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 25 23 470.08 0.71 2 2 26 24 470.09 0.71 3 2 27 25 470.10 0.71 4 2 96 94 469.96 0.74 5 2 98 96 470.07 0.71 6 2 101 99 470.09 0.71 7 2 102 100 470.04 0.71 8 2 103 101 469.99 0.73 9 2 104 102 469.62 0.62 10 3 24 21 470.09 0.71 11 3 25 22 470.10 0.71 12 3 104 101 469.96 0.74 13 4 22 18 470.07 0.71 14 4 23 19 470.09 0.71 15 4 24 20 470.10 0.71 16 4 33 29 470.09 0.71 17 4 94 90 469.96 0.74 18 4 95 91 470.08 0.71 19 4 96 92 470.09 0.71 20 4 104 100 470.07 0.71 21 4 105 101 470.00 0.73 22 4 106 102 469.85 0.69 23 5 22 17 470.09 0.71 24 5 23 18 470.10 0.71 25 6 21 15 470.09 0.71 26 6 22 16 470.10 0.71 27 6 94 88 470.09 0.71 28 6 106 100 470.09 0.71 29 6 107 101 470.00 0.73 30 6 108 102 469.94 0.73 31 7 10 3 771.05 1.79 32 7 21 14 470.11 0.71 33 7 108 101 469.98 0.73 34 8 107 99 470.10 0.71 35 8 108 100 469.99 0.73 36 8 109 101 469.98 0.73 37 9 109 100 469.99 0.73 38 9 111 102 469.96 0.73 39 10 18 8 495.75 12.11 40 10 20 10 470.14 0.71 41 10 109 99 470.09 0.71 42 10 110 100 469.98 0.73 43 10 111 101 469.97 0.73 44 11 110 99 470.09 0.71 45 11 111 100 469.97 0.73 46 11 113 102 469.95 0.73 47 11 213 202 60.91 0.81 48 11 214 203 62.34 0.28 49 12 16 4 706.56 2.02 50 12 18 6 568.43 48.43 51 12 84 72 488.08 8.27 52 12 110 98 470.11 0.71 53 12 111 99 470.04 0.71 54 12 112 100 469.95 0.73 55 12 113 101 469.95 0.73 56 12 213 201 63.34 0.18 57 13 16 3 743.20 6.08 58 13 113 100 469.96 0.73 59 13 114 101 469.94 0.73 60 13 115 102 469.94 0.73 61 13 212 199 63.48 0.26 62 13 213 200 63.60 0.18 63 14 84 70 493.79 11.12 64 14 85 71 493.79 11.12 65 14 112 98 470.08 0.72 66 14 113 99 470.00 0.73 67 14 114 100 469.91 0.72 68 14 184 170 64.97 0.21 69 15 83 68 494.61 11.51 70 15 84 69 494.29 11.36 71 15 85 70 494.19 11.30 72 16 83 67 494.69 11.54 73 16 84 68 494.66 11.54 74 17 81 64 494.86 11.60 75 17 82 65 494.78 11.55 76 17 83 66 494.77 11.55 77 18 80 62 495.18 11.57 78 18 81 63 494.97 11.63 79 18 84 66 494.77 11.55 80 18 110 92 470.19 0.72 81 19 78 59 495.67 11.67 82 19 79 60 495.36 11.66 83 19 80 61 495.25 11.60 84 20 35 15 495.62 11.76 85 20 78 58 495.68 11.67 86 20 79 59 495.38 11.65 87 20 81 61 495.38 11.65 88 20 92 72 494.72 11.46 89 20 110 90 469.99 0.73 90 21 35 14 495.75 11.71 91 21 78 57 495.69 11.68 92 22 33 11 495.85 11.68 93 22 35 13 495.75 11.70 94 22 78 56 495.82 11.64 95 22 94 72 494.83 11.35 96 24 27 3 780.95 0.62 97 24 31 7 570.11 48.12 98 24 33 9 495.97 11.64 99 24 96 72 495.03 11.23 100 26 101 75 482.93 4.18 101 27 31 4 711.62 0.01 102 27 96 69 495.93 10.78 103 27 98 71 495.37 10.39 104 27 101 74 486.12 5.78 105 28 31 3 789.42 0.24 106 28 101 73 517.39 1.23 107 29 52 23 669.23 3.83 108 29 53 24 669.15 3.81 109 29 54 25 669.00 3.83 110 30 51 21 669.30 3.83 111 30 52 22 669.24 3.83 112 30 53 23 669.19 3.82 113 31 51 20 669.31 3.83 114 31 52 21 669.25 3.83 115 31 96 65 519.16 0.84 116 31 97 66 518.96 0.81 117 31 98 67 518.72 0.89 118 32 49 17 669.58 3.79 119 32 50 18 669.52 3.79 120 32 51 19 669.31 3.83 121 32 96 64 519.11 0.87 122 32 97 65 518.95 0.83 123 33 49 16 669.58 3.79 124 33 50 17 669.54 3.79 125 33 76 43 602.73 0.88 126 33 77 44 602.10 0.78 127 33 94 61 519.56 0.96 128 33 95 62 519.44 0.93 129 33 96 63 519.06 0.91 130 34 46 12 671.21 3.69 131 34 48 14 669.71 3.76 132 34 49 15 669.58 3.79 133 34 94 60 519.58 0.97 134 34 95 61 519.45 0.92 135 34 97 63 519.44 0.92 136 35 46 11 671.24 3.69 137 35 47 12 670.53 3.60 138 35 48 13 670.08 3.81 139 35 73 38 602.76 0.90 140 35 77 42 602.84 0.92 141 35 78 43 602.83 0.93 142 35 79 44 602.47 0.86 143 35 92 57 520.22 1.15 144 35 93 58 520.07 1.18 145 35 94 59 519.58 0.98 146 36 44 8 671.54 3.79 147 36 45 9 671.30 3.68 148 36 46 10 671.25 3.68 149 36 47 11 671.22 3.69 150 36 92 56 520.26 1.15 151 36 93 57 520.10 1.17 152 36 95 59 520.04 1.20 153 37 44 7 671.59 3.81 154 37 45 8 671.53 3.78 155 37 47 10 671.25 3.68 156 37 65 28 668.41 4.03 157 37 71 34 602.92 0.87 158 37 90 53 520.60 1.09 159 37 91 54 520.40 1.13 160 37 92 55 520.33 1.15 161 38 43 5 671.67 3.83 162 38 44 6 671.60 3.81 163 38 90 52 520.62 1.09 164 38 91 53 520.49 1.10 165 38 93 55 520.38 1.13 166 39 42 3 709.28 2.36 167 39 43 4 679.75 7.87 168 39 45 6 671.61 3.81 169 39 65 26 668.53 4.03 170 44 93 49 520.41 1.13 171 44 105 61 495.53 12.61 172 45 64 19 668.75 3.90 173 45 65 20 668.51 4.00 174 46 62 16 669.07 3.87 175 46 63 17 668.63 3.97 176 47 61 14 669.13 3.87 177 47 62 15 668.78 3.87 178 47 63 16 668.57 3.97 179 47 71 24 602.83 0.91 180 47 79 32 602.78 0.89 181 47 92 45 520.26 1.15 182 48 60 12 669.15 3.85 183 48 61 13 668.79 3.87 184 48 62 14 668.62 3.95 185 48 73 25 602.76 0.90 186 49 59 10 669.15 3.85 187 49 60 11 669.06 3.85 188 49 62 13 668.62 3.95 189 50 57 7 669.24 3.83 190 50 58 8 669.15 3.85 191 50 59 9 669.00 3.83 192 50 73 23 602.25 0.79 193 51 57 6 669.16 3.83 194 51 58 7 669.10 3.85 195 52 55 3 763.81 0.69 196 52 56 4 692.15 2.43 197 52 57 5 669.10 3.85 198 52 75 23 602.27 0.81 199 52 76 24 602.25 0.82 200 53 56 3 724.89 2.71 201 57 74 17 602.32 0.80 202 57 75 18 602.32 0.80 203 57 77 20 602.24 0.83 204 59 73 14 602.32 0.81 205 61 71 10 602.68 0.92 206 61 72 11 602.74 0.90 207 63 66 3 753.01 2.62 208 63 67 4 741.37 0.20 209 63 71 8 602.85 0.91 210 67 70 3 722.25 1.28 211 67 71 4 715.44 4.69 212 67 81 14 602.98 0.91 213 67 82 15 602.95 0.91 214 67 83 16 602.93 0.92 215 67 84 17 602.78 0.93 216 67 88 21 520.85 1.20 217 69 82 13 602.95 0.91 218 69 83 14 602.95 0.91 219 71 79 8 603.49 0.81 220 71 81 10 602.98 0.92 221 72 79 7 603.49 0.81 222 72 80 8 603.35 0.76 223 73 77 4 677.63 6.06 224 73 78 5 603.71 0.73 225 73 79 6 603.50 0.82 226 73 80 7 603.48 0.80 227 74 77 3 722.59 7.70 228 74 78 4 635.33 15.06 229 74 80 6 603.53 0.82 230 79 92 13 520.14 1.19 231 81 88 7 520.45 1.19 232 81 92 11 520.08 1.24 233 81 110 29 494.42 12.82 234 84 88 4 702.78 5.78 235 84 112 28 494.37 12.85 236 85 88 3 735.14 0.23 237 85 112 27 494.55 12.77 238 86 89 3 729.07 3.27 239 86 112 26 494.56 12.77 240 86 147 61 64.45 0.15 241 86 182 96 64.97 0.21 242 86 183 97 64.81 0.20 243 86 184 98 64.70 0.21 244 88 92 4 775.40 1.86 245 88 110 22 495.05 12.69 246 88 112 24 494.60 12.76 247 89 109 20 495.22 12.71 248 89 110 21 494.93 12.74 249 89 111 22 494.70 12.72 250 89 112 23 494.65 12.73 251 89 147 58 64.01 0.04 252 90 109 19 495.15 12.69 253 90 110 20 495.08 12.71 254 91 107 16 495.31 12.68 255 91 108 17 495.25 12.66 256 91 109 18 494.94 12.66 257 92 107 15 495.24 12.64 258 92 108 16 495.18 12.67 259 92 110 18 494.75 12.68 260 93 105 12 495.45 12.61 261 93 106 13 495.38 12.62 262 93 107 14 495.17 12.67 263 94 105 11 495.43 12.60 264 94 106 12 495.38 12.58 265 95 103 8 495.50 12.60 266 95 104 9 495.45 12.59 267 95 105 10 495.35 12.56 268 96 103 7 495.49 12.59 269 96 104 8 495.40 12.55 270 97 102 5 539.99 6.41 271 97 103 6 495.49 12.59 272 98 101 3 729.52 1.96 273 98 102 4 603.41 35.41 274 99 102 3 736.51 4.09 275 112 147 35 64.42 0.16 276 113 147 34 64.45 0.15 277 113 148 35 64.42 0.16 278 113 211 98 63.31 0.30 279 113 212 99 63.45 0.24 280 113 213 100 63.69 0.15 281 114 146 32 64.75 0.16 282 114 147 33 64.52 0.12 283 114 184 70 64.98 0.21 284 115 210 95 63.58 0.24 285 115 220 105 62.09 0.26 286 116 143 27 64.84 0.29 287 116 144 28 65.03 0.21 288 116 145 29 65.01 0.21 289 116 146 30 64.94 0.18 290 116 150 34 64.69 0.20 291 116 210 94 64.70 0.20 292 116 220 104 63.48 0.23 293 117 144 27 65.07 0.20 294 117 145 28 65.06 0.21 295 117 220 103 64.55 0.15 296 118 220 102 64.58 0.15 297 119 141 22 67.54 0.78 298 119 142 23 65.88 0.12 299 119 206 87 64.61 0.21 300 119 207 88 64.71 0.20 301 119 208 89 64.83 0.23 302 119 220 101 64.70 0.20 303 119 221 102 64.56 0.16 304 119 222 103 63.47 0.22 305 119 223 104 63.48 0.21 306 120 141 21 67.56 0.77 307 120 142 22 67.55 0.79 308 120 144 24 67.57 0.78 309 121 139 18 69.28 1.51 310 121 140 19 68.39 1.12 311 121 141 20 67.59 0.75 312 121 154 33 67.22 0.89 313 121 206 85 64.81 0.24 314 121 222 101 64.69 0.19 315 121 223 102 64.65 0.21 316 121 225 104 63.47 0.15 317 122 139 17 69.30 1.51 318 122 140 18 68.52 1.13 319 123 138 15 69.34 1.52 320 123 139 16 69.31 1.52 321 123 225 102 64.56 0.18 322 124 127 3 773.99 0.58 323 124 128 4 714.42 1.01 324 124 137 13 69.56 1.48 325 124 138 14 69.45 1.46 326 124 139 15 69.35 1.51 327 125 228 103 54.72 0.19 328 125 230 105 54.71 0.19 329 126 230 104 54.72 0.18 330 127 230 103 54.26 0.04 331 128 136 8 116.52 0.74 332 128 137 9 114.85 1.56 333 128 138 10 107.13 4.27 334 128 195 67 125.30 0.26 335 128 227 99 64.47 0.14 336 128 228 100 61.76 0.72 337 128 229 101 54.22 0.07 338 128 230 102 52.02 0.81 339 129 132 3 745.90 1.37 340 129 136 7 304.39 9.76 341 129 195 66 126.69 0.42 342 129 229 100 59.81 0.01 343 129 230 101 54.27 0.03 344 130 195 65 126.72 0.44 345 130 196 66 130.11 1.55 346 130 197 67 127.31 0.18 347 130 229 99 64.10 0.04 348 132 136 4 747.85 0.39 349 133 194 61 168.75 1.46 350 134 194 60 169.94 1.39 351 135 169 34 171.48 1.11 352 135 172 37 171.01 0.88 353 135 192 57 170.98 0.88 354 135 193 58 170.21 1.26 355 135 194 59 169.96 1.40 356 136 192 56 171.63 1.20 357 136 193 57 171.46 1.12 358 136 195 59 170.89 1.54 359 137 190 53 173.56 0.72 360 137 191 54 173.40 0.80 361 137 192 55 171.74 1.17 362 138 191 53 173.62 0.82 363 138 192 54 172.00 1.25 364 138 193 55 172.15 1.34 365 138 195 57 171.96 1.25 366 138 225 87 64.69 0.20 367 138 227 89 57.41 0.32 368 139 154 15 182.64 2.64 369 139 190 51 178.62 1.03 370 139 191 52 174.06 0.99 371 139 225 86 64.62 0.19 372 140 154 14 182.75 2.68 373 140 188 48 184.78 1.56 374 140 189 49 183.93 1.42 375 140 190 50 179.02 0.84 376 141 152 11 184.88 1.67 377 141 154 13 182.77 2.67 378 141 188 47 184.79 1.56 379 141 189 48 184.18 1.52 380 141 206 65 169.20 1.94 381 142 187 45 185.08 1.62 382 142 188 46 184.82 1.55 383 143 150 7 191.05 0.23 384 143 152 9 185.08 1.62 385 143 186 43 209.13 0.48 386 143 187 44 185.09 1.63 387 143 208 65 169.15 1.96 388 144 186 42 209.16 0.49 389 145 180 35 256.82 2.34 390 145 184 39 256.10 1.99 391 145 185 40 250.38 0.24 392 145 186 41 228.37 2.25 393 146 150 4 722.70 0.92 394 146 184 38 257.02 2.27 395 146 185 39 256.05 1.98 396 147 184 37 257.19 2.28 397 147 185 38 257.27 2.23 398 148 185 37 257.31 2.23 399 148 211 63 168.98 1.91 400 149 177 28 257.32 2.22 401 149 185 36 257.41 2.19 402 150 185 35 258.58 1.86 403 150 187 37 258.06 1.86 404 150 208 58 169.84 1.89 405 150 209 59 169.47 2.07 406 151 187 36 258.56 1.88 407 151 207 56 170.25 2.09 408 151 208 57 169.81 1.90 409 151 209 58 169.46 2.07 410 152 173 21 258.16 1.81 411 152 187 35 258.60 1.86 412 152 188 36 258.59 1.87 413 152 189 37 258.15 1.82 414 152 206 54 170.25 2.09 415 152 207 55 169.87 1.92 416 152 208 56 169.52 2.09 417 153 160 7 305.60 0.08 418 153 206 53 170.25 2.08 419 153 207 54 170.03 2.00 420 153 209 56 169.85 1.92 421 154 160 6 308.14 1.35 422 154 161 7 305.57 0.09 423 154 173 19 258.50 1.84 424 154 189 35 258.62 1.86 425 154 190 36 258.61 1.86 426 154 191 37 258.16 1.79 427 154 205 51 170.30 2.06 428 154 206 52 170.19 2.10 429 154 225 71 68.29 1.47 430 155 159 4 440.25 45.70 431 155 160 5 308.16 1.35 432 155 161 6 305.59 0.09 433 155 204 49 170.44 2.11 434 155 205 50 170.31 2.06 435 155 206 51 170.28 2.08 436 155 207 52 170.28 2.08 437 155 209 54 170.29 2.08 438 155 219 64 96.54 1.71 439 156 159 3 724.55 0.40 440 156 161 5 326.96 1.59 441 156 193 37 258.42 1.78 442 156 199 43 199.59 5.34 443 156 202 46 170.66 2.12 444 156 203 47 170.62 2.10 445 156 204 48 170.49 2.09 446 157 202 45 171.66 1.62 447 157 203 46 170.63 2.10 448 161 191 30 259.76 2.06 449 161 193 32 259.31 1.97 450 161 204 43 170.60 2.15 451 163 171 8 259.76 2.06 452 163 172 9 259.77 2.06 453 163 173 10 259.96 2.08 454 163 191 28 259.92 2.06 455 163 193 30 259.76 2.06 456 164 168 4 746.25 0.27 457 164 171 7 294.08 4.79 458 164 172 8 276.01 5.96 459 164 173 9 276.05 5.96 460 165 173 8 276.05 5.96 461 166 172 6 310.48 1.78 462 168 171 3 755.92 3.39 463 168 172 4 722.04 4.06 464 170 193 23 260.43 1.87 465 170 194 24 260.35 1.90 466 171 192 21 260.48 1.86 467 171 193 22 260.43 1.87 468 172 191 19 263.21 0.89 469 172 192 20 262.67 0.78 470 173 189 16 264.32 1.22 471 173 190 17 264.29 1.23 472 173 191 18 263.21 0.89 473 174 189 15 264.33 1.22 474 174 190 16 264.31 1.22 475 174 192 18 264.29 1.22 476 175 187 12 264.93 1.24 477 175 188 13 264.38 1.23 478 175 189 14 264.33 1.22 479 176 187 11 265.01 1.28 480 176 188 12 264.62 1.18 481 177 185 8 313.56 3.21 482 177 186 9 294.99 4.28 483 177 187 10 276.04 6.79 484 178 185 7 313.70 3.15 485 178 186 8 296.43 3.82 486 179 183 4 652.10 11.98 487 179 184 5 333.42 0.06 488 179 185 6 313.71 3.15 489 180 183 3 725.06 8.09 490 180 184 4 517.09 91.86 491 180 186 6 321.26 6.13 492 193 204 11 170.45 2.15 493 195 199 4 710.51 0.54 494 195 227 32 64.70 0.18 495 195 229 34 63.68 0.23 496 196 199 3 739.03 4.62 497 197 200 3 740.37 0.35 498 198 201 3 765.74 4.71 499 198 202 4 725.48 1.04 500 199 202 3 721.62 5.59 501 199 227 28 65.06 0.03 502 200 229 29 64.94 0.02 503 200 231 31 64.91 0.01 504 201 226 25 65.62 0.04 505 202 226 24 65.45 0.13 506 203 224 21 65.77 0.08 507 203 225 22 65.67 0.10 508 203 226 23 65.09 0.05 509 204 224 20 65.70 0.08 510 204 225 21 65.54 0.09 511 204 227 23 65.01 0.01 512 205 221 16 174.53 54.00 513 205 222 17 69.99 2.06 514 205 223 18 68.50 1.43 515 205 224 19 65.45 0.14 516 205 225 20 65.45 0.14 517 206 221 15 174.71 54.09 518 206 222 16 174.09 54.19 519 207 219 12 297.76 1.76 520 207 220 13 291.67 3.56 521 207 221 14 180.69 50.93 522 208 219 11 300.25 0.54 523 208 220 12 297.28 1.95 524 209 218 9 305.93 2.70 525 209 219 10 300.84 0.32 526 210 217 7 319.07 3.95 527 210 218 8 305.94 2.70 528 210 219 9 305.93 2.70 529 210 220 10 305.93 2.70 530 211 216 5 328.66 0.58 531 211 217 6 320.36 3.38 532 212 215 3 744.07 2.58 533 212 216 4 339.55 4.05 534 212 217 5 322.44 2.35 535 212 218 6 322.44 2.35 536 213 216 3 735.50 2.92