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 11 136 125 46.91 2.00 2 12 132 120 48.95 1.15 3 12 133 121 48.97 1.15 4 12 134 122 48.97 1.15 5 12 135 123 48.55 1.25 6 12 136 124 46.93 2.00 7 13 17 4 636.91 1.16 8 13 131 118 48.93 1.14 9 14 17 3 701.86 2.40 10 14 133 119 53.88 0.07 11 15 133 118 60.77 3.35 12 16 19 3 700.26 0.84 13 17 20 3 698.13 4.25 14 17 21 4 669.52 2.73 15 17 65 48 79.70 0.34 16 17 67 50 78.11 0.04 17 18 21 3 674.57 0.01 18 18 22 4 641.09 2.33 19 18 23 5 637.24 0.41 20 18 25 7 625.07 4.18 21 18 26 8 619.93 4.66 22 18 65 47 79.72 0.33 23 18 66 48 79.72 0.33 24 18 96 78 79.85 0.34 25 18 99 81 79.89 0.35 26 19 23 4 637.26 0.40 27 19 26 7 622.04 5.70 28 19 28 9 611.37 11.01 29 20 23 3 725.09 1.85 30 21 67 46 79.88 0.34 31 21 94 73 79.88 0.34 32 22 25 3 696.38 2.53 33 22 26 4 682.15 4.34 34 22 36 14 80.00 0.39 35 22 96 74 79.86 0.34 36 23 26 3 681.68 4.58 37 23 27 4 681.66 4.58 38 23 28 5 639.61 1.02 39 23 29 6 625.90 4.05 40 23 30 7 621.13 5.17 41 23 31 8 621.13 5.17 42 23 34 11 568.88 2.16 43 24 27 3 681.79 4.65 44 24 28 4 659.84 6.32 45 24 30 6 625.90 4.06 46 25 99 74 80.73 0.12 47 30 34 4 674.24 0.03 48 31 34 3 717.73 2.44 49 33 85 52 202.25 0.62 50 34 85 51 202.80 0.77 51 35 83 48 202.67 0.83 52 35 92 57 186.27 1.15 53 35 94 59 186.22 1.15 54 36 93 57 186.25 1.15 55 36 94 58 186.25 1.15 56 36 95 59 186.24 1.15 57 36 96 60 186.26 1.16 58 37 94 57 186.28 1.16 59 37 95 58 186.27 1.16 60 37 105 68 186.28 1.16 61 37 106 69 186.28 1.16 62 37 107 70 190.48 0.86 63 38 107 69 199.98 0.89 64 39 70 31 202.84 0.76 65 39 72 33 202.86 0.76 66 39 89 50 203.10 0.80 67 39 90 51 202.97 0.81 68 39 91 52 202.93 0.79 69 39 92 53 202.86 0.76 70 39 93 54 202.83 0.76 71 39 106 67 202.91 0.78 72 39 107 68 202.91 0.78 73 39 108 69 202.90 0.79 74 40 44 4 647.03 7.89 75 40 48 8 203.10 0.80 76 40 88 48 211.37 1.45 77 40 89 49 203.11 0.80 78 40 107 67 203.03 0.80 79 40 108 68 203.07 0.79 80 40 109 69 203.08 0.79 81 41 44 3 673.58 4.00 82 41 48 7 591.60 15.11 83 41 85 44 227.25 2.44 84 41 86 45 227.25 2.44 85 41 87 46 222.51 0.16 86 41 88 47 218.48 1.30 87 42 48 6 421.50 103.60 88 43 88 45 230.47 4.06 89 44 48 4 677.15 5.78 90 44 88 44 230.59 4.00 91 44 89 45 230.47 4.06 92 44 109 65 232.72 0.24 93 45 75 30 260.57 1.21 94 45 109 64 262.56 0.18 95 46 75 29 260.46 1.26 96 46 109 63 277.86 4.34 97 47 109 62 290.51 0.32 98 47 110 63 289.57 0.39 99 47 181 134 290.88 0.14 100 48 108 60 290.98 0.12 101 48 109 61 290.94 0.12 102 48 180 132 290.95 0.12 103 49 107 58 291.09 0.13 104 49 108 59 291.02 0.12 105 49 109 60 291.00 0.11 106 49 110 61 290.98 0.12 107 49 145 96 290.94 0.12 108 49 180 131 290.97 0.12 109 49 181 132 290.93 0.12 110 49 183 134 290.91 0.13 111 50 105 55 291.20 0.12 112 50 106 56 291.16 0.12 113 50 107 57 291.11 0.13 114 50 177 127 290.99 0.13 115 50 180 130 291.01 0.12 116 50 181 131 290.97 0.12 117 50 182 132 290.94 0.12 118 50 183 133 290.94 0.12 119 51 104 53 291.27 0.10 120 51 105 54 291.21 0.12 121 51 106 55 291.16 0.12 122 51 108 57 291.15 0.11 123 51 126 75 291.00 0.11 124 51 143 92 290.97 0.12 125 51 145 94 290.99 0.12 126 51 183 132 290.94 0.12 127 52 103 51 291.38 0.13 128 52 104 52 291.26 0.10 129 52 105 53 291.25 0.10 130 52 177 125 291.07 0.13 131 52 182 130 291.00 0.13 132 52 183 131 290.97 0.12 133 52 184 132 290.94 0.13 134 52 185 133 290.92 0.13 135 53 103 50 291.47 0.10 136 53 104 51 291.38 0.14 137 53 184 131 290.94 0.12 138 53 185 132 290.92 0.13 139 53 186 133 290.91 0.13 140 54 62 8 431.83 69.58 141 54 101 47 292.38 0.07 142 54 102 48 291.92 0.09 143 54 103 49 291.56 0.09 144 54 104 50 291.55 0.09 145 54 184 130 291.00 0.12 146 54 186 132 290.91 0.12 147 54 187 133 290.91 0.13 148 55 62 7 431.85 69.58 149 55 63 8 431.79 69.59 150 55 66 11 291.60 0.04 151 55 97 42 292.22 0.10 152 55 104 49 292.23 0.11 153 55 130 75 291.16 0.14 154 55 187 132 290.92 0.13 155 55 189 134 290.88 0.14 156 56 60 4 628.37 3.46 157 56 61 5 584.64 10.87 158 56 62 6 431.86 69.56 159 56 63 7 431.82 69.58 160 56 186 130 291.00 0.12 161 56 187 131 290.93 0.12 162 56 188 132 290.91 0.12 163 56 189 133 290.90 0.12 164 57 60 3 691.57 3.25 165 57 61 4 629.02 3.12 166 57 63 6 431.97 69.55 167 57 189 132 290.89 0.13 168 58 190 132 290.84 0.14 169 62 101 39 561.52 1.39 170 63 66 3 703.83 1.19 171 63 97 34 561.60 1.42 172 63 132 69 465.18 1.27 173 63 189 126 290.88 0.14 174 64 97 33 561.61 1.42 175 64 98 34 561.66 1.43 176 64 99 35 561.66 1.43 177 64 100 36 561.70 1.42 178 64 102 38 560.29 0.78 179 65 97 32 562.32 1.42 180 65 133 68 466.08 1.71 181 66 96 30 562.84 1.62 182 66 97 31 562.54 1.48 183 66 130 64 466.48 1.65 184 66 131 65 466.20 1.66 185 66 132 66 466.08 1.71 186 67 94 27 563.21 1.72 187 67 95 28 563.04 1.69 188 67 96 29 562.93 1.66 189 67 130 63 466.51 1.65 190 67 131 64 466.21 1.66 191 68 94 26 563.21 1.72 192 68 95 27 563.04 1.69 193 68 96 28 563.03 1.71 194 68 104 36 562.79 1.81 195 68 128 60 466.69 1.62 196 68 129 61 466.62 1.65 197 68 130 62 466.54 1.65 198 68 187 119 290.99 0.14 199 69 92 23 563.66 1.73 200 69 93 24 563.43 1.79 201 69 94 25 563.22 1.73 202 69 128 59 466.74 1.64 203 69 129 60 466.65 1.64 204 69 131 62 466.62 1.65 205 70 92 22 563.75 1.78 206 70 93 23 563.55 1.75 207 70 106 36 562.78 1.80 208 70 126 56 466.98 1.65 209 70 127 57 466.80 1.67 210 70 128 58 466.77 1.65 211 71 79 8 566.27 1.81 212 71 81 10 566.16 1.83 213 71 91 20 563.80 1.77 214 71 92 21 563.77 1.78 215 71 126 55 467.14 1.58 216 71 127 56 466.85 1.66 217 72 79 7 566.28 1.81 218 72 89 17 565.13 1.75 219 72 91 19 563.80 1.77 220 72 108 36 562.75 1.73 221 72 109 37 562.44 1.66 222 72 111 39 559.81 0.97 223 72 126 54 467.25 1.64 224 73 77 4 610.07 12.81 225 73 78 5 595.85 12.95 226 73 79 6 566.28 1.81 227 73 89 16 565.23 1.77 228 73 111 38 559.82 0.97 229 73 112 39 560.38 1.26 230 73 114 41 558.11 0.73 231 74 77 3 676.58 4.08 232 74 78 4 604.64 8.56 233 74 80 6 595.83 12.96 234 74 89 15 565.16 1.74 235 74 111 37 561.22 1.64 236 74 112 38 560.49 1.28 237 75 109 34 562.64 1.67 238 75 110 35 562.46 1.66 239 75 112 37 560.49 1.28 240 77 112 35 560.38 1.26 241 77 113 36 559.57 0.85 242 77 114 37 558.64 0.47 243 79 91 12 564.31 1.85 244 79 114 35 558.49 0.56 245 79 125 46 467.64 1.66 246 79 127 48 467.54 1.64 247 80 89 9 565.25 1.81 248 80 91 11 564.31 1.85 249 82 87 5 664.59 4.58 250 83 90 7 565.27 1.82 251 83 92 9 565.23 1.84 252 84 87 3 672.60 2.30 253 84 90 6 593.24 6.93 254 85 90 5 638.76 5.00 255 87 90 3 713.52 5.17 256 89 108 19 562.89 1.78 257 89 109 20 562.88 1.79 258 95 104 9 562.83 1.84 259 95 105 10 562.80 1.83 260 95 106 11 562.44 1.66 261 96 104 8 562.82 1.84 262 97 102 5 562.90 1.83 263 97 103 6 562.87 1.83 264 97 104 7 562.79 1.85 265 98 101 3 676.09 2.78 266 98 102 4 573.36 3.39 267 98 103 5 562.91 1.83 268 103 184 81 291.00 0.12 269 104 185 81 290.95 0.12 270 108 126 18 467.22 1.62 271 110 145 35 465.21 1.47 272 110 147 37 462.42 2.28 273 110 148 38 443.82 4.24 274 110 183 73 291.04 0.15 275 111 124 13 467.55 1.67 276 111 125 14 467.53 1.65 277 111 126 15 467.52 1.65 278 111 145 34 465.88 1.76 279 113 121 8 469.82 1.81 280 113 122 9 469.54 1.86 281 113 124 11 467.66 1.66 282 114 121 7 469.82 1.81 283 114 122 8 469.55 1.86 284 114 125 11 468.99 2.01 285 115 119 4 615.43 17.27 286 115 120 5 469.89 1.83 287 115 121 6 469.82 1.81 288 115 122 7 469.82 1.81 289 116 119 3 669.70 3.01 290 116 120 4 609.71 20.12 291 116 122 6 469.76 1.89 292 116 156 40 405.02 0.60 293 120 156 36 405.07 0.62 294 121 156 35 405.02 0.60 295 122 125 3 802.59 4.17 296 122 142 20 466.34 1.75 297 122 155 33 404.99 0.59 298 122 156 34 404.99 0.60 299 122 157 35 404.95 0.60 300 123 144 21 466.14 1.76 301 123 151 28 405.15 0.67 302 123 152 29 405.14 0.66 303 123 155 32 404.99 0.60 304 124 144 20 466.12 1.76 305 124 145 21 466.11 1.75 306 124 148 24 448.24 3.54 307 124 151 27 405.17 0.68 308 125 142 17 466.16 1.75 309 125 143 18 466.12 1.75 310 125 144 19 465.92 1.76 311 125 145 20 465.92 1.76 312 126 142 16 466.12 1.74 313 126 143 17 465.95 1.75 314 126 145 19 465.92 1.76 315 127 141 14 466.15 1.74 316 127 142 15 465.95 1.75 317 128 140 12 466.14 1.74 318 128 141 13 466.09 1.72 319 128 143 15 465.88 1.76 320 128 185 57 291.06 0.14 321 128 187 59 290.95 0.12 322 129 138 9 466.18 1.73 323 129 139 10 466.15 1.74 324 129 140 11 466.00 1.73 325 130 135 5 644.81 2.26 326 130 138 8 466.16 1.75 327 130 139 9 466.14 1.74 328 130 187 57 291.00 0.14 329 130 189 59 290.93 0.12 330 131 138 7 466.17 1.76 331 132 135 3 690.99 0.84 332 135 138 3 711.06 5.09 333 135 139 4 697.97 0.45 334 135 189 54 291.01 0.14 335 139 189 50 290.97 0.14 336 139 197 58 154.18 2.65 337 140 197 57 149.21 0.19 338 140 198 58 147.44 0.69 339 140 200 60 145.12 1.66 340 141 170 29 346.96 0.85 341 141 185 44 291.08 0.15 342 141 187 46 290.95 0.12 343 141 195 54 164.79 0.18 344 141 196 55 161.75 0.18 345 141 197 56 147.64 0.59 346 141 198 57 145.50 1.66 347 142 157 15 396.19 1.59 348 142 170 28 346.97 0.85 349 142 185 43 291.07 0.14 350 142 198 56 147.44 0.69 351 143 170 27 346.98 0.85 352 143 172 29 346.77 0.88 353 143 185 42 291.03 0.14 354 144 152 8 469.74 0.86 355 144 155 11 404.98 0.60 356 144 157 13 404.44 0.53 357 144 158 14 403.10 0.03 358 144 170 26 347.04 0.87 359 144 171 27 346.97 0.84 360 144 172 28 346.95 0.84 361 145 148 3 686.38 0.70 362 145 152 7 602.18 4.24 363 145 171 26 347.04 0.84 364 145 172 27 346.94 0.85 365 145 183 38 291.12 0.18 366 146 171 25 347.07 0.86 367 146 172 26 347.05 0.85 368 146 173 27 346.97 0.84 369 146 174 28 346.86 0.89 370 147 174 27 346.86 0.89 371 147 183 36 291.18 0.14 372 148 151 3 682.34 0.30 373 148 152 4 678.21 2.79 374 149 152 3 679.52 2.15 375 149 153 4 678.23 2.80 376 150 153 3 687.29 1.92 377 150 154 4 685.55 1.06 378 151 154 3 695.62 3.57 379 151 155 4 685.54 1.06 380 152 155 3 693.23 4.71 381 152 158 6 649.91 1.36 382 152 171 19 347.13 0.86 383 153 159 6 661.33 3.91 384 154 159 5 670.35 0.60 385 155 158 3 682.07 0.09 386 155 159 4 670.36 0.60 387 156 159 3 677.25 2.83 388 156 160 4 670.36 0.60 389 157 160 3 678.67 2.13 390 157 198 41 161.97 0.10 391 158 161 3 696.93 1.79 392 158 167 9 347.64 0.83 393 158 170 12 347.52 0.90 394 159 167 8 464.79 56.97 395 161 166 5 656.95 4.65 396 161 167 6 599.19 2.01 397 161 170 9 590.13 6.24 398 161 196 35 165.18 0.24 399 161 198 37 165.00 0.20 400 163 166 3 687.78 2.60 401 163 167 4 671.28 0.28 402 164 167 3 681.82 2.73 403 164 168 4 675.28 1.73 404 165 168 3 706.68 6.88 405 166 169 3 690.04 2.73 406 166 194 28 168.40 0.18 407 166 195 29 167.41 0.05 408 166 196 30 165.45 0.10 409 167 170 3 696.26 6.16 410 167 171 4 677.89 0.33 411 168 171 3 676.68 0.04 412 169 185 16 291.18 0.15 413 169 193 24 168.09 0.32 414 169 194 25 166.62 0.03 415 169 195 26 165.22 0.02 416 169 196 27 165.21 0.02 417 170 185 15 291.08 0.15 418 170 195 25 165.28 0.05 419 170 196 26 165.08 0.04 420 170 198 28 164.71 0.21 421 171 185 14 291.06 0.16 422 172 183 11 291.16 0.16 423 172 184 12 291.07 0.15 424 172 185 13 291.03 0.17 425 173 183 10 291.19 0.15 426 173 184 11 291.11 0.14 427 174 181 7 443.38 74.98 428 174 182 8 292.10 0.54 429 174 183 9 291.14 0.13 430 175 181 6 472.45 60.48 431 175 182 7 320.81 13.81 432 176 179 3 688.19 3.11 433 176 180 4 597.84 1.38 434 176 181 5 597.00 1.79 435 176 182 6 443.34 75.02 436 177 180 3 664.31 3.12 437 177 182 5 473.31 60.91 438 187 195 8 165.12 0.01 439 187 197 10 164.94 0.01 440 188 192 4 689.69 1.47 441 188 193 5 449.13 76.48 442 188 194 6 256.51 45.66 443 188 195 7 256.49 45.66 444 188 197 9 256.50 45.66 445 189 194 5 445.48 74.66 446 189 197 8 378.75 107.14 447 190 194 4 558.42 26.62 448 191 194 3 663.56 1.60