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 1 141 140 23.44 0.72 2 2 134 132 39.18 0.06 3 3 7 4 520.92 1.74 4 3 8 5 520.94 1.73 5 3 11 8 491.53 0.86 6 3 131 128 47.22 0.36 7 3 134 131 40.66 0.69 8 3 135 132 38.96 0.17 9 3 138 135 38.96 0.17 10 4 7 3 529.95 4.54 11 4 8 4 524.97 3.75 12 5 8 3 525.56 3.45 13 5 9 4 525.55 3.45 14 5 80 75 53.86 1.19 15 6 9 3 526.71 4.03 16 6 10 4 525.56 3.45 17 7 10 3 525.54 3.46 18 7 11 4 525.35 3.55 19 7 131 124 74.67 0.88 20 7 134 127 74.69 0.88 21 8 11 3 522.29 2.04 22 8 12 4 516.79 0.73 23 8 77 69 74.70 0.88 24 8 80 72 74.70 0.88 25 8 81 73 74.70 0.88 26 8 135 127 74.70 0.89 27 8 138 130 74.70 0.89 28 9 12 3 522.67 2.22 29 9 13 4 517.50 1.08 30 10 13 3 529.76 1.33 31 10 14 4 521.96 1.14 32 10 127 117 90.48 0.11 33 10 128 118 90.37 0.11 34 10 131 121 90.34 0.10 35 11 14 3 536.09 1.89 36 11 15 4 530.72 2.31 37 11 77 66 90.33 0.10 38 11 131 120 90.38 0.11 39 11 132 121 90.33 0.10 40 11 135 124 90.33 0.10 41 12 15 3 532.04 1.66 42 12 16 4 532.31 1.52 43 12 77 65 90.39 0.11 44 12 78 66 90.39 0.11 45 12 80 68 90.39 0.12 46 13 16 3 532.54 1.40 47 13 17 4 526.99 1.38 48 14 17 3 532.54 1.41 49 14 18 4 526.75 1.27 50 14 116 102 98.25 0.26 51 14 120 106 98.98 0.48 52 14 123 109 98.92 0.50 53 14 124 110 98.84 0.47 54 14 132 118 94.09 0.67 55 15 18 3 528.25 4.03 56 15 19 4 524.74 2.27 57 15 70 55 98.02 0.21 58 15 73 58 96.08 1.12 59 15 74 59 94.12 0.68 60 15 77 62 94.12 0.69 61 15 78 63 94.17 0.70 62 15 132 117 98.03 0.19 63 16 19 3 528.43 3.95 64 16 20 4 524.71 2.26 65 17 20 3 533.86 1.74 66 17 25 8 449.76 3.84 67 17 120 103 101.58 0.05 68 17 123 106 100.06 0.81 69 18 21 3 535.02 1.16 70 18 22 4 498.97 2.92 71 18 25 7 421.44 7.90 72 18 70 52 99.02 0.49 73 18 116 98 100.02 0.83 74 19 78 59 98.73 0.51 75 21 24 3 545.08 4.34 76 21 25 4 516.87 1.73 77 22 25 3 526.52 3.10 78 22 26 4 512.34 0.54 79 22 67 45 132.85 0.86 80 22 70 48 128.94 0.15 81 23 26 3 523.34 0.86 82 23 27 4 510.82 0.24 83 23 63 40 160.97 9.50 84 23 67 44 158.22 10.78 85 24 27 3 527.61 0.61 86 24 28 4 517.15 0.68 87 24 119 95 176.88 1.09 88 25 28 3 530.78 0.98 89 25 29 4 517.15 0.67 90 25 70 45 161.24 9.36 91 25 116 91 175.62 1.97 92 25 119 94 176.88 1.09 93 25 120 95 176.88 1.09 94 26 29 3 530.78 0.98 95 26 30 4 513.06 1.38 96 26 66 40 161.25 9.36 97 26 70 44 161.24 9.35 98 27 30 3 531.38 0.69 99 27 31 4 518.13 3.40 100 27 57 30 217.98 4.63 101 27 63 36 178.84 0.73 102 28 31 3 530.67 1.71 103 28 32 4 522.11 1.42 104 28 115 87 177.68 0.96 105 28 119 91 177.34 0.87 106 29 32 3 526.66 0.85 107 29 33 4 522.12 1.42 108 29 70 41 178.84 0.73 109 29 108 79 178.38 0.70 110 29 111 82 178.16 0.76 111 29 112 83 178.12 0.75 112 29 115 86 177.88 0.86 113 30 33 3 522.71 1.49 114 30 34 4 516.04 0.49 115 30 62 32 208.81 1.44 116 30 66 36 178.97 0.67 117 30 108 78 178.42 0.72 118 31 34 3 526.16 1.27 119 31 35 4 518.79 1.88 120 31 53 22 218.88 4.61 121 31 56 25 218.52 4.40 122 31 57 26 218.85 4.63 123 31 62 31 217.95 4.63 124 32 35 3 522.87 2.93 125 32 36 4 501.03 2.67 126 32 111 79 178.16 0.77 127 32 114 82 178.12 0.77 128 32 115 83 178.09 0.79 129 33 36 3 527.23 0.76 130 33 37 4 518.65 0.30 131 33 40 7 415.24 19.10 132 33 107 74 178.55 0.76 133 33 108 75 178.42 0.72 134 33 111 78 178.16 0.77 135 34 37 3 524.84 1.95 136 34 38 4 494.45 3.36 137 34 40 6 422.55 22.75 138 34 41 7 415.19 19.08 139 34 44 10 348.18 14.43 140 34 56 22 228.49 0.14 141 34 62 28 228.38 0.17 142 35 38 3 536.03 1.02 143 35 53 18 230.16 0.98 144 37 40 3 538.05 5.01 145 37 107 70 178.71 0.70 146 37 110 73 178.69 0.69 147 38 41 3 542.72 5.48 148 39 42 3 526.33 2.72 149 39 104 65 178.85 0.67 150 39 107 68 178.77 0.69 151 40 43 3 532.86 0.55 152 40 44 4 520.70 1.06 153 40 104 64 178.77 0.69 154 40 107 67 178.75 0.69 155 41 44 3 533.96 0.01 156 41 47 6 382.89 3.03 157 41 48 7 295.93 11.89 158 41 50 9 292.66 10.27 159 41 56 15 239.69 2.80 160 42 48 6 304.11 7.81 161 43 98 55 178.94 0.76 162 43 99 56 179.03 0.70 163 43 100 57 179.02 0.70 164 43 101 58 179.06 0.68 165 43 104 61 178.95 0.66 166 44 47 3 522.03 0.80 167 44 48 4 494.99 5.96 168 44 65 21 230.68 0.07 169 45 48 3 539.84 1.29 170 46 49 3 600.28 0.35 171 46 61 15 236.94 2.71 172 47 50 3 535.37 0.98 173 47 61 14 231.90 0.20 174 47 62 15 231.86 0.20 175 47 65 18 231.81 0.21 176 50 55 5 463.50 6.52 177 50 56 6 406.11 22.18 178 50 59 9 296.24 3.38 179 50 62 12 270.27 3.92 180 51 55 4 525.03 3.35 181 52 55 3 525.04 3.35 182 52 56 4 525.03 3.35 183 53 56 3 530.30 0.71 184 53 57 4 525.03 3.35 185 54 57 3 523.05 2.35 186 54 58 4 517.63 0.35 187 55 58 3 528.84 0.55 188 55 59 4 514.48 0.27 189 56 59 3 535.16 1.71 190 56 62 6 465.49 2.77 191 59 62 3 522.48 2.81 192 59 63 4 509.29 0.76 193 60 63 3 525.91 3.04 194 60 64 4 509.29 0.76 195 61 64 3 524.88 0.65 196 61 65 4 507.55 0.24 197 62 65 3 524.87 0.65 198 62 66 4 507.56 0.24 199 63 66 3 524.88 0.65 200 63 67 4 516.64 4.77 201 64 67 3 519.99 3.10 202 64 68 4 516.65 4.77 203 65 68 3 522.89 0.29 204 65 69 4 510.50 1.70 205 66 69 3 528.23 2.48 206 66 70 4 513.02 0.46 207 67 70 3 528.23 2.47 208 67 71 4 509.81 2.04 209 68 71 3 533.40 0.12 210 68 72 4 514.06 4.62 211 69 72 3 529.37 2.14 212 69 73 4 511.61 1.27 213 69 108 39 178.69 0.72 214 70 73 3 518.79 0.33 215 70 74 4 513.28 0.23 216 71 74 3 518.56 2.85 217 71 75 4 518.56 2.85 218 72 75 3 527.84 7.23 219 72 76 4 516.78 3.74 220 73 76 3 518.55 2.85 221 73 77 4 516.77 3.75 222 73 112 39 178.68 0.71 223 73 136 63 176.50 0.73 224 74 77 3 526.31 1.02 225 74 78 4 516.77 3.74 226 75 78 3 527.75 2.54 227 75 79 4 515.96 3.35 228 76 79 3 533.89 2.82 229 76 80 4 518.79 1.94 230 76 83 7 264.93 0.97 231 76 86 10 218.41 11.43 232 76 87 11 240.99 0.13 233 76 90 14 218.36 11.43 234 76 139 63 174.88 0.92 235 77 80 3 527.07 1.25 236 77 132 55 176.98 0.76 237 77 135 58 176.55 0.74 238 79 82 3 503.61 5.99 239 79 83 4 499.99 7.80 240 79 86 7 365.12 3.91 241 81 138 57 176.70 0.66 242 83 86 3 520.34 1.33 243 83 87 4 519.23 1.87 244 83 138 55 176.67 0.65 245 83 142 59 174.05 1.03 246 84 87 3 530.62 3.32 247 84 88 4 525.06 1.43 248 85 88 3 542.82 2.77 249 85 89 4 530.66 3.29 250 86 89 3 553.22 2.42 251 86 90 4 526.21 1.20 252 87 90 3 529.78 0.01 253 87 91 4 524.18 0.95 254 87 139 52 175.28 1.24 255 87 142 55 173.11 0.75 256 87 143 56 171.62 0.32 257 88 91 3 526.84 0.87 258 88 92 4 524.18 0.95 259 88 146 58 168.14 0.42 260 89 92 3 522.05 3.27 261 89 93 4 517.73 2.28 262 90 93 3 528.14 0.23 263 90 94 4 514.99 3.62 264 90 139 49 175.69 1.02 265 90 143 53 171.30 0.14 266 91 94 3 525.88 0.90 267 91 95 4 509.80 1.02 268 91 143 52 168.91 0.37 269 91 146 55 160.83 1.16 270 91 147 56 159.32 0.41 271 91 150 59 152.52 1.67 272 92 95 3 530.97 4.38 273 92 96 4 505.40 2.16 274 92 150 58 154.43 0.29 275 93 96 3 531.85 3.93 276 93 97 4 493.55 7.78 277 93 98 5 435.53 5.74 278 94 98 4 422.03 1.00 279 94 99 5 410.12 6.95 280 94 100 6 350.50 17.70 281 94 147 53 159.31 0.42 282 95 99 4 410.12 6.95 283 95 147 52 159.27 0.42 284 95 150 55 153.29 3.01 285 95 152 57 102.72 4.24 286 96 99 3 529.54 2.24 287 99 152 53 102.84 4.30 288 100 104 4 516.01 4.92 289 100 105 5 513.84 6.00 290 100 147 47 159.28 0.42 291 100 152 52 102.84 4.30 292 101 104 3 524.78 0.54 293 101 105 4 520.71 2.57 294 101 152 51 105.63 2.91 295 101 154 53 20.63 2.91 296 102 105 3 521.26 2.29 297 102 106 4 513.90 5.97 298 102 140 38 171.76 0.23 299 102 143 41 168.74 0.36 300 102 144 42 163.43 0.06 301 102 147 45 159.24 0.41 302 102 154 52 19.64 2.42 303 103 106 3 519.32 6.58 304 103 107 4 513.90 5.97 305 104 107 3 519.20 3.33 306 104 108 4 517.65 4.09 307 105 108 3 529.33 1.57 308 105 109 4 517.82 4.20 309 105 140 35 171.62 0.30 310 105 143 38 168.64 0.32 311 105 147 42 159.24 0.41 312 106 109 3 529.62 1.43 313 106 110 4 517.82 4.20 314 106 140 34 171.62 0.30 315 107 110 3 524.38 0.92 316 107 111 4 517.06 4.58 317 108 111 3 511.48 0.97 318 108 112 4 508.98 0.21 319 109 112 3 513.80 4.68 320 109 113 4 511.97 1.70 321 109 136 27 176.11 0.84 322 109 140 31 171.62 0.30 323 110 113 3 526.47 1.66 324 110 114 4 512.90 1.24 325 111 114 3 528.31 1.59 326 111 115 4 523.45 4.02 327 112 115 3 532.80 3.85 328 112 116 4 523.46 4.01 329 112 136 24 176.15 0.86 330 113 116 3 523.47 4.01 331 113 117 4 523.46 4.01 332 113 124 11 268.77 6.19 333 113 129 16 197.33 9.41 334 113 132 19 197.11 9.46 335 113 133 20 197.09 9.45 336 113 136 23 176.50 0.72 337 114 117 3 528.86 1.31 338 114 118 4 512.86 1.28 339 115 118 3 519.79 3.22 340 115 119 4 513.33 1.51 341 116 119 3 522.52 3.08 342 116 120 4 480.64 3.85 343 116 124 8 274.79 3.90 344 116 132 16 240.58 0.57 345 117 121 4 455.43 6.05 346 117 124 7 268.89 6.13 347 117 129 12 240.57 0.55 348 118 121 3 556.10 1.55 349 120 123 3 516.95 1.72 350 120 124 4 456.76 0.65 351 121 124 3 466.13 3.71 352 123 128 5 469.10 8.58 353 124 128 4 474.72 5.78 354 124 129 5 469.10 8.58 355 124 132 8 444.26 0.15 356 125 128 3 515.20 2.69 357 125 129 4 500.48 2.50 358 126 129 3 507.51 0.83 359 126 130 4 500.56 2.46 360 127 130 3 519.52 1.54 361 127 131 4 491.84 1.92 362 128 131 3 521.48 4.59 363 128 132 4 491.97 1.86 364 129 132 3 528.05 1.30 365 129 133 4 502.29 3.29 366 130 133 3 513.22 1.66 367 130 134 4 502.29 3.29 368 131 134 3 520.03 1.81 369 131 135 4 506.89 1.35 370 132 135 3 519.08 2.29 371 132 136 4 502.66 3.47 372 133 136 3 519.84 1.74 373 133 137 4 502.38 3.61 374 134 137 3 513.95 2.16 375 134 138 4 492.38 1.20 376 135 138 3 517.48 0.39 377 135 139 4 511.73 1.38 378 136 139 3 511.73 1.38 379 136 140 4 511.74 1.39 380 137 140 3 512.52 0.99 381 137 141 4 511.73 1.39 382 138 141 3 513.92 2.18 383 138 142 4 511.74 1.37 384 139 142 3 520.74 2.20 385 139 143 4 512.55 1.89 386 140 143 3 524.11 0.52 387 140 144 4 518.87 2.10 388 141 144 3 519.43 1.83 389 141 145 4 518.90 2.10 390 142 145 3 518.97 2.06 391 142 146 4 519.62 1.73 392 143 146 3 519.62 1.73 393 143 147 4 514.56 0.80 394 144 147 3 521.88 2.85 395 144 148 4 519.61 1.72 396 145 148 3 501.86 7.15 397 145 149 4 495.22 10.47 398 146 149 3 510.35 2.90 399 146 150 4 503.79 6.17 400 147 150 3 514.50 0.81 401 147 151 4 495.17 10.47 402 147 152 5 416.60 9.04 403 147 154 7 269.20 7.93 404 148 151 3 508.92 3.57 405 148 152 4 459.48 3.42