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 8 11 3 677.43 1.25 2 8 12 4 673.15 3.38 3 8 115 107 100.93 3.55 4 9 12 3 677.44 1.25 5 9 13 4 673.15 3.38 6 10 13 3 676.49 1.71 7 10 14 4 676.48 1.71 8 10 109 99 113.00 0.50 9 10 111 101 105.22 4.38 10 10 115 105 104.17 4.83 11 11 14 3 672.03 2.83 12 11 15 4 672.04 2.83 13 11 41 30 108.09 2.93 14 11 115 104 104.17 4.83 15 12 15 3 674.12 1.79 16 12 16 4 672.04 2.83 17 13 16 3 682.44 1.67 18 13 17 4 678.82 0.01 19 13 105 92 132.22 0.24 20 13 108 95 132.22 0.24 21 13 109 96 132.18 0.25 22 13 112 99 130.71 0.38 23 14 17 3 690.62 2.42 24 14 18 4 678.82 0.01 25 14 41 27 131.59 0.05 26 14 69 55 130.80 0.42 27 14 97 83 132.28 0.20 28 14 102 88 132.21 0.23 29 14 105 91 132.21 0.23 30 14 112 98 131.59 0.07 31 15 18 3 678.82 0.01 32 15 41 26 131.77 0.04 33 15 43 28 132.14 0.22 34 15 95 80 132.19 0.21 35 17 97 80 132.57 0.25 36 17 105 88 132.41 0.33 37 18 95 77 132.57 0.26 38 18 96 78 132.57 0.26 39 18 97 79 132.57 0.26 40 19 95 76 133.39 0.04 41 19 96 77 133.28 0.02 42 20 43 23 133.93 0.25 43 20 93 73 134.28 0.42 44 20 94 74 133.47 0.03 45 20 95 75 133.41 0.04 46 21 93 72 134.76 0.21 47 21 94 73 133.94 0.24 48 21 96 75 134.11 0.16 49 22 92 70 228.42 34.97 50 22 93 71 134.99 0.16 51 23 27 4 625.00 12.05 52 23 29 6 506.82 4.38 53 23 88 65 454.51 0.32 54 23 91 68 456.54 0.70 55 23 92 69 317.76 4.28 56 23 94 71 218.37 29.94 57 24 27 3 679.18 0.86 58 24 88 64 473.16 0.83 59 24 91 67 466.69 1.32 60 25 88 63 473.88 0.47 61 25 89 64 474.98 0.05 62 25 90 65 473.88 0.47 63 25 91 66 473.37 0.21 64 26 87 61 477.43 1.07 65 26 88 62 477.14 1.05 66 26 89 63 476.63 0.68 67 27 87 60 477.99 0.97 68 27 88 61 477.95 0.97 69 28 31 3 724.52 2.91 70 28 86 58 478.58 0.83 71 28 87 59 478.41 0.77 72 29 47 18 478.67 0.84 73 29 70 41 478.11 0.60 74 29 86 57 478.69 0.85 75 29 87 58 478.67 0.84 76 29 88 59 478.69 0.86 77 29 94 65 476.71 0.65 78 30 40 10 478.09 0.58 79 30 70 40 478.69 0.77 80 30 71 41 476.74 0.66 81 30 82 52 480.28 0.73 82 30 84 54 480.18 0.68 83 30 85 55 479.85 0.64 84 30 86 56 478.93 0.83 85 31 34 3 683.49 1.22 86 31 82 51 480.55 0.70 87 31 85 54 480.17 0.68 88 32 51 19 480.44 0.66 89 32 82 50 480.55 0.69 90 32 83 51 480.49 0.62 91 32 84 52 480.25 0.67 92 32 85 53 480.20 0.69 93 33 81 48 481.04 0.57 94 33 82 49 480.87 0.64 95 34 81 47 483.51 1.39 96 34 82 48 481.07 0.58 97 35 80 45 487.07 1.34 98 36 74 38 487.50 1.57 99 36 80 44 487.09 1.34 100 36 81 45 487.06 1.35 101 36 82 46 486.79 1.37 102 36 99 63 478.01 0.93 103 37 82 45 487.25 1.39 104 37 98 61 478.12 0.89 105 37 99 62 478.00 0.93 106 38 71 33 492.46 1.55 107 38 82 44 488.86 2.06 108 38 96 58 478.56 0.88 109 38 97 59 478.49 0.90 110 38 98 60 478.04 0.93 111 38 99 61 478.03 0.93 112 39 69 30 492.84 1.54 113 39 70 31 492.77 1.55 114 39 71 32 492.47 1.55 115 39 72 33 492.36 1.56 116 39 96 57 478.56 0.89 117 39 97 58 478.49 0.89 118 39 99 60 478.04 0.93 119 39 102 63 460.45 1.54 120 39 116 77 143.05 2.00 121 40 69 29 492.84 1.54 122 40 70 30 492.78 1.54 123 40 71 31 492.70 1.52 124 40 82 42 491.07 1.53 125 40 94 54 480.27 0.66 126 40 95 55 479.65 0.78 127 40 96 56 478.57 0.90 128 41 67 26 494.13 1.56 129 41 68 27 493.23 1.56 130 41 69 28 492.85 1.54 131 41 94 53 480.28 0.66 132 41 95 54 480.24 0.65 133 42 45 3 725.86 5.58 134 42 47 5 649.90 10.14 135 42 64 22 494.75 1.34 136 42 65 23 494.50 1.47 137 42 66 24 494.32 1.55 138 42 67 25 494.22 1.57 139 42 68 26 494.06 1.53 140 42 70 28 493.24 1.42 141 42 93 51 480.82 0.59 142 42 94 52 480.28 0.66 143 43 66 23 494.49 1.47 144 43 93 50 480.84 0.60 145 43 94 51 480.81 0.58 146 43 95 52 480.80 0.58 147 44 66 22 494.54 1.50 148 44 92 48 485.30 0.91 149 44 93 49 481.04 0.58 150 45 65 20 494.89 1.42 151 45 66 21 494.84 1.43 152 45 90 45 487.21 1.43 153 45 91 46 487.01 1.36 154 45 92 47 483.69 0.10 155 46 64 18 494.92 1.42 156 46 65 19 494.87 1.43 157 46 88 42 487.50 1.52 158 46 89 43 487.43 1.51 159 46 90 44 487.39 1.51 160 46 92 46 486.02 1.25 161 47 63 16 495.16 1.31 162 47 64 17 495.13 1.31 163 47 70 23 494.61 1.52 164 47 86 39 489.44 2.08 165 47 87 40 488.19 1.86 166 47 88 41 487.49 1.53 167 47 89 42 487.43 1.52 168 47 92 45 486.07 1.27 169 48 62 14 495.32 1.29 170 48 63 15 495.24 1.31 171 48 86 38 489.75 1.97 172 48 87 39 488.50 1.79 173 49 60 11 495.94 1.25 174 49 61 12 495.77 1.19 175 49 62 13 495.42 1.33 176 49 64 15 495.40 1.33 177 49 84 35 492.39 1.50 178 49 85 36 492.00 1.50 179 49 86 37 489.94 1.84 180 50 58 8 496.61 1.35 181 50 59 9 496.35 1.24 182 50 60 10 496.12 1.33 183 50 84 34 492.44 1.50 184 50 85 35 492.31 1.46 185 50 87 37 491.79 1.39 186 51 58 7 496.62 1.34 187 51 59 8 496.57 1.35 188 51 61 10 496.14 1.34 189 51 83 32 492.57 1.50 190 51 84 33 492.44 1.50 191 51 85 34 492.44 1.50 192 52 57 5 496.68 1.34 193 52 58 6 496.63 1.34 194 52 85 33 492.50 1.51 195 53 57 4 500.01 0.33 196 58 87 29 492.49 1.53 197 58 174 116 67.35 0.12 198 59 174 115 67.12 0.15 199 59 175 116 67.27 0.21 200 59 176 117 67.30 0.21 201 59 177 118 67.91 0.52 202 60 63 3 784.84 7.98 203 60 171 111 66.92 0.12 204 60 174 114 67.00 0.16 205 60 175 115 66.97 0.16 206 61 84 23 492.49 1.48 207 61 130 69 108.59 0.48 208 63 89 26 487.47 1.51 209 63 153 90 37.04 0.17 210 63 167 104 45.66 0.05 211 63 171 108 66.70 0.15 212 63 175 112 66.83 0.17 213 64 68 4 610.28 4.48 214 64 70 6 496.98 1.11 215 64 123 59 141.73 1.76 216 65 68 3 685.99 0.14 217 65 153 88 36.70 0.24 218 65 154 89 36.63 0.21 219 67 119 52 142.96 2.00 220 68 119 51 142.91 2.02 221 68 123 55 142.72 1.98 222 69 112 43 143.24 1.96 223 69 115 46 143.03 1.99 224 69 116 47 142.97 2.00 225 69 119 50 142.94 2.01 226 69 123 54 142.88 2.04 227 70 86 16 487.28 1.44 228 70 94 24 480.32 0.68 229 71 82 11 489.15 1.98 230 71 99 28 478.27 0.81 231 72 75 3 691.84 0.73 232 72 76 4 691.84 0.73 233 72 116 44 143.03 1.99 234 72 120 48 143.00 2.00 235 72 123 51 142.94 2.03 236 73 80 7 497.06 0.99 237 73 83 10 490.93 1.14 238 73 120 47 143.01 2.00 239 74 77 3 690.44 0.93 240 74 80 6 497.03 0.98 241 74 99 25 478.03 0.92 242 75 99 24 478.03 0.92 243 75 102 27 477.37 0.78 244 75 103 28 469.73 0.76 245 75 116 41 143.36 1.97 246 76 113 37 280.78 2.27 247 76 120 44 143.29 1.96 248 77 80 3 721.51 0.77 249 78 103 25 477.07 0.51 250 82 99 17 478.02 0.93 251 88 92 4 546.98 19.97 252 97 101 4 674.11 2.48 253 97 102 5 663.23 1.74 254 97 105 8 645.19 6.86 255 98 101 3 678.57 0.27 256 98 102 4 674.01 2.54 257 99 102 3 689.27 4.63 258 99 103 4 674.48 2.76 259 100 103 3 687.22 2.43 260 100 104 4 674.61 2.69 261 101 104 3 679.58 5.18 262 101 105 4 674.64 2.68 263 102 105 3 683.55 4.00 264 102 106 4 672.42 1.56 265 102 112 10 509.71 0.60 266 102 116 14 321.77 87.19 267 103 106 3 676.87 1.50 268 103 107 4 683.69 4.08 269 104 107 3 688.56 2.02 270 104 108 4 672.40 1.56 271 105 108 3 688.19 1.83 272 105 109 4 667.36 0.23 273 105 112 7 604.86 10.63 274 106 109 3 688.19 1.83 275 106 110 4 640.85 7.37 276 106 112 6 593.27 16.43 277 106 113 7 534.76 11.92 278 109 112 3 714.53 5.38 279 110 113 3 700.76 0.24 280 110 114 4 672.02 5.08 281 111 114 3 681.09 9.61 282 111 115 4 670.25 0.45 283 112 115 3 696.98 1.65 284 112 116 4 666.22 2.47 285 113 116 3 680.18 4.51 286 113 117 4 666.22 2.48 287 114 117 3 678.64 3.73 288 114 118 4 667.05 2.06 289 115 118 3 678.91 1.77 290 115 119 4 667.12 2.08 291 116 119 3 693.37 3.48 292 116 120 4 667.12 2.08 293 117 120 3 667.40 1.34 294 117 121 4 664.27 1.47 295 118 121 3 695.66 2.85 296 118 122 4 665.10 1.06 297 119 122 3 682.79 3.59 298 119 123 4 663.12 0.07 299 120 123 3 679.78 5.10 300 120 124 4 673.23 2.75 301 121 124 3 677.18 0.78 302 121 125 4 668.20 5.26 303 122 125 3 674.15 2.29 304 122 126 4 668.21 5.25 305 123 126 3 679.79 5.11 306 123 127 4 668.52 3.03 307 124 127 3 682.30 3.85 308 124 128 4 668.52 3.03 309 125 128 3 683.21 4.30 310 125 129 4 668.31 3.15 311 126 129 3 683.21 4.30 312 126 130 4 668.31 3.15 313 127 130 3 668.87 2.87 314 127 131 4 667.01 2.49 315 128 131 3 684.26 4.88 316 128 132 4 667.48 2.75 317 129 132 3 683.85 4.00 318 129 133 4 667.47 2.75 319 130 133 3 671.00 0.98 320 130 134 4 666.88 2.46 321 130 175 45 104.95 18.20 322 131 134 3 696.57 8.66 323 131 135 4 664.78 3.50 324 132 135 3 687.31 6.23 325 132 136 4 654.64 1.68 326 133 136 3 695.51 2.12 327 133 137 4 645.58 6.21 328 133 142 9 169.80 51.05 329 133 145 12 169.79 51.05 330 134 142 8 408.88 65.56 331 134 176 42 173.91 2.31 332 137 141 4 640.53 0.97 333 137 142 5 637.52 2.48 334 137 145 8 605.00 0.06 335 138 141 3 690.91 1.39 336 138 142 4 670.74 2.37 337 139 142 3 672.88 1.55 338 139 143 4 670.74 2.37 339 139 178 39 257.89 1.48 340 139 182 43 257.80 1.42 341 139 186 47 256.88 0.96 342 140 143 3 675.86 0.04 343 140 144 4 670.95 2.46 344 140 186 46 256.88 0.96 345 140 190 50 256.86 0.95 346 141 144 3 670.96 2.46 347 141 145 4 671.25 2.31 348 142 145 3 689.19 0.74 349 142 146 4 671.25 2.31 350 142 176 34 259.75 1.56 351 142 178 36 259.81 1.55 352 143 146 3 689.19 0.74 353 143 147 4 671.25 2.31 354 143 172 29 259.62 1.51 355 143 176 33 259.95 1.63 356 143 183 40 259.33 1.56 357 143 186 43 258.96 1.39 358 143 187 44 258.74 1.49 359 143 190 47 258.54 1.40 360 144 147 3 683.38 3.73 361 144 148 4 671.78 0.73 362 144 190 46 258.24 1.40 363 145 148 3 677.70 0.89 364 145 149 4 676.54 0.65 365 146 149 3 676.55 0.65 366 146 150 4 675.53 0.14 367 146 175 29 260.19 1.66 368 146 176 30 260.18 1.66 369 147 150 3 695.21 0.44 370 147 151 4 669.42 2.92 371 147 165 18 259.69 1.56 372 147 172 25 260.17 1.66 373 147 187 40 259.55 1.58 374 147 190 43 259.38 1.53 375 147 196 49 258.25 1.40 376 147 203 56 258.56 1.41 377 147 205 58 243.57 1.89 378 148 151 3 691.00 2.06 379 148 152 4 676.38 4.42 380 148 205 57 244.57 1.79 381 149 152 3 683.68 0.79 382 149 153 4 683.67 0.79 383 150 153 3 682.01 5.88 384 150 156 6 420.60 63.87 385 150 165 15 260.20 1.64 386 150 167 17 260.31 1.58 387 150 175 25 261.08 1.49 388 151 156 5 283.81 2.15 389 151 163 12 259.26 1.53 390 151 165 14 260.20 1.62 391 151 205 54 256.26 2.16 392 153 156 3 670.28 0.61 393 156 163 7 261.27 1.50 394 156 164 8 261.18 1.53 395 156 165 9 260.93 1.65 396 157 163 6 261.50 1.59 397 157 164 7 261.04 1.59 398 158 163 5 261.51 1.58 399 159 162 3 672.19 4.38 400 159 163 4 263.43 0.63 401 159 164 5 263.29 0.70 402 159 204 45 260.83 1.59 403 161 206 45 260.82 1.58 404 162 205 43 260.82 1.59 405 162 206 44 260.31 1.53 406 163 204 41 261.27 1.36 407 163 205 42 260.80 1.59 408 164 202 38 261.95 1.54 409 164 203 39 261.41 1.32 410 164 204 40 261.16 1.30 411 165 202 37 262.08 1.60 412 165 203 38 261.65 1.44 413 165 205 40 261.38 1.33 414 166 201 35 262.29 1.52 415 166 202 36 262.08 1.61 416 167 171 4 672.19 1.38 417 167 172 5 672.14 1.35 418 167 201 34 262.37 1.50 419 167 203 36 262.29 1.52 420 168 171 3 672.23 1.38 421 168 172 4 672.22 1.36 422 168 201 33 262.51 1.43 423 169 172 3 672.24 1.37 424 169 173 4 672.24 1.36 425 169 180 11 264.49 1.55 426 169 181 12 264.55 1.54 427 169 183 14 264.28 1.53 428 169 184 15 264.41 1.59 429 169 187 18 264.23 1.51 430 170 173 3 673.59 2.02 431 170 174 4 672.26 1.35 432 170 180 10 264.49 1.55 433 171 174 3 673.60 2.02 434 171 175 4 672.24 1.34 435 172 175 3 676.53 0.77 436 172 176 4 672.23 1.33 437 172 183 11 264.34 1.56 438 172 187 15 264.30 1.55 439 172 203 31 263.64 1.56 440 173 176 3 672.23 1.33 441 173 177 4 640.21 9.12 442 173 178 5 274.71 2.12 443 173 183 10 264.46 1.56 444 178 182 4 665.99 2.19 445 178 183 5 647.81 6.28 446 179 182 3 677.44 3.52 447 179 183 4 649.28 6.16 448 180 183 3 665.99 2.19 449 180 184 4 659.06 1.27 450 181 184 3 677.40 3.29 451 181 185 4 660.94 1.98 452 182 185 3 678.43 2.78 453 182 186 4 660.21 2.33 454 183 186 3 676.14 0.32 455 183 187 4 655.57 4.67 456 184 187 3 676.56 0.52 457 184 188 4 665.01 0.03 458 185 188 3 677.54 1.68 459 185 189 4 672.89 0.65 460 186 189 3 675.21 0.75 461 186 190 4 668.38 2.90 462 187 190 3 678.44 2.13 463 187 191 4 670.12 2.03 464 187 196 9 309.35 8.03 465 187 203 16 268.69 1.03 466 188 191 3 675.05 0.67 467 188 192 4 663.75 1.16 468 189 192 3 677.29 5.62 469 189 193 4 663.72 1.17 470 190 193 3 671.61 2.62 471 190 194 4 671.45 2.69 472 190 195 5 601.44 5.50 473 190 196 6 580.15 16.14 474 191 194 3 659.26 2.80 475 191 196 5 428.71 51.65 476 191 197 6 309.35 8.03 477 191 198 7 309.35 8.03 478 194 206 12 268.79 1.19 479 195 206 11 268.24 0.91 480 196 203 7 269.13 1.23 481 196 204 8 268.94 1.19 482 196 205 9 268.22 0.90 483 196 206 10 268.22 0.90 484 197 203 6 269.12 1.23 485 197 204 7 269.00 1.19 486 197 206 9 268.92 1.18 487 198 202 4 549.41 8.00 488 198 203 5 269.12 1.23 489 199 202 3 656.84 0.67