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 5 500.50 3.06 2 2 10 8 475.45 15.42 3 2 130 128 34.04 3.45 4 2 133 131 25.73 1.59 5 2 134 132 25.62 1.54 6 2 137 135 25.62 1.55 7 3 6 3 518.73 0.52 8 3 7 4 513.25 3.25 9 4 7 3 520.87 0.56 10 4 8 4 509.16 1.20 11 5 8 3 513.26 3.25 12 5 9 4 509.29 1.20 13 6 9 3 511.31 2.20 14 6 10 4 509.29 1.20 15 6 130 124 67.30 0.61 16 6 133 127 67.31 0.62 17 7 10 3 511.82 0.06 18 7 11 4 514.25 1.28 19 7 76 69 67.31 0.62 20 7 79 72 67.31 0.61 21 7 80 73 67.34 0.62 22 7 134 127 67.31 0.62 23 7 137 130 67.31 0.62 24 8 11 3 514.26 1.29 25 8 12 4 514.24 1.30 26 9 12 3 514.25 1.30 27 9 13 4 514.25 1.30 28 9 126 117 80.34 1.36 29 9 127 118 80.28 1.38 30 9 130 121 80.19 1.40 31 10 13 3 524.44 0.39 32 10 14 4 510.40 3.22 33 10 76 66 80.21 1.41 34 10 130 120 80.23 1.42 35 10 131 121 80.20 1.41 36 10 134 124 80.18 1.40 37 11 14 3 512.68 2.08 38 11 15 4 511.04 2.90 39 11 76 65 80.27 1.43 40 11 77 66 80.31 1.43 41 11 79 68 80.34 1.41 42 12 15 3 520.17 1.74 43 13 16 3 529.58 2.96 44 13 17 4 507.30 0.03 45 13 123 110 86.13 0.71 46 13 127 114 86.12 0.71 47 13 131 118 86.09 0.71 48 14 17 3 519.40 5.75 49 14 18 4 507.16 0.54 50 14 69 55 178.06 3.79 51 14 72 58 126.83 19.64 52 14 73 59 86.10 0.72 53 14 76 62 86.09 0.72 54 14 77 63 86.09 0.72 55 14 131 117 86.12 0.71 56 15 18 3 508.08 0.09 57 15 19 4 507.16 0.55 58 16 19 3 513.16 0.69 59 16 24 8 419.09 8.35 60 16 119 103 99.34 0.96 61 17 20 3 512.13 1.20 62 17 21 4 486.20 0.42 63 17 24 7 415.32 6.48 64 17 69 52 210.87 2.76 65 17 115 98 99.36 0.96 66 18 21 3 511.38 1.57 67 18 77 59 160.72 3.42 68 20 23 3 518.46 3.33 69 20 24 4 506.03 0.66 70 21 24 3 519.27 0.77 71 21 25 4 506.88 1.07 72 21 66 45 212.75 2.95 73 21 69 48 212.37 3.12 74 21 70 49 212.72 2.94 75 22 25 3 506.89 1.07 76 22 26 4 512.32 3.79 77 22 62 40 213.57 2.84 78 22 66 44 213.03 2.93 79 23 26 3 532.96 3.18 80 23 27 4 512.88 3.60 81 23 62 39 213.67 2.84 82 24 27 3 518.69 0.70 83 24 28 4 512.42 3.83 84 24 69 45 213.03 2.93 85 24 114 90 158.10 3.53 86 24 115 91 158.09 3.53 87 24 118 94 154.79 2.10 88 24 119 95 154.80 2.10 89 25 28 3 518.68 0.70 90 25 29 4 512.49 3.79 91 25 65 40 213.13 2.97 92 25 69 44 213.04 2.93 93 26 29 3 521.38 2.04 94 26 30 4 512.48 3.79 95 26 61 35 213.71 2.85 96 26 62 36 213.69 2.84 97 26 65 39 213.59 2.83 98 27 30 3 523.00 1.22 99 27 31 4 512.51 3.81 100 27 114 87 158.13 3.54 101 27 118 91 157.57 3.40 102 28 31 3 519.02 3.21 103 28 32 4 512.51 3.81 104 28 69 41 213.64 2.81 105 28 107 79 158.77 3.52 106 28 110 82 158.58 3.56 107 28 111 83 158.41 3.57 108 28 114 86 158.14 3.54 109 29 32 3 513.26 3.43 110 29 33 4 512.47 3.83 111 29 61 32 214.25 2.58 112 29 64 35 213.73 2.83 113 29 65 36 213.69 2.81 114 29 107 78 158.78 3.52 115 30 33 3 509.59 2.38 116 30 34 4 498.22 1.52 117 30 52 22 222.37 6.25 118 30 55 25 221.36 5.78 119 30 56 26 221.41 5.77 120 30 61 31 214.41 2.62 121 31 34 3 516.31 0.98 122 31 35 4 496.97 2.14 123 31 110 79 158.70 3.54 124 31 113 82 158.53 3.62 125 31 114 83 158.52 3.62 126 31 117 86 158.23 3.48 127 32 35 3 506.75 1.20 128 32 36 4 487.66 2.52 129 32 39 7 317.85 6.41 130 32 106 74 158.84 3.50 131 32 107 75 158.81 3.52 132 32 110 78 158.71 3.52 133 33 37 4 460.80 5.63 134 33 39 6 351.63 4.68 135 33 40 7 296.68 8.89 136 33 43 10 287.73 5.14 137 33 46 13 261.61 0.04 138 33 55 22 222.50 6.27 139 33 61 28 221.59 5.83 140 34 37 3 529.31 0.70 141 34 52 18 222.97 6.04 142 34 55 21 222.97 6.04 143 36 39 3 531.16 2.81 144 36 106 70 159.34 3.35 145 36 109 73 159.09 3.48 146 37 40 3 527.83 1.55 147 38 41 3 526.15 2.39 148 38 103 65 160.00 3.21 149 38 106 68 159.97 3.21 150 39 42 3 530.90 0.01 151 39 43 4 526.15 2.39 152 39 103 64 159.83 3.28 153 39 106 67 159.49 3.33 154 40 43 3 527.01 2.18 155 40 46 6 418.09 25.65 156 40 47 7 302.07 1.60 157 40 55 15 243.65 2.38 158 41 47 6 341.41 15.34 159 42 97 55 160.67 3.34 160 42 98 56 160.67 3.34 161 42 99 57 160.58 3.35 162 42 103 61 160.48 3.39 163 43 46 3 522.42 1.64 164 43 47 4 515.05 2.33 165 43 64 21 224.72 6.92 166 44 47 3 530.88 1.71 167 44 48 4 532.62 0.83 168 45 48 3 598.38 2.78 169 45 60 15 231.43 3.64 170 46 49 3 533.49 1.27 171 46 60 14 231.43 3.62 172 46 61 15 231.40 3.64 173 46 64 18 231.38 3.64 174 48 54 6 504.92 0.45 175 49 54 5 468.30 2.38 176 49 55 6 444.08 6.70 177 49 58 9 293.83 0.38 178 49 61 12 275.01 6.12 179 50 54 4 508.94 1.55 180 51 54 3 512.97 1.49 181 51 55 4 508.94 1.55 182 52 55 3 510.21 2.19 183 52 56 4 506.37 0.82 184 53 56 3 508.60 1.38 185 53 57 4 506.37 0.82 186 54 57 3 506.37 0.82 187 54 58 4 505.12 0.29 188 55 58 3 505.23 0.34 189 55 61 6 450.36 9.79 190 58 61 3 524.02 3.39 191 58 62 4 511.85 2.04 192 59 62 3 516.08 0.07 193 59 63 4 511.85 2.04 194 60 63 3 511.85 2.04 195 60 64 4 511.84 2.04 196 61 64 3 512.35 1.79 197 61 65 4 511.84 2.05 198 62 65 3 510.36 0.81 199 62 66 4 505.87 0.99 200 63 66 3 508.80 0.47 201 63 67 4 508.72 0.52 202 64 67 3 510.11 0.18 203 64 68 4 508.69 0.53 204 65 68 3 511.81 1.02 205 65 69 4 508.77 0.49 206 66 69 3 522.76 1.59 207 66 70 4 509.56 2.41 208 67 70 3 523.05 2.10 209 67 71 4 511.82 3.51 210 68 71 3 521.60 1.38 211 68 72 4 511.83 3.50 212 68 107 39 158.75 3.51 213 69 72 3 521.59 1.38 214 69 73 4 512.19 3.32 215 69 111 42 158.51 3.52 216 70 73 3 521.08 1.12 217 70 74 4 512.19 3.31 218 71 74 3 509.96 2.20 219 71 75 4 509.95 2.20 220 72 75 3 509.93 2.19 221 72 76 4 511.78 1.27 222 72 111 39 158.61 3.47 223 72 135 63 152.83 2.13 224 72 138 66 151.22 1.87 225 73 76 3 516.33 1.02 226 73 77 4 508.84 0.24 227 74 77 3 529.00 2.32 228 74 78 4 513.38 2.50 229 75 78 3 529.17 2.24 230 75 82 7 273.42 9.44 231 75 85 10 202.96 17.54 232 75 86 11 202.96 17.54 233 75 89 14 161.05 3.42 234 75 138 63 151.66 1.78 235 76 79 3 511.30 0.99 236 76 134 58 152.94 2.10 237 78 81 3 501.72 2.98 238 78 82 4 405.50 8.60 239 78 85 7 312.12 9.79 240 80 137 57 153.03 2.12 241 82 85 3 518.35 0.46 242 82 86 4 518.35 0.46 243 82 137 55 153.02 2.10 244 82 141 59 151.38 1.95 245 83 86 3 530.05 3.85 246 83 87 4 518.37 0.46 247 84 87 3 530.56 3.62 248 84 88 4 530.56 3.62 249 85 88 3 548.60 0.08 250 85 89 4 530.06 3.87 251 86 89 3 530.07 3.87 252 86 90 4 523.28 0.48 253 86 138 52 151.93 2.10 254 86 141 55 150.66 2.09 255 86 142 56 150.00 2.39 256 87 90 3 520.08 1.12 257 87 91 4 511.37 1.67 258 87 145 58 148.91 2.78 259 88 91 3 517.90 3.03 260 88 92 4 508.05 0.03 261 89 92 3 537.75 3.93 262 89 93 4 506.22 1.51 263 89 138 49 151.94 2.10 264 89 142 53 149.91 2.43 265 90 93 3 512.42 4.59 266 90 94 4 505.91 1.66 267 90 142 52 149.74 2.51 268 90 145 55 146.83 1.73 269 90 146 56 145.71 1.19 270 91 94 3 520.31 0.65 271 91 95 4 500.56 3.75 272 91 149 58 134.20 0.07 273 92 95 3 519.67 0.96 274 92 96 4 470.75 5.67 275 92 97 5 454.31 13.88 276 93 97 4 431.68 2.58 277 93 98 5 405.38 6.99 278 93 99 6 316.92 2.54 279 93 142 49 149.81 2.48 280 93 146 53 145.69 1.16 281 94 98 4 405.38 7.00 282 94 146 52 145.69 1.15 283 94 149 55 134.10 0.03 284 94 151 57 112.17 1.61 285 95 98 3 527.88 2.96 286 95 149 54 137.87 0.31 287 95 151 56 120.33 1.52 288 99 103 4 514.85 0.48 289 99 104 5 514.85 0.48 290 99 146 47 145.69 1.16 291 100 103 3 523.00 3.58 292 100 104 4 514.86 0.48 293 100 153 53 37.34 3.29 294 101 104 3 523.00 3.58 295 101 105 4 514.87 0.48 296 101 143 42 147.94 1.99 297 101 146 45 145.67 1.16 298 101 152 51 45.05 0.49 299 101 153 52 35.09 4.42 300 102 105 3 526.98 1.59 301 102 106 4 514.85 0.48 302 102 153 51 38.05 2.75 303 103 106 3 517.05 0.62 304 103 107 4 512.38 1.72 305 104 107 3 527.38 2.54 306 104 108 4 509.06 0.04 307 104 139 35 150.32 2.30 308 104 142 38 149.72 2.50 309 105 108 3 514.35 2.06 310 105 109 4 512.94 1.90 311 105 139 34 150.32 2.30 312 106 109 3 519.39 1.45 313 106 110 4 514.16 1.28 314 107 110 3 514.16 1.28 315 107 111 4 506.07 1.80 316 108 111 3 514.16 1.28 317 108 112 4 505.44 2.12 318 108 135 27 152.86 2.17 319 108 139 31 150.32 2.30 320 109 112 3 517.70 3.06 321 109 113 4 499.34 5.15 322 110 113 3 502.97 4.28 323 110 114 4 499.32 5.19 324 111 114 3 521.86 5.46 325 111 115 4 504.13 2.77 326 111 135 24 152.99 2.11 327 112 115 3 522.91 4.94 328 112 116 4 487.87 0.53 329 112 123 11 252.81 9.23 330 112 131 19 153.06 2.11 331 112 132 20 153.03 2.10 332 112 135 23 153.02 2.10 333 113 116 3 525.16 3.81 334 113 117 4 501.14 6.23 335 114 117 3 509.40 2.10 336 114 118 4 486.47 0.18 337 115 118 3 523.76 3.60 338 115 119 4 478.31 2.34 339 115 123 8 274.37 1.14 340 115 131 16 153.06 2.11 341 116 120 4 462.25 2.21 342 116 123 7 272.12 0.42 343 116 128 12 252.78 9.25 344 117 120 3 536.85 2.17 345 119 122 3 514.34 1.58 346 119 123 4 481.10 9.85 347 120 123 3 514.31 2.54 348 122 127 5 490.52 5.01 349 123 127 4 491.36 4.60 350 123 128 5 490.54 5.03 351 123 131 8 472.25 4.12 352 124 127 3 521.63 2.50 353 124 128 4 495.92 2.40 354 125 128 3 508.68 3.98 355 125 129 4 514.55 2.11 356 126 129 3 518.74 0.04 357 126 130 4 514.55 2.12 358 127 130 3 518.73 0.03 359 127 131 4 500.65 9.06 360 128 131 3 516.75 1.02 361 128 132 4 513.66 2.57 362 129 132 3 516.28 1.26 363 129 133 4 515.73 1.53 364 130 133 3 520.09 3.32 365 130 134 4 508.85 0.34 366 131 134 3 518.33 4.20 367 131 135 4 514.18 2.33 368 132 135 3 520.06 0.60 369 132 136 4 503.69 2.92 370 133 136 3 514.19 2.33 371 133 137 4 503.76 2.88 372 134 137 3 511.96 0.74 373 134 138 4 507.95 0.78 374 135 138 3 504.74 2.89 375 135 139 4 498.03 0.02 376 136 139 3 508.59 2.65 377 136 140 4 501.22 1.04 378 137 140 3 515.15 0.64 379 137 141 4 498.76 0.20 380 138 141 3 515.29 0.64 381 138 142 4 498.77 0.20 382 139 142 3 511.26 3.46 383 139 143 4 498.77 0.20 384 140 143 3 504.73 2.78 385 140 144 4 501.34 1.08 386 141 144 3 508.53 4.82 387 141 145 4 501.27 1.12 388 142 145 3 508.60 4.79 389 142 146 4 503.65 2.31 390 143 146 3 507.72 4.34 391 143 147 4 501.27 1.12 392 143 152 9 348.20 28.69 393 144 147 3 519.91 5.07 394 144 148 4 498.79 0.12 395 145 148 3 516.30 0.70 396 145 149 4 497.40 0.58 397 146 149 3 507.32 3.79 398 146 150 4 498.46 0.03 399 146 151 5 464.94 1.58 400 146 152 6 407.67 1.00 401 147 150 3 508.87 5.18 402 147 151 4 484.97 6.76 403 147 152 5 464.23 1.25