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 12 166 154 36.48 0.67 2 13 166 153 44.47 0.12 3 13 167 154 44.92 0.29 4 14 166 152 44.93 0.29 5 15 100 85 44.94 0.29 6 15 164 149 44.70 0.24 7 15 165 150 44.93 0.28 8 15 166 151 44.93 0.29 9 15 187 172 36.73 0.02 10 15 188 173 25.89 1.02 11 16 27 11 45.59 0.42 12 16 164 148 44.94 0.28 13 16 165 149 44.98 0.28 14 16 185 169 44.99 0.29 15 16 186 170 44.88 0.31 16 16 187 171 43.09 0.56 17 16 188 172 38.51 0.59 18 17 27 10 45.69 0.39 19 17 163 146 44.98 0.29 20 17 164 147 44.97 0.28 21 17 186 169 44.98 0.29 22 17 187 170 44.95 0.28 23 17 188 171 44.83 0.30 24 18 27 9 45.97 0.52 25 18 46 28 45.59 0.42 26 18 55 37 45.58 0.42 27 18 144 126 45.48 0.38 28 18 161 143 45.05 0.32 29 18 163 145 45.15 0.36 30 18 165 147 45.51 0.39 31 19 23 4 277.68 108.94 32 19 27 8 46.11 0.57 33 19 160 141 45.36 0.36 34 19 161 142 45.42 0.38 35 20 184 164 47.79 0.70 36 20 186 166 46.19 0.56 37 22 160 138 46.20 0.56 38 23 159 136 46.08 0.61 39 23 160 137 46.08 0.61 40 26 29 3 583.54 3.03 41 26 142 116 75.03 0.57 42 26 143 117 64.84 0.83 43 26 144 118 56.75 1.41 44 26 145 119 51.17 2.06 45 26 146 120 51.18 2.06 46 26 147 121 69.91 11.41 47 26 182 156 88.77 0.36 48 27 143 116 82.38 0.52 49 27 181 154 95.00 0.35 50 27 182 155 93.39 0.21 51 27 185 158 78.87 0.17 52 28 142 114 92.13 0.42 53 28 143 115 84.59 0.61 54 28 180 152 100.44 0.12 55 28 181 153 96.98 0.61 56 28 182 154 97.77 0.40 57 28 185 157 83.89 0.39 58 29 140 111 100.41 0.30 59 29 141 112 99.86 0.29 60 29 142 113 92.14 0.42 61 29 147 118 98.28 0.18 62 29 179 150 106.39 1.85 63 29 180 151 102.03 0.27 64 30 140 110 101.99 0.23 65 30 141 111 100.31 0.32 66 30 143 113 100.27 0.29 67 30 170 140 100.43 0.30 68 30 176 146 126.20 1.88 69 30 178 148 125.19 1.76 70 30 179 149 109.70 0.20 71 31 138 107 115.39 1.98 72 31 139 108 110.84 0.38 73 31 140 109 102.04 0.25 74 31 176 145 126.25 1.89 75 31 177 146 126.19 1.89 76 31 178 147 126.06 1.88 77 32 37 5 516.62 0.18 78 32 138 106 123.56 1.20 79 32 139 107 117.87 1.06 80 32 141 109 116.80 1.29 81 32 170 138 125.48 1.88 82 32 171 139 125.52 1.89 83 32 172 140 126.03 1.92 84 32 175 143 126.26 1.89 85 32 176 144 126.26 1.89 86 32 177 145 126.27 1.89 87 33 36 3 554.34 0.44 88 33 37 4 531.59 3.54 89 33 137 104 136.02 1.39 90 33 175 142 126.28 1.89 91 33 177 144 126.30 1.89 92 34 37 3 541.40 1.36 93 34 60 26 141.00 0.56 94 34 131 97 144.77 0.09 95 34 132 98 156.18 2.73 96 34 134 100 162.10 3.33 97 34 136 102 162.10 3.35 98 34 137 103 142.72 0.29 99 34 139 105 127.14 1.47 100 35 132 97 165.77 1.51 101 35 137 102 162.08 3.33 102 36 174 138 154.30 0.75 103 36 175 139 146.03 0.84 104 37 40 3 576.46 3.98 105 37 131 94 170.38 1.38 106 37 172 135 148.27 1.84 107 37 175 138 163.84 1.52 108 38 172 134 167.93 0.44 109 38 174 136 168.16 0.42 110 39 171 132 167.94 0.43 111 39 172 133 168.02 0.48 112 40 106 66 173.27 1.11 113 40 107 67 171.95 1.76 114 40 131 91 173.25 2.12 115 40 171 131 168.24 0.39 116 41 105 64 173.50 1.09 117 41 106 65 173.27 1.11 118 41 171 130 168.27 0.38 119 42 104 62 177.10 1.57 120 42 105 63 176.50 1.40 121 42 169 127 168.30 0.36 122 42 170 128 168.25 0.39 123 42 171 129 168.35 0.38 124 43 103 60 178.31 1.03 125 43 104 61 177.10 1.57 126 43 168 125 168.31 0.36 127 43 169 126 168.33 0.36 128 44 55 11 177.03 1.54 129 44 56 12 177.10 1.56 130 44 69 25 178.33 1.02 131 44 102 58 185.26 1.02 132 44 103 59 180.80 0.45 133 44 165 121 167.65 0.44 134 44 166 122 168.29 0.36 135 44 167 123 168.31 0.36 136 44 168 124 168.31 0.36 137 44 170 126 168.56 0.38 138 45 100 55 206.03 2.52 139 45 101 56 193.14 1.21 140 45 102 57 185.30 1.02 141 45 165 120 168.09 0.40 142 45 166 121 168.31 0.35 143 45 167 122 168.34 0.36 144 46 95 49 209.62 1.21 145 46 100 54 218.17 3.54 146 46 101 55 198.56 0.22 147 46 103 57 194.35 0.60 148 46 161 115 168.78 0.41 149 46 164 118 168.08 0.47 150 47 98 51 272.79 1.10 151 47 99 52 254.16 3.92 152 47 100 53 223.86 0.74 153 47 163 116 168.32 0.35 154 47 164 117 168.29 0.36 155 48 71 23 222.59 1.40 156 48 95 47 257.64 2.81 157 48 96 48 257.82 2.90 158 48 97 49 275.72 0.76 159 48 98 50 275.64 0.79 160 48 161 113 168.84 0.41 161 48 162 114 168.55 0.37 162 48 163 115 168.33 0.35 163 49 96 47 269.73 2.64 164 49 97 48 275.88 0.83 165 49 98 49 275.87 0.83 166 50 71 21 265.09 0.61 167 50 96 46 276.19 0.91 168 50 160 110 176.27 1.27 169 50 161 111 169.01 0.36 170 50 162 112 168.88 0.39 171 51 71 20 268.18 0.82 172 51 72 21 276.04 0.98 173 51 73 22 276.05 0.99 174 51 74 23 275.13 0.64 175 51 94 43 276.22 0.92 176 51 96 45 277.89 1.67 177 52 71 19 275.95 0.98 178 52 72 20 276.04 0.98 179 52 157 105 192.02 0.95 180 52 158 106 188.84 0.01 181 52 161 109 169.53 0.29 182 53 70 17 276.73 1.17 183 53 71 18 277.89 1.67 184 53 157 104 197.19 0.53 185 53 158 105 192.03 0.94 186 53 159 106 183.90 1.16 187 53 160 107 181.24 1.15 188 53 161 108 168.87 0.39 189 54 68 14 275.95 0.97 190 54 69 15 277.89 1.67 191 54 70 16 277.89 1.67 192 54 144 90 278.75 1.77 193 54 145 91 278.36 1.80 194 54 146 92 277.81 2.08 195 54 157 103 199.25 0.37 196 54 159 105 187.69 0.57 197 54 161 107 168.78 0.39 198 55 69 14 278.24 1.81 199 55 70 15 278.29 1.82 200 55 71 16 278.33 1.81 201 55 143 88 278.89 1.77 202 55 144 89 278.76 1.77 203 55 161 106 168.77 0.40 204 56 67 11 278.30 1.83 205 56 68 12 278.29 1.83 206 56 69 13 278.30 1.83 207 56 105 49 278.32 1.82 208 56 141 85 279.34 1.89 209 56 142 86 278.93 1.77 210 56 143 87 278.91 1.77 211 56 144 88 278.89 1.77 212 56 170 114 204.69 0.78 213 57 62 5 541.03 3.11 214 57 66 9 278.30 1.83 215 57 67 10 278.30 1.83 216 57 68 11 278.30 1.83 217 57 141 84 279.36 1.88 218 57 142 85 279.32 1.88 219 57 145 88 278.91 1.77 220 57 146 89 278.80 1.76 221 57 147 90 278.79 1.76 222 57 148 91 278.81 1.77 223 58 66 8 278.30 1.83 224 58 67 9 278.31 1.83 225 58 140 82 279.38 1.88 226 58 141 83 279.37 1.88 227 59 62 3 558.63 0.28 228 59 65 6 485.85 0.23 229 59 66 7 278.31 1.83 230 59 139 80 279.44 1.88 231 59 140 81 279.44 1.89 232 60 65 5 505.12 0.18 233 60 134 74 278.59 1.69 234 60 136 76 279.05 1.80 235 60 138 78 279.44 1.88 236 60 139 79 279.44 1.88 237 61 64 3 552.31 1.99 238 61 65 4 509.97 2.13 239 61 66 5 511.45 1.39 240 62 66 4 521.49 3.62 241 62 140 78 279.65 1.83 242 62 148 86 279.44 1.88 243 63 66 3 599.32 2.96 244 64 81 17 278.59 1.82 245 64 82 18 278.54 1.84 246 65 81 16 278.64 1.82 247 65 82 17 278.58 1.82 248 65 134 69 279.62 1.86 249 66 79 13 279.23 1.64 250 66 80 14 278.90 1.74 251 66 81 15 278.76 1.77 252 66 148 82 279.74 1.81 253 66 153 87 279.58 1.81 254 66 154 88 279.57 1.81 255 67 78 11 279.41 1.73 256 67 79 12 279.22 1.64 257 67 80 13 278.94 1.72 258 67 105 38 279.81 1.83 259 67 112 45 279.59 1.82 260 68 77 9 279.67 1.79 261 68 78 10 279.39 1.72 262 68 79 11 279.31 1.68 263 68 146 78 279.83 1.80 264 68 153 85 279.71 1.80 265 68 157 89 279.54 1.79 266 69 76 7 368.32 46.11 267 69 77 8 279.67 1.79 268 69 78 9 279.43 1.73 269 69 103 34 279.99 1.81 270 69 105 36 279.83 1.83 271 69 114 45 279.85 1.85 272 70 76 6 368.32 46.11 273 70 77 7 279.68 1.79 274 71 74 3 539.72 0.99 275 71 75 4 495.13 5.35 276 71 76 5 368.32 46.11 277 71 95 24 370.81 3.52 278 71 96 25 370.88 3.52 279 71 157 86 240.78 21.27 280 71 161 90 169.14 0.42 281 72 75 3 538.28 1.71 282 72 77 5 493.28 4.49 283 72 79 7 493.30 4.48 284 72 155 83 279.87 1.81 285 72 156 84 279.86 1.80 286 72 157 85 240.78 21.27 287 73 94 21 370.88 3.52 288 74 94 20 370.88 3.52 289 74 95 21 370.91 3.52 290 74 96 22 370.92 3.52 291 75 92 17 370.88 3.52 292 75 93 18 370.89 3.52 293 75 94 19 370.90 3.51 294 76 90 14 370.84 3.51 295 76 91 15 370.88 3.52 296 76 92 16 370.89 3.52 297 76 93 17 370.92 3.51 298 76 95 19 370.96 3.51 299 76 114 38 370.90 3.52 300 76 116 40 370.96 3.50 301 77 88 11 370.84 3.51 302 77 89 12 370.85 3.51 303 77 90 13 370.87 3.52 304 78 87 9 370.84 3.51 305 78 88 10 370.87 3.52 306 78 89 11 370.88 3.52 307 78 114 36 371.01 3.50 308 78 122 44 371.00 3.52 309 78 124 46 370.91 3.51 310 79 87 8 370.85 3.51 311 79 88 9 370.87 3.52 312 79 153 74 282.17 1.47 313 79 154 75 282.18 1.47 314 79 155 76 282.17 1.48 315 80 85 5 509.23 3.92 316 80 86 6 415.11 18.62 317 80 87 7 370.88 3.52 318 80 124 44 371.05 3.52 319 80 127 47 370.94 3.51 320 80 154 74 282.90 1.70 321 81 85 4 522.82 0.91 322 81 86 5 428.54 25.34 323 82 85 3 532.71 0.03 324 82 86 4 516.49 0.28 325 82 127 45 371.38 3.50 326 84 126 42 371.44 3.50 327 84 127 43 371.44 3.50 328 84 128 44 371.44 3.52 329 84 129 45 371.44 3.52 330 85 127 42 371.44 3.50 331 86 154 68 282.91 1.70 332 87 124 37 371.63 3.45 333 87 127 40 371.72 3.50 334 87 154 67 282.81 1.66 335 88 154 66 282.19 1.48 336 88 155 67 282.18 1.48 337 89 122 33 371.72 3.50 338 89 124 35 371.74 3.49 339 91 121 30 371.72 3.50 340 91 122 31 371.73 3.50 341 92 121 29 371.72 3.50 342 93 116 23 371.75 3.48 343 93 121 28 371.84 3.47 344 95 101 6 371.70 3.49 345 95 103 8 371.92 3.45 346 95 116 21 371.92 3.44 347 97 101 4 578.38 1.67 348 100 164 64 168.30 0.36 349 100 165 65 168.44 0.33 350 100 166 66 168.56 0.39 351 101 117 16 461.68 6.76 352 102 116 14 461.68 6.75 353 102 117 15 461.69 6.76 354 102 118 16 461.73 6.76 355 103 114 11 461.72 6.78 356 103 115 12 461.70 6.76 357 104 114 10 461.75 6.78 358 104 115 11 461.71 6.76 359 105 112 7 461.73 6.78 360 105 113 8 461.75 6.78 361 105 114 9 461.75 6.79 362 106 112 6 461.75 6.78 363 106 113 7 461.76 6.78 364 106 115 9 461.81 6.78 365 107 111 4 503.39 7.78 366 107 112 5 461.75 6.78 367 107 128 21 461.67 6.83 368 107 131 24 460.97 6.40 369 108 111 3 535.82 3.79 370 108 113 5 484.20 1.84 371 110 126 16 462.03 6.92 372 110 127 17 462.04 6.91 373 110 128 18 462.00 6.89 374 111 123 12 462.06 6.83 375 111 124 13 462.05 6.90 376 111 125 14 462.05 6.91 377 111 127 16 462.06 6.91 378 112 123 11 462.12 6.87 379 112 124 12 462.06 6.90 380 112 127 15 462.09 6.91 381 113 120 7 462.01 6.75 382 113 122 9 462.20 6.83 383 113 123 10 462.13 6.87 384 114 120 6 467.81 3.95 385 114 121 7 462.20 6.83 386 114 122 8 462.22 6.83 387 115 119 4 484.66 3.16 388 115 120 5 467.81 3.95 389 116 119 3 539.03 2.15 390 116 121 5 477.12 0.62 391 120 123 3 617.91 0.91 392 124 127 3 561.38 0.79 393 130 133 3 535.69 0.66 394 130 134 4 514.96 2.07 395 131 134 3 532.48 0.48 396 131 139 8 462.67 6.87 397 138 177 39 463.38 6.77 398 139 171 32 463.69 6.74 399 140 147 7 483.82 2.70 400 141 170 29 463.75 6.82 401 141 171 30 463.91 6.80 402 142 145 3 560.94 0.55 403 142 147 5 490.47 0.61 404 143 165 22 463.17 6.86 405 143 168 25 464.13 6.71 406 143 170 27 464.18 6.73 407 146 149 3 572.54 1.39 408 146 150 4 526.75 4.38 409 146 153 7 510.28 2.65 410 146 159 13 463.88 6.66 411 148 152 4 532.57 3.77 412 148 153 5 517.54 0.61 413 149 152 3 537.62 1.04 414 150 153 3 544.03 2.17 415 150 156 6 481.31 0.65 416 150 157 7 480.33 1.13 417 150 159 9 464.75 6.59 418 151 156 5 492.12 3.24 419 153 156 3 533.64 2.30 420 153 157 4 539.86 0.81