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 10 54 44 27.43 0.28 2 10 69 59 24.80 0.24 3 11 53 42 39.24 2.68 4 12 16 4 207.40 0.48 5 12 17 5 207.38 0.47 6 12 50 38 58.35 1.77 7 12 53 41 50.48 2.12 8 12 66 54 31.61 0.51 9 12 71 59 27.85 0.48 10 13 16 3 221.76 1.69 11 13 17 4 210.59 2.06 12 13 53 40 67.73 0.30 13 14 17 3 221.76 1.69 14 14 18 4 217.51 0.33 15 15 18 3 217.88 0.15 16 15 19 4 217.72 0.23 17 15 36 21 93.29 6.42 18 15 38 23 89.34 8.27 19 15 46 31 70.48 0.90 20 16 19 3 222.27 1.43 21 16 20 4 218.23 0.03 22 16 46 30 70.47 0.90 23 16 49 33 70.05 0.71 24 16 50 34 69.94 0.76 25 16 53 37 69.96 0.76 26 17 20 3 227.79 1.33 27 17 21 4 216.83 0.05 28 17 71 54 39.70 1.54 29 18 21 3 216.72 0.77 30 18 22 4 217.18 0.48 31 18 36 18 94.64 7.10 32 19 22 3 223.62 3.46 33 19 23 4 217.20 0.48 34 19 32 13 114.39 2.87 35 19 36 17 94.72 7.13 36 19 43 24 78.61 4.93 37 19 46 27 70.70 0.97 38 19 47 28 70.62 0.94 39 20 23 3 217.20 0.48 40 20 24 4 217.21 0.49 41 20 47 27 70.66 0.95 42 20 50 30 70.63 0.95 43 20 62 42 62.91 0.19 44 20 63 43 62.59 0.32 45 20 66 46 62.02 0.23 46 20 72 52 39.47 0.07 47 21 24 3 227.84 1.32 48 21 25 4 223.56 3.46 49 21 72 51 40.76 1.01 50 22 25 3 229.11 0.69 51 22 26 4 224.22 3.12 52 22 27 5 209.90 3.08 53 22 32 10 114.52 2.81 54 22 35 13 122.45 1.16 55 22 36 14 115.07 2.53 56 23 26 3 229.11 0.69 57 23 27 4 210.80 2.63 58 23 32 9 134.08 0.94 59 23 47 24 78.60 4.92 60 23 59 36 64.66 0.91 61 23 63 40 62.89 0.18 62 24 63 39 62.97 0.14 63 24 72 48 43.01 0.07 64 24 74 50 38.04 0.77 65 27 31 4 208.21 1.79 66 27 32 5 202.81 0.91 67 27 35 8 196.22 2.31 68 28 31 3 221.18 3.04 69 28 32 4 208.59 1.13 70 29 32 3 224.84 1.41 71 29 33 4 209.71 1.04 72 29 43 14 94.66 7.16 73 29 47 18 94.66 7.16 74 29 59 30 64.67 0.92 75 30 33 3 220.05 2.68 76 30 34 4 215.06 0.56 77 30 40 10 124.92 0.11 78 31 34 3 217.79 1.58 79 31 35 4 214.43 0.85 80 32 35 3 217.75 0.80 81 32 36 4 214.69 0.73 82 32 43 11 123.40 0.59 83 33 36 3 216.25 0.04 84 33 37 4 212.40 0.14 85 33 38 5 152.89 5.49 86 33 39 6 153.23 5.10 87 33 40 7 141.94 8.40 88 33 43 10 123.47 0.57 89 34 37 3 213.38 0.64 90 38 42 4 213.68 0.46 91 38 43 5 212.84 0.88 92 38 46 8 199.25 2.94 93 39 42 3 213.75 0.43 94 39 43 4 213.75 0.43 95 40 43 3 218.84 2.10 96 40 44 4 213.78 0.45 97 41 44 3 215.81 0.35 98 41 45 4 215.59 0.46 99 42 45 3 219.17 1.33 100 42 46 4 215.63 0.44 101 43 46 3 218.22 1.55 102 43 47 4 215.63 0.43 103 44 47 3 215.64 0.43 104 44 48 4 213.46 0.66 105 45 48 3 224.11 0.39 106 45 49 4 214.44 1.15 107 46 49 3 224.11 0.39 108 46 50 4 209.90 0.27 109 47 50 3 216.37 2.35 110 47 51 4 209.78 0.16 111 47 59 12 93.59 6.62 112 48 51 3 216.59 3.56 113 48 52 4 210.58 0.56 114 49 52 3 215.40 2.88 115 49 53 4 210.58 0.56 116 50 53 3 214.06 0.49 117 50 54 4 205.41 2.02 118 51 54 3 214.06 0.49 119 51 55 4 204.04 1.34 120 51 56 5 181.93 7.77 121 51 58 7 122.78 4.35 122 51 59 8 119.55 5.97 123 51 62 11 91.00 4.13 124 52 55 3 210.37 1.84 125 54 62 8 110.06 1.23 126 54 65 11 95.07 6.11 127 54 66 12 95.17 6.16 128 54 69 15 94.62 5.90 129 56 61 5 193.71 2.73 130 56 62 6 163.75 5.68 131 56 65 9 153.29 10.90 132 57 61 4 208.18 4.49 133 58 61 3 215.22 0.96 134 58 62 4 205.87 3.25 135 59 62 3 217.47 0.15 136 59 63 4 212.25 1.74 137 60 63 3 219.45 0.84 138 60 64 4 213.54 1.10 139 61 64 3 219.69 1.26 140 61 65 4 213.56 1.09 141 62 65 3 213.62 1.06 142 62 66 4 213.78 0.97 143 63 66 3 213.77 0.96 144 63 67 4 213.78 0.96 145 63 72 9 129.99 1.72 146 64 67 3 215.56 1.84 147 64 68 4 210.55 0.67 148 65 68 3 216.56 1.33 149 65 69 4 215.55 1.83 150 66 69 3 217.25 0.99 151 66 70 4 215.55 1.83 152 66 71 5 171.62 0.96 153 66 72 6 139.53 3.05 154 67 70 3 217.25 0.99 155 67 72 5 139.53 3.05 156 67 73 6 139.53 3.05 157 67 74 7 130.93 1.25