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 90 72 66.27 1.11 2 18 91 73 67.56 1.70 3 18 101 83 66.28 1.11 4 18 191 173 68.11 1.95 5 19 22 3 738.21 1.45 6 19 188 169 68.21 1.97 7 19 191 172 68.17 1.97 8 20 188 168 68.22 1.95 9 20 189 169 68.20 1.96 10 20 190 170 68.17 1.97 11 20 191 171 68.17 1.97 12 21 187 166 68.64 2.02 13 22 27 5 602.87 8.11 14 22 28 6 582.37 1.77 15 22 31 9 566.17 1.04 16 22 187 165 69.02 1.96 17 22 188 166 68.91 1.90 18 23 167 144 101.45 1.06 19 24 27 3 673.76 4.10 20 24 28 4 657.39 1.99 21 25 28 3 660.87 0.24 22 25 29 4 651.04 4.46 23 25 162 137 107.09 0.66 24 25 163 138 117.97 1.44 25 25 164 139 122.36 0.21 26 25 166 141 114.23 0.62 27 25 167 142 106.69 0.20 28 26 29 3 660.87 0.24 29 26 30 4 651.04 4.46 30 27 30 3 660.93 0.27 31 27 31 4 656.76 1.59 32 28 31 3 668.43 1.70 33 28 32 4 656.75 1.58 34 28 162 134 123.15 0.54 35 28 167 139 123.05 0.56 36 28 185 157 117.97 1.43 37 28 186 158 122.36 0.38 38 28 187 159 117.98 1.43 39 28 188 160 115.13 0.02 40 29 32 3 671.28 2.85 41 29 33 4 645.54 5.53 42 29 156 127 123.17 0.54 43 29 161 132 123.19 0.54 44 29 162 133 123.16 0.54 45 30 33 3 668.01 1.90 46 30 34 4 644.98 5.82 47 31 34 3 660.45 0.18 48 31 88 57 123.23 0.58 49 31 90 59 123.22 0.58 50 31 149 118 123.25 0.57 51 31 188 157 123.23 0.56 52 32 148 116 123.25 0.57 53 32 149 117 123.25 0.57 54 32 152 120 123.26 0.57 55 32 153 121 123.27 0.58 56 32 156 124 123.76 0.48 57 32 162 130 123.83 0.50 58 32 188 156 123.48 0.64 59 32 189 157 123.31 0.58 60 33 153 120 123.51 0.58 61 33 156 123 123.81 0.50 62 34 88 54 124.67 0.71 63 34 149 115 123.95 0.43 64 34 153 119 123.97 0.42 65 36 86 50 125.32 0.41 66 36 87 51 125.32 0.41 67 36 88 52 125.29 0.42 68 36 149 113 124.34 0.55 69 37 86 49 125.34 0.42 70 37 87 50 125.35 0.42 71 38 85 47 125.60 0.41 72 38 86 48 125.55 0.42 73 38 139 101 114.11 1.64 74 38 150 112 125.55 0.42 75 39 42 3 713.52 2.17 76 39 57 18 127.03 0.64 77 39 59 20 127.03 0.64 78 39 64 25 127.01 0.64 79 39 84 45 125.61 0.41 80 39 85 46 125.61 0.41 81 39 87 48 125.78 0.48 82 40 84 44 125.62 0.41 83 41 82 41 125.96 0.53 84 41 83 42 125.95 0.53 85 42 80 38 128.78 1.62 86 42 82 40 126.53 0.77 87 42 83 41 126.52 0.77 88 42 85 43 126.59 0.80 89 43 80 37 131.31 0.36 90 43 81 38 131.33 0.37 91 43 82 39 128.78 1.62 92 44 55 11 131.72 0.15 93 44 79 35 133.72 0.03 94 44 80 36 133.03 0.12 95 45 55 10 133.71 0.03 96 45 79 34 133.75 0.04 97 46 54 8 133.76 0.04 98 46 55 9 133.71 0.03 99 46 68 22 133.74 0.02 100 46 76 30 133.94 0.04 101 46 77 31 133.96 0.04 102 46 79 33 133.96 0.04 103 47 53 6 139.62 2.79 104 47 54 7 133.95 0.04 105 47 56 9 134.31 0.18 106 48 52 4 611.52 1.54 107 49 52 3 640.52 0.32 108 49 54 5 582.94 11.58 109 49 56 7 535.64 2.19 110 49 65 16 137.68 0.33 111 49 67 18 134.57 0.21 112 52 67 15 139.50 0.24 113 52 69 17 139.13 0.30 114 53 67 14 139.52 0.24 115 53 68 15 139.50 0.24 116 53 73 20 139.48 0.23 117 54 65 11 142.63 0.96 118 54 66 12 140.79 0.40 119 54 67 13 139.63 0.21 120 55 65 10 142.64 0.96 121 55 66 11 142.47 0.96 122 55 68 13 142.46 0.96 123 55 80 25 142.63 0.97 124 56 64 8 142.73 0.96 125 56 65 9 142.66 0.96 126 56 97 41 143.00 0.86 127 57 63 6 541.88 8.86 128 57 64 7 142.91 0.88 129 57 66 9 142.89 0.88 130 57 85 28 142.76 0.96 131 58 61 3 698.38 2.94 132 58 62 4 642.66 3.16 133 58 63 5 388.03 85.78 134 59 62 3 705.17 1.09 135 59 64 5 638.12 1.26 136 62 92 30 216.96 0.83 137 62 98 36 216.91 0.84 138 63 97 34 216.99 0.84 139 63 98 35 216.99 0.81 140 64 87 23 216.36 0.76 141 64 98 34 217.02 0.83 142 65 97 32 217.11 0.85 143 65 98 33 217.09 0.84 144 65 99 34 217.06 0.84 145 65 100 35 217.06 0.84 146 66 80 14 217.21 0.84 147 66 85 19 217.13 0.86 148 66 100 34 217.08 0.85 149 66 101 35 217.09 0.84 150 66 102 36 217.08 0.85 151 66 104 38 217.11 0.84 152 67 99 32 217.18 0.84 153 67 100 33 217.15 0.84 154 67 101 34 217.09 0.84 155 67 102 35 217.09 0.84 156 68 72 4 635.70 0.25 157 68 73 5 560.28 0.29 158 68 76 8 371.78 78.03 159 68 80 12 217.40 0.85 160 68 104 36 217.18 0.84 161 69 72 3 697.26 3.46 162 69 101 32 217.19 0.84 163 69 191 122 217.12 0.83 164 69 192 123 217.11 0.83 165 70 73 3 676.49 1.60 166 70 192 122 217.13 0.83 167 71 74 3 681.30 0.41 168 71 75 4 657.86 3.02 169 71 196 125 217.15 0.84 170 72 75 3 661.95 0.98 171 72 76 4 636.82 0.04 172 72 102 30 217.22 0.85 173 72 195 123 217.13 0.82 174 73 77 4 629.39 3.33 175 74 77 3 658.35 1.43 176 76 79 3 660.58 5.69 177 76 80 4 642.63 3.29 178 76 83 7 598.46 3.50 179 76 104 28 217.41 0.88 180 80 83 3 688.03 2.54 181 80 85 5 666.98 2.09 182 80 104 24 243.60 0.81 183 82 107 25 285.57 1.07 184 83 104 21 285.65 1.03 185 83 105 22 285.63 1.03 186 83 106 23 285.56 1.07 187 83 107 24 285.57 1.07 188 84 104 20 285.67 1.02 189 84 105 21 285.67 1.02 190 84 109 25 285.62 1.04 191 85 103 18 285.66 1.02 192 85 104 19 285.68 1.02 193 86 103 17 285.68 1.02 194 86 145 59 285.57 1.07 195 86 146 60 285.56 1.07 196 86 149 63 285.56 1.08 197 86 150 64 285.56 1.07 198 87 98 11 285.93 0.99 199 87 100 13 285.75 1.03 200 88 100 12 285.77 1.02 201 88 145 57 285.73 1.03 202 88 149 61 285.59 1.07 203 89 92 3 755.09 6.70 204 89 98 9 285.93 0.99 205 89 99 10 285.93 1.00 206 90 99 9 285.97 0.98 207 90 101 11 285.89 1.00 208 90 188 98 285.71 1.03 209 90 191 101 285.85 1.00 210 91 98 7 286.05 1.00 211 91 99 8 286.00 0.99 212 92 96 4 619.72 9.46 213 92 97 5 417.92 66.75 214 92 98 6 286.05 1.00 215 93 96 3 664.58 0.86 216 93 97 4 592.56 19.38 217 100 145 45 292.52 0.13 218 101 145 44 292.52 0.13 219 101 191 90 292.35 0.06 220 101 194 93 292.53 0.13 221 102 145 43 292.55 0.12 222 102 194 92 292.54 0.12 223 102 195 93 292.56 0.13 224 103 143 40 292.57 0.14 225 103 145 42 292.55 0.12 226 103 194 91 292.56 0.13 227 104 197 93 292.79 0.20 228 105 109 4 663.08 0.67 229 105 141 36 293.06 0.30 230 105 142 37 293.03 0.29 231 105 143 38 292.78 0.20 232 106 109 3 663.27 0.58 233 106 140 34 332.20 1.86 234 106 141 35 294.39 0.38 235 109 139 30 365.69 2.26 236 109 140 31 366.82 2.82 237 109 141 32 352.22 0.20 238 110 139 29 386.24 0.18 239 110 140 30 379.18 2.31 240 111 138 27 407.20 1.76 241 111 139 28 408.68 0.21 242 112 137 25 431.60 0.07 243 112 138 26 431.48 0.14 244 112 139 27 431.45 0.12 245 113 136 23 431.63 0.09 246 113 137 24 431.64 0.09 247 113 138 25 431.62 0.09 248 114 135 21 431.93 0.08 249 114 136 22 431.87 0.06 250 114 137 23 431.68 0.10 251 114 200 86 431.77 0.04 252 115 134 19 431.91 0.08 253 115 135 20 431.87 0.11 254 115 136 21 431.88 0.06 255 116 134 18 432.04 0.11 256 116 135 19 431.93 0.08 257 116 137 21 431.97 0.07 258 116 203 87 431.93 0.07 259 116 204 88 431.91 0.07 260 116 205 89 431.89 0.07 261 116 206 90 431.87 0.07 262 117 133 16 432.10 0.11 263 117 204 87 431.95 0.07 264 117 205 88 431.91 0.07 265 117 206 89 431.91 0.07 266 118 132 14 432.19 0.15 267 118 133 15 432.11 0.11 268 118 134 16 432.07 0.12 269 118 135 17 432.07 0.12 270 118 154 36 431.95 0.07 271 118 206 88 431.91 0.07 272 118 208 90 431.91 0.07 273 119 131 12 432.23 0.14 274 119 132 13 432.21 0.14 275 119 206 87 431.95 0.07 276 119 207 88 431.92 0.07 277 119 208 89 431.91 0.07 278 120 130 10 432.26 0.15 279 120 131 11 432.23 0.14 280 120 155 35 431.95 0.07 281 120 159 39 431.95 0.07 282 120 208 88 431.92 0.07 283 120 210 90 431.90 0.07 284 121 128 7 432.43 0.16 285 121 129 8 432.39 0.18 286 121 130 9 432.26 0.15 287 121 207 86 431.97 0.07 288 121 208 87 431.94 0.07 289 121 209 88 431.91 0.07 290 121 210 89 431.90 0.07 291 122 128 6 484.41 26.14 292 122 129 7 432.41 0.18 293 122 159 37 431.99 0.07 294 122 166 44 431.92 0.07 295 122 210 88 431.91 0.07 296 122 212 90 431.69 0.07 297 123 127 4 601.97 21.68 298 123 128 5 484.41 26.15 299 123 209 86 431.97 0.07 300 123 210 87 431.94 0.07 301 123 211 88 431.89 0.07 302 123 212 89 431.87 0.06 303 124 127 3 647.04 1.90 304 124 212 88 431.76 0.01 305 131 159 28 431.97 0.06 306 133 159 26 431.98 0.04 307 134 154 20 432.33 0.10 308 135 147 12 432.38 0.12 309 135 150 15 432.37 0.12 310 135 151 16 432.33 0.11 311 135 154 19 432.33 0.11 312 135 206 71 432.27 0.10 313 137 142 5 574.38 4.73 314 137 147 10 432.41 0.11 315 137 200 63 435.11 1.16 316 137 203 66 432.41 0.12 317 139 146 7 636.73 4.46 318 139 200 61 495.46 0.18 319 140 199 59 495.60 0.23 320 140 200 60 495.56 0.22 321 141 197 56 496.85 0.15 322 141 198 57 496.18 0.05 323 141 200 59 495.65 0.21 324 142 146 4 648.68 1.47 325 142 147 5 647.48 0.88 326 142 197 55 496.88 0.15 327 142 198 56 496.31 0.10 328 142 200 58 496.44 0.03 329 142 203 61 496.26 0.01 330 143 146 3 668.48 3.54 331 143 147 4 652.18 0.28 332 143 194 51 497.20 0.01 333 143 196 53 497.12 0.06 334 143 197 54 496.88 0.15 335 144 147 3 652.52 0.45 336 144 148 4 648.73 1.44 337 144 173 29 496.65 0.10 338 144 181 37 496.43 0.14 339 144 183 39 496.29 0.06 340 144 189 45 497.31 0.04 341 144 193 49 497.22 0.01 342 144 196 52 497.19 0.03 343 144 198 54 497.00 0.13 344 145 148 3 669.30 0.69 345 145 149 4 651.06 0.84 346 145 189 44 497.30 0.04 347 145 194 49 497.22 0.01 348 146 149 3 661.62 3.52 349 146 150 4 647.51 0.91 350 147 150 3 693.13 6.01 351 147 151 4 647.45 0.92 352 147 173 26 497.03 0.15 353 147 198 51 497.46 0.16 354 147 203 56 497.47 0.28 355 148 151 3 661.68 3.45 356 148 152 4 647.27 0.85 357 148 183 35 497.26 0.01 358 148 189 41 497.40 0.01 359 149 152 3 669.92 1.20 360 149 153 4 647.26 0.84 361 150 153 3 645.91 0.17 362 150 154 4 650.06 1.23 363 151 154 3 658.79 3.14 364 151 155 4 650.07 1.23 365 151 171 20 497.78 0.21 366 151 173 22 497.87 0.29 367 151 206 55 497.53 0.39 368 151 208 57 497.11 0.29 369 152 155 3 654.60 0.04 370 152 156 4 646.56 0.53 371 152 161 9 543.21 1.34 372 152 162 10 543.21 1.34 373 152 171 19 497.85 0.25 374 152 183 31 498.20 0.31 375 152 184 32 498.30 0.32 376 152 185 33 498.22 0.36 377 152 187 35 499.18 0.24 378 152 188 36 499.12 0.28 379 152 189 37 499.08 0.26 380 153 156 3 652.59 0.97 381 153 157 4 646.29 0.68 382 154 157 3 663.75 2.34 383 154 158 4 646.28 0.67 384 154 159 5 644.61 1.47 385 155 159 4 636.09 1.68 386 155 160 5 636.08 1.68 387 155 161 6 592.54 10.13 388 155 171 16 498.23 0.29 389 155 185 30 499.15 0.22 390 155 208 53 497.55 0.40 391 156 161 5 552.48 3.28 392 156 162 6 552.48 3.28 393 159 210 51 497.39 0.33 394 160 163 3 676.54 1.72 395 160 166 6 520.73 8.68 396 161 166 5 518.35 7.49 397 161 167 6 518.35 7.49 398 161 185 24 502.50 0.40 399 161 210 49 497.51 0.39 400 162 166 4 534.48 5.95 401 162 167 5 518.36 7.49 402 162 185 23 502.52 0.40 403 165 212 47 497.09 0.36 404 165 213 48 497.02 0.34 405 166 210 44 497.53 0.42 406 166 212 46 497.02 0.34 407 167 185 18 513.37 0.59 408 167 186 19 510.87 0.35 409 168 185 17 513.50 0.65 410 168 186 18 510.87 0.35 411 168 210 42 497.44 0.50 412 168 211 43 497.38 0.48 413 169 184 15 513.76 0.66 414 169 185 16 513.65 0.64 415 169 209 40 497.59 0.45 416 169 210 41 497.44 0.49 417 169 211 42 497.38 0.48 418 170 182 12 514.83 0.24 419 170 183 13 514.60 0.27 420 170 184 14 513.85 0.60 421 170 185 15 513.72 0.66 422 170 208 38 497.62 0.46 423 170 209 39 497.59 0.45 424 171 182 11 514.84 0.24 425 171 183 12 514.66 0.30 426 171 185 14 514.00 0.61 427 171 206 35 497.81 0.46 428 171 207 36 497.68 0.47 429 171 208 37 497.61 0.45 430 172 180 8 515.31 0.08 431 172 181 9 515.06 0.18 432 172 182 10 514.85 0.24 433 172 206 34 497.82 0.46 434 172 207 35 497.67 0.48 435 173 180 7 515.32 0.09 436 173 181 8 515.08 0.18 437 173 183 10 515.07 0.18 438 173 198 25 501.44 0.10 439 173 203 30 500.44 0.10 440 173 205 32 498.63 0.38 441 173 206 33 497.85 0.46 442 174 177 3 668.80 2.60 443 174 203 29 500.50 0.07 444 174 204 30 499.68 0.09 445 174 205 31 499.34 0.06 446 175 178 3 685.95 3.11 447 175 179 4 591.30 1.02 448 175 181 6 531.06 3.15 449 175 198 23 501.90 0.41 450 175 202 27 500.60 0.10 451 175 203 28 500.55 0.09 452 176 202 26 500.82 0.00 453 176 204 28 500.56 0.10 454 177 204 27 500.57 0.09 455 181 193 12 512.48 1.14 456 181 198 17 501.99 0.38 457 182 193 11 512.48 1.14 458 183 189 6 515.19 0.21 459 183 193 10 515.17 0.21 460 184 187 3 688.66 3.92 461 185 208 23 497.63 0.46 462 185 210 25 497.44 0.50 463 188 194 6 652.51 1.42 464 189 193 4 669.45 1.29 465 189 194 5 647.18 1.37 466 190 193 3 674.78 0.82 467 190 194 4 669.45 1.29 468 191 194 3 669.79 1.12 469 193 196 3 662.24 2.17 470 198 203 5 607.27 16.64 471 199 202 3 648.08 1.70 472 199 203 4 643.07 0.64 473 200 203 3 666.13 1.52 474 203 206 3 778.21 3.63