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 25 24 30.33 0.57 2 1 117 116 27.84 0.77 3 2 5 3 849.92 2.25 4 2 6 4 841.84 1.33 5 2 72 70 28.09 0.59 6 2 114 112 26.46 0.90 7 2 115 113 27.80 0.74 8 2 116 114 28.21 0.58 9 2 117 115 30.99 0.24 10 3 6 3 844.97 0.23 11 3 7 4 841.83 1.33 12 4 7 3 857.38 5.31 13 4 8 4 841.83 1.33 14 4 160 156 57.37 0.34 15 4 161 157 56.09 0.97 16 5 8 3 841.81 1.33 17 5 9 4 815.36 1.31 18 5 20 15 36.13 0.76 19 5 105 100 33.54 0.73 20 6 104 98 33.55 0.73 21 6 105 99 33.54 0.73 22 6 106 100 36.30 0.65 23 6 114 108 36.33 0.66 24 7 106 99 42.16 1.08 25 9 20 11 60.64 1.32 26 9 23 14 61.69 1.25 27 9 105 96 61.26 1.26 28 9 106 97 61.39 1.30 29 10 105 95 61.40 1.31 30 10 106 96 61.39 1.30 31 11 105 94 61.44 1.32 32 12 19 7 512.23 94.20 33 12 20 8 206.21 73.65 34 12 74 62 61.48 1.32 35 12 76 64 61.41 1.32 36 12 105 93 61.47 1.32 37 12 112 100 61.43 1.33 38 13 17 4 786.88 4.58 39 13 18 5 742.02 5.30 40 13 19 6 533.04 85.62 41 13 76 63 61.46 1.33 42 13 149 136 61.45 1.33 43 14 17 3 823.50 1.79 44 14 18 4 771.20 3.26 45 14 20 6 706.99 1.41 46 17 238 221 67.52 0.43 47 18 238 220 67.54 0.43 48 19 22 3 863.79 0.22 49 19 74 55 67.50 0.44 50 19 76 57 67.51 0.43 51 19 149 130 67.51 0.43 52 19 150 131 67.52 0.43 53 19 151 132 67.51 0.43 54 19 236 217 68.48 0.05 55 19 238 219 67.56 0.43 56 20 23 3 849.13 1.08 57 21 24 3 855.15 4.10 58 21 25 4 820.25 2.71 59 21 74 53 67.63 0.48 60 21 236 215 77.67 1.77 61 22 25 3 839.19 2.21 62 22 26 4 813.40 0.73 63 22 236 214 69.63 0.48 64 23 26 3 870.51 3.69 65 23 159 136 158.39 2.41 66 24 157 133 152.75 0.74 67 24 158 134 158.16 2.37 68 24 159 135 158.17 2.38 69 25 153 128 108.42 1.67 70 25 155 130 152.75 0.74 71 25 156 131 155.08 0.85 72 25 157 132 154.21 0.42 73 25 158 133 158.99 2.56 74 25 236 211 108.42 1.67 75 26 158 132 159.43 2.62 76 26 159 133 160.90 2.16 77 27 232 205 162.69 1.06 78 27 234 207 162.20 0.98 79 27 235 208 153.83 0.21 80 27 236 209 151.12 1.56 81 28 236 208 158.38 2.26 82 29 154 125 163.12 0.68 83 29 233 204 164.03 0.70 84 29 234 205 163.56 0.78 85 29 235 206 162.43 1.02 86 29 236 207 162.15 1.04 87 29 237 208 160.13 1.53 88 30 52 22 164.18 0.70 89 30 154 124 163.91 0.74 90 31 49 18 164.21 0.71 91 31 50 19 164.19 0.71 92 31 51 20 164.14 0.72 93 31 52 21 164.22 0.72 94 31 150 119 161.90 1.14 95 31 152 121 163.27 0.77 96 31 154 123 164.06 0.69 97 31 237 206 163.21 0.77 98 31 238 207 162.43 1.02 99 32 49 17 164.22 0.72 100 32 50 18 164.21 0.72 101 33 47 14 164.22 0.71 102 33 48 15 164.25 0.70 103 33 49 16 164.22 0.72 104 33 75 42 163.70 0.82 105 33 148 115 163.10 0.76 106 33 150 117 163.40 0.73 107 33 240 207 163.22 0.72 108 33 241 208 161.94 1.15 109 34 47 13 164.28 0.70 110 34 48 14 164.31 0.70 111 34 50 16 164.34 0.71 112 35 45 10 164.31 0.70 113 35 47 12 164.31 0.71 114 35 148 113 163.56 0.77 115 35 241 206 163.44 0.71 116 35 243 208 162.25 1.01 117 36 39 3 890.97 5.61 118 36 45 9 164.36 0.71 119 36 46 10 164.38 0.71 120 36 243 207 163.25 0.70 121 37 243 206 163.31 0.73 122 37 244 207 163.19 0.72 123 38 243 205 163.55 0.78 124 38 244 206 163.10 0.68 125 38 246 208 162.18 1.04 126 39 45 6 355.97 3.16 127 39 132 93 164.40 0.72 128 39 243 204 163.66 0.80 129 39 244 205 163.32 0.74 130 39 245 206 162.36 0.97 131 39 246 207 162.34 0.97 132 40 43 3 856.44 3.85 133 40 132 92 164.53 0.77 134 40 246 206 162.37 0.97 135 40 248 208 157.08 1.92 136 41 133 92 164.52 0.78 137 41 134 93 164.44 0.74 138 41 135 94 164.53 0.79 139 41 143 102 164.03 0.62 140 41 245 204 163.55 0.77 141 41 246 205 163.30 0.73 142 41 248 207 162.24 1.03 143 42 88 46 166.25 0.82 144 42 131 89 164.66 0.75 145 42 132 90 164.62 0.76 146 42 133 91 164.62 0.76 147 42 134 92 164.57 0.78 148 43 88 45 166.26 0.82 149 43 131 88 165.16 0.56 150 43 132 89 164.71 0.77 151 44 84 40 165.99 0.76 152 44 88 44 166.26 0.82 153 44 93 49 170.62 0.81 154 44 129 85 166.10 0.74 155 44 130 86 165.96 0.77 156 44 131 87 165.21 0.56 157 45 81 36 166.05 0.74 158 45 129 84 166.16 0.76 159 45 130 85 166.01 0.76 160 45 132 87 165.99 0.77 161 45 243 198 163.59 0.78 162 46 93 47 171.94 0.40 163 46 96 50 172.07 0.36 164 46 127 81 170.20 0.62 165 46 128 82 166.29 0.81 166 47 75 28 166.94 0.47 167 47 127 80 171.68 0.26 168 47 128 81 166.96 0.48 169 47 130 83 166.28 0.81 170 48 125 77 175.00 0.54 171 48 126 78 173.47 1.07 172 48 127 79 171.75 0.29 173 49 73 24 173.53 1.00 174 49 75 26 171.69 0.24 175 49 125 76 175.08 0.57 176 49 126 77 173.50 1.06 177 49 128 79 173.47 1.07 178 49 150 101 170.18 0.65 179 50 124 74 175.99 0.24 180 50 125 75 175.48 0.38 181 51 71 20 176.06 0.21 182 51 72 21 176.06 0.21 183 51 73 22 175.99 0.23 184 51 124 73 176.03 0.23 185 51 126 75 176.01 0.24 186 51 152 101 175.21 0.55 187 51 153 102 176.00 0.24 188 51 154 103 176.06 0.22 189 52 154 102 176.16 0.26 190 53 69 16 177.93 0.01 191 53 71 18 177.09 0.29 192 53 120 67 179.21 0.66 193 53 121 68 179.22 0.65 194 53 154 101 176.19 0.25 195 54 57 3 861.13 0.64 196 55 121 66 189.61 4.54 197 55 124 69 185.77 2.62 198 57 69 12 349.07 8.10 199 57 233 176 233.53 0.52 200 58 66 8 530.62 86.30 201 58 67 9 349.83 7.98 202 58 69 11 349.14 8.11 203 58 233 175 240.42 0.96 204 59 66 7 543.40 79.92 205 59 67 8 362.21 2.14 206 59 68 9 353.95 6.27 207 59 69 10 349.79 7.97 208 59 155 96 240.43 0.96 209 59 156 97 240.51 0.96 210 59 233 174 240.43 0.96 211 60 64 4 771.00 11.93 212 60 65 5 743.53 1.76 213 60 66 6 702.99 0.15 214 60 156 96 240.71 0.92 215 60 167 107 241.28 0.82 216 60 168 108 240.84 0.93 217 60 210 150 241.44 0.78 218 60 231 171 241.01 0.93 219 61 64 3 833.07 2.43 220 61 65 4 750.89 1.87 221 61 66 5 743.25 1.60 222 61 67 6 743.22 1.60 223 61 156 95 240.97 0.92 224 61 167 106 241.41 0.77 225 62 156 94 241.28 0.81 226 63 209 146 305.08 0.96 227 64 167 103 305.08 0.99 228 64 209 145 305.07 0.96 229 64 210 146 304.78 1.06 230 69 120 51 691.32 0.67 231 69 154 85 308.03 0.29 232 69 155 86 308.11 0.40 233 69 233 164 308.37 0.38 234 69 234 165 308.29 0.40 235 70 117 47 691.54 0.70 236 70 118 48 691.42 0.70 237 70 119 49 691.39 0.69 238 70 120 50 691.38 0.70 239 70 154 84 308.32 0.40 240 70 155 85 308.35 0.38 241 71 116 45 691.73 0.71 242 71 117 46 691.64 0.72 243 71 118 47 691.56 0.70 244 71 120 49 691.43 0.68 245 71 123 52 691.41 0.70 246 71 126 55 691.12 0.72 247 71 153 82 308.34 0.40 248 71 154 83 308.36 0.39 249 72 115 43 691.73 0.72 250 72 116 44 691.73 0.71 251 72 152 80 308.43 0.41 252 72 153 81 308.41 0.40 253 73 114 41 691.80 0.70 254 73 115 42 691.75 0.71 255 73 128 55 691.30 0.66 256 73 151 78 308.43 0.42 257 73 152 79 308.43 0.41 258 74 112 38 691.90 0.67 259 74 113 39 691.82 0.69 260 74 114 40 691.80 0.70 261 74 150 76 308.45 0.42 262 74 151 77 308.44 0.42 263 75 112 37 691.93 0.67 264 75 113 38 691.83 0.70 265 75 128 53 691.54 0.69 266 75 130 55 691.14 0.71 267 75 148 73 308.62 0.52 268 75 149 74 308.51 0.45 269 75 150 75 308.45 0.42 270 76 111 35 692.11 0.69 271 76 112 36 691.95 0.68 272 76 148 72 308.63 0.52 273 76 149 73 308.55 0.47 274 77 81 4 801.83 4.13 275 77 111 34 692.11 0.69 276 77 113 36 692.10 0.69 277 77 130 53 691.45 0.70 278 77 148 71 308.64 0.51 279 78 81 3 845.81 1.76 280 78 111 33 692.28 0.69 281 78 146 68 308.68 0.53 282 78 147 69 308.69 0.52 283 78 148 70 308.69 0.50 284 79 111 32 692.29 0.69 285 79 141 62 316.07 2.79 286 80 133 53 690.45 1.02 287 80 141 61 316.10 2.81 288 81 111 30 692.48 0.69 289 81 130 49 691.68 0.66 290 81 131 50 691.58 0.64 291 81 132 51 691.14 0.71 292 81 133 52 690.77 0.87 293 81 146 65 308.70 0.52 294 81 243 162 308.46 0.41 295 81 245 164 305.32 0.66 296 82 110 28 692.49 0.69 297 82 130 48 691.68 0.66 298 82 131 49 691.65 0.66 299 83 102 19 692.47 0.70 300 83 113 30 692.51 0.71 301 83 129 46 691.78 0.68 302 84 89 5 776.31 3.91 303 84 129 45 691.78 0.69 304 84 130 46 691.77 0.69 305 84 131 47 691.72 0.67 306 85 88 3 835.66 0.29 307 85 89 4 825.24 4.92 308 85 131 46 691.77 0.69 309 86 89 3 833.91 0.58 310 86 94 8 774.56 3.17 311 88 131 43 691.82 0.68 312 89 93 4 824.17 1.50 313 89 94 5 818.33 3.14 314 89 129 40 691.90 0.66 315 90 93 3 824.18 1.50 316 90 94 4 830.68 1.76 317 91 94 3 830.68 1.76 318 91 95 4 845.27 2.31 319 92 95 3 866.24 0.70 320 92 96 4 845.28 2.31 321 93 96 3 852.02 5.67 322 93 97 4 833.94 3.37 323 94 97 3 835.75 2.47 324 94 98 4 835.74 2.47 325 95 98 3 835.74 2.46 326 96 127 31 692.27 0.56 327 97 100 3 860.12 3.77 328 97 102 5 833.99 3.00 329 97 127 30 692.25 0.55 330 97 129 32 692.25 0.54 331 99 123 24 692.96 0.52 332 100 115 15 693.83 0.60 333 100 118 18 693.27 0.68 334 100 123 23 692.95 0.52 335 100 126 26 692.54 0.43 336 101 115 14 693.84 0.60 337 102 113 11 694.08 0.56 338 102 114 12 693.88 0.60 339 102 115 13 693.83 0.60 340 102 126 24 692.62 0.38 341 102 127 25 692.53 0.41 342 102 128 26 692.21 0.46 343 102 129 27 692.01 0.39 344 103 113 10 694.09 0.56 345 103 114 11 693.88 0.61 346 104 107 3 854.16 5.90 347 104 109 5 763.21 2.01 348 104 110 6 714.86 0.26 349 104 112 8 694.57 0.47 350 104 113 9 694.09 0.56 351 105 109 4 809.79 6.98 352 105 112 7 696.20 1.28 353 105 114 9 694.10 0.56 354 106 109 3 831.87 2.64 355 107 110 3 880.71 2.73 356 109 112 3 854.69 5.21 357 113 128 15 691.56 0.69 358 113 130 17 691.40 0.70 359 115 126 11 692.56 0.36 360 115 128 13 692.12 0.33 361 118 123 5 759.47 6.11 362 118 126 8 717.21 1.23 363 119 122 3 852.38 5.95 364 119 123 4 810.02 4.44 365 120 123 3 821.78 1.54 366 120 124 4 778.52 3.41 367 123 126 3 850.61 7.62 368 132 245 113 303.11 1.74 369 133 141 8 516.26 92.08 370 133 245 112 307.88 0.26 371 134 137 3 835.62 3.43 372 134 138 4 808.93 5.92 373 135 138 3 825.11 2.18 374 135 141 6 516.51 92.02 375 135 142 7 516.50 92.02 376 135 143 8 516.31 92.06 377 135 245 110 308.47 0.40 378 138 141 3 853.30 2.31 379 139 142 3 923.19 0.28 380 141 146 5 840.22 3.27 381 141 245 104 308.83 0.19 382 142 146 4 893.10 3.73 383 142 245 103 308.83 0.19 384 143 245 102 308.83 0.19 385 143 246 103 308.82 0.18 386 143 247 104 308.57 0.29 387 143 248 105 308.80 0.18 388 144 244 100 309.08 0.10 389 144 245 101 308.90 0.14 390 145 242 97 309.29 0.01 391 145 243 98 309.25 0.01 392 145 244 99 309.03 0.06 393 146 242 96 309.28 0.01 394 146 243 97 309.21 0.01 395 146 245 99 309.04 0.06 396 147 241 94 309.36 0.04 397 147 242 95 309.23 0.03 398 148 240 92 309.41 0.06 399 148 241 93 309.31 0.07 400 148 243 95 309.30 0.07 401 149 239 90 310.35 0.24 402 149 240 91 309.37 0.08 403 150 238 88 310.59 0.28 404 150 239 89 310.51 0.30 405 151 236 85 313.07 0.20 406 151 237 86 312.38 0.09 407 151 238 87 310.65 0.24 408 152 236 84 313.62 0.07 409 152 237 85 312.65 0.01 410 153 235 82 313.82 0.07 411 153 236 83 313.63 0.07 412 154 234 80 313.94 0.10 413 154 235 81 313.91 0.10 414 154 236 82 313.91 0.10 415 154 237 83 313.92 0.10 416 155 234 79 313.94 0.10 417 156 167 11 351.98 2.16 418 156 168 12 349.51 1.82 419 157 166 9 352.12 2.18 420 158 165 7 352.79 1.90 421 158 166 8 352.15 2.19 422 158 168 10 352.05 2.22 423 158 169 11 351.87 2.29 424 158 232 74 320.01 0.76 425 159 163 4 739.29 5.00 426 159 164 5 720.33 3.79 427 159 165 6 363.54 0.87 428 160 163 3 826.84 0.76 429 160 164 4 747.33 17.26 430 160 165 5 720.36 3.77 431 160 166 6 720.32 3.79 432 165 169 4 833.74 0.69 433 165 170 5 830.41 0.98 434 165 171 6 806.65 1.61 435 166 169 3 893.38 1.12 436 166 171 5 837.99 1.43 437 167 171 4 854.99 0.96 438 167 208 41 431.49 2.54 439 167 209 42 431.30 2.64 440 167 211 44 430.73 2.50 441 167 231 64 373.81 2.12 442 168 231 63 373.80 2.11 443 168 232 64 373.73 2.15 444 169 211 42 431.49 2.54 445 169 231 62 373.81 2.11 446 170 226 56 431.89 2.31 447 170 228 58 430.31 2.12 448 170 230 60 397.84 4.36 449 170 231 61 404.75 0.90 450 171 207 36 432.03 2.31 451 171 208 37 433.55 3.06 452 171 211 40 431.94 2.31 453 171 226 55 432.43 2.50 454 171 227 56 431.91 2.32 455 171 228 57 431.45 2.35 456 172 224 52 443.23 1.23 457 172 225 53 438.15 1.29 458 172 226 54 432.44 2.50 459 172 227 55 432.42 2.52 460 173 194 21 483.44 0.49 461 173 205 32 460.25 0.77 462 173 221 48 471.31 1.68 463 173 222 49 472.87 1.36 464 173 223 50 472.54 1.29 465 173 224 51 448.96 0.14 466 173 225 52 448.86 0.12 467 173 227 54 433.17 2.87 468 174 203 29 529.83 2.91 469 174 205 31 478.60 2.17 470 174 223 49 480.40 2.02 471 175 194 19 558.32 2.35 472 175 196 21 585.27 1.06 473 175 201 26 585.32 1.10 474 175 203 28 552.18 2.12 475 175 221 46 505.05 3.53 476 175 223 48 480.41 2.02 477 176 194 18 585.22 1.08 478 176 196 20 585.35 1.09 479 176 221 45 505.05 3.53 480 176 222 46 505.03 3.54 481 176 223 47 489.98 2.75 482 177 194 17 585.34 1.09 483 177 195 18 585.35 1.09 484 177 196 19 585.35 1.09 485 177 220 43 507.15 3.51 486 177 221 44 506.18 3.71 487 178 194 16 585.50 1.08 488 178 195 17 585.48 1.07 489 178 218 40 507.65 3.49 490 178 219 41 507.41 3.46 491 178 220 42 507.28 3.45 492 179 182 3 917.05 0.79 493 179 192 13 585.69 0.97 494 179 193 14 585.87 0.90 495 179 194 15 585.65 1.01 496 179 215 36 507.81 3.58 497 179 216 37 508.03 3.47 498 179 217 38 507.99 3.42 499 179 218 39 507.73 3.52 500 179 219 40 507.57 3.48 501 179 221 42 507.40 3.46 502 180 193 13 586.19 0.94 503 180 195 15 586.12 0.90 504 181 192 11 586.25 0.92 505 181 193 12 586.19 0.94 506 181 217 36 508.19 3.41 507 182 190 8 586.43 0.90 508 182 191 9 586.35 0.92 509 182 192 10 586.25 0.92 510 182 213 31 509.57 3.02 511 182 215 33 508.54 3.45 512 182 216 34 508.45 3.46 513 182 217 35 508.33 3.45 514 183 190 7 586.54 0.96 515 183 191 8 586.39 0.90 516 184 189 5 643.48 27.39 517 184 190 6 586.59 0.94 518 184 213 29 525.76 0.35 519 185 188 3 818.70 2.46 520 185 189 4 723.59 5.83 521 185 190 5 586.81 0.92 522 185 191 6 586.81 0.92 523 185 206 21 586.31 0.97 524 187 209 22 586.10 0.99 525 188 209 21 585.85 1.03 526 189 207 18 586.24 0.97 527 189 208 19 586.09 1.02 528 189 209 20 585.47 1.09 529 190 206 16 586.28 0.99 530 190 207 17 586.18 0.98 531 190 211 21 581.88 2.60 532 190 213 23 512.08 2.73 533 191 204 13 586.43 1.02 534 191 205 14 586.35 1.02 535 191 206 15 586.25 1.01 536 192 204 12 586.44 1.03 537 192 205 13 586.38 1.01 538 192 207 15 586.36 1.00 539 192 213 21 509.39 3.16 540 192 215 23 508.54 3.45 541 192 227 35 507.36 3.38 542 193 202 9 587.31 0.91 543 193 203 10 587.17 0.89 544 193 204 11 586.57 0.96 545 194 202 8 587.31 0.91 546 194 203 9 587.24 0.91 547 194 205 11 587.16 0.89 548 194 221 27 507.40 3.48 549 195 201 6 589.40 0.09 550 195 202 7 587.31 0.91 551 196 199 3 850.00 0.85 552 196 200 4 774.85 3.52 553 196 201 5 589.40 0.09 554 197 200 3 808.64 3.43 555 205 227 22 507.44 3.40 556 207 211 4 833.69 3.00 557 207 213 6 737.59 2.92 558 207 227 20 507.70 3.34 559 207 228 21 507.59 3.38 560 208 211 3 885.05 4.84 561 211 228 17 507.72 3.33 562 211 229 18 507.63 3.29 563 211 231 20 506.97 3.37 564 212 228 16 507.62 3.27 565 212 229 17 507.58 3.27 566 213 227 14 507.65 3.29 567 213 228 15 507.45 3.33 568 214 227 13 507.59 3.27 569 214 228 14 507.49 3.24 570 214 229 15 507.32 3.26 571 215 219 4 811.88 1.40 572 215 221 6 651.47 30.84 573 215 227 12 507.56 3.27 574 216 219 3 839.11 7.16 575 221 225 4 761.28 7.00 576 221 227 6 618.02 57.09 577 222 225 3 824.05 0.48