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 8 471.94 2.27 2 2 130 128 47.80 0.22 3 2 133 131 38.13 2.62 4 2 134 132 32.33 0.97 5 2 137 135 32.30 0.98 6 3 6 3 514.98 1.62 7 3 7 4 513.50 2.37 8 4 7 3 517.48 2.88 9 4 8 4 513.71 2.25 10 4 79 75 57.91 2.59 11 5 8 3 513.71 2.25 12 5 9 4 513.71 2.25 13 6 9 3 527.40 4.26 14 6 10 4 513.69 2.25 15 6 130 124 71.53 0.56 16 6 133 127 71.53 0.56 17 7 10 3 510.62 0.46 18 7 11 4 506.77 2.38 19 7 76 69 72.08 0.82 20 7 79 72 72.08 0.82 21 7 80 73 72.09 0.82 22 7 134 127 72.06 0.82 23 7 137 130 72.14 0.84 24 8 11 3 524.62 2.87 25 8 12 4 506.77 2.38 26 9 12 3 526.83 1.76 27 9 13 4 518.32 2.49 28 9 126 117 83.21 0.86 29 9 127 118 83.11 0.83 30 9 130 121 83.11 0.83 31 10 13 3 529.67 0.34 32 10 14 4 513.74 0.02 33 10 76 66 83.11 0.83 34 10 130 120 83.11 0.83 35 10 131 121 83.11 0.83 36 10 134 124 82.98 0.78 37 11 14 3 515.64 0.96 38 11 15 4 513.73 0.01 39 11 76 65 83.14 0.81 40 11 77 66 83.14 0.82 41 11 79 68 83.15 0.81 42 12 15 3 521.42 3.85 43 12 16 4 513.75 0.02 44 12 122 110 94.92 0.32 45 13 16 3 521.69 3.98 46 13 17 4 509.67 2.02 47 13 115 102 91.48 1.01 48 13 119 106 95.97 0.12 49 13 122 109 94.92 0.32 50 13 123 110 94.84 0.35 51 13 131 118 89.73 1.24 52 14 17 3 517.90 0.70 53 14 18 4 510.04 4.63 54 14 69 55 90.95 1.52 55 14 72 58 89.91 1.21 56 14 73 59 89.70 1.29 57 14 76 62 89.70 1.30 58 14 77 63 89.71 1.30 59 15 18 3 511.90 3.70 60 15 19 4 516.46 1.42 61 16 19 3 518.95 0.18 62 16 24 8 434.34 11.33 63 16 119 103 99.68 0.93 64 16 122 106 98.84 1.31 65 17 20 3 525.54 2.05 66 17 21 4 492.94 3.79 67 17 24 7 433.28 10.80 68 17 69 52 175.15 0.47 69 17 115 98 98.85 1.32 70 18 21 3 515.44 1.58 71 18 77 59 97.39 1.13 72 20 23 3 520.04 0.97 73 20 24 4 510.15 3.96 74 20 118 98 134.66 1.04 75 21 24 3 516.85 0.61 76 21 25 4 512.65 0.97 77 21 66 45 178.12 0.04 78 21 69 48 177.27 0.39 79 22 25 3 515.60 1.24 80 22 26 4 512.66 0.97 81 22 62 40 179.48 0.05 82 22 66 44 178.09 0.02 83 23 26 3 513.88 0.37 84 23 27 4 512.65 0.96 85 23 118 95 166.49 0.68 86 24 27 3 522.36 4.61 87 24 28 4 512.27 0.78 88 24 69 45 178.18 0.07 89 24 114 90 167.87 0.27 90 24 115 91 167.86 0.27 91 24 118 94 167.58 0.13 92 24 119 95 167.59 0.13 93 25 28 3 515.91 1.40 94 25 29 4 511.78 0.67 95 25 65 40 178.17 0.06 96 25 69 44 178.18 0.07 97 26 29 3 516.38 1.09 98 26 30 4 511.43 0.49 99 26 56 30 212.59 0.73 100 26 62 36 179.78 0.13 101 27 30 3 519.38 1.05 102 27 31 4 507.30 2.58 103 27 114 87 168.16 0.12 104 27 118 91 167.88 0.00 105 28 31 3 513.34 0.43 106 28 32 4 507.29 2.56 107 28 69 41 179.16 0.16 108 28 107 79 168.74 0.07 109 28 110 82 168.45 0.04 110 28 111 83 168.37 0.04 111 28 114 86 168.18 0.12 112 29 32 3 508.97 1.75 113 29 33 4 502.26 5.08 114 29 61 32 194.72 0.36 115 29 64 35 186.56 1.43 116 29 65 36 179.74 0.06 117 29 107 78 168.84 0.05 118 30 33 3 517.39 1.60 119 30 34 4 506.59 2.92 120 30 52 22 218.28 0.68 121 30 55 25 214.93 0.42 122 30 56 26 215.61 0.20 123 30 61 31 208.15 1.14 124 31 34 3 518.12 1.24 125 31 35 4 499.23 5.62 126 31 110 79 168.60 0.12 127 31 113 82 168.41 0.09 128 31 114 83 168.45 0.18 129 32 35 3 513.30 0.43 130 32 36 4 504.74 2.87 131 32 39 7 368.91 15.43 132 32 106 74 168.91 0.04 133 32 107 75 168.85 0.06 134 32 110 78 168.59 0.14 135 33 36 3 518.68 0.12 136 33 37 4 460.38 2.38 137 33 39 6 385.61 23.78 138 33 40 7 330.24 15.96 139 33 43 10 297.72 1.95 140 33 46 13 254.22 2.50 141 33 55 22 218.41 0.65 142 33 61 28 218.38 0.65 143 34 37 3 520.54 1.05 144 34 52 18 221.15 1.08 145 36 39 3 526.64 4.42 146 36 106 70 169.08 0.03 147 37 40 3 512.51 0.84 148 38 41 3 512.52 0.84 149 38 103 65 169.84 0.04 150 38 106 68 169.28 0.05 151 39 42 3 522.95 4.87 152 39 43 4 520.38 4.52 153 39 103 64 169.25 0.07 154 39 106 67 169.09 0.03 155 40 43 3 524.56 1.13 156 40 46 6 379.53 10.61 157 40 47 7 344.43 28.12 158 40 49 9 271.69 3.81 159 40 55 15 237.83 0.96 160 41 47 6 305.06 4.59 161 42 97 55 170.50 0.29 162 42 98 56 170.49 0.29 163 42 99 57 170.34 0.27 164 42 100 58 170.38 0.26 165 42 103 61 170.19 0.20 166 43 46 3 524.02 1.36 167 43 47 4 496.25 5.50 168 43 64 21 228.19 4.30 169 44 47 3 526.92 1.27 170 45 48 3 597.94 1.47 171 45 60 15 228.46 4.38 172 45 64 19 228.37 4.35 173 46 49 3 534.37 0.52 174 46 60 14 228.46 4.38 175 46 61 15 228.40 4.34 176 46 64 18 228.32 4.33 177 49 54 5 401.66 16.02 178 49 55 6 346.62 9.95 179 49 58 9 272.74 7.85 180 49 61 12 252.96 1.21 181 50 54 4 499.07 3.58 182 51 54 3 500.45 0.72 183 51 55 4 488.31 1.81 184 52 55 3 502.08 1.54 185 52 56 4 495.18 1.62 186 53 56 3 512.21 2.36 187 53 57 4 499.87 0.45 188 54 57 3 509.54 1.03 189 54 58 4 500.31 0.68 190 55 58 3 520.74 0.78 191 55 61 6 396.84 4.67 192 58 61 3 522.40 2.83 193 58 62 4 505.47 2.23 194 59 62 3 509.86 0.70 195 59 63 4 503.94 2.99 196 60 63 3 504.61 3.32 197 60 64 4 504.61 3.32 198 61 64 3 525.56 0.89 199 61 65 4 504.57 3.33 200 62 65 3 503.56 2.54 201 62 66 4 503.56 2.54 202 63 66 3 513.84 1.37 203 63 67 4 510.97 1.18 204 64 67 3 510.98 1.17 205 64 68 4 510.96 1.18 206 65 68 3 521.95 5.88 207 65 69 4 511.75 0.78 208 66 69 3 521.96 5.87 209 66 70 4 510.90 1.19 210 67 70 3 518.25 2.48 211 67 71 4 511.75 0.77 212 68 71 3 522.88 2.28 213 68 72 4 505.91 1.30 214 68 107 39 168.94 0.04 215 69 72 3 523.45 0.12 216 69 73 4 509.26 0.90 217 70 73 3 518.55 3.75 218 70 74 4 509.31 0.88 219 71 74 3 518.85 2.50 220 71 75 4 512.24 0.58 221 72 75 3 520.58 1.63 222 72 76 4 512.25 0.59 223 72 111 39 168.90 0.07 224 72 135 63 166.33 0.31 225 72 138 66 165.78 0.30 226 73 76 3 517.88 2.01 227 73 77 4 512.60 0.42 228 74 77 3 515.52 0.91 229 74 78 4 513.14 0.28 230 75 78 3 536.54 0.48 231 75 79 4 518.55 2.98 232 75 82 7 252.08 1.16 233 75 85 10 178.70 4.36 234 75 89 14 178.72 4.36 235 75 138 63 165.86 0.29 236 76 79 3 532.14 1.73 237 76 134 58 166.56 0.42 238 78 81 3 511.44 0.15 239 78 82 4 438.55 4.63 240 78 85 7 361.45 24.21 241 80 137 57 166.70 0.39 242 82 85 3 521.38 0.33 243 82 86 4 509.05 1.37 244 82 137 55 166.72 0.38 245 82 141 59 165.78 0.32 246 83 86 3 516.08 0.26 247 83 87 4 510.35 1.82 248 84 88 4 523.83 0.14 249 85 88 3 543.65 0.02 250 85 89 4 521.71 1.01 251 86 89 3 528.82 2.52 252 86 90 4 521.71 1.01 253 86 138 52 166.10 0.24 254 86 141 55 165.69 0.30 255 86 142 56 162.99 0.29 256 86 145 59 161.40 0.57 257 87 90 3 522.41 0.86 258 87 91 4 521.71 1.01 259 87 145 58 159.74 0.10 260 88 91 3 517.99 0.86 261 88 92 4 517.98 0.86 262 89 92 3 518.97 0.37 263 89 93 4 512.41 1.92 264 89 138 49 166.03 0.27 265 89 142 53 162.22 0.68 266 90 93 3 513.40 2.42 267 90 94 4 512.41 1.92 268 90 142 52 161.72 0.71 269 90 145 55 156.13 0.09 270 90 146 56 155.63 0.14 271 91 94 3 515.85 0.19 272 91 95 4 505.51 0.70 273 91 149 58 150.88 0.30 274 92 95 3 526.84 5.31 275 92 96 4 480.77 4.79 276 92 97 5 463.08 13.61 277 93 97 4 445.17 4.65 278 93 98 5 398.09 28.18 279 93 99 6 369.50 42.45 280 93 146 53 154.66 0.58 281 94 98 4 419.37 17.53 282 94 146 52 154.00 0.29 283 94 149 55 145.96 1.34 284 94 151 57 95.60 3.23 285 95 98 3 516.03 0.09 286 95 149 54 150.85 0.33 287 95 151 56 119.23 2.16 288 98 151 53 108.34 3.13 289 99 103 4 512.39 0.48 290 99 104 5 512.38 0.49 291 99 146 47 153.58 0.50 292 99 153 54 36.25 0.45 293 100 103 3 521.73 0.46 294 100 104 4 514.79 0.71 295 100 153 53 26.52 2.32 296 101 104 3 522.21 3.00 297 101 105 4 512.45 0.46 298 101 142 41 161.58 0.84 299 101 143 42 157.46 0.83 300 101 146 45 152.57 0.98 301 101 153 52 26.06 2.34 302 102 105 3 521.51 3.35 303 102 106 4 512.45 0.47 304 103 106 3 517.73 3.10 305 103 107 4 512.46 0.47 306 104 107 3 525.83 1.12 307 104 108 4 505.06 0.94 308 104 139 35 162.60 0.51 309 104 142 38 159.68 0.07 310 105 108 3 519.48 4.29 311 105 109 4 508.91 0.99 312 105 139 34 162.61 0.51 313 106 109 3 508.73 1.08 314 106 110 4 502.54 0.12 315 107 110 3 510.75 1.27 316 107 111 4 503.23 0.21 317 108 111 3 511.23 1.51 318 108 112 4 503.93 2.14 319 108 135 27 165.56 0.18 320 108 139 31 162.60 0.51 321 109 112 3 512.67 0.30 322 109 113 4 503.98 1.55 323 110 113 3 507.41 3.20 324 110 114 4 503.99 1.55 325 111 114 3 508.27 2.69 326 111 115 4 498.81 1.04 327 111 135 24 165.56 0.18 328 112 115 3 511.85 0.89 329 112 116 4 505.90 2.10 330 112 123 11 299.53 1.24 331 112 128 16 166.37 0.33 332 112 131 19 166.03 0.40 333 112 132 20 166.00 0.39 334 112 135 23 165.61 0.20 335 113 116 3 515.25 2.58 336 113 117 4 510.09 0.00 337 114 117 3 512.43 1.17 338 114 118 4 505.90 2.09 339 115 118 3 522.61 3.12 340 115 119 4 498.51 0.93 341 115 123 8 316.94 9.94 342 115 131 16 187.93 0.70 343 116 119 3 527.86 0.15 344 116 120 4 498.50 0.93 345 116 123 7 316.94 9.94 346 117 120 3 542.95 1.62 347 119 122 3 523.53 8.29 348 119 123 4 479.94 5.16 349 120 123 3 490.75 1.94 350 120 124 4 479.94 5.16 351 122 127 5 484.72 2.54 352 123 127 4 487.78 4.07 353 123 128 5 484.73 2.53 354 123 131 8 439.87 3.71 355 124 127 3 514.49 1.19 356 124 128 4 499.85 2.73 357 125 128 3 508.56 0.15 358 125 129 4 501.32 3.46 359 126 129 3 511.11 1.42 360 126 130 4 501.34 3.46 361 127 130 3 517.31 1.29 362 127 131 4 499.87 2.73 363 128 131 3 515.00 0.14 364 128 132 4 504.87 5.22 365 129 132 3 512.11 1.60 366 129 133 4 509.53 2.89 367 130 133 3 516.75 0.03 368 130 134 4 512.34 1.48 369 131 134 3 516.75 0.03 370 131 135 4 510.80 2.25 371 132 135 3 511.04 2.83 372 132 136 4 500.18 3.06 373 133 136 3 507.37 0.99 374 133 137 4 506.04 0.12 375 134 137 3 505.58 0.10 376 134 138 4 505.59 0.10 377 135 138 3 505.58 0.11 378 135 139 4 506.38 0.51 379 136 139 3 510.72 1.65 380 136 140 4 500.10 2.84 381 137 140 3 517.06 1.09 382 137 141 4 500.55 2.86 383 138 141 3 519.14 0.06 384 138 142 4 504.12 1.07 385 139 142 3 508.63 2.37 386 139 143 4 505.75 1.88 387 140 143 3 515.20 2.85 388 140 144 4 505.76 1.88 389 141 144 3 511.80 1.14 390 141 145 4 507.98 0.78 391 142 145 3 512.74 1.60 392 142 146 4 505.76 1.89 393 143 146 3 507.22 1.16 394 143 147 4 504.98 1.47 395 143 152 9 234.50 14.71 396 144 147 3 513.87 3.82 397 144 148 4 504.37 1.16 398 145 148 3 518.68 1.26 399 145 149 4 508.70 1.01 400 146 149 3 514.75 1.03 401 146 150 4 508.70 1.01 402 146 151 5 363.53 30.72 403 146 152 6 265.56 23.97 404 146 153 7 253.37 6.21 405 147 150 3 508.70 1.00 406 147 152 5 253.27 6.21