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 36 21 307.97 0.55 2 15 37 22 307.97 0.55 3 15 38 23 308.19 0.76 4 15 39 24 308.95 0.89 5 16 36 20 308.47 0.78 6 16 37 21 309.02 1.05 7 17 20 3 748.41 2.46 8 17 34 17 308.45 0.79 9 17 35 18 308.77 0.93 10 17 36 19 308.48 0.78 11 18 35 17 309.43 0.93 12 18 36 18 309.44 0.95 13 18 37 19 309.48 0.95 14 18 43 25 309.75 0.81 15 19 34 15 309.55 0.90 16 19 35 16 309.49 0.94 17 20 32 12 309.44 0.95 18 20 33 13 309.67 0.84 19 20 34 14 309.55 0.90 20 20 50 30 307.30 0.54 21 21 32 11 309.67 0.84 22 21 33 12 309.69 0.84 23 22 25 3 709.27 4.33 24 22 31 9 309.76 0.81 25 22 32 10 309.70 0.85 26 23 31 8 309.83 0.80 27 23 32 9 309.85 0.80 28 23 33 10 309.87 0.81 29 24 30 6 385.17 36.86 30 24 31 7 309.86 0.80 31 25 29 4 615.41 2.44 32 25 30 5 385.16 36.86 33 25 52 27 309.65 0.83 34 26 29 3 644.56 3.31 35 26 52 26 309.83 0.81 36 27 52 25 309.85 0.81 37 28 51 23 309.88 0.80 38 28 52 24 309.85 0.81 39 28 53 25 309.85 0.81 40 29 49 20 310.05 0.78 41 29 50 21 309.95 0.78 42 29 51 22 309.88 0.80 43 29 52 23 309.87 0.80 44 30 49 19 310.06 0.78 45 30 50 20 310.01 0.78 46 30 51 21 309.97 0.79 47 30 52 22 309.91 0.81 48 31 47 16 310.18 0.79 49 31 48 17 310.10 0.79 50 31 49 18 310.06 0.78 51 32 47 15 310.18 0.79 52 32 48 16 310.12 0.80 53 32 50 18 310.11 0.80 54 33 45 12 310.53 0.72 55 33 46 13 310.43 0.77 56 34 45 11 310.53 0.72 57 34 46 12 310.43 0.77 58 34 48 14 310.21 0.79 59 35 43 8 476.56 3.55 60 35 44 9 389.71 39.85 61 35 45 10 310.53 0.72 62 36 43 7 476.50 3.52 63 36 44 8 389.73 39.86 64 36 45 9 389.73 39.86 65 36 46 10 389.70 39.84 66 37 41 4 597.41 5.01 67 37 42 5 509.01 3.72 68 38 41 3 648.77 4.77 69 38 42 4 550.06 0.31 70 38 44 6 493.10 4.16 71 46 135 89 325.53 3.20 72 48 136 88 325.56 3.20 73 49 136 87 325.59 3.20 74 49 137 88 325.56 3.19 75 49 138 89 325.62 3.19 76 50 138 88 325.66 3.17 77 51 60 9 325.68 3.18 78 51 98 47 325.63 3.19 79 51 139 88 325.69 3.19 80 53 98 45 339.67 1.71 81 54 58 4 645.77 2.72 82 54 60 6 513.70 4.70 83 54 138 84 401.85 0.18 84 54 139 85 364.28 0.80 85 54 140 86 357.12 2.62 86 55 58 3 660.37 1.30 87 55 59 4 651.33 0.06 88 55 60 5 593.22 11.37 89 55 99 44 355.08 2.75 90 55 100 45 355.87 3.15 91 55 101 46 354.57 2.88 92 59 99 40 449.84 1.06 93 59 129 70 419.16 4.83 94 59 140 81 448.93 0.86 95 59 141 82 425.72 2.77 96 59 142 83 411.19 3.12 97 60 98 38 449.85 1.06 98 60 99 39 449.84 1.06 99 60 139 79 449.76 1.10 100 60 140 80 449.70 1.10 101 61 97 36 449.88 1.07 102 61 98 37 449.85 1.05 103 61 99 38 449.85 1.06 104 61 140 79 449.77 1.09 105 61 141 80 449.69 1.10 106 61 142 81 449.69 1.10 107 62 96 34 450.06 1.09 108 62 97 35 449.99 1.11 109 62 99 37 449.99 1.10 110 62 105 43 449.72 1.10 111 62 108 46 449.75 1.10 112 62 109 47 449.72 1.10 113 62 141 79 449.74 1.10 114 62 142 80 449.71 1.10 115 62 144 82 449.62 1.12 116 63 94 31 450.36 1.02 117 63 95 32 450.11 1.08 118 63 96 33 450.07 1.09 119 63 141 78 449.81 1.09 120 63 142 79 449.76 1.10 121 63 143 80 449.72 1.09 122 63 144 81 449.71 1.09 123 63 196 133 100.87 0.50 124 64 94 30 450.41 0.99 125 64 95 31 450.30 1.03 126 64 109 45 449.92 1.16 127 64 113 49 449.97 1.13 128 64 144 80 449.72 1.09 129 64 146 82 449.63 1.11 130 65 94 29 450.49 0.99 131 65 143 78 449.83 1.10 132 65 144 79 449.75 1.10 133 65 145 80 449.71 1.09 134 65 146 81 449.70 1.09 135 65 200 135 99.23 0.06 136 66 76 10 451.31 0.84 137 66 77 11 450.72 1.01 138 66 78 12 450.56 0.97 139 66 94 28 450.56 0.99 140 66 95 29 450.54 0.99 141 66 113 47 450.35 1.02 142 66 146 80 449.72 1.09 143 66 148 82 449.60 1.13 144 67 75 8 451.40 0.84 145 67 76 9 451.31 0.84 146 67 77 10 451.12 0.84 147 67 145 78 449.82 1.09 148 67 146 79 449.74 1.10 149 67 147 80 449.66 1.12 150 67 148 81 449.63 1.11 151 68 75 7 451.40 0.84 152 68 76 8 451.36 0.84 153 68 78 10 451.22 0.80 154 68 119 51 450.50 1.00 155 68 148 80 449.64 1.11 156 68 150 82 448.13 1.21 157 69 75 6 451.42 0.84 158 69 147 78 449.80 1.10 159 69 148 79 449.73 1.10 160 69 149 80 449.70 1.10 161 69 150 81 449.62 1.11 162 70 73 3 635.92 1.15 163 70 76 6 521.60 11.96 164 70 150 80 449.68 1.11 165 70 151 81 449.62 1.11 166 71 151 80 449.69 1.11 167 74 176 102 199.84 0.86 168 75 174 99 200.25 0.96 169 75 175 100 199.79 0.83 170 76 172 96 200.87 0.66 171 76 173 97 200.25 0.96 172 76 174 98 199.74 0.87 173 76 175 99 198.84 1.22 174 77 94 17 475.69 0.32 175 77 172 95 200.57 0.81 176 77 173 96 200.22 0.95 177 77 175 98 194.68 2.38 178 77 178 101 137.62 0.32 179 77 200 123 102.87 0.86 180 78 95 17 475.43 0.45 181 78 117 39 453.27 1.24 182 78 119 41 452.88 1.16 183 78 148 70 449.63 1.12 184 78 170 92 201.31 0.47 185 78 171 93 201.20 0.51 186 78 172 94 199.88 0.88 187 79 92 13 476.22 0.27 188 79 93 14 476.13 0.24 189 79 94 15 475.91 0.35 190 79 95 16 475.69 0.32 191 79 170 91 201.27 0.47 192 79 171 92 201.02 0.58 193 79 173 94 199.97 0.83 194 79 178 99 137.60 0.31 195 79 182 103 125.17 1.58 196 79 197 118 102.79 0.93 197 80 92 12 482.25 2.75 198 80 93 13 476.18 0.26 199 80 94 14 476.16 0.25 200 80 95 15 475.93 0.19 201 80 116 36 454.48 1.59 202 80 117 37 454.38 1.61 203 80 168 88 201.44 0.47 204 80 169 89 201.34 0.48 205 80 170 90 201.26 0.46 206 81 90 9 494.56 0.65 207 81 91 10 493.79 0.42 208 81 92 11 489.73 0.98 209 81 168 87 201.45 0.47 210 81 169 88 201.39 0.47 211 81 171 90 201.33 0.48 212 81 189 108 105.33 0.47 213 81 191 110 104.83 0.30 214 82 90 8 494.80 0.53 215 82 91 9 494.55 0.64 216 82 93 11 494.04 0.42 217 82 167 85 201.47 0.48 218 82 168 86 201.44 0.47 219 83 88 5 600.25 7.49 220 83 89 6 528.39 2.79 221 83 90 7 494.81 0.54 222 84 87 3 635.57 1.65 223 84 88 4 616.15 11.71 224 84 89 5 545.62 4.49 225 84 91 7 518.31 1.19 226 84 93 9 505.09 3.33 227 85 88 3 634.53 2.52 228 87 91 4 657.11 0.28 229 87 192 105 105.08 0.38 230 90 191 101 105.02 0.40 231 90 192 102 104.84 0.31 232 91 191 100 104.81 0.29 233 91 192 101 104.25 0.39 234 92 171 79 201.26 0.47 235 92 182 90 121.53 1.50 236 92 185 93 117.17 3.69 237 92 191 99 104.73 0.27 238 92 192 100 104.25 0.39 239 92 193 101 104.19 0.38 240 92 194 102 103.97 0.49 241 92 197 105 102.92 0.99 242 93 194 101 102.59 1.02 243 93 197 104 102.03 0.90 244 94 196 102 102.03 0.90 245 94 197 103 101.14 0.46 246 94 200 106 100.41 0.62 247 95 113 18 454.50 1.58 248 95 116 21 454.61 1.56 249 95 117 22 454.60 1.57 250 96 112 16 454.63 1.57 251 96 116 20 454.88 1.50 252 97 112 15 454.75 1.55 253 98 111 13 455.43 1.49 254 99 103 4 619.31 5.06 255 99 105 6 547.97 10.16 256 99 108 9 455.43 1.50 257 99 142 43 449.81 1.12 258 100 103 3 635.68 2.77 259 103 107 4 632.25 1.45 260 103 108 5 623.16 2.78 261 103 111 8 622.64 3.06 262 104 107 3 643.40 3.35 263 104 108 4 633.53 0.81 264 105 108 3 652.89 1.28 265 105 109 4 635.89 1.97 266 105 126 21 451.30 1.13 267 105 142 37 449.88 1.11 268 105 144 39 449.84 1.10 269 106 109 3 645.66 2.85 270 106 110 4 645.04 2.55 271 106 123 17 454.68 1.42 272 106 126 20 451.36 1.16 273 106 144 38 449.85 1.11 274 107 110 3 646.30 2.54 275 107 111 4 635.94 2.00 276 108 111 3 649.94 0.12 277 108 112 4 642.57 3.79 278 109 112 3 649.91 0.12 279 109 113 4 634.86 0.07 280 109 144 35 449.83 1.09 281 110 113 3 642.81 0.22 282 110 114 4 637.33 1.28 283 110 121 11 478.07 3.12 284 110 122 12 455.25 1.44 285 110 123 13 455.17 1.41 286 110 146 36 449.72 1.09 287 111 114 3 660.47 1.71 288 111 115 4 637.87 1.02 289 112 115 3 653.17 5.36 290 112 116 4 637.87 1.02 291 113 116 3 660.50 1.70 292 113 117 4 637.80 0.99 293 113 118 5 623.72 2.40 294 113 119 6 571.34 4.04 295 113 121 8 533.43 0.93 296 113 146 33 449.72 1.09 297 113 148 35 449.61 1.10 298 114 117 3 658.09 0.52 299 114 118 4 606.55 1.61 300 114 119 5 593.21 4.36 301 114 120 6 571.31 4.02 302 115 160 45 201.68 0.44 303 115 161 46 201.59 0.47 304 115 162 47 201.58 0.47 305 116 160 44 201.78 0.44 306 116 166 50 201.47 0.47 307 116 170 54 201.26 0.48 308 117 158 41 202.07 0.51 309 117 160 43 201.83 0.46 310 117 170 53 201.24 0.49 311 118 158 40 202.06 0.50 312 118 159 41 201.98 0.50 313 118 160 42 201.77 0.42 314 119 148 29 449.64 1.08 315 119 155 36 202.93 0.69 316 119 158 39 202.07 0.51 317 120 148 28 449.69 1.11 318 120 154 34 203.12 0.65 319 120 155 35 203.06 0.62 320 121 146 25 449.79 1.08 321 121 147 26 449.72 1.09 322 121 148 27 449.61 1.07 323 122 146 24 449.81 1.09 324 122 147 25 449.76 1.09 325 123 144 21 449.94 1.10 326 123 145 22 449.88 1.10 327 123 146 23 449.80 1.10 328 124 145 21 449.93 1.10 329 124 146 22 449.86 1.10 330 124 147 23 449.85 1.10 331 125 144 19 449.99 1.08 332 125 145 20 449.89 1.12 333 126 142 16 450.07 1.11 334 126 143 17 450.01 1.09 335 126 144 18 449.96 1.08 336 127 142 15 450.09 1.12 337 127 143 16 450.03 1.10 338 128 142 14 450.13 1.11 339 129 140 11 450.31 1.07 340 129 141 12 450.26 1.09 341 129 142 13 450.20 1.09 342 130 140 10 450.34 1.07 343 130 141 11 450.31 1.06 344 130 143 13 450.29 1.07 345 131 134 3 659.70 3.35 346 131 139 8 450.39 1.08 347 131 140 9 450.38 1.08 348 132 139 7 450.44 1.08 349 132 140 8 450.43 1.08 350 132 141 9 450.42 1.08 351 132 196 64 96.08 0.16 352 133 136 3 650.08 2.07 353 133 137 4 613.38 1.03 354 134 137 3 650.08 2.07 355 141 196 55 100.50 0.60 356 148 155 7 522.48 1.95 357 149 152 3 658.09 1.10 358 149 155 6 539.44 10.43 359 150 155 5 539.45 10.44 360 152 155 3 643.07 0.89 361 152 156 4 608.85 4.54 362 153 156 3 647.38 3.33 363 155 158 3 644.26 5.52 364 162 166 4 517.80 2.00 365 163 166 3 660.02 2.11 366 171 185 14 313.82 92.67 367 173 178 5 573.75 1.46 368 173 181 8 525.12 9.40 369 173 182 9 525.03 9.36 370 173 185 12 512.63 3.42 371 174 177 3 653.68 0.34 372 174 178 4 603.91 1.38 373 174 181 7 573.09 1.79 374 175 178 3 629.84 0.88 375 175 204 29 100.61 1.15 376 177 180 3 663.04 4.33 377 177 181 4 645.31 4.29 378 178 181 3 650.88 1.52 379 178 182 4 648.62 2.64 380 178 200 22 104.02 0.49 381 178 201 23 103.54 0.72 382 178 204 26 101.03 1.15 383 179 182 3 650.88 1.52 384 179 183 4 648.62 2.63 385 179 198 19 104.33 0.36 386 179 201 22 103.57 0.71 387 179 202 23 103.55 0.71 388 179 205 26 100.84 1.05 389 180 183 3 657.86 1.99 390 180 184 4 650.87 1.50 391 180 205 25 103.57 0.71 392 181 184 3 664.37 1.83 393 181 185 4 650.87 1.50 394 182 185 3 652.86 0.50 395 182 186 4 650.12 1.78 396 182 193 11 104.81 0.35 397 182 197 15 104.50 0.35 398 182 198 16 104.33 0.43 399 182 201 19 104.10 0.47 400 183 186 3 660.88 3.62 401 183 187 4 649.86 1.90 402 183 198 15 104.80 0.35 403 184 187 3 646.49 0.20 404 184 188 4 633.42 1.78 405 185 188 3 638.03 4.04 406 185 189 4 625.75 1.14 407 185 191 6 560.98 3.50 408 186 190 4 586.74 1.07 409 186 191 5 555.64 3.44 410 186 193 7 518.13 9.81 411 193 197 4 639.18 7.00 412 193 198 5 622.59 1.43 413 194 197 3 644.74 4.22 414 194 198 4 628.80 1.20 415 195 198 3 644.65 4.19 416 195 199 4 637.99 3.40 417 196 199 3 649.34 1.84 418 196 200 4 635.59 4.60 419 197 200 3 649.35 1.83 420 197 201 4 643.28 0.78 421 198 201 3 643.28 0.78 422 198 202 4 635.50 4.67 423 199 202 3 650.12 2.65 424 199 203 4 638.37 3.88 425 200 203 3 656.16 0.38 426 200 204 4 639.93 3.10 427 201 204 3 641.28 3.77 428 201 205 4 638.37 3.88 429 202 205 3 639.93 3.10 430 202 206 4 638.37 3.88 431 203 206 3 638.18 3.79 432 203 207 4 637.16 4.29 433 204 207 3 645.86 0.96 434 204 208 4 638.40 3.67 435 205 208 3 651.86 0.21