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 3 53 50 87.83 1.39 2 4 8 4 654.26 3.97 3 4 9 5 638.60 3.85 4 4 12 8 631.89 2.42 5 4 50 46 88.48 1.72 6 4 53 49 88.49 1.72 7 5 8 3 655.63 3.85 8 5 9 4 655.09 3.58 9 6 9 3 674.19 1.54 10 6 10 4 656.99 3.18 11 7 10 3 661.52 1.06 12 7 11 4 657.20 3.06 13 7 37 30 122.06 0.19 14 7 46 39 104.75 0.32 15 8 11 3 668.81 0.66 16 8 12 4 656.10 0.31 17 8 49 41 104.69 0.31 18 8 50 42 104.70 0.31 19 8 53 45 103.28 0.54 20 9 12 3 659.68 2.03 21 9 13 4 655.78 0.15 22 9 16 7 651.10 2.50 23 10 13 3 655.86 0.12 24 10 14 4 655.92 0.22 25 10 35 25 122.36 0.21 26 11 14 3 666.44 0.60 27 11 15 4 656.01 0.27 28 11 31 20 122.23 0.15 29 11 35 24 122.23 0.14 30 11 37 26 122.22 0.14 31 11 46 35 105.17 0.15 32 11 47 36 105.16 0.14 33 11 50 39 105.12 0.16 34 12 15 3 657.53 0.91 35 12 16 4 656.01 0.27 36 12 50 38 104.78 0.33 37 12 55 43 103.03 0.50 38 12 56 44 102.84 0.59 39 12 68 56 79.04 0.01 40 13 16 3 679.75 3.93 41 13 17 4 654.59 0.97 42 13 91 78 50.00 0.46 43 14 17 3 679.79 3.90 44 14 18 4 653.73 1.39 45 14 31 17 122.56 0.13 46 14 34 20 122.61 0.15 47 14 35 21 122.61 0.15 48 15 18 3 680.77 3.41 49 15 19 4 666.53 0.97 50 15 26 11 123.66 0.01 51 15 31 16 122.59 0.14 52 15 47 32 120.61 0.55 53 15 50 35 107.50 0.60 54 15 56 41 102.85 0.60 55 15 66 51 80.12 0.10 56 15 68 53 79.14 0.04 57 16 19 3 666.53 0.97 58 16 20 4 649.23 1.69 59 16 68 52 79.14 0.04 60 16 91 75 51.30 0.27 61 17 20 3 670.70 1.10 62 17 21 4 657.84 0.71 63 17 87 70 51.11 0.17 64 17 90 73 50.77 0.40 65 17 91 74 51.20 0.22 66 18 21 3 664.22 2.47 67 18 22 4 643.77 1.03 68 18 23 5 641.86 1.98 69 18 24 6 501.32 45.91 70 18 25 7 277.06 52.62 71 18 26 8 273.13 54.58 72 19 22 3 666.12 3.40 73 19 23 4 601.95 4.64 74 19 24 5 599.58 5.83 75 19 25 6 280.00 54.03 76 19 68 49 80.25 0.22 77 20 87 67 51.62 0.33 78 21 86 65 52.10 0.47 79 21 87 66 51.62 0.34 80 24 64 40 83.28 0.72 81 25 64 39 83.27 0.72 82 25 66 41 81.64 0.02 83 26 30 4 642.11 0.60 84 26 31 5 642.03 0.56 85 26 64 38 83.27 0.72 86 26 66 40 83.21 0.72 87 27 30 3 666.04 3.90 88 27 31 4 653.86 5.22 89 27 64 37 83.26 0.72 90 28 31 3 666.04 3.90 91 28 32 4 652.71 1.13 92 28 40 12 148.43 0.42 93 28 43 15 145.24 1.34 94 28 44 16 145.20 1.32 95 28 47 19 145.18 1.31 96 28 58 30 102.28 0.86 97 28 66 38 83.24 0.71 98 29 32 3 670.12 1.86 99 29 33 4 652.02 1.51 100 29 40 11 255.44 53.93 101 30 33 3 676.94 6.30 102 30 34 4 650.59 2.23 103 30 64 34 83.42 0.79 104 31 34 3 685.98 1.79 105 31 35 4 652.04 1.49 106 31 37 6 633.94 2.68 107 31 43 12 145.94 1.65 108 31 47 16 145.22 1.31 109 32 35 3 680.60 4.48 110 32 36 4 650.57 2.23 111 32 37 5 618.30 5.12 112 32 39 7 380.47 0.74 113 32 40 8 373.38 2.59 114 32 43 11 148.37 0.44 115 33 36 3 652.37 3.12 116 37 42 5 642.40 2.03 117 37 43 6 630.13 9.30 118 37 46 9 612.38 5.67 119 38 42 4 658.85 4.63 120 39 42 3 665.69 1.22 121 39 43 4 666.39 0.87 122 40 43 3 668.52 1.93 123 40 44 4 666.38 0.87 124 41 44 3 668.51 1.93 125 41 45 4 666.39 0.86 126 42 45 3 671.73 1.15 127 42 46 4 667.15 0.47 128 43 46 3 677.35 2.00 129 43 47 4 661.91 1.36 130 44 47 3 665.99 0.12 131 44 48 4 657.72 0.70 132 45 48 3 666.00 0.12 133 45 49 4 662.08 1.83 134 46 49 3 660.62 2.00 135 46 50 4 659.72 2.44 136 47 50 3 670.88 7.29 137 47 51 4 657.67 1.53 138 47 56 9 479.84 50.31 139 47 58 11 120.28 9.99 140 47 66 19 79.72 0.06 141 48 51 3 671.99 6.74 142 48 52 4 652.96 0.82 143 48 58 10 156.03 0.16 144 49 52 3 655.44 3.35 145 49 53 4 653.70 3.52 146 50 53 3 668.98 8.31 147 50 54 4 648.00 0.68 148 50 55 5 625.25 0.06 149 50 56 6 488.43 46.02 150 51 54 3 648.77 0.27 151 51 56 5 597.89 13.62 152 51 58 7 265.45 50.20 153 54 69 15 78.99 0.03 154 54 70 16 78.99 0.03 155 55 68 13 79.03 0.04 156 55 69 14 78.99 0.03 157 56 66 10 79.86 0.01 158 56 67 11 79.55 0.03 159 56 68 12 79.03 0.02 160 56 69 13 79.00 0.03 161 57 66 9 79.91 0.01 162 57 67 10 79.72 0.06 163 57 69 12 79.20 0.03 164 58 65 7 80.88 0.02 165 59 65 6 80.53 0.15 166 68 71 3 712.67 1.33 167 70 73 3 783.93 3.12 168 74 99 25 564.37 0.48 169 75 98 23 564.43 0.45 170 75 99 24 564.36 0.47 171 75 100 25 564.30 0.48 172 75 102 27 564.22 0.49 173 76 97 21 564.50 0.47 174 76 98 22 564.44 0.45 175 76 100 24 564.41 0.46 176 76 102 26 564.37 0.47 177 76 109 33 563.98 0.51 178 76 110 34 563.86 0.52 179 76 111 35 563.79 0.49 180 76 112 36 563.78 0.49 181 77 94 17 565.29 0.26 182 77 96 19 564.72 0.47 183 77 97 20 564.53 0.46 184 77 110 33 563.98 0.51 185 77 111 34 563.85 0.52 186 77 112 35 563.85 0.52 187 78 94 16 565.30 0.26 188 78 95 17 565.29 0.26 189 78 96 18 565.23 0.24 190 78 98 20 564.62 0.43 191 78 112 34 563.87 0.51 192 78 113 35 563.86 0.51 193 78 114 36 563.85 0.52 194 78 130 52 298.99 2.44 195 79 82 3 758.92 0.06 196 79 88 9 565.43 0.32 197 79 89 10 565.43 0.31 198 79 93 14 565.36 0.27 199 79 94 15 565.32 0.26 200 79 111 32 563.98 0.50 201 79 112 33 563.95 0.50 202 79 113 34 563.87 0.51 203 79 114 35 563.86 0.51 204 80 93 13 565.39 0.28 205 80 95 15 565.32 0.26 206 80 114 34 563.86 0.51 207 81 93 12 565.53 0.24 208 82 88 6 565.83 0.21 209 82 93 11 565.53 0.24 210 82 148 66 301.27 2.17 211 82 153 71 301.26 2.16 212 83 86 3 673.49 5.62 213 83 92 9 565.87 0.23 214 83 93 10 565.85 0.22 215 83 148 65 301.36 2.14 216 84 148 64 301.37 2.14 217 84 151 67 301.35 2.14 218 85 151 66 301.82 2.37 219 86 90 4 601.11 3.60 220 86 92 6 599.23 4.54 221 86 93 7 579.88 5.13 222 86 148 62 301.37 2.14 223 87 90 3 644.81 2.25 224 87 93 6 601.99 3.17 225 87 148 61 301.26 2.16 226 88 93 5 601.99 3.17 227 88 111 23 564.17 0.49 228 88 148 60 301.14 2.21 229 88 153 65 301.24 2.17 230 88 189 101 295.82 0.97 231 89 94 5 598.89 1.62 232 89 111 22 564.10 0.47 233 90 93 3 673.63 0.77 234 90 94 4 655.22 5.79 235 91 94 3 665.77 0.98 236 94 97 3 826.16 4.33 237 95 114 19 563.87 0.51 238 98 112 14 563.86 0.52 239 98 130 32 298.12 2.00 240 98 198 100 225.37 4.65 241 100 104 4 681.43 3.58 242 100 105 5 677.24 5.68 243 100 196 96 237.88 10.27 244 101 104 3 677.23 5.69 245 102 105 3 689.73 2.64 246 102 108 6 564.57 0.23 247 102 109 7 563.96 0.48 248 103 108 5 565.64 0.26 249 105 108 3 682.23 1.46 250 105 109 4 649.25 3.71 251 105 132 27 296.39 1.25 252 105 193 88 277.48 0.71 253 105 194 89 277.19 0.70 254 105 196 91 277.19 0.70 255 106 193 87 280.43 1.57 256 107 134 27 295.98 1.12 257 107 191 84 295.84 1.08 258 107 193 86 280.48 1.55 259 108 134 26 295.96 1.11 260 109 132 23 296.26 1.19 261 109 133 24 295.97 1.11 262 109 193 84 277.80 0.60 263 110 133 23 296.26 1.19 264 110 134 24 295.96 1.12 265 110 135 25 295.94 1.13 266 111 132 21 296.38 1.19 267 111 133 22 296.12 1.18 268 111 135 24 295.95 1.14 269 112 130 18 299.00 2.44 270 112 131 19 298.04 2.01 271 112 132 20 296.37 1.21 272 112 196 84 241.24 8.76 273 113 130 17 299.01 2.44 274 113 131 18 298.06 2.02 275 113 133 20 298.01 2.02 276 113 146 33 298.03 2.00 277 113 153 40 300.05 2.41 278 113 155 42 298.52 2.14 279 114 128 14 299.67 2.48 280 114 129 15 299.52 2.41 281 114 130 16 299.01 2.44 282 115 125 10 300.28 2.56 283 115 126 11 300.41 2.60 284 115 127 12 300.37 2.60 285 115 128 13 300.13 2.70 286 115 129 14 299.58 2.44 287 115 131 16 299.50 2.40 288 116 127 11 313.30 2.45 289 117 127 10 319.03 0.40 290 118 121 3 643.26 4.29 291 118 126 8 334.62 2.73 292 118 127 9 326.10 1.35 293 118 171 53 344.53 1.76 294 118 174 56 344.44 1.72 295 119 156 37 344.00 1.88 296 119 169 50 344.19 1.79 297 119 170 51 344.44 1.71 298 119 171 52 344.53 1.76 299 119 174 55 344.39 1.74 300 120 123 3 681.41 0.29 301 120 124 4 636.56 1.42 302 120 125 5 376.11 5.07 303 120 144 24 344.06 1.86 304 120 155 35 344.12 1.84 305 120 156 36 344.15 1.84 306 120 157 37 344.31 1.77 307 120 168 48 344.44 1.72 308 120 169 49 344.44 1.71 309 120 170 50 344.50 1.74 310 121 124 3 644.62 5.45 311 121 125 4 594.47 8.20 312 121 126 5 375.30 5.47 313 121 170 49 344.78 1.71 314 121 171 50 344.94 1.67 315 122 170 48 344.87 1.67 316 122 171 49 345.01 1.66 317 123 144 21 344.77 1.70 318 123 157 34 345.02 1.66 319 123 170 47 345.03 1.66 320 124 197 73 277.88 0.64 321 125 129 4 618.08 15.13 322 125 131 6 361.12 2.00 323 125 144 19 345.04 1.65 324 125 195 70 277.88 0.64 325 126 129 3 665.45 2.97 326 126 197 71 274.31 1.17 327 129 195 66 277.31 0.53 328 129 197 68 238.03 10.28 329 130 195 65 266.19 1.38 330 130 196 66 256.88 0.94 331 130 198 68 238.00 10.29 332 131 146 15 347.14 1.71 333 131 155 24 346.98 1.79 334 131 192 61 345.07 1.67 335 131 194 63 325.23 3.75 336 131 195 64 272.06 0.56 337 132 192 60 345.30 1.56 338 132 193 61 344.93 1.60 339 132 194 62 325.26 3.75 340 133 146 13 347.31 1.68 341 133 190 57 347.01 1.53 342 133 191 58 346.25 1.43 343 133 193 60 345.29 1.56 344 134 190 56 347.29 1.65 345 134 191 57 346.47 1.53 346 134 193 59 345.73 1.37 347 135 189 54 347.50 1.62 348 135 190 55 347.29 1.66 349 136 139 3 736.99 3.19 350 136 188 52 347.85 1.70 351 136 189 53 347.69 1.67 352 136 190 54 347.39 1.64 353 136 191 55 347.39 1.64 354 137 188 51 347.90 1.73 355 139 143 4 658.09 2.06 356 139 145 6 356.92 1.22 357 139 158 19 356.45 1.00 358 139 188 49 348.45 1.56 359 139 191 52 347.72 1.66 360 140 143 3 677.32 1.55 361 140 158 18 356.45 1.00 362 141 158 17 356.45 1.00 363 141 159 18 356.36 1.05 364 141 160 19 356.37 1.04 365 142 157 15 357.92 0.94 366 142 158 16 357.31 1.02 367 143 157 14 358.14 0.89 368 143 158 15 358.07 0.88 369 143 191 48 348.39 1.62 370 144 155 11 360.23 1.06 371 144 156 12 358.99 0.97 372 144 157 13 358.22 0.89 373 144 191 47 348.50 1.57 374 144 192 48 348.27 1.60 375 145 155 10 360.23 1.06 376 145 156 11 360.10 1.04 377 145 158 13 359.00 0.98 378 145 188 43 351.90 1.65 379 145 190 45 348.99 1.73 380 146 153 7 365.95 3.75 381 146 154 8 360.51 1.13 382 146 155 9 360.24 1.06 383 146 188 42 351.93 1.64 384 146 189 43 351.29 1.65 385 146 190 44 349.97 2.04 386 147 153 6 426.35 33.95 387 147 154 7 360.67 1.11 388 147 167 20 360.20 1.08 389 147 186 39 353.94 1.62 390 147 187 40 353.38 1.47 391 147 188 41 352.41 1.88 392 148 151 3 663.32 4.19 393 148 152 4 529.24 19.25 394 148 153 5 426.36 33.95 395 148 186 38 353.94 1.62 396 148 187 39 353.88 1.64 397 148 189 41 352.62 1.79 398 149 152 3 646.70 2.15 399 149 154 5 564.02 33.84 400 149 167 18 360.56 1.14 401 149 177 28 360.53 1.14 402 149 179 30 358.91 1.05 403 149 184 35 356.89 0.77 404 149 185 36 356.79 0.76 405 149 186 37 354.03 1.66 406 150 184 34 356.91 0.76 407 150 185 35 356.81 0.76 408 154 167 13 489.93 1.08 409 154 177 23 487.22 2.44 410 156 167 11 490.81 1.25 411 156 168 12 491.03 1.20 412 156 169 13 491.03 1.20 413 156 177 21 490.97 1.23 414 157 167 10 491.04 1.19 415 157 168 11 491.04 1.19 416 157 170 13 491.41 1.27 417 158 165 7 492.61 1.08 418 158 167 9 491.12 1.21 419 159 165 6 492.62 1.08 420 159 166 7 491.15 1.22 421 159 168 9 491.39 1.26 422 160 165 5 492.69 1.05 423 161 164 3 646.18 2.42 424 161 165 4 493.95 1.68 425 161 166 5 492.70 1.05 426 163 181 18 491.24 1.22 427 163 182 19 491.22 1.22 428 164 178 14 491.68 1.17 429 164 179 15 491.53 1.22 430 164 180 16 491.39 1.18 431 164 181 17 491.39 1.19 432 164 182 18 491.39 1.18 433 165 178 13 491.69 1.17 434 165 179 14 491.58 1.21 435 165 181 16 491.50 1.19 436 165 186 21 359.58 1.11 437 166 177 11 491.79 1.15 438 166 178 12 491.70 1.17 439 167 176 9 491.88 1.13 440 167 177 10 491.79 1.15 441 167 179 12 491.78 1.15 442 167 186 19 359.57 1.10 443 168 176 8 491.90 1.13 444 169 174 5 492.74 1.32 445 169 175 6 492.72 1.31 446 169 176 7 491.97 1.17 447 171 174 3 667.81 6.24 448 179 184 5 538.63 20.16 449 179 186 7 493.32 1.17 450 180 183 3 675.89 4.20 451 180 184 4 623.53 9.07 452 181 184 3 662.34 2.25 453 181 186 5 495.80 0.82