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 4 35 31 54.34 1.53 2 5 33 28 74.28 2.44 3 5 34 29 54.45 1.48 4 5 35 30 54.45 1.48 5 5 36 31 54.43 1.48 6 5 98 93 59.13 0.44 7 5 99 94 54.43 1.48 8 5 100 95 54.41 1.49 9 6 32 26 83.23 1.16 10 6 33 27 80.23 0.20 11 6 98 92 54.62 1.39 12 7 30 23 90.39 0.93 13 7 31 24 90.38 0.93 14 7 95 88 90.36 0.93 15 7 96 89 90.31 0.90 16 7 97 90 75.71 0.17 17 7 98 91 70.18 0.32 18 8 30 22 90.40 0.93 19 8 31 23 90.39 0.93 20 8 33 25 90.38 0.94 21 8 34 26 90.38 0.94 22 9 28 19 90.81 0.93 23 9 29 20 90.53 0.96 24 9 30 21 90.42 0.93 25 10 28 18 90.84 0.92 26 10 29 19 90.66 0.97 27 11 26 15 90.92 0.92 28 11 27 16 90.91 0.91 29 11 28 17 90.86 0.92 30 12 17 5 117.67 0.24 31 12 25 13 94.33 0.70 32 12 26 14 90.92 0.92 33 12 27 15 90.92 0.92 34 12 29 17 90.89 0.91 35 13 16 3 131.11 2.29 36 13 17 4 123.56 1.98 37 13 25 12 93.38 0.23 38 13 26 13 91.56 0.64 39 14 17 3 122.83 2.34 40 14 21 7 95.20 0.43 41 14 23 9 94.91 0.53 42 14 25 11 94.64 0.55 43 15 21 6 95.20 0.43 44 15 22 7 95.19 0.43 45 15 23 8 94.93 0.54 46 17 27 10 94.88 0.53 47 17 29 12 94.42 0.42 48 17 93 76 94.39 0.48 49 19 90 71 94.90 0.50 50 19 93 74 94.89 0.49 51 21 80 59 142.81 0.15 52 22 83 61 159.05 0.96 53 23 81 58 115.09 1.03 54 23 82 59 113.74 1.71 55 23 83 60 118.67 0.27 56 25 80 55 95.21 0.45 57 25 81 56 97.39 0.67 58 27 78 51 94.93 0.51 59 27 79 52 95.00 0.49 60 27 80 53 95.02 0.51 61 28 78 50 94.92 0.51 62 32 70 38 90.37 0.94 63 32 71 39 90.39 0.93 64 32 72 40 90.40 0.93 65 33 70 37 90.36 0.94 66 34 70 36 90.35 0.93 67 35 67 32 90.43 0.93 68 36 67 31 90.38 0.93 69 36 68 32 90.36 0.93 70 36 69 33 89.77 0.65 71 36 70 34 64.90 0.21 72 37 40 3 236.55 0.22 73 37 67 30 90.11 0.96 74 39 68 29 90.35 0.93 75 39 100 61 165.60 27.75 76 40 44 4 232.01 1.79 77 40 45 5 235.71 0.21 78 40 48 8 203.00 8.96 79 40 66 26 90.53 0.86 80 40 67 27 90.36 0.93 81 40 68 28 90.36 0.93 82 41 44 3 236.00 0.14 83 44 66 22 90.66 0.80 84 44 67 23 90.66 0.80 85 44 68 24 90.66 0.80 86 47 56 9 141.27 1.47 87 47 64 17 90.94 0.88 88 47 65 18 90.89 0.86 89 47 66 19 90.67 0.81 90 48 66 18 90.78 0.84 91 50 55 5 230.94 2.90 92 50 56 6 221.59 7.57 93 51 56 5 225.05 3.05 94 51 63 12 90.98 0.89 95 51 64 13 90.95 0.88 96 59 64 5 157.09 26.87 97 68 100 32 55.97 0.74 98 69 99 30 90.36 0.93 99 69 100 31 54.58 1.40 100 70 98 28 84.18 1.39 101 70 99 29 55.48 0.96 102 71 98 27 90.26 0.91 103 71 99 28 64.92 0.21 104 72 75 3 197.56 0.39 105 72 95 23 90.41 0.93 106 72 97 25 90.39 0.93 107 72 98 26 90.37 0.93 108 73 97 24 90.40 0.93 109 73 98 25 90.39 0.93 110 73 99 26 90.39 0.93 111 74 95 21 90.59 0.93 112 74 96 22 90.48 0.95 113 74 97 23 90.42 0.93 114 75 92 17 90.23 0.94 115 75 94 19 90.84 0.92 116 75 95 20 90.73 0.90 117 75 96 21 90.55 0.93 118 76 92 16 90.42 0.93 119 76 93 17 90.86 0.92 120 76 94 18 90.86 0.92 121 76 96 20 90.84 0.92 122 77 89 12 94.86 0.48 123 77 90 13 94.69 0.43 124 77 91 14 93.20 0.03 125 77 92 15 92.86 0.12 126 78 89 11 94.89 0.49 127 78 90 12 94.86 0.50 128 78 93 15 93.12 0.01 129 78 94 16 91.64 0.56 130 79 87 8 97.61 0.58 131 79 88 9 94.89 0.49 132 79 89 10 94.89 0.49 133 80 87 7 97.91 0.72 134 80 88 8 97.56 0.56 135 81 86 5 102.03 0.65 136 81 87 6 98.64 0.35 137 82 85 3 126.03 3.22 138 82 86 4 111.78 1.04 139 82 88 6 106.20 1.75 140 90 93 3 167.16 2.90