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 2 27 25 59.26 0.31 2 2 29 27 58.38 0.10 3 2 90 88 56.44 0.34 4 2 92 90 56.88 0.37 5 2 93 91 56.87 0.37 6 2 97 95 55.78 0.04 7 3 25 22 59.66 0.31 8 3 26 23 59.48 0.38 9 4 23 19 60.02 0.20 10 4 24 20 59.90 0.21 11 4 25 21 59.66 0.30 12 4 33 29 59.44 0.39 13 4 88 84 58.21 0.04 14 4 90 86 57.09 0.40 15 4 97 93 56.83 0.37 16 4 98 94 56.55 0.34 17 4 99 95 55.10 0.14 18 4 100 96 56.39 0.34 19 5 23 18 60.03 0.20 20 5 24 19 59.95 0.23 21 5 100 95 56.49 0.35 22 6 21 15 61.20 0.24 23 6 22 16 61.08 0.26 24 6 23 17 60.13 0.20 25 6 86 80 60.88 0.10 26 6 87 81 60.68 0.07 27 6 88 82 60.13 0.20 28 6 99 93 56.79 0.38 29 6 100 94 56.66 0.37 30 6 101 95 56.50 0.36 31 6 102 96 56.45 0.35 32 7 21 14 61.20 0.24 33 7 22 15 61.18 0.24 34 8 11 3 139.97 1.09 35 8 21 13 61.23 0.24 36 8 102 94 56.55 0.34 37 9 101 92 56.82 0.37 38 9 102 93 56.55 0.35 39 9 103 94 56.54 0.34 40 10 103 93 56.54 0.34 41 11 19 8 89.24 0.35 42 11 102 91 56.85 0.38 43 11 103 92 56.70 0.39 44 11 104 93 56.55 0.35 45 11 105 94 56.50 0.33 46 12 105 93 56.53 0.34 47 12 107 95 55.74 0.58 48 13 17 4 117.31 0.37 49 13 19 6 103.23 0.46 50 13 78 65 122.56 0.47 51 13 105 92 56.76 0.36 52 13 106 93 56.44 0.36 53 13 107 94 56.42 0.35 54 14 17 3 125.09 1.59 55 14 78 64 132.37 0.18 56 14 107 93 56.44 0.36 57 15 78 63 135.75 1.86 58 15 80 65 141.22 2.88 59 16 77 61 192.45 14.96 60 16 78 62 194.74 13.43 61 17 76 59 247.44 0.89 62 17 77 60 241.22 2.19 63 17 78 61 233.84 5.87 64 18 74 56 254.84 2.27 65 18 75 57 247.48 0.91 66 18 76 58 247.44 0.89 67 19 75 56 254.83 2.23 68 19 104 85 56.77 0.37 69 21 35 14 249.77 4.80 70 21 102 81 56.77 0.35 71 21 104 83 56.61 0.38 72 29 92 63 170.95 7.78 73 36 98 62 63.65 3.68 74 78 104 26 56.90 0.36 75 78 106 28 56.70 0.39 76 79 106 27 56.81 0.35 77 80 106 26 56.84 0.35 78 83 103 20 56.93 0.35 79 83 104 21 56.81 0.35 80 83 105 22 56.80 0.35 81 83 106 23 56.78 0.36 82 84 103 19 56.88 0.35 83 84 104 20 56.81 0.35 84 85 101 16 56.93 0.35 85 85 102 17 56.88 0.35 86 85 103 18 56.77 0.35 87 86 101 15 56.88 0.35 88 86 102 16 56.82 0.36 89 86 104 18 56.77 0.35 90 87 98 11 63.57 3.67 91 87 99 12 63.45 3.62 92 87 100 13 62.52 3.18 93 87 101 14 56.77 0.35 94 88 98 10 63.54 3.68 95 88 99 11 63.41 3.64 96 89 96 7 75.77 1.74 97 89 97 8 63.82 3.81 98 89 98 9 63.52 3.69 99 90 93 3 168.39 2.81 100 90 95 5 123.64 1.26 101 90 96 6 77.45 2.58 102 90 97 7 74.63 2.28 103 91 96 5 86.31 0.70 104 93 96 3 127.73 1.02