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 37 34 99.44 0.14 2 3 38 35 99.43 0.14 3 3 41 38 101.50 0.46 4 4 34 30 100.04 0.17 5 4 38 34 101.27 0.40 6 4 52 48 99.41 0.15 7 5 52 47 101.29 0.39 8 6 38 32 103.30 0.10 9 6 42 36 104.14 0.10 10 6 51 45 101.72 0.56 11 6 52 46 101.51 0.46 12 6 97 91 103.52 0.10 13 6 98 92 104.05 0.07 14 7 11 4 549.72 0.04 15 7 13 6 497.67 6.21 16 7 14 7 445.34 2.73 17 7 50 43 102.33 0.30 18 7 51 44 102.31 0.29 19 7 52 45 103.09 0.03 20 7 53 46 102.36 0.30 21 7 98 91 104.72 0.14 22 8 11 3 578.48 1.02 23 8 14 6 505.55 3.26 24 8 97 89 104.77 0.14 25 8 98 90 104.74 0.14 26 8 100 92 105.20 0.18 27 9 14 5 518.03 3.37 28 9 98 89 105.20 0.18 29 9 99 90 105.06 0.24 30 9 147 138 85.45 0.10 31 9 160 151 21.91 0.03 32 9 164 155 14.10 0.32 33 11 14 3 558.56 0.46 34 12 15 3 544.69 0.27 35 12 16 4 543.39 0.38 36 13 16 3 555.89 3.90 37 13 53 40 108.02 0.10 38 14 50 36 107.45 0.20 39 14 51 37 107.45 0.20 40 14 98 84 107.35 0.15 41 14 145 131 89.06 1.59 42 14 147 133 85.76 0.11 43 15 145 130 89.06 1.59 44 15 146 131 89.06 1.59 45 15 147 132 89.06 1.59 46 15 150 135 84.06 0.48 47 16 50 34 108.64 0.16 48 16 55 39 109.31 0.34 49 16 145 129 92.88 0.32 50 17 143 126 107.14 0.03 51 18 50 32 109.33 0.34 52 18 55 37 109.35 0.34 53 18 56 38 109.37 0.35 54 18 57 39 109.19 0.39 55 18 143 125 107.78 0.29 56 19 55 36 109.42 0.34 57 19 56 37 109.42 0.34 58 19 57 38 109.40 0.35 59 20 57 37 109.81 0.15 60 20 80 60 110.64 0.27 61 21 24 3 611.98 9.12 62 21 28 7 486.62 0.03 63 21 56 35 110.73 0.23 64 21 57 36 110.73 0.23 65 21 58 37 110.73 0.24 66 21 79 58 110.74 0.24 67 21 80 59 110.74 0.23 68 23 28 5 520.91 2.36 69 24 28 4 522.70 3.25 70 24 79 55 139.89 0.51 71 24 80 56 139.88 0.51 72 24 117 93 139.91 0.51 73 24 118 94 139.91 0.51 74 24 119 95 139.91 0.51 75 24 121 97 141.14 0.11 76 25 28 3 539.05 0.56 77 25 29 4 526.61 1.30 78 26 29 3 532.08 4.03 79 26 30 4 532.13 4.00 80 27 30 3 540.08 0.52 81 27 31 4 533.81 3.18 82 28 31 3 534.25 3.40 83 28 32 4 532.73 3.71 84 28 56 28 159.46 0.58 85 28 58 30 159.31 0.50 86 28 79 51 164.18 0.49 87 29 32 3 544.83 2.34 88 29 33 4 545.48 2.67 89 29 119 90 180.02 0.93 90 29 120 91 183.50 2.35 91 30 33 3 545.48 2.67 92 30 34 4 544.01 1.95 93 31 34 3 547.75 1.53 94 31 35 4 545.44 2.68 95 31 54 23 183.55 2.44 96 31 56 25 184.33 2.04 97 31 58 27 183.55 2.44 98 32 35 3 545.44 2.69 99 32 36 4 545.42 2.69 100 32 58 26 184.34 2.05 101 32 60 28 183.62 2.42 102 32 77 45 189.72 0.62 103 32 79 47 187.34 0.56 104 32 119 87 193.34 0.76 105 33 36 3 543.90 0.50 106 33 37 4 526.52 0.67 107 33 119 86 194.62 0.77 108 34 37 3 544.07 1.99 109 34 38 4 525.27 1.42 110 35 38 3 549.75 0.51 111 35 39 4 536.50 4.19 112 35 47 12 194.77 0.82 113 35 48 13 194.77 0.82 114 35 49 14 194.77 0.82 115 35 52 17 194.76 0.81 116 35 58 23 194.78 0.81 117 35 59 24 194.77 0.82 118 35 60 25 194.84 0.79 119 36 39 3 548.84 0.41 120 36 40 4 538.27 4.87 121 36 60 24 194.84 0.80 122 36 62 26 197.31 1.48 123 36 72 36 197.36 1.47 124 36 75 39 194.93 0.79 125 37 40 3 557.52 2.85 126 37 41 4 538.06 4.97 127 38 41 3 549.42 0.10 128 38 42 4 538.06 4.97 129 38 52 14 195.01 0.71 130 39 42 3 548.82 0.41 131 39 43 4 536.57 5.71 132 39 44 5 485.75 13.05 133 39 45 6 448.07 1.30 134 39 46 7 313.56 59.62 135 39 47 8 195.08 0.70 136 39 60 21 195.37 0.57 137 39 62 23 198.59 1.71 138 39 97 58 197.69 1.69 139 40 43 3 545.32 1.33 140 40 70 30 241.48 1.63 141 42 97 55 238.82 0.85 142 44 70 26 260.23 5.25 143 44 97 53 246.38 0.16 144 45 61 16 259.92 5.26 145 45 62 17 259.99 5.24 146 45 63 18 260.05 5.24 147 45 64 19 260.17 5.28 148 45 70 25 260.24 5.25 149 45 131 86 248.72 0.33 150 46 60 14 259.98 5.24 151 46 61 15 259.98 5.24 152 46 97 51 249.13 0.17 153 46 139 93 248.09 0.07 154 47 51 4 538.73 0.82 155 47 52 5 526.82 6.78 156 47 59 12 260.00 5.23 157 47 60 13 260.04 5.24 158 47 97 50 249.44 0.01 159 47 139 92 248.59 0.30 160 48 51 3 548.95 2.48 161 48 58 10 260.01 5.23 162 48 59 11 260.00 5.23 163 48 139 91 248.75 0.36 164 48 142 94 248.40 0.39 165 48 143 95 247.58 0.12 166 49 52 3 550.12 4.87 167 49 53 4 543.36 1.50 168 49 54 5 478.66 5.24 169 49 56 7 265.99 3.63 170 49 58 9 260.01 5.23 171 50 53 3 543.36 1.51 172 50 54 4 508.50 6.60 173 50 55 5 491.39 1.84 174 50 142 92 248.60 0.48 175 51 96 45 252.07 0.42 176 51 97 46 252.06 0.42 177 51 98 47 252.06 0.42 178 51 139 88 249.06 0.38 179 51 142 91 248.59 0.48 180 54 58 4 567.68 1.83 181 56 143 87 249.46 0.88 182 57 79 22 262.24 4.28 183 57 80 23 260.97 4.90 184 57 81 24 260.98 4.89 185 57 143 86 249.46 0.89 186 57 144 87 249.46 0.89 187 58 78 20 262.35 4.23 188 58 79 21 261.85 4.48 189 58 143 85 249.64 1.00 190 59 77 18 262.56 4.22 191 59 78 19 262.38 4.24 192 59 81 22 262.38 4.24 193 59 139 80 250.92 1.34 194 59 140 81 250.75 1.27 195 59 143 84 250.14 1.26 196 60 75 15 263.20 4.02 197 60 76 16 263.00 4.05 198 60 77 17 262.56 4.22 199 61 75 14 263.24 4.03 200 61 76 15 263.05 4.07 201 61 78 17 263.00 4.06 202 61 132 71 251.76 1.55 203 61 135 74 251.48 1.47 204 61 136 75 251.49 1.47 205 61 139 78 251.18 1.44 206 62 70 8 263.49 4.08 207 62 71 9 263.49 4.08 208 62 72 10 263.43 4.05 209 62 74 12 263.26 4.03 210 62 75 13 263.24 4.03 211 63 131 68 251.87 1.64 212 63 132 69 251.86 1.64 213 63 135 72 251.82 1.63 214 64 68 4 448.13 1.23 215 64 69 5 263.86 4.08 216 64 70 6 263.58 4.09 217 65 68 3 538.03 5.05 218 65 69 4 504.86 2.98 219 65 71 6 263.94 4.12 220 65 74 9 263.72 4.15 221 67 71 4 611.10 1.36 222 71 74 3 550.81 0.96 223 71 75 4 529.52 3.97 224 72 75 3 537.45 0.01 225 76 116 40 414.25 2.14 226 76 126 50 302.69 1.04 227 76 132 56 252.43 1.75 228 77 116 39 418.36 0.09 229 77 118 41 415.09 0.19 230 77 119 42 421.28 0.45 231 78 81 3 564.86 0.43 232 78 114 36 408.41 0.77 233 78 116 38 418.36 0.09 234 78 136 58 252.38 1.80 235 79 116 37 421.42 0.69 236 79 117 38 421.69 0.56 237 79 118 39 421.98 0.70 238 79 119 40 422.05 0.69 239 80 116 36 421.95 0.70 240 80 117 37 421.99 0.70 241 81 115 34 421.96 0.69 242 81 116 35 421.96 0.70 243 81 140 59 303.45 6.89 244 81 143 62 296.49 5.42 245 82 114 32 422.00 0.68 246 82 115 33 422.00 0.69 247 83 112 29 422.44 0.45 248 83 113 30 422.43 0.47 249 83 114 31 422.03 0.67 250 83 136 53 369.19 1.02 251 83 137 54 354.26 6.40 252 83 140 57 331.93 0.97 253 84 113 29 422.69 0.59 254 84 114 30 422.55 0.68 255 84 115 31 422.47 0.72 256 84 125 41 422.45 0.73 257 85 112 27 422.76 0.58 258 85 113 28 422.74 0.59 259 86 109 23 423.42 0.70 260 86 111 25 423.20 0.72 261 86 112 26 422.77 0.58 262 87 109 22 423.43 0.70 263 87 110 23 423.42 0.70 264 87 111 24 423.21 0.72 265 88 109 21 423.47 0.70 266 88 110 22 423.40 0.71 267 89 107 18 423.83 0.74 268 89 108 19 423.74 0.78 269 89 109 20 423.49 0.70 270 89 110 21 423.47 0.70 271 90 107 17 423.86 0.74 272 90 108 18 423.78 0.77 273 90 110 20 423.51 0.71 274 90 130 40 422.54 0.76 275 90 134 44 420.78 0.62 276 91 105 14 424.22 0.74 277 91 106 15 424.12 0.71 278 91 107 16 423.86 0.74 279 92 105 13 424.25 0.75 280 92 106 14 424.20 0.75 281 92 131 39 422.56 0.78 282 92 134 42 421.92 0.70 283 93 103 10 424.45 0.82 284 93 104 11 424.28 0.75 285 93 105 12 424.26 0.74 286 94 103 9 424.45 0.82 287 94 104 10 424.43 0.82 288 94 106 12 424.26 0.74 289 94 108 14 424.29 0.76 290 94 134 40 422.31 0.84 291 94 138 44 412.22 2.37 292 94 148 54 343.68 1.03 293 95 102 7 424.51 0.83 294 95 103 8 424.44 0.82 295 95 138 43 420.74 0.67 296 95 148 53 344.06 1.02 297 96 99 3 532.38 0.73 298 96 100 4 519.29 5.81 299 96 138 42 421.05 0.51 300 96 142 46 392.84 0.54 301 96 148 52 353.43 5.70 302 97 100 3 547.72 2.65 303 99 102 3 563.75 2.54 304 99 148 49 361.38 1.74 305 99 149 50 361.27 1.78 306 99 160 61 286.67 1.68 307 102 148 46 353.50 5.67 308 102 149 47 344.14 1.06 309 102 152 50 343.66 0.98 310 102 160 58 158.75 65.51 311 102 163 61 144.46 61.87 312 104 148 44 343.57 0.99 313 104 152 48 329.83 1.86 314 104 156 52 298.13 5.83 315 104 159 55 290.92 2.38 316 105 152 47 328.98 1.44 317 106 148 42 337.89 1.63 318 106 151 45 328.97 1.44 319 106 152 46 326.47 2.68 320 108 134 26 411.18 2.85 321 108 137 29 386.32 1.66 322 108 138 30 384.35 2.64 323 108 141 33 371.28 1.65 324 108 148 40 337.89 1.63 325 108 151 43 328.97 1.44 326 109 112 3 587.66 3.27 327 109 137 28 384.29 2.62 328 110 129 19 422.48 0.74 329 110 130 20 422.39 0.76 330 110 133 23 407.49 0.07 331 111 128 17 422.56 0.79 332 111 129 18 422.16 0.81 333 112 127 15 422.61 0.81 334 112 128 16 422.47 0.83 335 112 133 21 383.60 1.93 336 112 136 24 373.84 2.46 337 112 137 25 373.68 2.53 338 113 125 12 422.74 0.81 339 113 126 13 422.62 0.82 340 113 127 14 422.60 0.82 341 114 125 11 422.75 0.81 342 114 126 12 422.64 0.83 343 114 136 22 369.33 0.95 344 114 140 26 331.96 0.96 345 115 123 8 422.92 0.79 346 115 124 9 422.86 0.80 347 115 125 10 422.76 0.81 348 116 123 7 422.92 0.79 349 116 124 8 422.88 0.80 350 116 126 10 422.84 0.81 351 117 121 4 447.45 10.76 352 117 122 5 446.74 11.12 353 117 123 6 422.93 0.78 354 118 121 3 540.09 5.08 355 118 122 4 452.16 8.41 356 118 124 6 422.96 0.76 357 126 132 6 515.65 6.87 358 126 136 10 471.88 1.84 359 128 132 4 517.88 5.75 360 128 133 5 505.26 1.78 361 128 136 8 490.47 9.16 362 129 132 3 554.49 1.37 363 129 133 4 507.41 2.68 364 130 133 3 540.48 0.21 365 130 134 4 535.38 0.97 366 131 134 3 547.69 2.80 367 131 135 4 534.73 1.30 368 132 135 3 539.76 0.16 369 132 136 4 537.01 1.54 370 133 136 3 546.37 3.46 371 133 137 4 537.02 1.53 372 134 137 3 537.03 1.53 373 134 138 4 535.35 0.70 374 135 138 3 535.37 0.70 375 135 139 4 535.34 0.69 376 136 139 3 543.23 1.56 377 136 140 4 538.37 0.06 378 137 140 3 544.29 2.35 379 137 141 4 538.38 0.06 380 138 141 3 549.58 1.74 381 138 142 4 538.39 0.06 382 138 148 10 337.90 1.62 383 139 142 3 545.09 3.31 384 139 143 4 545.10 3.31 385 140 143 3 554.14 1.22 386 140 144 4 545.44 3.14 387 141 144 3 546.08 2.81 388 141 145 4 545.02 3.34 389 141 146 5 498.29 7.92 390 141 151 10 425.70 0.87 391 142 145 3 542.38 0.97 392 142 146 4 527.63 1.78 393 142 147 5 514.76 4.66 394 146 150 4 535.12 0.40 395 146 151 5 535.11 0.40 396 147 150 3 543.40 3.74 397 148 151 3 537.15 0.59 398 148 152 4 535.14 0.41 399 149 152 3 543.29 2.00 400 149 160 11 159.13 65.41 401 152 156 4 530.15 2.67 402 152 157 5 520.95 5.46 403 152 160 8 485.56 6.04 404 153 156 3 543.11 1.74 405 153 157 4 535.22 0.14 406 154 157 3 544.21 1.19 407 154 158 4 541.82 0.01 408 155 158 3 555.94 0.29 409 155 159 4 541.83 0.01 410 156 159 3 539.84 1.01 411 156 160 4 536.76 0.54 412 157 160 3 546.76 2.94 413 157 161 4 539.21 0.69 414 158 161 3 543.06 1.23 415 158 162 4 537.69 1.46 416 159 162 3 546.16 2.78 417 159 163 4 539.27 0.67 418 160 163 3 553.27 0.78 419 160 164 4 531.40 4.59 420 161 164 3 545.13 2.66