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 2 27 25 47.91 0.47 2 2 76 74 44.47 0.33 3 2 77 75 43.92 0.06 4 3 25 22 48.30 0.27 5 3 26 23 48.43 0.24 6 3 78 75 40.16 0.51 7 4 7 3 283.44 0.36 8 4 23 19 47.57 0.39 9 4 24 20 48.39 0.23 10 4 25 21 48.35 0.29 11 4 78 74 46.99 0.16 12 4 79 75 46.97 0.17 13 4 80 76 38.47 0.35 14 5 24 19 48.59 0.18 15 5 25 20 48.59 0.20 16 6 23 17 48.59 0.18 17 6 24 18 48.61 0.18 18 7 22 15 48.69 0.15 19 7 23 16 48.66 0.15 20 7 80 73 48.01 0.28 21 8 21 13 99.90 25.46 22 8 22 14 48.70 0.16 23 8 23 15 48.70 0.17 24 8 34 26 48.56 0.19 25 8 71 63 48.02 0.28 26 8 72 64 48.53 0.21 27 8 73 65 48.59 0.19 28 8 80 72 48.55 0.20 29 8 81 73 48.51 0.20 30 8 82 74 47.18 0.24 31 9 21 12 106.81 28.89 32 9 82 73 47.63 0.10 33 10 82 72 48.47 0.18 34 10 83 73 47.26 0.25 35 11 19 8 184.43 7.50 36 11 20 9 183.33 8.05 37 11 21 10 174.76 3.77 38 11 83 72 48.56 0.18 39 11 84 73 47.66 0.10 40 11 85 74 47.66 0.10 41 12 85 73 47.81 0.03 42 13 17 4 255.06 1.72 43 13 18 5 237.69 0.52 44 13 63 50 104.10 0.10 45 13 84 71 48.64 0.14 46 13 85 72 48.50 0.15 47 13 86 73 47.62 0.09 48 13 87 74 47.27 0.26 49 14 17 3 277.55 1.88 50 14 87 73 47.63 0.09 51 14 88 74 47.16 0.26 52 14 89 75 46.73 0.14 53 15 62 47 105.91 0.69 54 15 63 48 105.52 0.60 55 15 64 49 104.29 0.01 56 15 65 50 104.31 0.01 57 15 86 71 48.52 0.16 58 15 87 72 48.44 0.18 59 15 88 73 47.20 0.29 60 16 62 46 105.91 0.69 61 16 63 47 107.15 0.71 62 17 61 44 107.99 0.51 63 17 62 45 107.49 0.60 64 18 59 41 109.37 0.88 65 18 60 42 108.07 0.53 66 18 61 43 108.00 0.50 67 19 59 40 109.44 0.84 68 19 60 41 109.07 1.02 69 19 63 44 108.00 0.52 70 19 84 65 48.62 0.16 71 20 58 38 111.36 1.04 72 20 59 39 111.28 1.03 73 21 34 13 114.09 0.49 74 21 57 36 111.67 1.10 75 21 58 37 111.52 1.11 76 21 60 39 111.45 1.02 77 21 71 50 105.21 0.33 78 21 82 61 53.25 0.05 79 21 84 63 52.98 0.12 80 22 34 12 114.31 0.58 81 22 56 34 113.46 0.34 82 22 57 35 111.67 1.09 83 23 34 11 136.46 11.63 84 23 56 33 113.48 0.33 85 23 73 50 105.18 0.32 86 23 80 57 64.62 0.29 87 24 55 31 113.62 0.30 88 25 30 5 268.56 0.42 89 25 56 31 114.36 0.58 90 25 75 50 105.13 0.33 91 25 78 53 91.75 0.21 92 28 54 26 138.70 0.59 93 30 56 26 151.65 3.21 94 30 75 45 105.20 0.32 95 31 51 20 151.81 3.27 96 32 51 19 151.88 3.27 97 32 73 41 105.46 0.29 98 32 74 42 105.27 0.34 99 32 75 43 105.15 0.33 100 33 73 40 105.40 0.33 101 33 74 41 105.25 0.33 102 34 41 7 236.78 0.55 103 34 49 15 160.29 0.51 104 34 56 22 152.99 3.75 105 34 57 23 152.42 3.50 106 34 58 24 152.34 3.47 107 34 71 37 107.03 0.38 108 34 73 39 105.21 0.33 109 35 38 3 267.44 0.20 110 35 39 4 248.77 0.48 111 35 40 5 236.91 0.48 112 35 41 6 236.91 0.49 113 35 72 37 105.48 0.33 114 36 39 3 269.92 0.39 115 36 41 5 261.74 2.83 116 36 67 31 108.20 0.63 117 36 70 34 107.88 0.58 118 36 84 48 53.17 0.03 119 37 69 32 107.96 0.55 120 37 70 33 107.95 0.55 121 41 47 6 230.62 3.48 122 43 47 4 241.05 0.77 123 43 49 6 223.56 6.75 124 44 47 3 264.91 0.56 125 46 60 14 153.22 3.71 126 46 62 16 153.19 3.71 127 47 60 13 153.21 3.73 128 48 59 11 153.23 3.73 129 48 61 13 153.22 3.73 130 49 58 9 191.57 5.40 131 50 57 7 212.96 2.76 132 51 55 4 261.81 0.35 133 51 56 5 212.97 2.77 134 51 57 6 212.97 2.77 135 52 55 3 292.94 2.75 136 53 56 3 294.99 1.74 137 56 73 17 105.22 0.33 138 60 63 3 294.80 0.85 139 60 67 7 244.19 0.78 140 63 67 4 263.60 0.01 141 63 86 23 48.63 0.14 142 64 67 3 282.61 1.46 143 64 86 22 48.67 0.14 144 65 68 3 283.17 1.18 145 65 86 21 48.68 0.14 146 65 87 22 48.66 0.13 147 65 88 23 48.66 0.14 148 67 84 17 52.70 0.01 149 67 86 19 50.38 0.69 150 68 84 16 53.01 0.10 151 68 85 17 50.48 0.73 152 68 86 18 50.48 0.73 153 69 84 15 53.09 0.06 154 70 82 12 53.40 0.02 155 70 83 13 53.20 0.04 156 70 84 14 53.20 0.04 157 71 81 10 53.77 0.01 158 71 82 11 53.59 0.07 159 71 84 13 53.41 0.03 160 72 80 8 139.23 7.12 161 72 81 9 53.76 0.01 162 73 79 6 186.94 0.59 163 73 80 7 141.35 7.70 164 74 79 5 190.75 1.31 165 75 78 3 267.40 6.27