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 8 474.47 2.79 2 2 130 128 43.09 0.14 3 2 133 131 30.05 0.10 4 2 134 132 29.99 0.08 5 2 137 135 29.94 0.08 6 3 6 3 518.99 0.41 7 3 7 4 507.25 0.73 8 4 7 3 513.45 2.36 9 4 8 4 495.65 6.53 10 4 79 75 57.55 2.50 11 5 8 3 513.36 2.32 12 5 9 4 507.26 0.73 13 6 9 3 520.58 7.42 14 6 10 4 500.61 4.05 15 6 130 124 67.70 1.35 16 6 133 127 67.70 1.35 17 7 10 3 510.78 0.53 18 7 11 4 500.60 4.04 19 7 76 69 70.92 0.25 20 7 79 72 67.76 1.32 21 7 80 73 70.92 0.24 22 7 134 127 67.75 1.33 23 7 137 130 67.80 1.31 24 8 11 3 524.37 2.75 25 8 12 4 504.01 2.34 26 9 12 3 526.57 1.64 27 9 13 4 515.26 1.21 28 9 126 117 81.81 1.27 29 9 127 118 81.72 1.27 30 9 130 121 81.72 1.27 31 10 13 3 526.58 1.64 32 10 14 4 515.45 1.12 33 10 76 66 81.70 1.25 34 10 130 120 81.74 1.26 35 10 131 121 81.67 1.28 36 10 134 124 81.61 1.32 37 11 14 3 515.46 1.12 38 11 15 4 515.45 1.12 39 11 76 65 81.74 1.26 40 11 77 66 81.76 1.26 41 11 79 68 81.77 1.25 42 12 15 3 522.00 1.94 43 12 16 4 515.44 1.11 44 12 122 110 90.84 1.45 45 13 16 3 525.31 2.18 46 13 17 4 513.84 2.39 47 13 115 102 90.76 1.47 48 13 119 106 91.05 1.45 49 13 122 109 90.94 1.46 50 13 123 110 90.84 1.45 51 13 131 118 87.44 0.24 52 14 17 3 518.71 0.04 53 14 18 4 518.71 0.04 54 14 69 55 90.67 1.49 55 14 72 58 90.24 1.62 56 14 73 59 89.07 1.56 57 14 76 62 88.29 1.17 58 14 77 63 88.80 0.92 59 15 18 3 514.58 2.11 60 15 19 4 519.99 0.59 61 16 19 3 519.99 0.59 62 16 119 103 101.72 0.01 63 16 122 106 100.35 0.53 64 17 20 3 520.12 0.67 65 17 21 4 497.08 6.10 66 17 24 7 420.23 5.50 67 17 69 52 174.97 0.62 68 17 115 98 91.25 1.40 69 18 21 3 518.70 0.04 70 18 77 59 133.34 19.88 71 20 23 3 526.58 2.54 72 20 24 4 512.46 1.09 73 20 118 98 134.74 0.99 74 21 24 3 515.38 0.10 75 21 25 4 512.45 1.10 76 21 66 45 179.15 0.51 77 21 69 48 179.08 0.53 78 22 25 3 516.60 0.73 79 22 26 4 515.36 1.35 80 22 62 40 180.26 0.32 81 22 66 44 179.13 0.51 82 23 26 3 522.12 4.73 83 23 27 4 513.64 0.49 84 23 118 95 165.50 1.95 85 24 27 3 520.71 1.31 86 24 28 4 510.32 0.05 87 24 69 45 179.31 0.51 88 24 114 90 167.00 2.12 89 24 115 91 166.97 2.12 90 24 118 94 165.52 1.95 91 24 119 95 165.54 1.95 92 25 28 3 514.18 0.01 93 25 29 4 511.53 0.54 94 25 65 40 179.39 0.55 95 25 69 44 179.32 0.51 96 26 29 3 514.90 0.09 97 26 30 4 511.17 0.36 98 26 56 30 233.06 0.83 99 26 62 36 181.41 0.59 100 27 30 3 519.12 0.93 101 27 31 4 508.73 1.59 102 27 114 87 167.00 2.12 103 27 118 91 165.97 1.76 104 28 31 3 518.01 0.03 105 28 32 4 508.73 1.59 106 28 69 41 179.77 0.51 107 28 107 79 167.77 2.04 108 28 110 82 167.44 2.09 109 28 111 83 167.37 2.09 110 28 114 86 167.00 2.12 111 29 32 3 519.45 0.33 112 29 33 4 507.68 2.12 113 29 61 32 201.56 1.92 114 29 64 35 182.31 0.26 115 29 65 36 180.88 0.92 116 29 107 78 167.84 2.02 117 30 33 3 515.28 2.41 118 30 34 4 506.37 2.78 119 30 52 22 235.41 1.25 120 30 55 25 233.66 0.66 121 30 56 26 235.21 1.18 122 31 34 3 517.87 1.11 123 31 35 4 505.59 2.40 124 31 110 79 167.59 2.06 125 31 113 82 167.47 2.12 126 31 114 83 167.34 2.18 127 32 35 3 510.45 0.03 128 32 36 4 505.57 2.41 129 32 39 7 366.25 1.38 130 32 106 74 167.84 2.02 131 32 107 75 167.85 2.02 132 32 110 78 167.59 2.07 133 33 36 3 514.89 1.78 134 33 37 4 491.59 4.17 135 33 39 6 366.25 1.38 136 33 40 7 334.50 13.86 137 33 43 10 297.19 4.79 138 33 46 13 252.41 1.41 139 33 55 22 235.88 1.43 140 33 61 28 235.27 1.18 141 34 37 3 533.51 0.02 142 34 52 18 235.93 1.43 143 34 55 21 235.93 1.43 144 36 39 3 514.44 2.02 145 36 106 70 168.04 2.04 146 37 40 3 525.94 3.38 147 38 41 3 521.51 5.58 148 38 103 65 168.49 2.02 149 38 106 68 168.31 2.08 150 39 42 3 527.46 2.61 151 39 43 4 525.83 1.79 152 39 103 64 168.22 2.06 153 39 106 67 168.21 2.06 154 40 43 3 525.84 1.79 155 40 46 6 384.15 15.90 156 40 47 7 269.57 4.64 157 40 49 9 265.08 6.88 158 40 55 15 250.96 1.02 159 41 47 6 287.56 6.77 160 42 97 55 169.24 2.16 161 42 98 56 169.21 2.15 162 42 99 57 168.95 2.08 163 42 100 58 169.19 2.16 164 42 103 61 168.69 2.14 165 43 46 3 523.77 1.24 166 43 47 4 482.47 5.34 167 43 64 21 238.62 0.79 168 44 47 3 529.47 0.01 169 45 48 3 603.06 1.44 170 45 60 15 238.96 0.88 171 45 64 19 238.88 0.89 172 46 49 3 536.96 0.72 173 46 60 14 238.94 0.86 174 46 61 15 238.87 0.89 175 46 64 18 238.78 0.84 176 47 50 3 608.04 2.02 177 49 54 5 439.99 13.03 178 49 55 6 394.43 9.84 179 49 58 9 280.39 4.03 180 49 61 12 255.97 0.60 181 50 54 4 519.78 7.83 182 51 54 3 504.69 0.28 183 51 55 4 504.69 0.28 184 52 55 3 508.66 1.70 185 52 56 4 504.69 0.28 186 53 56 3 509.61 1.22 187 53 57 4 504.69 0.28 188 54 57 3 504.68 0.27 189 54 58 4 504.65 0.25 190 55 58 3 505.20 0.04 191 55 61 6 415.87 0.34 192 58 61 3 533.14 2.79 193 58 62 4 506.67 1.73 194 59 62 3 505.90 2.54 195 59 63 4 501.37 4.84 196 60 63 3 505.94 2.56 197 60 64 4 517.46 3.17 198 61 64 3 517.47 3.17 199 61 65 4 517.47 3.17 200 62 65 3 520.98 1.43 201 62 66 4 517.50 3.16 202 63 66 3 520.99 1.43 203 63 67 4 517.50 3.16 204 64 67 3 517.51 3.17 205 64 68 4 517.51 3.17 206 65 68 3 517.97 2.94 207 65 69 4 517.37 3.24 208 66 69 3 518.93 2.46 209 66 70 4 510.67 1.31 210 67 70 3 522.99 2.33 211 67 71 4 511.49 0.89 212 68 71 3 523.29 0.29 213 68 72 4 510.65 1.31 214 68 107 39 167.78 2.06 215 69 72 3 523.20 0.24 216 69 73 4 505.96 0.81 217 70 73 3 523.78 2.21 218 70 74 4 510.37 0.10 219 71 74 3 521.10 3.55 220 71 75 4 513.36 0.06 221 72 75 3 525.44 1.38 222 72 76 4 512.35 0.56 223 72 111 39 167.61 2.03 224 72 135 63 163.88 1.86 225 72 138 66 163.35 1.90 226 73 76 3 516.58 2.66 227 73 77 4 512.38 0.54 228 74 77 3 536.29 0.35 229 74 78 4 512.38 0.54 230 75 78 3 523.83 5.88 231 75 79 4 517.91 3.30 232 75 82 7 209.93 3.20 233 75 85 10 178.77 2.31 234 75 89 14 178.61 2.39 235 75 138 63 163.79 1.76 236 76 79 3 529.54 3.02 237 76 131 55 164.38 1.74 238 76 134 58 164.10 1.78 239 78 81 3 502.79 2.44 240 78 82 4 502.55 2.33 241 78 85 7 301.96 6.40 242 80 137 57 164.18 1.81 243 82 85 3 518.14 1.94 244 82 86 4 510.99 0.20 245 82 137 55 164.22 1.78 246 82 141 59 163.46 1.92 247 83 86 3 515.21 0.04 248 83 87 4 511.00 0.21 249 84 88 4 516.77 0.51 250 85 88 3 543.25 0.53 251 85 89 4 516.74 0.51 252 86 89 3 520.49 0.94 253 86 90 4 514.17 1.79 254 86 138 52 163.49 1.93 255 86 141 55 162.69 2.18 256 86 142 56 160.66 1.68 257 86 145 59 157.86 0.92 258 87 90 3 517.17 0.71 259 87 91 4 513.14 2.31 260 88 91 3 518.33 1.08 261 88 92 4 513.20 2.29 262 89 92 3 516.25 2.01 263 89 93 4 513.20 2.28 264 89 138 49 163.46 1.93 265 90 93 3 514.89 3.14 266 90 94 4 512.19 1.79 267 90 142 52 158.92 0.82 268 90 145 55 153.19 0.45 269 90 146 56 152.41 0.28 270 91 94 3 525.15 2.66 271 91 95 4 512.15 1.79 272 91 149 58 147.97 1.78 273 92 95 3 513.87 0.96 274 92 96 4 495.40 10.17 275 92 97 5 495.39 10.17 276 93 97 4 440.59 8.53 277 93 98 5 440.56 8.52 278 93 99 6 305.56 2.01 279 93 146 53 151.05 0.41 280 94 98 4 384.95 19.28 281 94 146 52 151.03 0.40 282 94 149 55 145.70 1.47 283 94 151 57 108.47 2.81 284 95 98 3 520.35 2.12 285 95 149 54 146.95 0.84 286 95 151 56 121.24 8.40 287 98 151 53 102.09 0.38 288 99 103 4 513.62 0.73 289 99 104 5 509.38 2.85 290 99 146 47 150.77 0.50 291 100 103 3 518.26 1.02 292 100 104 4 513.65 0.74 293 100 152 52 49.88 2.23 294 101 104 3 514.20 1.01 295 101 105 4 511.47 1.82 296 101 139 38 159.57 1.04 297 101 142 41 157.90 0.91 298 101 143 42 154.69 0.08 299 101 146 45 150.13 0.80 300 101 152 51 46.86 0.73 301 102 105 3 515.27 0.07 302 102 106 4 509.42 2.85 303 103 106 3 513.65 0.73 304 103 107 4 515.25 0.07 305 104 107 3 521.34 3.12 306 104 108 4 515.25 0.07 307 104 139 35 159.03 0.83 308 104 142 38 157.50 0.70 309 105 108 3 513.46 0.96 310 105 109 4 513.44 0.96 311 105 139 34 159.03 0.83 312 106 109 3 521.46 3.03 313 106 110 4 513.38 1.01 314 107 110 3 511.80 1.79 315 107 111 4 501.76 0.95 316 108 111 3 519.09 2.66 317 108 112 4 501.77 0.95 318 108 135 27 163.59 1.83 319 108 139 31 159.01 0.83 320 109 112 3 520.67 5.15 321 109 113 4 501.71 0.92 322 110 113 3 522.31 0.12 323 110 114 4 498.31 0.79 324 111 114 3 522.31 0.12 325 111 115 4 500.48 1.88 326 111 135 24 163.59 1.83 327 112 115 3 516.96 2.79 328 112 116 4 498.57 2.83 329 112 123 11 261.69 0.33 330 112 131 19 163.78 1.90 331 112 132 20 163.64 1.83 332 112 135 23 163.61 1.83 333 113 116 3 512.98 1.70 334 113 117 4 509.34 0.12 335 114 117 3 509.50 2.64 336 114 118 4 505.63 0.70 337 115 118 3 517.55 0.59 338 115 119 4 495.90 4.13 339 115 123 8 285.25 12.11 340 115 131 16 184.57 8.50 341 116 120 4 481.84 2.90 342 116 123 7 293.25 15.93 343 117 120 3 539.18 2.78 344 119 122 3 526.65 0.27 345 119 123 4 490.54 0.14 346 120 123 3 491.47 0.58 347 120 124 4 491.44 0.59 348 122 127 5 480.11 14.07 349 123 127 4 489.85 9.21 350 123 128 5 461.97 5.21 351 123 131 8 426.98 9.68 352 124 127 3 514.59 0.89 353 124 128 4 508.34 0.01 354 125 128 3 508.34 0.01 355 125 129 4 504.37 1.98 356 126 129 3 505.80 1.27 357 126 130 4 509.26 3.00 358 127 130 3 514.75 0.27 359 127 131 4 507.85 3.71 360 128 131 3 518.03 1.35 361 128 132 4 507.87 3.73 362 129 132 3 518.03 1.35 363 129 133 4 504.68 5.32 364 130 133 3 515.76 0.22 365 130 134 4 512.10 1.61 366 131 134 3 515.76 0.23 367 131 135 4 510.56 2.38 368 132 135 3 514.83 0.69 369 132 136 4 499.60 3.11 370 133 136 3 511.16 1.15 371 133 137 4 505.62 0.09 372 134 137 3 499.51 0.80 373 134 138 4 505.14 0.15 374 135 138 3 506.11 0.32 375 135 139 4 506.55 0.43 376 136 139 3 510.47 1.53 377 136 140 4 506.04 0.15 378 137 140 3 513.76 0.30 379 137 141 4 506.05 0.14 380 138 141 3 520.37 3.42 381 138 142 4 506.04 0.14 382 139 142 3 513.50 0.07 383 139 143 4 506.03 0.14 384 140 143 3 513.69 3.35 385 140 144 4 506.03 0.14 386 141 144 3 510.74 1.42 387 141 145 4 506.91 0.50 388 142 145 3 513.46 0.99 389 142 146 4 503.67 1.11 390 143 146 3 508.69 1.39 391 143 147 4 503.28 1.31 392 144 147 3 513.45 3.77 393 144 148 4 505.40 0.25 394 145 148 3 510.65 2.00 395 145 149 4 505.36 0.23 396 146 149 3 510.55 2.88 397 146 150 4 502.99 1.42 398 146 151 5 368.05 2.26 399 146 152 6 368.05 2.26 400 147 150 3 508.75 1.98