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 12 4 650.35 3.38 2 8 115 107 176.78 49.65 3 9 12 3 663.88 1.52 4 9 13 4 658.81 0.84 5 10 13 3 658.96 0.78 6 10 14 4 663.70 1.59 7 10 111 101 181.65 48.55 8 10 112 102 179.23 49.53 9 10 115 105 179.24 49.54 10 11 14 3 668.18 0.64 11 11 15 4 663.76 1.56 12 11 41 30 179.71 49.62 13 11 115 104 179.25 49.53 14 12 15 3 668.18 0.64 15 12 16 4 668.18 0.64 16 13 16 3 674.86 2.03 17 13 17 4 671.54 0.53 18 13 105 92 219.73 53.65 19 13 108 95 219.74 53.66 20 13 109 96 219.62 53.60 21 13 112 99 219.58 53.59 22 14 17 3 677.67 3.44 23 14 18 4 670.02 0.28 24 14 41 27 219.62 53.62 25 14 69 55 219.61 53.61 26 14 97 83 220.23 53.54 27 14 102 88 219.86 53.64 28 14 105 91 219.78 53.68 29 14 112 98 219.58 53.60 30 15 18 3 672.28 0.85 31 15 41 26 219.70 53.66 32 15 43 28 219.65 53.63 33 15 95 80 219.74 53.65 34 17 97 80 222.75 53.51 35 17 101 84 222.62 53.50 36 17 105 88 222.02 53.20 37 18 95 77 222.75 53.51 38 18 96 78 222.79 53.49 39 18 97 79 222.79 53.49 40 19 95 76 223.53 53.22 41 19 96 77 223.55 53.23 42 19 97 78 223.49 53.23 43 20 43 23 226.10 52.09 44 20 93 73 226.22 52.05 45 20 94 74 223.59 53.22 46 20 95 75 223.56 53.23 47 21 93 72 227.88 52.85 48 21 94 73 226.16 52.08 49 21 96 75 226.09 52.11 50 22 92 70 326.26 3.75 51 22 93 71 227.92 52.86 52 23 27 4 590.41 23.45 53 23 29 6 491.48 0.67 54 23 91 68 437.10 4.12 55 23 92 69 327.06 4.14 56 23 94 71 326.35 3.81 57 23 96 73 304.74 14.91 58 24 27 3 667.84 4.26 59 24 88 64 456.34 3.08 60 24 91 67 443.16 2.61 61 25 88 63 464.44 0.79 62 25 89 64 458.21 3.22 63 25 90 65 452.87 4.88 64 25 91 66 452.69 4.96 65 26 87 61 466.26 0.68 66 26 88 62 466.13 0.66 67 27 87 60 468.29 1.68 68 27 88 61 466.36 0.71 69 28 31 3 707.52 1.26 70 28 85 57 469.90 2.03 71 28 86 58 469.25 1.97 72 28 87 59 468.30 1.69 73 29 47 18 469.37 2.00 74 29 70 41 466.32 0.75 75 29 86 57 469.59 2.10 76 29 88 59 469.56 2.10 77 29 94 65 466.70 0.90 78 30 40 10 466.68 0.91 79 30 70 40 466.73 0.90 80 30 71 41 466.34 0.73 81 30 82 52 470.31 2.00 82 30 84 54 470.22 2.06 83 30 85 55 470.06 2.04 84 30 86 56 469.88 2.00 85 31 34 3 668.61 2.07 86 31 82 51 470.47 2.00 87 31 85 54 470.17 2.08 88 32 82 50 470.41 2.04 89 32 83 51 470.35 2.02 90 32 84 52 470.26 2.06 91 32 85 53 470.25 2.06 92 33 81 48 471.52 1.98 93 33 82 49 471.38 2.00 94 34 81 47 472.08 1.74 95 34 82 48 472.05 1.72 96 36 74 38 478.11 0.02 97 36 80 44 478.17 0.06 98 36 81 45 478.09 0.09 99 36 82 46 476.33 0.38 100 36 99 63 469.36 2.21 101 37 82 45 478.23 0.04 102 37 98 61 469.41 2.20 103 37 99 62 469.36 2.21 104 38 71 33 484.42 1.44 105 38 82 44 479.51 0.27 106 38 97 59 469.62 2.17 107 38 98 60 469.40 2.19 108 38 99 61 469.38 2.21 109 39 69 30 484.75 1.39 110 39 70 31 484.56 1.42 111 39 71 32 484.42 1.44 112 39 72 33 484.37 1.45 113 39 96 57 469.68 2.18 114 39 97 58 469.63 2.17 115 39 99 60 469.45 2.25 116 39 102 63 465.57 4.04 117 39 116 77 228.99 53.19 118 40 69 29 484.87 1.44 119 40 70 30 484.59 1.44 120 40 82 42 483.68 1.50 121 40 94 54 470.25 2.04 122 40 95 55 470.14 2.02 123 40 96 56 469.75 2.14 124 41 67 26 485.95 1.15 125 41 68 27 485.79 1.12 126 41 69 28 484.88 1.44 127 41 94 53 470.29 2.02 128 41 95 54 470.14 2.02 129 42 45 3 716.61 1.66 130 42 47 5 601.88 10.63 131 42 64 22 486.29 0.97 132 42 65 23 486.25 1.00 133 42 66 24 486.10 1.07 134 42 67 25 485.98 1.13 135 42 68 26 485.85 1.16 136 42 70 28 485.34 1.33 137 42 93 51 470.78 2.00 138 42 94 52 470.30 2.02 139 43 66 23 486.48 1.10 140 43 93 50 470.82 2.00 141 43 94 51 470.79 2.00 142 43 95 52 470.79 2.00 143 44 66 22 486.59 1.14 144 44 92 48 472.63 1.14 145 44 93 49 472.49 1.19 146 45 65 20 486.64 1.15 147 45 66 21 486.64 1.15 148 45 90 45 478.25 0.10 149 45 91 46 478.25 0.10 150 45 92 47 472.68 1.16 151 46 64 18 486.78 1.11 152 46 65 19 486.64 1.15 153 46 88 42 479.09 0.18 154 46 89 43 479.00 0.14 155 46 90 44 478.69 0.13 156 46 92 46 476.10 0.55 157 47 63 16 487.04 1.03 158 47 64 17 486.82 1.08 159 47 70 23 486.54 1.12 160 47 86 39 483.40 1.58 161 47 87 40 479.64 0.23 162 47 88 41 479.01 0.14 163 47 89 42 479.00 0.14 164 47 92 45 478.14 0.15 165 48 62 14 487.18 0.96 166 48 63 15 487.04 1.02 167 48 85 37 484.12 1.58 168 48 86 38 483.69 1.45 169 48 87 39 483.38 1.58 170 48 89 41 479.04 0.14 171 49 60 11 488.39 1.38 172 49 61 12 488.35 1.40 173 49 62 13 487.23 0.98 174 49 64 15 487.10 1.05 175 49 84 35 484.26 1.53 176 49 85 36 484.12 1.58 177 49 86 37 483.76 1.49 178 50 58 8 488.85 1.29 179 50 59 9 488.69 1.30 180 50 60 10 488.41 1.38 181 50 84 34 484.28 1.53 182 50 85 35 484.16 1.56 183 50 87 37 484.13 1.58 184 51 58 7 488.86 1.29 185 51 59 8 488.85 1.29 186 51 61 10 488.48 1.41 187 51 84 33 484.38 1.49 188 51 85 34 484.38 1.48 189 52 57 5 491.11 1.57 190 52 58 6 489.05 1.20 191 52 85 33 484.43 1.47 192 53 56 3 669.86 0.71 193 53 57 4 493.62 2.15 194 58 87 29 484.37 1.48 195 58 174 116 56.97 0.14 196 59 130 71 213.48 48.86 197 59 134 75 201.96 48.73 198 59 174 115 56.91 0.14 199 59 175 116 56.93 0.14 200 59 176 117 56.93 0.14 201 59 177 118 56.94 0.14 202 60 63 3 776.08 6.04 203 60 130 70 213.44 48.84 204 60 171 111 56.80 0.10 205 60 174 114 56.87 0.12 206 60 175 115 56.69 0.10 207 61 84 23 484.33 1.51 208 61 130 69 208.87 51.09 209 63 89 26 479.23 0.03 210 63 171 108 52.95 0.21 211 63 175 112 56.36 0.01 212 64 68 4 633.39 3.19 213 64 69 5 602.54 12.23 214 64 70 6 506.34 3.02 215 64 123 59 227.94 53.27 216 65 68 3 672.99 3.72 217 67 119 52 228.39 53.41 218 68 119 51 228.38 53.41 219 68 123 55 228.34 53.41 220 69 112 43 229.36 53.01 221 69 115 46 228.59 53.37 222 69 116 47 228.47 53.39 223 69 119 50 228.40 53.41 224 69 123 54 228.37 53.40 225 70 86 16 478.86 0.09 226 71 82 11 483.47 1.57 227 71 99 28 469.48 2.25 228 72 75 3 672.69 1.30 229 72 76 4 685.73 5.46 230 72 116 44 228.99 53.19 231 72 120 48 228.55 53.34 232 72 123 51 228.45 53.38 233 73 83 10 483.43 1.58 234 73 120 47 228.83 53.20 235 74 77 3 680.00 4.61 236 74 80 6 485.57 2.30 237 74 99 25 469.41 2.27 238 75 99 24 469.35 2.25 239 75 102 27 468.92 2.41 240 75 103 28 464.61 1.85 241 75 116 41 229.81 52.91 242 76 113 37 303.86 16.02 243 76 120 44 229.75 52.89 244 77 80 3 703.00 2.60 245 78 103 25 467.27 1.30 246 82 99 17 469.37 2.21 247 88 92 4 642.64 6.20 248 97 101 4 663.07 0.83 249 97 102 5 651.57 4.92 250 97 105 8 645.25 2.60 251 98 101 3 675.69 3.59 252 98 102 4 662.81 0.70 253 99 102 3 669.38 0.54 254 99 103 4 662.83 0.70 255 100 103 3 671.27 3.27 256 100 104 4 662.92 0.66 257 101 104 3 662.93 0.66 258 101 105 4 662.92 0.66 259 102 105 3 668.36 0.01 260 102 106 4 662.64 0.80 261 102 112 10 230.69 52.59 262 102 116 14 229.87 52.94 263 103 106 3 664.70 1.83 264 103 107 4 664.74 1.84 265 104 107 3 668.88 0.23 266 104 108 4 662.58 0.77 267 105 108 3 661.02 1.51 268 105 109 4 652.77 2.54 269 106 109 3 667.31 3.08 270 106 110 4 628.46 10.77 271 106 112 6 592.63 7.89 272 106 113 7 519.31 6.84 273 109 112 3 694.93 0.70 274 110 113 3 681.52 0.83 275 110 114 4 668.34 2.36 276 111 114 3 670.76 1.15 277 111 115 4 664.22 4.42 278 112 115 3 668.90 4.64 279 112 116 4 651.66 0.95 280 113 116 3 661.78 1.40 281 113 117 4 654.37 2.29 282 114 117 3 674.34 2.95 283 114 118 4 662.88 0.48 284 115 118 3 673.86 4.38 285 115 119 4 662.90 0.48 286 116 119 3 670.83 4.45 287 116 120 4 661.43 1.24 288 117 120 3 661.47 1.22 289 117 121 4 661.34 1.29 290 118 121 3 661.49 1.23 291 118 122 4 661.29 1.31 292 119 122 3 669.10 1.81 293 119 123 4 655.32 4.29 294 120 123 3 664.08 2.62 295 120 124 4 656.32 1.56 296 121 124 3 669.09 1.81 297 121 125 4 662.47 1.51 298 122 125 3 669.08 1.81 299 122 126 4 656.32 1.56 300 123 126 3 660.07 0.53 301 123 127 4 655.16 2.27 302 124 127 3 674.62 5.44 303 124 128 4 657.62 1.04 304 125 128 3 667.24 1.07 305 125 129 4 660.27 0.77 306 126 129 3 665.59 1.90 307 126 130 4 660.83 0.48 308 127 130 3 657.70 1.07 309 127 131 4 659.21 0.32 310 128 131 3 664.53 2.35 311 128 132 4 659.11 3.02 312 129 132 3 661.89 1.62 313 129 133 4 657.15 2.02 314 130 133 3 664.07 2.71 315 130 134 4 656.13 1.49 316 130 175 45 91.93 17.32 317 131 134 3 679.20 4.85 318 131 135 4 656.12 1.49 319 132 135 3 668.19 1.65 320 132 136 4 655.68 1.26 321 133 136 3 665.55 1.30 322 133 137 4 650.22 3.98 323 133 142 9 147.65 10.67 324 134 142 8 225.58 24.87 325 134 176 42 161.83 48.33 326 137 141 4 641.13 10.58 327 137 142 5 641.13 10.57 328 138 141 3 667.23 5.04 329 138 142 4 658.83 3.87 330 139 142 3 668.69 4.32 331 139 143 4 658.83 3.87 332 139 176 37 196.34 33.27 333 139 178 39 196.24 33.30 334 139 182 43 196.14 33.34 335 139 186 47 195.90 33.26 336 140 143 3 670.73 3.51 337 140 144 4 658.84 3.85 338 140 186 46 195.86 33.24 339 140 189 49 195.79 33.27 340 140 190 50 195.71 33.30 341 141 144 3 665.12 0.71 342 141 145 4 658.84 3.85 343 142 145 3 665.95 1.12 344 142 146 4 656.01 5.25 345 142 176 34 196.47 33.26 346 142 177 35 196.69 33.35 347 143 146 3 662.65 1.90 348 143 147 4 663.76 1.34 349 143 172 29 196.50 33.25 350 143 176 33 196.73 33.37 351 143 178 35 196.71 33.36 352 143 183 40 196.19 33.29 353 143 186 43 196.03 33.31 354 143 187 44 196.00 33.30 355 143 190 47 195.88 33.32 356 144 147 3 679.73 1.23 357 144 148 4 679.73 1.23 358 144 190 46 195.83 33.30 359 145 148 3 674.33 3.93 360 145 149 4 674.32 3.93 361 146 149 3 674.29 3.95 362 146 150 4 674.32 3.94 363 146 172 26 196.75 33.33 364 146 175 29 196.79 33.35 365 146 176 30 196.78 33.35 366 147 150 3 682.37 0.07 367 147 151 4 663.94 1.25 368 147 165 18 197.21 33.19 369 147 172 25 196.79 33.35 370 147 187 40 196.16 33.27 371 147 190 43 196.16 33.26 372 147 196 49 189.97 31.76 373 147 203 56 187.20 32.10 374 147 205 58 171.93 30.37 375 148 151 3 670.47 1.61 376 148 205 57 172.29 30.52 377 149 152 3 685.48 4.25 378 149 153 4 664.40 1.45 379 150 153 3 664.40 1.45 380 150 156 6 526.86 13.32 381 150 165 15 206.84 28.41 382 150 167 17 197.18 33.20 383 150 172 22 197.08 33.24 384 151 156 5 526.87 13.32 385 151 163 12 206.83 28.38 386 151 165 14 206.83 28.41 387 151 205 54 172.74 30.74 388 152 156 4 568.31 8.53 389 153 156 3 659.86 3.48 390 156 163 7 342.95 79.42 391 156 164 8 217.25 23.42 392 156 165 9 212.19 25.75 393 157 163 6 343.00 79.41 394 157 164 7 217.26 23.43 395 158 162 4 590.69 7.63 396 158 163 5 343.01 79.41 397 159 162 3 611.44 2.75 398 159 163 4 527.62 12.89 399 159 164 5 527.62 12.89 400 159 204 45 189.41 31.70 401 161 204 43 189.46 31.69 402 161 206 45 189.26 31.70 403 162 205 43 189.28 31.70 404 163 204 41 189.31 31.68 405 163 205 42 189.22 31.70 406 164 202 38 189.32 31.68 407 164 203 39 189.28 31.69 408 164 204 40 189.21 31.70 409 165 202 37 189.29 31.69 410 165 203 38 189.24 31.69 411 166 201 35 189.31 31.68 412 167 171 4 660.74 3.06 413 167 172 5 652.41 7.23 414 167 175 8 627.50 5.03 415 167 201 34 189.28 31.67 416 167 203 36 189.26 31.68 417 168 171 3 670.12 1.10 418 168 172 4 663.86 1.54 419 168 201 33 189.28 31.68 420 169 172 3 669.87 1.47 421 169 173 4 667.38 0.23 422 169 180 11 203.97 30.75 423 169 183 14 200.91 32.28 424 169 184 15 200.90 32.28 425 169 187 18 200.89 32.27 426 169 201 32 189.28 31.67 427 170 173 3 669.22 0.69 428 170 174 4 667.38 0.23 429 170 180 10 203.97 30.76 430 171 174 3 667.38 0.23 431 171 175 4 667.38 0.23 432 172 175 3 667.36 0.24 433 172 176 4 667.36 0.24 434 172 183 11 203.96 30.75 435 173 176 3 664.25 1.31 436 173 177 4 614.34 0.04 437 173 178 5 422.21 53.38 438 173 183 10 203.97 30.75 439 178 182 4 645.90 8.83 440 178 183 5 644.47 1.69 441 179 182 3 661.46 3.18 442 179 183 4 661.81 0.90 443 180 183 3 663.93 1.95 444 180 184 4 661.81 0.89 445 181 184 3 664.88 2.00 446 181 185 4 661.80 0.89 447 182 185 3 661.79 0.89 448 182 186 4 661.77 0.88 449 183 186 3 668.97 2.72 450 183 187 4 648.18 3.14 451 184 187 3 662.01 0.82 452 184 188 4 657.45 1.46 453 185 188 3 669.73 1.14 454 185 189 4 657.44 1.46 455 186 189 3 663.25 4.38 456 186 190 4 658.69 0.83 457 187 190 3 662.46 0.06 458 187 191 4 658.69 0.83 459 187 196 9 230.49 19.03 460 187 203 16 182.96 30.57 461 188 191 3 658.83 0.75 462 188 192 4 658.68 0.82 463 189 192 3 651.81 2.78 464 189 193 4 651.63 2.69 465 190 193 3 656.16 0.39 466 190 194 4 647.04 4.94 467 190 195 5 572.31 1.88 468 190 196 6 546.71 14.59 469 191 194 3 649.29 0.32 470 191 196 5 511.66 2.19 471 191 197 6 349.80 78.73 472 191 198 7 230.44 19.05 473 194 206 12 172.51 30.61 474 195 205 10 172.89 30.78 475 195 206 11 172.35 30.54 476 196 203 7 195.82 27.80 477 196 204 8 179.27 31.55 478 196 205 9 172.88 30.77 479 196 206 10 172.30 30.51 480 197 203 6 192.87 26.32 481 197 204 7 179.43 31.48 482 197 206 9 179.42 31.48 483 198 203 5 194.16 26.96 484 199 202 3 691.61 1.71