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 2 10 8 477.93 0.06 2 2 130 128 42.73 0.24 3 2 133 131 34.07 1.43 4 2 134 132 33.59 1.60 5 2 137 135 33.59 1.60 6 3 6 3 520.76 2.18 7 3 7 4 502.35 10.66 8 4 7 3 513.80 4.93 9 4 8 4 497.98 7.13 10 4 79 75 52.28 2.50 11 5 8 3 518.80 2.36 12 5 9 4 504.10 4.07 13 6 9 3 517.63 2.69 14 6 10 4 504.29 3.97 15 6 130 124 70.91 0.41 16 6 133 127 70.98 0.37 17 7 10 3 511.72 0.63 18 7 11 4 511.34 0.42 19 7 76 69 71.20 0.47 20 7 79 72 71.21 0.47 21 7 80 73 71.44 0.58 22 7 134 127 71.17 0.45 23 7 137 130 71.20 0.47 24 8 11 3 517.08 3.15 25 8 12 4 505.58 2.47 26 8 79 71 80.93 0.72 27 9 12 3 514.96 2.54 28 9 13 4 511.55 0.51 29 9 126 117 82.62 0.99 30 9 127 118 82.56 0.99 31 9 130 121 82.50 1.01 32 10 13 3 525.83 3.71 33 10 14 4 511.55 0.51 34 10 76 66 82.56 1.00 35 10 130 120 82.57 0.99 36 10 131 121 82.51 1.00 37 10 134 124 82.48 1.01 38 11 14 3 515.49 1.47 39 11 15 4 515.90 2.68 40 11 76 65 82.58 0.99 41 11 77 66 82.59 0.99 42 11 79 68 82.59 0.99 43 12 15 3 522.20 0.48 44 12 16 4 520.31 0.47 45 13 16 3 524.96 1.27 46 13 17 4 520.31 0.47 47 13 115 102 91.37 0.97 48 13 122 109 92.86 1.67 49 13 123 110 91.38 0.98 50 13 127 114 90.68 0.79 51 13 131 118 90.22 0.57 52 14 17 3 524.95 1.26 53 14 18 4 520.29 0.47 54 14 69 55 128.62 19.71 55 14 72 58 90.67 0.79 56 14 73 59 90.63 0.78 57 14 76 62 90.62 0.79 58 14 77 63 90.62 0.79 59 14 131 117 90.68 0.79 60 15 18 3 520.89 0.77 61 15 19 4 520.88 0.77 62 16 19 3 528.28 2.26 63 16 24 8 466.86 2.66 64 16 119 103 100.61 0.58 65 16 122 106 100.53 0.62 66 17 20 3 532.86 0.03 67 17 21 4 508.61 2.17 68 17 24 7 395.95 0.65 69 17 69 52 174.96 0.79 70 17 115 98 100.01 0.88 71 18 21 3 515.58 1.60 72 18 77 59 133.23 15.36 73 20 23 3 521.91 0.83 74 20 24 4 508.87 2.02 75 20 118 98 155.69 0.89 76 21 24 3 519.10 2.23 77 21 25 4 508.86 2.02 78 21 66 45 176.17 1.31 79 21 69 48 175.68 1.12 80 22 25 3 516.97 1.17 81 22 26 4 516.97 1.17 82 22 62 40 177.96 1.98 83 22 66 44 176.17 1.31 84 23 26 3 518.07 1.87 85 23 27 4 517.35 2.23 86 23 118 95 165.30 1.26 87 24 27 3 520.74 1.30 88 24 28 4 517.25 2.27 89 24 69 45 177.62 2.06 90 24 114 90 166.68 1.88 91 24 115 91 166.67 1.89 92 24 118 94 165.31 1.26 93 24 119 95 165.30 1.26 94 25 28 3 522.57 0.39 95 25 29 4 508.49 1.70 96 25 65 40 177.85 1.96 97 25 69 44 177.60 2.08 98 26 29 3 526.87 2.54 99 26 30 4 513.94 3.93 100 26 56 30 217.66 4.48 101 26 61 35 189.62 1.46 102 26 62 36 178.14 1.96 103 27 30 3 532.54 5.38 104 27 31 4 505.58 0.25 105 27 114 87 166.69 1.89 106 27 118 91 165.31 1.26 107 28 31 3 521.25 1.09 108 28 32 4 503.99 0.81 109 28 69 41 178.06 1.97 110 28 107 79 167.12 1.88 111 28 110 82 167.02 1.86 112 28 111 83 166.97 1.86 113 28 114 86 166.68 1.88 114 29 32 3 527.92 2.25 115 29 33 4 504.01 0.81 116 29 61 32 203.30 2.65 117 29 64 35 191.19 3.25 118 29 65 36 183.69 4.29 119 30 33 3 516.38 4.40 120 30 34 4 512.91 5.25 121 30 52 22 233.44 0.65 122 30 55 25 232.94 0.76 123 30 56 26 233.41 0.65 124 31 34 3 523.47 0.85 125 31 35 4 515.53 3.11 126 31 110 79 167.08 1.87 127 31 113 82 166.91 1.89 128 31 114 83 166.90 1.88 129 32 35 3 523.51 0.06 130 32 36 4 500.34 1.93 131 32 39 7 414.43 1.74 132 32 106 74 167.14 1.88 133 32 107 75 167.12 1.87 134 32 110 78 167.06 1.86 135 33 36 3 522.57 0.41 136 33 37 4 477.73 5.09 137 33 39 6 419.95 1.02 138 33 40 7 361.97 21.23 139 33 43 10 361.98 21.24 140 33 55 22 234.35 0.65 141 33 61 28 233.11 0.83 142 34 37 3 519.59 2.77 143 34 51 17 234.56 0.67 144 34 52 18 234.49 0.64 145 34 55 21 234.49 0.64 146 36 39 3 532.83 0.08 147 36 106 70 167.30 1.85 148 37 40 3 521.12 0.31 149 37 41 4 516.04 2.85 150 38 41 3 531.14 4.10 151 38 103 65 167.84 1.79 152 38 106 68 167.78 1.81 153 39 42 3 526.13 0.50 154 39 43 4 522.87 2.14 155 39 103 64 167.56 1.77 156 39 106 67 167.53 1.79 157 40 43 3 521.65 1.45 158 40 46 6 405.81 12.09 159 40 47 7 325.99 22.90 160 40 49 9 268.26 3.89 161 41 47 6 315.19 17.50 162 42 97 55 168.10 1.78 163 42 98 56 168.09 1.78 164 42 99 57 167.97 1.79 165 42 103 61 167.88 1.81 166 43 46 3 519.50 2.17 167 43 47 4 490.31 2.69 168 43 64 21 234.57 0.57 169 44 47 3 529.22 1.57 170 45 48 3 597.82 3.62 171 45 64 19 234.60 0.55 172 46 49 3 534.33 1.58 173 46 60 14 234.62 0.55 174 46 61 15 234.61 0.56 175 46 64 18 234.60 0.56 176 49 54 5 432.68 12.26 177 49 55 6 371.43 0.04 178 49 58 9 276.77 7.07 179 49 61 12 255.88 0.57 180 50 54 4 511.47 5.46 181 51 54 3 513.59 4.40 182 51 55 4 511.47 5.46 183 52 55 3 514.78 3.80 184 52 56 4 511.45 5.46 185 53 56 3 523.27 0.44 186 53 57 4 511.46 5.46 187 54 57 3 523.27 0.44 188 54 58 4 498.62 6.88 189 55 58 3 518.70 1.85 190 55 61 6 408.45 18.50 191 58 61 3 531.00 5.66 192 58 62 4 507.02 2.50 193 59 62 3 527.17 7.58 194 59 63 4 507.03 2.50 195 60 63 3 518.06 3.02 196 60 64 4 507.63 2.18 197 61 64 3 520.92 1.44 198 61 65 4 507.63 2.18 199 62 65 3 521.17 1.31 200 62 66 4 507.66 2.16 201 63 66 3 514.23 1.91 202 63 67 4 510.68 3.68 203 64 67 3 520.37 1.16 204 64 68 4 504.31 0.49 205 65 68 3 521.12 1.54 206 65 69 4 504.31 0.49 207 66 69 3 529.67 3.25 208 66 70 4 505.05 1.48 209 67 70 3 527.03 4.58 210 67 71 4 509.99 3.95 211 68 71 3 530.13 3.02 212 68 72 4 509.74 4.07 213 69 72 3 517.25 0.31 214 69 73 4 513.36 0.04 215 70 73 3 518.14 0.76 216 70 74 4 513.36 0.05 217 71 74 3 521.75 1.04 218 71 75 4 508.94 2.27 219 72 75 3 516.03 0.85 220 72 76 4 505.60 3.94 221 72 111 39 166.98 1.86 222 72 135 63 163.03 1.21 223 73 76 3 518.50 0.38 224 73 77 4 503.14 5.17 225 74 77 3 521.03 1.60 226 74 78 4 518.11 0.18 227 75 78 3 529.87 2.82 228 75 82 7 244.72 0.92 229 75 85 10 187.09 1.59 230 75 86 11 184.80 0.46 231 75 89 14 184.79 0.45 232 75 138 63 162.78 1.21 233 76 79 3 527.05 4.23 234 76 134 58 163.05 1.22 235 78 81 3 504.33 7.97 236 78 82 4 394.06 24.64 237 78 85 7 359.73 7.48 238 80 137 57 162.98 1.27 239 82 85 3 528.49 1.02 240 82 86 4 515.74 0.97 241 82 137 55 162.97 1.27 242 82 141 59 161.03 1.44 243 83 86 3 524.58 0.94 244 83 87 4 518.83 1.86 245 83 145 62 159.73 1.38 246 84 87 3 532.48 0.47 247 84 88 4 534.50 1.49 248 85 88 3 553.51 3.85 249 85 89 4 516.66 0.80 250 86 89 3 522.05 0.33 251 86 90 4 514.95 0.70 252 86 138 52 162.75 1.19 253 86 141 55 160.88 1.39 254 86 142 56 160.32 1.25 255 87 90 3 523.24 2.60 256 87 91 4 515.26 0.26 257 87 145 58 159.19 1.27 258 88 91 3 521.38 1.68 259 88 92 4 515.26 0.25 260 89 92 3 522.46 1.06 261 89 93 4 515.26 0.25 262 89 138 49 162.78 1.21 263 89 142 53 159.99 1.25 264 90 93 3 516.17 0.69 265 90 94 4 507.37 0.60 266 90 142 52 159.88 1.28 267 90 145 55 152.20 0.07 268 90 146 56 150.99 0.48 269 90 149 59 141.61 1.83 270 91 94 3 519.17 1.38 271 91 95 4 501.11 0.87 272 91 96 5 494.01 2.03 273 91 149 58 141.60 1.83 274 92 96 4 455.20 1.72 275 92 97 5 455.20 1.73 276 93 97 4 436.62 10.98 277 93 98 5 427.74 15.41 278 93 99 6 398.01 30.24 279 93 146 53 150.85 0.55 280 94 98 4 407.57 25.47 281 94 146 52 149.26 1.32 282 94 149 55 138.89 0.48 283 94 151 57 92.46 4.62 284 95 98 3 528.34 4.25 285 98 151 53 98.78 1.46 286 99 103 4 508.25 2.29 287 99 104 5 507.77 2.52 288 99 146 47 149.27 1.32 289 99 151 52 92.47 4.62 290 100 103 3 527.91 0.82 291 100 104 4 516.51 4.34 292 100 151 51 92.45 4.62 293 100 153 53 31.80 1.98 294 101 104 3 516.51 4.34 295 101 105 4 508.26 2.29 296 101 142 41 159.60 1.15 297 101 143 42 155.40 0.01 298 101 146 45 149.08 1.24 299 101 153 52 22.61 2.62 300 102 105 3 510.32 1.25 301 102 106 4 508.26 2.28 302 103 106 3 509.88 3.08 303 103 107 4 505.70 0.99 304 104 107 3 516.11 6.21 305 104 108 4 505.07 1.31 306 104 138 34 162.78 1.11 307 104 139 35 160.18 1.15 308 104 142 38 159.30 1.03 309 105 108 3 513.31 0.33 310 105 109 4 505.06 1.31 311 105 139 34 160.19 1.15 312 106 109 3 506.25 0.98 313 106 110 4 503.40 2.15 314 107 110 3 503.73 2.33 315 107 111 4 506.88 3.06 316 108 111 3 514.21 0.60 317 108 112 4 508.56 2.25 318 108 135 27 162.97 1.12 319 108 139 31 160.19 1.15 320 109 112 3 518.08 1.33 321 109 113 4 506.94 3.08 322 110 113 3 518.08 1.33 323 110 114 4 508.60 2.27 324 111 114 3 524.96 2.11 325 111 115 4 508.65 2.23 326 111 135 24 163.06 1.13 327 112 115 3 514.66 0.77 328 112 116 4 508.65 2.23 329 112 123 11 251.69 4.64 330 112 128 16 163.43 1.17 331 112 131 19 163.26 1.11 332 112 132 20 163.25 1.13 333 112 135 23 163.18 1.13 334 113 116 3 510.18 1.47 335 113 117 4 508.54 2.18 336 114 117 3 506.88 1.36 337 114 118 4 501.85 1.16 338 115 118 3 509.40 5.28 339 115 119 4 483.51 4.67 340 115 123 8 268.88 3.55 341 115 131 16 200.13 3.25 342 116 120 4 437.05 7.12 343 116 123 7 268.81 3.58 344 116 128 12 223.94 8.65 345 117 120 3 537.93 2.45 346 119 122 3 525.70 1.75 347 119 123 4 455.61 1.65 348 120 123 3 510.37 1.34 349 122 127 5 494.05 1.09 350 123 127 4 494.05 1.09 351 123 128 5 494.05 1.09 352 123 131 8 442.17 3.25 353 124 127 3 514.01 0.61 354 124 128 4 494.15 1.07 355 125 128 3 520.16 3.69 356 125 129 4 506.18 1.10 357 126 129 3 513.37 0.46 358 126 130 4 512.23 1.92 359 127 130 3 516.54 0.23 360 127 131 4 512.24 1.92 361 128 131 3 514.53 3.06 362 128 132 4 507.23 4.42 363 129 132 3 514.53 3.07 364 129 133 4 510.20 5.91 365 130 133 3 518.06 1.98 366 130 134 4 509.53 5.57 367 131 134 3 514.50 0.44 368 131 135 4 505.30 3.46 369 132 135 3 514.74 0.33 370 132 136 4 497.42 1.80 371 133 136 3 521.70 1.79 372 133 137 4 504.60 5.40 373 134 137 3 521.78 2.84 374 134 138 4 502.84 4.55 375 135 138 3 513.07 1.52 376 135 139 4 496.14 2.43 377 136 139 3 524.20 2.00 378 136 140 4 496.05 2.39 379 137 140 3 517.98 0.40 380 137 141 4 506.20 5.47 381 138 141 3 516.59 0.28 382 138 142 4 516.36 0.39 383 139 142 3 516.37 0.39 384 139 143 4 516.36 0.39 385 140 143 3 524.65 1.35 386 140 144 4 521.52 2.20 387 141 144 3 521.52 2.21 388 141 145 4 521.52 2.20 389 142 145 3 521.33 2.31 390 142 146 4 521.29 2.31 391 143 146 3 521.46 2.24 392 143 147 4 521.46 2.24 393 144 147 3 521.52 0.43 394 144 148 4 516.57 0.20 395 145 148 3 521.26 2.15 396 145 149 4 516.47 0.25 397 146 149 3 518.50 0.75 398 146 150 4 505.20 5.88 399 146 151 5 313.87 19.50 400 146 152 6 274.64 2.42 401 146 153 7 258.17 2.10 402 147 150 3 518.08 0.56 403 147 152 5 274.42 2.29