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 15 37 22 307.57 0.65 2 15 38 23 307.62 0.67 3 15 39 24 307.65 0.67 4 16 36 20 307.68 0.69 5 16 37 21 307.74 0.71 6 17 20 3 769.84 1.44 7 17 34 17 307.79 0.76 8 17 35 18 307.82 0.74 9 17 36 19 307.69 0.69 10 18 35 17 307.85 0.75 11 18 36 18 307.83 0.74 12 18 37 19 307.87 0.73 13 18 43 25 307.92 0.76 14 19 34 15 307.92 0.77 15 19 35 16 307.89 0.76 16 20 32 12 307.98 0.80 17 20 33 13 307.94 0.77 18 20 34 14 307.93 0.77 19 20 50 30 306.89 0.38 20 21 32 11 308.07 0.84 21 21 33 12 307.97 0.79 22 22 30 8 398.89 46.24 23 22 31 9 308.26 0.94 24 22 32 10 308.14 0.87 25 23 31 8 398.89 46.23 26 23 32 9 308.27 0.92 27 23 33 10 308.20 0.86 28 24 30 6 398.92 46.23 29 24 31 7 398.90 46.23 30 25 29 4 615.41 2.44 31 25 30 5 398.92 46.23 32 25 52 27 307.83 0.70 33 26 29 3 630.97 3.48 34 27 52 25 307.91 0.72 35 28 51 23 307.95 0.72 36 28 52 24 307.93 0.72 37 28 53 25 307.86 0.70 38 28 98 70 218.14 5.38 39 29 49 20 308.07 0.69 40 29 50 21 308.00 0.69 41 29 51 22 307.91 0.69 42 29 52 23 307.87 0.69 43 30 49 19 308.06 0.66 44 30 50 20 308.01 0.68 45 30 51 21 307.94 0.67 46 30 52 22 307.88 0.67 47 31 48 17 308.11 0.65 48 31 49 18 308.00 0.64 49 32 47 15 308.17 0.61 50 32 48 16 308.12 0.62 51 32 50 18 308.04 0.61 52 33 45 12 309.12 0.67 53 33 46 13 308.69 0.52 54 34 45 11 309.16 0.66 55 34 46 12 308.72 0.51 56 34 48 14 308.12 0.56 57 35 43 8 397.64 44.27 58 35 44 9 310.22 0.57 59 35 45 10 309.38 0.66 60 36 43 7 397.66 44.27 61 36 44 8 397.60 44.26 62 36 45 9 310.20 0.56 63 36 46 10 310.18 0.57 64 37 41 4 597.41 5.01 65 37 42 5 533.30 8.06 66 38 41 3 648.77 4.77 67 38 42 4 569.20 7.45 68 38 44 6 508.93 3.76 69 46 135 89 43.95 3.91 70 48 136 88 43.94 3.90 71 49 136 87 43.96 3.91 72 49 137 88 43.95 3.90 73 49 138 89 45.30 3.27 74 50 138 88 179.84 64.00 75 51 60 9 311.17 1.45 76 51 139 88 311.07 1.49 77 53 98 45 311.62 1.36 78 54 57 3 677.82 3.81 79 54 59 5 531.07 10.40 80 54 60 6 320.58 3.10 81 54 138 84 417.42 0.50 82 54 140 86 362.26 0.01 83 55 101 46 471.75 2.00 84 56 101 45 479.06 0.09 85 57 99 42 472.12 1.82 86 57 101 44 482.68 0.70 87 58 129 71 402.87 1.04 88 58 140 82 453.86 0.43 89 58 142 84 403.34 3.05 90 59 99 40 483.73 0.39 91 59 129 70 419.12 0.29 92 59 140 81 453.54 0.32 93 59 141 82 420.86 0.56 94 59 142 83 408.04 0.70 95 60 98 38 483.76 0.39 96 60 99 39 483.74 0.38 97 60 139 79 454.19 0.54 98 60 140 80 454.11 0.53 99 61 97 36 483.80 0.40 100 61 98 37 483.76 0.39 101 61 99 38 483.75 0.39 102 61 140 79 454.20 0.54 103 61 141 80 454.12 0.53 104 61 142 81 454.12 0.53 105 62 96 34 483.97 0.44 106 62 97 35 483.82 0.41 107 62 99 37 483.81 0.41 108 62 105 43 483.32 0.48 109 62 108 46 483.24 0.52 110 62 109 47 483.15 0.48 111 62 141 79 454.17 0.55 112 62 142 80 454.13 0.54 113 62 144 82 454.09 0.53 114 63 94 31 484.34 0.56 115 63 95 32 484.26 0.52 116 63 96 33 483.96 0.45 117 63 141 78 454.22 0.54 118 63 142 79 454.19 0.54 119 63 143 80 454.14 0.54 120 63 144 81 454.13 0.54 121 64 94 30 484.44 0.59 122 64 95 31 484.29 0.55 123 64 109 45 483.34 0.48 124 64 113 49 483.25 0.45 125 64 144 80 454.14 0.54 126 64 146 82 454.07 0.52 127 65 94 29 484.71 0.48 128 65 143 78 454.23 0.54 129 65 144 79 454.19 0.54 130 65 145 80 454.13 0.54 131 65 146 81 454.12 0.53 132 65 200 135 96.24 0.99 133 66 77 11 485.63 0.58 134 66 78 12 485.57 0.58 135 66 94 28 485.45 0.63 136 66 95 29 485.01 0.59 137 66 113 47 483.34 0.47 138 66 146 80 454.12 0.53 139 66 148 82 454.07 0.52 140 67 75 8 485.79 0.58 141 67 76 9 485.76 0.55 142 67 77 10 485.63 0.58 143 67 145 78 454.23 0.54 144 67 146 79 454.18 0.54 145 67 147 80 454.12 0.53 146 67 148 81 454.11 0.53 147 68 75 7 485.84 0.57 148 68 76 8 485.76 0.56 149 68 78 10 485.66 0.58 150 68 119 51 480.87 0.87 151 68 148 80 454.12 0.53 152 68 150 82 451.11 0.87 153 68 172 104 201.24 0.53 154 69 75 6 485.87 0.58 155 69 147 78 454.22 0.54 156 69 148 79 454.18 0.55 157 69 149 80 454.12 0.53 158 69 150 81 454.10 0.53 159 70 73 3 634.51 0.45 160 70 76 6 505.29 3.36 161 70 150 80 454.12 0.54 162 70 151 81 454.10 0.53 163 71 151 80 454.15 0.55 164 74 176 102 200.84 0.59 165 75 174 99 200.99 0.60 166 75 175 100 200.87 0.58 167 76 172 96 201.22 0.54 168 76 173 97 201.09 0.56 169 76 174 98 200.89 0.58 170 76 175 99 199.47 0.91 171 77 94 17 493.82 0.32 172 77 172 95 201.20 0.55 173 77 173 96 200.97 0.62 174 77 175 98 194.68 2.39 175 77 178 101 137.69 0.29 176 77 200 123 99.78 1.85 177 78 95 17 491.90 0.64 178 78 117 39 482.70 0.66 179 78 119 41 482.39 0.77 180 78 148 70 454.09 0.52 181 78 170 92 201.69 0.41 182 78 171 93 201.31 0.56 183 78 172 94 201.10 0.54 184 79 92 13 496.79 0.56 185 79 93 14 495.17 0.04 186 79 94 15 493.85 0.30 187 79 95 16 491.92 0.64 188 79 170 91 201.66 0.40 189 79 171 92 201.25 0.53 190 79 173 94 201.09 0.55 191 79 178 99 137.72 0.29 192 79 182 103 130.50 2.01 193 79 197 118 99.76 1.84 194 80 91 11 498.63 1.25 195 80 92 12 497.06 0.68 196 80 93 13 496.75 0.57 197 80 94 14 495.12 0.07 198 80 95 15 493.80 0.33 199 80 116 36 483.07 0.52 200 80 117 37 482.82 0.59 201 80 168 88 201.81 0.43 202 80 169 89 201.76 0.42 203 80 170 90 201.53 0.46 204 81 90 9 498.75 1.28 205 81 91 10 498.40 1.15 206 81 92 11 498.15 1.22 207 81 168 87 201.83 0.43 208 81 169 88 201.76 0.43 209 81 171 90 201.56 0.48 210 81 189 108 104.39 1.81 211 81 191 110 101.64 1.65 212 82 90 8 506.16 4.98 213 82 91 9 498.74 1.28 214 82 93 11 498.60 1.25 215 82 167 85 201.87 0.44 216 82 168 86 201.82 0.44 217 83 88 5 600.24 7.47 218 83 89 6 528.28 2.78 219 83 90 7 506.18 4.99 220 84 87 3 655.83 3.14 221 84 88 4 618.91 1.86 222 84 89 5 541.52 5.08 223 84 91 7 513.94 1.10 224 84 93 9 513.95 1.10 225 85 88 3 631.11 4.24 226 87 91 4 657.11 0.28 227 87 192 105 102.10 1.90 228 90 191 101 102.07 1.88 229 90 192 102 101.62 1.66 230 91 191 100 101.62 1.65 231 91 192 101 101.15 1.59 232 92 171 79 201.53 0.48 233 92 182 90 128.06 2.96 234 92 185 93 121.69 1.54 235 92 191 99 101.62 1.64 236 92 192 100 101.11 1.43 237 92 193 101 100.02 1.80 238 92 194 102 100.02 1.80 239 92 197 105 99.80 1.86 240 93 194 101 99.77 1.85 241 93 197 104 99.70 1.81 242 94 196 102 99.00 1.51 243 94 197 103 99.65 1.84 244 94 200 106 97.12 1.35 245 95 113 18 483.17 0.49 246 95 116 21 482.41 0.78 247 95 117 22 482.36 0.76 248 96 112 16 483.17 0.49 249 96 116 20 482.36 0.76 250 97 112 15 483.12 0.48 251 98 111 13 483.16 0.49 252 98 112 14 483.15 0.49 253 99 103 4 613.04 0.70 254 99 105 6 522.15 6.34 255 99 108 9 483.15 0.49 256 99 142 43 454.21 0.55 257 100 103 3 636.65 2.29 258 103 107 4 633.56 0.79 259 103 108 5 631.50 0.23 260 103 111 8 623.50 2.62 261 104 107 3 653.24 1.56 262 104 108 4 638.74 1.79 263 105 108 3 652.89 1.28 264 105 109 4 641.14 0.59 265 105 126 21 454.15 0.53 266 105 142 37 454.20 0.55 267 105 144 39 454.13 0.54 268 106 109 3 650.52 0.42 269 106 110 4 641.16 0.60 270 106 123 17 454.48 0.69 271 106 126 20 454.19 0.55 272 106 144 38 454.16 0.55 273 107 110 3 650.53 0.42 274 107 111 4 641.85 3.92 275 108 111 3 650.25 0.28 276 108 112 4 641.87 3.91 277 109 112 3 650.00 0.15 278 109 113 4 641.14 0.61 279 109 144 35 454.18 0.56 280 110 113 3 642.21 3.73 281 110 114 4 637.86 1.02 282 110 121 11 454.56 0.68 283 110 122 12 454.55 0.69 284 110 123 13 454.53 0.69 285 110 146 36 454.13 0.54 286 111 114 3 660.47 1.71 287 111 115 4 637.87 1.02 288 112 115 3 651.90 6.00 289 112 116 4 640.76 2.46 290 113 116 3 654.79 4.55 291 113 117 4 632.95 3.41 292 113 118 5 618.16 0.72 293 113 119 6 547.24 1.25 294 113 146 33 454.17 0.56 295 113 148 35 454.03 0.52 296 114 118 4 600.02 7.01 297 114 119 5 555.73 2.98 298 114 120 6 534.17 5.28 299 115 160 45 202.06 0.48 300 115 161 46 201.92 0.44 301 115 162 47 201.87 0.45 302 116 160 44 202.08 0.48 303 116 166 50 201.87 0.44 304 116 168 52 201.71 0.40 305 116 170 54 201.52 0.41 306 117 158 41 202.28 0.45 307 117 160 43 202.08 0.48 308 117 170 53 201.52 0.41 309 118 158 40 202.26 0.45 310 118 159 41 202.16 0.46 311 118 160 42 202.06 0.48 312 119 148 29 454.07 0.53 313 119 155 36 203.11 0.57 314 119 158 39 202.28 0.44 315 120 148 28 454.13 0.55 316 120 154 34 203.40 0.43 317 120 155 35 203.35 0.44 318 121 146 25 454.21 0.56 319 121 147 26 454.16 0.55 320 121 148 27 454.12 0.56 321 122 146 24 454.23 0.57 322 122 147 25 454.17 0.56 323 123 144 21 454.34 0.54 324 123 145 22 454.32 0.55 325 123 146 23 454.22 0.58 326 124 145 21 454.34 0.55 327 124 146 22 454.30 0.54 328 124 147 23 454.23 0.58 329 125 144 19 454.38 0.54 330 125 145 20 454.32 0.55 331 126 144 18 454.37 0.53 332 127 142 15 454.44 0.52 333 127 143 16 454.43 0.52 334 128 142 14 454.57 0.51 335 129 140 11 454.69 0.48 336 129 141 12 454.68 0.48 337 129 142 13 454.59 0.51 338 130 140 10 454.70 0.48 339 130 141 11 454.69 0.49 340 130 143 13 454.67 0.48 341 131 134 3 657.16 2.08 342 131 139 8 454.73 0.48 343 131 140 9 454.71 0.48 344 132 139 7 454.77 0.47 345 132 141 9 454.76 0.48 346 132 196 64 91.08 0.29 347 133 136 3 650.08 2.07 348 133 137 4 595.53 12.24 349 134 137 3 650.08 2.07 350 141 196 55 93.83 0.41 351 148 155 7 521.62 2.46 352 149 152 3 652.82 1.08 353 149 155 6 539.41 10.45 354 150 155 5 539.44 10.44 355 152 155 3 652.86 3.72 356 152 156 4 609.15 5.46 357 153 156 3 647.38 3.33 358 155 158 3 644.26 5.52 359 160 170 10 201.70 0.40 360 162 166 4 544.12 4.55 361 163 166 3 655.12 4.57 362 171 185 14 130.56 2.00 363 173 178 5 546.10 1.06 364 173 181 8 523.42 1.66 365 173 182 9 523.35 1.62 366 173 185 12 523.41 1.65 367 174 177 3 647.31 2.84 368 174 178 4 606.34 0.29 369 174 181 7 554.21 8.32 370 175 178 3 624.35 0.88 371 175 204 29 96.91 1.10 372 177 180 3 653.71 0.34 373 177 181 4 632.09 2.19 374 178 181 3 647.40 2.57 375 178 182 4 632.76 2.47 376 178 200 22 100.17 1.89 377 178 201 23 100.08 1.93 378 178 204 26 99.08 1.81 379 179 182 3 650.86 1.51 380 179 183 4 645.79 4.04 381 179 198 19 100.61 1.81 382 179 201 22 100.08 1.93 383 179 202 23 100.08 1.93 384 179 205 26 98.70 2.00 385 180 183 3 657.86 1.99 386 180 184 4 650.88 1.50 387 180 205 25 98.92 1.89 388 181 184 3 652.90 0.52 389 181 185 4 650.92 1.50 390 182 185 3 664.40 1.85 391 182 186 4 650.93 1.50 392 182 193 11 101.51 1.55 393 182 197 15 101.39 1.54 394 182 201 19 100.17 1.88 395 183 186 3 661.01 3.54 396 183 187 4 650.93 1.50 397 183 198 15 101.45 1.52 398 184 187 3 673.63 0.83 399 184 188 4 650.86 1.46 400 185 188 3 655.21 0.22 401 185 189 4 649.96 1.91 402 185 191 6 537.74 0.02 403 186 190 4 621.20 0.54 404 186 191 5 528.56 4.55 405 186 193 7 304.69 98.36 406 187 190 3 635.87 0.26 407 193 197 4 640.21 6.49 408 193 198 5 628.14 0.47 409 194 197 3 644.74 4.22 410 194 198 4 640.52 6.33 411 195 198 3 654.91 0.87 412 195 199 4 641.50 1.64 413 196 199 3 654.84 0.91 414 196 200 4 641.50 1.64 415 197 200 3 653.46 0.22 416 197 201 4 641.94 1.86 417 198 201 3 646.84 1.00 418 198 202 4 636.75 4.04 419 199 202 3 637.73 3.56 420 199 203 4 637.72 3.56 421 200 203 3 638.33 3.85 422 200 204 4 639.79 3.03 423 201 204 3 638.33 3.85 424 201 205 4 644.92 0.47 425 202 205 3 649.64 1.77 426 202 206 4 644.87 0.44 427 203 206 3 644.89 0.45 428 203 207 4 635.36 5.20 429 204 207 3 645.77 0.92 430 204 208 4 634.60 5.55 431 205 208 3 645.07 0.57