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 5 484.44 2.37 2 2 10 8 460.40 3.83 3 2 130 128 47.41 0.09 4 2 133 131 38.62 2.23 5 2 134 132 33.98 0.12 6 2 137 135 33.05 0.58 7 3 6 3 509.00 0.64 8 3 7 4 514.42 2.05 9 4 7 3 515.20 1.67 10 4 8 4 514.44 2.05 11 4 79 75 56.67 1.45 12 5 8 3 515.76 2.69 13 5 9 4 514.66 1.94 14 6 9 3 516.01 2.62 15 6 10 4 514.65 1.94 16 6 130 124 62.33 0.43 17 6 133 127 62.34 0.43 18 7 10 3 515.98 2.60 19 7 11 4 511.47 0.35 20 7 76 69 62.37 0.46 21 7 79 72 62.34 0.44 22 7 80 73 66.31 1.52 23 7 134 127 62.40 0.45 24 7 137 130 62.40 0.45 25 8 11 3 519.26 1.45 26 8 12 4 507.10 1.83 27 9 12 3 523.35 0.88 28 9 13 4 511.78 0.95 29 9 126 117 80.94 1.07 30 9 127 118 80.33 1.04 31 9 130 121 80.18 0.99 32 10 13 3 523.35 0.88 33 10 14 4 511.79 0.95 34 10 76 66 80.34 1.04 35 10 130 120 80.30 1.05 36 10 131 121 80.17 1.01 37 10 134 124 79.70 0.79 38 11 14 3 517.17 1.75 39 11 15 4 511.78 0.95 40 11 76 65 80.35 1.03 41 11 77 66 80.36 1.03 42 11 79 68 80.36 1.03 43 12 15 3 526.42 2.23 44 12 16 4 526.42 2.23 45 12 122 110 92.42 0.04 46 13 16 3 526.45 2.22 47 13 17 4 512.66 1.06 48 13 115 102 92.30 0.01 49 13 119 106 92.56 0.03 50 13 122 109 92.50 0.01 51 13 123 110 92.42 0.04 52 13 131 118 91.39 0.23 53 14 17 3 513.72 0.54 54 14 18 4 512.66 1.05 55 14 69 55 92.08 0.09 56 14 72 58 91.42 0.24 57 14 73 59 91.34 0.21 58 14 76 62 89.62 0.66 59 14 77 63 90.91 0.01 60 14 131 117 91.97 0.09 61 15 18 3 525.16 3.08 62 15 19 4 512.35 0.89 63 16 19 3 518.22 1.88 64 16 119 103 97.33 0.25 65 16 122 106 96.66 0.58 66 17 20 3 525.83 1.93 67 17 21 4 504.09 3.24 68 17 24 7 437.84 6.87 69 17 69 52 180.72 2.58 70 17 115 98 92.65 0.04 71 18 21 3 511.75 2.33 72 18 77 59 170.92 1.68 73 20 23 3 527.56 4.41 74 20 24 4 508.30 3.75 75 20 118 98 149.78 6.62 76 21 24 3 524.90 0.09 77 21 25 4 508.33 3.73 78 21 66 45 187.12 2.23 79 21 69 48 184.22 3.08 80 22 25 3 508.66 3.86 81 22 26 4 508.36 3.71 82 22 62 40 188.82 1.39 83 22 66 44 187.15 2.22 84 23 26 3 523.64 0.85 85 23 27 4 518.92 3.21 86 23 118 95 163.65 0.09 87 24 27 3 523.58 0.88 88 24 28 4 504.75 1.88 89 24 69 45 187.15 2.23 90 24 114 90 164.63 0.01 91 24 115 91 164.63 0.01 92 24 118 94 163.69 0.07 93 24 119 95 163.74 0.07 94 25 28 3 519.55 2.29 95 25 29 4 508.19 0.16 96 25 65 40 187.16 2.21 97 25 69 44 187.15 2.23 98 26 29 3 519.11 0.70 99 26 30 4 504.75 1.88 100 26 61 35 189.09 1.52 101 26 62 36 188.90 1.42 102 27 30 3 519.09 0.71 103 27 31 4 502.45 3.01 104 27 114 87 164.65 0.01 105 27 118 91 164.03 0.20 106 28 31 3 520.79 0.14 107 28 32 4 502.09 3.20 108 28 69 41 188.88 1.41 109 28 107 79 165.56 0.04 110 28 110 82 165.33 0.01 111 28 111 83 165.12 0.06 112 28 114 86 164.78 0.06 113 29 32 3 519.59 0.47 114 29 33 4 501.94 3.12 115 29 61 32 189.22 1.46 116 29 64 35 189.21 1.47 117 29 65 36 188.97 1.38 118 29 107 78 165.57 0.05 119 30 33 3 534.86 3.24 120 30 34 4 503.57 2.38 121 30 52 22 222.39 2.19 122 30 55 25 220.88 1.44 123 30 56 26 220.99 1.50 124 30 61 31 214.43 0.49 125 31 34 3 514.81 1.94 126 31 35 4 504.49 4.85 127 31 110 79 165.41 0.01 128 31 113 82 165.31 0.02 129 32 35 3 514.81 1.94 130 32 36 4 497.91 1.60 131 32 39 7 417.97 31.12 132 32 106 74 165.59 0.06 133 32 107 75 165.59 0.06 134 32 110 78 165.41 0.01 135 33 36 3 512.56 0.82 136 33 37 4 478.12 3.83 137 33 39 6 389.19 6.75 138 33 40 7 344.17 0.23 139 33 43 10 344.50 0.39 140 33 46 13 260.27 5.51 141 33 55 22 233.84 2.98 142 33 61 28 222.93 2.44 143 34 37 3 522.10 0.32 144 34 52 18 227.41 0.26 145 36 39 3 525.24 3.00 146 36 106 70 166.53 0.35 147 37 40 3 521.78 1.27 148 38 41 3 525.71 0.69 149 38 103 65 166.96 0.44 150 38 106 68 166.91 0.44 151 39 42 3 528.69 1.17 152 39 43 4 519.91 2.21 153 39 103 64 166.78 0.46 154 39 106 67 166.72 0.42 155 40 43 3 522.00 1.02 156 40 46 6 315.24 5.24 157 40 47 7 273.67 0.81 158 40 49 9 273.19 1.05 159 40 55 15 254.21 4.99 160 41 47 6 312.35 6.68 161 42 97 55 167.40 0.41 162 42 98 56 167.41 0.41 163 42 99 57 167.29 0.39 164 42 100 58 167.38 0.40 165 42 103 61 166.94 0.46 166 43 46 3 524.33 6.59 167 43 47 4 491.53 5.79 168 43 64 21 235.85 3.91 169 44 47 3 524.22 1.36 170 45 48 3 606.06 0.26 171 45 60 15 237.30 3.48 172 45 63 18 236.15 4.05 173 46 49 3 528.35 0.71 174 46 60 14 236.14 4.05 175 46 61 15 236.09 4.03 176 46 64 18 236.09 4.03 177 49 54 5 480.69 1.18 178 49 55 6 344.17 8.53 179 49 58 9 289.49 0.38 180 49 61 12 278.73 5.71 181 50 54 4 507.18 0.17 182 51 54 3 509.65 1.40 183 51 55 4 514.13 3.64 184 52 55 3 515.04 3.19 185 52 56 4 514.13 3.64 186 53 56 3 516.89 2.27 187 53 57 4 514.13 3.64 188 54 57 3 517.17 2.14 189 54 58 4 507.20 0.18 190 55 58 3 517.17 2.14 191 55 61 6 406.13 6.96 192 58 61 3 508.12 0.37 193 58 62 4 509.27 4.05 194 59 62 3 515.83 0.78 195 59 63 4 502.90 7.24 196 60 63 3 515.26 1.07 197 60 64 4 513.69 0.29 198 61 64 3 517.60 0.11 199 61 65 4 505.75 2.77 200 62 65 3 516.12 0.85 201 62 66 4 508.17 1.57 202 63 66 3 526.88 0.35 203 63 67 4 508.16 1.57 204 64 67 3 508.61 4.60 205 64 68 4 506.50 3.35 206 65 68 3 516.55 0.62 207 65 69 4 506.51 3.35 208 66 69 3 529.61 3.54 209 66 70 4 497.00 0.03 210 67 70 3 521.92 0.30 211 67 71 4 512.08 4.62 212 68 71 3 521.91 0.30 213 68 72 4 503.05 1.59 214 68 107 39 165.56 0.04 215 69 72 3 507.19 2.16 216 69 73 4 503.67 1.91 217 70 73 3 517.71 0.92 218 70 74 4 506.48 0.96 219 71 74 3 519.70 3.84 220 71 75 4 511.84 0.10 221 72 75 3 515.13 1.41 222 72 76 4 507.10 2.71 223 72 111 39 165.38 0.00 224 72 135 63 162.97 0.04 225 72 138 66 162.16 0.28 226 73 76 3 516.61 1.45 227 73 77 4 506.26 3.14 228 74 77 3 517.46 1.88 229 74 78 4 510.05 1.82 230 75 78 3 528.38 1.07 231 75 82 7 240.71 2.18 232 75 85 10 193.34 6.12 233 75 89 14 186.88 2.89 234 75 138 63 162.56 0.09 235 76 79 3 523.13 3.70 236 76 134 58 163.10 0.09 237 78 81 3 511.57 3.13 238 78 82 4 391.75 41.03 239 78 85 7 284.11 2.26 240 80 137 57 163.12 0.06 241 82 85 3 517.01 1.80 242 82 86 4 505.30 0.43 243 82 137 55 163.17 0.08 244 82 141 59 162.12 0.19 245 83 86 3 520.50 5.17 246 83 87 4 507.37 0.16 247 83 145 62 161.50 0.14 248 84 88 4 524.89 0.60 249 85 88 3 551.18 0.94 250 85 89 4 520.07 3.02 251 86 89 3 520.45 2.83 252 86 90 4 515.88 0.93 253 86 138 52 162.71 0.05 254 86 141 55 162.15 0.27 255 86 142 56 161.60 0.10 256 87 90 3 527.35 0.62 257 87 91 4 522.33 4.19 258 87 145 58 161.00 0.35 259 88 91 3 526.66 2.02 260 88 92 4 506.74 0.12 261 89 92 3 527.71 2.77 262 89 93 4 506.67 0.14 263 89 138 49 162.71 0.06 264 89 142 53 161.57 0.10 265 90 93 3 524.14 4.54 266 90 94 4 506.66 0.15 267 90 142 52 161.18 0.27 268 90 145 55 153.81 0.09 269 90 146 56 152.93 0.51 270 91 94 3 524.14 4.54 271 91 95 4 508.44 1.76 272 91 149 58 146.06 1.33 273 92 95 3 530.89 4.42 274 92 96 4 459.44 12.04 275 92 97 5 427.76 9.98 276 93 97 4 407.73 0.04 277 93 98 5 379.04 14.38 278 93 99 6 296.57 9.19 279 93 146 53 152.94 0.52 280 94 98 4 334.72 7.79 281 94 146 52 149.80 0.16 282 94 149 55 143.67 0.62 283 94 151 57 58.55 1.99 284 95 149 54 147.26 0.98 285 95 151 56 124.50 0.64 286 99 103 4 511.01 1.27 287 99 104 5 505.82 0.81 288 99 146 47 149.72 0.12 289 100 103 3 526.20 1.07 290 100 104 4 511.01 1.27 291 101 104 3 511.02 1.27 292 101 105 4 511.00 1.27 293 101 139 38 161.60 0.15 294 101 142 41 160.71 0.28 295 101 143 42 156.27 0.07 296 101 146 45 147.80 0.70 297 102 105 3 511.01 1.27 298 102 106 4 506.37 1.05 299 103 106 3 507.98 0.27 300 103 107 4 505.84 0.80 301 104 107 3 514.72 3.64 302 104 108 4 506.29 0.42 303 104 139 35 161.60 0.15 304 104 142 38 160.47 0.15 305 105 108 3 513.40 3.15 306 105 109 4 507.77 0.33 307 105 139 34 161.61 0.15 308 106 109 3 518.14 1.01 309 106 110 4 509.56 1.32 310 107 110 3 513.86 3.15 311 107 111 4 509.58 1.33 312 108 111 3 514.95 0.17 313 108 112 4 511.16 2.12 314 108 135 27 162.29 0.27 315 108 139 31 161.65 0.14 316 109 112 3 515.00 0.20 317 109 113 4 509.40 1.41 318 110 113 3 512.68 1.35 319 110 114 4 509.37 1.40 320 111 114 3 521.32 5.67 321 111 115 4 510.98 2.21 322 111 135 24 162.29 0.27 323 112 115 3 519.70 6.49 324 112 116 4 509.32 1.38 325 112 123 11 262.04 7.42 326 112 128 16 163.15 0.04 327 112 131 19 162.97 0.04 328 112 132 20 162.99 0.04 329 112 135 23 162.35 0.27 330 113 116 3 529.11 1.78 331 113 117 4 508.23 1.93 332 114 117 3 509.41 1.34 333 114 118 4 504.10 0.14 334 115 118 3 523.58 1.93 335 115 119 4 488.71 1.12 336 115 123 8 267.38 4.76 337 115 131 16 176.30 6.54 338 116 120 4 468.38 4.97 339 116 123 7 267.38 4.76 340 117 120 3 536.66 2.58 341 119 122 3 519.07 4.17 342 119 123 4 456.13 3.29 343 120 123 3 506.02 2.35 344 122 127 5 480.23 2.74 345 123 127 4 480.33 2.69 346 123 128 5 480.34 2.69 347 123 131 8 456.12 9.30 348 124 127 3 512.21 2.71 349 124 128 4 499.76 2.23 350 125 128 3 505.26 0.53 351 125 129 4 506.26 1.02 352 126 129 3 518.65 2.85 353 126 130 4 507.16 0.80 354 127 130 3 507.43 0.94 355 127 131 4 507.16 0.80 356 128 131 3 516.36 3.53 357 128 132 4 501.41 3.70 358 129 132 3 528.06 2.33 359 129 133 4 507.17 0.82 360 130 133 3 507.16 0.83 361 130 134 4 501.44 3.68 362 131 134 3 506.51 1.14 363 131 135 4 505.25 1.77 364 132 135 3 516.39 3.69 365 132 136 4 495.33 0.63 366 133 136 3 520.17 1.79 367 133 137 4 487.76 3.52 368 134 137 3 511.22 3.49 369 134 138 4 491.92 5.30 370 135 138 3 506.44 1.10 371 135 139 4 514.24 4.16 372 136 139 3 515.85 3.35 373 136 140 4 516.02 3.27 374 137 140 3 517.26 3.89 375 137 141 4 516.03 3.27 376 138 141 3 517.28 3.88 377 138 142 4 516.06 3.25 378 139 142 3 517.29 3.87 379 139 143 4 509.01 0.29 380 140 143 3 525.32 0.10 381 140 144 4 511.00 0.70 382 141 144 3 521.26 1.12 383 141 145 4 515.02 1.28 384 142 145 3 520.09 1.25 385 142 146 4 511.03 0.71 386 143 146 3 515.73 3.06 387 143 147 4 510.84 0.81 388 143 152 9 235.64 15.22 389 144 147 3 511.01 0.89 390 144 148 4 510.97 0.88 391 145 148 3 513.96 3.88 392 145 149 4 504.28 4.22 393 146 149 3 514.48 4.09 394 146 150 4 500.52 2.34 395 146 151 5 354.61 1.33 396 146 152 6 287.41 5.67 397 147 150 3 509.25 6.71 398 147 152 5 283.81 17.68