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 9 8 213.62 1.06 2 1 46 45 33.21 0.30 3 1 51 50 28.22 2.19 4 2 5 3 233.65 1.59 5 2 6 4 231.58 2.62 6 3 6 3 233.65 1.59 7 3 7 4 233.64 1.59 8 4 7 3 233.68 1.58 9 4 8 4 233.66 1.58 10 4 31 27 48.48 1.17 11 4 34 30 48.49 1.17 12 4 42 38 47.49 1.36 13 5 8 3 233.65 1.56 14 5 9 4 233.50 1.51 15 5 42 37 47.61 1.30 16 5 45 40 47.49 1.36 17 5 46 41 47.43 1.32 18 6 9 3 233.50 1.51 19 6 10 4 232.31 2.10 20 7 10 3 231.08 0.70 21 7 11 4 228.87 0.40 22 7 30 23 48.81 1.14 23 7 31 24 48.94 1.21 24 8 11 3 235.83 0.58 25 8 12 4 228.36 0.17 26 8 27 19 48.31 1.12 27 8 31 23 48.95 1.21 28 8 42 34 47.91 1.31 29 8 43 35 47.89 1.31 30 8 46 38 47.68 1.28 31 8 52 44 47.56 1.32 32 9 12 3 241.19 2.54 33 9 13 4 227.76 0.46 34 9 46 37 47.69 1.28 35 9 51 42 47.59 1.30 36 9 65 56 47.44 1.28 37 10 13 3 231.27 2.21 38 11 14 3 257.56 0.43 39 11 22 11 48.61 1.18 40 11 30 19 49.02 1.19 41 12 22 10 48.61 1.18 42 12 27 15 49.00 1.19 43 12 52 40 47.74 1.26 44 12 64 52 47.63 1.30 45 12 65 53 47.61 1.29 46 13 65 52 47.63 1.31 47 14 17 3 232.47 2.01 48 14 18 4 230.46 1.54 49 15 18 3 234.21 1.14 50 15 19 4 239.84 1.69 51 16 19 3 241.05 2.29 52 17 22 5 201.99 3.71 53 21 62 41 69.86 2.53 54 22 26 4 230.16 2.58 55 22 27 5 230.15 2.57 56 22 62 40 71.81 1.56 57 22 63 41 69.84 2.53 58 23 26 3 237.08 0.88 59 23 27 4 233.10 1.68 60 23 57 34 72.67 1.65 61 23 60 37 72.67 1.65 62 23 61 38 72.58 1.67 63 23 62 39 72.04 1.65 64 24 27 3 237.81 0.17 65 24 28 4 230.62 2.37 66 24 36 12 73.42 1.37 67 24 39 15 73.36 1.36 68 24 40 16 72.94 1.56 69 24 43 19 72.72 1.63 70 24 60 36 72.69 1.65 71 24 61 37 72.61 1.67 72 24 63 39 72.55 1.63 73 25 28 3 230.19 2.58 74 25 29 4 230.17 2.59 75 25 36 11 73.43 1.38 76 26 29 3 239.78 1.76 77 26 30 4 233.81 4.46 78 27 30 3 239.50 1.61 79 27 31 4 234.63 0.38 80 27 39 12 72.95 1.57 81 27 43 16 72.75 1.62 82 27 63 36 72.69 1.65 83 28 31 3 236.81 1.46 84 28 36 8 73.44 1.38 85 28 39 11 72.95 1.56 86 29 32 3 240.75 0.41 87 31 34 3 244.59 1.69 88 31 39 8 153.14 7.06 89 34 38 4 226.83 1.10 90 34 39 5 226.81 1.09 91 34 42 8 213.03 3.10 92 35 38 3 233.74 2.19 93 35 39 4 226.93 1.05 94 36 39 3 230.25 0.43 95 36 40 4 226.93 1.05 96 37 40 3 233.69 0.10 97 37 41 4 226.94 1.06 98 38 41 3 242.59 4.55 99 38 42 4 226.94 1.06 100 39 42 3 233.69 0.10 101 39 43 4 226.91 1.07 102 40 43 3 234.86 0.07 103 40 44 4 226.91 1.07 104 40 61 21 136.84 1.45 105 40 63 23 136.65 1.50 106 41 44 3 230.19 1.22 107 41 45 4 226.25 0.74 108 42 45 3 232.99 0.62 109 42 46 4 230.11 2.06 110 43 46 3 227.22 3.50 111 43 47 4 221.58 0.73 112 43 52 9 136.66 1.51 113 43 63 20 136.66 1.50 114 44 47 3 228.00 2.49 115 44 48 4 220.03 1.45 116 45 48 3 228.05 2.46 117 45 49 4 220.03 1.45 118 46 49 3 231.10 0.34 119 46 50 4 219.97 1.45 120 46 51 5 182.77 7.90 121 46 52 6 147.41 3.33 122 47 50 3 219.96 1.49 123 47 52 5 146.38 2.83 124 47 53 6 136.66 1.52 125 47 54 7 136.91 1.48 126 47 63 16 137.56 1.72 127 50 66 16 136.78 1.54 128 51 65 14 137.78 1.66 129 51 66 15 137.72 1.63 130 52 63 11 138.03 1.69 131 52 64 12 137.93 1.73 132 52 65 13 137.78 1.66 133 52 66 14 137.78 1.66 134 53 63 10 138.04 1.68 135 53 64 11 138.00 1.69 136 53 65 12 137.94 1.72 137 53 66 13 137.80 1.66 138 53 67 14 137.81 1.66 139 53 68 15 137.80 1.65 140 53 69 16 137.75 1.64 141 54 61 7 138.72 1.87 142 54 62 8 138.28 1.75 143 54 63 9 138.04 1.68 144 55 61 6 138.75 1.88 145 55 62 7 138.63 1.84 146 55 69 14 137.84 1.69 147 56 60 4 171.67 3.77 148 56 61 5 138.75 1.88 149 57 60 3 232.67 0.02 150 57 61 4 157.47 2.25 151 57 62 5 157.46 2.24 152 65 68 3 233.06 0.15 153 67 70 3 244.28 2.12 154 67 71 4 232.90 0.18 155 68 71 3 238.26 2.75 156 68 72 4 232.91 0.18 157 69 72 3 240.65 1.56 158 69 73 4 232.92 0.18 159 70 73 3 232.95 0.16 160 70 74 4 232.88 0.15 161 71 74 3 233.09 0.09