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 1 375 381 6 19.41 1.09 2 380 422 42 53.73 0.89 3 383 387 4 191.75 0.81 4 383 388 5 189.74 0.16 5 383 391 8 185.07 1.62 6 383 412 29 88.12 0.71 7 383 415 32 82.21 0.18 8 383 419 36 73.95 0.48 9 383 420 37 72.23 1.31 10 383 423 40 65.28 1.02 11 384 387 3 197.14 1.17 12 384 388 4 191.77 0.83 13 384 415 31 87.23 1.11 14 385 388 3 201.58 1.94 15 385 389 4 195.55 1.05 16 386 389 3 201.58 1.94 17 386 390 4 195.50 1.03 18 386 413 27 88.41 0.79 19 387 390 3 197.28 0.24 20 387 391 4 195.47 1.05 21 387 412 25 88.24 0.70 22 387 413 26 88.25 0.70 23 387 414 27 88.25 0.70 24 387 415 28 88.21 0.71 25 388 391 3 201.12 1.52 26 388 392 4 195.47 1.06 27 388 423 35 82.79 0.71 28 388 427 39 77.59 0.07 29 389 392 3 197.47 3.34 30 389 393 4 192.05 0.65 31 390 393 3 195.78 2.50 32 390 394 4 187.73 1.53 33 390 410 20 90.20 0.12 34 390 411 21 90.20 0.12 35 390 412 22 90.06 0.10 36 391 394 3 192.80 1.01 37 391 395 4 187.72 1.53 38 391 403 12 93.55 1.10 39 391 406 15 90.33 0.16 40 391 412 21 90.09 0.12 41 391 420 29 87.94 0.73 42 391 423 32 87.06 0.34 43 391 424 33 82.83 0.71 44 391 427 36 82.03 0.74 45 392 395 3 199.84 1.35 46 392 396 4 187.98 1.98 47 392 424 32 83.19 0.87 48 392 433 41 49.29 1.20 49 393 396 3 191.22 0.36 50 393 397 4 187.98 1.98 51 393 410 17 90.33 0.17 52 394 397 3 192.14 0.73 53 394 398 4 187.87 2.04 54 394 406 12 90.34 0.16 55 394 410 16 90.32 0.17 56 395 398 3 198.30 0.65 57 395 399 4 178.10 0.03 58 395 400 5 152.47 9.72 59 395 403 8 112.12 3.31 60 395 406 11 93.37 1.06 61 395 424 29 86.84 0.24 62 398 402 4 200.28 1.46 63 398 406 8 100.70 2.33 64 398 409 11 97.28 0.65 65 398 410 12 96.24 0.12 66 399 402 3 230.30 1.09 67 399 406 7 165.85 8.62 68 400 403 3 243.93 0.76 69 400 424 24 89.21 0.17 70 400 428 28 85.95 0.61 71 402 405 3 200.62 0.33 72 402 406 4 196.24 1.85 73 403 406 3 194.57 1.02 74 403 407 4 191.42 0.56 75 403 417 14 89.39 0.27 76 403 420 17 89.53 0.27 77 403 421 18 89.53 0.27 78 403 424 21 89.46 0.24 79 404 407 3 196.16 0.23 80 404 408 4 194.59 1.01 81 405 408 3 197.62 0.97 82 405 409 4 194.59 1.01 83 406 409 3 196.13 0.24 84 406 410 4 191.88 0.34 85 406 412 6 190.09 1.23 86 406 420 14 89.56 0.27 87 407 410 3 201.12 2.29 88 407 412 5 183.78 0.26 89 407 415 8 93.05 0.21 90 407 416 9 91.30 0.49 91 407 417 10 89.94 0.16 92 407 420 13 89.75 0.18 93 412 415 3 203.41 0.00 94 412 420 8 162.47 0.48 95 414 419 5 193.41 1.36 96 415 419 4 190.65 2.74 97 415 420 5 190.55 2.70 98 416 419 3 195.46 2.38 99 416 420 4 194.22 0.96 100 417 420 3 194.24 0.95 101 417 421 4 194.23 0.95 102 418 421 3 197.86 2.77 103 418 422 4 194.22 0.95 104 419 422 3 194.16 0.93 105 419 423 4 188.35 1.64 106 420 423 3 199.11 1.10 107 420 424 4 189.35 2.08 108 421 424 3 195.03 0.94 109 421 425 4 190.38 1.57 110 422 425 3 193.80 0.32 111 422 426 4 190.38 1.57 112 423 426 3 196.67 1.11 113 423 427 4 193.69 1.24 114 424 427 3 195.45 0.36 115 424 428 4 193.68 1.25 116 424 433 9 159.75 0.78 117 425 428 3 201.34 1.08 118 425 429 4 191.61 2.29 119 426 429 3 199.41 3.87 120 426 430 4 184.29 1.35 121 426 431 5 176.50 2.52 122 427 430 3 203.97 1.59 123 427 431 4 170.41 0.36 124 427 432 5 170.40 0.35 125 427 433 6 170.38 0.35 126 428 432 4 170.38 0.35 127 428 433 5 170.35 0.34 128 429 432 3 198.47 1.15