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 81 78 33.47 0.59 2 3 82 79 32.86 0.41 3 3 153 150 28.77 0.80 4 4 81 77 33.52 0.57 5 5 78 73 33.52 0.57 6 5 79 74 33.52 0.57 7 5 80 75 33.48 0.58 8 5 81 76 33.54 0.57 9 5 156 151 33.02 0.35 10 6 10 4 558.46 1.28 11 6 78 72 33.55 0.56 12 6 79 73 33.57 0.55 13 6 81 75 33.79 0.48 14 7 77 70 33.60 0.54 15 7 78 71 33.60 0.54 16 7 79 72 33.65 0.52 17 8 79 71 34.35 0.26 18 9 15 6 386.97 0.80 19 9 79 70 34.40 0.24 20 9 104 95 36.61 0.80 21 10 13 3 598.75 2.28 22 10 81 71 225.28 2.29 23 10 101 91 338.44 1.03 24 11 99 88 338.50 1.03 25 11 101 90 338.47 1.02 26 12 99 87 338.51 1.03 27 12 100 88 338.47 1.02 28 12 101 89 338.48 1.02 29 13 81 68 338.31 1.06 30 13 100 87 338.50 1.03 31 13 101 88 338.50 1.03 32 13 102 89 338.44 1.03 33 13 103 90 338.41 1.03 34 13 104 91 308.44 3.79 35 14 96 82 338.60 1.02 36 14 100 86 338.55 1.02 37 14 102 88 338.51 1.03 38 14 103 89 338.43 1.03 39 14 104 90 338.42 1.03 40 15 46 31 338.59 1.02 41 15 47 32 338.58 1.02 42 15 79 64 338.44 1.03 43 15 104 89 338.44 1.03 44 16 45 29 338.66 1.01 45 16 46 30 338.59 1.02 46 16 47 31 338.58 1.02 47 16 79 63 338.50 1.04 48 16 104 88 338.51 1.03 49 16 105 89 338.44 1.03 50 16 106 90 338.44 1.03 51 17 44 27 338.69 0.99 52 17 45 28 338.67 1.01 53 17 46 29 338.64 1.02 54 17 47 30 338.63 1.02 55 17 53 36 338.50 1.03 56 17 56 39 338.43 1.03 57 17 57 40 338.41 1.03 58 17 105 88 338.49 1.03 59 17 106 89 338.44 1.03 60 18 43 25 338.81 0.96 61 18 44 26 338.70 0.99 62 18 57 39 338.49 1.04 63 18 106 88 338.51 1.03 64 18 107 89 338.44 1.03 65 18 108 90 338.44 1.03 66 19 42 23 339.30 0.73 67 19 43 24 339.29 0.73 68 19 44 25 338.79 0.97 69 19 57 38 338.51 1.03 70 19 58 39 338.51 1.03 71 19 60 41 338.50 1.03 72 19 61 42 338.44 1.03 73 19 107 88 338.50 1.03 74 19 108 89 338.44 1.03 75 19 110 91 338.42 1.03 76 20 28 8 362.51 10.87 77 20 42 22 339.30 0.73 78 20 107 87 338.53 1.03 79 20 108 88 338.49 1.03 80 20 109 89 338.44 1.03 81 20 110 90 338.44 1.03 82 20 157 137 96.62 0.01 83 20 161 141 95.92 0.31 84 21 28 7 362.51 10.87 85 21 29 8 355.86 7.54 86 21 61 40 338.55 1.02 87 21 67 46 338.49 1.02 88 21 70 49 338.41 1.02 89 21 110 89 338.44 1.03 90 21 111 90 338.44 1.03 91 21 112 91 337.92 0.90 92 21 136 115 175.28 0.89 93 22 26 4 445.85 4.78 94 22 27 5 405.84 1.08 95 22 28 6 374.37 16.80 96 22 73 51 338.54 1.03 97 22 109 87 338.54 1.03 98 22 110 88 338.49 1.03 99 22 111 89 338.44 1.03 100 22 112 90 338.43 1.04 101 22 164 142 95.89 0.30 102 22 165 143 91.36 0.79 103 23 26 3 547.56 3.08 104 23 27 4 457.53 1.86 105 23 112 89 338.44 1.04 106 23 116 93 269.56 2.42 107 23 136 113 175.49 0.79 108 26 139 113 172.82 0.52 109 26 164 138 95.92 0.32 110 26 165 139 91.36 0.79 111 27 136 109 174.33 0.41 112 27 137 110 173.99 0.26 113 27 138 111 166.24 0.34 114 27 139 112 166.24 0.34 115 28 42 14 350.24 4.60 116 28 136 108 174.31 0.40 117 28 137 109 173.72 0.15 118 28 138 110 166.24 0.34 119 28 139 111 151.12 0.92 120 28 142 114 128.06 1.76 121 28 158 130 96.70 0.01 122 28 165 137 88.03 0.88 123 29 42 13 350.24 4.60 124 29 43 14 350.24 4.60 125 29 65 36 338.56 1.03 126 29 67 38 338.53 1.02 127 29 119 90 195.39 0.87 128 29 121 92 195.31 0.83 129 29 134 105 183.69 0.17 130 29 135 106 181.95 0.67 131 29 136 107 174.28 0.39 132 30 40 10 351.75 5.21 133 30 41 11 351.65 5.24 134 30 134 104 183.71 0.17 135 30 135 105 183.62 0.17 136 30 137 107 174.27 0.40 137 30 142 112 127.92 1.88 138 31 40 9 351.78 5.21 139 31 41 10 351.71 5.23 140 31 121 90 195.16 0.92 141 31 131 100 193.78 0.98 142 31 133 102 192.50 0.52 143 31 134 103 183.71 0.17 144 32 36 4 535.52 0.51 145 32 37 5 408.41 2.26 146 32 39 7 356.83 7.71 147 32 40 8 354.56 6.59 148 32 131 99 193.79 0.98 149 32 132 100 193.78 0.98 150 32 133 101 193.19 0.85 151 33 36 3 551.93 0.44 152 33 39 6 392.19 3.85 153 33 41 8 380.19 2.05 154 33 130 97 193.86 0.97 155 33 131 98 193.79 0.98 156 33 147 114 104.10 0.14 157 34 128 94 194.03 0.96 158 34 129 95 194.03 0.96 159 34 130 96 193.99 0.98 160 34 131 97 193.84 0.96 161 34 132 98 193.69 1.04 162 36 39 3 553.96 0.69 163 37 40 3 622.53 0.35 164 38 145 107 108.95 2.50 165 39 147 108 104.06 0.15 166 40 133 93 193.15 0.69 167 40 134 94 185.60 0.46 168 40 135 95 183.70 0.17 169 40 145 105 104.12 0.15 170 40 146 106 104.06 0.15 171 40 147 107 104.06 0.15 172 41 131 90 193.75 0.97 173 41 142 101 113.37 2.77 174 41 146 105 103.56 0.09 175 41 150 109 102.42 0.15 176 41 154 113 96.68 0.00 177 42 107 65 338.56 1.03 178 42 142 100 116.50 1.19 179 42 154 112 96.64 0.01 180 42 157 115 96.64 0.01 181 43 61 18 338.43 1.02 182 43 107 64 338.54 1.03 183 43 131 88 191.86 0.27 184 44 105 61 338.55 1.03 185 44 107 63 338.48 1.03 186 45 60 15 338.30 1.03 187 46 60 14 338.30 1.03 188 47 51 4 506.40 13.64 189 47 52 5 465.94 1.35 190 47 53 6 414.20 2.19 191 47 56 9 341.47 0.49 192 47 79 32 344.70 4.12 193 48 51 3 538.99 2.66 194 51 55 4 552.73 2.52 195 52 55 3 555.94 0.92 196 52 56 4 547.47 5.15 197 53 56 3 556.16 0.81 198 53 57 4 547.45 5.16 199 53 79 26 351.81 7.61 200 53 106 53 351.64 7.54 201 53 108 55 351.48 7.52 202 54 57 3 556.15 0.80 203 54 58 4 550.02 3.87 204 54 72 18 351.37 7.52 205 54 108 54 351.48 7.52 206 54 110 56 351.45 7.53 207 55 58 3 558.59 1.79 208 55 59 4 545.22 4.07 209 56 59 3 556.60 0.83 210 56 60 4 540.62 1.87 211 57 60 3 565.78 5.39 212 57 61 4 545.36 1.92 213 57 108 51 351.60 7.53 214 57 110 53 351.56 7.54 215 58 61 3 551.31 1.05 216 58 62 4 545.56 1.82 217 58 110 52 351.58 7.54 218 59 62 3 553.38 0.96 219 59 63 4 550.57 0.68 220 60 63 3 562.54 3.62 221 60 64 4 550.33 0.57 222 61 64 3 563.84 2.97 223 61 65 4 559.86 5.34 224 61 67 6 470.86 1.76 225 62 65 3 564.36 3.08 226 62 66 4 495.22 7.40 227 62 67 5 470.86 1.76 228 62 68 6 431.17 1.57 229 64 121 57 193.90 0.96 230 64 130 66 193.47 0.93 231 64 131 67 193.63 0.92 232 65 118 53 195.37 0.90 233 65 119 54 195.12 0.82 234 65 120 55 195.10 0.83 235 65 121 56 193.90 0.96 236 65 131 66 193.72 0.95 237 66 118 52 195.36 0.90 238 67 70 3 621.78 1.32 239 67 112 45 351.68 7.57 240 67 118 51 195.36 0.90 241 67 119 52 195.12 0.81 242 69 112 43 351.68 7.58 243 69 113 44 351.62 7.58 244 69 114 45 350.55 7.99 245 70 110 40 352.18 7.58 246 70 111 41 352.05 7.58 247 70 112 42 351.67 7.58 248 70 113 43 351.64 7.57 249 71 110 39 352.23 7.59 250 71 111 40 352.14 7.57 251 71 113 42 352.00 7.57 252 72 75 3 636.82 1.18 253 72 109 37 352.52 7.58 254 72 110 38 352.35 7.56 255 73 109 36 352.55 7.58 256 73 110 37 352.51 7.59 257 73 111 38 352.47 7.61 258 73 164 91 89.51 0.18 259 74 108 34 352.64 7.61 260 74 109 35 352.55 7.58 261 74 161 87 95.93 0.30 262 74 164 90 83.76 0.16 263 75 107 32 352.87 7.65 264 75 108 33 352.64 7.61 265 75 109 34 352.64 7.61 266 75 160 85 96.02 0.27 267 75 161 86 95.92 0.30 268 76 106 30 352.97 7.63 269 76 107 31 352.88 7.65 270 76 157 81 96.37 0.12 271 76 160 84 95.92 0.30 272 76 161 85 95.92 0.30 273 77 160 83 95.92 0.30 274 78 106 28 354.22 7.93 275 78 156 78 96.48 0.07 276 78 160 82 95.92 0.30 277 79 104 25 355.08 7.91 278 79 105 26 355.01 7.88 279 79 106 27 354.22 7.93 280 80 103 23 355.26 7.91 281 80 104 24 355.13 7.92 282 80 105 25 355.07 7.91 283 80 107 27 355.01 7.88 284 80 153 73 96.36 0.10 285 80 156 76 96.23 0.17 286 80 157 77 96.16 0.21 287 81 103 22 355.26 7.91 288 81 104 23 355.18 7.91 289 82 103 21 355.31 7.90 290 82 149 67 96.44 0.06 291 82 152 70 96.25 0.15 292 82 153 71 96.23 0.16 293 83 89 6 527.74 1.01 294 83 101 18 356.10 7.88 295 83 102 19 355.65 8.06 296 84 88 4 550.43 0.03 297 84 89 5 540.11 5.17 298 84 92 8 473.06 2.23 299 84 102 18 356.10 7.88 300 84 103 19 356.10 7.88 301 85 88 3 571.60 1.20 302 85 89 4 550.48 0.03 303 86 89 3 559.13 0.35 304 86 90 4 555.94 1.24 305 87 90 3 564.64 0.83 306 87 91 4 554.61 0.58 307 88 91 3 554.56 0.60 308 88 92 4 550.47 0.01 309 89 92 3 556.44 2.98 310 89 93 4 526.89 7.54 311 89 94 5 535.82 3.08 312 90 94 4 526.86 7.53 313 91 95 4 541.19 5.42 314 92 95 3 551.41 0.33 315 92 96 4 551.41 0.33 316 92 101 9 356.96 8.04 317 92 102 10 356.94 8.03 318 93 96 3 574.61 4.22 319 93 100 7 365.33 3.94 320 93 101 8 356.95 8.04 321 94 97 3 553.64 0.01 322 96 100 4 470.65 4.29 323 107 153 46 96.63 0.01 324 107 154 47 96.62 0.01 325 107 157 50 96.16 0.21 326 108 161 53 95.92 0.31 327 109 161 52 95.92 0.31 328 109 164 55 85.14 0.84 329 109 165 56 81.88 0.78 330 112 115 3 657.11 3.02 331 112 116 4 586.72 1.08 332 112 136 24 183.61 0.17 333 115 118 3 574.00 0.06 334 116 119 3 561.90 1.68 335 116 134 18 193.39 1.02 336 116 136 20 192.06 0.41 337 119 134 15 193.15 0.90 338 119 136 17 193.15 0.90 339 121 129 8 193.99 0.95 340 121 130 9 193.93 0.98 341 121 131 10 193.76 0.96 342 121 132 11 193.75 0.96 343 121 133 12 193.74 0.96 344 121 134 13 193.41 0.93 345 122 129 7 194.00 0.95 346 137 141 4 523.84 0.98 347 137 142 5 517.26 0.84 348 137 145 8 484.53 1.49 349 138 141 3 538.66 4.46 350 138 142 4 538.67 4.45 351 139 142 3 557.28 4.85 352 139 143 4 557.28 4.85 353 139 158 19 399.88 7.04 354 139 165 26 86.38 0.04 355 140 143 3 557.28 4.85 356 140 144 4 547.07 0.24 357 140 155 15 400.15 7.00 358 140 158 18 400.02 7.06 359 141 144 3 547.09 0.24 360 141 145 4 547.06 0.24 361 142 145 3 553.48 1.75 362 142 146 4 529.91 0.70 363 142 154 12 425.81 0.15 364 143 146 3 548.63 0.68 365 143 151 8 416.56 13.13 366 143 154 11 408.63 8.75 367 143 155 12 406.14 9.97 368 143 158 15 406.15 9.97 369 146 150 4 547.42 0.48 370 146 151 5 520.42 6.57 371 146 154 8 494.69 4.61 372 147 150 3 571.65 0.12 373 147 151 4 544.38 1.03 374 148 151 3 547.40 0.48 375 148 152 4 546.37 0.05 376 149 153 4 549.54 0.81 377 150 153 3 553.73 2.90 378 150 154 4 547.34 0.30 379 151 154 3 559.61 5.83 380 151 155 4 547.34 0.30 381 152 155 3 547.34 0.30 382 152 156 4 547.33 0.31 383 153 156 3 562.96 3.79 384 153 157 4 547.48 0.41 385 154 157 3 547.46 0.42 386 154 158 4 547.37 0.23 387 155 158 3 554.06 3.57 388 155 159 4 555.09 3.05 389 156 159 3 556.41 2.39 390 156 160 4 560.01 0.58 391 157 160 3 564.27 1.53 392 157 161 4 560.00 0.58 393 158 161 3 560.00 0.58 394 158 162 4 560.70 0.23 395 158 165 7 521.46 1.47 396 159 162 3 567.65 0.97 397 159 163 4 577.65 0.42 398 160 163 3 610.85 3.06 399 160 164 4 574.15 1.32 400 161 164 3 563.68 0.26 401 161 165 4 553.96 3.13 402 162 165 3 554.38 3.35