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 18 17 41.66 1.16 2 1 19 18 41.66 1.16 3 1 62 61 41.64 1.18 4 1 63 62 41.66 1.16 5 2 14 12 95.06 27.75 6 2 15 13 94.95 27.73 7 2 63 61 41.67 1.16 8 2 64 62 41.66 1.16 9 3 14 11 95.20 27.74 10 3 15 12 95.06 27.78 11 3 17 14 94.94 27.72 12 3 26 23 41.76 1.15 13 3 56 53 41.79 1.16 14 3 61 58 41.78 1.16 15 3 62 59 41.79 1.16 16 3 65 62 41.66 1.17 17 3 67 64 41.63 1.17 18 4 12 8 149.01 1.24 19 4 13 9 95.67 27.89 20 4 14 10 95.35 27.82 21 4 64 60 41.80 1.15 22 4 65 61 41.75 1.14 23 4 66 62 41.66 1.16 24 4 67 63 41.63 1.17 25 5 12 7 149.15 1.18 26 5 13 8 95.69 27.89 27 5 15 10 95.67 27.89 28 5 30 25 41.80 1.15 29 5 67 62 41.66 1.16 30 5 69 64 41.58 1.16 31 6 10 4 186.57 1.20 32 6 11 5 157.41 0.96 33 6 12 6 149.18 1.16 34 6 66 60 41.81 1.15 35 6 67 61 41.70 1.17 36 6 68 62 41.66 1.16 37 6 69 63 41.62 1.17 38 7 10 3 220.62 4.12 39 7 11 4 180.12 4.42 40 7 13 6 166.69 3.75 41 7 34 27 42.01 1.19 42 8 36 28 41.97 1.20 43 8 69 61 41.70 1.16 44 8 70 62 41.66 1.17 45 8 71 63 41.60 1.16 46 13 33 20 134.72 0.42 47 13 34 21 134.43 0.55 48 14 33 19 135.84 0.05 49 15 26 11 136.20 0.01 50 15 29 14 136.03 0.06 51 15 30 15 136.03 0.06 52 15 33 18 136.02 0.06 53 16 29 13 136.25 0.05 54 17 21 4 226.61 0.65 55 17 26 9 150.41 0.86 56 17 29 12 141.02 2.31 57 17 56 39 111.82 0.14 58 18 21 3 232.83 1.61 59 18 56 38 111.86 0.15 60 19 56 37 111.89 0.17 61 19 57 38 111.81 0.14 62 20 55 35 112.55 0.15 63 21 25 4 228.15 2.23 64 21 26 5 224.56 0.43 65 21 29 8 218.07 1.01 66 21 55 34 112.56 0.15 67 21 56 35 112.56 0.15 68 22 25 3 230.69 1.85 69 22 26 4 232.75 0.82 70 22 54 32 112.97 0.26 71 22 55 33 112.59 0.14 72 23 26 3 234.42 0.01 73 23 27 4 236.09 0.83 74 23 43 20 134.60 0.43 75 23 50 27 113.50 0.17 76 23 51 28 113.49 0.18 77 23 52 29 113.23 0.29 78 23 54 31 112.98 0.26 79 23 56 33 112.60 0.14 80 23 59 36 112.64 0.12 81 24 27 3 236.09 0.83 82 24 28 4 236.12 0.82 83 24 52 28 113.23 0.29 84 24 53 29 113.23 0.29 85 25 28 3 235.92 2.37 86 25 29 4 232.84 0.83 87 26 29 3 232.84 0.83 88 26 30 4 232.83 0.83 89 26 43 17 145.62 1.11 90 26 56 30 112.58 0.14 91 26 67 41 97.78 0.27 92 27 30 3 232.84 0.83 93 27 31 4 232.83 0.83 94 27 38 11 164.34 0.87 95 27 41 14 152.07 4.08 96 27 43 16 145.76 1.04 97 27 52 25 113.23 0.29 98 28 31 3 229.09 2.47 99 28 32 4 228.92 0.33 100 29 32 3 233.60 0.41 101 29 33 4 231.17 0.80 102 30 33 3 236.27 1.75 103 30 34 4 225.55 0.85 104 30 35 5 224.81 1.22 105 30 41 11 168.55 1.21 106 30 43 13 159.38 0.42 107 30 69 39 97.64 0.22 108 31 34 3 236.28 1.76 109 31 35 4 216.13 1.16 110 31 36 5 210.86 3.79 111 31 37 6 207.28 3.45 112 31 38 7 197.37 7.20 113 31 41 10 181.48 3.10 114 32 35 3 236.28 1.76 115 36 40 4 221.58 1.34 116 36 41 5 205.55 3.66 117 36 69 33 97.78 0.29 118 36 71 35 97.40 0.29 119 37 40 3 235.52 0.95 120 37 41 4 230.84 3.29 121 38 41 3 233.19 2.12 122 39 72 33 97.37 0.30 123 40 71 31 97.40 0.29 124 40 72 32 97.31 0.27 125 40 73 33 97.17 0.27 126 41 69 28 97.78 0.29 127 41 70 29 97.67 0.24 128 41 72 31 97.24 0.24 129 42 49 7 150.10 1.84 130 42 68 26 97.94 0.33 131 42 69 27 97.73 0.25 132 42 70 28 97.66 0.24 133 42 72 30 97.25 0.23 134 43 49 6 150.12 1.84 135 43 50 7 145.88 3.87 136 43 67 24 97.95 0.33 137 43 68 25 97.75 0.26 138 43 69 26 97.73 0.25 139 44 47 3 238.04 1.15 140 44 48 4 198.87 4.21 141 44 49 5 158.81 2.50 142 44 67 23 97.96 0.33 143 44 68 24 97.76 0.24 144 44 70 26 97.74 0.25 145 45 48 3 236.50 1.92 146 45 50 5 196.56 5.34 147 45 59 14 112.64 0.15 148 45 61 16 112.53 0.12 149 45 65 20 98.69 0.28 150 45 66 21 98.20 0.29 151 45 67 22 97.96 0.33 152 49 72 23 97.48 0.14 153 50 59 9 132.25 9.64 154 50 61 11 130.81 8.96 155 50 67 17 97.95 0.33 156 51 54 3 241.12 0.45 157 51 59 8 183.50 1.10 158 54 58 4 227.88 0.57 159 54 59 5 227.87 0.57 160 55 58 3 231.60 0.36 161 55 59 4 229.53 1.40 162 56 59 3 231.94 0.20 163 56 60 4 227.87 0.57 164 56 61 5 209.78 1.19 165 57 60 3 229.50 1.41 166 61 65 4 185.80 2.21 167 61 67 6 179.31 2.90 168 62 65 3 229.53 1.57