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 24 420.63 32.04 2 1 95 94 347.32 0.41 3 1 96 95 346.57 0.13 4 2 23 21 420.83 32.01 5 2 95 93 347.81 0.45 6 2 96 94 347.49 0.44 7 2 97 95 346.25 0.13 8 2 99 97 345.04 0.46 9 2 134 132 228.13 0.26 10 3 22 19 420.98 31.95 11 3 23 20 420.82 32.01 12 3 93 90 348.95 0.30 13 3 95 92 348.00 0.50 14 3 97 94 347.75 0.45 15 3 98 95 345.35 0.30 16 3 99 96 345.04 0.46 17 3 134 131 228.13 0.26 18 4 21 17 421.53 31.81 19 4 22 18 421.39 31.76 20 4 99 95 345.35 0.30 21 4 134 130 228.13 0.26 22 4 135 131 228.12 0.25 23 4 138 134 227.97 0.21 24 5 19 14 422.95 31.45 25 5 20 15 421.94 31.71 26 5 21 16 421.56 31.80 27 5 86 81 359.54 0.57 28 5 89 84 359.29 0.70 29 5 90 85 358.49 0.29 30 5 93 88 358.04 0.07 31 5 98 93 347.88 0.42 32 5 99 94 347.50 0.44 33 5 100 95 345.16 0.42 34 5 101 96 345.41 0.28 35 5 135 130 228.15 0.25 36 5 138 133 228.02 0.23 37 6 19 13 422.96 31.45 38 6 20 14 422.72 31.35 39 6 86 80 361.82 0.89 40 6 101 95 346.00 0.01 41 6 129 123 231.32 0.12 42 6 135 129 228.49 0.32 43 6 138 132 228.10 0.23 44 6 139 133 227.96 0.20 45 7 10 3 609.20 1.81 46 7 17 10 423.26 31.44 47 7 18 11 423.10 31.50 48 7 19 12 422.96 31.45 49 7 82 75 361.94 0.93 50 7 86 79 361.90 0.91 51 7 142 135 221.49 0.84 52 8 17 9 423.31 31.41 53 8 18 10 423.13 31.48 54 8 142 134 224.20 1.39 55 8 143 135 221.57 0.79 56 8 146 138 208.97 0.58 57 9 12 3 533.35 2.46 58 9 17 8 423.31 31.41 59 9 146 137 215.82 0.34 60 9 164 155 118.18 1.78 61 9 188 179 56.30 1.31 62 10 17 7 423.36 31.41 63 10 78 68 362.51 0.97 64 10 82 72 362.49 0.98 65 10 103 93 347.68 0.51 66 10 188 178 56.32 1.32 67 10 191 181 47.24 1.55 68 11 164 153 118.17 1.77 69 11 191 180 47.38 1.62 70 12 146 134 223.81 1.35 71 12 163 151 118.23 1.77 72 12 164 152 118.20 1.76 73 12 188 176 56.34 1.33 74 12 191 179 47.36 1.61 75 13 163 150 118.25 1.77 76 13 164 151 118.23 1.77 77 13 165 152 118.22 1.76 78 13 170 157 116.58 1.04 79 13 174 161 103.46 0.83 80 13 187 174 56.40 1.33 81 13 188 175 56.34 1.33 82 13 191 178 47.38 1.62 83 13 193 180 41.02 0.82 84 14 153 139 186.90 0.57 85 14 160 146 118.59 1.82 86 14 163 149 118.25 1.77 87 14 170 156 116.56 1.07 88 14 174 160 103.89 0.64 89 14 177 163 99.73 0.92 90 14 186 172 56.43 1.33 91 14 187 173 56.37 1.32 92 15 66 51 463.42 10.52 93 15 150 135 199.69 0.58 94 15 153 138 177.95 0.61 95 15 186 171 56.38 1.32 96 15 188 173 56.33 1.32 97 16 63 47 463.62 10.60 98 16 64 48 463.52 10.54 99 16 65 49 463.48 10.54 100 16 66 50 463.43 10.51 101 16 149 133 202.14 0.15 102 16 188 172 56.32 1.32 103 17 63 46 463.68 10.51 104 17 64 47 463.49 10.53 105 17 69 52 445.88 1.74 106 17 78 61 403.43 19.43 107 17 81 64 403.38 19.46 108 17 82 65 403.28 19.42 109 17 85 68 403.19 19.43 110 17 188 171 56.30 1.32 111 18 61 43 463.93 10.48 112 18 62 44 463.81 10.47 113 18 63 45 463.61 10.47 114 18 142 124 221.62 0.81 115 18 145 127 217.04 0.87 116 18 146 128 204.66 0.66 117 19 61 42 463.92 10.46 118 19 62 43 463.82 10.47 119 19 82 63 403.25 19.52 120 19 85 66 402.93 19.57 121 19 86 67 402.85 19.57 122 19 89 70 402.52 19.47 123 20 60 40 464.17 10.33 124 20 61 41 463.80 10.40 125 20 89 69 402.44 19.53 126 20 138 118 228.04 0.24 127 20 141 121 224.96 0.80 128 20 142 122 220.51 0.36 129 21 59 38 464.26 10.34 130 21 60 39 464.17 10.30 131 21 89 68 400.30 20.60 132 21 93 72 397.98 19.90 133 22 53 31 715.34 2.62 134 22 57 35 561.11 2.23 135 22 58 36 472.30 8.76 136 22 59 37 464.54 10.46 137 22 93 71 398.01 20.30 138 22 134 112 228.31 0.24 139 22 137 115 228.11 0.24 140 22 138 116 228.02 0.23 141 22 141 119 221.53 0.86 142 23 57 34 646.12 1.58 143 23 58 35 534.38 0.41 144 23 93 70 398.31 21.39 145 24 134 110 228.68 0.30 146 27 134 107 230.17 0.09 147 30 133 103 230.48 0.20 148 30 134 104 230.42 0.21 149 30 137 107 229.33 0.26 150 31 133 102 230.50 0.20 151 35 133 98 230.53 0.18 152 35 136 101 229.97 0.21 153 35 137 102 229.81 0.28 154 35 140 105 229.13 0.20 155 38 140 102 229.37 0.11 156 39 129 90 232.75 1.18 157 43 147 104 220.49 0.37 158 43 151 108 202.84 0.26 159 46 140 94 228.96 0.28 160 46 143 97 228.21 0.20 161 46 144 98 226.52 0.29 162 46 147 101 219.78 0.56 163 47 144 97 227.03 0.64 164 47 148 101 210.03 2.22 165 49 140 91 228.77 0.20 166 50 140 90 228.21 0.15 167 50 141 91 228.13 0.18 168 50 144 94 220.06 0.58 169 51 148 97 210.03 2.21 170 53 137 84 228.89 0.23 171 53 141 88 228.01 0.23 172 54 141 87 228.03 0.23 173 54 145 91 219.77 0.55 174 58 92 34 400.74 20.58 175 58 93 35 399.31 20.96 176 59 141 82 223.37 0.04 177 60 89 29 401.81 20.03 178 60 92 32 398.75 19.55 179 60 93 33 398.42 19.68 180 61 89 28 402.46 19.53 181 61 92 31 400.17 18.86 182 61 141 80 226.49 0.21 183 61 145 84 208.78 0.69 184 62 85 23 402.97 19.59 185 62 88 26 402.60 19.46 186 62 89 27 402.32 19.46 187 62 92 30 400.54 18.66 188 63 145 82 219.09 0.06 189 64 68 4 528.42 2.75 190 64 69 5 528.20 2.85 191 64 72 8 493.31 0.84 192 64 85 21 403.18 19.49 193 65 68 3 537.54 1.80 194 65 69 4 528.43 2.75 195 66 69 3 533.38 0.60 196 66 70 4 535.92 1.01 197 66 185 119 56.48 1.34 198 66 186 120 56.41 1.32 199 66 187 121 56.37 1.32 200 66 188 122 56.25 1.31 201 67 70 3 539.16 0.61 202 67 71 4 537.84 0.05 203 68 71 3 542.31 0.09 204 68 72 4 537.85 0.05 205 69 72 3 541.56 1.35 206 69 73 4 537.82 0.04 207 69 78 9 405.06 19.98 208 69 81 12 404.39 19.91 209 69 188 119 56.31 1.32 210 70 73 3 545.47 3.20 211 70 188 118 56.32 1.32 212 70 189 119 56.29 1.32 213 70 190 120 53.67 0.93 214 71 74 3 555.64 1.82 215 71 190 119 56.20 1.32 216 72 75 3 555.50 1.75 217 72 76 4 524.88 1.37 218 72 81 9 405.55 20.39 219 72 84 12 405.55 20.39 220 73 76 3 538.20 0.20 221 73 78 5 468.85 10.71 222 73 190 117 54.39 1.32 223 73 191 118 54.09 1.38 224 74 190 116 55.54 1.07 225 76 80 4 518.60 5.13 226 76 81 5 518.04 5.40 227 76 84 8 518.00 5.38 228 77 80 3 540.09 1.10 229 77 81 4 536.11 0.81 230 78 81 3 547.04 1.55 231 78 82 4 536.29 0.71 232 78 191 113 44.08 0.03 233 79 82 3 542.30 0.00 234 79 83 4 531.11 1.88 235 79 103 24 348.00 0.47 236 80 83 3 535.65 4.14 237 80 84 4 534.84 3.73 238 81 84 3 548.54 2.34 239 81 85 4 546.25 1.98 240 82 85 3 547.06 1.58 241 82 86 4 531.62 1.27 242 82 103 21 347.99 0.47 243 83 86 3 549.84 0.19 244 83 87 4 531.62 1.26 245 83 110 27 264.63 0.54 246 83 113 30 264.54 0.55 247 83 114 31 264.54 0.55 248 83 117 34 264.43 0.54 249 84 87 3 551.50 0.64 250 84 88 4 545.00 2.35 251 85 88 3 547.88 0.92 252 85 89 4 545.00 2.35 253 86 89 3 552.80 1.33 254 86 90 4 544.97 2.37 255 86 100 14 348.17 0.53 256 86 101 15 348.17 0.53 257 86 114 28 264.52 0.55 258 87 90 3 551.12 0.43 259 87 91 4 540.98 0.38 260 87 114 27 264.52 0.55 261 87 117 30 263.48 0.65 262 87 118 31 263.25 0.58 263 88 91 3 551.12 0.43 264 88 92 4 540.51 0.78 265 89 92 3 547.96 2.01 266 89 93 4 540.47 0.80 267 90 93 3 549.69 0.06 268 90 94 4 524.29 1.75 269 90 95 5 524.27 1.76 270 90 98 8 348.33 0.48 271 90 100 10 348.17 0.53 272 90 114 24 264.44 0.58 273 90 118 28 263.07 0.50 274 90 120 30 262.82 0.54 275 90 122 32 261.76 0.49 276 91 94 3 533.88 2.50 277 91 118 27 263.07 0.50 278 91 120 29 262.99 0.51 279 94 120 26 262.37 0.40 280 95 98 3 561.37 1.56 281 95 120 25 262.36 0.41 282 96 121 25 261.42 0.52 283 97 121 24 260.48 0.99 284 97 123 26 260.14 1.03 285 98 121 23 261.91 0.42 286 98 122 24 259.50 0.84 287 98 123 25 259.37 0.90 288 99 123 24 259.31 0.88 289 99 132 33 228.40 0.29 290 99 135 36 228.13 0.25 291 100 114 14 264.33 0.53 292 100 122 22 261.99 0.46 293 100 123 23 260.19 1.09 294 100 124 24 258.87 1.03 295 100 125 25 255.88 0.47 296 100 128 28 231.31 0.12 297 101 127 26 239.34 1.94 298 101 128 27 231.32 0.12 299 101 129 28 231.31 0.12 300 101 135 34 228.50 0.32 301 102 107 5 264.58 0.55 302 102 110 8 264.48 0.53 303 102 124 22 261.16 0.59 304 102 125 23 259.13 1.00 305 103 110 7 265.00 0.35 306 104 107 3 582.35 1.54 307 106 109 3 577.61 0.42 308 107 110 3 551.05 2.61 309 107 111 4 548.44 3.92 310 107 124 17 262.48 0.52 311 107 125 18 262.44 0.52 312 107 126 19 262.26 0.43 313 108 111 3 552.61 1.83 314 108 112 4 538.67 0.69 315 109 112 3 547.34 0.81 316 109 113 4 539.77 4.59 317 110 113 3 547.56 0.70 318 110 114 4 535.31 2.35 319 110 124 14 262.56 0.55 320 111 114 3 539.77 4.58 321 111 115 4 533.42 1.42 322 111 122 11 262.87 0.51 323 111 124 13 262.56 0.56 324 112 115 3 538.91 1.61 325 112 116 4 533.00 1.63 326 113 116 3 540.24 4.27 327 113 117 4 527.20 1.27 328 114 117 3 543.12 2.83 329 114 118 4 527.12 1.25 330 114 122 8 262.90 0.51 331 115 118 3 553.93 1.77 332 115 119 4 510.95 3.25 333 115 120 5 448.06 22.36 334 115 121 6 263.16 0.52 335 115 122 7 263.01 0.57 336 118 122 4 564.18 1.83 337 125 128 3 530.00 2.54 338 125 131 6 304.38 37.03 339 125 132 7 304.38 37.04 340 127 130 3 574.67 4.11 341 128 131 3 550.43 0.91 342 128 132 4 500.35 3.92 343 128 135 7 228.61 0.34 344 129 135 6 228.62 0.34 345 129 136 7 228.48 0.32 346 129 139 10 228.15 0.21 347 132 135 3 541.87 0.69 348 132 136 4 532.50 4.00 349 133 136 3 541.74 0.21 350 133 137 4 532.49 3.99 351 134 137 3 540.91 0.21 352 134 138 4 532.49 3.99 353 135 138 3 531.16 3.37 354 135 139 4 527.34 1.42 355 136 139 3 536.81 2.64 356 136 140 4 535.51 1.99 357 137 140 3 536.20 2.33 358 137 141 4 533.72 4.12 359 138 141 3 548.79 2.75 360 138 142 4 534.45 4.49 361 139 142 3 546.21 1.35 362 139 143 4 533.74 4.13 363 140 143 3 543.35 0.04 364 140 144 4 540.04 1.69 365 141 144 3 543.89 2.02 366 141 145 4 533.87 4.08 367 142 145 3 554.84 0.32 368 142 146 4 533.87 4.08 369 143 146 3 540.28 0.87 370 143 147 4 533.82 4.04 371 144 147 3 540.28 0.88 372 144 148 4 533.80 4.04 373 145 148 3 545.12 0.27 374 145 149 4 534.60 3.63 375 146 149 3 543.31 2.15 376 146 150 4 533.76 4.03 377 146 162 16 118.25 1.78 378 146 164 18 118.23 1.77 379 147 150 3 536.41 2.48 380 147 151 4 532.64 3.47 381 148 151 3 536.90 4.63 382 148 152 4 530.90 2.60 383 149 152 3 535.09 4.70 384 149 153 4 530.89 2.60 385 150 153 3 539.18 1.54 386 150 154 4 531.02 0.16 387 150 160 10 118.84 1.84 388 151 154 3 541.46 0.41 389 151 155 4 531.02 0.18 390 152 155 3 543.11 0.19 391 152 156 4 533.78 1.15 392 153 156 3 539.58 2.48 393 153 157 4 530.63 0.43 394 153 160 7 262.58 73.70 395 153 186 33 56.35 1.31 396 154 157 3 537.96 3.29 397 154 158 4 496.99 9.20 398 154 159 5 248.55 62.97 399 154 160 6 118.90 1.85 400 154 161 7 118.91 1.85 401 157 177 20 100.64 0.83 402 157 184 27 56.51 1.34 403 157 186 29 56.54 1.36 404 159 173 14 116.09 0.92 405 160 163 3 578.63 1.07 406 160 169 9 117.05 1.27 407 160 170 10 116.64 1.06 408 160 173 13 110.51 0.41 409 160 177 17 100.81 0.74 410 161 167 6 118.17 1.77 411 161 169 8 116.61 1.05 412 161 170 9 116.62 1.06 413 162 167 5 118.48 1.61 414 162 170 8 116.62 1.06 415 163 170 7 116.59 1.06 416 164 167 3 548.25 0.83 417 164 170 6 207.71 29.95 418 165 171 6 120.48 2.62 419 165 193 28 38.98 1.83 420 166 171 5 526.74 1.08 421 167 170 3 539.50 1.33 422 167 171 4 536.79 2.75 423 168 171 3 537.09 2.61 424 168 172 4 536.79 2.75 425 169 172 3 547.71 2.70 426 169 173 4 534.12 1.36 427 170 173 3 536.87 2.72 428 170 174 4 534.11 1.35 429 171 174 3 542.45 2.81 430 171 175 4 531.46 2.67 431 172 175 3 534.09 1.36 432 172 176 4 542.42 2.81 433 173 176 3 545.58 1.71 434 173 177 4 542.39 2.81 435 174 177 3 542.46 2.80 436 174 178 4 539.57 4.22 437 174 187 13 56.48 1.33 438 174 193 19 56.26 1.31 439 174 197 23 33.69 0.76 440 175 178 3 550.24 1.09 441 175 179 4 529.59 1.26 442 176 179 3 537.25 2.57 443 176 180 4 529.59 1.26 444 177 180 3 540.53 0.95 445 177 181 4 529.59 1.26 446 177 183 6 56.69 1.30 447 177 184 7 58.66 0.34 448 177 187 10 56.68 1.30 449 178 181 3 541.54 2.94 450 178 183 5 208.15 40.36 451 178 194 16 56.24 1.32 452 178 197 19 37.12 0.58 453 178 198 20 33.65 0.79 454 183 187 4 529.70 1.93 455 183 189 6 102.00 19.84 456 184 187 3 551.52 3.05 457 187 194 7 437.93 10.97 458 188 191 3 534.50 0.65 459 188 194 6 437.94 10.97 460 189 194 5 437.94 10.97 461 189 198 9 92.57 14.05 462 191 194 3 547.63 2.33 463 191 195 4 530.23 1.79 464 192 195 3 540.37 6.84 465 192 196 4 529.12 2.35 466 193 196 3 552.71 3.00 467 193 197 4 530.25 1.79 468 194 197 3 549.91 0.82 469 194 198 4 530.19 1.83 470 195 198 3 531.79 2.60 471 195 199 4 527.49 0.46 472 196 199 3 539.32 3.71 473 196 200 4 523.17 1.70 474 197 200 3 519.45 0.31