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 7 5 478.61 3.66 2 2 10 8 478.45 3.73 3 2 130 128 37.58 0.41 4 2 133 131 30.49 1.52 5 2 134 132 29.95 1.79 6 2 137 135 26.25 0.07 7 3 6 3 517.12 11.83 8 3 7 4 494.45 3.22 9 4 7 3 501.43 0.26 10 4 8 4 505.11 2.10 11 5 8 3 505.11 2.10 12 5 9 4 505.11 2.10 13 6 9 3 506.07 1.62 14 6 10 4 505.10 2.11 15 6 130 124 61.31 2.23 16 6 133 127 61.26 2.23 17 7 10 3 506.32 1.50 18 7 11 4 501.95 3.68 19 7 76 69 61.30 2.23 20 7 79 72 61.30 2.23 21 7 80 73 61.32 2.24 22 7 134 127 61.30 2.23 23 7 137 130 61.31 2.23 24 8 11 3 516.37 3.53 25 8 12 4 500.62 1.21 26 9 12 3 511.81 1.02 27 9 13 4 505.85 3.82 28 9 126 117 79.48 0.51 29 9 127 118 78.92 0.69 30 9 130 121 78.81 0.71 31 10 13 3 520.12 3.14 32 10 14 4 507.99 2.75 33 10 76 66 78.84 0.69 34 10 130 120 78.91 0.68 35 10 131 121 78.81 0.71 36 10 134 124 78.80 0.70 37 11 14 3 511.93 1.08 38 11 15 4 512.39 1.31 39 11 76 65 78.91 0.68 40 11 77 66 78.89 0.69 41 11 79 68 78.88 0.67 42 12 15 3 519.80 1.61 43 12 16 4 519.29 1.87 44 13 16 3 524.13 3.79 45 13 17 4 516.40 0.42 46 13 115 102 82.89 0.14 47 13 123 110 82.73 0.32 48 13 127 114 81.92 0.07 49 13 131 118 81.47 0.12 50 14 17 3 516.29 0.36 51 14 18 4 508.74 2.29 52 14 69 55 82.02 0.02 53 14 72 58 81.90 0.07 54 14 73 59 81.84 0.06 55 14 76 62 81.41 0.15 56 14 77 63 81.84 0.07 57 14 131 117 81.95 0.07 58 15 18 3 514.49 5.15 59 15 19 4 506.20 1.53 60 16 19 3 518.94 1.12 61 16 24 8 448.30 6.83 62 16 119 103 102.94 3.37 63 16 122 106 106.89 1.34 64 17 20 3 517.99 0.65 65 17 21 4 479.88 3.50 66 17 24 7 436.58 12.69 67 17 69 52 97.81 1.09 68 17 115 98 98.17 1.07 69 18 21 3 510.55 4.36 70 18 77 59 97.77 1.17 71 20 23 3 520.18 2.29 72 20 24 4 499.47 4.42 73 21 24 3 505.64 5.82 74 21 25 4 498.00 2.13 75 21 66 45 122.25 0.64 76 21 69 48 112.80 1.24 77 22 25 3 506.63 5.33 78 22 26 4 487.78 2.98 79 22 62 40 129.94 0.84 80 22 66 44 126.20 0.40 81 23 26 3 521.70 2.21 82 23 27 4 495.47 0.85 83 24 27 3 524.16 1.54 84 24 28 4 496.90 1.56 85 24 69 45 132.66 0.08 86 24 114 90 142.72 2.21 87 24 115 91 144.41 1.36 88 24 118 94 149.00 0.25 89 24 119 95 150.63 1.06 90 25 28 3 515.12 4.79 91 25 29 4 499.79 2.88 92 25 65 40 132.85 0.01 93 25 69 44 132.66 0.08 94 26 29 3 519.12 0.97 95 26 30 4 499.67 2.94 96 26 56 30 153.67 0.42 97 26 61 35 147.96 0.12 98 26 62 36 147.96 0.12 99 26 65 39 147.25 0.43 100 27 30 3 513.29 1.94 101 27 31 4 495.44 0.83 102 27 56 29 153.99 0.55 103 27 114 87 149.59 0.03 104 27 118 91 152.50 0.31 105 28 31 3 516.23 0.47 106 28 32 4 497.86 2.15 107 28 107 79 148.96 0.24 108 28 110 82 149.03 0.24 109 28 111 83 149.02 0.24 110 28 114 86 151.31 0.76 111 29 32 3 506.23 0.19 112 29 33 4 497.82 2.17 113 29 61 32 153.68 0.45 114 29 64 35 153.52 0.55 115 29 65 36 153.19 0.59 116 29 107 78 149.07 0.23 117 30 33 3 511.01 3.27 118 30 34 4 502.85 0.35 119 30 52 22 154.19 0.51 120 30 55 25 154.10 0.54 121 30 56 26 154.10 0.54 122 30 61 31 153.81 0.48 123 31 34 3 517.79 0.50 124 31 35 4 496.43 2.85 125 31 110 79 152.69 0.29 126 31 113 82 153.73 0.45 127 31 114 83 153.74 0.46 128 32 35 3 515.22 0.79 129 32 36 4 491.85 0.80 130 32 39 7 405.14 31.71 131 32 106 74 152.62 0.30 132 32 107 75 152.67 0.32 133 32 110 78 153.63 0.48 134 33 36 3 506.29 5.98 135 33 37 4 467.01 0.79 136 33 39 6 424.88 21.85 137 33 40 7 297.04 51.88 138 33 43 10 288.69 56.06 139 33 46 13 154.52 0.60 140 33 55 22 154.44 0.60 141 33 61 28 154.34 0.58 142 34 37 3 521.24 0.39 143 34 52 18 154.47 0.58 144 34 55 21 154.46 0.58 145 36 39 3 525.46 0.67 146 36 106 70 153.34 0.60 147 37 40 3 525.46 0.67 148 37 41 4 516.71 0.54 149 38 41 3 518.75 0.85 150 38 103 65 153.46 0.67 151 38 106 68 153.84 0.49 152 39 42 3 519.10 0.66 153 39 43 4 512.62 2.58 154 39 103 64 153.24 0.58 155 39 106 67 153.82 0.48 156 40 43 3 513.81 0.07 157 40 46 6 357.26 0.55 158 40 47 7 164.18 2.19 159 40 49 9 165.03 4.35 160 40 55 15 155.18 0.56 161 41 47 6 238.05 32.09 162 42 97 55 153.23 0.58 163 42 98 56 153.25 0.57 164 42 99 57 152.96 0.42 165 42 100 58 153.48 0.66 166 42 103 61 153.83 0.49 167 43 46 3 511.79 1.69 168 43 47 4 502.67 0.42 169 43 64 21 155.06 0.60 170 44 47 3 517.12 0.20 171 45 48 3 561.23 1.77 172 45 60 15 155.22 0.56 173 45 64 19 155.15 0.58 174 46 49 3 524.99 1.64 175 46 60 14 155.22 0.56 176 46 61 15 155.16 0.58 177 46 64 18 155.15 0.58 178 47 50 3 570.26 3.35 179 48 54 6 471.98 6.62 180 49 54 5 465.58 9.81 181 49 55 6 447.38 18.91 182 49 58 9 258.75 36.22 183 49 61 12 163.44 3.48 184 50 54 4 511.49 0.92 185 51 54 3 511.49 0.92 186 51 55 4 511.49 0.92 187 52 55 3 511.49 0.92 188 52 56 4 511.49 0.92 189 53 56 3 511.50 0.91 190 53 57 4 504.95 2.35 191 54 57 3 511.50 0.92 192 54 58 4 499.18 0.54 193 55 58 3 513.31 1.81 194 55 61 6 419.17 4.82 195 58 61 3 505.88 1.28 196 58 62 4 502.09 0.61 197 59 62 3 502.10 0.61 198 59 63 4 501.93 0.70 199 60 63 3 504.50 1.81 200 60 64 4 495.75 2.40 201 61 64 3 512.91 2.40 202 61 65 4 495.72 2.41 203 62 65 3 503.90 0.76 204 62 66 4 495.86 2.48 205 63 66 3 505.84 1.64 206 63 67 4 502.67 3.23 207 64 67 3 509.45 0.17 208 64 68 4 509.44 0.17 209 65 68 3 509.71 0.29 210 65 69 4 509.45 0.17 211 66 69 3 520.20 1.82 212 66 70 4 500.55 4.61 213 67 70 3 524.02 4.82 214 67 71 4 500.55 4.61 215 68 71 3 515.47 0.54 216 68 72 4 502.44 3.40 217 68 107 39 159.57 0.66 218 69 72 3 513.06 1.09 219 69 73 4 493.66 1.01 220 70 73 3 510.60 0.14 221 70 74 4 507.06 1.91 222 71 74 3 517.08 3.39 223 71 75 4 501.03 1.11 224 72 75 3 514.26 4.83 225 72 76 4 513.37 5.28 226 72 111 39 165.50 0.61 227 72 135 63 165.49 0.53 228 72 138 66 165.09 0.67 229 73 76 3 514.28 4.82 230 73 77 4 505.87 1.53 231 74 77 3 530.87 0.20 232 74 78 4 506.41 1.25 233 75 78 3 519.70 5.39 234 75 82 7 166.30 0.77 235 75 85 10 165.69 0.48 236 75 86 11 165.69 0.48 237 75 89 14 165.69 0.48 238 75 138 63 167.96 1.60 239 76 79 3 509.47 0.28 240 76 131 55 188.56 8.30 241 76 134 58 172.58 0.33 242 78 81 3 500.29 1.61 243 78 82 4 328.50 42.40 244 78 85 7 302.73 6.01 245 80 137 57 260.80 1.52 246 82 85 3 507.33 0.84 247 82 86 4 493.06 0.41 248 82 137 55 299.47 6.08 249 82 141 59 290.06 7.29 250 83 86 3 509.17 1.74 251 83 87 4 497.30 2.52 252 83 145 62 295.81 4.50 253 84 88 4 516.71 2.77 254 85 88 3 543.75 1.80 255 85 89 4 510.07 0.55 256 86 89 3 519.29 1.45 257 86 90 4 508.78 0.10 258 86 138 52 300.47 5.75 259 86 141 55 300.41 5.76 260 86 142 56 300.41 5.76 261 86 145 59 300.38 5.75 262 87 90 3 511.58 0.21 263 87 91 4 507.58 0.49 264 87 145 58 300.40 5.75 265 88 91 3 510.44 0.93 266 88 92 4 505.17 0.70 267 89 92 3 513.61 0.77 268 89 93 4 505.18 0.71 269 89 138 49 300.61 5.78 270 90 93 3 521.46 1.75 271 90 94 4 509.58 2.91 272 90 142 52 300.46 5.77 273 90 145 55 300.43 5.76 274 90 146 56 300.42 5.75 275 91 94 3 518.29 0.17 276 91 95 4 497.90 0.39 277 91 149 58 299.24 5.58 278 92 95 3 521.04 0.59 279 92 96 4 472.76 0.66 280 92 97 5 449.18 11.13 281 93 97 4 438.62 13.05 282 93 98 5 424.88 19.91 283 93 99 6 321.97 0.28 284 93 146 53 300.51 5.76 285 94 98 4 424.87 19.91 286 94 146 52 300.51 5.76 287 94 149 55 299.99 5.86 288 94 151 57 296.85 4.75 289 95 98 3 521.10 0.59 290 95 149 54 300.03 5.88 291 98 151 53 298.12 5.00 292 99 103 4 511.68 1.61 293 99 104 5 510.03 0.78 294 99 146 47 301.33 5.87 295 99 151 52 298.12 5.00 296 100 103 3 518.27 2.23 297 100 104 4 512.13 1.49 298 100 146 46 301.34 5.87 299 100 151 51 298.12 5.00 300 100 152 52 297.00 4.84 301 100 153 53 276.81 2.34 302 101 104 3 515.97 3.38 303 101 105 4 512.16 1.48 304 101 139 38 301.56 5.90 305 101 142 41 301.56 5.90 306 101 143 42 301.47 5.91 307 101 146 45 301.44 5.92 308 102 105 3 512.55 1.28 309 102 106 4 512.16 1.48 310 103 106 3 514.56 2.67 311 103 107 4 513.73 0.69 312 104 107 3 516.13 1.89 313 104 108 4 513.73 0.69 314 104 138 34 301.79 5.90 315 104 139 35 301.68 5.93 316 104 142 38 301.63 5.90 317 104 146 42 301.58 5.92 318 105 108 3 516.13 1.89 319 105 109 4 513.67 0.66 320 105 139 34 301.79 5.90 321 106 109 3 520.96 4.30 322 106 110 4 509.06 1.62 323 107 110 3 505.85 3.21 324 107 111 4 509.04 1.61 325 108 111 3 509.95 1.16 326 108 112 4 509.04 1.61 327 108 135 27 301.89 5.92 328 108 139 31 301.83 5.92 329 109 112 3 517.58 2.65 330 109 113 4 505.81 3.22 331 110 113 3 509.05 1.62 332 110 114 4 502.82 1.76 333 111 114 3 511.15 0.48 334 111 115 4 508.25 0.96 335 111 135 24 302.28 6.00 336 112 115 3 510.75 0.28 337 112 116 4 508.27 0.96 338 112 123 11 304.22 6.21 339 112 128 16 302.82 5.97 340 112 131 19 302.82 5.97 341 112 132 20 302.78 5.96 342 112 135 23 302.70 6.00 343 113 116 3 515.37 2.58 344 113 117 4 507.71 1.25 345 114 117 3 507.71 1.25 346 114 118 4 507.70 1.24 347 115 118 3 514.04 0.98 348 115 119 4 491.37 8.12 349 115 123 8 304.24 6.21 350 115 131 16 303.42 6.01 351 116 119 3 506.43 0.60 352 116 120 4 469.05 1.82 353 116 123 7 305.44 6.81 354 116 128 12 304.25 6.21 355 117 120 3 521.02 3.27 356 119 122 3 503.56 6.15 357 119 123 4 441.43 10.51 358 123 127 4 502.11 6.59 359 123 128 5 483.81 1.73 360 123 131 8 470.93 8.22 361 124 127 3 513.74 0.82 362 124 128 4 503.05 6.15 363 125 128 3 511.99 1.69 364 125 129 4 506.15 4.62 365 126 129 3 512.01 1.69 366 126 130 4 508.59 3.39 367 127 130 3 513.85 1.08 368 127 131 4 506.12 4.60 369 128 131 3 512.62 1.70 370 128 132 4 505.74 0.33 371 129 132 3 512.32 1.54 372 129 133 4 505.75 0.33 373 130 133 3 507.02 0.88 374 130 134 4 505.75 0.34 375 131 134 3 506.55 0.74 376 131 135 4 509.23 1.41 377 132 135 3 510.98 0.54 378 132 136 4 508.24 1.91 379 133 136 3 512.40 0.18 380 133 137 4 499.73 5.55 381 134 137 3 503.00 3.92 382 134 138 4 500.61 5.12 383 135 138 3 509.12 0.85 384 135 139 4 509.36 0.73 385 136 139 3 516.09 4.10 386 136 140 4 501.99 1.74 387 137 140 3 509.36 0.73 388 137 141 4 502.49 1.49 389 138 141 3 509.11 0.61 390 138 142 4 507.11 0.82 391 139 142 3 507.11 0.82 392 139 143 4 507.10 0.82 393 140 143 3 509.33 0.62 394 140 144 4 509.37 0.65 395 141 144 3 509.38 0.65 396 141 145 4 509.42 0.67 397 142 145 3 509.42 0.67 398 142 146 4 509.40 0.67 399 143 146 3 509.54 0.71 400 143 147 4 509.40 0.67 401 144 147 3 509.41 0.68 402 144 148 4 509.40 0.68 403 145 148 3 508.01 1.40 404 145 149 4 507.58 1.60 405 146 149 3 522.65 0.14 406 146 150 4 499.94 5.42 407 146 151 5 323.57 2.82 408 147 150 3 504.51 3.14