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 18 112 94 34.17 0.41 2 18 113 95 34.07 0.39 3 18 114 96 33.97 0.39 4 19 112 93 34.19 0.41 5 19 113 94 34.20 0.41 6 19 115 96 34.36 0.40 7 20 111 91 34.24 0.40 8 20 112 92 34.22 0.41 9 21 111 90 34.29 0.38 10 21 113 92 34.34 0.39 11 22 25 3 667.75 3.58 12 22 26 4 654.05 1.28 13 23 26 3 664.74 2.04 14 23 27 4 654.12 1.30 15 23 82 59 64.00 0.61 16 23 83 60 66.00 0.38 17 23 105 82 63.16 0.23 18 23 108 85 53.76 0.01 19 24 27 3 671.00 0.83 20 24 28 4 656.11 2.29 21 25 28 3 673.75 0.54 22 25 29 4 659.96 0.36 23 26 29 3 679.88 1.53 24 26 34 8 321.36 69.86 25 26 121 95 61.52 1.39 26 26 123 97 65.99 0.39 27 27 34 7 321.36 69.87 28 27 77 50 133.20 26.05 29 27 82 55 73.82 0.45 30 29 32 3 726.84 0.63 31 32 114 82 443.63 0.62 32 32 115 83 443.63 0.62 33 32 119 87 443.59 0.63 34 32 120 88 443.58 0.62 35 32 121 89 443.15 0.48 36 33 74 41 459.09 8.34 37 33 119 86 443.63 0.62 38 33 120 87 443.61 0.62 39 33 121 88 443.59 0.62 40 34 74 40 459.10 8.34 41 34 75 41 459.04 8.32 42 34 77 43 459.04 8.31 43 34 121 87 443.61 0.62 44 34 123 89 443.59 0.62 45 35 73 38 459.12 8.35 46 35 74 39 459.10 8.34 47 35 75 40 459.10 8.34 48 35 120 85 443.67 0.62 49 35 121 86 443.63 0.62 50 35 122 87 443.61 0.63 51 35 123 88 443.60 0.62 52 36 72 36 459.24 8.30 53 36 73 37 459.22 8.30 54 36 75 39 459.18 8.30 55 36 82 46 459.00 8.29 56 36 86 50 458.92 8.26 57 36 123 87 443.61 0.63 58 36 125 89 443.59 0.62 59 37 70 33 459.59 8.45 60 37 71 34 459.51 8.45 61 37 72 35 459.24 8.30 62 37 73 36 459.25 8.29 63 37 86 49 458.98 8.28 64 37 122 85 443.69 0.64 65 37 123 86 443.64 0.62 66 37 124 87 443.61 0.63 67 37 125 88 443.60 0.63 68 38 70 32 459.66 8.45 69 38 71 33 459.60 8.45 70 38 86 48 459.12 8.24 71 38 90 52 459.07 8.21 72 38 125 87 443.61 0.63 73 39 58 19 460.74 8.77 74 39 59 20 460.40 8.62 75 39 70 31 459.69 8.44 76 39 124 85 443.69 0.64 77 39 125 86 443.63 0.62 78 39 126 87 443.59 0.62 79 39 127 88 443.59 0.62 80 39 188 149 164.16 0.23 81 39 192 153 152.99 0.20 82 40 58 18 460.75 8.77 83 40 59 19 460.55 8.70 84 40 94 54 458.87 8.02 85 40 98 58 456.19 6.75 86 40 127 87 443.61 0.62 87 40 129 89 443.51 0.65 88 40 134 94 346.07 0.69 89 40 137 97 322.49 0.82 90 41 56 15 464.69 9.37 91 41 57 16 464.26 9.38 92 41 58 17 460.75 8.77 93 41 126 85 443.68 0.64 94 41 127 86 443.63 0.62 95 41 128 87 443.60 0.62 96 41 129 88 443.57 0.64 97 41 134 93 346.39 0.71 98 41 192 151 156.74 0.27 99 42 56 14 464.70 9.37 100 42 57 15 464.45 9.36 101 42 128 86 443.62 0.62 102 42 129 87 443.60 0.62 103 42 130 88 443.56 0.63 104 42 131 89 406.43 0.03 105 42 134 92 346.43 0.71 106 43 55 12 464.77 9.39 107 43 56 13 464.70 9.37 108 43 128 85 443.68 0.64 109 43 129 86 443.65 0.63 110 43 131 88 443.04 0.88 111 44 54 10 466.80 10.32 112 44 55 11 464.78 9.39 113 44 56 12 464.77 9.39 114 44 57 13 464.73 9.38 115 44 131 87 443.56 0.63 116 46 53 7 476.56 5.75 117 46 54 8 475.41 6.27 118 47 50 3 640.16 3.60 119 47 51 4 608.69 4.33 120 47 52 5 495.44 4.04 121 47 53 6 476.56 5.75 122 47 54 7 476.56 5.75 123 48 51 3 666.52 1.19 124 48 52 4 579.20 10.42 125 48 54 6 481.38 3.54 126 48 160 112 293.14 0.11 127 48 162 114 292.54 0.05 128 51 163 112 292.76 0.17 129 52 160 108 292.77 0.17 130 53 160 107 292.58 0.07 131 54 57 3 719.24 7.30 132 54 159 105 292.58 0.07 133 54 160 106 292.42 0.01 134 55 159 104 292.55 0.06 135 55 194 139 161.89 0.35 136 55 195 140 162.91 0.09 137 56 128 72 443.70 0.63 138 56 159 103 291.62 0.29 139 56 192 136 164.25 0.21 140 56 194 138 156.57 1.81 141 57 134 77 346.41 0.71 142 57 156 99 292.61 0.08 143 58 156 98 292.56 0.07 144 58 157 99 291.72 0.24 145 58 159 101 290.75 0.22 146 58 185 127 167.49 0.12 147 58 189 131 165.73 0.09 148 58 194 136 154.24 0.83 149 59 70 11 469.73 5.66 150 59 134 75 346.09 0.70 151 59 137 78 322.36 0.66 152 59 138 79 317.56 1.62 153 59 154 95 293.11 0.14 154 59 155 96 292.61 0.06 155 59 156 97 291.74 0.24 156 60 69 9 472.60 4.25 157 60 70 10 469.73 5.66 158 60 71 11 469.72 5.66 159 60 154 94 293.02 0.17 160 60 155 95 292.91 0.21 161 60 157 97 290.81 0.51 162 60 172 112 172.58 0.19 163 60 177 117 171.22 0.17 164 60 181 121 169.91 0.32 165 60 185 125 167.07 0.26 166 61 68 7 488.88 0.98 167 61 69 8 484.01 1.39 168 61 71 10 469.75 5.67 169 61 93 32 461.29 6.95 170 61 94 33 461.18 6.91 171 61 151 90 293.60 0.25 172 61 153 92 293.31 0.22 173 61 154 93 293.04 0.17 174 61 155 94 292.93 0.21 175 62 66 4 628.54 10.99 176 62 67 5 518.47 4.69 177 62 68 6 497.90 5.47 178 62 151 89 293.60 0.25 179 62 152 90 293.42 0.19 180 62 153 91 293.34 0.21 181 63 66 3 655.13 2.31 182 63 67 4 555.39 13.76 183 63 68 5 518.45 4.71 184 63 69 6 501.11 3.93 185 63 150 87 293.70 0.29 186 63 152 89 293.43 0.20 187 63 178 115 171.22 0.18 188 64 149 85 293.77 0.31 189 64 150 86 293.71 0.30 190 64 152 88 293.57 0.27 191 65 178 113 171.25 0.18 192 67 176 109 171.25 0.18 193 67 177 110 171.21 0.18 194 67 178 111 171.10 0.21 195 68 155 87 293.01 0.17 196 68 172 104 171.53 0.26 197 68 175 107 171.30 0.18 198 68 176 108 171.25 0.18 199 68 177 109 171.05 0.21 200 68 178 110 170.91 0.27 201 68 181 113 169.51 0.59 202 69 178 109 168.55 0.33 203 69 181 112 167.39 0.14 204 70 124 54 443.63 0.62 205 70 181 111 166.79 0.17 206 70 184 114 167.03 0.24 207 70 185 115 166.26 0.09 208 71 90 19 462.82 6.32 209 71 93 22 462.56 6.18 210 71 94 23 462.56 6.18 211 72 86 14 462.87 6.33 212 72 89 17 462.83 6.30 213 72 90 18 462.81 6.31 214 72 93 21 462.59 6.16 215 73 89 16 462.86 6.29 216 74 89 15 462.88 6.27 217 74 120 46 443.73 0.61 218 75 82 7 463.10 6.23 219 75 85 10 462.95 6.25 220 75 86 11 462.95 6.25 221 76 79 3 668.71 1.46 222 76 80 4 625.70 3.19 223 80 84 4 627.09 4.52 224 81 84 3 654.00 0.97 225 81 85 4 643.10 3.27 226 82 85 3 660.06 0.78 227 82 86 4 651.50 2.22 228 82 123 41 443.70 0.62 229 82 125 43 443.65 0.65 230 83 86 3 665.93 2.69 231 83 87 4 654.54 0.70 232 83 103 20 444.48 0.27 233 83 104 21 444.45 0.26 234 83 105 22 444.44 0.26 235 83 125 42 443.65 0.61 236 84 87 3 661.72 1.61 237 84 88 4 657.57 0.46 238 85 88 3 666.15 1.11 239 85 89 4 655.82 1.33 240 86 89 3 660.30 1.81 241 86 90 4 654.09 0.51 242 86 103 17 444.46 0.26 243 86 125 39 443.63 0.62 244 87 90 3 669.13 2.60 245 87 91 4 659.99 2.45 246 88 91 3 664.44 0.26 247 88 92 4 658.35 3.31 248 89 92 3 666.68 3.92 249 89 93 4 655.58 4.69 250 90 93 3 666.67 3.93 251 90 94 4 653.25 5.79 252 90 98 8 565.69 6.20 253 90 103 13 447.93 1.46 254 91 94 3 666.67 3.93 255 91 95 4 629.36 4.63 256 91 96 5 581.64 5.88 257 91 98 7 531.90 11.01 258 91 99 8 497.93 5.19 259 92 144 52 293.88 0.38 260 92 145 53 293.81 0.35 261 92 146 54 293.76 0.34 262 93 144 51 293.92 0.37 263 93 146 53 293.76 0.33 264 93 151 58 293.51 0.24 265 94 98 4 654.41 1.51 266 94 137 43 300.77 1.94 267 94 140 46 294.83 0.24 268 94 141 47 294.05 0.46 269 94 144 50 293.92 0.37 270 94 154 60 293.23 0.15 271 95 98 3 690.31 1.54 272 95 144 49 293.89 0.38 273 96 99 3 673.65 1.08 274 96 140 44 294.87 0.25 275 97 100 3 684.74 1.85 276 97 101 4 654.46 1.50 277 97 137 40 304.59 3.79 278 97 140 43 294.97 0.19 279 98 101 3 669.72 5.66 280 98 137 39 305.11 3.54 281 101 127 26 443.69 0.62 282 101 129 28 443.45 0.66 283 102 127 25 443.68 0.61 284 103 107 4 648.51 1.17 285 103 125 22 443.72 0.62 286 103 127 24 443.56 0.64 287 104 107 3 685.41 3.49 288 104 108 4 659.21 2.76 289 104 125 21 443.75 0.64 290 105 108 3 660.93 1.90 291 106 109 3 795.73 1.11 292 107 125 18 443.75 0.64 293 107 126 19 443.74 0.65 294 107 127 20 443.63 0.65 295 108 123 15 443.88 0.64 296 108 125 17 443.75 0.64 297 109 124 15 443.87 0.64 298 109 125 16 443.81 0.65 299 109 126 17 443.81 0.65 300 109 187 78 164.81 0.20 301 110 123 13 443.93 0.64 302 110 124 14 443.87 0.65 303 111 121 10 444.09 0.63 304 111 122 11 443.97 0.64 305 111 123 12 443.93 0.64 306 112 121 9 444.10 0.63 307 112 122 10 444.00 0.65 308 112 180 68 166.56 0.16 309 113 120 7 444.18 0.65 310 113 121 8 444.10 0.62 311 114 119 5 444.27 0.61 312 114 120 6 444.24 0.62 313 114 179 65 166.54 0.18 314 114 180 66 166.54 0.18 315 115 118 3 646.04 0.54 316 115 119 4 444.27 0.61 317 122 180 58 166.59 0.18 318 122 184 62 166.13 0.05 319 124 184 60 166.22 0.10 320 124 187 63 164.43 0.12 321 124 188 64 163.22 0.20 322 126 187 61 165.84 0.05 323 126 188 62 163.49 0.11 324 126 191 65 154.47 0.71 325 126 192 66 148.54 0.06 326 129 133 4 650.40 0.50 327 129 134 5 644.27 2.56 328 129 137 8 629.52 0.92 329 130 133 3 656.38 2.48 330 130 134 4 656.37 2.48 331 131 134 3 656.37 2.48 332 131 135 4 656.36 2.48 333 132 135 3 668.76 3.73 334 132 136 4 649.79 0.18 335 133 136 3 668.76 3.73 336 133 137 4 655.75 2.77 337 134 137 3 657.60 1.85 338 134 138 4 646.46 1.88 339 135 138 3 651.57 0.67 340 135 139 4 649.06 0.58 341 135 156 21 293.50 0.29 342 136 139 3 649.24 0.48 343 136 140 4 646.76 0.75 344 137 140 3 656.14 0.24 345 137 141 4 640.37 2.45 346 137 154 17 293.53 0.27 347 138 141 3 653.62 1.02 348 138 154 16 293.54 0.27 349 138 156 18 293.49 0.28 350 139 142 3 694.72 1.21 351 140 143 3 670.54 2.38 352 140 144 4 643.51 0.89 353 141 144 3 651.45 3.08 354 141 147 6 546.30 1.92 355 141 154 13 293.52 0.27 356 142 147 5 543.26 0.42 357 144 147 3 648.69 3.45 358 145 149 4 667.45 1.38 359 145 150 5 646.81 0.90 360 146 149 3 665.49 2.02 361 146 150 4 637.51 5.53 362 146 151 5 615.82 16.29 363 147 151 4 630.35 9.03 364 148 151 3 663.44 2.60 365 148 152 4 634.41 7.00 366 149 152 3 688.81 0.93 367 151 154 3 743.17 1.71 368 155 172 17 173.20 0.21 369 157 169 12 173.38 0.26 370 157 172 15 173.16 0.23 371 157 185 28 168.50 0.36 372 158 168 10 173.36 0.27 373 158 169 11 173.38 0.26 374 158 172 14 173.33 0.27 375 159 169 10 173.38 0.24 376 159 189 30 167.15 0.12 377 159 194 35 154.80 1.08 378 160 168 8 173.71 0.12 379 160 169 9 173.41 0.25 380 161 165 4 567.94 1.71 381 161 166 5 525.00 5.56 382 161 167 6 335.66 80.75 383 161 170 9 173.75 0.13 384 161 203 42 105.18 1.66 385 162 165 3 647.41 4.16 386 162 167 5 505.53 4.17 387 162 168 6 505.51 4.17 388 164 167 3 691.00 1.28 389 165 170 5 602.73 0.41 390 165 206 41 101.80 0.29 391 166 170 4 602.57 0.33 392 166 171 5 603.26 0.69 393 166 206 40 99.95 0.04 394 167 171 4 641.75 0.25 395 168 171 3 669.45 3.69 396 168 172 4 650.13 3.54 397 169 172 3 650.15 3.54 398 169 173 4 650.71 3.27 399 169 189 20 168.10 0.32 400 169 195 26 154.25 0.82 401 169 203 34 100.44 0.26 402 170 173 3 653.12 2.06 403 170 174 4 656.30 3.66 404 170 203 33 99.98 0.03 405 170 206 36 99.86 0.01 406 170 207 37 93.09 1.03 407 171 174 3 662.46 0.58 408 172 175 3 678.67 3.90 409 172 177 5 666.21 1.30 410 172 185 13 170.44 0.28 411 173 177 4 680.72 5.96 412 173 182 9 170.44 0.29 413 173 185 12 170.41 0.29 414 173 186 13 170.37 0.28 415 173 203 30 99.98 0.03 416 173 204 31 99.94 0.04 417 173 207 34 91.44 1.72 418 174 207 33 91.39 1.71 419 177 181 4 600.52 6.84 420 177 182 5 567.36 4.75 421 178 181 3 669.27 1.35 422 180 183 3 655.46 5.25 423 180 184 4 642.93 0.34 424 181 184 3 652.96 5.34 425 181 185 4 643.83 0.11 426 182 185 3 648.35 2.10 427 182 186 4 647.58 0.35 428 182 204 22 99.92 0.04 429 183 186 3 649.71 1.42 430 183 187 4 647.58 0.35 431 184 187 3 659.90 6.52 432 184 188 4 647.58 0.35 433 185 188 3 651.84 1.78 434 185 189 4 648.49 0.10 435 186 189 3 653.99 0.70 436 186 190 4 648.49 0.10 437 186 200 14 100.00 0.08 438 186 204 18 99.92 0.04 439 187 190 3 658.47 1.56 440 187 191 4 642.88 3.06 441 188 191 3 654.01 0.68 442 188 192 4 633.90 5.46 443 189 193 4 627.28 8.70 444 189 194 5 549.79 12.56 445 189 195 6 520.90 1.88 446 189 200 11 518.12 3.21 447 190 193 3 657.81 2.60 448 190 195 5 549.78 12.56 449 190 196 6 518.35 3.14 450 190 197 7 518.34 3.14 451 190 200 10 494.86 8.54 452 195 199 4 622.05 10.87 453 195 200 5 622.16 10.80 454 195 203 8 585.58 1.52 455 196 199 3 643.85 5.75 456 196 200 4 643.49 1.91 457 197 200 3 651.63 1.85 458 197 201 4 645.88 1.02 459 198 201 3 651.63 1.85 460 198 202 4 651.49 1.79 461 199 202 3 656.28 1.43 462 199 203 4 651.56 1.76 463 200 203 3 651.77 1.65 464 200 204 4 647.79 0.12 465 201 204 3 653.73 0.67 466 201 205 4 647.79 0.12 467 202 205 3 647.81 0.12 468 202 206 4 641.00 2.04 469 203 206 3 651.57 1.77 470 203 207 4 641.07 2.08 471 204 207 3 647.94 5.51 472 204 208 4 647.94 5.50 473 205 208 3 653.81 2.57 474 205 209 4 647.95 5.50 475 206 209 3 651.81 1.57