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 8 472.37 1.54 2 2 130 128 47.27 0.03 3 2 133 131 41.44 0.96 4 2 134 132 32.52 0.72 5 2 137 135 32.45 0.69 6 3 6 3 512.88 2.65 7 3 7 4 513.20 2.50 8 4 7 3 515.74 3.75 9 4 8 4 513.22 2.49 10 4 79 75 58.91 1.76 11 5 8 3 513.21 2.48 12 5 9 4 513.22 2.49 13 6 9 3 526.56 4.18 14 6 10 4 513.42 2.38 15 6 130 124 66.75 1.18 16 6 133 127 66.80 1.15 17 7 10 3 515.97 2.35 18 7 11 4 505.34 1.68 19 7 76 69 66.88 1.13 20 7 79 72 66.86 1.13 21 7 80 73 67.16 0.98 22 7 134 127 66.86 1.13 23 7 137 130 66.86 1.13 24 8 11 3 524.12 2.62 25 8 12 4 506.25 2.14 26 9 12 3 526.32 1.52 27 9 13 4 514.98 1.32 28 9 126 117 82.78 0.65 29 9 127 118 82.73 0.64 30 9 130 121 82.73 0.64 31 10 13 3 525.01 1.99 32 10 14 4 515.17 1.24 33 10 76 66 82.72 0.63 34 10 130 120 82.73 0.64 35 10 131 121 82.73 0.64 36 10 134 124 82.72 0.64 37 11 14 3 515.17 1.23 38 11 15 4 515.16 1.23 39 11 76 65 82.78 0.64 40 11 77 66 82.73 0.62 41 11 79 68 82.75 0.62 42 12 15 3 523.38 2.88 43 12 16 4 520.11 3.70 44 12 122 110 89.67 1.07 45 13 16 3 523.64 3.01 46 13 17 4 515.66 1.48 47 13 115 102 89.52 1.10 48 13 119 106 89.92 0.97 49 13 122 109 89.67 1.06 50 13 123 110 89.66 1.07 51 13 131 118 88.55 1.04 52 14 17 3 518.12 0.25 53 14 18 4 518.46 0.08 54 14 69 55 89.34 1.00 55 14 72 58 89.00 0.83 56 14 73 59 88.05 1.28 57 14 76 62 88.05 1.29 58 14 77 63 88.07 1.28 59 15 18 3 518.46 0.08 60 15 19 4 516.34 0.98 61 16 19 3 518.46 0.09 62 16 119 103 95.34 3.43 63 16 122 106 95.34 3.43 64 17 20 3 525.04 1.80 65 17 21 4 491.21 4.02 66 17 24 7 405.04 2.48 67 17 69 52 130.31 19.28 68 17 115 98 90.15 0.83 69 18 21 3 514.94 1.83 70 18 77 59 130.05 19.18 71 20 23 3 519.54 0.72 72 20 24 4 510.15 3.97 73 20 118 98 133.88 1.42 74 21 24 3 519.54 0.72 75 21 25 4 513.90 2.10 76 21 66 45 175.77 1.19 77 21 69 48 175.72 1.16 78 22 25 3 518.85 0.38 79 22 26 4 513.91 2.10 80 22 62 40 179.60 0.01 81 22 66 44 176.06 1.31 82 23 26 3 520.65 5.46 83 23 27 4 513.89 2.08 84 23 118 95 165.99 0.42 85 24 27 3 521.85 4.87 86 24 28 4 511.78 1.02 87 24 69 45 176.15 1.28 88 24 114 90 166.22 0.60 89 24 115 91 166.26 0.58 90 24 118 94 166.00 0.42 91 24 119 95 166.19 0.52 92 25 28 3 513.76 0.04 93 25 29 4 510.98 0.57 94 25 65 40 177.34 1.11 95 25 69 44 176.15 1.28 96 26 29 3 517.42 0.07 97 26 30 4 508.47 1.46 98 26 55 29 234.00 4.17 99 26 56 30 230.19 6.07 100 27 30 3 518.88 0.80 101 27 31 4 512.82 0.69 102 27 114 87 167.81 0.18 103 27 118 91 167.59 0.18 104 28 31 3 510.49 0.49 105 28 32 4 508.50 1.48 106 28 69 41 182.15 0.20 107 28 107 79 168.44 0.21 108 28 110 82 168.22 0.18 109 28 111 83 168.20 0.18 110 28 114 86 167.82 0.18 111 29 32 3 519.20 0.20 112 29 33 4 508.46 1.49 113 29 61 32 207.94 1.03 114 29 64 35 204.88 0.18 115 29 65 36 187.92 1.93 116 29 107 78 168.45 0.21 117 30 33 3 516.90 1.34 118 30 34 4 506.41 2.52 119 30 52 22 245.67 0.78 120 30 55 25 243.99 0.04 121 30 56 26 245.68 0.81 122 30 61 31 212.38 0.22 123 31 34 3 517.62 0.99 124 31 35 4 494.20 3.56 125 31 110 79 168.29 0.14 126 31 113 82 168.05 0.07 127 31 114 83 168.05 0.07 128 32 35 3 514.67 1.68 129 32 36 4 494.35 3.48 130 32 39 7 432.82 4.30 131 32 106 74 168.58 0.22 132 32 107 75 168.46 0.21 133 32 110 78 168.30 0.14 134 33 36 3 519.47 0.52 135 33 37 4 493.36 3.96 136 33 39 6 432.83 4.31 137 33 40 7 315.85 1.88 138 33 43 10 302.30 4.90 139 33 46 13 254.95 1.20 140 33 55 22 249.09 0.03 141 33 61 28 246.14 0.60 142 34 37 3 527.60 2.98 143 34 50 16 251.31 0.52 144 34 51 17 249.64 0.08 145 34 52 18 249.18 0.01 146 34 55 21 249.16 0.01 147 36 39 3 523.91 5.78 148 36 106 70 168.65 0.20 149 37 40 3 525.68 3.50 150 38 41 3 520.25 4.58 151 38 103 65 169.00 0.10 152 38 106 68 168.93 0.09 153 39 42 3 527.21 2.73 154 39 43 4 515.15 2.04 155 39 103 64 168.91 0.10 156 39 106 67 168.70 0.17 157 40 43 3 520.49 0.62 158 40 46 6 349.92 24.91 159 40 47 7 279.55 4.33 160 40 49 9 270.94 6.32 161 40 55 15 252.17 0.94 162 41 47 6 300.37 3.53 163 42 97 55 169.59 0.22 164 42 98 56 169.59 0.22 165 42 99 57 169.57 0.23 166 42 100 58 169.57 0.23 167 42 103 61 169.37 0.29 168 43 46 3 523.52 1.11 169 43 47 4 498.88 6.82 170 43 64 21 249.81 0.81 171 44 47 3 526.42 1.52 172 45 48 3 596.31 0.65 173 45 60 15 250.37 0.59 174 45 64 19 249.87 0.81 175 46 49 3 533.87 0.77 176 46 60 14 249.91 0.81 177 46 61 15 249.86 0.82 178 46 64 18 249.85 0.82 179 49 54 5 434.19 2.16 180 49 55 6 377.23 26.32 181 49 58 9 290.60 0.46 182 49 61 12 252.34 0.96 183 50 54 4 501.84 2.19 184 51 54 3 502.36 2.43 185 51 55 4 502.32 2.44 186 52 55 3 502.43 2.47 187 52 56 4 502.07 2.56 188 53 56 3 519.50 5.83 189 53 57 4 502.07 2.56 190 54 57 3 508.06 1.77 191 54 58 4 502.07 2.56 192 55 58 3 514.25 3.52 193 55 61 6 407.60 0.04 194 58 61 3 532.89 2.92 195 58 62 4 505.64 2.31 196 59 62 3 517.00 3.37 197 59 63 4 504.00 3.13 198 60 63 3 517.03 3.38 199 60 64 4 504.12 3.08 200 61 64 3 525.06 0.64 201 61 65 4 508.71 0.77 202 62 65 3 510.34 0.04 203 62 66 4 511.70 0.72 204 63 66 3 517.14 1.99 205 63 67 4 511.73 0.74 206 64 67 3 509.90 1.66 207 64 68 4 509.92 1.67 208 65 68 3 525.82 3.94 209 65 69 4 511.24 1.02 210 66 69 3 527.81 2.94 211 66 70 4 511.25 1.02 212 67 70 3 531.63 3.94 213 67 71 4 511.24 1.02 214 68 71 3 522.99 0.39 215 68 72 4 507.49 1.29 216 68 107 39 168.52 0.24 217 69 72 3 518.11 2.06 218 69 73 4 502.51 2.53 219 70 73 3 526.88 0.41 220 70 74 4 505.50 3.96 221 71 74 3 520.08 1.88 222 71 75 4 505.60 3.91 223 72 75 3 520.08 1.88 224 72 76 4 510.82 1.29 225 72 111 39 168.42 0.30 226 72 135 63 166.12 0.61 227 72 138 66 165.45 0.41 228 73 76 3 516.33 2.79 229 73 77 4 509.13 0.80 230 74 77 3 530.50 3.00 231 74 78 4 512.07 0.67 232 75 78 3 536.04 0.23 233 75 82 7 205.33 5.49 234 75 85 10 176.35 3.51 235 75 89 14 176.35 3.51 236 75 138 63 165.62 0.41 237 76 79 3 525.22 5.19 238 76 134 58 166.22 0.63 239 78 81 3 503.14 2.88 240 78 82 4 403.34 21.73 241 78 85 7 283.81 2.83 242 80 137 57 166.23 0.63 243 82 85 3 519.59 1.22 244 82 86 4 499.36 4.76 245 82 137 55 166.24 0.63 246 82 141 59 165.33 0.50 247 83 86 3 515.58 0.01 248 83 87 4 505.72 1.58 249 84 88 4 526.27 3.29 250 85 88 3 543.15 0.23 251 85 89 4 521.40 0.86 252 86 89 3 526.27 3.29 253 86 90 4 511.24 0.91 254 86 138 52 165.62 0.46 255 86 141 55 165.17 0.57 256 86 142 56 164.42 0.93 257 86 145 59 158.77 1.25 258 87 90 3 521.42 0.85 259 87 91 4 516.38 1.67 260 88 91 3 521.53 0.91 261 88 92 4 510.87 1.06 262 89 92 3 518.47 0.62 263 89 93 4 510.86 1.06 264 89 138 49 165.58 0.43 265 89 142 53 161.08 0.59 266 90 93 3 512.97 2.14 267 90 94 4 505.81 1.39 268 90 142 52 160.63 0.38 269 90 145 55 155.38 0.23 270 90 146 56 151.19 0.13 271 91 94 3 517.73 1.23 272 91 95 4 503.85 2.37 273 91 149 58 147.62 0.83 274 92 95 3 526.34 5.56 275 92 96 4 480.47 4.38 276 92 97 5 469.75 0.98 277 93 97 4 420.61 18.31 278 93 98 5 416.84 20.18 279 93 99 6 323.44 7.01 280 93 146 53 151.16 0.15 281 94 98 4 416.83 20.18 282 94 146 52 149.30 0.04 283 94 149 55 142.22 0.10 284 94 151 57 79.35 3.90 285 95 98 3 515.53 0.16 286 95 149 54 143.80 0.48 287 95 151 56 118.72 2.42 288 98 151 53 87.28 0.34 289 99 103 4 509.59 2.74 290 99 104 5 509.61 2.75 291 99 146 47 148.56 0.41 292 100 103 3 522.98 0.17 293 100 104 4 513.94 1.14 294 100 153 53 27.27 4.17 295 101 104 3 521.72 2.75 296 101 105 4 510.95 2.63 297 101 142 41 160.49 0.45 298 101 143 42 156.95 0.57 299 101 146 45 148.00 0.68 300 101 153 52 17.96 0.51 301 102 105 3 521.17 3.02 302 102 106 4 510.48 2.32 303 103 106 3 519.02 1.96 304 103 107 4 510.48 2.31 305 104 107 3 519.10 2.10 306 104 108 4 508.38 1.26 307 104 139 35 161.54 0.54 308 104 142 38 158.92 0.26 309 105 108 3 513.05 0.92 310 105 109 4 513.04 0.91 311 105 139 34 161.59 0.52 312 106 109 3 519.23 3.85 313 106 110 4 513.06 0.92 314 107 110 3 513.06 0.92 315 107 111 4 501.23 2.33 316 108 111 3 518.83 2.79 317 108 112 4 506.51 0.84 318 108 135 27 165.06 0.43 319 108 139 31 161.58 0.52 320 109 112 3 519.85 2.52 321 109 113 4 508.44 1.81 322 110 113 3 514.61 4.91 323 110 114 4 506.71 1.18 324 111 114 3 525.98 0.55 325 111 115 4 508.06 0.51 326 111 135 24 165.11 0.45 327 112 115 3 520.13 0.15 328 112 116 4 509.58 0.24 329 112 123 11 276.30 8.07 330 112 128 16 166.16 0.64 331 112 131 19 165.58 0.53 332 112 132 20 165.52 0.56 333 112 135 23 165.14 0.46 334 113 116 3 519.77 0.33 335 113 117 4 509.58 0.25 336 114 117 3 507.78 3.50 337 114 118 4 509.10 0.49 338 115 118 3 517.30 0.47 339 115 119 4 498.70 2.65 340 115 123 8 294.19 0.88 341 115 131 16 186.61 5.18 342 116 119 3 525.38 1.24 343 116 120 4 493.56 1.55 344 116 123 7 283.16 4.65 345 117 120 3 545.44 3.21 346 119 122 3 519.38 5.15 347 119 123 4 465.98 2.55 348 120 123 3 509.97 9.85 349 120 124 4 489.26 0.50 350 122 127 5 475.73 9.17 351 123 127 4 478.14 10.37 352 123 128 5 473.24 0.32 353 123 131 8 438.91 3.93 354 124 127 3 512.10 1.89 355 124 128 4 500.25 4.04 356 125 128 3 508.09 0.11 357 125 129 4 505.54 1.39 358 126 129 3 508.09 0.11 359 126 130 4 505.55 1.39 360 127 130 3 512.62 3.64 361 127 131 4 504.04 0.64 362 128 131 3 514.50 0.39 363 128 132 4 514.49 0.39 364 129 132 3 517.78 1.24 365 129 133 4 515.30 0.01 366 130 133 3 515.32 0.00 367 130 134 4 511.84 1.73 368 131 134 3 515.51 0.10 369 131 135 4 504.49 5.41 370 132 135 3 514.58 0.57 371 132 136 4 503.61 4.92 372 133 136 3 510.91 1.27 373 133 137 4 504.90 0.28 374 134 137 3 509.03 1.77 375 134 138 4 504.98 0.30 376 135 138 3 505.78 0.10 377 135 139 4 506.34 0.54 378 136 139 3 512.60 2.59 379 136 140 4 505.79 0.25 380 137 140 3 519.02 2.58 381 137 141 4 505.80 0.26 382 138 141 3 520.12 3.54 383 138 142 4 506.37 0.54 384 139 142 3 509.38 1.99 385 139 143 4 505.74 0.29 386 140 143 3 514.73 2.58 387 140 144 4 507.48 1.04 388 141 144 3 512.59 1.51 389 141 145 4 507.49 1.04 390 142 145 3 513.21 0.86 391 142 146 4 505.32 2.12 392 143 146 3 509.65 0.06 393 143 147 4 508.83 0.46 394 143 152 9 234.63 15.03 395 144 147 3 513.24 3.64 396 144 148 4 507.83 0.97 397 145 148 3 510.84 2.10 398 145 149 4 506.70 1.53 399 146 149 3 511.24 0.73 400 146 150 4 502.80 3.46 401 146 151 5 427.04 29.67 402 146 152 6 241.32 11.73 403 147 150 3 502.83 3.48 404 147 152 5 291.75 13.53