565.28 4.17 178 64 102 38 564.11 3.95 179 65 99 34 565.33 4.16 180 65 132 67 473.90 0.83 181 65 133 68 473.88 0.82 182 66 96 30 565.87 3.89 183 66 97 31 565.69 3.98 184 66 130 64 474.06 0.86 185 66 131 65 474.00 0.84 186 66 132 66 473.91 0.83 187 67 94 27 566.52 4.08 188 67 95 28 566.34 4.05 189 67 96 29 565.98 3.94 190 67 130 63 474.09 0.88 191 67 131 64 474.00 0.84 192 68 94 26 566.52 4.08 193 68 95 27 566.39 4.08 194 68 96 28 566.24 4.00 195 68 104 36 565.88 4.04 196 68 128 60 474.38 0.83 197 68 129 61 474.19 0.85 198 68 130 62 474.13 0.85 199 68 187 119 293.13 1.15 200 69 92 23 566.98 4.00 201 69 93 24 566.71 4.03 202 69 94 25 566.56 4.07 203 69 128 59 474.39 0.83 204 69 129 60 474.31 0.80 205 69 131 62 474.19 0.85 206 70 92 22 566.98 4.00 207 70 93 23 566.75 4.02 208 70 106 36 565.90 4.04 209 70 126 56 474.64 0.77 210 70 127 57 474.50 0.82 211 70 128 58 474.39 0.83 212 71 79 8 568.93 3.89 213 71 81 10 568.73 3.97 214 71 91 20 567.03 4.00 215 71 92 21 567.02 4.00 216 71 126 55 474.67 0.76 217 71 127 56 474.51 0.81 218 72 79 7 573.62 6.23 219 72 89 17 567.88 3.96 220 72 91 19 567.06 4.00 221 72 108 36 565.85 4.01 222 72 109 37 565.79 4.01 223 72 111 39 564.03 4.05 224 72 126 54 474.72 0.76 225 73 77 4 610.91 12.39 226 73 78 5 573.64 6.24 227 73 79 6 568.93 3.88 228 73 89 16 567.89 3.95 229 73 111 38 564.07 4.05 230 73 112 39 564.04 4.05 231 73 114 41 563.26 4.05 232 74 77 3 676.58 4.08 233 74 78 4 592.68 2.59 234 74 80 6 573.66 6.22 235 74 89 15 567.89 3.95 236 74 111 37 564.33 3.94 237 74 112 38 564.12 4.04 238 75 109 34 565.90 4.04 239 75 110 35 565.75 4.06 240 75 112 37 564.13 4.04 241 76 112 36 564.40 3.97 242 77 112 35 563.83 3.94 243 77 113 36 563.83 3.94 244 77 114 37 563.70 3.93 245 79 91 12 567.24 4.08 246 79 114 35 563.59 4.00 247 79 125 46 475.25 0.73 248 79 127 48 475.09 0.79 249 80 89 9 567.85 3.93 250 80 91 11 567.26 4.09 251 82 87 5 664.60 4.58 252 83 87 4 672.74 2.23 253 83 90 7 567.76 3.94 254 83 92 9 567.72 3.96 255 84 87 3 679.00 5.50 256 84 90 6 590.11 5.45 257 87 90 3 713.93 4.96 258 89 108 19 565.89 4.06 259 89 109 20 565.89 4.05 260 95 104 9 565.93 4.07 261 95 105 10 565.92 4.07 262 95 106 11 565.85 4.08 263 96 104 8 565.94 4.07 264 97 102 5 566.08 4.05 265 97 103 6 566.02 4.05 266 97 104 7 565.95 4.08 267 98 101 3 676.09 2.77 268 98 102 4 566.10 4.05 269 98 103 5 566.09 4.05 270 103 184 81 293.17 1.14 271 104 185 81 293.12 1.15 272 108 126 18 474.92 0.85 273 110 145 35 473.21 0.76 274 110 147 37 472.41 0.71 275 110 148 38 439.93 4.59 276 110 183 73 293.20 1.17 277 111 124 13 475.12 0.78 278 111 125 14 475.13 0.79 279 111 126 15 475.05 0.83 280 111 145 34 473.58 0.81 281 113 121 8 475.99 0.83 282 113 122 9 475.73 0.90 283 113 124 11 475.32 0.74 284 114 121 7 476.00 0.83 285 114 122 8 475.81 0.86 286 114 125 11 475.47 0.80 287 115 119 4 649.45 0.26 288 115 120 5 476.24 0.78 289 115 121 6 476.02 0.83 290 115 122 7 476.02 0.83 291 116 119 3 659.58 5.33 292 116 120 4 649.44 0.26 293 116 122 6 476.17 0.77 294 116 156 40 403.86 0.92 295 120 156 36 403.88 0.93 296 121 156 35 403.84 0.93 297 122 125 3 787.91 1.48 298 122 142 20 474.07 0.85 299 122 155 33 403.56 1.04 300 122 156 34 403.47 1.09 301 122 157 35 403.37 1.04 302 123 144 21 473.82 0.84 303 123 151 28 404.22 1.00 304 123 152 29 404.16 1.04 305 123 155 32 403.47 1.09 306 124 144 20 473.76 0.83 307 124 145 21 473.74 0.82 308 124 148 24 434.42 1.85 309 124 151 27 404.23 1.01 310 125 142 17 473.85 0.84 311 125 143 18 473.75 0.82 312 125 144 19 473.56 0.79 313 125 145 20 473.56 0.80 314 126 142 16 473.80 0.83 315 126 143 17 473.59 0.78 316 126 145 19 473.56 0.80 317 127 141 14 473.82 0.83 318 127 142 15 473.58 0.78 319 128 140 12 473.82 0.83 320 128 141 13 473.73 0.81 321 128 143 15 473.42 0.79 322 128 185 57 293.19 1.15 323 128 187 59 293.13 1.15 324 129 138 9 473.86 0.83 325 129 139 10 473.82 0.83 326 129 140 11 473.76 0.82 327 130 135 5 638.88 5.22 328 130 138 8 473.84 0.83 329 130 139 9 473.76 0.82 330 130 187 57 293.16 1.15 331 130 189 59 293.07 1.16 332 131 138 7 473.80 0.83 333 132 135 3 690.99 0.84 334 135 138 3 711.06 5.09 335 135 139 4 690.25 4.31 336 135 189 54 293.14 1.15 337 139 189 50 293.12 1.15 338 139 197 58 148.25 0.28 339 140 197 57 147.55 0.63 340 140 198 58 147.15 0.59 341 140 200 60 144.38 1.37 342 141 170 29 348.79 1.80 343 141 185 44 293.23 1.16 344 141 187 46 293.13 1.15 345 141 195 54 164.71 0.14 346 141 196 55 163.07 0.58 347 141 197 56 147.21 0.62 348 141 198 57 145.06 1.69 349 142 157 15 398.99 1.50 350 142 170 28 348.77 1.81 351 142 185 43 293.22 1.15 352 142 198 56 147.20 0.62 353 143 170 27 348.82 1.79 354 143 172 29 348.64 1.77 355 143 185 42 293.17 1.15 356 144 152 8 404.19 0.99 357 144 155 11 403.47 1.09 358 144 157 13 402.88 1.15 359 144 158 14 401.31 1.35 360 144 170 26 348.87 1.80 361 144 171 27 348.79 1.79 362 144 172 28 348.75 1.80 363 145 148 3 685.99 1.60 364 145 152 7 599.14 3.31 365 145 171 26 348.82 1.79 366 145 172 27 348.78 1.79 367 145 183 38 293.28 1.13 368 146 171 25 348.88 1.80 369 146 172 26 348.83 1.79 370 146 173 27 348.76 1.80 371 146 174 28 348.73 1.82 372 147 174 27 348.78 1.81 373 147 183 36 293.35 1.16 374 148 151 3 677.38 0.90 375 148 152 4 679.52 2.14 376 149 152 3 683.62 0.09 377 149 153 4 679.52 2.15 378 150 153 3 686.37 0.83 379 150 154 4 685.56 1.06 380 151 154 3 695.62 3.57 381 151 155 4 685.54 1.06 382 152 155 3 683.64 0.09 383 152 158 6 649.77 1.90 384 152 171 19 348.99 1.81 385 153 159 6 661.31 3.88 386 154 159 5 666.99 1.05 387 155 158 3 682.07 0.09 388 155 159 4 667.00 1.05 389 156 159 3 677.08 2.92 390 156 160 4 670.16 0.53 391 157 160 3 680.64 1.17 392 157 198 41 159.17 0.12 393 158 161 3 696.93 1.79 394 158 167 9 478.48 62.60 395 158 170 12 349.20 1.79 396 159 167 8 584.38 3.35 397 161 166 5 663.43 1.42 398 161 167 6 617.77 1.39 399 161 170 9 621.06 1.92 400 161 196 35 165.56 0.34 401 161 198 37 164.37 0.12 402 162 167 5 672.58 2.17 403 163 166 3 684.96 4.01 404 163 167 4 677.83 0.46 405 164 167 3 682.10 2.59 406 164 168 4 677.83 0.45 407 165 168 3 692.45 0.30 408 166 169 3 684.37 3.06 409 166 194 28 168.17 0.28 410 166 195 29 166.34 0.35 411 166 196 30 165.10 0.07 412 167 170 3 702.21 3.19 413 167 171 4 677.75 0.41 414 168 171 3 677.65 0.45 415 169 185 16 293.30 1.14 416 169 193 24 166.37 0.34 417 169 194 25 166.17 0.26 418 169 195 26 165.00 0.11 419 169 196 27 164.83 0.18 420 170 185 15 293.24 1.16 421 170 195 25 164.82 0.18 422 170 196 26 164.73 0.15 423 170 198 28 164.72 0.14 424 171 185 14 293.21 1.15 425 172 183 11 293.30 1.14 426 172 184 12 293.27 1.14 427 172 185 13 293.20 1.15 428 173 183 10 293.31 1.14 429 173 184 11 293.29 1.14 430 174 181 7 445.57 73.86 431 174 182 8 294.03 0.83 432 174 183 9 293.31 1.14 433 175 181 6 445.59 73.87 434 175 182 7 295.17 1.31 435 176 179 3 687.94 3.23 436 176 180 4 474.06 60.50 437 176 181 5 445.59 73.87 438 176 182 6 445.56 73.87 439 177 180 3 664.31 3.12 440 177 182 5 446.61 73.39 441 187 195 8 164.76 0.16 442 187 197 10 164.72 0.14 443 188 192 4 685.11 3.76 444 188 193 5 455.98 77.45 445 188 194 6 321.99 12.86 446 188 195 7 230.25 32.90 447 188 197 9 230.25 32.91 448 189 194 5 455.97 77.45 449 189 197 8 444.55 74.24 450 190 194 4 458.75 76.07 451 191 194 3 663.56 1.60