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 19 18 47.99 1.09 2 1 56 55 48.00 1.09 3 1 61 60 48.04 1.10 4 1 62 61 48.04 1.10 5 1 63 62 48.02 1.09 6 2 14 12 48.06 1.09 7 2 15 13 47.93 1.10 8 2 63 61 48.05 1.10 9 2 64 62 48.04 1.09 10 3 14 11 48.10 1.10 11 3 15 12 48.05 1.09 12 3 17 14 48.08 1.09 13 3 61 58 48.06 1.10 14 3 64 61 48.04 1.09 15 3 65 62 48.04 1.09 16 3 67 64 48.00 1.10 17 4 12 8 48.23 1.07 18 4 13 9 48.13 1.10 19 4 14 10 48.12 1.11 20 4 64 60 48.11 1.11 21 4 65 61 48.08 1.10 22 4 66 62 48.01 1.10 23 4 67 63 48.01 1.10 24 5 12 7 48.24 1.06 25 5 13 8 48.16 1.10 26 5 15 10 48.15 1.10 27 5 30 25 48.11 1.11 28 5 43 38 48.00 1.10 29 5 67 62 48.04 1.09 30 5 69 64 47.92 1.12 31 6 11 5 175.03 0.03 32 6 12 6 138.14 4.71 33 6 66 60 48.11 1.10 34 6 67 61 48.09 1.10 35 6 68 62 48.02 1.10 36 6 69 63 47.98 1.12 37 7 10 3 236.81 2.25 38 7 11 4 186.27 5.57 39 7 13 6 161.81 6.58 40 7 69 62 48.02 1.11 41 8 69 61 48.08 1.10 42 8 70 62 47.99 1.11 43 11 34 23 128.82 7.11 44 13 30 17 129.55 7.47 45 13 33 20 130.07 7.61 46 13 34 21 129.57 7.46 47 14 33 19 130.43 7.47 48 15 26 11 130.30 7.71 49 15 29 14 130.27 7.66 50 15 30 15 130.40 7.48 51 15 33 18 130.48 7.45 52 16 29 13 130.82 7.46 53 17 21 4 227.04 2.90 54 17 26 9 149.98 1.74 55 17 29 12 149.97 1.74 56 17 56 39 118.31 2.36 57 18 21 3 236.48 0.52 58 18 56 38 118.31 2.36 59 19 55 36 118.47 2.42 60 19 56 37 118.31 2.36 61 19 57 38 117.92 2.21 62 20 55 35 118.50 2.41 63 21 25 4 230.12 0.18 64 21 26 5 227.80 0.98 65 21 55 34 118.56 2.42 66 21 56 35 118.53 2.43 67 22 25 3 236.53 3.02 68 22 26 4 230.13 0.18 69 22 52 30 122.50 0.54 70 22 54 32 121.31 1.06 71 22 55 33 121.28 1.06 72 23 26 3 234.59 2.27 73 23 27 4 230.19 0.21 74 23 43 20 136.94 4.04 75 23 50 27 122.56 0.53 76 23 51 28 122.54 0.55 77 23 52 29 122.51 0.54 78 23 54 31 122.30 0.60 79 23 56 33 121.33 1.04 80 23 59 36 121.42 1.01 81 24 27 3 232.46 1.29 82 24 28 4 230.19 0.21 83 24 52 28 122.51 0.53 84 25 28 3 233.49 1.44 85 25 29 4 232.42 0.91 86 26 29 3 232.65 1.02 87 26 30 4 232.44 0.92 88 26 43 17 141.50 2.44 89 26 56 30 121.99 0.71 90 27 30 3 234.84 1.54 91 27 31 4 232.53 0.88 92 27 38 11 173.50 1.07 93 27 41 14 157.25 0.79 94 27 43 16 155.50 1.62 95 27 52 25 122.59 0.49 96 28 31 3 235.81 1.06 97 28 32 4 232.65 1.03 98 28 38 10 183.94 2.70 99 29 32 3 234.25 0.24 100 29 33 4 232.75 0.99 101 30 33 3 234.28 0.25 102 30 34 4 225.89 0.23 103 30 35 5 225.44 0.42 104 30 36 6 216.90 0.68 105 30 41 11 183.78 2.62 106 30 43 13 168.54 3.68 107 30 69 39 99.64 0.07 108 31 34 3 237.15 1.18 109 31 35 4 215.75 0.40 110 31 36 5 202.31 2.62 111 31 37 6 202.25 2.65 112 31 38 7 188.79 0.71 113 31 41 10 184.60 2.80 114 36 40 4 232.90 0.88 115 36 41 5 226.74 3.94 116 36 69 33 99.73 0.04 117 36 71 35 99.10 0.12 118 37 40 3 241.62 0.95 119 37 41 4 232.90 0.88 120 38 41 3 232.90 0.88 121 39 72 33 98.36 0.04 122 40 71 31 98.38 0.03 123 40 72 32 98.32 0.05 124 40 73 33 98.31 0.06 125 41 69 28 99.72 0.04 126 41 70 29 99.14 0.15 127 41 71 30 98.39 0.02 128 41 72 31 98.37 0.03 129 42 49 7 164.82 1.40 130 42 68 26 100.00 0.09 131 42 69 27 99.47 0.00 132 42 70 28 99.11 0.17 133 42 72 30 98.37 0.03 134 43 49 6 164.84 1.41 135 43 50 7 144.28 8.87 136 43 67 24 100.02 0.10 137 43 68 25 99.72 0.04 138 43 69 26 99.14 0.15 139 44 47 3 244.00 1.03 140 44 48 4 188.94 2.91 141 44 49 5 164.91 1.38 142 44 50 6 164.91 1.38 143 44 67 23 100.02 0.10 144 44 68 24 99.73 0.04 145 44 70 26 99.61 0.07 146 45 48 3 237.59 0.33 147 45 50 5 189.38 3.12 148 45 59 14 122.64 0.45 149 45 61 16 122.45 0.46 150 45 65 20 101.14 0.31 151 45 66 21 100.62 0.20 152 45 67 22 100.02 0.10 153 48 59 11 132.34 4.36 154 50 59 9 156.99 3.71 155 50 61 11 142.82 9.63 156 50 67 17 100.02 0.10 157 51 54 3 237.13 1.59 158 51 59 8 188.28 1.79 159 54 58 4 228.03 0.27 160 54 59 5 228.05 0.27 161 55 58 3 235.16 0.01 162 55 59 4 234.83 0.15 163 56 59 3 236.71 0.79 164 56 60 4 230.00 1.25 165 56 61 5 217.20 1.47 166 57 60 3 234.59 0.27 167 61 65 4 213.49 3.56 168 61 67 6 185.12 1.04 169 62 65 3 238.50 0.54