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 5 187 182 30.50 0.76 2 5 237 232 48.39 0.27 3 6 187 181 31.29 0.36 4 6 189 183 36.91 0.42 5 6 237 231 48.68 0.38 6 6 238 232 47.71 0.59 7 6 242 236 36.94 0.40 8 6 247 241 29.73 0.38 9 7 176 169 38.95 0.34 10 7 186 179 38.35 0.18 11 7 187 180 37.74 0.01 12 7 188 181 37.62 0.07 13 7 189 182 37.62 0.07 14 7 235 228 53.63 0.26 15 7 236 229 51.95 0.12 16 7 237 230 48.72 0.40 17 7 238 231 48.59 0.34 18 8 189 181 39.03 0.38 19 8 235 227 63.72 0.66 20 8 236 228 58.98 2.33 21 8 238 230 50.64 0.54 22 9 188 179 43.19 0.78 23 9 189 180 42.68 0.53 24 9 190 181 42.68 0.52 25 9 192 183 48.06 0.68 26 9 193 184 47.22 0.71 27 9 233 224 64.28 0.38 28 9 234 225 70.53 0.49 29 9 235 226 67.55 1.98 30 10 233 223 70.66 0.53 31 10 234 224 71.06 0.32 32 10 236 226 77.80 0.39 33 11 14 3 616.29 0.01 34 11 193 182 59.16 0.18 35 11 231 220 70.56 0.50 36 11 232 221 70.89 0.42 37 11 233 222 71.09 0.34 38 12 232 220 75.07 0.70 39 12 233 221 77.56 0.46 40 12 234 222 80.47 0.21 41 13 231 218 78.32 0.14 42 13 232 219 77.72 0.43 43 14 196 182 80.53 0.24 44 14 229 215 80.69 0.33 45 14 230 216 79.73 0.64 46 14 231 217 79.30 0.52 47 15 51 36 92.21 0.60 48 15 52 37 95.11 0.75 49 15 221 206 90.70 0.04 50 15 229 214 90.02 0.21 51 15 230 215 87.77 1.43 52 15 232 217 93.98 0.13 53 16 52 36 97.34 1.57 54 16 53 37 97.34 1.57 55 16 54 38 98.57 2.18 56 16 228 212 90.94 0.11 57 16 229 213 90.91 0.10 58 17 21 4 545.38 4.26 59 17 23 6 94.92 0.46 60 17 36 19 101.05 0.30 61 17 54 37 104.37 0.71 62 17 223 206 92.67 0.47 63 17 224 207 91.33 0.17 64 17 227 210 91.00 0.08 65 17 228 211 92.59 0.49 66 17 229 212 92.90 0.59 67 17 230 213 95.36 0.59 68 18 21 3 545.38 4.26 69 18 47 29 156.88 1.47 70 18 227 209 95.40 0.61 71 19 226 207 95.28 0.63 72 19 227 208 128.06 16.95 73 19 228 209 96.28 0.18 74 20 43 23 171.37 8.67 75 20 226 206 154.02 6.70 76 21 36 15 170.80 8.39 77 21 38 17 170.80 8.42 78 21 47 26 171.40 8.65 79 21 225 204 161.94 4.01 80 21 226 205 161.92 4.00 81 22 38 16 170.88 8.46 82 22 39 17 170.96 8.51 83 22 40 18 171.36 8.67 84 22 67 45 171.34 8.68 85 22 206 184 171.05 8.54 86 22 225 203 161.95 4.01 87 22 226 204 170.78 8.40 88 23 26 3 626.42 1.82 89 23 36 13 171.38 8.66 90 23 37 14 171.35 8.67 91 23 38 15 171.35 8.68 92 23 209 186 169.43 7.73 93 23 210 187 161.96 4.00 94 23 223 200 162.00 4.00 95 23 224 201 164.72 5.37 96 23 225 202 170.19 8.11 97 24 37 13 171.39 8.68 98 24 38 14 171.42 8.68 99 24 39 15 171.39 8.69 100 24 67 43 171.40 8.69 101 24 68 44 171.35 8.69 102 24 69 45 170.80 8.42 103 24 70 46 170.01 8.03 104 24 155 131 170.73 8.39 105 24 156 132 165.97 6.00 106 24 209 185 171.34 8.68 107 24 225 201 171.33 8.62 108 25 36 11 171.69 8.79 109 25 37 12 171.41 8.68 110 25 69 44 171.35 8.67 111 25 70 45 169.80 7.91 112 25 71 46 161.96 3.99 113 25 156 131 170.78 8.40 114 26 34 8 172.30 9.00 115 26 35 9 171.75 8.78 116 26 36 10 171.71 8.80 117 26 156 130 170.95 8.45 118 26 158 132 168.60 7.27 119 26 210 184 171.56 8.73 120 26 211 185 172.24 9.08 121 26 212 186 172.27 9.08 122 26 221 195 172.38 9.11 123 26 223 197 172.25 9.02 124 26 230 204 171.40 8.56 125 27 34 7 172.36 9.03 126 27 35 8 171.75 8.80 127 27 71 44 171.65 8.75 128 27 72 45 171.50 8.69 129 27 73 46 171.48 8.69 130 27 78 51 171.70 8.78 131 27 212 185 172.29 9.07 132 28 32 4 528.89 3.23 133 28 33 5 172.38 9.02 134 28 34 6 172.37 9.03 135 28 51 23 180.37 12.76 136 28 212 184 172.91 9.36 137 28 213 185 176.84 11.33 138 28 214 186 178.06 11.96 139 28 216 188 178.15 11.98 140 28 219 191 178.16 11.95 141 28 221 193 175.92 10.83 142 29 33 4 332.50 71.04 143 29 35 6 172.40 9.02 144 29 73 44 171.77 8.79 145 29 93 64 172.28 9.06 146 30 33 3 561.10 3.42 147 30 93 63 200.55 22.09 148 30 216 186 179.90 12.84 149 32 50 18 255.22 18.41 150 32 51 19 255.23 18.41 151 32 52 20 255.27 18.42 152 32 219 187 182.35 13.21 153 33 48 15 255.30 18.40 154 33 49 16 255.25 18.39 155 33 57 24 255.21 18.39 156 34 48 14 255.31 18.40 157 34 49 15 255.26 18.39 158 34 51 17 255.36 18.41 159 34 212 178 181.56 13.36 160 34 221 187 182.66 13.07 161 34 230 196 172.56 8.00 162 35 47 12 255.32 18.39 163 35 48 13 255.31 18.39 164 35 71 36 206.14 24.81 165 35 73 38 206.19 24.82 166 35 78 43 207.09 25.21 167 35 93 58 223.94 22.42 168 35 96 61 241.68 24.54 169 36 46 10 255.33 18.39 170 36 47 11 255.33 18.39 171 36 49 13 255.37 18.41 172 36 71 35 207.22 25.34 173 37 45 8 255.34 18.39 174 37 46 9 255.33 18.39 175 37 68 31 207.30 25.38 176 37 69 32 207.12 25.29 177 37 71 34 207.22 25.34 178 37 80 43 207.36 25.37 179 38 43 5 378.48 43.19 180 38 44 6 255.34 18.39 181 38 45 7 255.34 18.39 182 38 47 9 255.38 18.41 183 38 68 30 228.50 23.97 184 39 43 4 383.26 45.56 185 39 44 5 255.34 18.39 186 39 67 28 239.91 25.01 187 39 68 29 228.54 23.99 188 40 43 3 564.38 10.01 189 40 44 4 255.35 18.39 190 40 67 27 241.00 25.56 191 40 226 186 200.72 3.81 192 41 64 23 255.27 18.45 193 41 65 24 253.46 19.36 194 41 66 25 251.54 20.32 195 41 67 26 243.02 24.58 196 41 83 42 249.66 21.27 197 41 84 43 251.61 20.29 198 42 61 19 255.63 18.51 199 42 64 22 253.99 17.80 200 43 226 183 197.80 2.46 201 44 61 17 255.66 18.51 202 44 62 18 255.52 18.46 203 44 66 22 242.78 24.73 204 44 67 23 242.38 24.92 205 44 68 24 241.53 25.34 206 45 59 14 256.25 18.80 207 45 60 15 255.66 18.50 208 45 61 16 255.62 18.49 209 45 62 17 255.61 18.49 210 45 80 35 242.62 25.03 211 46 59 13 256.27 18.80 212 46 60 14 256.11 18.73 213 46 71 25 231.58 30.55 214 46 78 32 241.81 25.44 215 46 80 34 230.31 31.19 216 46 91 45 242.99 25.30 217 46 96 50 243.34 25.19 218 47 56 9 258.12 19.66 219 47 58 11 257.81 19.55 220 47 59 12 256.27 18.80 221 47 96 49 256.26 18.80 222 48 56 8 258.18 19.64 223 48 57 9 258.13 19.66 224 48 58 10 257.94 19.59 225 48 96 48 257.76 19.50 226 49 54 5 539.83 4.03 227 49 55 6 258.44 19.75 228 49 56 7 258.18 19.63 229 49 57 8 258.29 19.69 230 50 54 4 577.86 0.36 231 50 55 5 406.74 54.39 232 50 57 7 258.43 19.73 233 51 219 168 227.40 35.43 234 51 221 170 227.35 35.41 235 51 230 179 203.47 7.77 236 56 59 3 605.12 5.91 237 58 94 36 269.63 19.48 238 58 95 37 269.63 19.48 239 58 96 38 269.64 19.49 240 59 96 37 269.66 19.49 241 60 91 31 270.50 19.07 242 60 96 36 269.67 19.49 243 60 98 38 270.82 18.98 244 62 66 4 498.90 16.14 245 62 68 6 269.58 19.50 246 62 80 18 273.50 17.71 247 62 82 20 270.45 19.09 248 62 89 27 277.43 15.95 249 62 91 29 286.49 12.18 250 63 66 3 558.81 0.77 251 66 82 16 327.76 33.24 252 66 85 19 350.08 44.41 253 66 87 21 344.00 40.85 254 66 89 23 316.20 26.26 255 67 82 15 350.09 44.40 256 67 83 16 349.93 44.51 257 68 80 12 350.75 43.52 258 68 82 14 350.53 44.20 259 69 80 11 351.55 43.77 260 69 81 12 350.62 44.24 261 69 82 13 350.66 44.27 262 69 83 14 350.69 44.28 263 69 109 40 350.68 44.27 264 69 110 41 350.67 44.27 265 70 80 10 351.60 43.80 266 70 81 11 351.45 43.88 267 70 110 40 350.72 44.28 268 70 111 41 350.69 44.27 269 70 112 42 350.68 44.26 270 71 78 7 351.89 43.58 271 71 79 8 351.63 43.78 272 71 80 9 351.61 43.80 273 71 112 41 351.62 43.81 274 72 78 6 351.97 43.61 275 72 79 7 351.94 43.63 276 72 112 40 351.70 43.83 277 72 113 41 351.67 43.83 278 72 114 42 351.69 43.83 279 72 119 47 351.66 43.81 280 73 76 3 578.53 0.97 281 73 77 4 354.99 42.11 282 73 78 5 352.00 43.60 283 73 93 20 373.13 33.04 284 73 114 41 352.07 43.68 285 74 77 3 544.17 5.18 286 74 79 5 352.43 43.43 287 74 114 40 352.10 43.68 288 74 116 42 352.05 43.69 289 74 117 43 352.05 43.69 290 74 119 45 352.09 43.67 291 74 133 59 352.00 43.66 292 76 92 16 400.66 19.30 293 76 93 17 400.66 19.30 294 77 90 13 400.69 19.34 295 77 91 14 400.67 19.31 296 77 99 22 400.68 19.32 297 78 89 11 400.80 19.37 298 78 90 12 400.73 19.34 299 78 91 13 400.70 19.33 300 78 93 15 400.76 19.32 301 78 96 18 400.76 19.32 302 79 89 10 400.80 19.37 303 79 90 11 400.74 19.34 304 79 102 23 400.81 19.39 305 79 112 33 359.75 39.99 306 79 119 40 364.25 37.68 307 79 133 54 377.39 31.09 308 79 136 57 396.61 21.47 309 80 88 8 400.83 19.39 310 80 89 9 400.81 19.38 311 80 91 11 400.85 19.36 312 80 102 22 400.84 19.39 313 80 112 32 364.31 37.72 314 81 87 6 400.85 19.39 315 81 88 7 400.83 19.39 316 81 102 21 400.85 19.39 317 81 104 23 400.76 19.46 318 81 106 25 395.80 21.96 319 81 109 28 361.90 38.91 320 81 110 29 361.98 38.95 321 81 112 31 372.07 33.87 322 82 85 3 567.52 3.17 323 82 87 5 400.88 19.41 324 82 89 7 400.88 19.37 325 82 109 27 368.97 35.45 326 83 108 25 389.41 25.82 327 83 109 26 376.21 31.99 328 83 110 27 377.44 31.34 329 84 108 24 401.77 20.13 330 85 104 19 404.48 21.15 331 85 108 23 402.11 20.00 332 85 109 24 402.11 20.00 333 86 103 17 404.49 21.16 334 86 104 18 404.47 21.16 335 86 105 19 404.46 21.15 336 86 106 20 404.38 21.12 337 87 101 14 404.77 21.23 338 87 102 15 404.57 21.20 339 87 103 16 404.54 21.18 340 88 101 13 404.89 21.27 341 88 102 14 404.62 21.22 342 88 103 15 404.60 21.17 343 89 98 9 405.11 21.15 344 89 100 11 405.05 21.22 345 89 101 12 404.89 21.27 346 89 102 13 404.89 21.27 347 90 98 8 405.12 21.15 348 90 99 9 405.14 21.16 349 90 100 10 405.05 21.23 350 90 101 11 405.05 21.22 351 90 102 12 405.06 21.21 352 90 136 46 401.75 19.57 353 91 96 5 405.17 21.11 354 91 97 6 405.17 21.12 355 91 98 7 405.12 21.15 356 91 99 8 405.15 21.16 357 92 95 3 555.88 2.75 358 92 96 4 405.19 21.12 359 92 97 5 405.18 21.12 360 92 99 7 405.16 21.18 361 93 96 3 551.10 4.05 362 98 101 3 649.54 1.61 363 100 136 36 421.06 15.47 364 102 112 10 419.70 15.61 365 102 136 34 421.06 15.47 366 103 136 33 423.31 14.36 367 104 108 4 572.41 0.49 368 104 109 5 508.82 10.71 369 104 131 27 421.10 15.46 370 105 129 24 421.32 15.61 371 105 136 31 427.12 13.03 372 105 137 32 427.05 13.05 373 105 138 33 425.43 13.71 374 106 109 3 614.93 3.39 375 106 112 6 526.21 5.28 376 106 121 15 425.47 13.85 377 106 122 16 421.65 15.77 378 106 123 17 421.63 15.78 379 106 129 23 421.39 15.63 380 106 131 25 427.12 13.03 381 107 123 16 425.51 13.87 382 107 125 18 427.25 14.76 383 108 123 15 428.44 13.92 384 110 122 12 429.69 14.25 385 110 123 13 429.66 14.25 386 110 124 14 429.67 14.24 387 110 153 43 301.35 49.93 388 110 154 44 297.34 51.93 389 110 155 45 296.25 52.48 390 110 169 59 275.94 62.66 391 111 121 10 430.22 14.01 392 111 122 11 429.75 14.23 393 111 155 44 294.79 53.29 394 111 156 45 294.75 53.31 395 111 157 46 294.48 53.45 396 112 120 8 430.72 13.87 397 112 121 9 430.31 14.02 398 112 157 45 295.55 53.69 399 113 119 6 430.94 13.86 400 113 120 7 430.84 13.91 401 113 157 44 295.62 53.72 402 113 158 45 295.59 53.74 403 113 159 46 295.30 53.88 404 113 164 51 278.81 62.12 405 114 117 3 586.80 2.33 406 114 118 4 470.56 5.95 407 114 119 5 430.92 13.87 408 114 120 6 430.93 13.87 409 114 159 45 295.61 53.74 410 115 118 3 580.40 1.36 411 115 120 5 431.19 13.78 412 115 159 44 295.71 53.77 413 117 133 16 489.84 19.62 414 118 130 12 489.76 19.62 415 118 131 13 489.78 19.63 416 118 133 15 489.84 19.61 417 118 139 21 489.76 19.63 418 119 130 11 489.79 19.62 419 119 131 12 489.80 19.62 420 119 133 14 490.08 19.50 421 119 136 17 490.20 19.46 422 120 128 8 489.77 19.63 423 120 129 9 489.79 19.62 424 120 130 10 489.79 19.62 425 120 157 37 313.11 62.34 426 120 159 39 313.04 62.46 427 120 164 44 295.06 70.23 428 120 179 59 300.73 73.13 429 121 128 7 489.79 19.62 430 121 129 8 489.79 19.62 431 121 131 10 490.18 19.48 432 121 157 36 317.53 64.63 433 122 127 5 489.78 19.62 434 122 129 7 489.90 19.58 435 122 154 32 319.07 63.83 436 122 155 33 319.44 64.07 437 122 157 35 319.06 65.44 438 123 129 6 490.29 19.46 439 124 152 28 471.53 10.35 440 124 153 29 464.75 7.41 441 124 154 30 464.93 7.32 442 125 152 27 471.77 10.23 443 125 153 28 471.38 10.08 444 125 154 29 471.26 10.00 445 126 142 16 490.84 19.23 446 126 143 17 490.72 19.24 447 126 144 18 490.16 19.44 448 126 150 24 471.81 10.28 449 126 151 25 471.81 10.25 450 126 152 26 471.43 10.05 451 126 154 28 469.04 8.84 452 127 141 14 490.86 19.20 453 127 142 15 490.81 19.21 454 127 143 16 490.78 19.22 455 127 154 27 469.03 8.35 456 128 141 13 490.94 19.24 457 128 142 14 490.90 19.22 458 128 144 16 490.81 19.22 459 128 154 26 327.26 62.55 460 128 157 29 321.53 65.59 461 128 164 36 304.22 74.12 462 128 177 49 303.44 74.49 463 129 138 9 491.27 19.16 464 129 140 11 491.16 19.21 465 129 141 12 491.06 19.18 466 130 138 8 491.31 19.18 467 130 139 9 491.21 19.19 468 130 140 10 491.17 19.21 469 130 142 12 491.14 19.20 470 130 179 49 303.60 74.56 471 131 136 5 491.39 19.21 472 131 137 6 491.38 19.21 473 131 138 7 491.32 19.18 474 131 139 8 491.31 19.19 475 132 135 3 547.32 2.62 476 132 136 4 491.40 19.21 477 132 137 5 491.42 19.21 478 132 139 7 491.33 19.19 479 133 136 3 551.34 2.50 480 138 141 3 637.66 1.31 481 140 180 40 332.51 88.23 482 142 179 37 332.41 88.36 483 142 180 38 332.97 88.08 484 142 181 39 332.91 88.06 485 142 182 40 332.88 88.04 486 144 150 6 500.75 4.17 487 144 151 7 500.67 4.17 488 144 154 10 500.61 4.20 489 144 177 33 331.75 88.64 490 144 182 38 332.97 88.08 491 144 184 40 351.12 78.95 492 145 148 3 567.80 1.82 493 145 149 4 509.01 0.04 494 145 150 5 500.75 4.17 495 145 151 6 500.75 4.17 496 145 184 39 355.29 76.91 497 146 149 3 536.65 2.96 498 146 151 5 501.52 3.79 499 146 184 38 355.30 76.91 500 146 187 41 477.62 15.75 501 146 247 101 331.69 88.65 502 146 248 102 331.59 88.67 503 146 252 106 318.34 84.36 504 147 248 101 331.63 88.65 505 149 248 99 331.00 88.95 506 149 252 103 313.07 87.08 507 150 252 102 309.51 85.53 508 151 154 3 628.22 0.65 509 151 168 17 332.30 88.91 510 151 175 24 331.23 89.36 511 151 184 33 478.26 15.84 512 151 187 36 520.22 5.13 513 151 252 101 303.27 87.98 514 152 168 16 332.93 89.25 515 153 167 14 335.11 90.33 516 153 168 15 331.97 89.73 517 153 169 16 331.50 90.03 518 153 170 17 332.04 89.76 519 154 157 3 652.40 1.64 520 154 166 12 334.68 90.12 521 154 167 13 335.04 90.36 522 154 168 14 332.05 89.77 523 154 175 21 326.06 92.77 524 154 177 23 364.37 78.59 525 155 166 11 345.69 95.67 526 155 167 12 342.61 95.31 527 155 169 14 334.58 92.89 528 155 209 54 536.14 2.05 529 155 225 70 536.67 2.04 530 156 166 10 346.59 96.67 531 156 167 11 345.26 97.14 532 156 209 53 536.17 2.04 533 156 210 54 536.52 2.10 534 156 211 55 536.59 2.08 535 157 164 7 427.74 57.03 536 157 165 8 373.48 83.73 537 157 166 9 347.18 96.53 538 158 164 6 537.42 2.33 539 158 165 7 427.74 57.02 540 158 211 53 537.30 2.25 541 158 212 54 542.74 0.36 542 158 213 55 559.27 7.87 543 159 162 3 592.16 0.89 544 159 163 4 561.95 6.06 545 159 164 5 537.47 2.34 546 159 179 20 588.63 4.01 547 159 213 54 568.90 3.12 548 160 163 3 568.88 3.12 549 160 165 5 568.35 2.89 550 160 211 51 571.76 4.55 551 160 213 53 569.38 2.90 552 160 220 60 602.74 3.16 553 161 213 52 611.93 1.34 554 162 179 17 612.04 1.39 555 163 176 13 611.18 1.05 556 163 177 14 611.99 1.41 557 163 185 22 612.00 1.36 558 164 175 11 612.06 1.39 559 164 176 12 612.05 1.39 560 164 177 13 612.04 1.39 561 164 179 15 612.12 1.36 562 165 174 9 612.04 1.39 563 165 175 10 612.05 1.39 564 165 176 11 612.05 1.39 565 165 188 23 612.06 1.38 566 165 211 46 627.12 5.99 567 165 220 55 693.78 28.10 568 165 235 70 688.18 29.31 569 166 174 8 612.06 1.39 570 166 175 9 612.06 1.39 571 166 177 11 612.20 1.38 572 166 211 45 665.71 1.00 573 167 173 6 612.06 1.39 574 167 174 7 612.07 1.39 575 167 208 41 662.20 23.46 576 167 209 42 641.49 13.11 577 167 210 43 665.96 1.12 578 167 211 44 707.64 19.96 579 168 171 3 612.21 1.31 580 168 173 5 612.09 1.38 581 168 175 7 612.31 1.31 582 168 187 19 700.52 18.82 583 168 251 83 611.96 1.34 584 170 253 83 612.00 1.40 585 171 250 79 612.08 1.39 586 171 251 80 612.12 1.38 587 171 253 82 611.99 1.42