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 1 46 45 35.10 0.31 2 2 5 3 221.84 0.48 3 2 6 4 227.16 0.47 4 3 6 3 236.71 2.75 5 3 7 4 227.72 0.18 6 3 45 42 35.09 0.31 7 3 46 43 37.52 0.76 8 4 7 3 227.73 0.18 9 4 8 4 225.28 1.07 10 4 53 49 37.52 0.76 11 4 56 52 37.20 0.72 12 5 8 3 229.35 0.86 13 5 9 4 225.30 1.08 14 6 9 3 227.55 0.04 15 6 10 4 227.71 0.14 16 7 10 3 229.47 1.00 17 7 11 4 227.71 0.14 18 7 41 34 40.26 0.09 19 7 42 35 40.14 0.15 20 7 45 38 40.58 0.06 21 7 56 49 39.87 0.12 22 8 11 3 230.88 0.30 23 8 12 4 227.69 0.15 24 9 12 3 230.43 0.53 25 9 13 4 219.88 0.25 26 10 13 3 220.79 0.01 27 10 14 4 219.97 0.21 28 10 38 28 45.16 2.39 29 10 41 31 45.33 2.28 30 11 14 3 231.76 1.81 31 11 15 4 219.92 0.24 32 11 38 27 45.26 2.34 33 11 56 45 40.09 0.11 34 11 63 52 38.99 0.24 35 12 15 3 220.08 0.16 36 12 16 4 219.93 0.24 37 13 16 3 231.71 0.48 38 13 17 4 219.92 0.23 39 14 18 4 216.36 1.54 40 14 31 17 72.09 0.24 41 14 63 49 39.95 0.10 42 15 19 4 218.96 0.14 43 16 19 3 229.13 3.71 44 16 20 4 230.03 3.25 45 17 20 3 239.60 1.93 46 17 21 4 223.05 1.92 47 17 27 10 86.73 0.73 48 17 31 14 82.18 0.62 49 18 21 3 233.78 4.83 50 18 28 10 85.09 0.46 51 18 31 13 82.34 0.70 52 18 67 49 39.47 0.11 53 18 70 52 39.30 0.17 54 21 24 3 167.63 22.48 55 21 27 6 114.62 1.25 56 21 28 7 105.33 2.81 57 21 70 49 39.32 0.17 58 21 73 52 34.43 2.30 59 23 26 3 234.53 1.18 60 24 27 3 190.16 3.34 61 24 28 4 160.05 0.89 62 24 29 5 175.37 1.21 63 24 70 46 39.47 0.11 64 24 71 47 39.34 0.18 65 24 72 48 39.33 0.17 66 25 29 4 190.26 8.65 67 25 71 46 39.44 0.12 68 26 29 3 231.41 2.58 69 27 30 3 239.96 0.97 70 28 31 3 211.92 0.45 71 28 32 4 220.18 1.27 72 28 67 39 40.11 0.12 73 28 70 42 39.48 0.10 74 28 71 43 39.44 0.11 75 29 32 3 234.08 0.95 76 30 33 3 223.25 0.27 77 30 34 4 223.26 0.25 78 31 34 3 225.69 1.46 79 31 35 4 223.32 0.28 80 31 67 36 42.34 0.98 81 32 35 3 230.36 0.88 82 32 36 4 227.96 2.09 83 32 64 32 42.56 0.99 84 32 67 35 42.50 0.96 85 33 36 3 233.44 0.65 86 33 37 4 230.37 0.89 87 34 37 3 228.86 1.64 88 34 38 4 225.62 3.26 89 35 38 3 226.22 2.96 90 35 39 4 226.24 2.95 91 35 60 25 43.12 1.22 92 35 63 28 42.96 1.15 93 35 64 29 42.91 1.17 94 35 67 32 42.88 1.14 95 36 39 3 231.86 0.14 96 36 40 4 221.94 0.24 97 37 41 4 216.81 0.48 98 38 42 4 195.05 5.24 99 38 56 18 52.59 0.08 100 38 60 22 49.47 1.17 101 39 42 3 209.94 1.71 102 39 43 4 215.59 1.11 103 39 57 18 52.45 0.03 104 40 44 4 209.66 4.09 105 41 44 3 209.66 4.08 106 41 45 4 182.15 7.05 107 42 45 3 225.16 0.45 108 42 53 11 69.03 3.47 109 43 48 5 115.81 1.56 110 45 49 4 226.80 1.26 111 45 52 7 186.12 4.44 112 45 53 8 163.47 15.76 113 46 52 6 201.31 5.55 114 49 52 3 221.86 0.92 115 49 53 4 207.48 8.62 116 50 53 3 228.23 0.09 117 50 54 4 222.46 1.22 118 51 54 3 224.22 2.10 119 51 55 4 228.30 0.06 120 52 55 3 250.13 2.08 121 53 56 3 227.97 0.11 122 53 57 4 227.51 0.34 123 54 57 3 227.52 0.34 124 54 58 4 227.50 0.35 125 55 58 3 234.46 3.13 126 55 59 4 227.92 0.11 127 56 59 3 228.44 0.15 128 56 60 4 216.04 1.96 129 57 61 4 226.09 1.32 130 58 61 3 226.11 1.32 131 58 62 4 226.11 1.32 132 59 62 3 228.76 0.01 133 59 63 4 226.09 1.32 134 60 63 3 228.75 0.01 135 60 64 4 226.74 0.99 136 61 64 3 232.03 1.09 137 61 65 4 224.96 0.10 138 62 66 4 215.52 0.75 139 63 67 4 225.18 1.92 140 64 67 3 226.29 1.36 141 64 68 4 225.26 1.88 142 65 68 3 225.26 1.88 143 65 69 4 226.77 1.12 144 66 69 3 232.27 1.15 145 66 70 4 226.76 1.12 146 67 70 3 226.76 1.14 147 67 71 4 226.47 1.22 148 68 71 3 232.50 1.80 149 69 72 3 233.04 1.53 150 69 73 4 220.77 1.44 151 70 73 3 222.42 1.03