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 8 457.25 4.90 2 2 130 128 40.19 0.21 3 2 133 131 21.30 1.65 4 2 134 132 19.09 0.55 5 2 137 135 19.09 0.55 6 3 6 3 498.57 0.10 7 3 7 4 505.79 3.90 8 4 7 3 527.26 0.81 9 4 8 4 506.38 3.81 10 4 79 75 60.94 2.55 11 5 8 3 519.27 3.19 12 5 9 4 519.27 3.19 13 6 9 3 519.27 3.19 14 6 10 4 519.27 3.19 15 6 130 124 66.75 2.76 16 6 133 127 66.75 2.76 17 7 10 3 517.37 2.25 18 7 11 4 502.16 2.03 19 7 76 69 66.85 2.80 20 7 79 72 66.84 2.81 21 7 80 73 66.87 2.81 22 7 134 127 66.85 2.80 23 7 137 130 66.85 2.80 24 8 11 3 517.29 1.63 25 8 12 4 508.00 4.98 26 9 12 3 508.56 4.71 27 9 13 4 508.00 4.99 28 9 126 117 90.56 0.56 29 9 127 118 90.40 0.49 30 9 130 121 90.39 0.49 31 10 13 3 515.37 1.30 32 10 14 4 513.07 2.46 33 10 76 66 90.39 0.49 34 10 130 120 90.45 0.51 35 10 131 121 90.39 0.49 36 10 134 124 90.38 0.49 37 11 14 3 513.58 2.20 38 11 15 4 513.57 2.21 39 11 76 65 90.48 0.51 40 11 77 66 90.67 0.60 41 11 79 68 90.70 0.61 42 12 15 3 515.36 1.31 43 12 16 4 512.25 0.24 44 12 122 110 95.44 0.34 45 13 16 3 515.13 1.20 46 13 17 4 509.73 1.47 47 13 115 102 95.33 0.39 48 13 122 109 95.45 0.34 49 13 123 110 95.42 0.34 50 13 127 114 95.08 0.30 51 13 131 118 94.67 0.48 52 14 17 3 509.76 1.49 53 14 18 4 507.44 0.33 54 14 69 55 166.47 0.93 55 14 72 58 94.81 0.42 56 14 73 59 94.68 0.48 57 14 76 62 94.68 0.47 58 14 77 63 94.68 0.48 59 14 131 117 95.07 0.29 60 15 18 3 507.44 0.33 61 15 19 4 509.94 0.93 62 16 19 3 511.71 1.59 63 16 24 8 421.60 0.52 64 16 119 103 97.14 0.45 65 16 122 106 97.14 0.45 66 17 20 3 522.99 2.62 67 17 21 4 492.03 0.74 68 17 24 7 417.59 2.50 69 17 69 52 183.72 1.53 70 17 115 98 97.14 0.45 71 18 21 3 502.10 3.17 72 18 77 59 171.34 1.24 73 20 23 3 506.44 0.14 74 20 24 4 502.59 1.78 75 20 118 98 148.90 0.36 76 21 24 3 511.06 1.57 77 21 25 4 502.61 1.77 78 21 66 45 186.03 2.43 79 21 69 48 185.62 2.23 80 22 25 3 510.47 1.86 81 22 26 4 510.47 1.86 82 22 62 40 186.27 2.35 83 22 66 44 186.03 2.41 84 23 26 3 521.94 3.05 85 23 27 4 511.07 1.59 86 23 118 95 162.31 0.66 87 24 27 3 521.06 3.40 88 24 28 4 512.20 1.03 89 24 69 45 186.02 2.42 90 24 114 90 162.91 0.92 91 24 115 91 162.91 0.92 92 24 118 94 162.34 0.67 93 24 119 95 162.34 0.67 94 25 28 3 521.06 3.40 95 25 29 4 512.20 1.03 96 25 65 40 186.06 2.41 97 25 69 44 186.02 2.42 98 26 29 3 519.18 4.44 99 26 30 4 511.88 0.89 100 26 56 30 199.80 0.83 101 26 61 35 186.40 2.40 102 26 62 36 186.36 2.38 103 27 30 3 512.75 1.22 104 27 31 4 511.98 0.85 105 27 114 87 162.98 0.92 106 27 118 91 162.41 0.68 107 28 31 3 525.86 0.99 108 28 32 4 511.97 0.84 109 28 69 41 186.30 2.35 110 28 107 79 163.41 0.95 111 28 110 82 163.30 0.94 112 28 111 83 163.28 0.94 113 28 114 86 162.99 0.92 114 29 32 3 517.09 3.40 115 29 33 4 511.95 0.84 116 29 61 32 194.56 0.56 117 29 64 35 194.42 0.56 118 29 65 36 192.18 0.54 119 30 33 3 510.07 0.10 120 30 34 4 503.06 3.60 121 30 52 22 202.86 1.49 122 30 55 25 202.56 1.61 123 30 56 26 202.59 1.60 124 31 34 3 519.13 2.75 125 31 35 4 503.04 3.59 126 31 110 79 163.34 0.93 127 31 113 82 163.29 0.92 128 31 114 83 163.16 0.98 129 32 35 3 519.79 2.43 130 32 36 4 493.49 0.03 131 32 39 7 418.79 2.71 132 32 106 74 163.44 0.95 133 32 107 75 163.44 0.94 134 32 110 78 163.34 0.93 135 33 36 3 516.76 3.94 136 33 37 4 456.62 13.33 137 33 39 6 425.62 0.69 138 33 40 7 327.47 1.38 139 33 43 10 326.00 0.65 140 33 46 13 244.38 1.64 141 33 55 22 203.03 1.46 142 33 61 28 202.83 1.48 143 34 37 3 523.97 0.34 144 36 39 3 531.67 1.79 145 36 106 70 163.56 0.97 146 37 40 3 514.51 0.31 147 37 41 4 514.52 0.30 148 38 41 3 522.49 2.91 149 38 103 65 164.88 0.51 150 38 106 68 164.22 0.83 151 39 42 3 524.72 0.51 152 39 43 4 514.51 0.30 153 39 103 64 164.03 0.75 154 39 106 67 163.67 0.93 155 40 43 3 515.86 0.98 156 40 46 6 410.94 33.55 157 40 47 7 256.43 0.00 158 40 55 15 214.49 1.04 159 42 97 55 165.94 0.43 160 42 98 56 165.94 0.43 161 42 99 57 165.73 0.41 162 42 100 58 165.87 0.40 163 42 103 61 165.29 0.35 164 43 46 3 506.85 2.33 165 43 47 4 484.68 0.51 166 43 64 21 203.51 1.44 167 45 48 3 553.18 1.42 168 46 49 3 522.13 2.34 169 46 60 14 208.54 3.68 170 46 61 15 203.60 1.40 171 46 64 18 203.79 1.31 172 49 54 5 459.14 3.10 173 49 55 6 340.76 3.30 174 49 58 9 262.77 1.53 175 49 61 12 256.76 1.70 176 50 54 4 494.54 2.28 177 51 54 3 512.89 3.60 178 51 55 4 483.35 2.47 179 52 55 3 501.98 6.02 180 52 56 4 486.41 0.94 181 53 56 3 510.32 1.84 182 53 57 4 497.79 4.60 183 54 57 3 508.29 0.83 184 54 58 4 483.95 2.32 185 55 58 3 514.20 1.78 186 55 61 6 421.68 4.32 187 58 61 3 512.11 3.08 188 58 62 4 505.07 2.27 189 59 62 3 507.00 1.46 190 59 63 4 492.93 3.81 191 60 63 3 503.42 1.44 192 60 64 4 485.79 3.12 193 61 64 3 507.82 7.88 194 61 65 4 485.79 3.13 195 62 65 3 496.99 1.78 196 62 66 4 500.04 1.57 197 63 66 3 518.02 2.32 198 63 67 4 504.60 0.71 199 64 67 3 510.66 2.32 200 64 68 4 504.60 0.71 201 65 68 3 508.40 1.18 202 65 69 4 497.61 2.77 203 66 69 3 507.19 0.54 204 66 70 4 497.50 2.82 205 67 70 3 515.12 2.56 206 67 71 4 501.70 4.21 207 68 71 3 518.81 0.72 208 68 72 4 510.42 0.14 209 69 72 3 514.04 1.67 210 69 73 4 503.33 3.41 211 70 73 3 513.38 1.99 212 70 74 4 513.38 2.00 213 71 74 3 526.70 4.75 214 71 75 4 509.78 0.20 215 72 75 3 518.42 0.93 216 72 76 4 512.29 1.09 217 72 111 39 163.32 0.92 218 72 135 63 161.05 1.02 219 73 76 3 525.39 5.33 220 73 77 4 514.37 0.06 221 74 77 3 530.56 2.75 222 74 78 4 514.37 0.06 223 75 78 3 521.29 3.52 224 75 79 4 521.28 3.52 225 75 82 7 247.25 0.83 226 75 85 10 243.34 1.08 227 75 86 11 238.75 1.21 228 75 89 14 243.34 1.09 229 75 138 63 160.25 1.28 230 76 79 3 534.60 3.17 231 76 131 55 161.31 1.03 232 76 134 58 161.18 0.98 233 78 81 3 495.40 2.00 234 78 82 4 445.23 15.87 235 78 85 7 335.03 10.75 236 80 137 57 161.21 1.03 237 82 85 3 515.23 0.13 238 82 86 4 501.01 0.78 239 82 137 55 161.21 1.03 240 82 141 59 159.87 1.18 241 83 86 3 512.85 1.32 242 83 87 4 508.94 2.87 243 84 87 3 521.27 0.01 244 84 88 4 531.58 0.72 245 85 88 3 536.08 2.94 246 86 89 3 531.57 0.73 247 86 90 4 512.45 1.12 248 86 138 52 160.69 1.08 249 86 141 55 159.56 1.30 250 86 142 56 158.54 0.81 251 87 90 3 521.20 0.27 252 87 91 4 501.49 2.89 253 88 91 3 519.08 0.79 254 88 92 4 510.77 1.68 255 89 92 3 522.40 2.44 256 89 93 4 498.63 4.40 257 89 138 49 160.75 1.06 258 90 93 3 516.56 0.49 259 90 94 4 494.78 2.47 260 90 142 52 154.97 0.15 261 90 145 55 140.62 1.03 262 90 146 56 134.91 1.80 263 90 149 59 133.66 1.71 264 91 94 3 508.62 4.46 265 91 95 4 485.71 7.00 266 91 149 58 133.56 1.65 267 92 95 3 506.93 3.60 268 92 96 4 460.47 1.60 269 92 97 5 439.59 4.79 270 93 97 4 397.89 19.54 271 93 98 5 366.81 4.00 272 93 99 6 316.84 3.67 273 93 146 53 134.91 1.79 274 93 151 58 67.62 2.94 275 94 98 4 397.89 19.54 276 94 146 52 134.91 1.79 277 94 149 55 132.55 1.18 278 94 151 57 64.95 1.61 279 95 98 3 527.04 3.14 280 98 151 53 65.00 1.59 281 99 103 4 496.57 4.09 282 99 104 5 498.69 3.04 283 99 146 47 134.96 1.76 284 99 151 52 64.95 1.61 285 100 103 3 518.81 2.38 286 100 104 4 503.15 0.81 287 100 151 51 64.95 1.61 288 100 152 52 60.06 1.78 289 101 104 3 503.15 0.81 290 101 105 4 503.16 0.81 291 101 139 38 159.49 1.25 292 101 142 41 157.45 0.87 293 101 143 42 143.53 0.14 294 101 146 45 134.90 1.79 295 101 152 51 47.20 0.51 296 102 105 3 503.94 0.42 297 102 106 4 503.17 0.81 298 103 106 3 504.09 0.48 299 103 107 4 503.17 0.81 300 104 107 3 515.44 0.63 301 104 108 4 503.08 0.77 302 104 138 34 160.23 1.28 303 104 139 35 158.57 0.80 304 104 142 38 157.47 1.14 305 105 108 3 515.45 0.62 306 105 109 4 512.57 3.75 307 105 139 34 158.62 0.82 308 106 109 3 520.31 1.80 309 106 110 4 510.19 4.94 310 107 110 3 519.75 0.17 311 107 111 4 510.17 4.96 312 108 111 3 520.11 0.02 313 108 112 4 520.11 0.01 314 108 135 27 161.03 0.99 315 108 139 31 158.56 0.79 316 109 112 3 518.38 0.89 317 109 113 4 506.48 6.83 318 110 113 3 510.86 4.64 319 110 114 4 493.60 4.29 320 111 114 3 514.93 5.96 321 111 115 4 501.47 0.38 322 111 135 24 161.04 0.98 323 112 115 3 502.74 0.81 324 112 116 4 501.47 0.39 325 112 123 11 249.25 5.25 326 112 131 19 161.09 0.97 327 112 132 20 161.08 0.97 328 112 135 23 161.06 0.99 329 113 116 3 502.58 0.89 330 113 117 4 501.53 0.36 331 114 117 3 506.71 0.81 332 114 118 4 496.48 2.15 333 115 118 3 517.80 0.84 334 115 119 4 476.73 5.95 335 115 123 8 285.87 4.54 336 115 131 16 184.14 10.54 337 116 120 4 457.09 1.08 338 116 123 7 273.41 10.78 339 117 120 3 524.87 2.62 340 119 122 3 506.87 0.48 341 119 123 4 449.48 7.67 342 120 123 3 493.86 4.12 343 122 127 5 482.16 1.30 344 123 127 4 482.16 1.30 345 123 128 5 480.56 2.08 346 123 131 8 436.01 17.14 347 124 127 3 510.81 0.01 348 124 128 4 483.16 0.81 349 125 128 3 506.30 2.25 350 125 129 4 485.37 0.29 351 126 129 3 515.38 2.31 352 126 130 4 496.20 0.63 353 127 130 3 511.08 2.96 354 127 131 4 491.72 2.88 355 128 131 3 509.79 3.60 356 128 132 4 502.14 0.24 357 129 132 3 507.60 2.96 358 129 133 4 507.60 2.96 359 130 133 3 521.92 4.20 360 130 134 4 508.22 2.65 361 131 134 3 511.50 2.27 362 131 135 4 494.31 6.32 363 132 135 3 508.73 0.89 364 132 136 4 494.45 6.25 365 133 136 3 499.00 3.97 366 133 137 4 496.19 5.38 367 134 137 3 504.09 1.43 368 134 138 4 504.07 1.43 369 135 138 3 504.31 1.30 370 135 139 4 504.05 1.42 371 136 139 3 504.06 1.41 372 136 140 4 491.65 4.83 373 137 140 3 502.05 2.41 374 137 141 4 490.03 5.63 375 138 141 3 508.94 1.14 376 138 142 4 501.12 0.09 377 139 142 3 506.31 2.46 378 139 143 4 501.11 0.08 379 140 143 3 505.93 2.27 380 140 144 4 501.15 0.04 381 141 144 3 511.32 0.43 382 141 145 4 501.28 0.04 383 142 145 3 504.92 1.79 384 142 146 4 499.33 1.02 385 143 146 3 507.18 2.38 386 143 147 4 506.65 2.64 387 143 152 9 244.36 3.04 388 144 147 3 517.87 2.52 389 144 148 4 506.64 2.64 390 145 148 3 506.85 2.99 391 145 149 4 500.04 0.41 392 146 149 3 512.50 0.17 393 146 150 4 500.93 0.03 394 146 151 5 440.19 10.14 395 146 152 6 274.06 2.52 396 147 150 3 500.98 0.05 397 147 151 4 480.92 0.72 398 147 152 5 274.28 2.41