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 49.98 0.60 2 12 132 120 50.26 0.74 3 12 133 121 50.54 0.76 4 12 134 122 50.38 0.80 5 12 135 123 50.16 0.70 6 12 136 124 50.10 0.67 7 13 17 4 637.78 2.02 8 13 131 118 50.25 0.74 9 14 17 3 697.31 0.12 10 14 133 119 51.58 1.25 11 15 133 118 56.47 1.23 12 16 19 3 702.60 0.33 13 17 20 3 698.13 4.25 14 17 21 4 676.58 0.81 15 17 65 48 79.69 0.35 16 17 67 50 78.81 0.37 17 18 21 3 676.59 0.80 18 18 22 4 637.89 0.56 19 18 23 5 637.80 0.52 20 18 25 7 621.21 5.35 21 18 26 8 611.82 8.86 22 18 65 47 80.06 0.47 23 18 66 48 79.95 0.46 24 18 96 78 80.12 0.47 25 18 99 81 80.36 0.58 26 19 23 4 637.85 0.58 27 19 26 7 611.83 8.84 28 19 28 9 611.75 8.81 29 20 23 3 722.68 3.06 30 21 67 46 80.14 0.47 31 21 94 73 80.14 0.46 32 22 25 3 682.93 4.08 33 22 26 4 667.36 3.05 34 22 36 14 80.23 0.50 35 22 96 74 80.28 0.54 36 23 26 3 681.64 4.59 37 23 27 4 660.37 2.86 38 23 28 5 642.04 0.26 39 23 29 6 624.12 4.95 40 23 30 7 621.13 5.17 41 23 31 8 621.13 5.17 42 23 34 11 100.03 0.24 43 24 27 3 681.76 4.66 44 24 28 4 656.65 4.72 45 24 30 6 624.11 4.95 46 25 99 74 80.39 0.60 47 30 34 4 674.24 0.03 48 31 34 3 722.84 0.11 49 33 85 52 203.49 1.40 50 34 85 51 203.84 1.55 51 35 83 48 203.83 1.55 52 35 92 57 189.74 0.59 53 35 94 59 189.71 0.60 54 36 93 57 189.74 0.59 55 36 94 58 189.72 0.59 56 36 95 59 189.72 0.59 57 36 96 60 189.73 0.59 58 37 94 57 189.75 0.60 59 37 95 58 189.73 0.59 60 37 105 68 189.74 0.59 61 37 106 69 189.74 0.59 62 37 107 70 191.85 0.44 63 38 107 69 193.34 0.02 64 39 70 31 203.89 1.55 65 39 72 33 203.93 1.54 66 39 89 50 204.27 1.46 67 39 90 51 204.14 1.48 68 39 91 52 204.09 1.50 69 39 92 53 204.05 1.49 70 39 93 54 203.88 1.54 71 39 106 67 203.91 1.54 72 39 107 68 203.93 1.53 73 39 108 69 203.91 1.54 74 40 44 4 645.75 8.53 75 40 48 8 204.28 1.44 76 40 88 48 210.93 1.68 77 40 89 49 204.27 1.46 78 40 107 67 204.21 1.47 79 40 108 68 204.20 1.44 80 40 109 69 204.25 1.45 81 41 44 3 687.27 0.57 82 41 48 7 255.50 20.61 83 41 85 44 230.72 4.17 84 41 86 45 230.86 4.13 85 41 87 46 230.69 4.11 86 41 88 47 212.18 1.84 87 42 48 6 613.02 7.83 88 43 88 45 230.93 4.12 89 44 48 4 677.14 5.78 90 44 88 44 230.94 4.12 91 44 89 45 230.93 4.12 92 44 109 65 233.89 2.62 93 45 75 30 260.53 1.09 94 45 109 64 265.68 1.73 95 46 75 29 260.53 1.09 96 46 109 63 284.36 2.23 97 47 109 62 292.00 0.76 98 47 110 63 290.61 0.78 99 47 181 134 292.07 0.76 100 48 108 60 292.19 0.76 101 48 109 61 292.11 0.76 102 48 180 132 292.13 0.74 103 49 107 58 292.28 0.74 104 49 108 59 292.22 0.75 105 49 109 60 292.20 0.74 106 49 110 61 292.17 0.74 107 49 145 96 292.14 0.73 108 49 180 131 292.13 0.74 109 49 181 132 292.10 0.74 110 49 183 134 292.06 0.75 111 50 105 55 292.50 0.78 112 50 106 56 292.40 0.74 113 50 107 57 292.28 0.74 114 50 177 127 292.15 0.73 115 50 180 130 292.17 0.74 116 50 181 131 292.13 0.74 117 50 182 132 292.08 0.76 118 50 183 133 292.08 0.76 119 51 104 53 292.63 0.83 120 51 105 54 292.58 0.82 121 51 106 55 292.45 0.76 122 51 108 57 292.41 0.74 123 51 126 75 292.20 0.74 124 51 143 92 292.14 0.74 125 51 145 94 292.17 0.74 126 51 183 132 292.11 0.75 127 52 103 51 292.71 0.83 128 52 104 52 292.63 0.83 129 52 105 53 292.60 0.83 130 52 177 125 292.24 0.73 131 52 182 130 292.17 0.74 132 52 183 131 292.12 0.74 133 52 184 132 292.09 0.76 134 52 185 133 292.10 0.75 135 53 103 50 292.75 0.84 136 53 104 51 292.71 0.83 137 53 184 131 292.12 0.75 138 53 185 132 292.10 0.75 139 53 186 133 292.05 0.74 140 54 62 8 293.73 0.59 141 54 101 47 293.44 0.70 142 54 102 48 293.01 0.81 143 54 103 49 292.86 0.82 144 54 104 50 292.85 0.82 145 54 184 130 292.17 0.74 146 54 186 132 292.10 0.75 147 54 187 133 292.10 0.75 148 55 62 7 293.88 0.67 149 55 63 8 293.56 0.65 150 55 66 11 292.76 0.86 151 55 97 42 293.32 0.66 152 55 104 49 293.07 0.79 153 55 130 75 292.60 0.85 154 55 187 132 292.08 0.73 155 55 189 134 292.04 0.74 156 56 60 4 628.38 3.46 157 56 61 5 602.86 1.75 158 56 62 6 449.46 78.45 159 56 63 7 293.88 0.67 160 56 186 130 292.16 0.74 161 56 187 131 292.12 0.75 162 56 188 132 292.06 0.73 163 56 189 133 292.06 0.73 164 57 60 3 691.55 3.26 165 57 61 4 602.87 1.77 166 57 63 6 429.47 67.06 167 57 189 132 292.07 0.73 168 58 190 132 292.05 0.74 169 62 101 39 564.40 2.89 170 63 66 3 703.83 1.19 171 63 97 34 564.27 2.77 172 63 132 69 466.61 2.48 173 63 189 126 292.07 0.73 174 64 97 33 564.56 2.90 175 64 98 34 564.59 2.90 176 64 99 35 564.59 2.90 177 64 100 36 565.01 2.73 178 64 101 37 564.80 2.85 179 64 102 38 559.79 1.10 180 65 97 32 564.88 2.79 181 65 133 68 467.07 2.58 182 66 96 30 565.35 2.64 183 66 97 31 565.09 2.76 184 66 130 64 467.31 2.50 185 66 131 65 467.18 2.54 186 66 132 66 467.07 2.59 187 67 94 27 565.93 2.69 188 67 95 28 565.84 2.68 189 67 96 29 565.38 2.62 190 67 130 63 467.32 2.50 191 67 131 64 467.19 2.54 192 68 94 26 565.93 2.69 193 68 95 27 565.84 2.68 194 68 96 28 565.83 2.68 195 68 104 36 565.48 2.62 196 68 128 60 467.57 2.58 197 68 129 61 467.42 2.53 198 68 130 62 467.33 2.50 199 68 187 119 292.13 0.74 200 69 92 23 566.21 2.68 201 69 93 24 566.00 2.71 202 69 94 25 565.95 2.69 203 69 128 59 467.58 2.58 204 69 129 60 467.54 2.59 205 69 131 62 467.43 2.54 206 70 92 22 566.22 2.68 207 70 93 23 566.11 2.65 208 70 106 36 565.48 2.62 209 70 126 56 467.93 2.59 210 70 127 57 467.70 2.59 211 70 128 58 467.59 2.58 212 71 79 8 586.41 5.76 213 71 81 10 568.69 3.02 214 71 91 20 566.34 2.68 215 71 92 21 566.22 2.68 216 71 126 55 467.96 2.60 217 71 127 56 467.79 2.63 218 72 79 7 586.47 5.74 219 72 89 17 567.50 2.50 220 72 91 19 566.36 2.68 221 72 108 36 565.43 2.64 222 72 109 37 565.36 2.65 223 72 111 39 557.54 0.69 224 72 126 54 467.97 2.60 225 73 77 4 610.89 12.40 226 73 78 5 598.47 11.64 227 73 79 6 586.56 5.70 228 73 89 16 567.59 2.54 229 73 111 38 559.12 0.80 230 73 114 41 556.84 0.86 231 74 77 3 676.53 4.10 232 74 78 4 611.76 5.01 233 74 80 6 603.94 8.93 234 74 89 15 567.48 2.50 235 74 111 37 563.09 2.75 236 74 112 38 563.07 2.75 237 75 109 34 565.33 2.66 238 75 110 35 565.28 2.67 239 75 112 37 563.04 2.75 240 77 112 35 557.88 0.61 241 77 113 36 557.88 0.61 242 77 114 37 557.64 0.50 243 79 91 12 566.63 2.68 244 79 114 35 557.50 0.67 245 79 125 46 468.55 2.50 246 79 127 48 468.30 2.52 247 80 89 9 567.61 2.52 248 80 91 11 566.62 2.67 249 82 87 5 661.34 6.21 250 83 90 7 567.97 2.66 251 83 92 9 567.53 2.52 252 84 87 3 672.60 2.30 253 84 90 6 576.55 1.55 254 85 90 5 641.46 3.65 255 87 90 3 713.52 5.17 256 89 108 19 564.85 2.30 257 89 109 20 564.81 2.31 258 95 104 9 566.08 2.32 259 95 105 10 566.05 2.33 260 95 106 11 565.81 2.41 261 96 104 8 566.08 2.32 262 97 102 5 567.31 2.83 263 97 103 6 566.27 2.31 264 97 104 7 566.09 2.31 265 98 101 3 676.09 2.78 266 98 102 4 567.34 2.82 267 98 103 5 567.34 2.83 268 103 184 81 292.16 0.74 269 104 185 81 292.11 0.75 270 108 126 18 467.98 2.59 271 110 145 35 466.75 2.48 272 110 147 37 466.13 2.43 273 110 148 38 441.53 5.38 274 110 183 73 292.17 0.74 275 111 124 13 468.21 2.52 276 111 125 14 468.19 2.51 277 111 126 15 468.19 2.52 278 111 145 34 466.93 2.52 279 113 121 8 469.93 2.20 280 113 122 9 469.81 2.19 281 113 124 11 468.42 2.47 282 114 121 7 470.00 2.17 283 114 122 8 469.81 2.19 284 114 125 11 469.10 2.35 285 115 119 4 642.52 3.72 286 115 120 5 470.32 2.18 287 115 121 6 470.00 2.18 288 115 122 7 470.00 2.17 289 116 119 3 664.12 0.22 290 116 120 4 645.90 2.03 291 116 122 6 470.21 2.24 292 116 156 40 403.21 0.74 293 120 156 36 403.51 0.86 294 121 156 35 403.25 0.74 295 122 125 3 800.89 5.01 296 122 142 20 467.30 2.54 297 122 155 33 402.93 0.83 298 122 156 34 402.87 0.80 299 122 157 35 402.81 0.77 300 123 144 21 467.07 2.56 301 123 151 28 403.88 1.00 302 123 152 29 403.87 0.99 303 123 155 32 402.86 0.80 304 124 144 20 467.03 2.54 305 124 145 21 467.00 2.55 306 124 148 24 441.64 2.60 307 124 151 27 403.94 1.02 308 125 142 17 467.07 2.56 309 125 143 18 467.03 2.54 310 125 144 19 466.89 2.55 311 125 145 20 466.91 2.54 312 126 142 16 467.05 2.56 313 126 143 17 466.94 2.54 314 126 145 19 466.88 2.54 315 127 141 14 467.06 2.56 316 127 142 15 466.93 2.55 317 128 140 12 467.06 2.56 318 128 141 13 466.98 2.60 319 128 143 15 466.81 2.52 320 128 185 57 292.19 0.74 321 128 187 59 292.13 0.74 322 129 138 9 467.08 2.56 323 129 139 10 467.06 2.56 324 129 140 11 466.99 2.59 325 130 135 5 658.32 2.52 326 130 138 8 467.06 2.56 327 130 139 9 467.05 2.56 328 130 187 57 292.15 0.73 329 130 189 59 292.09 0.76 330 131 138 7 467.03 2.57 331 132 135 3 690.99 0.84 332 135 138 3 715.63 2.80 333 135 139 4 697.97 0.45 334 135 189 54 292.13 0.75 335 139 189 50 292.11 0.75 336 139 197 58 149.21 0.19 337 140 197 57 147.55 0.64 338 140 198 58 145.09 1.68 339 140 200 60 145.00 1.69 340 141 170 29 345.29 0.56 341 141 185 44 292.21 0.73 342 141 187 46 292.13 0.74 343 141 195 54 164.85 0.13 344 141 196 55 163.68 0.27 345 141 197 56 147.35 0.70 346 141 198 57 146.12 1.17 347 142 157 15 395.75 0.64 348 142 170 28 345.30 0.56 349 142 185 43 292.20 0.73 350 142 198 56 147.22 0.63 351 143 170 27 345.31 0.56 352 143 172 29 345.19 0.61 353 143 185 42 292.17 0.74 354 144 152 8 403.78 0.96 355 144 155 11 402.86 0.80 356 144 157 13 402.32 0.52 357 144 158 14 400.95 0.68 358 144 170 26 345.41 0.59 359 144 171 27 345.29 0.57 360 144 172 28 345.29 0.57 361 145 148 3 685.99 1.60 362 145 152 7 602.53 10.89 363 145 171 26 345.40 0.59 364 145 183 38 292.21 0.74 365 146 171 25 345.44 0.59 366 146 172 26 345.40 0.59 367 146 173 27 345.35 0.58 368 146 174 28 345.31 0.57 369 146 183 37 292.25 0.74 370 147 174 27 345.32 0.57 371 147 183 36 292.24 0.75 372 148 151 3 682.75 0.51 373 148 152 4 676.01 0.39 374 149 152 3 679.50 2.14 375 149 153 4 679.50 2.14 376 150 153 3 687.91 1.61 377 150 154 4 685.55 1.06 378 151 154 3 695.62 3.57 379 151 155 4 685.54 1.06 380 152 155 3 693.19 4.73 381 152 158 6 649.16 2.18 382 152 171 19 345.54 0.61 383 153 159 6 660.43 4.38 384 154 159 5 663.33 2.93 385 155 158 3 682.07 0.09 386 155 159 4 670.08 0.41 387 156 159 3 677.79 2.56 388 156 160 4 670.09 0.41 389 157 160 3 689.41 5.55 390 157 198 41 161.59 0.32 391 158 161 3 689.41 5.55 392 158 167 9 345.66 0.67 393 158 170 12 345.68 0.64 394 159 167 8 529.63 24.55 395 161 166 5 659.27 5.96 396 161 167 6 634.46 4.75 397 161 170 9 542.22 30.83 398 161 196 35 166.06 0.20 399 161 198 37 165.37 0.04 400 163 166 3 684.95 4.02 401 163 167 4 677.88 0.48 402 164 167 3 685.84 0.72 403 164 168 4 677.83 0.45 404 165 168 3 692.45 0.30 405 166 169 3 683.87 3.31 406 166 194 28 169.38 0.32 407 166 195 29 167.50 0.06 408 166 196 30 166.12 0.23 409 167 170 3 687.27 2.44 410 167 171 4 680.57 1.01 411 168 171 3 680.57 1.01 412 169 185 16 292.25 0.73 413 169 193 24 168.09 0.32 414 169 194 25 167.00 0.15 415 169 195 26 165.35 0.03 416 169 196 27 165.35 0.03 417 170 185 15 292.22 0.73 418 170 195 25 165.35 0.03 419 170 196 26 165.31 0.04 420 170 198 28 165.19 0.10 421 172 183 11 292.25 0.74 422 172 184 12 292.21 0.74 423 172 185 13 292.12 0.74 424 173 183 10 292.25 0.74 425 173 184 11 292.22 0.73 426 174 181 7 443.71 74.95 427 174 182 8 321.10 13.67 428 174 183 9 292.22 0.76 429 175 181 6 443.74 74.95 430 175 182 7 321.12 13.68 431 176 179 3 687.94 3.23 432 176 180 4 538.45 27.60 433 176 181 5 445.59 74.03 434 176 182 6 443.73 74.95 435 177 180 3 664.31 3.12 436 177 182 5 472.31 60.67 437 187 195 8 165.08 0.04 438 187 197 10 165.00 0.01 439 188 192 4 685.11 3.76 440 188 193 5 474.82 63.65 441 188 194 6 256.54 45.62 442 188 195 7 165.22 0.02 443 188 197 9 165.34 0.03 444 189 194 5 470.28 61.38 445 189 197 8 256.51 45.63 446 190 194 4 549.99 22.41 447 191 194 3 665.83 0.97