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 5 480.44 0.93 2 2 130 128 41.01 1.19 3 2 133 131 32.61 1.19 4 2 134 132 26.63 1.76 5 2 137 135 26.64 1.76 6 3 6 3 495.32 6.44 7 3 7 4 491.63 3.43 8 4 7 3 519.89 2.82 9 4 8 4 497.93 0.28 10 4 79 75 63.23 0.18 11 5 8 3 503.04 0.62 12 5 9 4 500.13 0.83 13 6 9 3 509.90 4.14 14 6 10 4 496.01 2.89 15 6 130 124 68.09 0.95 16 6 133 127 68.10 0.95 17 7 10 3 505.13 2.29 18 7 11 4 493.28 1.52 19 7 76 69 68.11 0.96 20 7 79 72 68.11 0.96 21 7 80 73 68.17 0.96 22 7 134 127 68.13 0.94 23 7 137 130 68.16 0.95 24 8 11 3 534.40 0.72 25 8 12 4 509.10 0.18 26 9 12 3 542.53 3.34 27 9 13 4 509.09 0.18 28 9 126 117 79.98 1.11 29 9 127 118 79.74 1.09 30 9 130 121 79.73 1.08 31 10 14 4 510.55 4.33 32 10 76 66 79.80 1.12 33 10 130 120 79.73 1.09 34 10 131 121 79.70 1.10 35 10 134 124 79.56 1.16 36 11 14 3 518.39 0.41 37 11 15 4 510.55 4.33 38 11 76 65 79.89 1.16 39 11 77 66 79.90 1.17 40 11 79 68 79.90 1.16 41 12 15 3 518.92 0.14 42 12 16 4 510.55 4.33 43 13 16 3 523.36 2.08 44 13 17 4 513.60 2.52 45 13 115 102 83.06 0.50 46 13 123 110 83.07 0.50 47 13 127 114 80.77 1.23 48 13 131 118 80.59 1.26 49 14 17 3 513.61 2.51 50 14 18 4 513.60 2.51 51 14 69 55 80.73 1.24 52 14 72 58 80.67 1.22 53 14 73 59 80.56 1.27 54 14 76 62 80.56 1.27 55 14 77 63 80.56 1.27 56 15 18 3 519.08 2.86 57 15 19 4 522.99 0.91 58 16 19 3 523.00 0.90 59 16 119 103 105.66 1.60 60 16 122 106 105.43 1.54 61 17 20 3 529.37 1.80 62 17 21 4 498.73 5.26 63 17 24 7 413.75 19.88 64 17 69 52 136.03 20.55 65 17 115 98 96.98 2.72 66 18 21 3 522.19 1.79 67 18 77 59 130.40 19.45 68 20 23 3 515.46 1.30 69 20 24 4 508.81 2.92 70 20 118 98 136.75 0.01 71 21 24 3 513.78 2.14 72 21 25 4 510.53 3.77 73 21 66 45 153.97 13.91 74 21 69 48 153.69 14.04 75 22 25 3 510.94 3.56 76 22 26 4 504.75 6.66 77 22 62 40 175.75 3.11 78 22 66 44 156.60 12.68 79 23 26 3 514.66 1.70 80 23 27 4 508.77 2.93 81 23 118 95 164.88 0.30 82 24 27 3 504.11 0.60 83 24 28 4 503.69 0.39 84 24 69 45 175.20 3.43 85 24 114 90 166.44 1.06 86 24 115 91 166.44 1.06 87 24 118 94 164.91 0.32 88 24 119 95 164.91 0.32 89 25 28 3 504.12 0.59 90 25 29 4 504.24 0.65 91 25 65 40 175.75 3.15 92 25 69 44 175.21 3.43 93 26 29 3 516.40 1.10 94 26 30 4 507.48 0.97 95 26 56 30 209.25 4.62 96 26 61 35 176.81 3.60 97 26 62 36 176.12 3.22 98 27 30 3 520.14 1.09 99 27 31 4 511.70 3.08 100 27 114 87 167.67 0.45 101 27 118 91 165.97 0.18 102 28 31 3 517.94 0.01 103 28 32 4 511.70 3.08 104 28 69 41 176.34 3.33 105 28 107 79 168.09 0.48 106 28 110 82 167.97 0.48 107 28 111 83 167.78 0.40 108 28 114 86 167.69 0.45 109 29 32 3 518.36 0.22 110 29 33 4 503.14 0.14 111 29 61 32 185.21 0.77 112 29 64 35 177.66 3.77 113 29 65 36 177.36 3.76 114 29 107 78 168.10 0.48 115 30 33 3 507.40 2.96 116 30 34 4 499.66 1.59 117 30 52 22 211.87 3.63 118 30 55 25 209.77 4.50 119 30 56 26 210.16 4.30 120 30 61 31 198.56 3.71 121 31 34 3 514.48 0.58 122 31 35 4 495.96 1.99 123 31 110 79 168.00 0.48 124 31 113 82 167.99 0.48 125 31 114 83 167.91 0.51 126 32 35 3 501.65 0.52 127 32 36 4 495.95 2.00 128 32 39 7 433.57 11.64 129 32 106 74 168.15 0.47 130 32 107 75 168.12 0.48 131 32 110 78 168.02 0.48 132 33 37 4 494.82 2.56 133 33 39 6 431.94 12.46 134 33 40 7 431.91 12.46 135 33 43 10 360.51 23.25 136 33 46 13 251.38 1.23 137 33 55 22 211.99 3.70 138 34 37 3 530.85 1.35 139 34 52 18 212.19 3.79 140 36 39 3 518.73 1.17 141 36 106 70 168.25 0.52 142 37 40 3 526.44 4.54 143 37 41 4 513.79 0.14 144 38 41 3 515.21 0.56 145 38 42 4 513.79 0.13 146 38 103 65 168.94 0.40 147 38 106 68 168.85 0.39 148 39 42 3 522.88 3.27 149 39 43 4 515.20 0.56 150 39 103 64 168.69 0.34 151 39 106 67 168.69 0.34 152 40 43 3 516.19 1.34 153 40 46 6 393.23 15.75 154 40 47 7 268.93 7.52 155 42 97 55 169.31 0.38 156 42 98 56 169.30 0.36 157 42 99 57 169.15 0.38 158 43 46 3 522.54 3.67 159 43 47 4 498.35 2.75 160 43 64 21 214.28 3.75 161 44 47 3 530.73 0.64 162 45 48 3 578.80 2.10 163 45 60 15 222.72 0.34 164 45 64 19 214.47 3.76 165 46 49 3 530.93 0.50 166 46 60 14 222.73 0.34 167 46 61 15 222.69 0.33 168 46 64 18 222.63 0.34 169 47 50 3 596.15 0.80 170 49 54 5 476.43 2.62 171 49 55 6 432.12 19.53 172 49 58 9 289.12 0.35 173 49 61 12 275.26 7.25 174 50 54 4 504.44 0.36 175 51 54 3 504.56 0.30 176 51 55 4 504.48 0.34 177 52 55 3 510.47 2.65 178 52 56 4 504.49 0.34 179 53 56 3 517.60 0.91 180 53 57 4 504.47 0.35 181 54 57 3 504.49 0.35 182 54 58 4 493.04 5.38 183 55 58 3 507.65 1.23 184 55 61 6 409.50 2.97 185 58 61 3 536.14 1.29 186 58 62 4 502.19 0.51 187 59 62 3 507.92 4.42 188 59 63 4 507.91 4.42 189 60 63 3 508.80 3.99 190 60 64 4 507.36 4.70 191 61 64 3 520.28 1.76 192 61 65 4 507.52 4.62 193 62 65 3 520.27 1.76 194 62 66 4 513.72 1.51 195 63 66 3 508.25 2.44 196 63 67 4 506.25 1.45 197 64 67 3 511.50 0.88 198 64 68 4 509.54 0.21 199 65 68 3 516.51 1.24 200 65 69 4 509.56 0.22 201 66 69 3 519.74 4.35 202 66 70 4 507.48 1.29 203 67 70 3 523.71 2.36 204 67 71 4 510.30 2.69 205 68 71 3 526.10 1.17 206 68 72 4 510.73 2.92 207 68 107 39 168.34 0.35 208 69 72 3 513.26 1.66 209 69 73 4 513.26 1.66 210 70 73 3 533.70 0.24 211 70 74 4 509.57 3.50 212 71 74 3 529.01 2.59 213 71 75 4 509.58 3.50 214 72 75 3 520.18 1.83 215 72 76 4 506.86 2.14 216 72 111 39 168.31 0.30 217 72 135 63 165.53 0.35 218 72 138 66 164.73 0.33 219 73 76 3 511.97 2.63 220 73 77 4 501.73 0.77 221 74 78 4 512.66 1.02 222 75 78 3 526.82 4.38 223 75 79 4 512.92 0.90 224 75 82 7 283.95 3.17 225 75 85 10 240.66 4.12 226 75 86 11 235.09 0.65 227 75 138 63 164.95 0.26 228 76 79 3 526.83 4.38 229 76 134 58 165.81 0.27 230 76 135 59 165.80 0.27 231 78 81 3 513.09 2.08 232 78 82 4 478.60 4.67 233 78 84 6 466.55 10.70 234 78 85 7 356.10 9.51 235 80 137 57 165.85 0.25 236 82 85 3 528.29 0.61 237 82 86 4 513.09 2.10 238 82 137 55 165.84 0.25 239 82 141 59 164.72 0.36 240 83 86 3 516.22 0.54 241 83 87 4 513.09 2.10 242 84 88 4 529.52 4.91 243 85 88 3 540.67 0.67 244 85 89 4 524.46 2.39 245 86 89 3 524.47 2.38 246 86 90 4 518.55 0.57 247 86 138 52 165.06 0.19 248 86 141 55 164.43 0.32 249 86 142 56 161.56 0.66 250 87 90 3 524.46 2.38 251 87 91 4 519.67 4.77 252 87 145 58 160.09 1.01 253 88 91 3 516.79 0.31 254 88 92 4 508.98 0.13 255 89 92 3 509.12 0.19 256 89 93 4 507.10 0.74 257 89 138 49 165.06 0.19 258 89 142 53 161.56 0.66 259 90 93 3 516.12 3.72 260 90 94 4 499.32 3.14 261 90 142 52 161.40 0.73 262 90 145 55 154.95 0.44 263 90 146 56 151.57 0.20 264 91 94 3 514.34 3.66 265 91 95 4 494.37 0.80 266 91 145 54 159.13 1.51 267 91 149 58 147.46 0.61 268 92 95 3 514.69 2.58 269 92 96 4 492.86 1.55 270 92 97 5 454.70 20.62 271 93 97 4 403.56 9.63 272 93 98 5 380.11 21.36 273 93 99 6 291.94 5.11 274 93 146 53 151.24 0.36 275 94 146 52 151.22 0.35 276 94 151 57 72.16 8.64 277 95 151 56 111.74 3.86 278 99 103 4 507.69 0.32 279 99 104 5 505.22 0.93 280 99 146 47 151.19 0.36 281 100 103 3 513.25 2.46 282 100 104 4 507.70 0.32 283 101 104 3 507.75 0.30 284 101 105 4 507.69 0.32 285 101 143 42 152.96 0.74 286 101 146 45 150.31 0.60 287 101 152 51 41.74 0.06 288 102 105 3 511.29 1.76 289 102 106 4 508.98 0.97 290 103 106 3 507.97 1.48 291 103 107 4 507.94 1.49 292 104 107 3 516.36 2.50 293 104 108 4 508.13 1.61 294 104 138 34 162.65 0.14 295 104 139 35 161.52 0.69 296 104 142 38 157.08 0.49 297 105 108 3 516.37 2.50 298 105 109 4 516.38 2.50 299 105 139 34 161.53 0.69 300 106 109 3 511.73 0.16 301 106 110 4 510.75 0.33 302 107 110 3 518.69 1.34 303 107 111 4 508.35 1.53 304 108 111 3 508.36 1.53 305 108 112 4 508.35 1.52 306 108 135 27 163.75 0.22 307 108 139 31 161.59 0.66 308 109 112 3 520.70 0.35 309 109 113 4 506.68 0.76 310 110 113 3 506.40 0.61 311 110 114 4 484.23 0.51 312 111 114 3 514.17 3.12 313 111 115 4 490.96 2.88 314 111 135 24 163.75 0.23 315 112 115 3 495.67 1.09 316 112 116 4 497.66 6.21 317 112 128 16 163.97 0.29 318 112 131 19 163.96 0.30 319 112 132 20 163.92 0.28 320 112 135 23 163.75 0.23 321 113 116 3 506.72 6.86 322 113 117 4 493.24 0.12 323 114 117 3 510.99 1.90 324 114 118 4 493.25 0.12 325 115 118 3 508.34 0.38 326 115 119 4 489.25 2.12 327 115 123 8 260.48 2.58 328 115 131 16 170.52 3.00 329 116 119 3 508.54 0.12 330 116 120 4 479.53 1.26 331 116 123 7 260.48 2.58 332 119 122 3 496.07 0.38 333 119 123 4 363.43 21.67 334 123 127 4 483.22 7.83 335 123 128 5 462.56 4.65 336 123 131 8 431.92 10.68 337 124 127 3 524.01 0.82 338 124 128 4 497.88 0.52 339 125 128 3 506.64 3.87 340 125 129 4 501.06 2.12 341 126 130 4 505.38 0.04 342 127 130 3 512.59 0.47 343 127 131 4 506.28 0.48 344 128 131 3 511.26 2.01 345 128 132 4 511.26 2.01 346 129 132 3 511.27 2.02 347 129 133 4 510.38 2.46 348 130 133 3 518.56 1.62 349 130 134 4 515.09 0.11 350 131 134 3 515.10 0.11 351 131 135 4 509.84 2.73 352 132 135 3 517.83 2.19 353 132 136 4 508.91 2.27 354 133 136 3 523.42 0.61 355 133 137 4 501.98 0.87 356 134 137 3 507.02 0.79 357 134 138 4 502.43 1.15 358 135 138 3 506.49 0.29 359 135 139 4 503.78 1.81 360 136 139 3 513.47 3.03 361 136 140 4 503.29 1.49 362 137 140 3 512.89 3.31 363 137 141 4 506.44 0.07 364 138 141 3 525.88 0.67 365 138 142 4 506.89 0.29 366 139 142 3 524.85 1.18 367 139 143 4 506.90 0.29 368 140 143 3 517.14 4.62 369 140 144 4 513.74 2.92 370 141 144 3 513.74 2.92 371 141 145 4 508.50 0.51 372 142 145 3 524.12 1.34 373 142 146 4 508.50 0.51 374 143 146 3 511.19 0.15 375 143 147 4 507.88 0.83 376 143 152 9 265.83 2.72 377 144 147 3 510.22 0.34 378 144 148 4 507.88 0.83 379 145 148 3 511.18 2.50 380 145 149 4 505.88 0.14 381 146 149 3 502.13 0.78 382 146 150 4 501.98 0.84 383 146 151 5 414.66 8.30 384 146 152 6 355.56 18.39 385 147 150 3 506.49 3.10 386 147 151 4 488.88 5.70 387 147 152 5 430.55 5.20