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 1 371 477 106 118.84 1.18 2 371 478 107 118.67 1.18 3 371 479 108 118.75 1.23 4 371 480 109 118.77 1.24 5 372 396 24 339.54 1.72 6 372 397 25 326.30 0.04 7 372 398 26 310.62 0.52 8 372 401 29 282.71 0.75 9 372 405 33 272.11 1.69 10 372 479 107 118.82 1.24 11 372 480 108 118.80 1.25 12 373 395 22 391.41 0.09 13 373 396 23 358.28 4.50 14 373 397 24 339.38 1.64 15 373 480 107 118.81 1.25 16 373 481 108 118.84 1.25 17 374 394 20 499.20 2.90 18 374 395 21 391.41 0.08 19 374 396 22 358.64 4.37 20 374 405 31 282.70 0.76 21 374 407 33 280.92 1.39 22 374 431 57 282.75 0.73 23 374 460 86 162.69 0.50 24 374 480 106 118.95 1.22 25 374 486 112 118.74 1.23 26 374 487 113 118.69 1.24 27 375 395 20 419.13 1.67 28 375 397 22 388.38 1.59 29 375 486 111 118.78 1.23 30 375 487 112 118.73 1.23 31 375 488 113 118.67 1.24 32 376 440 64 282.77 0.70 33 376 458 82 165.66 0.56 34 376 460 84 165.38 0.45 35 376 488 112 118.78 1.23 36 376 490 114 118.70 1.23 37 376 491 115 118.62 1.22 38 376 492 116 104.48 2.60 39 379 491 112 118.73 1.23 40 379 492 113 118.66 1.23 41 379 493 114 118.64 1.22 42 380 493 113 118.63 1.23 43 380 495 115 118.60 1.24 44 381 492 111 118.75 1.23 45 381 493 112 118.67 1.24 46 381 494 113 118.62 1.23 47 381 495 114 118.62 1.23 48 382 495 113 118.59 1.24 49 382 497 115 118.55 1.26 50 383 444 61 282.67 0.65 51 383 494 111 118.74 1.23 52 383 495 112 118.67 1.24 53 383 496 113 118.62 1.23 54 383 497 114 118.54 1.27 55 384 496 112 118.67 1.25 56 384 497 113 118.54 1.27 57 384 498 114 118.53 1.26 58 384 499 115 118.53 1.26 59 385 444 59 282.60 0.66 60 385 447 62 281.75 0.42 61 385 448 63 276.23 0.45 62 385 451 66 219.03 1.80 63 385 496 111 118.70 1.24 64 385 497 112 118.64 1.25 65 385 498 113 118.50 1.26 66 385 500 115 118.03 1.03 67 388 443 55 282.76 0.69 68 388 444 56 282.75 0.69 69 389 441 52 282.88 0.69 70 389 442 53 282.78 0.70 71 389 443 54 282.73 0.72 72 390 440 50 282.97 0.70 73 390 441 51 282.80 0.71 74 390 442 52 282.75 0.70 75 390 456 66 172.52 1.44 76 390 494 104 118.67 1.23 77 391 439 48 282.96 0.70 78 391 440 49 282.81 0.70 79 391 441 50 282.76 0.70 80 392 439 47 282.83 0.70 81 392 440 48 282.79 0.70 82 392 442 50 282.73 0.72 83 392 458 66 168.79 0.82 84 392 492 100 118.70 1.24 85 392 494 102 118.47 1.23 86 393 437 44 282.97 0.70 87 393 438 45 282.83 0.70 88 393 439 46 282.76 0.70 89 394 429 35 282.81 0.70 90 394 431 37 282.98 0.70 91 394 437 43 282.85 0.69 92 394 438 44 282.79 0.71 93 394 440 46 282.72 0.72 94 394 460 66 165.41 0.46 95 395 436 41 282.93 0.72 96 395 437 42 282.79 0.70 97 396 401 5 373.07 0.50 98 396 403 7 368.93 0.29 99 396 405 9 308.75 0.55 100 396 431 35 282.80 0.71 101 396 432 36 283.01 0.72 102 396 435 39 282.97 0.71 103 396 436 40 282.78 0.71 104 401 405 4 412.61 0.82 105 401 478 77 118.97 1.23 106 402 433 31 295.32 3.54 107 403 431 28 305.57 1.32 108 403 466 63 141.84 1.69 109 403 467 64 134.44 5.29 110 403 478 75 118.98 1.23 111 404 430 26 305.64 1.31 112 404 431 27 305.57 1.32 113 404 432 28 305.50 1.31 114 404 465 61 144.22 0.52 115 404 466 62 141.80 1.66 116 405 429 24 305.94 1.33 117 405 430 25 305.80 1.30 118 405 431 26 305.62 1.30 119 405 463 58 158.22 0.10 120 405 464 59 150.79 2.59 121 405 465 60 144.03 0.60 122 405 478 73 119.11 1.22 123 405 480 75 118.99 1.23 124 406 428 22 306.18 1.26 125 406 429 23 305.93 1.33 126 406 430 24 305.80 1.30 127 406 462 56 163.19 0.47 128 406 463 57 161.55 0.70 129 406 464 58 150.82 2.59 130 406 466 60 144.38 0.46 131 407 428 21 306.20 1.26 132 407 429 22 305.94 1.33 133 407 431 24 305.91 1.34 134 407 460 53 165.38 0.46 135 407 461 54 163.60 0.39 136 407 462 55 163.19 0.47 137 407 463 56 162.41 0.38 138 407 486 79 118.88 1.22 139 408 427 19 306.45 1.34 140 408 428 20 306.20 1.25 141 408 460 52 166.61 0.16 142 408 461 53 163.80 0.29 143 408 462 54 163.47 0.42 144 409 425 16 306.67 1.31 145 409 426 17 306.57 1.34 146 409 427 18 306.56 1.34 147 409 428 19 306.37 1.29 148 409 429 20 306.36 1.29 149 409 440 31 305.50 1.30 150 409 458 49 170.91 1.95 151 409 459 50 170.51 1.95 152 409 460 51 166.62 0.16 153 410 424 14 306.69 1.32 154 410 426 16 306.57 1.33 155 410 458 48 170.92 1.95 156 410 459 49 170.84 1.96 157 411 418 7 319.38 0.83 158 411 423 12 307.06 1.26 159 411 424 13 306.70 1.31 160 411 425 14 306.70 1.31 161 411 442 31 305.46 1.28 162 411 456 45 171.89 1.78 163 411 457 46 171.46 1.96 164 411 458 47 170.92 1.95 165 412 456 44 171.90 1.79 166 412 457 45 171.50 1.95 167 412 459 47 171.31 2.00 168 413 416 3 379.03 2.38 169 413 417 4 323.98 3.10 170 413 418 5 323.97 3.10 171 414 457 43 172.69 1.55 172 415 454 39 177.83 0.73 173 415 455 40 174.10 1.12 174 416 421 5 364.39 3.18 175 416 422 6 364.40 3.19 176 416 454 38 174.12 1.12 177 417 420 3 400.72 1.52 178 417 421 4 366.48 2.14 179 417 422 5 366.49 2.14 180 418 422 4 366.49 2.15 181 418 424 6 363.98 3.10 182 419 422 3 398.77 1.79 183 419 423 4 368.91 0.92 184 419 424 5 364.36 3.16 185 419 445 26 305.30 1.36 186 420 445 25 305.32 1.36 187 420 447 27 305.05 1.32 188 421 445 24 305.10 1.31 189 421 447 26 304.87 1.26 190 421 454 33 177.90 0.77 191 422 443 21 305.48 1.28 192 422 444 22 305.16 1.35 193 422 445 23 305.09 1.31 194 422 454 32 177.90 0.77 195 422 455 33 174.23 0.93 196 422 456 34 174.04 0.99 197 422 496 74 118.70 1.24 198 423 442 19 305.51 1.30 199 423 443 20 305.38 1.32 200 423 445 22 305.09 1.32 201 425 441 16 305.51 1.30 202 425 442 17 305.17 1.33 203 429 438 9 305.46 1.29 204 429 440 11 305.12 1.28 205 430 438 8 305.43 1.30 206 431 435 4 356.51 1.17 207 431 438 7 305.15 1.25 208 432 435 3 386.59 1.73 209 435 438 3 404.01 0.73 210 440 458 18 170.97 1.92 211 442 456 14 172.52 1.60 212 444 496 52 118.67 1.24 213 447 451 4 429.11 1.14 214 447 454 7 363.50 3.16 215 448 451 3 472.55 0.34 216 448 498 50 118.73 1.25 217 448 500 52 118.53 1.27 218 448 501 53 115.72 0.12 219 449 501 52 118.27 1.39 220 450 501 51 107.00 0.21 221 451 454 3 395.63 0.92 222 451 498 47 118.71 1.24 223 451 501 50 92.14 0.45 224 451 502 51 68.12 0.83 225 452 504 52 38.30 1.32 226 453 495 42 118.82 1.22 227 453 504 51 38.30 1.32 228 453 507 54 30.76 0.86 229 454 495 41 118.78 1.23 230 454 496 42 118.76 1.23 231 455 493 38 118.84 1.22 232 455 494 39 118.78 1.23 233 455 495 40 118.70 1.25 234 455 496 41 118.70 1.25 235 456 493 37 118.79 1.23 236 456 494 38 118.78 1.23 237 456 496 40 118.70 1.25 238 457 491 34 118.84 1.22 239 457 492 35 118.80 1.23 240 457 493 36 118.70 1.25 241 457 509 52 13.19 0.75 242 458 490 32 118.84 1.22 243 458 491 33 118.78 1.23 244 458 492 34 118.73 1.24 245 458 494 36 118.70 1.24 246 459 490 31 118.81 1.22 247 459 491 32 118.78 1.23 248 460 486 26 118.91 1.21 249 460 490 30 118.78 1.23 250 463 480 17 119.13 1.20 251 463 483 20 118.97 1.23 252 463 484 21 118.89 1.22 253 463 485 22 118.89 1.22 254 464 471 7 151.36 15.07 255 465 473 8 119.28 1.16 256 465 478 13 119.12 1.21 257 465 479 14 119.05 1.23 258 467 476 9 119.20 1.18 259 467 478 11 119.12 1.21 260 468 476 8 119.21 1.18 261 473 476 3 398.82 2.09 262 475 483 8 190.63 1.78 263 476 479 3 411.63 2.12 264 479 482 3 439.21 1.28 265 479 483 4 365.69 2.12 266 480 483 3 414.56 3.58 267 480 484 4 364.20 1.39 268 480 485 5 358.32 1.55 269 480 486 6 357.08 2.14 270 481 484 3 393.98 3.48 271 481 485 4 374.24 1.62 272 486 490 4 362.81 2.19 273 493 509 16 12.70 0.76 274 497 504 7 260.35 27.73 275 498 501 3 421.01 0.55 276 498 502 4 361.37 0.47 277 499 502 3 361.38 0.47