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 5 486.13 3.61 2 2 10 8 460.32 4.54 3 2 130 128 44.29 0.12 4 2 133 131 36.93 0.53 5 2 134 132 33.65 0.98 6 2 137 135 33.64 0.98 7 3 6 3 511.65 2.85 8 3 7 4 501.10 10.04 9 4 7 3 517.07 2.06 10 4 8 4 500.13 0.07 11 4 79 75 57.36 3.24 12 5 8 3 519.65 0.77 13 5 9 4 510.85 5.17 14 6 9 3 517.26 1.96 15 6 10 4 510.08 5.55 16 6 130 124 66.42 1.97 17 6 133 127 66.42 1.97 18 7 10 3 505.24 3.78 19 7 11 4 502.57 5.06 20 7 76 69 66.51 1.92 21 7 79 72 66.52 1.92 22 7 80 73 66.53 1.93 23 7 134 127 66.52 1.94 24 7 137 130 66.53 1.93 25 8 11 3 519.30 2.97 26 8 12 4 510.12 1.31 27 9 12 3 526.57 0.67 28 9 13 4 510.44 1.21 29 9 126 117 82.60 0.24 30 9 127 118 82.15 0.14 31 9 130 121 82.13 0.14 32 10 13 3 526.57 0.67 33 10 14 4 513.09 0.14 34 10 76 66 82.29 0.24 35 10 130 120 82.16 0.14 36 10 131 121 82.14 0.14 37 10 134 124 82.08 0.17 38 11 14 3 522.45 2.73 39 11 15 4 515.53 0.85 40 11 76 65 82.36 0.21 41 11 77 66 82.37 0.21 42 11 79 68 82.35 0.22 43 12 15 3 532.36 0.76 44 12 16 4 525.42 4.22 45 13 16 3 534.77 0.45 46 13 17 4 525.42 4.22 47 13 115 102 90.48 0.67 48 13 123 110 90.48 0.67 49 13 127 114 88.06 1.75 50 13 131 118 87.67 1.62 51 14 17 3 518.94 0.85 52 14 18 4 516.68 0.27 53 14 69 55 131.87 23.66 54 14 72 58 87.69 1.62 55 14 73 59 87.63 1.64 56 14 76 62 87.63 1.64 57 14 77 63 87.64 1.65 58 14 131 117 88.14 1.79 59 15 18 3 525.71 0.27 60 15 19 4 522.46 2.71 61 16 19 3 527.06 0.42 62 16 24 8 454.05 4.45 63 16 119 103 100.61 2.54 64 16 122 106 100.61 2.54 65 17 20 3 527.06 0.42 66 17 21 4 510.84 8.52 67 17 24 7 433.01 4.22 68 17 69 52 181.81 0.24 69 17 115 98 95.75 0.13 70 18 21 3 522.14 2.88 71 18 77 59 132.25 19.61 72 20 23 3 524.09 3.95 73 20 24 4 515.21 0.58 74 20 118 98 137.08 0.46 75 21 24 3 519.94 1.06 76 21 25 4 515.21 0.58 77 21 66 45 184.33 1.20 78 21 69 48 184.15 1.17 79 22 25 3 518.62 0.42 80 22 26 4 515.21 0.58 81 22 62 40 185.10 1.04 82 22 66 44 184.34 1.21 83 23 26 3 517.10 0.35 84 23 27 4 516.44 0.03 85 23 118 95 165.60 0.20 86 24 27 3 516.45 0.03 87 24 28 4 516.45 0.03 88 24 69 45 184.33 1.21 89 24 114 90 162.50 1.00 90 24 115 91 167.09 1.33 91 24 118 94 167.10 0.09 92 24 119 95 167.93 0.18 93 25 28 3 516.45 0.03 94 25 29 4 516.45 0.03 95 25 65 40 184.88 1.08 96 25 69 44 184.33 1.21 97 26 29 3 528.83 3.42 98 26 30 4 508.26 2.52 99 26 56 30 214.36 0.72 100 26 62 36 185.16 1.01 101 27 30 3 521.38 3.06 102 27 31 4 509.82 3.27 103 27 114 87 170.26 0.18 104 27 118 91 170.14 0.15 105 28 31 3 514.54 0.92 106 28 32 4 509.85 3.27 107 28 69 41 185.18 1.03 108 28 107 79 171.03 0.12 109 28 110 82 170.91 0.11 110 28 111 83 170.74 0.04 111 28 114 86 170.33 0.15 112 29 32 3 514.54 0.93 113 29 33 4 512.36 2.02 114 29 61 32 194.94 1.75 115 29 64 35 188.08 1.17 116 29 65 36 186.52 1.63 117 29 107 78 171.03 0.12 118 30 33 3 521.34 2.57 119 30 34 4 505.12 5.63 120 30 52 22 218.18 2.61 121 30 55 25 214.46 0.75 122 30 56 26 218.05 2.54 123 30 61 31 212.22 0.36 124 31 34 3 516.25 0.07 125 31 35 4 510.07 3.15 126 31 110 79 170.91 0.12 127 31 113 82 170.85 0.14 128 31 114 83 170.56 0.28 129 32 35 3 523.19 1.14 130 32 36 4 497.45 1.84 131 32 39 7 432.93 9.69 132 32 106 74 171.06 0.12 133 32 107 75 171.05 0.12 134 32 110 78 170.92 0.12 135 33 36 3 518.53 1.20 136 33 37 4 475.42 9.76 137 33 39 6 406.88 3.33 138 33 40 7 341.23 10.81 139 33 43 10 317.89 2.21 140 33 55 22 223.40 0.00 141 33 61 28 223.22 0.01 142 34 37 3 521.46 0.27 143 36 39 3 524.39 0.69 144 36 106 70 171.13 0.10 145 37 40 3 523.39 1.10 146 38 41 3 523.39 1.10 147 38 103 65 171.34 0.14 148 38 106 68 171.31 0.13 149 39 42 3 529.02 0.47 150 39 43 4 522.76 3.60 151 39 103 64 171.25 0.13 152 39 106 67 171.19 0.10 153 40 43 3 519.44 1.94 154 40 46 6 377.86 18.11 155 40 47 7 306.14 0.04 156 40 49 9 292.22 1.52 157 40 55 15 246.73 0.68 158 42 97 55 172.09 0.10 159 42 98 56 172.09 0.09 160 42 99 57 171.97 0.05 161 42 100 58 172.03 0.07 162 42 103 61 171.69 0.04 163 43 46 3 519.12 0.26 164 43 47 4 498.10 0.23 165 43 64 21 245.41 0.65 166 44 47 3 529.27 2.89 167 45 48 3 584.39 1.86 168 45 60 15 246.11 0.91 169 45 63 18 246.06 0.93 170 45 64 19 245.94 0.88 171 46 49 3 545.35 1.17 172 46 60 14 246.09 0.89 173 46 61 15 245.96 0.88 174 46 64 18 245.96 0.90 175 47 50 3 550.26 3.38 176 48 54 6 502.25 4.52 177 49 54 5 478.75 16.11 178 49 55 6 452.22 12.44 179 49 58 9 294.48 0.58 180 49 61 12 272.33 4.57 181 50 54 4 515.40 2.04 182 51 54 3 515.40 2.03 183 51 55 4 515.40 2.04 184 52 55 3 518.77 3.71 185 52 56 4 515.43 2.04 186 53 56 3 521.89 2.16 187 53 57 4 518.77 3.72 188 54 57 3 521.90 2.16 189 54 58 4 515.39 2.06 190 55 58 3 518.74 3.73 191 55 61 6 444.04 20.77 192 58 61 3 519.07 0.16 193 58 62 4 519.09 0.14 194 59 62 3 519.10 0.14 195 59 63 4 519.09 0.14 196 60 63 3 524.03 2.61 197 60 64 4 519.08 0.14 198 61 64 3 524.03 2.61 199 61 65 4 519.08 0.14 200 62 65 3 522.23 1.71 201 62 66 4 519.01 0.11 202 63 66 3 529.91 2.12 203 63 67 4 518.90 0.17 204 64 67 3 518.90 0.16 205 64 68 4 518.89 0.16 206 65 68 3 522.11 1.78 207 65 69 4 515.38 1.58 208 66 69 3 523.37 2.42 209 66 70 4 515.42 1.54 210 67 70 3 527.42 0.39 211 67 71 4 515.42 1.54 212 68 71 3 519.55 0.52 213 68 72 4 515.38 1.51 214 68 107 39 171.14 0.06 215 69 72 3 508.29 3.49 216 69 73 4 506.88 2.83 217 70 73 3 518.27 0.89 218 70 74 4 510.72 4.66 219 71 74 3 510.72 4.66 220 71 75 4 510.71 4.66 221 72 75 3 514.33 5.69 222 72 76 4 512.12 0.21 223 72 111 39 171.00 0.01 224 72 135 63 169.27 0.07 225 72 138 66 168.47 0.18 226 73 76 3 525.27 0.22 227 73 77 4 513.37 0.46 228 74 77 3 520.27 2.71 229 74 78 4 520.27 2.71 230 74 85 11 228.17 14.48 231 75 78 3 527.06 2.84 232 75 79 4 513.38 0.73 233 75 82 7 256.35 0.41 234 75 85 10 228.12 14.46 235 75 86 11 228.12 14.46 236 75 89 14 228.25 14.40 237 75 138 63 168.77 0.12 238 76 79 3 517.60 3.58 239 76 131 55 169.53 0.15 240 76 134 58 169.42 0.13 241 78 81 3 509.87 0.16 242 78 82 4 383.86 4.14 243 78 85 7 310.94 2.12 244 80 137 57 169.39 0.12 245 82 85 3 524.85 1.75 246 82 86 4 514.29 1.42 247 82 137 55 169.38 0.12 248 82 141 59 168.54 0.14 249 83 86 3 525.77 1.29 250 83 87 4 524.85 1.75 251 84 87 3 530.60 2.94 252 84 88 4 530.60 2.94 253 85 88 3 567.38 1.01 254 86 89 3 522.59 1.06 255 86 90 4 510.96 0.46 256 86 138 52 169.12 0.01 257 86 141 55 168.28 0.24 258 86 142 56 167.85 0.23 259 87 90 3 527.20 1.24 260 87 91 4 505.19 0.55 261 88 91 3 513.27 0.70 262 88 92 4 506.68 1.12 263 89 92 3 523.84 3.55 264 89 93 4 506.67 1.12 265 89 138 49 169.12 0.01 266 89 142 53 167.37 0.23 267 90 93 3 518.33 3.27 268 90 94 4 506.67 1.12 269 90 142 52 167.27 0.18 270 90 145 55 155.70 0.09 271 90 146 56 152.17 0.80 272 90 149 59 149.75 0.01 273 91 94 3 522.15 0.41 274 91 95 4 503.09 0.66 275 91 149 58 151.55 0.91 276 92 95 3 523.49 3.38 277 92 96 4 479.98 0.20 278 92 97 5 469.99 4.79 279 93 97 4 439.74 19.93 280 93 98 5 360.04 6.37 281 93 99 6 285.92 2.50 282 93 146 53 152.19 0.80 283 94 98 4 332.89 7.22 284 94 146 52 152.17 0.80 285 94 149 55 145.40 0.48 286 94 151 57 70.42 0.80 287 95 149 54 149.83 0.04 288 98 151 53 75.33 0.36 289 99 103 4 504.49 0.11 290 99 104 5 493.82 3.19 291 99 146 47 152.09 0.83 292 99 151 52 67.17 0.89 293 100 103 3 521.70 1.47 294 100 104 4 504.49 0.11 295 100 151 51 67.11 0.85 296 100 153 53 18.54 0.58 297 101 104 3 503.53 1.66 298 101 105 4 503.68 1.73 299 101 139 38 167.85 0.12 300 101 142 41 166.31 0.65 301 101 143 42 157.75 0.60 302 101 146 45 152.06 0.79 303 101 153 52 18.50 0.60 304 102 105 3 515.61 4.24 305 102 106 4 504.83 1.15 306 103 106 3 504.83 1.15 307 103 107 4 503.86 0.65 308 104 107 3 515.88 4.02 309 104 108 4 495.04 3.75 310 104 139 35 167.84 0.11 311 104 142 38 163.16 1.72 312 104 146 42 152.06 0.79 313 105 108 3 515.27 4.33 314 105 109 4 515.37 4.28 315 105 139 34 167.85 0.12 316 106 109 3 527.12 1.60 317 106 110 4 523.72 0.10 318 107 110 3 523.71 0.10 319 107 111 4 523.71 0.10 320 108 111 3 523.74 0.12 321 108 112 4 523.71 0.10 322 108 135 27 169.03 0.18 323 108 139 31 167.84 0.12 324 109 112 3 523.70 0.10 325 109 113 4 517.49 3.00 326 110 113 3 515.35 5.33 327 110 114 4 503.54 0.58 328 111 114 3 524.41 0.18 329 111 115 4 509.85 1.29 330 111 135 24 169.15 0.24 331 112 115 3 518.63 3.09 332 112 116 4 509.86 1.29 333 112 123 11 240.38 5.58 334 112 128 16 169.50 0.23 335 112 131 19 169.44 0.20 336 112 132 20 169.44 0.20 337 112 135 23 169.40 0.20 338 113 116 3 518.64 3.08 339 113 117 4 518.64 3.08 340 114 117 3 522.60 1.10 341 114 118 4 508.68 1.89 342 115 118 3 520.95 0.29 343 115 119 4 502.72 1.09 344 115 123 8 255.34 1.69 345 115 131 16 191.66 1.96 346 116 119 3 523.14 0.76 347 116 120 4 502.85 1.02 348 116 123 7 255.13 1.79 349 117 120 3 534.53 0.79 350 119 122 3 503.00 0.48 351 119 123 4 402.31 2.17 352 123 127 4 476.75 4.11 353 123 128 5 469.49 0.48 354 123 131 8 432.86 9.39 355 124 127 3 511.47 1.79 356 124 128 4 504.70 0.17 357 125 128 3 504.71 0.17 358 125 129 4 504.70 0.17 359 126 129 3 516.50 0.57 360 126 130 4 503.22 0.58 361 127 130 3 511.20 2.08 362 127 131 4 501.37 1.51 363 128 131 3 504.56 1.25 364 128 132 4 483.13 2.62 365 129 132 3 512.21 3.89 366 129 133 4 499.75 2.33 367 130 133 3 513.60 3.19 368 130 134 4 503.95 0.24 369 131 134 3 507.42 1.45 370 131 135 4 504.50 0.52 371 132 135 3 513.30 3.39 372 132 136 4 504.50 0.53 373 133 136 3 518.36 5.64 374 133 137 4 504.50 0.53 375 134 137 3 518.63 5.50 376 134 138 4 504.55 0.51 377 135 138 3 514.20 3.29 378 135 139 4 513.19 3.80 379 136 139 3 514.21 3.30 380 136 140 4 513.20 3.81 381 137 140 3 521.29 0.24 382 137 141 4 513.39 3.70 383 138 141 3 524.89 0.83 384 138 142 4 513.79 3.98 385 139 142 3 515.71 3.03 386 139 143 4 513.79 3.98 387 140 143 3 526.38 1.31 388 140 144 4 513.60 4.08 389 141 144 3 517.88 3.92 390 141 145 4 507.74 1.15 391 142 145 3 507.94 1.04 392 142 146 4 507.73 1.15 393 143 146 3 508.23 0.91 394 143 147 4 506.12 1.96 395 144 147 3 511.77 0.14 396 144 148 4 507.12 1.01 397 145 148 3 515.47 4.70 398 145 149 4 507.12 1.01 399 146 149 3 507.64 0.76 400 146 150 4 501.72 3.71 401 146 151 5 392.57 45.51 402 146 153 7 254.11 2.86 403 147 150 3 502.22 3.47