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 16 139 129 48.18 2.16 2 16 140 130 49.05 1.18 3 16 142 132 49.52 1.23 4 16 143 133 59.41 0.27 5 16 144 134 60.77 0.38 6 16 156 145 58.01 0.42 7 16 157 146 55.95 0.69 8 16 158 147 57.61 0.29 9 16 189 181 57.95 0.03 10 16 190 182 49.04 1.20 11 16 194 186 44.12 1.27 12 17 143 132 60.86 0.34 13 17 144 133 60.84 0.35 14 17 145 134 60.88 0.34 15 17 147 135 60.88 0.34 16 17 188 178 60.80 0.39 17 17 188 179 60.77 0.38 18 17 189 180 60.68 0.38 19 17 191 182 60.74 0.38 20 17 220 212 60.77 0.39 21 17 221 213 60.79 0.38 22 18 158 145 60.79 0.39 23 18 188 177 60.93 0.32 24 18 188 178 60.79 0.39 25 19 157 143 60.79 0.39 26 19 158 144 60.79 0.39 27 20 156 141 64.56 0.67 28 20 157 142 62.78 0.04 29 21 71 54 101.56 0.96 30 21 154 138 68.59 0.42 31 21 155 139 67.51 0.14 32 21 156 140 64.64 0.70 33 22 26 4 464.00 5.66 34 22 27 5 441.25 3.37 35 22 71 53 108.22 1.44 36 22 155 138 67.53 0.14 37 22 156 139 67.53 0.14 38 22 157 140 67.52 0.14 39 23 26 3 494.44 0.56 40 23 71 52 109.62 1.34 41 24 71 51 109.63 1.34 42 24 77 57 149.03 0.43 43 24 117 99 169.05 4.85 44 25 28 3 494.04 0.20 45 25 116 97 179.96 0.88 46 25 117 98 169.05 4.85 47 27 30 3 497.95 1.02 48 27 137 116 134.40 2.94 49 27 139 118 133.23 5.33 50 27 155 133 141.21 4.05 51 27 157 135 134.34 4.68 52 27 200 181 136.11 3.79 53 27 207 188 139.38 2.44 54 28 116 94 182.60 0.33 55 28 117 95 180.44 0.71 56 28 118 96 180.36 0.75 57 28 119 97 180.30 0.73 58 29 45 19 178.62 0.71 59 29 46 20 180.30 0.73 60 29 119 96 180.37 0.75 61 29 120 97 180.28 0.76 62 29 121 98 178.50 0.80 63 30 43 16 180.27 0.74 64 30 44 17 180.30 0.73 65 30 139 115 177.55 0.73 66 30 141 117 180.30 0.73 67 30 155 130 180.30 0.73 68 30 198 176 179.69 0.71 69 31 43 15 180.35 0.74 70 31 44 16 180.37 0.75 71 31 45 17 181.09 0.81 72 31 46 18 186.09 0.23 73 31 52 24 186.31 0.14 74 31 66 39 186.55 0.18 75 31 67 40 186.49 0.20 76 31 68 41 186.41 0.19 77 31 141 116 180.38 0.74 78 32 40 11 186.83 0.01 79 32 42 13 186.15 0.18 80 32 66 38 187.43 0.05 81 32 67 39 186.87 0.02 82 32 70 42 186.42 0.20 83 32 73 45 186.03 0.21 84 32 141 115 180.94 0.48 85 33 40 10 186.97 0.00 86 33 41 11 186.71 0.08 87 33 42 12 186.16 0.18 88 33 54 24 186.49 0.21 89 33 58 28 186.31 0.14 90 33 59 29 186.91 0.03 91 33 65 35 187.52 0.03 92 33 65 36 187.55 0.03 93 33 66 37 187.51 0.04 94 33 106 79 187.58 0.03 95 34 38 7 390.84 1.91 96 34 39 8 187.31 0.10 97 34 40 9 187.01 0.02 98 34 41 10 186.92 0.03 99 34 65 34 187.55 0.03 100 34 65 35 187.58 0.03 101 34 67 37 187.62 0.03 102 34 73 43 187.24 0.03 103 35 38 6 396.95 1.14 104 35 39 7 390.54 1.77 105 35 41 9 187.46 0.03 106 35 63 31 187.55 0.02 107 35 64 32 187.57 0.03 108 35 65 33 187.56 0.02 109 36 36 3 534.04 1.25 110 36 37 4 449.10 2.18 111 36 38 5 396.95 1.14 112 36 64 31 187.57 0.03 113 36 37 3 492.10 0.53 114 36 38 4 443.11 11.86 115 36 39 5 417.95 1.85 116 38 64 26 230.22 0.63 117 38 65 27 229.84 0.63 118 38 65 28 228.28 0.86 119 40 73 34 204.00 0.04 120 40 141 104 194.28 1.01 121 40 151 113 190.16 0.40 122 40 193 158 190.13 0.42 123 41 65 24 315.38 5.42 124 41 193 157 190.19 0.40 125 42 193 156 191.63 0.30 126 42 195 158 206.48 0.95 127 43 195 157 216.66 0.76 128 43 196 158 220.72 1.28 129 43 197 159 214.88 0.20 130 44 196 157 230.28 0.60 131 44 197 158 230.22 0.65 132 44 198 159 230.47 0.78 133 45 121 79 233.12 0.54 134 45 198 158 230.63 0.77 135 45 209 169 231.44 0.89 136 46 68 23 366.22 0.59 137 46 108 65 370.45 0.48 138 46 112 69 312.19 1.11 139 46 114 71 288.31 2.95 140 46 118 75 240.15 1.74 141 46 119 76 233.33 0.58 142 46 120 77 233.30 0.58 143 46 121 78 233.19 0.54 144 47 105 61 381.53 0.78 145 47 120 76 233.30 0.57 146 47 123 79 233.24 0.57 147 47 238 198 70.78 0.71 148 47 242 202 31.71 0.46 149 48 120 75 233.34 0.59 150 48 242 201 31.71 0.47 151 49 108 62 380.61 0.58 152 49 111 65 329.38 1.13 153 49 112 66 323.82 2.75 154 49 114 68 312.04 1.17 155 49 120 74 233.34 0.58 156 50 107 60 379.94 0.24 157 50 108 61 379.09 0.12 158 50 110 63 362.38 4.51 159 50 111 64 328.24 0.56 160 51 89 39 381.89 0.83 161 51 105 57 381.49 0.74 162 51 106 58 381.23 0.86 163 51 107 59 379.46 0.04 164 51 108 60 380.47 0.54 165 51 241 197 48.88 1.19 166 51 242 198 31.71 0.47 167 51 245 201 21.08 1.27 168 52 66 15 381.26 0.86 169 52 105 56 381.30 0.88 170 52 106 57 381.24 0.86 171 52 108 59 381.19 0.84 172 53 103 53 381.83 0.81 173 53 104 54 381.60 0.90 174 53 105 55 381.29 0.89 175 53 123 73 233.16 0.55 176 53 209 161 231.68 0.83 177 53 212 164 230.96 0.77 178 53 231 185 107.80 1.61 179 53 238 192 72.87 0.29 180 54 103 52 381.74 0.86 181 54 104 53 381.57 0.94 182 54 106 55 381.36 0.86 183 54 196 147 230.38 0.55 184 54 212 163 230.96 0.76 185 55 102 50 381.74 0.90 186 55 103 51 381.69 0.89 187 55 104 52 381.57 0.94 188 55 196 146 230.74 0.69 189 55 212 162 231.03 0.73 190 55 213 163 231.00 0.74 191 56 90 35 381.54 0.92 192 56 94 39 381.88 0.83 193 56 102 49 381.62 0.95 194 56 103 50 381.53 0.94 195 56 104 51 380.10 0.32 196 57 94 38 381.88 0.84 197 57 102 48 381.69 0.91 198 57 195 143 230.69 0.70 199 57 214 162 230.06 0.58 200 58 65 7 396.23 4.79 201 58 195 142 229.58 0.33 202 58 196 143 230.31 0.59 203 59 65 6 396.48 4.66 204 59 88 30 368.51 1.34 205 59 90 32 380.72 1.38 206 59 104 48 381.27 0.87 207 59 106 50 371.78 1.15 208 60 94 35 382.17 0.78 209 60 96 37 382.16 0.78 210 61 65 4 563.82 1.80 211 65 85 21 381.90 0.84 212 65 88 24 382.19 0.77 213 65 82 17 382.35 0.69 214 65 83 18 382.16 0.76 215 65 84 19 381.86 0.83 216 65 85 20 381.91 0.84 217 66 82 16 382.38 0.70 218 66 83 17 382.19 0.77 219 66 85 19 382.16 0.77 220 66 106 42 382.20 0.77 221 66 108 44 381.98 0.83 222 67 70 3 505.69 1.68 223 67 80 13 382.67 0.61 224 67 81 14 382.49 0.67 225 67 82 15 382.36 0.69 226 68 80 12 382.66 0.61 227 68 81 13 382.61 0.61 228 68 112 46 380.00 0.71 229 68 118 52 248.19 2.46 230 69 79 10 382.73 0.60 231 69 80 11 382.68 0.60 232 69 117 50 248.25 2.46 233 69 118 51 248.26 2.46 234 70 73 3 530.38 3.89 235 70 77 7 387.80 1.06 236 70 80 10 382.71 0.59 237 70 141 73 235.00 0.08 238 71 77 6 389.65 1.87 239 71 141 72 235.10 0.12 240 71 154 84 235.00 0.10 241 71 155 85 234.97 0.09 242 72 75 3 500.68 3.12 243 72 77 5 408.32 2.12 244 72 153 82 235.15 0.03 245 72 154 83 235.15 0.03 246 73 141 70 235.34 0.04 247 73 152 80 235.25 0.07 248 73 153 81 235.24 0.06 249 74 153 80 235.25 0.07 250 76 80 4 497.06 2.48 251 77 80 3 527.49 4.92 252 79 117 40 286.05 8.93 253 81 112 33 380.25 0.59 254 81 113 34 379.99 0.71 255 81 115 36 377.56 0.15 256 81 118 39 248.65 2.62 257 83 108 27 383.66 0.73 258 83 109 28 383.37 0.69 259 83 110 29 383.20 0.70 260 83 112 31 381.53 1.36 261 84 108 26 383.80 0.70 262 84 109 27 383.53 0.65 263 85 88 3 577.81 4.87 264 85 106 23 384.31 0.52 265 85 107 24 384.21 0.55 266 85 108 25 384.01 0.59 267 86 107 23 384.23 0.55 268 86 108 24 384.17 0.55 269 86 109 25 384.08 0.58 270 87 106 21 384.45 0.57 271 87 107 22 384.34 0.52 272 87 245 164 19.46 0.68 273 88 105 19 384.54 0.56 274 88 106 20 384.47 0.58 275 89 104 17 384.67 0.51 276 89 105 18 384.62 0.52 277 89 237 154 85.00 0.77 278 89 241 158 47.09 0.39 279 89 245 162 21.59 1.65 280 90 103 15 385.11 0.55 281 90 104 16 384.67 0.51 282 90 237 153 85.11 0.82 283 91 94 3 491.93 1.53 284 91 101 12 385.44 0.53 285 91 103 14 385.25 0.48 286 91 234 149 106.04 1.02 287 91 237 152 85.37 0.69 288 92 237 151 100.98 0.32 289 93 101 10 385.56 0.47 290 94 99 5 427.80 3.48 291 94 100 8 385.61 0.48 292 94 101 9 385.56 0.47 293 94 102 10 385.54 0.47 294 95 98 3 489.43 6.40 295 98 99 3 495.85 0.58 296 99 100 3 479.31 2.93 297 99 180 84 231.74 0.81 298 99 215 120 231.28 0.84 299 99 175 78 230.89 0.77 300 99 177 80 231.64 0.84 301 99 180 83 231.72 0.82 302 100 180 81 231.51 0.86 303 101 234 137 108.64 1.13 304 102 214 114 230.94 0.77 305 102 229 131 122.59 0.98 306 103 229 130 122.57 0.98 307 103 234 135 105.34 0.95 308 103 237 138 87.66 0.46 309 103 238 139 83.52 0.13 310 104 237 137 85.00 0.76 311 105 237 136 84.95 0.76 312 105 238 137 76.72 0.20 313 105 241 140 31.78 0.43 314 105 242 141 31.75 0.44 315 108 112 4 501.69 0.61 316 112 118 6 424.33 7.35 317 113 118 5 424.57 7.46 318 114 118 4 424.56 7.46 319 114 119 5 424.55 7.46 320 114 120 6 424.56 7.46 321 115 118 3 481.42 4.08 322 115 119 4 470.05 9.76 323 121 209 90 235.72 0.07 324 122 206 86 236.33 0.03 325 122 207 87 236.02 0.03 326 122 208 88 235.75 0.09 327 122 209 89 235.75 0.09 328 123 231 112 108.03 1.56 329 123 235 116 89.48 0.45 330 123 238 119 80.79 0.26 331 124 128 4 483.37 0.94 332 124 208 86 236.33 0.03 333 124 209 87 236.22 0.07 334 124 210 88 236.06 0.12 335 124 231 111 108.68 1.85 336 124 232 112 107.76 1.59 337 124 235 115 94.84 1.58 338 125 128 3 495.41 0.64 339 125 232 111 108.66 1.86 340 125 235 114 97.26 0.40 341 126 232 110 108.67 1.85 342 126 235 113 103.11 2.52 343 127 232 109 108.72 1.87 344 128 210 84 378.59 44.50 345 128 232 108 109.52 2.29 346 129 230 105 121.12 0.66 347 130 134 4 482.25 2.24 348 130 136 6 482.06 2.35 349 130 162 31 482.29 2.21 350 130 201 73 480.67 2.54 351 130 203 75 493.80 2.94 352 130 210 82 437.95 21.25 353 131 134 3 504.14 4.20 354 131 162 30 482.71 2.19 355 132 162 29 482.71 2.19 356 132 163 30 482.70 2.19 357 132 164 31 482.53 2.27 358 132 167 34 482.74 2.17 359 133 161 27 486.24 3.94 360 133 162 28 482.96 2.26 361 134 161 26 528.02 0.65 362 134 162 27 502.06 10.54 363 135 159 23 674.29 1.25 364 136 160 23 672.62 0.70 365 136 162 25 641.70 1.22 366 136 199 65 564.08 0.70 367 136 200 66 650.48 4.49 368 137 199 64 608.71 1.54 369 138 190 54 472.95 7.27 370 138 194 58 527.33 2.28 371 138 198 62 631.75 2.67 372 138 213 77 535.67 0.34 373 138 226 92 135.75 0.29 374 138 228 94 125.20 0.28 375 139 198 61 646.02 5.37 376 140 194 56 534.62 0.49 377 141 194 55 536.24 0.10 378 142 192 52 535.68 0.30 379 142 193 53 536.13 0.12 380 142 194 54 536.24 0.10 381 143 191 50 535.44 0.36 382 143 192 51 536.23 0.10 383 145 191 48 536.43 0.12 384 147 191 47 536.44 0.12 385 147 219 76 536.15 0.11 386 147 220 77 536.03 0.07 387 148 192 47 545.92 4.60 388 151 192 44 536.23 0.10 389 151 193 45 536.38 0.03 390 158 188 33 498.62 7.13 391 159 188 32 498.94 15.57 392 160 188 31 498.94 15.58 393 160 189 32 484.01 11.44 394 160 226 71 137.00 0.18 395 160 228 73 136.76 0.11 396 163 225 67 137.19 0.18 397 168 225 62 167.43 13.86 398 171 223 56 249.78 11.36 399 171 224 57 249.77 11.36 400 171 223 55 232.91 3.23 401 171 224 56 225.78 6.80 402 171 225 57 225.78 6.80 403 172 224 55 225.77 6.82 404 172 225 56 225.77 6.82 405 172 227 58 189.47 24.88 406 176 227 54 137.24 0.18 407 178 230 55 137.07 0.19 408 179 229 53 137.12 0.18 409 179 230 54 136.92 0.21 410 179 234 58 122.41 0.99 411 180 227 50 137.15 0.18 412 180 228 51 137.12 0.18 413 180 230 53 132.91 0.71 414 181 227 49 137.12 0.18 415 181 228 50 137.00 0.19 416 181 230 52 122.59 0.97 417 182 225 46 137.19 0.18 418 182 226 47 137.15 0.18 419 182 227 48 137.00 0.18 420 183 225 45 137.16 0.17 421 183 226 46 137.12 0.18 422 183 228 48 137.00 0.19 423 184 225 44 137.13 0.15 424 185 221 39 355.78 38.85 425 185 222 40 321.61 41.10 426 185 223 41 224.38 7.50 427 185 224 42 188.02 25.07 428 185 225 43 137.12 0.17 429 187 221 36 438.61 5.57 430 187 221 37 362.12 42.02 431 187 222 38 359.31 43.38 432 188 221 35 567.03 31.97 433 188 221 34 629.75 0.63 434 189 221 33 618.54 6.23 435 189 226 39 136.86 0.23 436 190 194 4 605.58 4.06 437 190 226 38 136.75 0.22 438 191 194 3 538.11 1.52 439 194 197 3 536.71 0.23 440 199 211 12 666.20 2.05 441 199 228 31 122.61 0.97 442 201 210 9 663.04 0.48 443 209 231 24 108.04 1.57 444 210 230 22 109.90 1.99 445 210 231 23 108.04 1.57 446 211 228 19 122.61 0.97 447 211 229 20 122.54 0.97 448 211 231 22 108.05 1.57 449 212 228 18 122.61 0.97 450 212 229 19 122.52 0.96 451 212 231 21 107.86 1.64 452 213 226 15 135.50 0.17 453 213 228 17 128.60 2.02 454 214 227 15 135.19 0.21 455 214 228 16 133.19 0.20 456 214 229 17 128.95 1.85 457 215 226 13 137.00 0.23 458 215 227 14 136.57 0.32 459 216 220 5 527.88 2.74 460 216 226 12 137.12 0.17 461 217 224 9 194.29 22.55 462 218 224 7 486.05 4.21 463 221 224 3 477.93 2.71 464 229 234 5 475.34 5.34 465 230 233 3 502.24 2.96 466 230 234 4 488.71 0.94 467 231 234 3 496.98 0.33 468 231 235 4 480.31 2.87 469 231 238 7 457.79 0.18 470 232 235 3 496.16 0.74 471 234 237 3 475.79 1.96 472 234 238 4 469.82 4.95 473 235 238 3 481.17 0.73 474 235 239 4 471.14 4.28 475 236 239 3 484.71 2.50 476 236 240 4 468.64 4.83 477 237 240 3 476.04 1.83 478 237 241 4 469.36 5.17 479 238 241 3 477.30 1.21 480 238 242 4 466.30 3.65 481 239 242 3 482.09 4.25 482 239 243 4 466.06 3.76 483 240 243 3 487.16 2.50 484 240 244 4 466.34 3.62 485 241 244 3 489.04 0.71 486 241 245 4 459.54 0.57