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 1 452 482 30 51.32 6.13 2 454 459 5 204.25 0.40 3 454 477 23 57.43 3.85 4 454 493 39 48.09 7.00 5 455 458 3 212.39 0.77 6 455 459 4 210.69 0.67 7 455 496 41 48.09 6.96 8 456 459 3 214.55 0.31 9 456 460 4 207.69 1.32 10 456 496 40 48.42 7.12 11 457 460 3 213.16 1.01 12 457 461 4 209.75 0.30 13 458 461 3 214.72 0.23 14 458 462 4 210.25 0.55 15 459 462 3 217.07 2.04 16 459 463 4 210.25 0.55 17 459 473 14 105.55 0.61 18 459 493 34 48.73 7.08 19 459 496 37 48.70 7.08 20 459 497 38 48.57 7.05 21 460 463 3 210.24 0.56 22 460 464 4 209.03 1.16 23 460 500 40 48.43 7.12 24 460 515 55 27.95 0.40 25 461 464 3 210.23 0.55 26 461 465 4 208.81 0.16 27 462 465 3 206.11 1.55 28 462 466 4 203.96 0.48 29 462 468 6 180.74 3.15 30 462 473 11 139.31 0.42 31 462 476 14 128.43 1.17 32 463 466 3 211.05 5.05 33 463 468 5 180.74 3.16 34 463 473 10 146.99 3.42 35 463 500 37 48.70 7.07 36 463 513 50 34.95 0.51 37 463 514 51 31.04 0.67 38 463 515 52 28.01 0.37 39 464 515 51 28.01 0.37 40 467 507 40 35.62 0.55 41 467 512 45 35.25 0.61 42 467 513 46 35.22 0.63 43 467 514 47 35.08 0.67 44 468 472 4 206.01 0.59 45 468 473 5 203.62 0.60 46 468 476 8 193.17 3.17 47 468 512 44 35.22 0.62 48 468 513 45 35.20 0.63 49 469 472 3 212.23 1.50 50 469 473 4 207.84 1.48 51 469 511 42 35.29 0.59 52 469 512 43 35.20 0.63 53 469 513 44 35.20 0.63 54 470 473 3 213.77 0.72 55 470 474 4 211.97 0.68 56 470 513 43 35.20 0.63 57 471 474 3 214.87 0.17 58 471 475 4 211.96 0.68 59 472 475 3 215.78 1.22 60 472 476 4 211.96 0.68 61 473 476 3 216.93 0.65 62 473 497 24 54.36 4.39 63 474 477 3 216.52 0.47 64 474 478 4 188.17 3.23 65 474 490 16 55.05 4.38 66 475 478 3 210.13 3.66 67 477 482 5 123.08 4.90 68 477 489 12 59.11 2.59 69 478 489 11 58.66 2.36 70 484 489 5 191.47 0.45 71 485 488 3 203.63 1.28 72 485 489 4 199.49 0.79 73 486 489 3 212.61 0.82 74 486 490 4 210.17 0.82 75 487 490 3 213.00 1.01 76 487 491 4 210.17 0.82 77 488 491 3 211.26 0.29 78 488 492 4 211.10 0.35 79 489 492 3 213.44 0.28 80 489 493 4 211.25 0.29 81 490 493 3 217.93 0.17 82 490 494 4 208.03 1.20 83 491 494 3 214.36 1.96 84 491 495 4 208.85 0.78 85 492 495 3 217.94 0.18 86 492 496 4 213.28 2.50 87 493 496 3 217.00 0.65 88 493 497 4 213.15 2.56 89 494 497 3 211.96 0.45 90 494 498 4 194.81 3.38 91 495 498 3 213.37 0.23 92 495 499 4 206.76 0.62 93 496 499 3 216.99 1.10 94 496 500 4 210.33 1.29 95 497 500 3 210.30 1.30 96 497 501 4 210.32 1.29 97 500 515 15 101.03 0.35 98 502 513 11 107.95 2.87 99 502 514 12 107.77 2.89 100 502 515 13 107.67 2.91 101 503 513 10 108.81 2.44 102 503 514 11 107.82 2.91 103 503 515 12 107.78 2.89 104 504 512 8 113.07 0.56 105 505 510 5 163.69 1.18 106 505 511 6 129.09 1.62 107 505 512 7 113.09 0.56 108 505 514 9 112.91 0.47 109 505 516 11 113.08 0.55 110 506 510 4 136.18 0.61 111 507 510 3 203.62 4.88 112 507 512 5 131.13 0.62