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 38 36 138.60 0.36 2 2 39 37 138.60 0.36 3 4 37 33 139.52 0.47 4 4 40 36 139.35 0.56 5 5 37 32 140.84 0.04 6 6 40 34 141.07 0.16 7 7 10 3 300.48 0.58 8 7 11 4 293.61 0.44 9 8 11 3 293.61 0.44 10 8 12 4 293.72 0.39 11 8 47 39 140.10 0.64 12 8 50 42 139.21 0.59 13 8 51 43 139.07 0.55 14 8 54 46 138.56 0.31 15 9 12 3 294.80 0.92 16 9 13 4 297.31 1.11 17 9 58 49 134.93 1.15 18 10 13 3 297.32 1.11 19 10 14 4 299.64 2.27 20 11 14 3 309.88 2.56 21 11 15 4 294.86 0.43 22 11 33 22 152.01 2.37 23 11 37 26 150.74 3.00 24 11 47 36 140.19 0.69 25 11 51 40 139.19 0.59 26 12 15 3 294.87 0.44 27 12 16 4 294.86 0.43 28 12 51 39 139.34 0.52 29 12 55 43 138.68 0.39 30 12 58 46 135.67 0.78 31 12 61 49 133.41 0.42 32 13 16 3 299.63 2.29 33 13 17 4 299.62 2.29 34 14 17 3 301.11 1.55 35 14 18 4 297.37 1.17 36 14 32 18 153.46 2.38 37 14 33 19 153.44 2.37 38 14 36 22 153.41 2.39 39 14 37 23 153.39 2.41 40 15 18 3 301.89 1.54 41 15 24 9 188.28 0.35 42 15 29 14 154.46 2.91 43 15 32 17 153.42 2.39 44 15 55 40 139.12 0.57 45 16 19 3 307.61 1.82 46 16 24 8 188.28 0.35 47 16 59 43 135.68 0.78 48 16 61 45 133.34 0.38 49 16 79 63 81.89 1.18 50 17 20 3 312.62 4.05 51 18 24 6 216.59 2.95 52 18 28 10 190.59 1.52 53 18 32 14 157.40 1.98 54 19 22 3 302.23 0.14 55 19 23 4 260.87 4.87 56 19 24 5 216.59 2.94 57 22 77 55 89.12 0.74 58 22 78 56 88.45 0.66 59 22 79 57 88.45 0.66 60 22 87 65 35.41 1.28 61 23 76 53 89.11 0.75 62 23 77 54 89.06 0.76 63 24 29 5 287.99 2.77 64 24 75 51 89.16 0.74 65 24 76 52 89.10 0.74 66 24 77 53 88.57 0.66 67 25 28 3 299.07 0.18 68 25 29 4 288.00 2.77 69 25 74 49 89.14 0.74 70 25 75 50 89.01 0.74 71 26 29 3 289.56 2.39 72 26 30 4 288.03 2.77 73 26 52 26 140.06 0.67 74 26 77 51 88.62 0.65 75 27 30 3 305.17 1.83 76 27 31 4 296.14 1.28 77 27 73 46 89.11 0.77 78 27 74 47 89.06 0.76 79 28 32 4 288.25 2.79 80 29 32 3 296.28 1.22 81 29 33 4 295.81 1.71 82 29 55 26 139.88 0.76 83 30 33 3 298.31 0.47 84 30 34 4 295.95 1.65 85 30 48 18 141.43 0.12 86 31 34 3 300.15 0.44 87 31 35 4 295.94 1.65 88 32 35 3 297.24 1.02 89 32 36 4 297.23 1.02 90 33 36 3 298.94 0.16 91 33 37 4 291.35 1.30 92 33 47 14 194.12 2.42 93 33 51 18 140.23 0.76 94 34 37 3 291.20 1.22 95 34 38 4 283.36 1.07 96 34 41 7 219.87 2.47 97 37 40 3 290.49 0.89 98 37 41 4 277.68 0.41 99 37 47 10 235.05 0.67 100 38 41 3 298.51 0.17 101 38 42 4 280.44 1.91 102 39 42 3 299.44 0.79 103 39 43 4 282.72 0.77 104 40 43 3 298.94 1.03 105 40 44 4 280.45 1.90 106 40 47 7 265.61 2.94 107 41 44 3 280.94 0.13 108 41 45 4 265.62 2.94 109 41 47 6 265.61 2.94 110 42 45 3 302.02 2.58 111 44 47 3 301.19 1.09 112 45 48 3 307.26 1.94 113 46 49 3 328.58 0.03 114 47 50 3 295.82 2.93 115 47 51 4 296.38 2.65 116 48 51 3 306.04 2.18 117 48 52 4 297.58 1.07 118 49 52 3 298.19 0.61 119 49 53 4 296.01 0.29 120 50 53 3 301.76 1.75 121 50 54 4 295.76 0.42 122 51 54 3 300.19 1.01 123 51 55 4 289.66 0.05 124 52 55 3 289.66 0.05 125 52 56 4 289.66 0.05 126 52 77 25 88.50 0.70 127 53 56 3 309.30 0.93 128 53 57 4 289.41 0.07 129 54 57 3 288.93 0.30 130 54 58 4 288.08 0.12 131 55 58 3 297.95 4.04 132 55 59 4 288.10 0.12 133 55 61 6 277.75 0.58 134 55 77 22 88.51 0.70 135 56 60 4 263.75 1.58 136 56 61 5 255.50 1.08 137 56 77 21 88.58 0.66 138 59 79 20 82.11 0.40 139 59 86 27 22.89 0.03 140 60 80 20 81.58 0.66 141 61 77 16 88.59 0.66 142 61 78 17 88.03 0.51 143 61 79 18 82.11 0.40 144 61 80 19 79.72 0.42 145 62 76 14 89.16 0.73 146 62 77 15 88.61 0.66 147 62 78 16 88.59 0.65 148 63 75 12 89.30 0.68 149 63 77 14 88.76 0.60 150 64 67 3 295.75 0.35 151 64 70 6 227.71 3.23 152 64 75 11 89.31 0.68 153 64 76 12 89.29 0.68 154 67 70 3 318.27 1.93 155 70 76 6 195.34 6.61 156 84 87 3 283.20 1.07 157 85 88 3 305.55 1.40 158 85 89 4 219.94 1.08 159 86 89 3 296.74 0.39 160 88 91 3 292.89 1.75 161 88 92 4 264.69 7.46 162 90 93 3 330.86 1.54