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 11 136 125 50.02 1.11 2 12 132 120 52.77 0.20 3 12 133 121 52.77 0.21 4 12 134 122 52.77 0.20 5 12 135 123 50.27 1.20 6 12 136 124 50.08 1.14 7 13 17 4 659.68 0.82 8 13 131 118 52.36 0.15 9 14 17 3 695.37 0.35 10 14 133 119 53.50 0.14 11 15 133 118 55.35 0.07 12 16 19 3 703.79 1.43 13 17 20 3 703.40 1.62 14 17 21 4 676.08 1.05 15 17 65 48 84.78 0.55 16 17 67 50 82.61 1.52 17 18 21 3 675.87 1.16 18 18 22 4 640.88 2.44 19 18 23 5 637.50 0.76 20 18 26 8 620.84 5.18 21 18 65 47 84.81 0.55 22 18 66 48 84.72 0.59 23 18 96 78 85.51 0.21 24 18 97 79 85.61 0.18 25 18 98 80 85.66 0.15 26 19 23 4 640.33 0.58 27 19 26 7 622.18 5.08 28 19 28 9 610.25 10.47 29 20 23 3 724.59 2.10 30 21 67 46 85.36 0.28 31 21 94 73 85.39 0.26 32 22 25 3 682.43 4.33 33 22 26 4 668.40 2.04 34 22 36 14 85.56 0.23 35 22 96 74 85.61 0.15 36 23 26 3 688.40 1.22 37 23 27 4 665.22 0.12 38 23 28 5 653.44 5.83 39 23 29 6 636.72 0.37 40 23 30 7 618.95 4.07 41 23 31 8 633.20 1.38 42 23 34 11 332.00 116.28 43 24 27 3 681.56 4.76 44 24 28 4 656.19 4.49 45 24 30 6 633.23 1.38 46 25 36 11 323.33 117.92 47 25 96 71 85.83 0.15 48 25 98 73 85.81 0.14 49 30 34 4 673.74 0.28 50 31 34 3 722.34 0.14 51 33 85 52 205.91 0.51 52 34 85 51 206.09 0.42 53 35 83 48 206.09 0.42 54 35 92 57 194.47 1.02 55 35 93 58 194.45 1.01 56 35 94 59 194.44 1.02 57 36 93 57 194.46 1.02 58 36 94 58 194.44 1.02 59 36 95 59 194.45 1.02 60 36 96 60 194.46 1.02 61 37 94 57 194.49 1.00 62 37 95 58 194.46 1.02 63 37 105 68 194.45 1.02 64 37 106 69 194.44 1.02 65 37 107 70 194.46 1.02 66 38 107 69 194.47 1.02 67 39 70 31 206.11 0.43 68 39 72 33 206.13 0.43 69 39 89 50 206.22 0.42 70 39 90 51 206.19 0.44 71 39 91 52 206.18 0.43 72 39 92 53 206.16 0.43 73 39 93 54 206.10 0.43 74 39 106 67 206.13 0.43 75 39 107 68 206.13 0.43 76 39 108 69 206.13 0.43 77 40 44 4 652.57 4.62 78 40 48 8 206.22 0.42 79 40 88 48 207.52 0.48 80 40 89 49 206.24 0.43 81 40 107 67 206.20 0.42 82 40 108 68 206.18 0.42 83 40 109 69 206.20 0.42 84 41 44 3 673.09 3.75 85 41 48 7 383.43 89.00 86 41 85 44 224.05 0.95 87 41 86 45 224.89 0.58 88 41 87 46 222.16 0.01 89 41 88 47 209.34 0.46 90 42 48 6 610.95 8.88 91 43 88 45 229.19 1.54 92 44 48 4 676.65 5.52 93 44 88 44 230.40 2.15 94 44 89 45 229.19 1.54 95 44 109 65 227.75 0.03 96 45 75 30 266.77 8.27 97 45 109 64 271.50 4.65 98 46 75 29 266.78 8.27 99 46 109 63 282.00 0.60 100 47 109 62 288.51 1.67 101 47 110 63 287.78 1.40 102 47 181 134 288.49 1.68 103 48 108 60 288.63 1.67 104 48 109 61 288.52 1.67 105 48 180 132 288.54 1.68 106 49 107 58 288.69 1.68 107 49 108 59 288.64 1.67 108 49 109 60 288.64 1.67 109 49 110 61 288.62 1.67 110 49 145 96 288.56 1.67 111 49 180 131 288.56 1.67 112 49 181 132 288.51 1.68 113 49 183 134 288.49 1.68 114 50 105 55 289.08 1.53 115 50 106 56 289.04 1.53 116 50 107 57 288.70 1.68 117 50 177 127 288.56 1.68 118 50 180 130 288.59 1.68 119 50 181 131 288.54 1.68 120 50 182 132 288.51 1.67 121 50 183 133 288.51 1.67 122 51 104 53 289.15 1.52 123 51 105 54 289.08 1.53 124 51 106 55 289.06 1.53 125 51 108 57 289.05 1.54 126 51 126 75 288.59 1.69 127 51 143 92 288.58 1.68 128 51 145 94 288.61 1.68 129 51 183 132 288.52 1.67 130 52 103 51 289.44 1.41 131 52 104 52 289.12 1.53 132 52 105 53 289.12 1.53 133 52 177 125 288.67 1.68 134 52 182 130 288.60 1.69 135 52 183 131 288.55 1.67 136 52 184 132 288.51 1.67 137 52 185 133 288.50 1.68 138 53 103 50 289.75 1.26 139 53 104 51 289.42 1.42 140 53 184 131 288.54 1.68 141 53 185 132 288.51 1.67 142 53 186 133 288.48 1.68 143 54 62 8 563.26 4.31 144 54 102 48 290.50 0.93 145 54 103 49 289.97 1.16 146 54 184 130 288.61 1.68 147 54 186 132 288.49 1.68 148 54 187 133 288.49 1.68 149 55 62 7 563.28 4.31 150 55 63 8 563.15 4.29 151 55 66 11 562.20 4.24 152 55 97 42 290.54 0.92 153 55 104 49 290.54 0.93 154 55 130 75 289.31 1.40 155 55 187 132 288.49 1.68 156 55 189 134 288.45 1.69 157 56 60 4 627.88 3.21 158 56 61 5 580.88 12.26 159 56 62 6 563.28 4.31 160 56 63 7 563.27 4.31 161 56 186 130 288.60 1.68 162 56 187 131 288.53 1.67 163 56 188 132 288.45 1.67 164 56 189 133 288.42 1.69 165 57 60 3 691.05 3.51 166 57 61 4 615.64 8.14 167 57 63 6 580.03 12.68 168 58 190 132 288.26 1.66 169 63 66 3 705.63 0.29 170 63 97 34 555.11 3.00 171 63 132 69 470.00 1.37 172 63 189 126 288.50 1.69 173 64 97 33 555.11 3.00 174 64 98 34 555.13 3.00 175 64 99 35 556.28 3.54 176 64 102 38 553.54 2.50 177 65 97 32 557.77 3.89 178 65 133 68 471.81 1.17 179 66 96 30 558.00 3.81 180 66 97 31 557.82 3.90 181 66 130 64 472.09 1.16 182 66 131 65 471.84 1.16 183 66 132 66 471.82 1.16 184 67 94 27 558.37 3.84 185 67 95 28 558.32 3.83 186 67 96 29 558.02 3.81 187 67 130 63 472.12 1.15 188 67 131 64 471.89 1.17 189 68 94 26 558.45 3.80 190 68 95 27 558.35 3.84 191 68 96 28 558.31 3.83 192 68 104 36 557.88 3.96 193 68 128 60 472.52 1.23 194 68 129 61 472.41 1.20 195 68 130 62 472.18 1.17 196 68 187 119 288.56 1.68 197 69 92 23 558.82 3.91 198 69 93 24 558.75 3.92 199 69 94 25 558.46 3.80 200 69 128 59 472.57 1.24 201 69 129 60 472.44 1.20 202 69 131 62 472.42 1.20 203 70 92 22 558.83 3.91 204 70 93 23 558.76 3.92 205 70 106 36 557.88 3.96 206 70 126 56 473.10 1.19 207 70 127 57 472.84 1.14 208 70 128 58 472.58 1.24 209 71 79 8 561.28 4.00 210 71 81 10 560.79 4.01 211 71 91 20 559.00 3.98 212 71 92 21 558.84 3.91 213 71 126 55 473.13 1.19 214 71 127 56 472.90 1.16 215 72 79 7 561.28 4.01 216 72 89 17 560.00 4.22 217 72 91 19 559.00 3.99 218 72 108 36 557.88 3.96 219 72 109 37 557.76 3.92 220 72 111 39 550.28 0.92 221 72 126 54 473.13 1.19 222 73 77 4 634.75 0.47 223 73 78 5 604.12 8.81 224 73 79 6 561.29 4.00 225 73 89 16 560.01 4.23 226 73 111 38 550.30 0.91 227 73 114 41 550.18 0.96 228 74 77 3 679.83 5.71 229 74 78 4 629.06 3.65 230 74 80 6 603.41 9.17 231 74 89 15 559.94 4.24 232 74 111 37 553.43 2.39 233 74 112 38 550.55 0.96 234 75 109 34 557.86 3.97 235 75 110 35 557.48 4.09 236 75 112 37 550.52 0.95 237 77 112 35 550.35 0.95 238 77 113 36 550.33 0.95 239 77 114 37 550.20 0.97 240 79 91 12 559.41 4.11 241 79 114 35 550.25 0.99 242 79 127 48 473.26 1.23 243 80 89 9 560.04 4.25 244 80 91 11 559.53 4.17 245 82 87 5 662.76 4.99 246 83 90 7 560.04 4.28 247 83 92 9 560.00 4.27 248 84 87 3 678.50 5.25 249 84 90 6 562.32 3.26 250 87 90 3 713.43 5.21 251 89 108 19 557.52 4.17 252 89 109 20 557.52 4.17 253 95 104 9 558.08 4.06 254 95 105 10 558.02 4.08 255 95 106 11 557.78 3.98 256 96 104 8 558.09 4.12 257 97 101 4 639.00 4.36 258 97 102 5 561.36 2.89 259 97 103 6 561.19 2.97 260 97 104 7 558.19 4.12 261 98 101 3 659.72 0.92 262 98 102 4 615.44 7.42 263 103 184 81 288.61 1.68 264 104 185 81 288.53 1.67 265 108 126 18 473.14 1.18 266 110 145 35 471.67 1.16 267 110 147 37 469.60 1.74 268 110 148 38 449.94 0.40 269 110 183 73 288.57 1.69 270 111 124 13 473.26 1.16 271 111 125 14 473.25 1.16 272 111 126 15 473.19 1.19 273 111 145 34 471.80 1.19 274 113 121 8 476.38 1.31 275 113 122 9 476.13 1.41 276 113 124 11 473.36 1.20 277 114 121 7 476.39 1.31 278 114 122 8 476.36 1.30 279 114 125 11 473.81 1.23 280 115 119 4 648.95 0.51 281 115 120 5 541.87 31.41 282 115 121 6 476.39 1.31 283 115 122 7 476.39 1.31 284 116 119 3 667.58 1.33 285 116 120 4 648.95 0.52 286 116 122 6 515.56 18.25 287 116 156 40 393.32 2.31 288 120 156 36 393.37 2.29 289 121 156 35 393.43 2.26 290 122 125 3 800.55 4.68 291 122 142 20 472.14 1.13 292 122 155 33 393.18 2.24 293 122 156 34 393.18 2.23 294 122 157 35 393.18 2.23 295 123 144 21 471.99 1.12 296 123 151 28 397.25 0.48 297 123 152 29 397.08 0.55 298 123 155 32 393.17 2.23 299 124 144 20 471.94 1.14 300 124 145 21 471.94 1.14 301 124 148 24 448.29 4.07 302 124 151 27 398.55 0.18 303 125 142 17 471.99 1.14 304 125 143 18 471.94 1.14 305 125 144 19 471.80 1.18 306 125 145 20 471.81 1.18 307 126 142 16 471.95 1.14 308 126 143 17 471.80 1.18 309 126 145 19 471.80 1.18 310 127 141 14 471.98 1.14 311 127 142 15 471.79 1.18 312 128 140 12 471.98 1.14 313 128 141 13 471.82 1.19 314 128 143 15 471.75 1.18 315 128 185 57 288.63 1.68 316 128 187 59 288.51 1.69 317 129 138 9 472.00 1.14 318 129 139 10 471.99 1.14 319 129 140 11 471.79 1.18 320 130 135 5 657.83 2.26 321 130 138 8 472.00 1.13 322 130 139 9 471.96 1.11 323 130 187 57 288.62 1.69 324 130 189 59 288.45 1.71 325 131 138 7 472.00 1.13 326 132 135 3 690.49 1.09 327 135 138 3 715.13 3.05 328 135 139 4 699.38 0.25 329 135 189 54 288.62 1.69 330 139 189 50 288.53 1.68 331 139 197 58 149.74 1.00 332 140 197 57 147.05 0.79 333 140 198 58 146.33 0.69 334 140 200 60 143.96 1.61 335 141 170 29 345.91 0.88 336 141 185 44 288.68 1.68 337 141 187 46 288.53 1.68 338 141 195 54 162.71 0.36 339 141 196 55 161.08 1.03 340 141 197 56 146.60 0.57 341 141 198 57 144.04 1.60 342 142 157 15 390.60 1.27 343 142 170 28 345.91 0.88 344 142 185 43 288.63 1.68 345 142 198 56 146.35 0.70 346 143 170 27 345.94 0.86 347 143 172 29 345.81 0.91 348 143 185 42 288.54 1.68 349 144 152 8 393.18 2.23 350 144 155 11 393.19 2.25 351 144 157 13 393.14 2.22 352 144 158 14 392.76 2.12 353 144 170 26 345.95 0.86 354 144 171 27 345.92 0.87 355 144 172 28 345.92 0.87 356 145 148 3 686.60 0.80 357 145 152 7 605.17 0.80 358 145 171 26 345.94 0.86 359 145 172 27 345.92 0.87 360 145 183 38 288.68 1.67 361 146 171 25 346.00 0.88 362 146 172 26 345.95 0.86 363 146 173 27 345.94 0.86 364 146 174 28 345.90 0.86 365 147 174 27 345.91 0.86 366 147 183 36 288.71 1.67 367 148 151 3 682.25 0.26 368 148 152 4 676.09 1.38 369 149 152 3 677.03 0.90 370 149 153 4 676.10 1.37 371 150 153 3 696.44 5.87 372 151 154 3 688.00 0.24 373 151 155 4 680.81 1.30 374 152 155 3 692.69 4.98 375 152 158 6 635.00 8.12 376 152 171 19 346.07 0.88 377 153 159 6 659.65 4.20 378 154 159 5 669.68 0.79 379 155 158 3 681.57 0.34 380 155 159 4 669.68 0.79 381 156 159 3 676.59 2.67 382 156 160 4 669.67 0.79 383 157 160 3 688.91 5.30 384 157 198 41 159.62 0.47 385 158 161 3 696.43 1.54 386 158 167 9 346.50 0.90 387 158 170 12 346.17 0.89 388 159 167 8 575.52 0.20 389 161 166 5 656.45 4.90 390 161 167 6 604.46 2.02 391 161 170 9 576.94 0.90 392 161 196 35 163.47 0.08 393 161 198 37 163.45 0.07 394 163 166 3 684.45 3.77 395 163 167 4 673.28 1.80 396 164 167 3 681.60 2.35 397 164 168 4 677.32 0.21 398 165 168 3 705.64 7.41 399 166 169 3 691.99 3.70 400 166 194 28 166.14 0.24 401 166 195 29 165.33 0.18 402 166 196 30 163.85 0.06 403 167 170 3 701.71 3.44 404 168 171 3 674.59 1.49 405 169 185 16 288.67 1.67 406 169 193 24 165.70 0.17 407 169 194 25 164.64 0.12 408 169 195 26 163.59 0.18 409 169 196 27 163.44 0.10 410 170 185 15 288.64 1.67 411 170 195 25 162.81 0.42 412 170 196 26 162.80 0.41 413 170 198 28 162.69 0.46 414 172 183 11 288.69 1.68 415 172 184 12 288.66 1.67 416 172 185 13 288.50 1.67 417 173 183 10 288.72 1.68 418 173 184 11 288.67 1.68 419 174 181 7 445.25 74.09 420 174 182 8 320.30 14.06 421 174 183 9 288.72 1.67 422 175 181 6 471.99 60.73 423 175 182 7 323.17 13.33 424 176 179 3 687.44 2.98 425 176 180 4 599.12 2.03 426 176 181 5 472.00 60.72 427 176 182 6 445.24 74.09 428 177 180 3 675.09 1.68 429 177 182 5 477.30 63.37 430 187 195 8 162.80 0.41 431 187 197 10 162.12 0.74 432 188 192 4 689.19 1.22 433 188 193 5 481.12 64.88 434 188 194 6 321.46 13.12 435 188 195 7 162.80 0.41 436 189 194 5 480.80 65.05 437 189 197 8 378.29 107.37 438 190 194 4 621.22 5.10 439 191 194 3 663.06 1.85