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 2 225 223 51.03 0.32 2 3 225 222 55.70 1.12 3 4 202 198 143.78 2.97 4 4 204 200 127.59 0.47 5 4 205 201 125.34 0.33 6 4 225 221 80.61 0.92 7 5 184 179 148.51 3.73 8 5 185 180 148.44 3.70 9 5 186 181 149.77 3.43 10 5 202 197 147.62 3.36 11 5 203 198 147.43 3.46 12 5 204 199 143.87 2.94 13 6 9 3 901.56 5.36 14 6 201 195 148.84 3.78 15 6 202 196 147.62 3.36 16 6 222 216 99.76 0.56 17 6 225 219 97.86 0.45 18 7 191 184 149.83 3.45 19 7 194 187 153.10 3.58 20 7 195 188 153.15 3.56 21 7 201 194 150.13 3.60 22 7 203 196 149.75 3.45 23 8 194 186 153.16 3.56 24 8 195 187 153.18 3.55 25 8 199 191 153.31 3.55 26 8 200 192 153.10 3.58 27 8 201 193 152.94 3.52 28 8 222 214 100.00 0.49 29 9 222 213 100.00 0.49 30 10 200 190 153.38 3.58 31 10 221 211 100.93 0.81 32 10 222 212 100.86 0.80 33 10 223 213 100.62 0.76 34 11 200 189 155.35 3.40 35 11 220 209 101.09 0.86 36 11 221 210 101.00 0.84 37 11 223 212 100.89 0.79 38 11 243 232 28.24 0.58 39 12 177 165 208.91 13.44 40 12 200 188 160.63 0.83 41 12 219 207 108.89 2.96 42 12 220 208 101.12 0.87 43 13 177 164 212.35 14.86 44 13 217 204 120.39 2.26 45 13 218 205 120.06 2.35 46 13 219 206 113.47 5.24 47 13 243 230 36.45 1.74 48 14 157 143 213.15 14.79 49 14 177 163 212.71 14.71 50 14 217 203 120.39 2.26 51 14 218 204 120.31 2.23 52 15 156 141 213.52 14.70 53 15 157 142 213.53 14.69 54 15 215 200 122.14 1.50 55 15 216 201 121.55 1.72 56 15 217 202 120.44 2.23 57 16 157 141 213.54 14.70 58 16 159 143 213.53 14.70 59 16 212 196 148.44 3.81 60 16 214 198 140.90 7.14 61 16 215 199 139.68 7.69 62 16 216 200 121.55 1.73 63 16 218 202 120.14 2.28 64 17 152 135 214.18 14.47 65 17 156 139 213.84 14.60 66 17 157 140 213.74 14.62 67 17 158 141 213.69 14.63 68 17 159 142 213.68 14.63 69 18 159 141 213.69 14.63 70 18 209 191 155.67 2.14 71 18 212 194 150.02 3.10 72 18 213 195 148.09 3.73 73 18 214 196 140.02 7.54 74 19 149 130 214.19 14.46 75 19 158 139 214.13 14.48 76 19 159 140 214.05 14.47 77 19 160 141 214.03 14.47 78 19 163 144 214.07 14.46 79 19 167 148 214.18 14.46 80 20 147 127 214.33 14.54 81 21 139 118 218.31 14.94 82 24 135 111 220.91 13.67 83 24 138 114 221.00 13.69 84 24 139 115 220.99 13.70 85 24 142 118 222.78 13.04 86 26 101 75 223.75 12.68 87 26 102 76 223.80 12.71 88 27 99 72 225.31 13.43 89 27 101 74 223.88 12.74 90 27 102 75 223.88 12.74 91 29 99 70 372.30 11.91 92 30 97 67 375.85 11.93 93 31 35 4 741.79 11.48 94 31 36 5 738.96 12.90 95 31 39 8 621.25 26.30 96 31 93 62 394.62 18.49 97 31 97 66 394.61 18.49 98 31 98 67 375.79 11.95 99 31 99 68 375.22 12.23 100 32 35 3 835.31 4.01 101 32 36 4 806.98 21.11 102 33 36 3 851.16 0.98 103 34 38 4 860.18 3.45 104 35 38 3 860.18 3.45 105 35 39 4 851.28 1.02 106 36 39 3 867.14 0.04 107 36 40 4 852.41 1.56 108 36 93 57 441.95 1.01 109 36 94 58 443.92 1.99 110 36 97 61 444.23 2.14 111 37 40 3 867.14 0.04 112 37 41 4 851.31 1.01 113 38 41 3 859.71 1.39 114 38 42 4 851.30 1.01 115 39 42 3 852.41 1.56 116 39 43 4 850.09 1.55 117 39 93 54 445.42 1.95 118 39 99 60 445.19 1.84 119 39 100 61 445.01 1.77 120 40 43 3 852.09 3.05 121 40 44 4 846.76 0.12 122 40 90 50 445.38 1.92 123 40 93 53 445.94 2.18 124 41 44 3 850.46 1.97 125 41 45 4 839.01 3.99 126 42 45 3 853.35 0.01 127 42 46 4 837.29 3.14 128 43 46 3 858.39 0.98 129 43 47 4 841.54 0.84 130 43 89 46 446.42 2.36 131 43 100 57 446.27 2.37 132 43 104 61 446.26 2.37 133 43 137 94 410.26 19.50 134 43 141 98 409.88 19.68 135 44 47 3 854.48 5.62 136 44 48 4 848.49 2.62 137 45 48 3 856.79 4.47 138 45 49 4 856.80 4.46 139 46 49 3 861.86 1.94 140 46 50 4 861.85 1.94 141 46 141 95 411.01 20.12 142 47 50 3 861.96 1.99 143 47 51 4 850.93 1.53 144 47 81 34 448.56 3.22 145 48 51 3 867.32 5.41 146 48 52 4 850.95 1.54 147 49 52 3 862.12 2.81 148 49 53 4 851.69 1.18 149 49 140 91 411.93 20.27 150 49 143 94 412.01 20.41 151 50 53 3 851.69 1.18 152 50 54 4 851.69 1.18 153 50 140 90 412.13 20.36 154 51 54 3 865.82 2.90 155 51 55 4 851.71 1.17 156 52 55 3 859.94 2.24 157 52 56 4 851.73 1.15 158 53 56 3 859.19 2.62 159 53 57 4 847.34 1.04 160 53 140 87 413.33 20.64 161 53 146 93 412.38 20.62 162 54 57 3 858.64 6.70 163 54 58 4 847.34 1.04 164 54 77 23 449.98 2.56 165 54 80 26 450.00 2.58 166 54 136 82 413.88 20.47 167 55 58 3 857.01 0.28 168 55 59 4 850.60 3.48 169 55 77 22 450.44 2.48 170 56 59 3 857.01 0.28 171 56 60 4 850.23 3.30 172 57 60 3 856.65 0.10 173 57 61 4 849.94 3.46 174 57 73 16 450.87 2.46 175 57 136 79 414.02 20.43 176 57 169 112 400.69 26.46 177 57 170 113 401.49 26.06 178 58 61 3 854.68 1.10 179 58 62 4 849.94 3.46 180 58 70 12 451.00 2.40 181 58 73 15 450.86 2.46 182 58 77 19 450.85 2.47 183 59 62 3 859.71 1.42 184 59 63 4 849.94 3.46 185 60 63 3 868.21 2.83 186 60 64 4 841.31 0.85 187 60 150 90 411.95 20.81 188 60 170 110 404.26 24.68 189 61 64 3 850.87 5.65 190 61 65 4 835.37 2.08 191 61 66 5 783.00 23.79 192 61 69 8 505.42 11.87 193 61 70 9 456.08 4.88 194 61 73 12 456.09 4.88 195 61 169 108 400.95 26.40 196 62 66 4 622.05 0.88 197 62 70 8 465.64 4.83 198 64 169 105 404.71 24.90 199 65 69 4 847.41 4.19 200 65 168 103 404.76 24.93 201 65 169 104 404.75 24.92 202 65 173 108 404.95 24.75 203 65 193 128 237.09 20.89 204 66 69 3 862.23 2.74 205 66 70 4 847.46 4.20 206 67 70 3 854.96 0.45 207 67 71 4 847.91 4.42 208 68 72 4 855.31 0.73 209 69 72 3 864.91 1.39 210 69 73 4 859.47 1.34 211 69 189 120 249.85 14.54 212 70 73 3 887.30 0.60 213 70 74 4 850.00 3.39 214 71 74 3 855.49 6.13 215 71 75 4 849.32 3.70 216 72 75 3 860.72 2.00 217 72 76 4 849.32 3.70 218 73 76 3 857.95 6.77 219 73 77 4 849.27 3.71 220 73 166 93 396.67 28.57 221 73 169 96 400.80 26.51 222 74 77 3 849.18 3.77 223 74 78 4 847.09 3.69 224 75 78 3 842.06 1.18 225 75 79 4 839.71 0.01 226 76 79 3 847.60 3.85 227 76 80 4 839.80 0.06 228 76 129 53 416.10 21.00 229 76 133 57 415.48 20.77 230 77 80 3 844.74 2.42 231 77 81 4 835.99 1.96 232 78 81 3 851.56 3.41 233 78 82 4 841.71 0.91 234 79 82 3 838.00 2.77 235 79 85 6 780.91 21.58 236 79 130 51 416.08 21.05 237 79 133 54 415.80 21.17 238 80 85 5 788.89 25.59 239 80 133 53 415.74 21.20 240 80 137 57 414.59 21.28 241 82 85 3 858.20 0.58 242 82 86 4 847.88 3.42 243 83 86 3 860.97 3.25 244 83 87 4 847.88 3.42 245 84 87 3 862.85 1.26 246 84 88 4 840.60 1.86 247 85 88 3 840.07 2.12 248 85 89 4 840.50 1.91 249 85 107 22 453.31 5.50 250 85 108 23 453.31 5.50 251 86 89 3 866.99 1.27 252 86 90 4 840.36 1.80 253 87 90 3 856.40 2.73 254 87 91 4 845.71 4.48 255 88 91 3 854.14 1.59 256 88 92 4 855.84 2.44 257 88 107 19 453.37 5.50 258 89 92 3 877.88 5.59 259 89 93 4 855.84 2.44 260 89 104 15 453.38 5.50 261 89 107 18 453.38 5.50 262 90 93 3 859.72 4.38 263 90 94 4 845.75 4.46 264 91 94 3 851.54 2.91 265 91 95 4 820.43 8.19 266 92 95 3 840.65 1.92 267 92 96 4 701.92 15.74 268 92 97 5 696.40 14.81 269 92 103 11 466.88 2.11 270 92 107 15 454.51 5.17 271 93 97 4 668.22 0.72 272 93 98 5 607.53 9.50 273 93 100 7 534.60 3.28 274 93 103 10 481.86 2.04 275 94 97 3 836.90 3.79 276 98 103 5 630.52 11.36 277 98 106 8 680.31 7.90 278 99 102 3 836.02 4.07 279 99 103 4 770.88 23.41 280 100 103 3 848.65 0.12 281 100 104 4 784.08 16.82 282 101 105 4 836.83 0.58 283 101 138 37 415.56 22.21 284 101 141 40 415.18 22.33 285 102 105 3 851.84 3.81 286 102 106 4 851.94 3.77 287 103 106 3 861.99 5.86 288 103 107 4 851.94 3.77 289 104 107 3 868.61 4.03 290 104 108 4 852.48 3.50 291 104 137 33 415.63 22.19 292 105 108 3 871.74 2.46 293 105 109 4 830.28 6.09 294 105 138 33 415.60 22.21 295 106 109 3 843.96 0.72 296 106 110 4 834.40 4.04 297 107 110 3 847.15 2.33 298 107 111 4 847.16 2.33 299 108 111 3 872.72 6.23 300 108 112 4 850.56 2.59 301 108 130 22 416.36 22.06 302 108 131 23 416.28 22.09 303 108 134 26 415.79 22.26 304 109 112 3 855.61 1.89 305 109 113 4 836.58 4.40 306 110 113 3 857.26 1.06 307 110 114 4 850.55 2.60 308 111 114 3 855.65 5.15 309 111 115 4 855.33 4.99 310 112 115 3 856.68 5.71 311 112 116 4 846.80 0.77 312 112 130 18 417.22 21.69 313 112 131 19 416.35 22.07 314 113 116 3 866.12 6.22 315 113 117 4 848.88 1.80 316 114 117 3 854.50 0.41 317 115 118 3 856.59 1.71 318 115 127 12 417.38 21.63 319 116 127 11 417.53 21.70 320 118 123 5 760.64 24.93 321 120 123 3 867.53 1.08 322 120 124 4 847.57 1.40 323 121 124 3 847.97 1.59 324 121 125 4 847.58 1.40 325 122 125 3 867.80 4.03 326 122 126 4 863.63 6.12 327 123 126 3 864.05 5.91 328 123 127 4 849.69 0.34 329 124 127 3 867.09 4.38 330 124 128 4 849.64 0.32 331 125 128 3 851.45 3.45 332 125 129 4 851.45 3.45 333 125 187 62 260.42 8.67 334 126 129 3 852.15 3.79 335 126 130 4 836.20 4.06 336 127 130 3 868.37 2.10 337 127 131 4 858.46 7.05 338 128 131 3 862.02 5.26 339 128 132 4 858.56 7.00 340 129 132 3 869.19 1.69 341 129 133 4 858.00 3.02 342 129 165 36 396.75 28.73 343 130 133 3 873.83 0.83 344 130 134 4 859.16 2.44 345 131 134 3 865.03 0.80 346 131 135 4 852.70 0.45 347 132 135 3 856.99 1.70 348 132 136 4 852.70 0.45 349 132 164 32 396.73 28.75 350 132 166 34 396.93 28.80 351 133 136 3 862.99 3.35 352 133 137 4 851.56 0.10 353 134 137 3 851.59 0.09 354 134 138 4 851.62 0.05 355 135 138 3 885.10 2.46 356 135 139 4 855.95 2.21 357 136 139 3 857.24 2.85 358 136 140 4 851.64 0.05 359 136 166 30 396.94 28.80 360 137 140 3 871.02 9.50 361 137 141 4 851.63 0.05 362 138 141 3 868.58 8.52 363 138 142 4 851.62 0.06 364 139 142 3 851.62 0.06 365 139 143 4 832.71 9.38 366 139 144 5 620.85 20.87 367 140 143 3 835.04 8.21 368 148 151 3 876.07 1.65 369 148 170 22 473.88 8.67 370 149 152 3 883.28 4.15 371 149 158 9 472.86 9.05 372 149 167 18 473.73 8.62 373 149 170 21 473.88 8.67 374 149 171 22 473.87 8.67 375 149 172 23 500.28 5.26 376 150 170 20 489.93 0.64 377 150 172 22 517.19 3.20 378 152 156 4 857.09 1.14 379 152 172 20 789.52 3.77 380 152 175 23 802.81 2.40 381 153 175 22 806.28 2.44 382 155 175 20 806.31 2.45 383 155 177 22 806.35 2.44 384 156 175 19 806.40 2.44 385 156 176 20 806.39 2.44 386 156 177 21 806.38 2.44 387 157 180 23 806.31 2.43 388 157 218 61 120.05 2.33 389 158 163 5 854.30 0.10 390 158 171 13 806.51 2.44 391 158 176 18 806.44 2.44 392 158 178 20 806.40 2.44 393 158 179 21 806.34 2.43 394 158 180 22 806.32 2.43 395 159 180 21 806.33 2.44 396 159 208 49 211.26 29.62 397 159 209 50 204.10 26.36 398 160 163 3 898.49 0.00 399 160 180 20 806.43 2.45 400 160 181 21 806.36 2.45 401 160 182 22 806.32 2.43 402 160 209 49 204.45 26.21 403 161 181 20 806.42 2.45 404 161 182 21 806.37 2.46 405 161 183 22 806.32 2.43 406 161 209 48 206.13 26.12 407 162 181 19 806.44 2.44 408 162 183 21 806.31 2.43 409 163 167 4 831.90 1.56 410 163 181 18 806.47 2.45 411 163 190 27 423.50 22.68 412 164 167 3 855.20 2.12 413 164 168 4 855.19 2.12 414 165 168 3 863.96 2.96 415 165 169 4 856.98 1.25 416 165 189 24 426.27 21.41 417 166 169 3 877.47 4.09 418 166 170 4 856.98 1.25 419 167 170 3 862.40 3.44 420 167 171 4 832.12 1.86 421 168 171 3 856.71 1.10 422 168 189 21 346.12 66.90 423 168 190 22 340.19 64.33 424 168 193 25 331.82 68.45 425 171 176 5 807.12 2.40 426 171 179 8 806.74 2.46 427 172 175 3 855.65 8.25 428 172 176 4 808.43 1.75 429 173 176 3 860.84 5.66 430 173 179 6 806.95 2.48 431 173 197 24 228.59 24.88 432 176 179 3 921.60 0.57 433 178 200 22 227.12 24.29 434 179 194 15 228.79 25.00 435 179 197 18 228.83 24.98 436 179 199 20 227.28 24.25 437 179 200 21 227.17 24.28 438 179 201 22 226.94 24.20 439 179 202 23 226.93 24.20 440 180 202 22 226.93 24.20 441 180 205 25 226.46 24.39 442 180 208 28 225.72 24.45 443 180 220 40 100.91 0.81 444 181 202 21 226.93 24.20 445 181 203 22 226.87 24.19 446 181 204 23 226.87 24.19 447 181 205 24 226.41 24.36 448 182 203 21 226.88 24.19 449 182 204 22 226.83 24.17 450 182 205 23 226.41 24.36 451 182 206 24 225.72 24.44 452 182 207 25 225.74 24.43 453 182 209 27 223.91 23.57 454 183 188 5 554.34 3.55 455 183 203 20 226.88 24.18 456 185 188 3 857.64 4.87 457 185 191 6 586.33 7.50 458 185 203 18 226.94 24.12 459 186 191 5 693.12 54.86 460 186 192 6 590.39 9.73 461 186 195 9 591.37 10.02 462 188 191 3 866.75 2.77 463 188 192 4 842.14 2.35 464 189 192 3 867.07 2.93 465 189 193 4 847.58 5.00 466 190 193 3 858.06 1.52 467 190 194 4 846.92 0.03 468 191 194 3 871.12 6.15 469 191 195 4 847.47 0.25 470 191 203 12 226.97 24.11 471 192 195 3 864.21 9.61 472 192 196 4 851.59 3.30 473 193 196 3 864.21 9.61 474 193 197 4 835.46 1.02 475 194 197 3 843.36 0.82 476 194 198 4 824.75 5.95 477 194 199 5 718.29 43.51 478 194 201 7 494.34 2.40 479 195 198 3 821.87 3.93 480 200 220 20 101.03 0.85 481 200 222 22 100.00 0.49 482 201 220 19 100.91 0.80 483 202 205 3 887.34 0.40 484 202 220 18 100.91 0.80 485 202 227 25 98.17 0.44 486 205 208 3 866.48 2.64 487 207 210 3 866.12 3.46 488 207 211 4 866.12 3.46 489 208 211 3 854.89 3.51 490 208 212 4 816.67 15.57 491 209 212 3 842.73 2.58 492 212 216 4 826.86 10.50 493 212 218 6 527.30 3.04 494 213 216 3 852.48 1.20 495 217 229 12 99.51 0.63 496 217 230 13 98.52 0.62 497 217 231 14 98.53 0.61 498 218 227 9 99.78 0.57 499 218 228 10 99.61 0.58 500 218 229 11 99.00 0.42 501 219 227 8 99.72 0.57 502 219 228 9 99.15 0.34 503 219 231 12 98.11 0.45 504 219 236 17 49.79 2.62 505 219 239 20 40.70 0.39 506 220 227 7 99.08 0.32 507 221 224 3 865.45 2.79 508 221 225 4 549.70 4.99 509 221 226 5 490.31 17.29 510 221 228 7 243.62 11.23 511 221 239 18 32.04 1.29 512 228 231 3 866.62 2.80 513 228 235 7 621.50 3.42 514 228 239 11 297.69 2.52 515 231 235 4 818.27 1.56 516 231 236 5 817.16 1.01 517 232 235 3 835.66 7.12 518 232 236 4 834.52 6.55 519 233 236 3 835.30 6.94 520 233 237 4 835.30 6.94 521 234 237 3 851.80 6.54 522 234 238 4 835.71 7.12 523 235 238 3 842.10 3.93 524 235 239 4 835.71 7.12 525 236 239 3 835.71 7.12 526 236 240 4 839.16 8.81 527 237 240 3 839.16 8.81 528 237 241 4 839.16 8.81 529 238 241 3 867.32 7.24 530 238 242 4 844.24 6.28 531 239 242 3 854.84 0.97 532 239 243 4 844.23 6.28 533 240 243 3 854.86 0.98 534 240 244 4 854.90 0.96 535 241 244 3 854.91 0.96 536 241 245 4 854.91 0.96 537 242 245 3 856.70 1.85 538 242 246 4 854.90 0.96 539 243 246 3 856.70 1.86 540 243 247 4 850.74 1.12 541 244 247 3 856.69 1.86 542 244 248 4 834.61 9.17 543 245 248 3 843.65 4.59 544 245 249 4 812.75 1.77 545 246 249 3 840.11 9.67