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 4 71 67 82.33 2.98 2 5 18 13 83.27 2.81 3 5 19 14 83.11 2.77 4 5 20 15 82.85 2.71 5 5 21 16 82.84 2.71 6 5 71 66 82.41 3.00 7 5 72 67 83.01 2.81 8 6 18 12 83.33 2.79 9 6 19 13 83.23 2.80 10 6 21 15 83.05 2.81 11 6 24 18 83.03 2.81 12 6 25 19 83.04 2.81 13 6 32 26 82.75 2.75 14 6 69 63 81.84 2.74 15 7 15 8 84.94 2.75 16 7 17 10 84.22 2.58 17 7 18 11 83.38 2.78 18 7 32 25 82.97 2.81 19 7 33 26 82.92 2.79 20 7 70 63 83.11 2.75 21 7 71 64 83.23 2.80 22 7 72 65 83.29 2.79 23 8 15 7 85.30 2.62 24 8 16 8 84.81 2.81 25 8 17 9 84.44 2.65 26 8 19 11 83.85 2.76 27 8 30 22 83.17 2.85 28 8 31 23 83.06 2.82 29 8 32 24 83.02 2.82 30 9 13 4 440.68 4.64 31 9 14 5 432.11 5.88 32 9 15 6 85.30 2.62 33 9 31 22 83.25 2.81 34 9 32 23 83.25 2.81 35 9 33 24 83.29 2.79 36 9 117 108 83.24 2.81 37 10 14 4 461.47 5.75 38 10 16 6 85.31 2.61 39 10 31 21 83.36 2.78 40 18 72 54 87.84 1.71 41 19 24 5 548.49 4.76 42 20 23 3 600.63 0.74 43 20 24 4 586.52 2.63 44 21 24 3 596.53 2.21 45 21 25 4 596.38 2.29 46 21 69 48 89.61 1.66 47 21 83 62 89.86 1.77 48 22 25 3 610.12 0.57 49 22 56 34 91.27 1.77 50 23 26 3 644.20 4.88 51 24 29 5 474.24 1.01 52 25 29 4 502.70 7.00 53 25 32 7 460.65 0.12 54 25 56 31 94.84 0.49 55 25 69 44 153.56 28.87 56 25 112 87 280.99 1.48 57 25 114 89 94.91 0.56 58 26 29 3 559.94 7.66 59 26 112 86 289.55 2.79 60 26 113 87 288.32 3.41 61 27 111 84 307.45 2.71 62 27 112 85 307.46 2.71 63 27 113 86 296.72 2.65 64 29 113 84 344.43 0.30 65 29 114 85 348.92 5.67 66 29 115 86 345.67 0.43 67 30 115 85 363.48 0.21 68 31 103 72 365.34 0.94 69 31 115 84 364.78 0.74 70 31 116 85 365.24 0.97 71 31 117 86 365.34 0.94 72 32 69 37 420.64 5.24 73 32 114 82 365.45 0.93 74 32 115 83 365.41 0.93 75 32 116 84 365.38 0.93 76 32 117 85 365.38 0.93 77 33 69 36 420.65 5.24 78 33 70 37 420.62 5.25 79 33 117 84 365.38 0.93 80 34 68 34 420.73 5.27 81 34 69 35 420.65 5.24 82 34 70 36 420.64 5.24 83 34 116 82 365.44 0.92 84 34 117 83 365.42 0.93 85 34 118 84 365.38 0.93 86 34 119 85 365.38 0.93 87 35 66 31 421.99 4.73 88 35 67 32 420.94 5.19 89 35 68 33 420.87 5.21 90 35 69 34 420.74 5.26 91 35 70 35 420.72 5.26 92 35 79 44 420.39 5.12 93 35 80 45 420.38 5.12 94 35 83 48 420.38 5.12 95 35 118 83 365.40 0.93 96 35 119 84 365.39 0.93 97 35 121 86 365.38 0.93 98 36 64 28 423.70 4.71 99 36 66 30 421.95 4.74 100 36 67 31 420.94 5.18 101 36 118 82 365.46 0.93 102 36 119 83 365.43 0.93 103 36 120 84 365.38 0.93 104 36 121 85 365.38 0.93 105 36 165 129 161.22 0.23 106 37 64 27 423.71 4.71 107 37 65 28 423.70 4.70 108 37 66 29 422.05 4.75 109 37 80 43 420.38 5.12 110 37 121 84 365.38 0.93 111 37 122 85 365.37 0.93 112 38 46 8 434.89 3.41 113 38 64 26 423.71 4.71 114 38 65 27 423.70 4.70 115 38 120 82 365.47 0.93 116 38 121 83 365.42 0.93 117 38 122 84 365.36 0.93 118 38 123 85 365.37 0.93 119 38 144 106 194.55 3.92 120 38 162 124 170.70 1.25 121 38 165 127 162.95 0.46 122 38 166 128 161.53 0.25 123 38 175 137 128.83 0.97 124 39 46 7 434.89 3.41 125 39 47 8 434.83 3.43 126 39 65 26 423.72 4.70 127 39 66 27 423.72 4.70 128 39 84 45 420.21 5.25 129 39 88 49 417.03 5.63 130 39 90 51 413.75 4.49 131 39 92 53 391.26 4.17 132 39 123 84 365.35 0.93 133 39 125 86 364.85 0.79 134 40 44 4 489.06 6.62 135 40 45 5 446.30 8.16 136 40 46 6 434.89 3.41 137 40 123 83 365.42 0.93 138 40 124 84 365.33 0.94 139 40 125 85 365.31 0.93 140 40 141 101 264.02 0.83 141 40 144 104 246.02 4.91 142 40 175 135 129.50 0.74 143 40 178 138 127.28 1.20 144 41 44 3 574.61 3.03 145 41 45 4 500.67 0.82 146 41 124 83 365.41 0.93 147 41 125 84 365.35 0.93 148 41 141 100 266.86 0.58 149 42 124 82 365.43 0.92 150 43 124 81 365.48 0.93 151 44 124 80 365.42 0.92 152 44 179 135 123.73 0.58 153 45 141 96 266.85 0.62 154 45 142 97 260.16 0.03 155 46 65 19 424.23 4.68 156 46 140 94 267.19 0.49 157 46 141 95 261.26 0.49 158 46 142 96 259.38 0.36 159 46 144 98 222.31 2.77 160 46 147 101 204.08 0.33 161 47 65 18 424.23 4.68 162 47 88 41 417.16 5.57 163 47 129 82 275.28 0.42 164 47 139 92 267.33 0.51 165 47 140 93 267.16 0.51 166 47 141 94 263.85 0.79 167 48 62 14 430.10 4.45 168 48 63 15 427.95 5.50 169 48 139 91 269.08 0.41 170 48 140 92 267.23 0.48 171 48 142 94 266.30 0.85 172 48 147 99 198.08 2.06 173 48 162 114 171.02 1.16 174 49 62 13 430.28 4.36 175 49 63 14 427.96 5.51 176 49 64 15 427.94 5.51 177 49 65 16 427.22 5.54 178 49 88 39 416.52 5.40 179 49 136 87 274.46 0.38 180 49 138 89 273.88 0.24 181 49 139 90 267.31 0.52 182 50 60 10 433.31 3.48 183 50 61 11 432.20 3.92 184 50 62 12 431.11 3.95 185 50 136 86 274.54 0.41 186 50 137 87 274.43 0.39 187 50 138 88 274.01 0.30 188 51 55 4 559.75 8.04 189 51 57 6 479.19 5.29 190 51 58 7 433.85 3.29 191 51 59 8 433.58 3.38 192 51 60 9 433.32 3.48 193 51 61 10 432.73 3.72 194 51 63 12 432.55 3.72 195 51 135 84 274.59 0.41 196 51 137 86 274.44 0.39 197 52 55 3 599.52 1.98 198 52 59 7 433.84 3.29 199 52 60 8 433.78 3.27 200 52 133 81 274.85 0.42 201 52 134 82 274.75 0.44 202 52 135 83 274.60 0.42 203 52 136 84 274.54 0.42 204 52 137 85 274.50 0.42 205 53 59 6 433.84 3.29 206 53 60 7 433.78 3.27 207 53 137 84 274.52 0.42 208 54 134 80 274.75 0.45 209 55 59 4 460.75 2.93 210 55 134 79 274.74 0.46 211 55 135 80 274.59 0.42 212 56 112 56 366.20 0.88 213 57 108 51 366.24 0.86 214 57 112 55 366.17 0.88 215 57 114 57 366.02 0.95 216 58 61 3 588.87 4.05 217 58 106 48 366.23 0.85 218 58 107 49 366.24 0.86 219 58 108 50 366.22 0.85 220 58 109 51 366.24 0.86 221 58 114 56 366.02 0.95 222 58 160 102 170.94 1.16 223 58 161 103 170.97 1.16 224 59 108 49 366.23 0.85 225 60 137 77 274.44 0.40 226 61 158 97 171.02 1.17 227 61 159 98 171.00 1.17 228 62 138 76 274.07 0.32 229 62 139 77 271.80 0.79 230 62 140 78 271.19 0.56 231 62 157 95 171.08 1.15 232 62 158 96 171.02 1.16 233 62 159 97 171.02 1.16 234 63 159 96 170.94 1.14 235 63 162 99 170.77 1.26 236 64 162 98 170.66 1.25 237 64 165 101 166.24 0.30 238 65 88 23 416.37 5.45 239 66 80 14 420.39 5.13 240 66 83 17 420.38 5.14 241 66 84 18 420.13 5.19 242 66 87 21 416.06 5.61 243 66 88 22 413.81 4.49 244 67 87 20 416.98 4.39 245 68 83 15 419.98 5.10 246 69 82 13 430.39 0.15 247 69 114 45 365.57 0.96 248 69 116 47 365.51 0.95 249 70 74 4 537.34 4.16 250 70 76 6 459.20 1.24 251 70 79 9 430.40 0.15 252 70 82 12 445.99 4.82 253 71 74 3 570.82 4.96 254 71 82 11 461.23 0.27 255 74 78 4 572.40 0.24 256 74 79 5 571.36 0.56 257 74 82 8 558.07 2.58 258 75 78 3 572.60 0.15 259 75 79 4 572.69 1.20 260 76 79 3 575.77 2.74 261 76 80 4 574.75 2.23 262 76 119 43 365.51 0.95 263 76 121 45 365.47 0.93 264 77 80 3 580.54 0.32 265 77 81 4 576.88 1.93 266 77 95 18 365.53 0.96 267 77 121 44 365.49 0.94 268 78 81 3 586.39 4.76 269 78 82 4 576.12 1.55 270 79 82 3 590.63 1.12 271 79 83 4 576.12 1.55 272 80 83 3 588.27 2.83 273 80 84 4 563.54 1.74 274 80 92 12 402.95 17.00 275 80 95 15 365.48 0.94 276 80 121 41 365.45 0.93 277 81 84 3 584.11 0.52 278 81 85 4 577.79 2.64 279 81 92 11 399.88 15.49 280 81 95 14 365.51 0.96 281 82 85 3 580.36 1.35 282 82 86 4 577.79 2.64 283 83 86 3 569.27 6.90 284 83 87 4 568.45 7.31 285 83 135 52 274.38 0.34 286 84 88 4 543.82 1.31 287 84 89 5 524.07 2.85 288 84 90 6 472.25 0.29 289 84 92 8 455.82 5.04 290 85 89 4 475.06 1.10 291 85 90 5 472.26 0.29 292 85 91 6 472.25 0.29 293 86 132 46 274.41 0.30 294 86 135 49 274.48 0.35 295 87 132 45 274.36 0.28 296 87 135 48 274.43 0.36 297 88 129 41 275.07 0.33 298 88 130 42 274.94 0.37 299 88 131 43 274.70 0.35 300 88 136 48 274.47 0.36 301 89 130 41 274.98 0.35 302 90 125 35 359.30 0.45 303 90 127 37 323.73 2.43 304 90 128 38 314.80 5.17 305 90 129 39 275.19 0.39 306 91 125 34 363.63 0.14 307 91 126 35 352.80 2.06 308 91 127 36 334.87 2.26 309 92 95 3 673.31 4.33 310 92 123 31 365.41 0.95 311 92 124 32 365.30 0.93 312 92 125 33 358.50 0.84 313 92 126 34 349.76 0.54 314 93 123 30 365.45 0.94 315 93 124 31 365.37 0.93 316 93 126 33 364.13 0.65 317 95 121 26 365.54 0.94 318 95 122 27 365.51 0.94 319 95 123 28 365.43 0.95 320 96 121 25 365.55 0.94 321 96 122 26 365.54 0.94 322 96 178 82 123.95 0.46 323 97 100 3 606.25 2.97 324 97 120 23 365.68 0.96 325 97 121 24 365.55 0.94 326 97 174 77 129.46 0.84 327 98 120 22 365.69 0.95 328 98 121 23 365.67 0.96 329 98 122 24 365.62 0.94 330 98 171 73 130.03 0.60 331 98 174 76 128.84 0.97 332 98 175 77 128.84 0.97 333 99 102 3 597.28 1.66 334 99 119 20 365.72 0.95 335 99 120 21 365.69 0.95 336 99 165 66 161.31 0.18 337 99 168 69 151.19 1.41 338 99 171 72 130.03 0.60 339 100 119 19 365.71 0.95 340 102 117 15 365.93 0.92 341 102 118 16 365.79 0.96 342 102 120 18 365.75 0.97 343 102 161 59 170.53 1.27 344 102 164 62 163.21 0.59 345 102 165 63 161.23 0.21 346 103 115 12 366.36 0.83 347 103 116 13 366.16 0.86 348 103 117 14 365.81 0.97 349 104 115 11 366.37 0.83 350 104 116 12 366.28 0.82 351 104 160 56 170.49 1.25 352 104 161 57 170.49 1.25 353 104 164 60 163.86 1.09 354 105 113 8 366.68 0.77 355 105 114 9 366.58 0.80 356 105 115 10 366.37 0.83 357 105 161 56 170.64 1.23 358 106 113 7 366.68 0.78 359 106 114 8 366.67 0.78 360 106 160 54 170.56 1.25 361 106 161 55 170.64 1.23 362 107 111 4 518.08 9.90 363 107 112 5 456.85 0.38 364 107 113 6 366.69 0.78 365 108 111 3 550.10 6.11 366 108 112 4 471.00 0.42 367 114 161 47 170.56 1.27 368 116 161 45 170.51 1.25 369 118 161 43 170.51 1.26 370 120 165 45 161.19 0.24 371 122 175 53 128.83 0.97 372 122 178 56 122.48 1.20 373 123 178 55 127.27 1.19 374 124 178 54 127.27 1.19 375 124 179 55 123.74 0.57 376 125 141 16 266.95 0.56 377 129 139 10 274.36 0.38 378 129 141 12 268.09 0.81 379 131 136 5 500.30 1.24 380 131 139 8 357.25 41.02 381 132 135 3 588.06 2.12 382 132 136 4 558.36 0.29 383 133 136 3 571.99 0.04 384 136 139 3 651.19 0.90 385 142 147 5 569.42 0.55 386 143 146 3 595.71 6.15 387 143 147 4 579.49 0.61 388 144 147 3 580.16 0.28 389 144 148 4 579.49 0.61 390 144 175 31 131.07 0.80 391 144 176 32 129.81 0.57 392 145 148 3 591.72 1.36 393 145 149 4 582.72 1.00 394 146 149 3 591.02 2.10 395 146 150 4 582.72 1.01 396 147 150 3 594.07 4.04 397 147 151 4 574.07 2.54 398 147 162 15 171.27 1.19 399 148 151 3 590.15 3.88 400 148 152 4 576.10 1.52 401 148 166 18 171.10 1.19 402 148 172 24 155.61 1.09 403 148 176 28 132.56 0.04 404 149 152 3 576.11 1.52 405 149 153 4 575.01 2.07 406 150 153 3 586.00 3.42 407 150 154 4 563.88 2.10 408 150 158 8 495.07 3.16 409 151 155 4 530.50 1.19 410 151 158 7 486.96 7.21 411 151 162 11 298.09 62.19 412 151 163 12 171.22 1.20 413 151 166 15 171.22 1.20 414 151 167 16 171.19 1.22 415 152 155 3 588.64 2.73 416 152 172 20 161.15 0.22 417 154 157 3 595.09 0.21 418 154 158 4 595.09 0.21 419 155 158 3 588.06 3.31 420 155 163 8 468.12 8.84 421 158 162 4 574.91 1.74 422 158 163 5 574.16 1.45 423 159 162 3 578.25 0.07 424 159 163 4 580.72 4.62 425 160 163 3 586.84 3.19 426 160 164 4 580.73 4.62 427 161 164 3 587.59 2.82 428 161 165 4 579.43 0.52 429 162 165 3 581.54 0.21 430 162 166 4 577.44 0.47 431 163 166 3 598.62 5.47 432 163 167 4 575.35 2.29 433 164 167 3 589.98 4.21 434 164 168 4 579.44 0.24 435 165 168 3 596.06 1.17 436 165 171 6 545.23 0.43 437 166 172 6 545.21 0.42 438 167 172 5 563.00 3.77 439 168 171 3 587.50 4.71 440 168 172 4 574.54 1.98 441 169 172 3 594.83 0.89 442 169 173 4 574.54 1.98 443 170 173 3 580.05 0.33 444 170 174 4 574.54 1.98 445 171 174 3 581.84 4.49 446 171 175 4 570.90 0.20 447 172 175 3 588.50 3.90 448 172 176 4 570.83 0.24 449 173 176 3 584.10 5.62 450 173 177 4 570.78 0.27 451 174 177 3 574.73 2.35 452 174 178 4 574.44 2.23 453 175 178 3 575.29 2.60 454 175 179 4 579.12 0.69 455 176 179 3 595.17 2.47