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 1 439 442 3 191.67 0.67 2 439 443 4 174.46 2.12 3 439 444 5 110.86 1.50 4 440 444 4 166.53 5.99 5 448 451 3 248.72 0.16 6 448 482 34 53.77 0.01 7 449 482 33 53.94 0.09 8 450 454 4 187.47 0.64 9 450 458 8 176.47 0.78 10 450 479 29 70.72 0.34 11 450 482 32 59.80 0.96 12 450 486 36 53.32 0.22 13 450 487 37 53.31 0.22 14 450 490 40 52.65 0.07 15 451 454 3 194.84 0.46 16 451 455 4 189.60 0.43 17 452 455 3 190.81 0.79 18 452 456 4 189.60 0.43 19 453 456 3 190.56 0.91 20 453 457 4 189.60 0.43 21 454 457 3 190.59 0.90 22 454 458 4 187.87 0.47 23 454 479 25 72.55 0.14 24 454 482 28 68.98 1.64 25 455 458 3 187.87 0.47 26 455 459 4 187.87 0.47 27 455 490 35 53.56 0.35 28 456 459 3 189.25 0.23 29 456 460 4 186.75 0.10 30 457 460 3 192.88 2.06 31 457 461 4 186.38 0.12 32 457 477 20 74.00 0.02 33 457 478 21 73.71 0.17 34 457 479 22 73.56 0.09 35 458 461 3 183.47 1.57 36 458 462 4 183.47 1.57 37 458 470 12 106.44 1.48 38 458 479 21 73.56 0.09 39 458 487 29 63.42 1.85 40 458 491 33 60.68 3.20 41 459 462 3 195.86 0.33 42 459 463 4 191.56 2.48 43 459 491 32 63.37 1.87 44 460 463 3 192.64 1.94 45 460 464 4 185.93 0.34 46 460 477 17 84.56 0.21 47 461 464 3 193.55 2.40 48 461 465 4 179.91 1.55 49 461 473 12 91.23 3.31 50 461 477 16 84.78 0.10 51 462 465 3 185.69 0.21 52 462 466 4 136.44 0.24 53 462 467 5 124.31 0.76 54 462 470 8 109.88 1.19 55 462 473 11 106.58 1.51 56 462 491 29 63.41 1.86 57 464 477 13 107.50 1.95 58 465 469 4 158.46 2.41 59 465 472 7 108.99 2.56 60 465 473 8 110.31 0.64 61 465 476 11 107.73 1.93 62 465 477 12 107.73 1.93 63 466 469 3 207.93 0.85 64 467 470 3 219.91 0.01 65 469 472 3 194.34 1.64 66 469 473 4 187.77 0.96 67 470 473 3 189.97 0.56 68 470 474 4 187.76 0.96 69 470 484 14 69.63 1.90 70 470 487 17 69.67 1.92 71 470 488 18 69.61 1.90 72 470 491 21 69.62 1.90 73 471 474 3 193.06 2.10 74 471 475 4 185.06 0.39 75 471 484 13 69.80 1.96 76 472 475 3 185.09 0.36 77 472 476 4 183.28 0.35 78 473 476 3 189.87 0.50 79 473 477 4 182.09 0.61 80 473 479 6 159.10 7.41 81 474 477 3 189.87 0.50 82 474 479 5 128.43 0.12 83 474 483 9 69.81 1.95 84 474 487 13 69.74 1.98 85 479 487 8 98.30 1.91 86 482 486 4 175.47 2.54 87 482 487 5 179.99 0.62 88 483 487 4 186.34 0.95 89 484 487 3 186.34 0.95 90 484 488 4 180.74 0.42 91 485 488 3 189.50 2.75 92 485 489 4 188.51 0.13 93 486 489 3 195.37 1.05 94 486 490 4 191.03 1.11 95 487 490 3 195.37 1.05 96 487 491 4 185.44 1.68 97 488 491 3 195.37 1.05 98 488 492 4 185.43 1.68 99 489 492 3 187.44 0.68 100 489 493 4 184.68 1.31 101 490 493 3 191.03 2.47 102 490 494 4 185.00 1.49 103 491 494 3 194.27 0.71 104 491 495 4 184.51 1.73 105 492 495 3 192.62 1.54 106 492 496 4 184.02 1.53 107 493 496 3 184.88 1.54 108 493 497 4 178.81 1.08 109 493 498 5 170.94 4.11 110 494 498 4 148.56 4.78 111 494 499 5 148.56 4.78 112 495 500 5 116.80 2.16