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 8 472.25 1.86 2 2 130 128 47.55 0.10 3 2 133 131 41.76 0.81 4 2 134 132 32.84 0.64 5 2 137 135 32.04 1.04 6 3 6 3 515.30 1.44 7 3 7 4 515.33 1.43 8 4 7 3 517.87 2.69 9 4 8 4 515.34 1.43 10 4 79 75 54.81 1.12 11 5 8 3 516.50 0.85 12 5 9 4 515.34 1.43 13 6 9 3 526.80 4.31 14 6 10 4 506.12 3.18 15 6 130 124 70.95 0.60 16 6 133 127 70.95 0.60 17 7 10 3 507.09 2.66 18 7 11 4 506.06 3.17 19 7 76 69 70.98 0.62 20 7 79 72 70.98 0.62 21 7 80 73 71.48 0.86 22 7 134 127 70.98 0.61 23 7 137 130 70.98 0.61 24 8 11 3 524.37 2.75 25 8 12 4 507.13 2.62 26 9 12 3 526.58 1.64 27 9 13 4 515.23 1.20 28 9 126 117 82.53 0.77 29 9 127 118 82.44 0.77 30 9 130 121 82.31 0.83 31 10 13 3 529.42 0.21 32 10 14 4 515.41 1.10 33 10 76 66 82.48 0.78 34 10 130 120 82.44 0.77 35 10 131 121 82.30 0.83 36 10 134 124 82.23 0.86 37 11 14 3 515.42 1.10 38 11 15 4 515.41 1.10 39 11 76 65 82.52 0.79 40 11 77 66 82.52 0.79 41 11 79 68 82.52 0.79 42 12 15 3 519.81 0.84 43 12 16 4 517.35 2.06 44 12 122 110 90.73 1.05 45 13 16 3 521.44 4.11 46 13 17 4 518.71 0.04 47 13 115 102 90.73 1.05 48 13 119 106 90.81 1.06 49 13 122 109 90.73 1.05 50 13 123 110 90.70 1.06 51 13 131 118 90.17 1.14 52 14 17 3 518.71 0.04 53 14 18 4 518.71 0.04 54 14 69 55 90.50 1.15 55 14 72 58 90.28 1.17 56 14 73 59 90.14 1.10 57 14 76 62 90.12 1.10 58 14 77 63 90.14 1.09 59 14 131 117 90.42 1.15 60 15 18 3 523.15 2.18 61 16 19 3 520.39 0.89 62 16 119 103 94.88 0.90 63 16 122 106 94.03 0.51 64 17 20 3 525.29 1.93 65 17 21 4 490.79 3.21 66 17 24 7 415.45 7.94 67 17 69 52 188.61 3.15 68 17 115 98 90.98 1.00 69 17 119 102 110.51 0.89 70 18 21 3 515.19 1.71 71 18 77 59 129.04 20.03 72 20 23 3 519.77 0.85 73 20 24 4 508.65 2.99 74 20 118 98 152.59 2.89 75 21 24 3 519.77 0.85 76 21 25 4 512.43 1.11 77 21 66 45 191.19 2.27 78 21 69 48 191.16 2.28 79 22 25 3 519.09 0.51 80 22 26 4 514.14 1.96 81 22 62 40 198.37 0.84 82 22 66 44 191.24 2.28 83 23 26 3 514.15 1.96 84 23 27 4 512.43 1.10 85 23 118 95 167.37 0.18 86 24 27 3 512.43 1.10 87 24 28 4 512.42 1.10 88 24 69 45 194.71 0.53 89 24 114 90 167.93 0.01 90 24 115 91 167.91 0.01 91 24 118 94 167.37 0.18 92 24 119 95 167.41 0.16 93 25 28 3 510.17 0.05 94 25 29 4 509.07 1.77 95 25 65 40 194.72 0.54 96 25 69 44 194.71 0.53 97 26 29 3 525.02 3.46 98 26 30 4 504.48 0.53 99 26 55 29 228.79 1.31 100 26 56 30 228.79 1.31 101 26 58 32 224.80 2.44 102 26 61 35 203.63 3.38 103 26 62 36 203.32 3.30 104 27 30 3 519.12 0.93 105 27 31 4 508.72 1.59 106 27 114 87 168.00 0.02 107 27 118 91 167.46 0.14 108 28 31 3 508.73 1.59 109 28 32 4 507.67 2.12 110 28 69 41 201.52 2.73 111 28 107 79 168.66 0.10 112 28 110 82 168.46 0.05 113 28 111 83 168.44 0.05 114 28 114 86 168.00 0.02 115 29 32 3 513.06 0.57 116 29 33 4 507.67 2.13 117 29 61 32 208.81 1.74 118 29 64 35 208.75 1.76 119 29 65 36 201.55 2.73 120 29 107 78 168.66 0.10 121 30 33 3 511.76 4.17 122 30 34 4 506.72 2.60 123 30 52 22 235.18 1.24 124 30 55 25 233.77 0.84 125 30 56 26 234.02 0.76 126 30 61 31 224.07 2.58 127 31 34 3 517.87 1.11 128 31 35 4 495.55 3.94 129 31 110 79 168.53 0.04 130 31 114 83 168.47 0.07 131 32 35 3 513.79 0.93 132 32 36 4 493.88 3.08 133 32 39 7 433.10 12.33 134 32 106 74 168.69 0.09 135 32 107 75 168.66 0.09 136 32 110 78 168.54 0.05 137 33 36 3 519.72 0.64 138 33 37 4 465.86 0.59 139 33 39 6 433.10 12.33 140 33 40 7 428.37 14.67 141 33 43 10 359.85 8.30 142 33 46 13 253.41 1.04 143 33 55 22 235.62 1.36 144 33 61 28 235.16 1.24 145 34 37 3 524.61 4.47 146 34 52 18 235.65 1.35 147 34 55 21 237.34 0.51 148 36 39 3 522.77 4.96 149 36 106 70 168.85 0.09 150 37 40 3 527.36 4.08 151 37 41 4 513.18 2.85 152 38 41 3 525.94 3.38 153 38 42 4 519.20 3.81 154 38 103 65 169.10 0.11 155 38 106 68 169.09 0.10 156 39 42 3 527.46 2.61 157 39 43 4 521.50 5.59 158 39 103 64 168.94 0.14 159 39 106 67 168.85 0.10 160 40 43 3 524.53 1.15 161 40 46 6 381.18 9.53 162 40 47 7 273.22 0.37 163 40 49 9 262.71 4.34 164 40 55 15 241.73 1.98 165 41 47 6 309.55 2.35 166 42 97 55 169.69 0.09 167 42 98 56 169.69 0.09 168 42 99 57 169.54 0.17 169 42 100 58 169.58 0.14 170 42 103 61 169.27 0.10 171 43 46 3 523.77 1.24 172 43 47 4 483.38 0.15 173 43 64 21 237.33 0.36 174 44 47 3 527.75 0.85 175 45 48 3 600.27 0.05 176 45 60 15 237.69 0.41 177 45 64 19 237.34 0.36 178 46 49 3 531.15 0.84 179 46 60 14 237.67 0.41 180 46 61 15 237.62 0.42 181 46 64 18 237.34 0.36 182 49 54 5 470.27 6.29 183 49 55 6 347.20 6.90 184 49 58 9 267.36 0.34 185 49 61 12 260.72 2.93 186 50 54 4 502.51 1.85 187 51 54 3 502.53 1.85 188 51 55 4 499.68 0.42 189 52 55 3 501.41 1.28 190 52 56 4 495.73 1.55 191 53 56 3 504.83 2.99 192 53 57 4 500.26 0.71 193 54 57 3 505.24 3.19 194 54 58 4 497.13 0.86 195 55 58 3 511.74 5.03 196 55 61 6 453.20 15.96 197 58 61 3 533.14 2.79 198 58 62 4 506.98 1.89 199 59 62 3 517.25 3.25 200 59 63 4 505.94 2.41 201 60 63 3 510.61 0.07 202 60 64 4 510.61 0.07 203 61 64 3 517.27 3.26 204 61 65 4 517.27 3.26 205 62 65 3 523.36 0.23 206 62 66 4 517.29 3.26 207 63 66 3 528.26 3.32 208 63 67 4 517.29 3.27 209 64 67 3 517.31 3.26 210 64 68 4 513.73 5.04 211 65 68 3 513.95 4.95 212 65 69 4 508.68 2.30 213 66 69 3 517.23 3.30 214 66 70 4 508.67 2.29 215 67 70 3 531.92 4.04 216 67 71 4 508.81 2.23 217 68 71 3 523.24 0.26 218 68 72 4 507.53 1.58 219 68 107 39 168.62 0.07 220 69 72 3 518.36 2.18 221 69 73 4 509.00 0.79 222 70 73 3 530.70 1.26 223 70 74 4 512.00 0.70 224 71 74 3 526.01 1.09 225 71 75 4 512.02 0.71 226 72 75 3 517.63 2.14 227 72 76 4 512.00 0.73 228 72 111 39 168.25 0.10 229 72 135 63 162.99 1.30 230 73 76 3 517.63 2.14 231 73 77 4 512.36 0.55 232 74 77 3 525.24 5.88 233 74 78 4 512.48 0.60 234 75 78 3 536.29 0.35 235 75 79 4 518.28 3.12 236 75 82 7 258.95 5.46 237 75 85 10 169.95 0.09 238 75 89 14 169.93 0.13 239 75 138 63 161.49 1.58 240 76 79 3 529.55 3.02 241 76 131 55 163.37 1.35 242 76 134 58 163.06 1.27 243 78 81 3 502.95 2.35 244 78 82 4 419.89 8.05 245 78 85 7 308.58 4.13 246 80 137 57 163.04 1.31 247 82 85 3 521.12 0.45 248 82 86 4 496.28 3.52 249 82 137 55 163.02 1.31 250 82 138 56 162.97 1.31 251 82 141 59 160.97 1.37 252 83 86 3 515.21 0.04 253 83 87 4 504.83 0.72 254 84 88 4 521.46 0.89 255 85 88 3 540.20 1.71 256 85 89 4 521.46 0.89 257 86 89 3 526.52 3.42 258 86 90 4 507.86 1.78 259 86 138 52 162.57 1.47 260 86 141 55 160.60 1.25 261 86 142 56 160.37 1.24 262 86 145 59 157.77 0.97 263 87 90 3 521.66 0.98 264 87 91 4 508.89 2.30 265 88 91 3 517.73 0.98 266 88 92 4 511.04 1.23 267 89 92 3 513.58 1.09 268 89 93 4 511.03 1.23 269 89 138 49 162.88 1.31 270 89 142 53 159.71 1.24 271 90 93 3 513.15 2.29 272 90 94 4 504.10 2.23 273 90 142 52 159.56 1.21 274 90 145 55 150.05 0.70 275 90 146 56 145.69 0.10 276 91 94 3 518.79 0.53 277 91 95 4 496.83 1.93 278 91 149 58 143.06 0.32 279 92 96 4 388.38 24.26 280 92 97 5 388.38 24.25 281 93 97 4 381.74 22.16 282 93 98 5 381.73 22.16 283 93 99 6 286.77 4.60 284 93 146 53 144.03 0.72 285 94 98 4 326.47 20.93 286 94 146 52 143.97 0.71 287 94 149 55 139.50 0.35 288 94 151 57 76.67 10.96 289 95 98 3 499.32 1.25 290 95 149 54 143.40 0.48 291 95 151 56 118.97 2.29 292 99 103 4 511.77 0.20 293 99 104 5 506.25 2.55 294 99 146 47 143.99 0.71 295 100 103 3 516.44 2.14 296 100 104 4 513.50 0.67 297 100 153 53 18.87 0.96 298 101 104 3 518.26 1.02 299 101 105 4 508.38 3.29 300 101 139 38 160.56 1.30 301 101 142 41 159.22 1.13 302 101 143 42 154.11 2.22 303 101 146 45 143.67 0.55 304 101 153 52 18.85 0.96 305 102 105 3 526.32 0.70 306 102 106 4 509.55 2.71 307 103 106 3 507.57 1.71 308 103 107 4 507.66 1.67 309 104 107 3 515.10 0.14 310 104 108 4 507.64 1.65 311 104 138 34 161.85 1.66 312 104 139 35 160.53 1.31 313 104 142 38 157.55 0.68 314 105 108 3 513.13 1.11 315 105 109 4 507.62 1.64 316 105 139 34 160.53 1.31 317 106 109 3 517.83 4.80 318 106 110 4 502.20 1.93 319 107 110 3 507.14 0.54 320 107 111 4 500.53 1.86 321 108 111 3 510.99 1.38 322 108 112 4 506.22 1.01 323 108 135 27 163.02 1.28 324 108 139 31 160.55 1.30 325 109 112 3 513.70 0.81 326 109 113 4 507.03 2.52 327 110 113 3 509.82 1.99 328 110 114 4 499.40 1.29 329 111 114 3 515.86 1.11 330 111 115 4 498.48 2.24 331 111 135 24 163.03 1.28 332 112 115 3 508.27 0.65 333 112 116 4 506.53 1.78 334 112 123 11 287.36 6.48 335 112 131 19 163.15 1.22 336 112 132 20 163.13 1.23 337 112 135 23 163.07 1.26 338 113 116 3 512.98 1.70 339 113 117 4 509.84 0.12 340 114 117 3 512.97 1.69 341 114 118 4 506.53 1.78 342 115 118 3 517.55 0.59 343 115 119 4 498.50 2.21 344 115 123 8 291.74 5.34 345 115 131 16 188.75 6.38 346 116 119 3 515.77 1.54 347 116 120 4 490.62 1.74 348 116 123 7 325.81 24.13 349 116 128 12 258.85 1.14 350 117 120 3 541.98 1.39 351 119 122 3 518.12 4.54 352 119 123 4 477.06 2.99 353 120 123 3 490.03 0.63 354 120 124 4 465.81 8.62 355 122 127 5 486.79 3.54 356 123 127 4 496.50 1.20 357 123 128 5 486.91 3.60 358 123 131 8 443.17 5.37 359 124 127 3 514.59 0.90 360 124 128 4 499.76 2.78 361 125 128 3 510.85 2.76 362 125 129 4 499.78 2.77 363 126 129 3 515.99 3.85 364 126 130 4 505.77 1.26 365 127 130 3 509.28 3.00 366 127 131 4 503.87 2.20 367 128 131 3 508.56 3.35 368 128 132 4 507.37 3.96 369 129 132 3 511.86 1.73 370 129 133 4 507.66 3.83 371 130 133 3 515.57 0.12 372 130 134 4 510.55 2.38 373 131 134 3 510.56 2.38 374 131 135 4 510.55 2.38 375 132 135 3 515.75 0.23 376 132 136 4 504.95 0.42 377 133 136 3 505.62 0.09 378 133 137 4 504.95 0.42 379 134 137 3 510.79 2.16 380 134 138 4 505.15 0.15 381 135 138 3 505.96 0.26 382 135 139 4 506.12 0.65 383 136 139 3 510.47 1.53 384 136 140 4 503.41 1.03 385 137 140 3 506.51 0.43 386 137 141 4 503.39 1.04 387 138 141 3 513.45 0.04 388 138 142 4 505.82 0.08 389 139 142 3 506.78 0.56 390 139 143 4 504.40 0.93 391 140 143 3 514.95 2.73 392 140 144 4 506.03 1.74 393 141 144 3 514.94 2.73 394 141 145 4 511.68 1.89 395 142 145 3 521.12 2.84 396 142 146 4 504.43 0.95 397 143 146 3 504.36 0.97 398 143 147 4 504.34 0.98 399 143 152 9 113.11 45.66 400 144 147 3 513.66 3.67 401 144 148 4 504.34 0.98 402 145 148 3 515.85 0.16 403 145 149 4 505.28 0.26 404 146 149 3 511.44 0.62 405 146 150 4 503.75 1.02 406 146 151 5 359.16 18.21 407 146 152 6 254.41 5.38 408 147 150 3 507.99 1.10 409 147 152 5 253.01 6.08