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 1 370 373 3 187.22 5.96 2 370 374 4 153.50 1.48 3 371 374 3 203.59 1.42 4 371 426 55 22.14 0.67 5 372 375 3 203.34 1.54 6 372 376 4 193.60 3.33 7 372 423 51 22.42 1.16 8 372 426 54 21.79 0.84 9 373 376 3 197.00 1.14 10 373 423 50 32.11 1.16 11 375 422 47 34.77 0.14 12 375 426 51 32.41 1.22 13 376 380 4 188.50 0.19 14 376 381 5 178.15 5.25 15 376 384 8 173.75 7.46 16 376 419 43 35.54 0.52 17 376 422 46 35.53 0.52 18 376 423 47 34.79 0.15 19 377 380 3 200.19 0.15 20 377 381 4 197.47 1.24 21 377 422 45 49.58 0.64 22 378 381 3 208.80 0.34 23 378 382 4 197.86 1.43 24 379 382 3 203.53 0.74 25 379 383 4 200.04 0.34 26 379 415 36 67.05 1.31 27 380 383 3 204.56 0.04 28 380 384 4 200.06 0.33 29 380 415 35 66.72 1.17 30 380 418 38 66.62 1.17 31 380 419 39 66.58 1.18 32 380 422 42 66.59 1.19 33 381 384 3 200.61 0.06 34 381 385 4 200.05 0.33 35 382 385 3 209.87 2.21 36 382 386 4 198.99 0.46 37 382 405 23 82.27 0.27 38 383 386 3 204.18 0.49 39 383 387 4 201.36 1.63 40 383 401 18 86.52 0.80 41 383 405 22 82.27 0.26 42 383 412 29 67.33 1.42 43 383 415 32 67.09 1.30 44 383 416 33 67.09 1.29 45 384 387 3 202.13 1.51 46 384 388 4 198.98 0.45 47 384 416 32 67.03 1.32 48 384 419 35 66.98 1.33 49 384 420 36 66.99 1.34 50 384 423 39 66.98 1.33 51 385 388 3 206.01 1.58 52 385 389 4 198.96 0.44 53 385 390 5 138.17 1.89 54 385 391 6 125.50 2.83 55 386 389 3 204.30 2.44 56 386 391 5 125.98 0.23 57 386 396 10 89.16 0.21 58 386 401 15 88.31 0.09 59 386 404 18 87.74 0.29 60 386 405 19 85.34 1.30 61 387 395 8 89.33 0.16 62 387 396 9 89.16 0.21 63 387 397 10 89.16 0.21 64 387 398 11 89.14 0.22 65 387 401 14 88.97 0.26 66 387 412 25 78.12 0.98 67 387 416 29 69.61 2.23 68 388 395 7 89.34 0.16 69 388 416 28 69.64 2.23 70 389 393 4 98.83 1.56 71 389 394 5 93.04 1.83 72 389 395 6 89.34 0.15 73 392 396 4 231.64 1.02 74 394 400 6 196.93 0.80 75 396 400 4 192.09 3.21 76 396 401 5 190.50 2.40 77 397 400 3 202.34 2.29 78 397 401 4 198.22 0.17 79 398 401 3 204.72 2.15 80 398 402 4 198.22 0.16 81 398 409 11 78.17 0.97 82 398 412 14 78.15 0.97 83 398 413 15 78.14 0.97 84 398 416 18 78.09 0.96 85 399 402 3 198.69 0.07 86 399 403 4 198.22 0.16 87 399 409 10 88.53 5.90 88 400 403 3 201.68 0.54 89 400 404 4 197.84 0.04 90 401 404 3 201.67 0.54 91 401 405 4 197.83 0.04 92 401 412 11 78.14 0.97 93 402 405 3 209.39 0.26 94 402 406 4 190.47 2.56 95 402 407 5 133.31 4.79 96 402 412 10 78.15 0.97 97 403 406 3 190.51 2.54 98 407 411 4 199.75 0.40 99 407 412 5 198.19 0.38 100 408 411 3 206.55 0.54 101 408 412 4 201.56 0.51 102 409 412 3 206.55 0.54 103 409 413 4 201.03 1.02 104 410 413 3 204.28 0.60 105 410 414 4 199.75 0.39 106 411 414 3 202.16 0.48 107 411 415 4 201.98 0.58 108 412 415 3 202.70 0.22 109 412 416 4 200.88 1.13 110 413 416 3 202.70 0.22 111 413 417 4 201.21 1.29 112 414 417 3 208.28 0.29 113 414 418 4 201.22 1.29 114 415 418 3 208.28 0.29 115 415 419 4 201.23 1.28 116 416 419 3 203.38 0.21 117 416 420 4 201.22 1.28 118 417 420 3 206.81 1.52 119 417 421 4 201.21 1.28 120 418 421 3 203.30 0.04 121 418 422 4 200.38 0.61 122 419 422 3 200.66 0.48 123 419 423 4 200.46 0.65 124 420 423 3 203.19 0.51 125 420 424 4 199.75 1.00 126 421 424 3 204.73 0.58 127 421 425 4 199.75 1.01 128 422 425 3 205.99 0.89 129 422 426 4 199.66 1.04 130 423 426 3 205.12 1.32 131 423 427 4 199.64 0.95 132 424 427 3 203.41 2.18 133 424 428 4 199.72 1.02 134 425 428 3 206.99 0.12