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 8 475.32 1.56 2 2 130 128 43.14 4.67 3 2 133 131 23.68 0.11 4 2 134 132 23.48 0.08 5 2 137 135 23.48 0.08 6 3 6 3 491.35 2.20 7 3 7 4 489.72 3.01 8 4 7 3 512.75 2.14 9 4 8 4 490.68 3.50 10 4 79 75 55.33 1.41 11 5 8 3 506.73 3.36 12 5 9 4 502.69 2.92 13 6 9 3 512.97 0.24 14 6 10 4 501.70 3.42 15 6 130 124 59.98 0.16 16 6 133 127 59.98 0.16 17 7 10 3 503.57 2.48 18 7 11 4 501.70 3.42 19 7 76 69 60.12 0.10 20 7 79 72 60.11 0.10 21 7 80 73 60.12 0.11 22 7 134 127 59.98 0.16 23 7 137 130 59.99 0.17 24 8 11 3 519.89 1.32 25 8 12 4 495.36 0.24 26 9 12 3 500.56 0.53 27 9 13 4 496.04 0.57 28 9 126 117 75.06 0.01 29 9 127 118 74.95 0.04 30 9 130 121 74.93 0.04 31 10 13 3 519.88 1.45 32 10 14 4 496.12 0.54 33 10 76 66 74.85 0.01 34 10 130 120 74.95 0.04 35 10 131 121 74.93 0.04 36 10 134 124 74.81 0.03 37 11 14 3 507.10 4.94 38 11 15 4 502.57 2.60 39 11 76 65 75.00 0.03 40 11 77 66 75.95 0.51 41 11 79 68 75.94 0.50 42 12 15 3 518.43 0.72 43 12 16 4 513.13 1.92 44 12 122 110 87.67 0.79 45 13 16 3 515.83 0.58 46 13 17 4 513.11 1.93 47 13 115 102 87.61 0.81 48 13 119 106 87.84 0.71 49 13 122 109 87.68 0.79 50 13 123 110 87.66 0.79 51 13 131 118 87.50 0.79 52 14 17 3 513.12 1.92 53 14 18 4 508.61 0.32 54 14 69 55 87.62 0.81 55 14 72 58 87.59 0.82 56 14 73 59 87.50 0.79 57 14 76 62 86.95 0.67 58 14 111 97 87.70 0.77 59 14 131 117 87.62 0.81 60 15 18 3 513.93 2.98 61 15 19 4 508.62 0.32 62 16 19 3 515.39 2.64 63 16 119 103 97.56 1.28 64 16 122 106 96.20 0.60 65 17 20 3 524.62 4.02 66 17 21 4 501.12 3.42 67 17 24 7 424.31 28.56 68 17 69 52 91.16 1.88 69 17 115 98 96.20 0.61 70 17 119 102 105.20 0.85 71 18 21 3 511.31 1.66 72 18 77 59 91.03 1.98 73 20 23 3 513.21 3.68 74 20 24 4 496.53 0.97 75 20 118 98 127.05 0.53 76 21 24 3 512.56 1.61 77 21 25 4 496.51 0.98 78 21 66 45 167.08 0.35 79 21 69 48 140.40 13.69 80 21 70 49 141.06 13.36 81 22 25 3 518.08 1.15 82 22 26 4 503.26 2.40 83 22 62 40 174.02 0.95 84 22 66 44 167.03 0.38 85 23 26 3 519.16 0.60 86 23 27 4 513.00 2.48 87 23 118 95 160.36 0.33 88 24 27 3 520.25 0.06 89 24 28 4 506.20 5.88 90 24 69 45 167.02 0.44 91 24 114 90 156.62 1.97 92 24 115 91 159.88 0.37 93 24 118 94 160.37 0.34 94 24 119 95 160.41 0.35 95 25 28 3 520.25 0.06 96 25 29 4 507.31 6.42 97 25 65 40 167.30 0.42 98 25 69 44 166.99 0.42 99 26 29 3 517.94 1.09 100 26 30 4 506.22 5.88 101 26 62 36 174.32 1.09 102 27 30 3 516.87 0.56 103 27 31 4 498.89 2.29 104 27 114 87 161.96 0.48 105 27 118 91 161.90 0.48 106 28 31 3 508.19 0.33 107 28 32 4 500.52 3.10 108 28 69 41 173.55 1.59 109 28 107 79 162.33 0.56 110 28 110 82 162.13 0.51 111 28 111 83 162.13 0.51 112 28 114 86 161.98 0.47 113 29 32 3 502.52 2.10 114 29 33 4 502.63 2.04 115 29 61 32 189.65 3.84 116 29 64 35 180.02 1.22 117 29 65 36 179.24 1.22 118 29 107 78 162.34 0.56 119 30 33 3 505.80 3.62 120 30 34 4 500.80 1.12 121 30 52 22 226.07 0.55 122 30 55 25 225.12 0.68 123 30 56 26 225.14 0.68 124 30 61 31 210.28 0.18 125 31 34 3 518.14 2.55 126 31 35 4 489.84 6.54 127 31 110 79 162.09 0.51 128 31 113 82 162.05 0.51 129 32 35 3 506.88 2.50 130 32 36 4 484.49 3.88 131 32 39 7 446.57 0.79 132 32 106 74 162.35 0.55 133 32 107 75 162.35 0.55 134 32 110 78 162.25 0.58 135 33 36 3 506.87 2.50 136 33 37 4 480.26 5.96 137 33 39 6 446.58 0.79 138 33 40 7 386.42 29.27 139 33 43 10 381.43 31.73 140 33 46 13 264.77 2.91 141 33 55 22 227.66 0.10 142 33 61 28 226.84 0.12 143 34 37 3 523.16 2.00 144 34 51 17 229.10 0.78 145 34 52 18 227.71 0.10 146 34 55 21 227.69 0.10 147 36 39 3 516.12 1.53 148 36 106 70 162.50 0.56 149 37 40 3 515.38 2.38 150 37 41 4 512.35 1.67 151 38 41 3 525.50 2.68 152 38 42 4 512.37 1.67 153 38 103 65 162.93 0.56 154 38 106 68 162.85 0.52 155 39 42 3 524.76 4.47 156 39 43 4 512.42 1.70 157 39 103 64 162.68 0.53 158 39 106 67 162.69 0.52 159 40 43 3 524.77 4.47 160 40 46 6 414.73 15.36 161 40 47 7 298.55 14.08 162 40 49 9 298.53 14.08 163 40 55 15 232.87 0.69 164 41 47 6 323.40 1.65 165 42 97 55 163.30 0.62 166 42 98 56 163.30 0.62 167 42 99 57 163.18 0.62 168 42 100 58 163.27 0.64 169 42 103 61 163.09 0.58 170 43 46 3 508.88 1.33 171 43 47 4 476.12 7.62 172 43 64 21 228.72 0.79 173 44 47 3 519.38 3.93 174 45 48 3 583.48 0.28 175 45 60 15 229.00 0.81 176 45 64 19 228.96 0.83 177 46 49 3 520.90 2.15 178 46 60 14 229.01 0.82 179 46 61 15 228.97 0.83 180 46 64 18 228.97 0.83 181 49 54 5 382.53 0.64 182 49 55 6 361.66 0.23 183 49 58 9 263.79 0.21 184 49 61 12 247.67 4.26 185 50 54 4 484.37 4.19 186 51 54 3 512.99 2.83 187 51 55 4 486.19 6.14 188 52 55 3 503.60 2.56 189 52 56 4 499.90 0.71 190 53 56 3 508.06 0.34 191 53 57 4 503.61 2.57 192 54 57 3 510.37 0.01 193 54 58 4 508.05 0.35 194 55 58 3 516.70 3.22 195 55 61 6 448.38 2.14 196 58 61 3 497.57 2.38 197 58 62 4 496.96 2.07 198 59 62 3 501.45 1.54 199 59 63 4 499.75 0.68 200 60 63 3 508.24 4.92 201 60 64 4 508.73 0.79 202 61 64 3 508.74 0.79 203 61 65 4 508.73 0.79 204 62 65 3 510.35 0.01 205 62 66 4 508.73 0.79 206 63 66 3 523.95 6.79 207 63 67 4 504.13 1.51 208 64 67 3 515.33 4.88 209 64 68 4 503.34 1.12 210 65 68 3 525.69 0.31 211 65 69 4 505.10 0.24 212 66 69 3 529.34 2.14 213 66 70 4 505.12 0.26 214 67 70 3 509.94 1.41 215 67 71 4 505.12 0.26 216 68 71 3 519.60 3.36 217 68 72 4 504.12 1.55 218 68 107 39 162.64 0.49 219 69 72 3 504.18 1.52 220 69 73 4 504.12 1.55 221 70 73 3 507.50 0.14 222 70 74 4 504.13 1.55 223 71 74 3 516.28 4.33 224 71 75 4 504.13 1.56 225 72 75 3 507.89 0.32 226 72 76 4 504.12 1.56 227 72 111 39 162.64 0.46 228 72 135 63 161.28 0.33 229 72 138 66 161.00 0.39 230 73 76 3 507.92 0.33 231 73 77 4 507.91 0.33 232 74 77 3 512.22 2.60 233 74 78 4 506.49 1.04 234 74 85 11 212.81 8.95 235 75 78 3 515.51 0.95 236 75 79 4 504.87 1.85 237 75 82 7 258.94 4.60 238 75 85 10 208.15 11.29 239 75 86 11 211.51 9.61 240 75 89 14 201.77 14.47 241 75 138 63 161.12 0.38 242 76 79 3 503.93 1.50 243 76 131 55 161.66 0.36 244 76 134 58 161.38 0.40 245 78 81 3 506.42 0.57 246 78 82 4 435.35 3.68 247 78 85 7 432.03 5.33 248 79 82 3 538.03 0.83 249 82 85 3 511.12 0.05 250 82 86 4 506.15 2.15 251 82 137 55 161.56 0.47 252 82 138 56 161.41 0.41 253 82 141 59 160.87 0.28 254 83 86 3 519.28 1.91 255 83 87 4 514.72 2.12 256 84 87 3 524.56 0.73 257 84 88 4 521.12 0.99 258 85 88 3 544.36 4.50 259 85 89 4 517.20 0.88 260 86 89 3 518.61 0.17 261 86 90 4 505.20 0.01 262 86 138 52 161.00 0.32 263 86 141 55 160.40 0.27 264 86 142 56 158.81 0.10 265 87 90 3 514.95 1.66 266 87 91 4 505.20 0.01 267 88 91 3 510.44 0.39 268 88 92 4 499.88 0.41 269 89 92 3 511.98 0.69 270 89 93 4 496.16 2.27 271 89 138 49 161.00 0.31 272 89 142 53 158.56 0.20 273 90 93 3 514.08 4.46 274 90 94 4 489.07 1.28 275 90 142 52 157.84 0.38 276 90 145 55 146.30 0.87 277 90 146 56 142.02 1.23 278 91 94 3 516.15 3.43 279 91 95 4 489.06 1.28 280 91 149 58 140.05 1.23 281 92 96 4 428.67 15.93 282 92 97 5 361.81 22.82 283 93 97 4 355.26 20.00 284 93 98 5 327.61 26.00 285 93 99 6 259.87 2.81 286 93 146 53 141.25 1.60 287 94 98 4 331.18 24.23 288 94 146 52 141.03 1.51 289 94 151 57 47.34 0.77 290 95 98 3 498.17 2.77 291 95 149 54 139.96 1.95 292 98 151 53 59.95 2.40 293 99 103 4 498.88 1.97 294 99 104 5 498.67 1.87 295 99 146 47 141.25 1.62 296 99 151 52 48.75 0.86 297 100 103 3 514.13 1.60 298 100 104 4 498.89 1.96 299 100 146 46 141.27 1.61 300 100 151 51 47.05 0.90 301 101 104 3 502.45 0.18 302 101 105 4 498.89 1.96 303 101 139 38 159.43 0.09 304 101 142 41 155.12 0.79 305 101 143 42 147.53 0.54 306 101 146 45 140.96 1.46 307 102 105 3 508.44 2.95 308 102 106 4 498.76 1.90 309 103 106 3 503.89 4.49 310 103 107 4 498.74 1.91 311 104 107 3 498.73 1.92 312 104 108 4 498.74 1.93 313 104 138 34 160.72 0.18 314 104 139 35 159.25 0.01 315 104 142 38 149.49 1.44 316 105 108 3 499.38 1.61 317 105 109 4 503.17 4.14 318 105 139 34 159.25 0.01 319 106 109 3 503.81 3.83 320 106 110 4 502.74 0.07 321 107 110 3 502.74 0.07 322 107 111 4 502.74 0.07 323 108 111 3 503.61 0.09 324 108 112 4 501.44 0.76 325 108 135 27 161.12 0.30 326 108 139 31 159.26 0.01 327 109 112 3 512.83 0.73 328 109 113 4 491.73 5.61 329 110 113 3 497.43 3.73 330 110 114 4 492.71 6.09 331 111 114 3 507.48 3.41 332 111 115 4 495.50 4.69 333 111 135 24 161.18 0.31 334 112 115 3 500.21 7.04 335 112 116 4 498.17 6.03 336 112 123 11 253.12 3.25 337 112 128 16 161.34 0.33 338 112 131 19 161.23 0.32 339 112 132 20 161.23 0.31 340 112 135 23 161.22 0.31 341 113 116 3 505.45 2.41 342 113 117 4 505.43 2.40 343 114 117 3 505.43 2.40 344 114 118 4 496.27 6.98 345 115 118 3 510.88 0.32 346 115 119 4 469.82 3.19 347 115 123 8 263.17 1.22 348 115 131 16 172.97 6.17 349 116 120 4 426.69 0.23 350 116 123 7 273.52 4.00 351 117 120 3 527.64 1.58 352 119 122 3 509.69 2.44 353 119 123 4 444.01 0.45 354 120 123 3 493.54 5.64 355 120 124 4 441.33 0.90 356 122 127 5 453.35 1.67 357 123 127 4 453.35 1.67 358 123 128 5 453.33 1.66 359 123 131 8 449.30 2.29 360 124 127 3 507.78 1.08 361 124 128 4 480.70 9.45 362 125 128 3 504.19 2.29 363 125 129 4 480.68 9.46 364 126 129 3 506.87 3.63 365 126 130 4 498.16 0.72 366 127 130 3 505.59 2.99 367 127 131 4 495.53 2.03 368 128 131 3 521.52 3.33 369 128 132 4 495.82 1.88 370 129 132 3 502.74 1.59 371 129 133 4 495.84 1.85 372 130 133 3 503.18 7.01 373 130 134 4 492.38 1.61 374 131 134 3 492.38 1.61 375 131 135 4 492.38 1.61 376 132 135 3 498.12 0.94 377 132 136 4 489.47 3.25 378 133 136 3 501.17 0.58 379 133 137 4 490.26 2.86 380 134 137 3 493.58 3.14 381 134 138 4 492.24 3.85 382 135 138 3 492.42 3.77 383 135 139 4 492.24 3.85 384 136 139 3 499.04 1.68 385 136 140 4 491.07 4.44 386 137 140 3 499.10 1.71 387 137 141 4 492.35 5.08 388 138 141 3 510.61 1.53 389 138 142 4 491.23 4.34 390 139 142 3 510.61 1.53 391 139 143 4 487.60 2.53 392 140 143 3 502.42 2.57 393 140 144 4 490.06 3.75 394 141 144 3 502.30 1.08 395 141 145 4 491.54 3.02 396 142 145 3 505.95 1.04 397 142 146 4 490.01 3.77 398 143 146 3 493.80 1.88 399 143 147 4 490.12 3.72 400 144 147 3 498.34 2.72 401 144 148 4 492.31 2.60 402 145 148 3 492.46 2.69 403 145 149 4 491.60 2.25 404 146 149 3 504.40 1.66 405 146 150 4 482.60 3.40 406 146 151 5 381.72 36.59 407 147 150 3 482.56 3.37