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 6 4 492.32 0.67 2 2 7 5 490.50 1.57 3 2 10 8 468.81 7.21 4 2 130 128 43.16 0.36 5 2 133 131 37.27 1.93 6 2 134 132 34.28 0.71 7 2 137 135 34.28 0.71 8 3 6 3 517.87 0.08 9 3 7 4 505.55 1.33 10 4 7 3 515.67 1.02 11 4 8 4 507.22 2.17 12 5 8 3 523.18 2.73 13 5 9 4 507.29 2.21 14 6 9 3 510.57 0.58 15 6 10 4 507.18 2.27 16 6 130 124 66.10 1.39 17 6 133 127 66.10 1.39 18 7 10 3 514.07 1.80 19 7 11 4 507.18 2.27 20 7 76 69 66.19 1.40 21 7 79 72 66.19 1.40 22 7 80 73 66.31 1.34 23 7 134 127 66.12 1.39 24 7 137 130 66.14 1.39 25 8 11 3 510.46 3.61 26 8 12 4 510.23 3.73 27 9 12 3 515.58 6.40 28 9 13 4 510.25 3.71 29 9 126 117 79.34 0.46 30 9 127 118 76.67 0.82 31 10 13 3 514.23 1.88 32 10 14 4 510.40 3.79 33 10 76 66 76.66 0.81 34 10 130 120 76.68 0.82 35 10 131 121 76.65 0.82 36 10 134 124 76.64 0.83 37 11 14 3 518.46 0.24 38 11 15 4 518.46 0.24 39 11 76 65 77.14 0.65 40 11 77 66 77.15 0.65 41 11 79 68 77.14 0.65 42 12 15 3 520.25 0.65 43 12 16 4 523.55 1.85 44 12 122 110 92.55 0.39 45 13 16 3 532.03 0.30 46 13 17 4 523.56 1.85 47 13 115 102 92.16 0.58 48 13 123 110 92.14 0.58 49 13 127 114 88.80 1.95 50 14 17 3 524.88 2.51 51 14 18 4 516.07 1.90 52 14 69 55 134.72 23.13 53 14 72 58 86.00 0.59 54 14 73 59 85.42 0.88 55 14 76 62 85.42 0.88 56 14 131 117 90.61 1.06 57 15 18 3 524.89 2.50 58 15 19 4 516.07 1.91 59 16 19 3 516.83 1.53 60 16 20 4 515.14 2.38 61 16 24 8 464.20 1.79 62 16 119 103 106.08 1.99 63 16 122 106 106.08 1.99 64 17 20 3 523.31 2.29 65 17 21 4 497.69 2.19 66 17 24 7 428.88 2.81 67 17 69 52 148.22 24.38 68 17 115 98 100.69 0.60 69 18 21 3 506.10 2.15 70 20 23 3 522.73 3.13 71 20 24 4 510.97 4.54 72 20 118 98 135.73 0.48 73 21 24 3 536.41 2.17 74 21 25 4 510.88 4.58 75 21 66 45 160.94 18.30 76 21 69 48 160.66 18.36 77 22 25 3 518.37 6.85 78 22 26 4 510.88 4.58 79 22 62 40 165.66 16.26 80 22 66 44 164.62 16.50 81 23 26 3 529.77 2.75 82 23 27 4 510.86 4.58 83 23 118 95 162.51 3.51 84 24 27 3 513.90 3.06 85 24 28 4 510.44 4.78 86 24 69 45 166.32 15.79 87 24 114 90 160.00 6.29 88 24 115 91 162.22 5.17 89 24 118 94 163.90 4.20 90 24 119 95 163.90 4.20 91 25 28 3 529.42 1.05 92 25 29 4 505.81 2.43 93 25 65 40 166.33 15.79 94 25 69 44 166.21 15.73 95 26 29 3 517.84 4.73 96 26 30 4 505.82 2.42 97 26 57 31 181.12 12.39 98 26 58 32 181.02 12.34 99 26 61 35 180.11 12.21 100 26 62 36 180.10 12.21 101 27 30 3 514.89 3.56 102 27 31 4 505.85 2.41 103 27 114 87 164.44 4.05 104 27 118 91 164.46 3.90 105 28 31 3 517.00 6.00 106 28 32 4 506.35 0.87 107 28 69 41 177.58 10.72 108 28 107 79 164.66 4.39 109 28 110 82 164.75 4.29 110 28 111 83 164.48 4.30 111 28 114 86 164.55 4.02 112 29 32 3 515.72 2.52 113 29 33 4 506.36 0.86 114 29 43 14 276.66 5.09 115 29 61 32 180.69 12.04 116 29 64 35 180.56 11.96 117 29 65 36 178.50 11.06 118 29 107 78 164.85 4.29 119 30 33 3 515.47 2.64 120 30 34 4 506.31 0.85 121 30 53 23 205.57 24.04 122 30 57 27 181.69 12.20 123 30 61 31 181.05 12.19 124 31 34 3 525.05 2.15 125 31 35 4 505.48 0.45 126 31 110 79 164.94 4.20 127 31 113 82 165.05 4.02 128 31 114 83 164.93 3.96 129 32 35 3 511.13 3.58 130 32 36 4 502.04 2.18 131 32 39 7 444.10 10.78 132 32 106 74 164.88 4.31 133 32 107 75 164.85 4.29 134 32 110 78 165.19 4.11 135 33 36 3 514.88 4.24 136 33 37 4 492.86 1.66 137 33 39 6 436.09 11.55 138 33 40 7 352.81 3.92 139 33 43 10 352.81 3.92 140 33 46 13 279.11 2.82 141 33 52 19 205.75 23.97 142 33 61 28 181.98 12.35 143 34 52 18 205.75 23.97 144 34 53 19 205.76 23.97 145 36 39 3 523.58 0.54 146 36 40 4 517.98 1.57 147 36 106 70 165.16 4.23 148 37 40 3 528.18 1.76 149 37 41 4 512.92 0.96 150 37 52 15 208.12 24.88 151 38 41 3 522.94 4.39 152 38 42 4 521.36 5.17 153 38 103 65 165.47 4.24 154 38 106 68 165.50 4.22 155 39 42 3 522.77 4.49 156 39 43 4 525.71 3.01 157 39 103 64 165.01 4.33 158 39 106 67 165.35 4.16 159 40 43 3 529.79 0.98 160 40 46 6 365.08 3.16 161 40 47 7 298.69 8.75 162 40 49 9 286.19 2.52 163 40 50 10 265.95 0.04 164 40 52 12 209.10 25.38 165 41 47 6 306.31 12.55 166 41 50 9 279.44 2.53 167 42 96 54 165.60 4.46 168 42 97 55 165.54 4.42 169 42 98 56 165.52 4.44 170 42 103 61 165.50 4.22 171 43 46 3 523.97 4.78 172 43 47 4 502.32 0.85 173 43 64 21 182.08 12.31 174 44 47 3 514.59 0.09 175 44 48 4 515.42 0.35 176 45 48 3 541.63 5.23 177 45 60 15 188.03 15.19 178 46 49 3 534.39 1.60 179 46 60 14 194.58 18.46 180 46 61 15 182.21 12.28 181 46 64 18 182.19 12.29 182 47 50 3 527.81 2.72 183 49 52 3 535.37 2.81 184 49 53 4 392.01 14.64 185 49 54 5 339.13 11.79 186 49 56 7 271.51 4.34 187 49 57 8 264.91 2.60 188 51 54 3 537.13 0.35 189 53 57 4 297.12 4.05 190 57 61 4 500.62 1.57 191 58 61 3 507.30 1.78 192 59 62 3 511.00 3.58 193 59 63 4 504.38 0.29 194 60 63 3 516.56 0.81 195 60 64 4 504.38 0.29 196 61 64 3 519.65 0.75 197 61 65 4 503.56 0.13 198 62 65 3 513.91 1.54 199 62 66 4 504.07 0.10 200 63 66 3 523.79 1.44 201 63 67 4 516.44 0.62 202 64 67 3 520.93 2.87 203 64 68 4 516.44 0.62 204 65 68 3 520.94 2.87 205 65 69 4 516.45 0.62 206 66 69 3 517.47 0.78 207 66 70 4 511.50 2.16 208 67 70 3 524.26 2.62 209 67 71 4 515.51 0.14 210 68 71 3 522.21 1.56 211 68 72 4 516.43 0.31 212 68 107 39 175.74 1.13 213 69 72 3 520.58 1.45 214 69 73 4 506.14 1.01 215 70 73 3 507.42 0.37 216 70 74 4 507.40 0.38 217 71 74 3 520.47 5.98 218 71 75 4 507.41 0.36 219 71 83 12 226.00 23.31 220 71 89 18 176.85 1.15 221 72 75 3 509.73 0.79 222 72 76 4 505.48 0.59 223 72 111 39 183.34 4.93 224 72 135 63 179.61 6.48 225 72 138 66 172.12 3.69 226 73 76 3 512.45 0.50 227 73 77 4 504.23 0.07 228 74 77 3 512.12 4.02 229 74 78 4 509.37 0.08 230 74 83 9 226.10 23.28 231 75 78 3 520.49 0.17 232 75 79 4 508.08 0.72 233 75 82 7 281.30 0.94 234 75 83 8 226.10 23.28 235 75 86 11 226.05 23.26 236 75 138 63 172.99 3.68 237 76 79 3 505.13 0.39 238 76 131 55 194.69 13.20 239 76 134 58 190.33 11.55 240 78 81 3 496.63 4.29 241 78 83 5 354.04 18.84 242 78 84 6 432.40 17.94 243 81 84 3 523.69 1.53 244 82 85 3 529.88 0.55 245 82 86 4 489.32 8.70 246 82 137 55 211.62 22.41 247 82 141 59 206.71 21.03 248 83 86 3 504.99 0.88 249 83 89 6 494.82 5.23 250 85 88 3 567.77 0.33 251 85 145 60 210.38 23.12 252 86 89 3 531.06 1.51 253 86 90 4 513.35 1.31 254 86 138 52 211.67 22.69 255 86 141 55 210.56 23.05 256 86 142 56 210.44 23.11 257 86 145 59 210.19 23.23 258 87 90 3 513.35 1.31 259 87 91 4 513.35 1.31 260 87 145 58 208.02 24.30 261 87 148 61 207.59 24.50 262 87 149 62 203.96 25.77 263 88 91 3 518.25 1.14 264 88 92 4 518.25 1.15 265 89 92 3 524.96 1.02 266 89 93 4 513.36 1.32 267 89 142 53 210.65 23.21 268 90 93 3 523.25 0.51 269 90 94 4 513.32 1.34 270 90 142 52 210.63 23.21 271 90 145 55 208.11 24.44 272 90 146 56 208.00 24.50 273 90 149 59 203.94 25.89 274 91 94 3 518.28 1.14 275 91 95 4 513.32 1.34 276 91 149 58 201.68 27.53 277 92 95 3 529.65 3.71 278 92 96 4 496.12 6.59 279 92 97 5 462.63 10.04 280 93 97 4 415.97 14.79 281 93 146 53 208.02 24.53 282 94 99 5 237.66 9.71 283 94 146 52 208.01 24.52 284 95 151 56 190.88 32.31 285 99 146 47 208.13 24.78 286 100 146 46 208.30 24.98 287 101 104 3 524.76 1.14 288 101 105 4 519.17 3.08 289 101 139 38 211.70 23.64 290 101 142 41 211.49 23.75 291 101 143 42 208.73 25.06 292 101 146 45 208.02 25.30 293 102 105 3 528.13 1.40 294 102 106 4 519.19 3.07 295 103 106 3 519.19 3.07 296 103 107 4 513.31 0.01 297 104 107 3 513.31 0.01 298 104 108 4 506.09 3.50 299 104 138 34 212.88 23.34 300 104 139 35 211.88 23.83 301 104 142 38 209.99 24.77 302 105 108 3 506.19 3.55 303 105 109 4 507.30 4.12 304 105 139 34 211.90 23.84 305 106 109 3 512.44 1.54 306 106 110 4 507.23 4.15 307 107 110 3 505.40 3.29 308 107 111 4 503.88 4.03 309 108 111 3 514.94 0.58 310 108 112 4 512.46 0.29 311 108 135 27 213.18 23.45 312 108 139 31 212.15 23.96 313 109 112 3 512.50 0.31 314 109 113 4 514.65 0.76 315 110 113 3 514.66 0.77 316 110 114 4 514.66 0.77 317 111 114 3 520.13 1.97 318 111 115 4 514.66 0.77 319 111 131 20 214.91 23.30 320 111 135 24 213.63 23.67 321 112 115 3 522.72 3.27 322 112 116 4 512.46 0.33 323 112 123 11 235.18 13.41 324 112 128 16 214.92 23.30 325 112 131 19 214.91 23.30 326 112 132 20 214.88 23.31 327 113 116 3 517.13 0.38 328 113 117 4 505.48 3.77 329 114 117 3 516.75 0.74 330 114 118 4 505.45 3.76 331 115 118 3 516.95 0.83 332 115 119 4 501.87 5.55 333 115 123 8 255.29 18.59 334 115 131 16 214.99 23.34 335 116 119 3 526.63 4.83 336 116 120 4 497.73 7.50 337 116 123 7 279.45 2.08 338 116 128 12 215.16 23.41 339 117 120 3 541.69 2.69 340 119 122 3 532.54 1.92 341 119 123 4 372.93 13.45 342 122 127 5 485.51 4.95 343 123 127 4 485.52 4.96 344 123 128 5 487.07 5.75 345 123 131 8 474.29 9.87 346 124 127 3 520.11 1.54 347 124 128 4 502.32 5.15 348 125 128 3 517.17 0.07 349 125 129 4 503.14 5.55 350 126 129 3 515.62 0.69 351 126 130 4 511.56 1.34 352 127 130 3 515.62 0.69 353 127 131 4 509.43 0.27 354 128 131 3 513.88 0.20 355 128 132 4 503.74 2.57 356 129 132 3 515.87 0.80 357 129 133 4 502.49 2.00 358 130 133 3 513.20 3.35 359 130 134 4 502.45 2.01 360 131 134 3 515.47 2.21 361 131 135 4 502.44 2.02 362 132 135 3 520.57 2.50 363 132 136 4 501.57 2.40 364 133 136 3 512.90 0.32 365 133 137 4 508.87 0.35 366 134 137 3 512.90 0.32 367 134 138 4 502.75 3.42 368 135 138 3 513.95 0.12 369 135 139 4 512.26 0.64 370 136 139 3 512.35 0.67 371 136 140 4 506.97 3.38 372 137 140 3 515.50 0.89 373 137 141 4 513.73 0.01 374 138 141 3 515.52 0.86 375 138 142 4 513.75 0.02 376 139 142 3 515.53 0.86 377 139 143 4 513.76 0.01 378 140 143 3 513.76 0.01 379 140 144 4 513.76 0.01 380 141 144 3 519.92 3.08 381 141 145 4 519.94 3.07 382 142 145 3 522.39 1.84 383 142 146 4 513.95 0.07 384 143 146 3 520.97 2.56 385 143 147 4 513.95 0.07 386 143 152 9 268.45 2.85 387 144 147 3 513.93 0.07 388 144 148 4 513.92 0.06 389 145 148 3 513.14 0.45 390 145 149 4 510.42 1.80 391 146 149 3 503.75 1.53 392 146 150 4 493.87 2.16 393 146 151 5 429.73 16.80 394 146 152 6 273.52 4.52 395 147 150 3 491.30 3.44 396 147 152 5 398.79 5.35 397 147 153 6 252.02 5.38