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 8 473.39 2.45 2 2 130 128 36.62 1.34 3 2 133 131 26.02 1.05 4 2 134 132 23.65 0.04 5 2 137 135 23.70 0.06 6 3 6 3 498.06 1.16 7 3 7 4 495.32 0.21 8 4 7 3 506.13 1.20 9 4 8 4 501.70 3.40 10 4 79 75 47.71 0.64 11 5 8 3 506.73 3.36 12 5 9 4 504.17 4.63 13 6 9 3 505.16 4.15 14 6 10 4 501.70 3.41 15 6 130 124 59.98 0.16 16 6 133 127 59.98 0.16 17 7 10 3 502.69 2.92 18 7 11 4 501.68 3.42 19 7 76 69 60.15 0.09 20 7 79 72 60.15 0.09 21 7 80 73 60.19 0.09 22 7 134 127 60.04 0.14 23 7 137 130 60.41 0.01 24 8 11 3 518.09 0.42 25 8 12 4 489.11 3.35 26 9 12 3 506.44 1.73 27 9 13 4 496.56 0.37 28 9 126 117 72.26 1.28 29 9 127 118 71.86 1.48 30 9 130 121 71.84 1.47 31 10 13 3 515.29 3.74 32 10 14 4 503.51 2.16 33 10 76 66 71.83 1.47 34 10 130 120 71.89 1.47 35 10 131 121 71.83 1.47 36 10 134 124 71.75 1.51 37 11 14 3 508.08 4.45 38 11 15 4 503.52 2.17 39 11 76 65 72.27 1.28 40 11 77 66 72.28 1.28 41 11 79 68 72.27 1.28 42 12 15 3 518.42 0.73 43 12 16 4 510.00 3.48 44 12 122 110 88.11 0.84 45 13 16 3 515.82 0.57 46 13 17 4 505.51 1.23 47 13 115 102 87.84 0.89 48 13 119 106 88.17 0.85 49 13 122 109 88.11 0.84 50 13 123 110 88.08 0.83 51 13 131 118 87.43 0.83 52 14 17 3 505.51 1.23 53 14 18 4 503.76 2.12 54 14 69 55 126.12 20.07 55 14 72 58 87.59 0.83 56 14 73 59 87.58 0.83 57 14 76 62 87.25 0.92 58 14 77 63 87.43 0.83 59 14 115 101 88.32 0.93 60 14 131 117 87.84 0.94 61 15 18 3 508.62 0.30 62 15 19 4 505.52 1.25 63 16 19 3 514.97 2.85 64 16 119 103 94.28 1.56 65 16 122 106 93.49 1.17 66 17 20 3 521.52 0.43 67 17 21 4 492.23 5.40 68 17 24 7 388.22 20.89 69 17 69 52 126.92 20.21 70 17 115 98 94.94 1.24 71 17 119 102 100.03 2.83 72 18 21 3 502.34 0.35 73 18 77 59 88.49 1.09 74 20 23 3 514.95 2.81 75 20 24 4 503.26 2.40 76 20 118 98 135.04 3.52 77 21 24 3 514.95 2.80 78 21 25 4 498.94 2.73 79 21 66 45 143.88 14.78 80 21 69 48 143.47 14.88 81 22 25 3 506.25 0.91 82 22 26 4 506.24 0.91 83 22 62 40 170.61 2.10 84 22 66 44 148.15 13.31 85 23 26 3 506.24 0.91 86 23 27 4 506.24 0.91 87 23 118 95 158.34 2.68 88 24 27 3 512.39 3.98 89 24 28 4 494.11 5.16 90 24 69 45 149.46 12.00 91 24 114 90 158.59 2.82 92 24 115 91 156.79 3.72 93 24 118 94 159.90 1.93 94 24 119 95 161.65 1.05 95 25 28 3 513.29 3.42 96 25 29 4 493.57 4.92 97 25 65 40 149.46 12.00 98 25 69 44 150.08 11.71 99 26 29 3 523.12 1.50 100 26 30 4 493.56 4.95 101 26 56 30 221.25 5.53 102 26 62 36 175.85 0.01 103 27 30 3 516.86 0.56 104 27 31 4 511.22 2.25 105 27 114 87 162.78 0.73 106 27 118 91 162.49 0.64 107 28 31 3 512.28 1.73 108 28 32 4 497.18 4.77 109 28 69 41 174.78 0.06 110 28 107 79 163.34 0.73 111 28 110 82 163.10 0.78 112 28 111 83 163.05 0.75 113 28 114 86 162.78 0.73 114 28 115 87 162.85 0.70 115 29 32 3 511.24 2.25 116 29 33 4 497.17 4.78 117 29 61 32 194.20 1.96 118 29 64 35 184.76 2.45 119 29 65 36 184.62 2.48 120 29 107 78 163.35 0.73 121 30 33 3 500.97 1.39 122 30 34 4 489.78 6.53 123 30 52 22 227.71 4.62 124 30 55 25 224.80 4.66 125 30 56 26 227.20 4.79 126 30 61 31 222.00 3.29 127 31 34 3 514.76 4.24 128 31 35 4 483.53 3.75 129 31 110 79 163.19 0.81 130 31 113 82 163.09 0.82 131 32 35 3 506.87 2.50 132 32 36 4 483.51 3.74 133 32 39 7 460.98 8.04 134 32 106 74 163.36 0.73 135 32 107 75 163.35 0.73 136 32 110 78 163.17 0.80 137 33 36 3 506.88 2.50 138 33 37 4 476.18 0.78 139 33 39 6 452.36 12.36 140 33 40 7 429.09 23.99 141 33 43 10 373.95 5.78 142 33 46 13 247.88 2.47 143 33 55 22 227.89 4.63 144 33 61 28 227.72 4.61 145 34 37 3 524.64 1.26 146 34 52 18 227.91 4.64 147 34 55 21 227.91 4.64 148 36 39 3 516.12 1.53 149 36 106 70 163.43 0.77 150 37 40 3 518.96 0.59 151 37 41 4 508.32 2.16 152 38 41 3 525.49 2.68 153 38 42 4 516.73 0.53 154 38 103 65 163.84 0.72 155 38 106 68 163.80 0.71 156 39 42 3 523.89 3.48 157 39 43 4 516.73 0.52 158 39 103 64 163.68 0.70 159 39 106 67 163.68 0.67 160 40 43 3 524.71 4.50 161 40 46 6 391.24 33.84 162 40 47 7 266.11 1.55 163 40 49 9 270.23 8.34 164 40 55 15 235.01 1.76 165 41 47 6 278.75 4.08 166 42 97 55 164.57 0.65 167 42 98 56 164.53 0.64 168 42 99 57 164.49 0.62 169 42 100 58 164.50 0.62 170 42 103 61 164.38 0.63 171 43 46 3 505.88 0.17 172 43 47 4 479.82 2.08 173 43 64 21 232.24 2.83 174 44 47 3 526.21 0.52 175 45 48 3 585.61 0.79 176 45 60 15 232.78 2.73 177 45 64 19 232.75 2.74 178 46 49 3 528.67 1.74 179 46 60 14 232.78 2.73 180 46 61 15 232.76 2.73 181 46 64 18 232.75 2.74 182 47 50 3 588.76 3.41 183 49 54 5 459.79 5.32 184 49 55 6 388.31 13.71 185 49 58 9 267.81 2.22 186 49 61 12 252.54 0.57 187 50 54 4 490.44 0.49 188 51 54 3 508.07 0.37 189 51 55 4 499.89 0.71 190 52 55 3 503.63 2.58 191 52 56 4 499.12 0.33 192 53 56 3 510.82 1.04 193 53 57 4 503.61 2.57 194 54 57 3 504.44 2.98 195 54 58 4 503.61 2.56 196 55 58 3 525.15 1.01 197 55 61 6 394.10 3.54 198 58 61 3 501.29 0.10 199 58 62 4 503.97 1.44 200 59 62 3 505.69 0.58 201 59 63 4 499.73 0.69 202 60 63 3 501.79 1.70 203 60 64 4 495.00 1.70 204 61 64 3 507.74 1.28 205 61 65 4 500.95 4.68 206 62 65 3 502.58 4.49 207 62 66 4 507.22 1.54 208 63 66 3 507.75 1.59 209 63 67 4 504.83 0.35 210 64 67 3 514.60 5.24 211 64 68 4 501.05 1.54 212 65 68 3 514.60 5.24 213 65 69 4 494.92 1.46 214 66 69 3 507.62 1.01 215 66 70 4 492.73 0.43 216 67 70 3 507.62 1.01 217 67 71 4 499.62 2.99 218 68 71 3 515.41 4.91 219 68 72 4 500.08 0.26 220 68 107 39 164.01 0.39 221 69 72 3 502.58 1.50 222 69 73 4 500.11 0.24 223 70 73 3 506.76 2.99 224 70 74 4 500.11 0.24 225 71 74 3 514.57 5.18 226 71 75 4 496.73 1.46 227 72 75 3 507.78 0.38 228 72 76 4 503.35 1.85 229 72 111 39 163.93 0.38 230 72 135 63 160.06 0.12 231 72 138 66 159.37 0.27 232 73 76 3 509.97 1.46 233 73 77 4 507.81 0.38 234 74 77 3 515.30 1.05 235 74 78 4 507.81 0.38 236 75 78 3 512.32 0.66 237 75 79 4 511.10 1.27 238 75 82 7 225.37 8.20 239 75 85 10 186.38 3.18 240 75 86 11 186.47 3.14 241 75 89 14 186.38 3.18 242 75 138 63 159.88 0.14 243 76 79 3 511.07 1.28 244 76 131 55 160.88 0.36 245 76 134 58 160.19 0.15 246 78 81 3 475.86 4.71 247 78 82 4 437.48 4.75 248 78 85 7 414.87 0.35 249 80 137 57 160.19 0.14 250 82 85 3 509.92 0.27 251 82 86 4 507.88 1.29 252 82 137 55 160.19 0.15 253 82 141 59 159.55 0.18 254 83 86 3 519.03 2.04 255 83 87 4 507.88 1.29 256 84 87 3 517.21 0.88 257 84 88 4 518.37 1.46 258 85 88 3 550.11 1.62 259 85 89 4 513.39 1.03 260 86 89 3 518.63 1.59 261 86 90 4 502.90 1.21 262 86 138 52 159.33 0.29 263 86 141 55 158.27 0.35 264 86 142 56 157.03 0.29 265 87 90 3 514.63 0.41 266 87 91 4 499.62 2.79 267 88 91 3 507.32 1.18 268 88 92 4 498.50 3.23 269 89 92 3 505.38 3.98 270 89 93 4 496.38 2.18 271 89 138 49 159.35 0.31 272 89 142 53 155.66 0.88 273 90 93 3 514.08 4.46 274 90 94 4 496.25 2.24 275 90 142 52 155.62 0.89 276 90 145 55 141.91 0.82 277 90 146 56 140.56 0.20 278 91 94 3 510.80 6.11 279 91 95 4 498.54 3.46 280 91 149 58 137.77 0.08 281 92 95 3 517.11 2.95 282 92 96 4 474.86 5.70 283 92 97 5 435.49 5.40 284 93 97 4 432.39 5.44 285 93 98 5 408.42 6.55 286 93 99 6 333.28 8.09 287 93 146 53 138.03 0.03 288 94 98 4 394.29 24.48 289 94 146 52 137.97 0.01 290 94 149 55 133.61 0.38 291 94 151 57 48.05 1.15 292 95 98 3 519.66 3.68 293 95 149 54 137.06 0.43 294 98 151 53 69.81 2.44 295 99 103 4 488.66 1.02 296 99 104 5 488.69 1.00 297 99 146 47 137.98 0.01 298 99 151 52 85.75 5.54 299 100 103 3 493.74 3.51 300 100 104 4 488.74 1.01 301 100 146 46 137.98 0.01 302 100 151 51 47.81 1.27 303 101 104 3 492.20 2.08 304 101 105 4 489.59 0.60 305 101 139 38 156.00 0.82 306 101 142 41 152.83 0.35 307 101 143 42 144.84 1.89 308 101 146 45 137.97 0.01 309 102 105 3 493.51 1.14 310 102 106 4 490.77 1.19 311 103 106 3 503.17 4.84 312 103 107 4 496.34 2.73 313 104 107 3 502.38 0.28 314 104 108 4 487.19 1.84 315 104 139 35 155.97 0.81 316 104 142 38 149.22 1.57 317 105 108 3 496.73 0.29 318 105 109 4 492.59 0.86 319 105 139 34 155.97 0.80 320 106 109 3 503.81 3.83 321 106 110 4 492.62 0.85 322 107 110 3 507.44 2.00 323 107 111 4 501.19 5.13 324 108 111 3 507.65 1.91 325 108 112 4 507.19 2.14 326 108 135 27 159.25 0.44 327 108 139 31 157.19 0.20 328 109 112 3 509.49 2.41 329 109 113 4 498.62 2.16 330 110 113 3 498.57 2.18 331 110 114 4 498.56 2.17 332 111 114 3 507.47 3.41 333 111 115 4 499.26 5.50 334 111 135 24 159.31 0.44 335 112 115 3 501.29 6.50 336 112 116 4 505.44 2.41 337 112 123 11 263.43 1.33 338 112 131 19 160.16 0.23 339 112 132 20 159.78 0.41 340 112 135 23 159.59 0.31 341 113 116 3 505.44 2.41 342 113 117 4 505.44 2.41 343 114 117 3 505.44 2.41 344 114 118 4 498.18 6.03 345 115 118 3 510.71 0.23 346 115 119 4 473.04 5.71 347 115 123 8 274.25 3.36 348 115 131 16 187.31 0.27 349 116 119 3 512.81 1.29 350 116 120 4 472.24 5.40 351 116 123 7 276.29 5.08 352 116 128 12 230.12 2.93 353 117 120 3 526.70 2.06 354 119 122 3 509.69 2.44 355 119 123 4 445.26 2.37 356 120 123 3 485.51 9.65 357 120 124 4 469.88 15.17 358 122 127 5 464.61 5.88 359 123 127 4 465.16 5.61 360 123 128 5 464.98 5.70 361 123 131 8 423.14 14.85 362 124 127 3 507.20 0.80 363 124 128 4 483.17 8.21 364 125 128 3 504.18 2.29 365 125 129 4 483.87 7.86 366 126 129 3 504.23 2.31 367 126 130 4 498.16 0.72 368 127 130 3 502.92 1.65 369 127 131 4 495.44 2.06 370 128 131 3 510.65 2.10 371 128 132 4 496.23 1.65 372 129 132 3 502.74 1.59 373 129 133 4 486.71 3.10 374 130 133 3 491.73 5.33 375 130 134 4 491.04 0.95 376 131 134 3 492.38 1.61 377 131 135 4 488.06 3.77 378 132 135 3 503.69 4.03 379 132 136 4 488.06 3.81 380 133 136 3 495.87 3.35 381 133 137 4 488.94 3.39 382 134 137 3 493.56 4.51 383 134 138 4 490.13 2.80 384 135 138 3 493.73 4.42 385 135 139 4 490.13 2.80 386 136 139 3 499.09 1.70 387 136 140 4 492.36 5.07 388 137 140 3 499.67 1.99 389 137 141 4 492.72 4.90 390 138 141 3 509.82 1.92 391 138 142 4 492.72 4.89 392 139 142 3 510.61 1.53 393 139 143 4 489.41 3.23 394 140 143 3 505.27 1.14 395 140 144 4 490.11 3.58 396 141 144 3 508.93 1.01 397 141 145 4 491.49 3.00 398 142 145 3 505.95 1.04 399 142 146 4 490.98 2.74 400 143 146 3 498.23 0.37 401 143 147 4 489.64 3.41 402 144 147 3 503.82 0.02 403 144 148 4 491.72 2.19 404 145 148 3 503.08 0.35 405 145 149 4 491.72 2.19 406 146 149 3 496.16 2.46 407 146 150 4 489.46 3.33 408 146 151 5 380.50 0.70 409 147 150 3 489.47 3.33