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 5 486.68 5.83 2 2 10 8 472.00 2.29 3 2 130 128 47.95 0.30 4 2 133 131 41.30 1.04 5 2 134 132 36.27 1.00 6 2 137 135 36.26 1.00 7 3 6 3 515.25 1.47 8 3 7 4 514.34 1.93 9 4 7 3 520.52 1.35 10 4 8 4 524.69 3.25 11 4 79 75 58.76 1.84 12 5 8 3 525.03 3.07 13 5 9 4 515.03 1.58 14 6 9 3 532.14 0.64 15 6 10 4 515.03 1.58 16 6 130 124 71.17 0.39 17 6 133 127 71.17 0.39 18 7 10 3 506.11 2.16 19 7 11 4 508.47 3.35 20 7 76 69 71.25 0.42 21 7 79 72 71.24 0.42 22 7 80 73 71.24 0.42 23 7 134 127 71.23 0.42 24 7 137 130 71.24 0.42 25 8 11 3 530.40 1.27 26 8 12 4 513.09 7.38 27 9 12 3 525.59 1.14 28 9 13 4 525.58 1.14 29 9 126 117 82.30 0.17 30 9 127 118 82.17 0.20 31 9 130 121 82.15 0.20 32 10 13 3 529.75 0.95 33 10 14 4 514.94 1.86 34 10 76 66 82.17 0.20 35 10 130 120 82.19 0.20 36 10 131 121 82.12 0.21 37 10 134 124 82.10 0.20 38 11 14 3 514.94 1.86 39 11 15 4 514.93 1.86 40 11 76 65 82.22 0.21 41 11 77 66 82.22 0.21 42 11 79 68 82.22 0.21 43 12 15 3 526.72 1.21 44 12 16 4 520.28 3.61 45 12 122 110 90.84 1.09 46 13 16 3 522.89 3.39 47 13 17 4 514.91 1.85 48 13 115 102 90.84 1.09 49 13 122 109 90.84 1.08 50 13 123 110 90.84 1.08 51 13 127 114 90.73 1.03 52 13 131 118 90.58 1.02 53 14 17 3 517.72 0.46 54 14 18 4 517.71 0.46 55 14 69 55 128.62 19.99 56 14 72 58 90.64 1.00 57 14 73 59 90.58 1.02 58 14 76 62 90.42 0.95 59 14 77 63 90.43 0.95 60 14 131 117 90.81 1.09 61 15 18 3 519.01 1.10 62 15 19 4 519.00 1.10 63 16 19 3 519.01 1.10 64 16 119 103 96.96 0.56 65 16 122 106 91.08 1.06 66 17 20 3 534.48 1.62 67 17 21 4 489.91 3.64 68 17 24 7 401.70 19.68 69 17 69 52 132.39 21.87 70 17 115 98 90.88 1.07 71 18 21 3 511.07 0.66 72 18 77 59 127.98 19.66 73 20 23 3 530.32 0.17 74 20 24 4 511.45 1.60 75 20 118 98 149.35 4.52 76 21 24 3 518.91 0.42 77 21 25 4 511.44 1.61 78 21 66 45 176.47 1.06 79 21 69 48 176.16 0.93 80 22 25 3 518.09 0.01 81 22 26 4 511.46 1.60 82 22 62 40 176.99 1.29 83 22 66 44 176.49 1.06 84 23 26 3 512.72 2.23 85 23 27 4 511.47 1.60 86 23 118 95 165.33 0.60 87 24 27 3 533.04 0.73 88 24 28 4 512.41 0.90 89 24 69 45 176.53 1.09 90 24 114 90 165.84 0.26 91 24 115 91 165.84 0.25 92 24 118 94 165.72 0.80 93 24 119 95 167.22 1.54 94 25 28 3 514.73 1.28 95 25 29 4 512.41 0.90 96 25 65 40 176.74 0.99 97 25 69 44 176.53 1.09 98 26 29 3 524.08 3.40 99 26 30 4 512.34 1.19 100 26 56 30 212.08 0.60 101 26 62 36 177.47 1.28 102 27 30 3 519.02 0.02 103 27 31 4 512.33 1.20 104 27 114 87 168.81 1.72 105 27 118 91 168.16 1.99 106 28 31 3 513.46 0.64 107 28 32 4 512.34 1.20 108 28 69 41 177.46 1.34 109 28 107 79 169.48 1.73 110 28 110 82 168.87 1.72 111 28 111 83 168.85 1.71 112 28 114 86 168.82 1.72 113 29 32 3 526.62 3.91 114 29 33 4 512.30 1.21 115 29 61 32 195.88 4.79 116 29 64 35 178.84 1.58 117 29 65 36 178.75 1.61 118 29 107 78 169.50 1.74 119 30 33 3 518.45 0.18 120 30 34 4 506.54 0.78 121 30 52 22 218.09 2.33 122 30 55 25 213.54 0.28 123 30 56 26 218.28 2.62 124 31 34 3 516.19 0.96 125 31 35 4 507.73 1.37 126 31 110 79 168.98 1.65 127 31 113 82 168.89 1.69 128 31 114 83 168.85 1.71 129 32 35 3 514.13 2.16 130 32 36 4 499.40 5.54 131 32 39 7 424.88 8.28 132 32 106 74 169.55 1.73 133 32 107 75 169.51 1.73 134 32 110 78 168.98 1.65 135 33 36 3 521.53 1.54 136 33 37 4 492.95 3.60 137 33 39 6 436.93 12.91 138 33 40 7 366.03 20.55 139 33 43 10 343.11 9.48 140 33 46 13 255.46 0.70 141 33 55 22 222.49 4.46 142 33 61 28 218.49 2.51 143 34 37 3 534.46 0.46 144 34 52 18 227.44 2.05 145 36 39 3 532.48 1.52 146 36 106 70 169.69 1.69 147 37 40 3 523.09 6.21 148 37 41 4 513.63 2.62 149 38 41 3 532.95 0.14 150 38 103 65 170.04 1.63 151 38 106 68 169.87 1.67 152 39 42 3 532.13 0.28 153 39 43 4 526.25 3.22 154 39 103 64 169.74 1.70 155 39 106 67 169.77 1.71 156 40 43 3 524.84 2.29 157 40 46 6 381.37 8.44 158 40 47 7 371.31 13.47 159 40 49 9 261.69 3.85 160 40 55 15 242.72 0.52 161 41 47 6 343.98 27.14 162 42 97 55 170.60 1.82 163 42 98 56 170.59 1.81 164 42 99 57 170.56 1.81 165 42 100 58 170.58 1.81 166 42 103 61 170.47 1.83 167 43 46 3 518.65 2.79 168 43 47 4 474.05 5.02 169 44 47 3 532.89 1.72 170 45 48 3 595.56 0.28 171 45 60 15 232.23 0.56 172 45 64 19 227.99 0.34 173 46 49 3 533.84 0.79 174 46 60 14 229.22 0.95 175 46 61 15 228.00 0.34 176 46 64 18 227.91 0.30 177 49 54 5 450.99 15.80 178 49 55 6 329.54 1.90 179 49 58 9 274.28 7.08 180 49 61 12 254.96 2.54 181 50 54 4 498.84 2.11 182 51 54 3 500.74 1.17 183 51 55 4 494.80 4.13 184 52 55 3 503.52 0.23 185 52 56 4 501.96 0.56 186 53 56 3 518.76 5.45 187 53 57 4 501.96 0.55 188 54 57 3 520.24 4.71 189 54 58 4 498.15 1.35 190 55 58 3 513.83 2.98 191 55 61 6 418.05 0.75 192 58 61 3 532.14 3.29 193 58 62 4 513.67 5.22 194 59 62 3 506.00 1.39 195 59 63 4 506.00 1.38 196 60 63 3 523.96 0.09 197 60 64 4 513.68 5.22 198 61 64 3 524.31 0.26 199 61 65 4 506.00 1.38 200 62 65 3 524.31 0.26 201 62 66 4 510.31 1.46 202 63 66 3 525.60 2.98 203 63 67 4 510.30 1.46 204 64 67 3 525.62 6.20 205 64 68 4 509.16 2.03 206 65 68 3 522.51 0.11 207 65 69 4 509.66 1.80 208 66 69 3 523.62 1.96 209 66 70 4 509.17 2.05 210 67 70 3 533.75 2.13 211 67 71 4 517.00 1.85 212 68 71 3 532.20 1.35 213 68 72 4 511.01 1.21 214 68 107 39 169.55 1.77 215 69 72 3 519.51 0.59 216 69 73 4 511.01 1.21 217 70 73 3 526.12 0.04 218 70 74 4 511.01 1.21 219 71 74 3 529.05 2.60 220 71 75 4 511.36 1.05 221 72 75 3 519.33 2.25 222 72 76 4 508.34 0.45 223 72 111 39 169.29 1.88 224 72 135 63 165.69 2.68 225 73 76 3 515.59 3.16 226 73 77 4 508.49 0.39 227 74 78 4 510.03 1.67 228 75 78 3 529.75 2.62 229 75 82 7 240.28 3.49 230 75 85 10 200.69 9.80 231 75 89 14 200.69 9.80 232 75 138 63 163.60 2.41 233 76 79 3 530.89 2.35 234 76 131 55 166.12 2.75 235 76 134 58 165.99 2.73 236 78 81 3 511.30 1.03 237 78 82 4 434.97 30.46 238 78 85 7 314.17 7.92 239 80 137 57 166.01 2.79 240 82 85 3 521.64 0.20 241 82 86 4 508.28 0.51 242 82 137 55 166.00 2.79 243 82 141 59 163.08 2.39 244 83 86 3 520.77 0.24 245 83 87 4 513.58 2.35 246 84 88 4 522.58 0.48 247 85 88 3 545.76 2.29 248 85 89 4 520.65 0.48 249 86 89 3 527.45 1.96 250 86 90 4 520.46 0.39 251 86 138 52 165.33 2.71 252 86 141 55 162.85 2.31 253 86 142 56 161.46 1.78 254 86 145 59 156.74 0.26 255 87 90 3 524.70 0.58 256 87 91 4 518.81 1.21 257 88 91 3 517.72 0.99 258 88 92 4 516.07 0.17 259 89 92 3 515.23 1.48 260 89 93 4 510.12 1.81 261 89 138 49 165.22 2.80 262 89 142 53 161.00 1.59 263 90 93 3 513.87 2.65 264 90 94 4 500.02 0.98 265 90 142 52 160.50 1.75 266 90 145 55 155.26 0.29 267 90 146 56 152.53 0.45 268 91 94 3 522.93 1.37 269 91 95 4 499.87 0.91 270 91 149 58 149.50 0.21 271 92 95 3 525.59 5.94 272 92 96 4 462.63 13.38 273 92 97 5 422.42 16.37 274 93 97 4 388.30 5.95 275 93 98 5 372.94 1.74 276 93 99 6 294.56 0.20 277 93 146 53 153.57 0.07 278 94 98 4 372.96 1.74 279 94 146 52 151.44 0.98 280 94 149 55 144.73 1.98 281 94 151 57 91.61 10.24 282 95 98 3 521.87 3.01 283 95 149 54 149.25 0.09 284 95 151 56 117.98 2.79 285 98 151 53 99.35 6.38 286 99 103 4 515.25 0.50 287 99 104 5 514.76 0.26 288 99 146 47 151.39 0.09 289 100 103 3 522.67 0.98 290 100 104 4 515.26 0.50 291 100 153 53 17.27 0.14 292 101 104 3 520.99 2.36 293 101 105 4 519.05 1.40 294 101 139 38 161.03 1.54 295 101 142 41 158.90 0.96 296 101 143 42 156.38 0.28 297 101 146 45 151.35 0.07 298 101 153 52 17.09 0.09 299 102 105 3 523.88 0.91 300 102 106 4 519.05 1.40 301 103 106 3 520.98 2.36 302 103 107 4 519.03 1.39 303 104 107 3 518.49 1.67 304 104 108 4 518.48 1.67 305 104 139 35 160.97 1.55 306 104 142 38 158.49 1.13 307 105 108 3 518.49 1.67 308 105 109 4 523.74 0.96 309 105 139 34 160.97 1.55 310 106 109 3 520.44 2.50 311 106 110 4 516.59 2.62 312 107 110 3 506.35 0.96 313 107 111 4 506.35 0.95 314 108 111 3 524.37 3.31 315 108 112 4 508.26 1.91 316 108 135 27 165.63 2.58 317 108 139 31 160.95 1.54 318 109 112 3 508.28 1.90 319 109 113 4 508.24 1.92 320 110 113 3 509.71 2.62 321 110 114 4 503.47 0.07 322 111 114 3 519.03 2.70 323 111 115 4 506.70 1.69 324 111 135 24 165.65 2.60 325 112 115 3 510.19 1.31 326 112 116 4 508.82 0.62 327 112 123 11 288.03 7.82 328 112 128 16 165.94 2.56 329 112 131 19 165.83 2.59 330 112 132 20 165.81 2.58 331 112 135 23 165.71 2.58 332 113 116 3 517.00 0.31 333 113 117 4 507.93 0.18 334 114 117 3 507.94 0.18 335 114 118 4 503.75 2.27 336 115 118 3 521.35 2.50 337 115 119 4 496.84 1.98 338 115 123 8 297.09 3.29 339 115 131 16 194.69 5.33 340 116 119 3 520.22 2.73 341 116 120 4 490.23 0.15 342 116 123 7 306.30 16.78 343 117 120 3 541.86 2.17 344 119 122 3 522.35 3.20 345 119 123 4 482.18 0.18 346 120 123 3 517.37 5.40 347 120 124 4 499.49 1.46 348 122 127 5 485.33 3.30 349 123 127 4 485.31 3.29 350 123 128 5 461.75 8.49 351 123 131 8 456.68 10.72 352 124 127 3 513.59 0.40 353 124 128 4 504.21 0.34 354 125 128 3 511.33 1.54 355 125 129 4 509.84 2.27 356 126 129 3 509.85 2.28 357 126 130 4 509.85 2.27 358 127 130 3 517.15 1.38 359 127 131 4 505.12 0.09 360 128 131 3 518.92 4.64 361 128 132 4 498.22 0.38 362 129 132 3 517.01 0.87 363 129 133 4 503.94 4.94 364 130 133 3 515.17 0.68 365 130 134 4 503.94 4.94 366 131 134 3 507.12 0.12 367 131 135 4 499.47 2.18 368 132 135 3 504.66 4.77 369 132 136 4 498.94 2.44 370 133 136 3 504.26 0.22 371 133 137 4 504.35 0.21 372 134 137 3 507.94 1.56 373 134 138 4 504.38 0.21 374 135 138 3 514.87 0.71 375 135 139 4 505.69 0.86 376 136 139 3 511.85 2.22 377 136 140 4 504.73 0.41 378 137 140 3 516.56 1.35 379 137 141 4 504.73 0.41 380 138 141 3 521.88 2.67 381 138 142 4 504.73 0.41 382 139 142 3 508.68 2.35 383 139 143 4 504.64 0.45 384 140 143 3 513.95 2.22 385 140 144 4 505.82 1.04 386 141 144 3 510.78 1.44 387 141 145 4 510.68 1.38 388 142 145 3 511.47 0.99 389 142 146 4 503.68 2.12 390 143 146 3 513.46 2.77 391 143 147 4 503.49 2.21 392 143 152 9 236.06 13.55 393 144 147 3 514.27 2.37 394 144 148 4 503.20 1.75 395 145 148 3 513.31 2.69 396 145 149 4 503.20 1.75 397 146 149 3 517.87 2.18 398 146 150 4 503.20 1.75 399 146 151 5 335.41 8.31 400 146 152 6 250.21 6.54 401 146 153 7 250.16 6.52 402 147 150 3 510.45 1.12 403 147 152 5 276.27 19.57