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 5 478.40 1.25 2 2 10 8 471.46 2.02 3 2 130 128 47.31 0.03 4 2 133 131 42.25 0.57 5 2 134 132 36.97 1.35 6 2 137 135 36.96 1.35 7 3 6 3 514.46 1.86 8 3 7 4 512.74 2.72 9 4 7 3 515.72 3.76 10 4 8 4 512.93 2.62 11 4 79 75 59.48 1.48 12 5 8 3 518.22 2.43 13 5 9 4 509.35 0.59 14 6 9 3 526.55 4.19 15 6 10 4 502.94 2.62 16 6 130 124 71.22 1.11 17 6 133 127 71.24 1.10 18 7 10 3 509.99 5.34 19 7 11 4 502.94 2.62 20 7 76 69 71.36 1.11 21 7 79 72 71.34 1.11 22 7 80 73 71.35 1.11 23 7 134 127 71.34 1.11 24 7 137 130 71.34 1.11 25 8 11 3 520.31 4.53 26 8 12 4 512.87 2.37 27 9 12 3 539.28 4.96 28 9 13 4 513.85 1.88 29 9 126 117 83.14 0.49 30 9 127 118 83.02 0.56 31 9 130 121 82.92 0.57 32 10 13 3 529.17 0.09 33 10 14 4 515.17 1.24 34 10 76 66 82.93 0.58 35 10 130 120 83.02 0.56 36 10 131 121 82.86 0.58 37 10 134 124 82.85 0.58 38 11 14 3 515.18 1.24 39 11 15 4 515.17 1.24 40 11 76 65 83.05 0.55 41 11 77 66 83.06 0.55 42 11 79 68 83.11 0.53 43 12 15 3 519.56 0.96 44 12 16 4 517.10 2.19 45 12 122 110 91.40 0.81 46 13 16 3 521.19 4.24 47 13 17 4 515.66 1.48 48 13 115 102 91.39 0.81 49 13 122 109 91.40 0.81 50 13 123 110 91.39 0.81 51 13 127 114 91.06 0.79 52 13 131 118 89.91 1.21 53 14 17 3 518.12 0.25 54 14 18 4 518.46 0.08 55 14 69 55 91.34 0.79 56 14 72 58 91.17 0.70 57 14 73 59 90.09 1.12 58 14 76 62 89.94 1.20 59 14 77 63 90.39 0.97 60 14 131 117 91.06 0.79 61 15 18 3 509.06 4.62 62 15 19 4 519.75 0.73 63 16 19 3 519.75 0.73 64 16 119 103 93.01 1.42 65 16 122 106 96.18 3.00 66 17 20 3 534.50 1.64 67 17 21 4 502.00 1.15 68 17 24 7 407.01 15.24 69 17 69 52 200.18 2.93 70 17 115 98 91.63 0.74 71 18 21 3 518.45 0.09 72 18 77 59 132.47 19.75 73 20 23 3 521.56 1.74 74 20 24 4 510.66 1.97 75 20 118 98 140.53 0.71 76 21 24 3 518.29 1.35 77 21 25 4 506.00 0.35 78 21 66 45 201.68 2.94 79 21 69 48 200.97 2.66 80 22 25 3 517.11 1.25 81 22 26 4 512.15 1.22 82 22 62 40 202.31 3.12 83 22 66 44 201.69 2.94 84 23 26 3 512.28 1.17 85 23 27 4 512.15 1.22 86 23 118 95 169.39 0.12 87 24 27 3 526.52 4.74 88 24 28 4 511.79 1.03 89 24 69 45 201.70 2.95 90 24 114 90 166.65 1.98 91 24 115 91 165.43 2.59 92 24 118 94 169.40 0.12 93 24 119 95 169.87 0.36 94 25 28 3 521.14 1.93 95 25 29 4 513.15 0.52 96 25 65 40 202.17 3.19 97 25 69 44 201.69 2.95 98 26 29 3 524.36 3.54 99 26 30 4 512.78 0.70 100 26 56 30 213.66 0.42 101 26 62 36 202.41 3.15 102 26 65 39 202.30 3.12 103 27 30 3 518.88 0.80 104 27 31 4 508.78 0.83 105 27 114 87 171.22 0.16 106 27 118 91 170.28 0.56 107 28 31 3 510.44 0.47 108 28 32 4 509.72 0.83 109 28 69 41 202.56 3.27 110 28 107 79 171.97 0.26 111 28 110 82 171.59 0.15 112 28 111 83 171.48 0.21 113 28 114 86 171.23 0.17 114 29 32 3 519.20 0.20 115 29 33 4 506.34 2.52 116 29 61 32 203.63 3.15 117 29 64 35 203.43 3.08 118 29 65 36 202.74 3.32 119 29 107 78 171.98 0.25 120 30 33 3 513.97 2.81 121 30 34 4 510.83 4.38 122 30 52 22 233.03 0.47 123 30 55 25 221.36 2.67 124 30 56 26 229.45 1.28 125 30 61 31 212.91 0.21 126 31 34 3 517.62 0.99 127 31 35 4 510.17 0.15 128 31 110 79 171.66 0.14 129 31 113 82 171.58 0.13 130 31 114 83 171.47 0.07 131 32 35 3 517.39 1.55 132 32 36 4 504.24 3.12 133 32 39 7 425.96 7.67 134 32 106 74 172.07 0.24 135 32 107 75 172.01 0.24 136 32 110 78 171.66 0.14 137 33 36 3 522.28 1.92 138 33 37 4 493.54 3.28 139 33 39 6 399.73 11.50 140 33 40 7 341.49 17.61 141 33 43 10 349.14 6.52 142 33 46 13 262.64 2.62 143 33 55 22 233.38 0.54 144 33 61 28 232.71 0.61 145 34 37 3 517.45 0.49 146 34 52 18 234.79 1.02 147 36 39 3 533.23 1.14 148 36 106 70 172.15 0.22 149 37 40 3 521.25 5.71 150 38 41 3 521.25 5.71 151 38 103 65 172.64 0.07 152 38 106 68 172.44 0.12 153 39 42 3 529.22 1.73 154 39 43 4 526.99 2.85 155 39 103 64 172.38 0.15 156 39 106 67 172.35 0.14 157 40 43 3 523.53 1.65 158 40 46 6 382.11 8.81 159 40 47 7 344.17 27.78 160 40 49 9 268.50 1.12 161 40 55 15 243.43 0.88 162 42 97 55 173.22 0.29 163 42 98 56 173.19 0.28 164 42 99 57 173.11 0.29 165 42 103 61 172.75 0.27 166 43 46 3 523.52 1.11 167 43 47 4 513.72 0.34 168 44 47 3 533.64 2.10 169 45 48 3 586.50 1.75 170 45 60 15 235.27 1.19 171 45 64 19 235.19 1.19 172 46 49 3 533.87 0.77 173 46 60 14 235.56 1.04 174 46 61 15 235.24 1.20 175 46 64 18 235.24 1.20 176 49 54 5 456.26 8.88 177 49 55 6 355.22 2.90 178 49 58 9 281.70 4.88 179 49 61 12 260.42 3.08 180 50 54 4 501.84 2.19 181 51 54 3 499.68 1.11 182 51 55 4 494.78 1.08 183 52 55 3 499.43 1.24 184 52 56 4 497.68 0.36 185 53 56 3 510.59 0.12 186 53 57 4 498.85 0.96 187 54 57 3 507.67 1.57 188 54 58 4 498.86 0.96 189 55 58 3 511.49 4.91 190 55 61 6 404.88 5.86 191 58 61 3 532.89 2.92 192 58 62 4 497.78 0.09 193 59 62 3 504.17 3.10 194 59 63 4 504.15 3.10 195 60 63 3 517.16 3.31 196 60 64 4 511.83 0.73 197 61 64 3 517.08 3.35 198 61 65 4 511.85 0.74 199 62 65 3 512.43 1.03 200 62 66 4 511.85 0.74 201 63 66 3 513.03 0.73 202 63 67 4 511.84 0.75 203 64 67 3 512.47 1.01 204 64 68 4 511.83 0.76 205 65 68 3 528.74 2.48 206 65 69 4 511.78 0.74 207 66 69 3 525.88 3.91 208 66 70 4 511.69 0.78 209 67 70 3 528.91 5.29 210 67 71 4 508.74 0.68 211 68 71 3 522.99 0.39 212 68 72 4 508.72 0.68 213 68 107 39 171.96 0.29 214 69 72 3 518.11 2.05 215 69 73 4 508.70 0.69 216 70 73 3 526.88 0.41 217 70 74 4 509.16 0.80 218 71 74 3 520.08 1.88 219 71 75 4 509.17 0.79 220 72 75 3 517.28 3.27 221 72 76 4 509.15 0.79 222 72 111 39 171.80 0.36 223 72 135 63 168.82 0.90 224 72 138 66 168.18 0.78 225 73 76 3 516.32 2.79 226 73 77 4 509.13 0.81 227 74 78 4 509.12 0.80 228 75 78 3 536.04 0.23 229 75 82 7 257.42 5.49 230 75 85 10 238.68 1.86 231 75 89 14 233.83 4.29 232 75 138 63 168.30 0.74 233 76 79 3 531.64 1.98 234 76 131 55 169.43 0.83 235 76 134 58 168.94 0.88 236 78 81 3 502.13 2.77 237 78 82 4 436.25 5.29 238 78 85 7 321.86 13.53 239 80 137 57 169.02 0.98 240 82 85 3 522.38 0.18 241 82 86 4 504.67 3.06 242 82 137 55 169.10 0.94 243 82 141 59 168.19 0.79 244 83 86 3 520.03 0.13 245 83 87 4 508.92 0.94 246 84 88 4 523.13 0.21 247 85 88 3 544.06 0.68 248 85 89 4 521.09 0.82 249 86 89 3 528.19 2.33 250 86 90 4 516.08 3.33 251 86 138 52 168.87 0.92 252 86 141 55 166.58 0.41 253 86 142 56 166.05 0.18 254 86 145 59 160.81 0.60 255 87 90 3 521.22 0.76 256 87 91 4 515.87 3.43 257 87 145 58 160.81 0.60 258 88 91 3 519.88 1.74 259 88 92 4 512.63 0.20 260 89 92 3 517.06 1.32 261 89 93 4 512.72 0.24 262 89 138 49 168.79 0.88 263 89 142 53 164.31 0.86 264 90 93 3 520.03 1.40 265 90 94 4 511.92 1.66 266 90 142 52 163.37 0.53 267 90 145 55 157.49 0.59 268 90 146 56 157.06 0.45 269 91 94 3 518.62 0.62 270 91 95 4 511.88 1.66 271 91 149 58 151.18 0.17 272 92 95 3 532.31 2.57 273 92 96 4 490.58 0.16 274 92 97 5 437.03 10.43 275 93 97 4 372.11 2.15 276 93 98 5 354.74 6.53 277 93 99 6 287.70 3.98 278 93 146 53 155.36 0.21 279 94 98 4 354.73 6.53 280 94 146 52 154.81 0.06 281 94 149 55 146.94 0.88 282 94 151 57 90.63 16.34 283 95 149 54 151.44 0.06 284 95 151 56 123.77 0.11 285 99 103 4 513.37 0.85 286 99 104 5 510.44 2.32 287 99 146 47 153.59 0.56 288 100 103 3 525.85 1.60 289 100 104 4 521.72 2.75 290 100 153 53 17.89 0.48 291 101 104 3 521.72 2.75 292 101 105 4 521.71 2.75 293 101 139 38 164.81 0.75 294 101 142 41 163.34 0.52 295 101 143 42 157.93 0.64 296 101 146 45 152.81 0.61 297 101 153 52 16.64 0.37 298 102 105 3 521.17 3.02 299 102 106 4 510.54 2.29 300 103 106 3 514.19 0.47 301 103 107 4 510.53 2.29 302 104 107 3 523.82 0.32 303 104 108 4 510.51 2.30 304 104 139 35 164.81 0.75 305 104 142 38 162.31 0.00 306 105 108 3 514.87 1.34 307 105 109 4 509.01 1.58 308 105 139 34 164.80 0.74 309 106 109 3 519.52 3.71 310 106 110 4 508.56 1.50 311 107 110 3 508.51 1.48 312 107 111 4 508.50 1.48 313 108 111 3 514.61 4.90 314 108 112 4 508.07 1.63 315 108 135 27 168.50 0.86 316 108 139 31 164.81 0.74 317 109 112 3 519.60 2.40 318 109 113 4 506.00 0.58 319 110 113 3 514.62 4.90 320 110 114 4 507.45 1.31 321 111 114 3 523.75 1.66 322 111 115 4 509.59 0.26 323 111 135 24 168.59 0.91 324 112 115 3 514.76 2.83 325 112 116 4 509.60 0.26 326 112 123 11 252.13 1.62 327 112 128 16 169.18 0.92 328 112 131 19 169.00 0.84 329 112 132 20 169.00 0.84 330 112 135 23 168.61 0.91 331 113 116 3 523.69 2.28 332 113 117 4 509.59 0.25 333 114 117 3 517.89 4.40 334 114 118 4 504.57 1.14 335 115 118 3 516.16 0.10 336 115 119 4 503.23 0.48 337 115 123 8 255.02 3.07 338 115 131 16 189.72 7.59 339 116 120 4 460.59 4.81 340 116 123 7 254.23 2.67 341 119 122 3 517.88 4.41 342 119 123 4 449.12 1.05 343 120 123 3 509.87 9.90 344 122 127 5 487.82 2.83 345 123 127 4 496.18 1.35 346 123 128 5 483.59 0.64 347 123 131 8 465.67 6.92 348 124 127 3 512.07 1.91 349 124 128 4 500.90 3.71 350 125 128 3 508.99 0.34 351 125 129 4 500.90 3.71 352 126 129 3 511.02 1.35 353 126 130 4 511.02 1.35 354 127 130 3 511.02 1.35 355 127 131 4 511.00 1.35 356 128 131 3 514.50 0.39 357 128 132 4 514.49 0.39 358 129 132 3 515.67 0.18 359 129 133 4 509.02 3.14 360 130 133 3 516.26 0.27 361 130 134 4 515.31 0.00 362 131 134 3 516.26 0.27 363 131 135 4 510.31 2.50 364 132 135 3 521.87 3.08 365 132 136 4 505.38 0.04 366 133 136 3 507.98 0.19 367 133 137 4 506.44 0.57 368 134 137 3 514.09 0.76 369 134 138 4 505.98 0.81 370 135 138 3 512.69 2.55 371 135 139 4 505.99 0.80 372 136 139 3 512.88 2.45 373 136 140 4 504.28 1.65 374 137 140 3 510.70 1.58 375 137 141 4 504.35 1.58 376 138 141 3 518.64 0.30 377 138 142 4 504.31 1.56 378 139 142 3 513.22 0.07 379 139 143 4 505.34 2.08 380 140 143 3 514.71 2.60 381 140 144 4 507.47 1.02 382 141 144 3 523.35 1.73 383 141 145 4 512.24 1.35 384 142 145 3 524.75 1.03 385 142 146 4 505.32 2.10 386 143 146 3 515.02 2.75 387 143 147 4 508.00 0.88 388 144 147 3 513.37 3.57 389 144 148 4 507.83 0.97 390 145 148 3 518.18 1.01 391 145 149 4 500.23 4.78 392 146 149 3 514.25 0.78 393 146 150 4 500.16 4.81 394 146 151 5 325.64 13.95 395 146 152 6 254.37 5.54 396 146 153 7 254.15 5.66 397 147 150 3 514.25 0.78 398 147 152 5 254.38 5.54