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 5 487.75 10.05 2 2 10 8 471.70 2.15 3 2 130 128 41.59 0.90 4 2 133 131 31.27 0.52 5 2 134 132 30.04 0.06 6 2 137 135 30.00 0.04 7 3 6 3 513.02 2.58 8 3 7 4 513.15 2.52 9 4 7 3 513.15 2.51 10 4 8 4 507.03 0.61 11 4 79 75 54.79 1.12 12 5 8 3 516.39 0.80 13 5 9 4 507.10 0.65 14 6 9 3 526.80 4.31 15 6 10 4 502.92 2.73 16 6 130 124 61.95 1.38 17 6 133 127 61.94 1.39 18 7 10 3 503.05 2.80 19 7 11 4 505.40 1.62 20 7 76 69 62.04 1.39 21 7 79 72 61.97 1.39 22 7 80 73 64.75 0.01 23 7 134 127 61.97 1.38 24 7 137 130 61.95 1.39 25 8 11 3 524.37 2.75 26 8 12 4 505.32 1.65 27 9 12 3 511.18 1.28 28 9 13 4 507.46 2.69 29 9 126 117 80.25 0.01 30 9 127 118 79.81 0.17 31 9 130 121 79.63 0.21 32 10 13 3 518.08 2.60 33 10 14 4 507.66 2.77 34 10 76 66 79.69 0.24 35 10 130 120 79.66 0.21 36 10 131 121 79.64 0.21 37 10 134 124 79.63 0.21 38 11 14 3 515.39 1.09 39 11 15 4 515.39 1.09 40 11 76 65 79.70 0.24 41 11 77 66 79.70 0.24 42 11 79 68 79.70 0.24 43 12 15 3 523.96 2.59 44 13 16 3 525.27 3.25 45 13 17 4 523.14 2.18 46 13 115 102 86.98 1.82 47 13 123 110 86.98 1.82 48 13 127 114 81.44 0.56 49 13 131 118 81.41 0.57 50 14 17 3 520.13 0.68 51 14 18 4 518.71 0.04 52 14 69 55 174.77 0.13 53 14 72 58 81.43 0.57 54 14 73 59 81.43 0.57 55 14 76 62 81.42 0.57 56 14 77 63 81.42 0.57 57 15 18 3 518.71 0.04 58 15 19 4 514.62 2.09 59 16 19 3 522.68 1.94 60 16 24 8 413.38 5.96 61 16 119 103 101.57 0.33 62 16 122 106 99.86 1.18 63 17 20 3 518.71 0.05 64 17 21 4 472.04 0.01 65 17 24 7 361.15 8.51 66 17 69 52 204.88 0.81 67 17 115 98 101.58 0.32 68 18 77 59 133.44 17.16 69 20 23 3 521.70 1.81 70 20 24 4 495.47 9.59 71 21 24 3 516.60 0.73 72 21 25 4 511.12 1.77 73 21 66 45 211.03 2.25 74 21 69 48 211.00 2.25 75 21 70 49 210.97 2.26 76 22 25 3 512.84 2.62 77 22 26 4 514.14 1.96 78 22 62 40 211.61 2.42 79 22 66 44 211.06 2.23 80 23 26 3 514.15 1.96 81 23 27 4 512.42 1.10 82 24 27 3 514.98 1.54 83 24 28 4 512.02 0.90 84 24 69 45 211.04 2.25 85 24 114 90 166.41 0.21 86 24 115 91 166.41 0.21 87 24 118 94 165.62 0.24 88 24 119 95 165.78 0.24 89 25 28 3 515.13 1.26 90 25 29 4 513.23 0.30 91 25 65 40 211.25 2.29 92 25 69 44 211.04 2.25 93 26 29 3 513.39 0.39 94 26 30 4 508.71 1.58 95 26 56 30 229.02 1.35 96 26 61 35 211.67 2.40 97 26 62 36 211.64 2.41 98 26 65 39 211.48 2.39 99 27 30 3 516.79 0.24 100 27 31 4 508.71 1.58 101 27 56 29 229.11 1.40 102 27 114 87 166.44 0.21 103 27 118 91 165.77 0.28 104 28 31 3 518.01 0.03 105 28 32 4 508.70 1.58 106 28 69 41 211.27 2.27 107 28 107 79 166.91 0.29 108 28 110 82 166.72 0.33 109 28 111 83 166.71 0.33 110 28 114 86 166.44 0.21 111 29 32 3 519.45 0.33 112 29 33 4 506.60 2.64 113 29 61 32 211.86 2.38 114 29 64 35 211.80 2.41 115 29 65 36 211.56 2.40 116 29 107 78 166.91 0.29 117 30 33 3 519.45 0.33 118 30 34 4 505.81 2.28 119 30 52 22 232.03 2.37 120 30 55 25 229.44 1.31 121 30 56 26 229.27 1.45 122 30 61 31 214.66 1.36 123 31 34 3 519.11 0.16 124 31 35 4 500.83 2.32 125 31 110 79 166.77 0.34 126 31 113 82 166.72 0.32 127 31 114 83 166.69 0.32 128 32 35 3 515.05 1.61 129 32 36 4 506.54 1.92 130 32 39 7 375.88 12.97 131 32 106 74 166.94 0.28 132 32 107 75 166.91 0.29 133 33 36 3 514.42 2.01 134 33 37 4 487.03 6.29 135 33 39 6 381.82 10.00 136 33 40 7 309.37 5.87 137 33 43 10 309.35 5.89 138 33 46 13 262.98 2.42 139 33 55 22 232.26 2.30 140 33 61 28 231.56 2.56 141 34 37 3 533.51 0.02 142 34 52 18 232.28 2.31 143 34 55 21 232.28 2.31 144 36 39 3 523.17 6.16 145 36 106 70 167.13 0.20 146 37 40 3 525.94 3.38 147 38 41 3 535.41 0.10 148 38 103 65 167.50 0.23 149 38 106 68 167.40 0.24 150 39 42 3 534.25 0.79 151 39 43 4 527.47 2.61 152 39 103 64 167.35 0.23 153 39 106 67 167.34 0.24 154 40 43 3 524.54 1.15 155 40 46 6 365.42 1.66 156 40 47 7 290.68 3.56 157 40 49 9 268.88 5.05 158 40 55 15 248.23 2.67 159 41 47 6 293.72 2.02 160 42 97 55 168.13 0.17 161 42 98 56 168.13 0.17 162 42 99 57 168.10 0.16 163 42 103 61 167.87 0.09 164 43 46 3 521.54 3.17 165 43 47 4 513.03 0.01 166 43 64 21 233.51 2.19 167 44 47 3 533.89 2.22 168 45 48 3 586.75 1.88 169 45 60 15 234.56 2.11 170 45 64 19 233.63 2.17 171 46 49 3 534.12 0.64 172 46 60 14 234.07 2.35 173 46 61 15 233.65 2.16 174 46 64 18 233.62 2.16 175 47 50 3 601.91 5.09 176 49 54 5 474.85 0.41 177 49 55 6 412.36 2.12 178 49 58 9 315.33 9.04 179 49 61 12 285.49 1.54 180 50 54 4 498.82 3.70 181 51 54 3 501.28 1.94 182 51 55 4 498.31 3.43 183 52 55 3 501.29 1.95 184 52 56 4 498.30 3.44 185 53 56 3 508.49 0.65 186 53 57 4 498.31 3.44 187 54 57 3 500.35 2.40 188 54 58 4 498.29 3.42 189 55 58 3 513.47 4.17 190 55 61 6 404.87 0.68 191 58 61 3 522.15 2.71 192 58 62 4 519.77 3.17 193 59 62 3 520.07 1.83 194 59 63 4 512.10 0.68 195 60 63 3 524.93 0.60 196 60 64 4 512.11 0.67 197 61 64 3 517.28 3.25 198 61 65 4 512.11 0.67 199 62 65 3 514.37 0.48 200 62 66 4 512.08 0.65 201 63 66 3 512.08 0.65 202 63 67 4 512.07 0.65 203 64 67 3 511.54 0.91 204 64 68 4 511.54 0.91 205 65 68 3 521.71 6.00 206 65 69 4 511.50 0.89 207 66 69 3 526.12 3.78 208 66 70 4 511.48 0.89 209 67 70 3 529.16 5.42 210 67 71 4 505.80 0.81 211 68 71 3 520.51 1.09 212 68 72 4 509.00 0.80 213 68 107 39 166.94 0.28 214 69 72 3 520.51 1.09 215 69 73 4 508.96 0.82 216 69 111 42 166.85 0.25 217 70 73 3 527.12 0.54 218 70 74 4 505.34 2.63 219 71 74 3 517.22 3.31 220 71 75 4 505.13 2.73 221 72 75 3 517.19 3.32 222 72 76 4 504.22 3.17 223 72 111 39 166.86 0.24 224 72 135 63 164.24 0.20 225 73 76 3 516.57 2.67 226 73 77 4 510.61 0.32 227 74 77 3 523.42 6.08 228 74 78 4 510.62 0.32 229 75 78 3 536.29 0.35 230 75 82 7 245.19 2.04 231 75 85 10 206.08 18.43 232 75 86 11 206.07 18.43 233 75 89 14 206.08 18.43 234 75 138 63 163.22 0.09 235 76 79 3 529.55 3.02 236 76 134 58 164.43 0.18 237 78 81 3 502.78 2.45 238 78 82 4 475.06 11.40 239 78 85 7 374.80 29.98 240 80 137 57 164.47 0.10 241 82 85 3 518.77 2.53 242 82 86 4 516.96 1.63 243 82 137 55 164.47 0.10 244 82 138 56 164.38 0.10 245 82 141 59 162.09 0.07 246 83 86 3 523.49 0.12 247 83 87 4 519.99 0.12 248 83 145 62 160.27 0.01 249 84 87 3 533.78 1.21 250 84 88 4 533.78 1.20 251 85 88 3 557.79 1.71 252 86 89 3 532.36 0.49 253 86 90 4 512.88 0.32 254 86 138 52 163.57 0.26 255 86 141 55 161.74 0.10 256 86 142 56 160.58 0.15 257 86 145 59 157.86 0.60 258 87 90 3 524.03 1.63 259 87 91 4 517.73 2.75 260 87 145 58 158.02 0.52 261 88 91 3 521.85 2.72 262 88 92 4 510.33 1.57 263 89 92 3 516.98 2.38 264 89 93 4 512.16 1.79 265 90 93 3 514.88 3.15 266 90 94 4 512.16 1.79 267 90 142 52 159.71 0.27 268 90 145 55 155.69 0.14 269 90 146 56 155.03 0.19 270 91 94 3 518.80 0.53 271 91 95 4 512.12 1.77 272 91 149 58 148.50 0.10 273 92 95 3 530.17 3.64 274 92 96 4 487.55 6.24 275 92 97 5 482.51 3.72 276 93 97 4 466.41 4.33 277 93 98 5 421.01 18.33 278 93 99 6 300.05 1.95 279 93 146 53 153.16 0.42 280 94 98 4 421.06 18.34 281 94 146 52 152.08 0.02 282 94 149 55 133.94 2.43 283 94 151 57 75.99 3.28 284 95 98 3 524.22 0.20 285 98 151 53 78.14 2.21 286 99 103 4 506.12 2.63 287 99 146 47 152.24 0.05 288 99 151 52 76.08 3.25 289 100 103 3 517.40 2.62 290 100 151 51 70.28 0.42 291 101 104 3 508.40 3.29 292 101 105 4 507.80 1.79 293 101 139 38 162.10 0.10 294 101 142 41 157.88 0.51 295 101 143 42 155.06 0.19 296 101 146 45 151.76 0.01 297 102 105 3 509.51 2.65 298 102 106 4 508.79 1.28 299 103 106 3 510.66 2.17 300 103 107 4 508.59 1.17 301 104 107 3 519.20 2.11 302 104 108 4 505.41 0.47 303 104 138 34 162.69 0.09 304 104 139 35 161.12 0.24 305 104 142 38 157.40 0.58 306 104 146 42 151.76 0.02 307 105 108 3 519.20 2.11 308 105 109 4 513.13 1.12 309 105 139 34 161.13 0.24 310 106 109 3 514.12 1.02 311 106 110 4 507.24 0.51 312 107 110 3 507.30 0.48 313 107 111 4 501.41 2.38 314 108 111 3 519.89 2.25 315 108 112 4 509.12 1.48 316 108 135 27 163.26 0.14 317 108 139 31 161.12 0.24 318 109 112 3 515.17 0.11 319 109 113 4 506.36 0.93 320 110 113 3 514.12 5.15 321 110 114 4 502.19 0.71 322 111 114 3 515.44 1.32 323 111 115 4 509.84 0.12 324 111 135 24 163.75 0.34 325 112 115 3 522.62 1.10 326 112 116 4 509.84 0.12 327 112 123 11 255.44 3.02 328 112 128 16 164.45 0.14 329 112 131 19 164.27 0.23 330 112 132 20 164.25 0.24 331 112 135 23 164.18 0.20 332 113 116 3 520.02 0.20 333 113 117 4 502.43 0.61 334 114 117 3 505.40 1.86 335 114 118 4 504.12 1.46 336 115 118 3 517.55 0.59 337 115 119 4 491.30 1.24 338 115 123 8 261.25 0.14 339 115 131 16 164.36 0.19 340 116 119 3 511.40 3.74 341 116 120 4 455.15 2.00 342 116 123 7 259.01 1.30 343 116 128 12 255.50 3.08 344 117 120 3 536.54 4.10 345 119 122 3 511.87 7.67 346 119 123 4 482.05 4.38 347 123 127 4 504.45 1.93 348 123 128 5 494.15 0.10 349 123 131 8 486.49 3.74 350 124 127 3 507.10 0.60 351 124 128 4 504.48 1.92 352 125 128 3 512.35 2.02 353 125 129 4 507.10 0.61 354 126 129 3 508.35 0.01 355 126 130 4 507.10 0.61 356 127 130 3 513.01 0.60 357 127 131 4 503.01 1.15 358 128 131 3 513.56 0.33 359 128 132 4 502.41 1.48 360 129 132 3 511.84 1.72 361 129 133 4 509.27 3.02 362 130 133 3 516.51 0.14 363 130 134 4 515.75 0.23 364 131 134 3 516.51 0.14 365 131 135 4 510.56 2.38 366 132 135 3 515.76 0.23 367 132 136 4 510.55 2.38 368 133 136 3 506.03 0.22 369 133 137 4 505.69 0.05 370 134 137 3 512.19 3.29 371 134 138 4 505.23 0.18 372 135 138 3 506.19 0.14 373 135 139 4 506.13 0.64 374 136 139 3 515.07 1.60 375 136 140 4 503.80 1.23 376 137 140 3 512.98 2.78 377 137 141 4 503.83 1.24 378 138 141 3 518.89 0.18 379 138 142 4 503.95 1.18 380 139 142 3 513.47 0.05 381 139 143 4 503.94 1.17 382 140 143 3 511.50 1.00 383 140 144 4 504.10 0.90 384 141 144 3 511.54 1.02 385 141 145 4 506.91 2.29 386 142 145 3 513.46 0.98 387 142 146 4 506.92 2.28 388 143 146 3 506.92 2.28 389 143 147 4 504.07 0.86 390 144 147 3 516.25 2.38 391 144 148 4 505.25 0.24 392 145 148 3 513.61 0.46 393 145 149 4 503.01 0.33 394 146 149 3 511.44 0.62 395 146 150 4 497.99 1.10 396 146 151 5 409.43 7.53 397 147 150 3 509.81 0.19