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 5 495.67 0.89 2 2 10 8 464.81 3.37 3 2 130 128 41.48 0.26 4 2 133 131 38.18 0.86 5 2 134 132 35.41 0.52 6 2 137 135 35.41 0.52 7 3 6 3 508.82 4.99 8 3 7 4 498.30 0.28 9 4 7 3 523.30 2.25 10 4 8 4 503.31 2.79 11 4 79 75 65.40 0.21 12 5 8 3 525.81 1.01 13 5 9 4 504.84 2.02 14 6 9 3 522.69 0.56 15 6 10 4 504.84 2.02 16 6 130 124 67.99 0.23 17 6 133 127 68.07 0.18 18 7 10 3 506.50 1.27 19 7 11 4 504.84 2.02 20 7 76 69 68.12 0.18 21 7 79 72 68.12 0.18 22 7 80 73 68.12 0.18 23 7 134 127 68.09 0.18 24 7 137 130 68.09 0.18 25 8 11 3 519.54 1.16 26 8 12 4 505.74 3.21 27 9 12 3 518.02 1.92 28 9 13 4 511.00 2.12 29 9 126 117 83.82 1.80 30 9 127 118 83.78 1.80 31 9 130 121 83.72 1.82 32 10 13 3 528.88 4.39 33 10 14 4 507.31 3.96 34 10 76 66 83.75 1.81 35 10 130 120 83.77 1.81 36 10 131 121 83.70 1.81 37 10 134 124 83.67 1.82 38 11 14 3 507.34 3.96 39 11 15 4 514.32 0.46 40 11 76 65 83.78 1.80 41 11 77 66 83.79 1.80 42 11 79 68 83.79 1.80 43 12 15 3 524.67 1.81 44 12 16 4 514.35 0.45 45 12 122 110 94.12 0.04 46 13 16 3 522.83 0.89 47 13 17 4 513.90 0.23 48 13 115 102 94.06 0.05 49 13 119 106 96.50 1.12 50 13 122 109 94.12 0.04 51 13 123 110 94.09 0.06 52 13 131 118 93.30 0.01 53 14 17 3 513.99 0.29 54 14 18 4 513.86 0.24 55 14 69 55 94.04 0.04 56 14 72 58 93.50 0.12 57 14 73 59 93.49 0.12 58 14 76 62 93.50 0.12 59 14 77 63 93.50 0.12 60 14 111 97 94.08 0.06 61 14 131 117 93.94 0.10 62 15 18 3 518.45 2.54 63 15 19 4 511.22 1.54 64 16 19 3 515.96 3.92 65 16 24 8 452.62 9.90 66 16 119 103 107.55 0.70 67 16 122 106 107.55 0.71 68 17 20 3 522.92 0.43 69 17 21 4 497.73 0.97 70 17 24 7 430.06 7.12 71 17 69 52 196.04 1.11 72 17 115 98 104.39 0.21 73 17 119 102 108.31 0.40 74 18 21 3 501.78 1.33 75 18 77 59 96.87 1.07 76 20 23 3 518.76 2.04 77 20 24 4 510.38 2.16 78 20 118 98 136.00 0.06 79 21 24 3 522.08 0.38 80 21 25 4 503.67 5.55 81 21 66 45 196.62 1.29 82 21 69 48 196.59 1.27 83 21 70 49 196.59 1.28 84 22 25 3 510.45 2.19 85 22 26 4 510.42 2.18 86 22 62 40 197.50 1.40 87 22 66 44 196.72 1.33 88 23 26 3 525.59 1.16 89 23 27 4 510.45 2.19 90 23 118 95 162.55 0.88 91 24 27 3 514.35 0.23 92 24 28 4 514.36 0.23 93 24 69 45 196.72 1.32 94 24 114 90 159.78 2.47 95 24 115 91 160.48 2.08 96 24 118 94 162.55 0.88 97 24 119 95 162.56 0.88 98 25 28 3 518.39 1.78 99 25 29 4 514.36 0.23 100 25 65 40 197.25 1.53 101 25 69 44 196.72 1.33 102 26 29 3 516.62 1.28 103 26 30 4 509.62 2.14 104 26 55 29 221.17 2.81 105 26 56 30 216.34 0.39 106 26 58 32 216.29 0.39 107 26 62 36 199.16 1.91 108 27 30 3 509.66 2.14 109 27 31 4 509.29 2.31 110 27 114 87 165.25 0.26 111 27 118 91 164.75 0.30 112 28 31 3 511.77 1.08 113 28 32 4 509.61 2.17 114 28 69 41 199.15 1.91 115 28 107 79 165.94 0.28 116 28 110 82 165.69 0.35 117 28 111 83 165.67 0.34 118 28 114 86 165.44 0.26 119 29 32 3 518.93 2.50 120 29 33 4 509.33 2.30 121 29 61 32 215.52 0.10 122 29 64 35 209.36 3.11 123 29 65 36 209.31 3.12 124 29 68 39 199.20 1.93 125 29 107 78 165.96 0.27 126 30 33 3 509.66 2.15 127 30 34 4 503.62 0.56 128 30 52 22 238.06 3.46 129 30 55 25 237.62 3.27 130 30 56 26 237.69 3.30 131 30 61 31 217.61 1.12 132 31 34 3 515.01 2.83 133 31 35 4 498.54 3.08 134 31 110 79 165.84 0.25 135 31 113 82 165.80 0.26 136 31 114 83 165.78 0.27 137 32 35 3 518.25 3.81 138 32 36 4 489.16 1.36 139 32 39 7 397.25 4.46 140 32 106 74 166.00 0.28 141 32 107 75 165.96 0.27 142 32 110 78 165.88 0.26 143 33 36 3 525.20 2.29 144 33 37 4 469.29 8.48 145 33 39 6 397.25 4.46 146 33 40 7 343.60 14.22 147 33 43 10 315.93 4.15 148 33 46 13 250.03 1.52 149 33 55 22 238.22 3.47 150 33 61 28 237.97 3.35 151 34 37 3 525.21 2.29 152 34 52 18 238.22 3.47 153 34 55 21 238.22 3.48 154 36 39 3 536.77 0.32 155 36 106 70 166.09 0.25 156 37 40 3 527.06 3.21 157 37 41 4 517.81 1.42 158 38 41 3 517.81 1.42 159 38 103 65 166.38 0.20 160 38 106 68 166.33 0.18 161 39 42 3 517.81 1.42 162 39 43 4 513.61 3.52 163 39 103 64 166.24 0.22 164 39 106 67 166.21 0.24 165 40 43 3 517.88 1.39 166 40 46 6 345.39 19.45 167 40 49 9 275.13 7.16 168 40 55 15 241.61 2.56 169 41 47 6 292.42 0.12 170 42 97 55 166.95 0.11 171 42 98 56 166.94 0.11 172 42 99 57 166.71 0.10 173 42 100 58 166.84 0.15 174 42 103 61 166.44 0.24 175 43 46 3 533.87 3.05 176 43 47 4 480.13 6.00 177 43 64 21 240.68 2.60 178 44 47 3 523.43 2.17 179 45 48 3 596.46 1.69 180 45 60 15 240.81 2.62 181 45 63 18 240.81 2.62 182 45 64 19 240.78 2.60 183 46 49 3 525.88 3.39 184 46 60 14 240.81 2.62 185 46 61 15 240.75 2.58 186 46 64 18 240.78 2.60 187 49 54 5 442.10 13.66 188 49 55 6 349.83 3.39 189 49 58 9 269.53 4.66 190 49 61 12 253.62 7.05 191 50 54 4 507.06 1.22 192 51 54 3 512.29 1.39 193 51 55 4 507.05 1.22 194 52 55 3 512.28 1.40 195 52 56 4 507.03 1.22 196 53 56 3 516.04 0.39 197 53 57 4 506.36 1.56 198 54 57 3 514.82 1.00 199 54 58 4 506.26 1.52 200 55 58 3 525.95 0.26 201 55 61 6 403.79 5.93 202 58 61 3 507.23 1.19 203 58 62 4 498.62 2.06 204 59 62 3 504.04 0.66 205 59 63 4 498.61 2.05 206 60 63 3 498.61 2.05 207 60 64 4 505.66 1.47 208 61 64 3 519.33 5.29 209 61 65 4 505.73 1.50 210 62 65 3 519.33 5.29 211 62 66 4 509.43 0.30 212 63 66 3 524.78 3.21 213 63 67 4 519.97 4.96 214 64 67 3 513.60 2.39 215 64 68 4 512.11 1.65 216 65 68 3 516.08 2.46 217 65 69 4 512.10 1.66 218 66 69 3 517.19 1.92 219 66 70 4 509.38 0.29 220 67 70 3 523.67 4.13 221 67 71 4 509.40 0.30 222 68 71 3 515.04 1.15 223 68 72 4 506.63 1.77 224 68 107 39 166.00 0.31 225 69 72 3 516.34 0.51 226 69 73 4 513.78 1.79 227 70 73 3 516.34 0.52 228 70 74 4 513.79 1.79 229 71 74 3 516.41 0.48 230 71 75 4 513.78 1.79 231 72 75 3 517.29 3.54 232 72 76 4 507.79 1.21 233 72 111 39 165.84 0.41 234 72 135 63 163.69 0.47 235 72 138 66 162.65 0.73 236 73 76 3 511.86 3.24 237 73 77 4 504.14 0.61 238 74 78 4 507.12 4.19 239 74 85 11 218.92 8.71 240 75 78 3 528.53 1.75 241 75 79 4 525.18 3.43 242 75 82 7 241.37 2.13 243 75 85 10 218.93 8.71 244 75 89 14 202.15 17.09 245 75 138 63 163.53 0.52 246 76 79 3 528.51 1.77 247 76 131 55 164.12 0.57 248 76 134 58 163.81 0.48 249 78 81 3 511.23 2.04 250 78 82 4 413.39 32.48 251 78 85 7 291.51 1.25 252 80 137 57 164.06 0.56 253 82 85 3 521.53 2.65 254 82 86 4 510.01 2.19 255 82 137 55 164.06 0.56 256 82 141 59 162.62 0.72 257 83 86 3 521.53 2.66 258 83 87 4 499.37 5.65 259 84 88 4 523.80 4.15 260 85 88 3 554.02 0.10 261 86 89 3 518.40 0.58 262 86 90 4 515.38 0.01 263 86 138 52 163.60 0.55 264 86 141 55 162.53 0.70 265 86 142 56 162.24 0.71 266 87 90 3 517.48 1.03 267 87 91 4 517.47 1.03 268 87 145 58 154.85 0.21 269 88 91 3 517.46 1.04 270 88 92 4 510.59 1.58 271 89 92 3 529.58 0.27 272 89 93 4 503.58 1.54 273 89 138 49 163.62 0.56 274 89 142 53 162.00 0.81 275 90 93 3 529.57 0.27 276 90 94 4 503.57 1.54 277 90 142 52 161.12 0.39 278 90 145 55 151.53 0.18 279 90 146 56 151.06 0.06 280 91 94 3 529.57 0.27 281 91 95 4 489.60 1.43 282 91 145 54 152.12 0.14 283 91 149 58 145.72 0.04 284 92 96 4 447.54 1.20 285 92 97 5 410.40 19.77 286 93 97 4 388.81 30.55 287 93 98 5 388.80 30.55 288 93 99 6 303.01 1.22 289 93 146 53 148.04 0.84 290 94 98 4 388.79 30.55 291 94 146 52 148.04 0.84 292 94 149 55 139.87 0.88 293 94 151 57 69.80 6.58 294 95 98 3 526.81 4.92 295 95 149 54 145.91 0.39 296 95 151 56 118.06 0.90 297 98 151 53 78.25 2.47 298 99 103 4 513.02 1.35 299 99 104 5 507.38 1.49 300 99 146 47 148.03 0.84 301 100 103 3 529.84 0.84 302 100 104 4 517.85 3.70 303 100 146 46 148.04 0.84 304 101 104 3 517.85 3.70 305 101 105 4 517.85 3.70 306 101 139 38 162.24 0.70 307 101 142 41 159.25 1.64 308 101 143 42 155.59 0.16 309 101 146 45 147.55 0.61 310 101 152 51 43.77 0.40 311 102 105 3 517.85 3.70 312 102 106 4 513.21 1.39 313 103 106 3 517.29 0.65 314 103 107 4 513.21 1.39 315 104 107 3 522.88 2.15 316 104 108 4 513.21 1.39 317 104 138 34 162.42 0.72 318 104 139 35 162.21 0.70 319 104 142 38 155.87 0.06 320 105 108 3 516.40 3.00 321 105 109 4 514.85 2.32 322 105 139 34 162.21 0.70 323 106 109 3 514.84 2.33 324 106 110 4 514.78 2.35 325 107 110 3 512.82 3.33 326 107 111 4 508.49 5.50 327 108 111 3 519.03 0.23 328 108 112 4 508.07 5.71 329 108 135 27 163.55 0.52 330 108 139 31 162.18 0.68 331 109 112 3 513.46 3.00 332 109 113 4 508.06 5.70 333 110 113 3 508.88 1.18 334 110 114 4 500.98 5.13 335 111 114 3 518.12 0.99 336 111 115 4 509.74 0.70 337 111 135 24 163.57 0.52 338 112 115 3 521.37 2.32 339 112 116 4 509.73 0.70 340 112 123 11 252.17 5.33 341 112 128 16 165.65 1.34 342 112 131 19 163.88 0.46 343 112 132 20 163.79 0.51 344 112 135 23 163.69 0.46 345 113 116 3 523.64 1.18 346 113 117 4 506.77 0.78 347 114 117 3 521.61 0.76 348 114 118 4 504.49 1.92 349 115 118 3 515.87 2.11 350 115 119 4 504.44 1.93 351 115 123 8 268.54 2.83 352 115 131 16 163.89 0.47 353 116 120 4 455.38 12.04 354 116 123 7 268.51 2.84 355 117 120 3 525.21 0.39 356 119 122 3 508.91 5.54 357 119 123 4 477.84 2.89 358 120 123 3 489.97 0.39 359 122 127 5 470.73 15.29 360 123 127 4 470.72 15.29 361 123 128 5 476.28 13.77 362 123 131 8 439.60 5.33 363 124 127 3 509.70 2.91 364 124 128 4 504.62 1.72 365 125 128 3 510.56 1.25 366 125 129 4 504.64 1.72 367 126 129 3 518.82 2.89 368 126 130 4 518.81 2.89 369 127 130 3 518.82 2.89 370 127 131 4 510.56 1.27 371 128 131 3 518.85 2.87 372 128 132 4 501.74 0.25 373 129 132 3 522.81 4.84 374 129 133 4 503.11 0.43 375 130 133 3 509.26 2.64 376 130 134 4 503.11 0.43 377 131 134 3 508.56 2.29 378 131 135 4 503.06 0.46 379 132 135 3 517.82 6.92 380 132 136 4 502.94 0.52 381 133 136 3 502.52 0.72 382 133 137 4 500.18 1.89 383 134 137 3 510.14 5.94 384 134 138 4 502.75 0.75 385 135 138 3 502.76 0.75 386 135 139 4 502.77 0.76 387 136 139 3 507.04 2.89 388 136 140 4 501.29 1.51 389 137 140 3 509.30 0.56 390 137 141 4 501.26 1.52 391 138 141 3 523.96 0.24 392 138 142 4 506.43 1.03 393 139 142 3 521.24 1.11 394 139 143 4 501.28 1.54 395 140 143 3 517.11 3.32 396 140 144 4 502.57 2.90 397 141 144 3 512.10 0.36 398 141 145 4 508.28 0.05 399 142 145 3 511.65 0.59 400 142 146 4 509.44 0.64 401 143 146 3 509.44 0.64 402 143 147 4 502.93 3.90 403 143 152 9 266.55 1.40 404 144 147 3 510.67 1.25 405 144 148 4 506.04 2.34 406 145 148 3 507.85 1.45 407 145 149 4 507.83 1.45 408 146 149 3 513.67 1.49 409 146 150 4 489.56 3.66 410 146 151 5 324.57 22.13 411 146 152 6 280.54 5.55 412 147 150 3 503.79 3.46 413 147 152 5 301.94 16.00