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 14 166 152 46.83 0.52 2 15 100 85 46.86 0.54 3 15 164 149 44.31 0.01 4 15 165 150 46.81 0.52 5 15 166 151 46.86 0.53 6 15 187 172 36.11 1.44 7 15 188 173 23.98 0.98 8 16 27 11 47.13 0.58 9 16 164 148 46.81 0.52 10 16 165 149 46.86 0.53 11 16 185 169 46.87 0.54 12 16 186 170 46.84 0.53 13 16 187 171 40.45 0.36 14 16 188 172 35.70 1.65 15 17 27 10 47.43 0.68 16 17 163 146 46.88 0.54 17 17 186 169 46.86 0.54 18 17 187 170 46.85 0.53 19 17 188 171 46.50 0.39 20 18 27 9 47.47 0.66 21 18 46 28 47.35 0.49 22 18 143 125 47.56 0.62 23 18 144 126 46.95 0.55 24 18 161 143 46.89 0.54 25 18 163 145 46.89 0.54 26 18 164 146 46.90 0.54 27 18 165 147 47.05 0.55 28 19 27 8 47.59 0.60 29 19 160 141 46.95 0.54 30 19 161 142 47.00 0.57 31 19 162 143 46.97 0.55 32 19 186 167 47.76 0.52 33 20 27 7 48.04 0.48 34 20 186 166 47.80 0.52 35 24 145 121 48.48 0.42 36 24 158 134 48.11 0.45 37 24 159 135 48.11 0.45 38 24 160 136 48.12 0.46 39 26 29 3 579.99 2.89 40 26 142 116 71.28 0.09 41 26 143 117 60.37 0.87 42 26 144 118 56.44 0.55 43 26 145 119 48.59 0.46 44 26 146 120 58.10 4.29 45 26 147 121 58.20 4.34 46 27 143 116 72.00 0.01 47 27 185 158 71.17 0.33 48 28 142 114 81.95 1.90 49 28 143 115 77.45 1.14 50 28 180 152 94.98 0.81 51 28 185 157 74.25 0.47 52 29 141 112 93.91 0.39 53 29 142 113 84.94 0.42 54 29 147 118 89.75 1.99 55 29 179 150 109.25 0.57 56 29 180 151 98.38 0.51 57 30 140 110 96.48 1.47 58 30 141 111 96.12 1.31 59 30 143 113 96.14 1.30 60 30 170 140 99.56 0.36 61 30 176 146 123.88 1.20 62 30 178 148 122.77 0.87 63 30 179 149 111.63 1.04 64 31 138 107 123.84 1.11 65 31 139 108 112.77 1.60 66 31 140 109 98.62 0.41 67 31 176 145 123.94 1.20 68 31 177 146 123.89 1.20 69 31 178 147 123.73 1.21 70 32 37 5 519.75 2.65 71 32 138 106 127.62 0.74 72 32 139 107 121.53 0.21 73 32 141 109 121.56 0.23 74 32 170 138 123.62 1.23 75 32 171 139 123.74 1.20 76 32 172 140 123.82 1.20 77 32 175 143 123.98 1.18 78 32 176 144 123.98 1.18 79 32 177 145 123.93 1.20 80 33 36 3 535.50 0.96 81 33 37 4 523.38 4.44 82 33 137 104 131.67 1.50 83 33 138 105 129.13 1.50 84 33 175 142 124.02 1.16 85 33 177 144 124.00 1.17 86 34 37 3 538.54 2.94 87 34 60 26 132.60 1.11 88 34 131 97 137.04 0.80 89 34 132 98 155.08 3.10 90 34 134 100 158.15 0.45 91 34 136 102 158.17 0.47 92 34 137 103 132.97 0.92 93 34 138 104 131.06 1.20 94 34 139 105 129.41 1.49 95 35 137 102 158.15 0.45 96 36 172 136 139.28 0.96 97 36 175 139 152.55 0.83 98 37 40 3 575.09 0.26 99 37 131 94 165.75 0.79 100 37 171 134 137.05 0.81 101 37 172 135 137.87 0.40 102 37 175 138 160.19 0.42 103 38 172 134 165.15 0.71 104 39 171 132 165.31 0.78 105 39 172 133 165.21 0.68 106 40 106 66 166.29 0.75 107 40 107 67 166.29 0.75 108 40 131 91 166.58 0.90 109 40 171 131 165.47 0.70 110 41 105 64 166.30 0.75 111 41 106 65 166.59 0.90 112 41 171 130 165.72 0.79 113 42 104 62 168.47 1.36 114 42 105 63 167.44 1.11 115 42 169 127 165.66 0.80 116 42 170 128 165.62 0.75 117 42 171 129 165.75 0.80 118 43 102 59 179.99 0.29 119 43 103 60 174.00 1.48 120 43 104 61 168.49 1.36 121 43 167 124 165.72 0.79 122 43 168 125 165.72 0.79 123 43 169 126 165.76 0.80 124 44 55 11 168.47 1.35 125 44 56 12 168.51 1.34 126 44 69 25 170.17 0.52 127 44 102 58 180.95 0.13 128 44 103 59 178.78 0.29 129 44 165 121 165.30 0.77 130 44 166 122 165.58 0.74 131 44 167 123 165.72 0.79 132 44 168 124 165.76 0.79 133 44 170 126 165.85 0.79 134 45 100 55 202.64 0.34 135 45 101 56 187.74 2.16 136 45 102 57 180.96 0.13 137 45 165 120 165.44 0.77 138 45 166 121 165.69 0.79 139 45 167 122 165.78 0.80 140 46 95 49 208.60 3.60 141 46 99 53 253.75 1.86 142 46 100 54 216.52 0.27 143 46 101 55 199.38 1.95 144 46 103 57 188.91 1.79 145 46 164 118 165.44 0.77 146 47 98 51 275.56 0.85 147 47 99 52 253.15 2.16 148 47 100 53 230.02 0.48 149 47 163 116 165.75 0.79 150 47 164 117 165.66 0.79 151 48 71 23 224.68 3.13 152 48 95 47 258.09 1.27 153 48 96 48 272.09 2.60 154 48 97 49 276.39 0.98 155 48 98 50 275.76 0.83 156 48 161 113 166.56 0.66 157 48 162 114 165.94 0.77 158 48 163 115 165.76 0.79 159 49 96 47 275.57 0.87 160 49 97 48 276.42 0.99 161 49 98 49 276.33 0.96 162 50 71 21 265.21 0.72 163 50 96 46 276.47 0.99 164 50 160 110 172.05 1.33 165 50 161 111 166.84 0.58 166 50 162 112 166.50 0.69 167 51 71 20 273.22 0.59 168 51 72 21 276.50 1.01 169 51 73 22 276.50 1.01 170 51 74 23 276.21 0.91 171 51 94 43 276.51 0.98 172 51 96 45 276.56 1.01 173 52 71 19 276.20 0.90 174 52 72 20 276.65 1.08 175 52 157 105 191.66 0.32 176 52 158 106 189.08 1.19 177 52 160 108 178.56 0.76 178 52 161 109 170.13 0.38 179 53 70 17 276.90 1.17 180 53 71 18 276.97 1.18 181 53 157 104 193.75 0.72 182 53 158 105 190.95 0.68 183 53 159 106 180.97 1.96 184 53 160 107 178.24 0.86 185 53 161 108 167.75 0.12 186 54 68 14 276.50 0.98 187 54 69 15 276.97 1.18 188 54 70 16 276.98 1.18 189 54 144 90 277.44 1.30 190 54 145 91 277.24 1.39 191 54 146 92 275.53 0.39 192 54 157 103 195.00 1.33 193 54 159 105 185.75 0.32 194 54 161 107 177.42 1.28 195 55 69 14 277.37 1.26 196 55 70 15 277.44 1.28 197 55 71 16 277.52 1.28 198 55 143 88 277.56 1.28 199 55 144 89 277.49 1.28 200 56 67 11 277.43 1.26 201 56 68 12 277.44 1.27 202 56 69 13 277.47 1.27 203 56 105 49 277.47 1.31 204 56 142 86 277.64 1.28 205 56 143 87 277.56 1.28 206 56 170 114 207.72 1.63 207 57 62 5 526.49 0.84 208 57 66 9 277.39 1.25 209 57 67 10 277.43 1.26 210 57 68 11 277.46 1.28 211 57 141 84 277.81 1.25 212 57 142 85 277.69 1.29 213 57 145 88 277.57 1.28 214 57 146 89 277.52 1.28 215 57 147 90 277.52 1.28 216 57 148 91 277.53 1.28 217 58 66 8 277.43 1.26 218 58 67 9 277.46 1.28 219 58 140 82 277.98 1.30 220 58 141 83 277.83 1.26 221 59 62 3 554.03 1.95 222 59 65 6 381.16 50.61 223 59 66 7 277.44 1.27 224 59 139 80 278.03 1.31 225 59 140 81 278.01 1.31 226 60 65 5 490.01 0.39 227 60 134 74 277.66 1.21 228 60 136 76 277.80 1.27 229 60 138 78 278.04 1.31 230 60 139 79 278.04 1.31 231 61 64 3 546.10 0.27 232 61 65 4 497.13 1.86 233 61 66 5 491.33 1.04 234 62 66 4 491.30 1.03 235 62 140 78 278.16 1.30 236 62 147 85 277.90 1.30 237 62 148 86 277.88 1.31 238 64 81 17 277.62 1.29 239 64 82 18 277.66 1.29 240 65 81 16 277.70 1.28 241 65 82 17 277.66 1.29 242 65 134 69 278.10 1.31 243 66 79 13 278.04 1.27 244 66 80 14 277.79 1.29 245 66 81 15 277.74 1.29 246 66 148 82 278.48 1.21 247 66 153 87 278.05 1.31 248 66 154 88 278.05 1.31 249 67 78 11 278.31 1.15 250 67 79 12 278.14 1.17 251 67 80 13 277.80 1.29 252 67 105 38 278.57 1.21 253 67 112 45 278.05 1.31 254 68 77 9 278.50 1.16 255 68 78 10 278.34 1.14 256 68 79 11 278.25 1.15 257 68 146 78 278.61 1.20 258 68 153 85 278.31 1.25 259 68 157 89 278.01 1.30 260 69 76 7 472.13 0.27 261 69 77 8 278.50 1.16 262 69 78 9 278.37 1.12 263 69 103 34 278.70 1.22 264 69 105 36 278.59 1.22 265 69 114 45 278.68 1.21 266 70 76 6 473.55 0.96 267 70 77 7 278.56 1.16 268 71 74 3 532.73 0.46 269 71 75 4 487.30 1.53 270 71 76 5 473.56 0.96 271 71 95 24 367.57 1.70 272 71 157 86 278.09 1.28 273 71 161 90 167.19 0.41 274 72 75 3 535.46 2.37 275 72 77 5 497.56 3.23 276 72 79 7 497.61 3.23 277 72 155 83 278.57 1.20 278 72 156 84 278.54 1.22 279 72 157 85 236.62 19.48 280 73 94 21 372.50 1.07 281 74 94 20 372.49 1.07 282 74 95 21 372.50 1.07 283 74 96 22 372.51 1.07 284 75 92 17 372.49 1.08 285 75 93 18 372.50 1.08 286 75 94 19 372.50 1.08 287 76 90 14 372.46 1.07 288 76 91 15 372.49 1.08 289 76 92 16 372.50 1.07 290 76 93 17 372.53 1.07 291 76 95 19 372.56 1.07 292 76 114 38 372.45 1.08 293 76 116 40 372.56 1.07 294 77 88 11 372.44 1.07 295 77 89 12 372.45 1.07 296 77 90 13 372.47 1.07 297 78 87 9 372.45 1.06 298 78 88 10 372.47 1.07 299 78 89 11 372.48 1.07 300 78 114 36 372.57 1.07 301 78 122 44 372.58 1.07 302 78 124 46 372.48 1.07 303 79 87 8 372.46 1.07 304 79 88 9 372.48 1.07 305 79 153 74 286.14 0.16 306 79 154 75 286.12 0.13 307 79 155 76 286.15 0.14 308 80 85 5 501.72 0.43 309 80 86 6 422.80 26.25 310 80 87 7 372.48 1.07 311 80 124 44 372.62 1.05 312 80 127 47 372.50 1.08 313 80 154 74 286.42 0.25 314 81 85 4 501.74 0.43 315 81 86 5 422.81 26.25 316 82 85 3 551.00 2.52 317 82 86 4 515.31 1.34 318 82 127 45 372.72 1.03 319 82 128 46 372.60 1.08 320 83 135 52 372.49 1.07 321 84 127 43 372.76 1.03 322 84 128 44 372.75 1.02 323 84 129 45 372.76 1.03 324 84 134 50 372.74 1.04 325 85 127 42 372.76 1.03 326 86 154 68 286.54 0.19 327 87 124 37 372.85 1.04 328 87 127 40 372.85 1.04 329 87 154 67 286.47 0.19 330 88 154 66 286.12 0.10 331 88 155 67 286.06 0.10 332 89 122 33 373.09 1.02 333 89 124 35 372.91 0.93 334 91 121 30 373.10 1.03 335 91 122 31 373.12 1.02 336 92 121 29 373.10 1.03 337 93 116 23 373.10 1.03 338 93 121 28 373.36 1.05 339 95 101 6 373.01 1.05 340 95 103 8 373.35 1.05 341 95 116 21 373.37 1.06 342 97 101 4 575.83 4.49 343 100 164 64 165.75 0.79 344 100 165 65 165.78 0.79 345 100 166 66 165.81 0.79 346 101 117 16 464.06 0.24 347 102 116 14 464.07 0.23 348 102 117 15 464.07 0.24 349 103 114 11 464.06 0.23 350 103 115 12 464.07 0.23 351 103 116 13 464.08 0.24 352 104 114 10 464.09 0.24 353 104 115 11 464.09 0.24 354 105 112 7 464.05 0.23 355 105 113 8 464.09 0.24 356 105 114 9 464.10 0.24 357 106 112 6 467.23 1.80 358 106 113 7 464.10 0.24 359 106 115 9 464.15 0.24 360 107 111 4 495.99 7.07 361 107 112 5 472.21 0.59 362 107 128 21 463.88 0.21 363 107 129 22 464.06 0.22 364 107 130 23 464.06 0.21 365 107 131 24 464.06 0.21 366 108 111 3 528.66 0.10 367 108 113 5 490.61 9.76 368 110 126 16 464.08 0.23 369 110 127 17 464.11 0.24 370 110 128 18 464.12 0.24 371 111 123 12 464.19 0.24 372 111 124 13 464.15 0.24 373 111 125 14 464.12 0.24 374 111 126 15 464.15 0.24 375 111 127 16 464.15 0.24 376 112 123 11 464.21 0.24 377 112 124 12 464.17 0.24 378 112 127 15 464.22 0.23 379 113 122 9 464.24 0.25 380 113 123 10 464.20 0.23 381 114 120 6 464.38 0.18 382 114 121 7 464.29 0.23 383 114 122 8 464.30 0.23 384 115 119 4 477.67 0.61 385 115 120 5 464.38 0.18 386 116 119 3 523.79 4.14 387 116 121 5 493.09 2.48 388 120 123 3 612.26 1.10 389 124 127 3 564.32 2.23 390 128 134 6 496.44 0.70 391 130 133 3 546.49 1.18 392 131 134 3 538.20 2.96 393 131 139 8 466.19 0.14 394 139 171 32 464.36 0.23 395 140 147 7 467.21 0.12 396 141 170 29 464.34 0.25 397 141 171 30 464.38 0.26 398 142 145 3 551.27 2.69 399 142 147 5 492.67 3.40 400 143 165 22 464.12 0.28 401 143 170 27 464.39 0.24 402 146 149 3 573.43 0.95 403 146 150 4 533.95 1.91 404 146 153 7 506.06 1.20 405 146 159 13 464.43 0.24 406 148 152 4 527.76 1.10 407 148 153 5 527.76 1.10 408 149 152 3 542.96 0.86 409 150 153 3 547.39 0.51 410 150 156 6 477.69 4.19 411 150 157 7 469.90 0.30 412 150 159 9 466.46 0.34 413 151 156 5 478.75 4.71 414 153 156 3 522.97 1.44 415 153 157 4 528.04 1.06