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 14 166 148 43.13 0.77 2 15 100 85 43.40 0.58 3 15 164 145 40.92 0.46 4 15 165 146 42.98 0.84 5 15 166 147 43.17 0.76 6 15 187 168 31.31 0.18 7 15 188 169 18.11 0.57 8 16 27 11 43.64 0.59 9 16 164 144 43.26 0.68 10 16 165 145 43.47 0.61 11 16 185 165 43.45 0.62 12 16 186 166 43.36 0.66 13 16 188 168 29.16 0.12 14 17 27 10 44.20 0.32 15 17 163 142 43.48 0.61 16 17 164 143 43.47 0.61 17 17 186 165 43.47 0.62 18 17 187 166 43.45 0.61 19 17 188 167 39.72 0.75 20 18 27 9 43.63 0.60 21 18 46 28 44.39 0.21 22 18 55 37 44.38 0.19 23 18 143 121 44.46 0.19 24 18 144 122 43.58 0.58 25 18 161 139 43.49 0.61 26 18 163 141 43.49 0.61 27 18 164 142 43.48 0.61 28 18 165 143 43.61 0.58 29 19 23 4 475.09 3.86 30 19 27 8 44.43 0.22 31 19 160 137 43.55 0.60 32 19 161 138 43.59 0.58 33 19 162 139 43.58 0.58 34 20 23 3 532.45 2.44 35 20 27 7 44.52 0.19 36 20 184 160 44.48 0.23 37 20 186 162 44.42 0.21 38 23 160 133 44.45 0.18 39 26 29 3 571.94 0.65 40 26 142 112 73.15 1.89 41 26 143 113 67.15 4.02 42 26 144 114 55.97 2.85 43 26 145 115 44.84 0.31 44 26 146 116 61.71 7.41 45 26 147 117 77.25 0.25 46 26 182 152 80.15 2.10 47 27 143 112 78.96 1.02 48 27 181 150 82.84 2.95 49 27 182 151 82.65 2.86 50 27 185 154 70.95 0.50 51 28 142 110 82.67 2.85 52 28 143 111 79.05 1.05 53 28 180 148 84.41 3.71 54 28 181 149 83.06 3.06 55 28 182 150 83.14 3.09 56 28 185 153 78.81 1.08 57 29 140 107 94.06 1.12 58 29 141 108 93.09 1.50 59 29 142 109 82.67 2.85 60 29 147 114 92.62 0.70 61 29 179 146 90.78 4.12 62 29 180 147 87.53 4.87 63 30 140 106 96.52 2.22 64 30 141 107 93.39 1.35 65 30 143 109 93.39 1.35 66 30 170 136 93.62 1.35 67 30 176 142 113.45 2.65 68 30 178 144 110.60 3.26 69 30 179 145 92.42 3.31 70 31 138 103 111.62 1.70 71 31 139 104 103.54 2.27 72 31 140 105 96.86 2.37 73 31 176 141 113.52 2.64 74 31 177 142 113.50 2.63 75 31 178 143 113.25 2.72 76 32 37 5 504.92 1.16 77 32 138 102 113.25 2.50 78 32 139 103 113.20 2.52 79 32 141 105 105.49 1.17 80 32 170 134 113.25 2.73 81 32 171 135 113.43 2.65 82 32 172 136 114.31 2.23 83 32 175 139 114.78 2.02 84 32 176 140 114.30 2.25 85 32 177 141 113.52 2.64 86 33 36 3 530.25 1.22 87 33 37 4 517.06 2.93 88 33 137 100 120.80 0.98 89 33 175 138 114.84 2.01 90 33 177 140 114.35 2.25 91 34 37 3 524.95 3.87 92 34 60 26 120.75 1.01 93 34 131 97 138.46 5.07 94 34 136 98 125.59 1.41 95 34 137 99 121.48 0.65 96 34 138 100 116.90 0.92 97 34 139 101 116.84 0.95 98 36 174 134 153.67 3.20 99 36 175 135 137.27 9.34 100 37 40 3 568.68 5.12 101 37 131 94 162.03 0.15 102 37 172 131 134.32 1.37 103 37 175 134 148.19 5.95 104 38 172 130 161.28 0.07 105 39 171 128 161.28 0.07 106 39 172 129 161.30 0.07 107 40 106 66 162.64 0.16 108 40 107 67 162.52 0.23 109 40 131 91 163.06 0.04 110 40 171 127 162.08 0.27 111 41 105 64 162.95 0.04 112 41 106 65 162.67 0.18 113 41 171 126 162.15 0.24 114 42 104 62 163.85 0.18 115 42 105 63 163.59 0.17 116 42 169 123 162.15 0.24 117 42 170 124 162.13 0.24 118 42 171 125 162.16 0.24 119 43 103 60 166.94 0.71 120 43 104 61 163.86 0.19 121 43 168 121 162.16 0.24 122 43 169 122 162.17 0.24 123 44 55 11 203.09 19.41 124 44 56 12 203.09 19.39 125 44 69 25 203.72 19.07 126 44 102 58 214.91 16.69 127 44 103 59 174.53 1.80 128 44 165 117 161.33 0.30 129 44 166 118 162.00 0.21 130 44 167 119 162.12 0.25 131 44 168 120 162.16 0.24 132 44 170 122 162.23 0.23 133 45 100 55 242.59 15.28 134 45 101 56 216.35 16.05 135 45 102 57 216.28 16.02 136 45 165 116 161.90 0.19 137 45 166 117 162.12 0.24 138 45 167 118 162.18 0.24 139 46 99 53 279.73 13.04 140 46 100 54 260.96 14.12 141 46 101 55 234.52 18.38 142 46 103 57 220.83 18.27 143 46 164 114 161.97 0.21 144 46 165 115 162.10 0.24 145 47 98 51 294.76 8.22 146 47 99 52 279.73 13.04 147 47 100 53 269.88 13.83 148 47 163 112 162.15 0.23 149 47 164 113 162.06 0.24 150 48 71 23 266.61 22.66 151 48 95 47 281.32 13.85 152 48 96 48 283.81 13.83 153 48 97 49 296.51 8.08 154 48 98 50 296.43 8.12 155 48 161 109 162.49 0.18 156 48 162 110 162.27 0.21 157 48 163 111 162.16 0.23 158 49 96 47 295.75 7.94 159 49 97 48 296.57 8.10 160 49 98 49 296.54 8.07 161 50 71 21 283.36 14.76 162 50 96 46 296.58 8.10 163 50 160 106 164.76 0.83 164 50 161 107 162.69 0.12 165 50 162 108 162.63 0.10 166 51 71 20 290.75 11.06 167 51 72 21 296.62 8.14 168 51 73 22 296.62 8.13 169 51 74 23 296.56 8.11 170 51 94 43 296.60 8.10 171 51 96 45 296.60 8.10 172 52 71 19 295.62 8.79 173 52 72 20 296.63 8.14 174 52 157 101 176.81 4.64 175 52 158 102 175.81 4.75 176 52 160 104 166.43 1.66 177 52 161 105 164.85 0.96 178 53 70 17 296.85 8.24 179 53 71 18 296.86 8.22 180 53 157 100 177.96 5.20 181 53 158 101 176.43 4.62 182 53 159 102 171.87 4.40 183 53 160 103 166.40 1.68 184 53 161 104 164.83 0.96 185 54 57 3 577.99 4.67 186 54 68 14 297.18 9.15 187 54 69 15 297.74 8.61 188 54 70 16 297.38 8.43 189 54 144 86 254.14 13.47 190 54 145 87 253.22 13.08 191 54 146 88 248.71 10.81 192 54 157 99 180.75 4.00 193 54 159 101 173.69 5.31 194 54 161 103 165.91 1.52 195 55 69 14 297.95 8.54 196 55 70 15 297.92 8.51 197 55 71 16 297.94 8.50 198 55 143 84 254.28 13.46 199 55 144 85 254.19 13.49 200 55 161 102 165.31 1.26 201 56 67 11 298.56 8.84 202 56 68 12 298.27 8.70 203 56 69 13 298.21 8.64 204 56 105 49 297.60 8.23 205 56 141 81 254.59 13.43 206 56 142 82 254.36 13.45 207 56 143 83 254.29 13.46 208 56 144 84 254.28 13.46 209 56 170 110 176.43 6.74 210 57 62 5 519.41 0.35 211 57 66 9 298.81 8.97 212 57 67 10 298.55 8.84 213 57 68 11 298.31 8.70 214 57 141 80 254.60 13.43 215 57 142 81 254.40 13.43 216 57 145 84 254.34 13.44 217 57 146 85 254.25 13.47 218 57 147 86 254.26 13.46 219 57 148 87 254.24 13.46 220 58 66 8 387.28 35.26 221 58 67 9 298.66 8.87 222 58 140 78 254.66 13.44 223 58 141 79 254.61 13.43 224 59 62 3 536.63 1.30 225 59 65 6 485.15 1.74 226 59 66 7 298.81 8.96 227 59 139 76 254.72 13.45 228 59 140 77 254.68 13.44 229 60 65 5 485.20 1.74 230 60 136 72 254.82 13.44 231 60 138 74 254.80 13.44 232 60 139 75 254.75 13.43 233 61 64 3 520.23 1.30 234 61 65 4 490.67 2.67 235 61 66 5 488.88 3.57 236 62 66 4 503.83 3.90 237 62 140 74 254.87 13.47 238 62 148 82 254.44 13.46 239 63 66 3 599.44 5.42 240 64 81 17 399.49 32.95 241 64 82 18 399.50 32.95 242 65 81 16 399.50 32.95 243 65 82 17 399.53 32.93 244 65 83 18 399.56 32.92 245 65 136 67 273.88 22.78 246 66 79 13 399.68 33.01 247 66 80 14 399.54 32.94 248 66 81 15 399.54 32.94 249 66 148 78 254.79 13.63 250 66 153 83 239.91 20.75 251 66 154 84 239.80 20.78 252 67 78 11 399.69 33.02 253 67 79 12 399.68 33.01 254 67 80 13 399.55 32.93 255 67 105 38 323.99 4.91 256 67 112 45 323.86 4.98 257 68 77 9 399.76 33.05 258 68 78 10 399.70 33.02 259 68 79 11 399.70 33.00 260 68 146 74 254.76 13.72 261 68 153 81 239.83 20.89 262 68 157 85 235.36 22.98 263 69 76 7 464.39 1.19 264 69 77 8 399.81 33.06 265 69 78 9 399.72 33.01 266 69 103 34 324.25 4.98 267 69 105 36 323.98 4.93 268 69 114 45 323.97 4.92 269 70 76 6 464.39 1.19 270 70 77 7 462.39 1.78 271 71 74 3 515.89 0.09 272 71 75 4 474.89 5.74 273 71 76 5 464.44 1.21 274 71 95 24 416.35 23.23 275 71 157 82 224.56 28.49 276 71 161 86 164.30 0.69 277 72 75 3 519.99 1.02 278 72 77 5 464.44 1.18 279 72 79 7 472.04 4.96 280 72 155 79 254.06 29.86 281 72 156 80 244.63 34.54 282 72 157 81 224.59 28.51 283 73 94 21 417.29 23.59 284 74 94 20 417.28 23.59 285 74 95 21 417.27 23.58 286 74 96 22 409.26 19.57 287 75 92 17 417.58 23.75 288 75 93 18 417.56 23.73 289 75 94 19 417.11 23.50 290 76 90 14 417.57 23.75 291 76 91 15 417.58 23.75 292 76 92 16 417.58 23.73 293 76 93 17 417.57 23.73 294 76 95 19 416.48 23.16 295 76 114 38 342.15 13.98 296 76 116 40 342.38 13.92 297 77 88 11 417.76 23.88 298 77 89 12 417.57 23.75 299 77 90 13 417.57 23.75 300 78 87 9 417.78 23.88 301 78 88 10 417.78 23.86 302 78 89 11 417.59 23.75 303 78 114 36 342.22 14.02 304 78 122 44 342.28 14.00 305 78 124 46 341.94 14.09 306 79 87 8 417.80 23.87 307 79 88 9 417.79 23.85 308 79 153 70 239.84 20.86 309 79 154 71 209.24 5.67 310 79 155 72 208.45 5.94 311 80 85 5 481.72 0.39 312 80 86 6 464.08 0.77 313 80 87 7 417.82 23.87 314 80 112 32 342.19 14.08 315 80 124 44 342.16 14.08 316 80 127 47 340.63 14.80 317 80 154 70 266.09 33.98 318 81 85 4 485.25 1.38 319 81 86 5 464.08 0.77 320 82 85 3 524.83 0.22 321 82 86 4 489.41 1.56 322 82 127 45 340.76 14.78 323 83 136 49 326.72 21.78 324 84 127 43 341.37 14.55 325 84 128 44 340.81 14.83 326 84 129 45 340.80 14.82 327 85 127 42 340.81 14.83 328 86 154 64 266.11 33.97 329 87 124 37 342.44 14.20 330 87 127 40 341.04 14.95 331 87 154 63 211.53 6.71 332 88 154 62 208.71 5.94 333 88 155 63 208.41 5.95 334 89 122 33 342.67 14.12 335 89 124 35 342.45 14.23 336 91 121 30 342.72 14.13 337 91 122 31 342.67 14.12 338 92 121 29 342.71 14.13 339 93 116 23 342.83 14.08 340 93 121 28 342.81 14.10 341 95 101 6 342.81 14.04 342 95 103 8 383.85 34.55 343 95 116 21 342.95 14.12 344 97 101 4 563.17 0.32 345 100 164 60 162.15 0.24 346 100 165 61 162.18 0.23 347 100 166 62 162.21 0.22 348 101 117 16 414.24 9.37 349 102 116 14 414.24 9.37 350 102 117 15 414.25 9.37 351 103 114 11 414.48 9.26 352 103 115 12 414.43 9.28 353 104 114 10 414.49 9.26 354 104 115 11 414.45 9.27 355 105 112 7 414.56 9.21 356 105 113 8 414.56 9.22 357 105 114 9 414.50 9.26 358 106 112 6 414.57 9.22 359 106 113 7 414.56 9.22 360 107 111 4 475.72 4.22 361 107 112 5 414.57 9.22 362 107 128 21 408.66 14.62 363 107 131 24 379.31 26.76 364 108 111 3 519.59 1.66 365 108 113 5 461.78 3.90 366 108 123 15 414.69 9.29 367 110 126 16 421.94 13.25 368 110 127 17 421.95 13.25 369 110 128 18 421.45 13.45 370 111 123 12 422.42 13.08 371 111 124 13 422.26 13.15 372 111 125 14 421.98 13.25 373 111 127 16 421.90 13.28 374 112 123 11 422.45 13.08 375 112 124 12 422.24 13.18 376 112 127 15 421.81 13.37 377 113 120 7 422.92 12.71 378 113 122 9 422.47 13.08 379 113 123 10 422.46 13.09 380 114 120 6 423.30 12.89 381 114 121 7 423.06 12.79 382 114 122 8 422.49 13.08 383 115 119 4 467.39 7.05 384 115 120 5 423.30 12.89 385 115 121 6 423.31 12.90 386 116 119 3 509.09 0.04 387 116 121 5 467.38 7.06 388 120 123 3 594.01 1.83 389 124 127 3 549.58 0.53 390 131 139 4 483.43 3.97 391 138 177 39 305.91 71.70 392 139 171 32 306.08 71.67 393 140 147 7 424.91 13.38 394 141 170 29 306.04 71.68 395 141 171 30 306.12 71.67 396 142 145 3 541.38 0.13 397 142 147 5 469.29 3.21 398 143 165 22 306.06 71.65 399 143 170 27 306.39 71.72 400 146 149 3 560.56 2.98 401 146 150 4 516.58 5.01 402 146 153 7 472.72 1.89 403 148 152 4 529.52 0.07 404 148 153 5 505.47 0.36 405 149 152 3 529.74 0.23 406 150 153 3 535.21 2.96 407 150 156 6 410.74 27.79 408 150 157 7 407.48 29.41 409 150 159 9 384.97 33.00 410 151 156 5 439.06 17.87 411 153 156 3 511.29 1.76 412 153 157 4 521.21 4.99