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 71 70 23.03 0.03 2 1 72 71 17.80 0.08 3 1 75 74 17.80 0.07 4 2 5 3 281.59 2.73 5 2 6 4 276.00 1.18 6 2 75 73 23.04 0.03 7 3 6 3 276.04 1.20 8 3 7 4 276.00 1.18 9 4 7 3 277.28 0.54 10 4 8 4 274.89 0.62 11 5 8 3 274.89 0.61 12 5 9 4 271.98 0.83 13 5 52 47 85.66 0.93 14 5 71 66 40.55 1.92 15 5 74 69 40.47 1.95 16 5 75 70 37.02 0.81 17 5 78 73 37.02 0.81 18 6 9 3 276.98 1.29 19 6 10 4 272.00 0.81 20 6 27 21 43.36 1.70 21 6 67 61 43.27 1.70 22 6 71 65 41.70 1.57 23 7 10 3 278.30 0.63 24 7 11 4 275.67 2.63 25 8 11 3 276.85 2.04 26 8 12 4 275.67 2.64 27 8 51 43 86.56 1.32 28 8 52 44 86.54 1.33 29 9 12 3 276.95 1.99 30 9 13 4 275.76 2.59 31 9 48 39 86.52 1.34 32 9 52 43 86.56 1.32 33 9 67 58 43.48 1.72 34 9 70 61 43.45 1.72 35 9 71 62 43.24 1.62 36 9 74 65 43.13 1.57 37 10 13 3 287.33 1.04 38 10 14 4 275.79 2.56 39 10 25 15 83.19 13.72 40 10 67 57 43.48 1.72 41 11 14 3 275.66 1.46 42 11 15 4 276.42 1.34 43 12 15 3 277.88 0.61 44 12 16 4 276.43 1.34 45 12 44 32 86.58 1.43 46 12 47 35 86.67 1.38 47 12 48 36 86.62 1.38 48 12 51 39 86.78 1.39 49 13 16 3 276.43 1.47 50 13 17 4 276.30 1.41 51 13 31 18 57.15 1.50 52 13 44 31 86.64 1.40 53 14 17 3 280.82 1.12 54 14 18 4 268.51 0.64 55 14 19 5 184.18 0.76 56 14 20 6 184.18 0.76 57 14 23 9 161.17 2.50 58 15 18 3 268.85 0.80 59 16 43 27 86.90 1.45 60 16 44 28 86.89 1.44 61 19 23 4 240.26 3.29 62 26 29 3 265.32 0.48 63 26 67 41 87.77 1.16 64 27 66 39 87.97 1.08 65 27 67 40 87.54 1.27 66 27 68 41 87.62 1.19 67 28 66 38 87.86 1.16 68 28 68 40 87.79 1.16 69 29 66 37 88.03 1.09 70 29 67 38 88.03 1.09 71 30 33 3 292.79 0.03 72 30 66 36 88.04 1.08 73 31 64 33 88.23 1.18 74 31 65 34 88.24 1.18 75 34 37 3 231.54 6.66 76 34 38 4 245.87 0.51 77 34 39 5 181.81 1.98 78 40 43 3 278.00 0.94 79 40 44 4 268.15 0.75 80 41 44 3 269.64 1.50 81 41 45 4 265.29 0.34 82 41 61 20 110.87 9.72 83 42 45 3 273.29 0.49 84 42 46 4 265.49 0.38 85 43 46 3 275.68 3.30 86 43 47 4 268.25 0.42 87 44 47 3 274.45 1.09 88 44 48 4 268.25 0.42 89 45 48 3 280.38 1.88 90 45 49 4 264.97 0.12 91 45 56 11 152.12 0.47 92 45 61 16 117.38 6.47 93 46 49 3 276.94 3.58 94 46 50 4 258.62 1.94 95 47 50 3 265.27 0.32 96 47 51 4 258.62 1.95 97 48 51 3 269.18 2.46 98 48 52 4 251.53 5.49 99 48 74 26 85.31 22.62 100 49 53 4 230.09 5.22 101 49 54 5 198.25 0.04 102 49 55 6 196.60 0.79 103 49 56 7 170.20 1.66 104 50 53 3 244.21 0.49 105 52 74 22 85.36 22.61 106 52 78 26 85.28 22.64 107 53 81 28 81.14 20.89 108 54 74 20 85.42 22.59 109 54 77 23 85.34 22.55 110 54 78 24 85.23 22.59 111 54 81 27 75.28 17.96 112 55 77 22 85.34 22.54 113 55 81 26 75.28 17.96 114 55 82 27 75.26 17.95 115 56 60 4 264.88 0.48 116 56 61 5 262.69 0.56 117 56 77 21 85.34 22.54 118 57 60 3 264.78 0.43 119 57 61 4 262.72 0.56 120 58 61 3 262.73 0.56 121 58 62 4 262.72 0.56 122 59 62 3 272.72 1.54 123 60 64 4 271.31 1.75 124 60 73 13 145.91 1.68 125 61 64 3 275.87 0.53 126 64 69 5 238.11 6.29 127 64 70 6 206.13 9.52 128 64 73 9 188.44 1.88 129 65 69 4 259.25 3.87 130 66 69 3 280.40 0.10 131 66 70 4 265.49 1.48 132 67 70 3 270.67 1.11 133 67 71 4 266.37 0.73 134 68 71 3 286.10 1.31 135 68 72 4 269.14 0.35 136 69 72 3 275.69 0.60 137 69 73 4 269.31 0.43 138 70 73 3 274.32 1.28 139 70 74 4 270.96 0.39 140 71 74 3 280.39 0.11 141 71 75 4 269.06 0.56 142 72 75 3 272.18 0.99 143 72 76 4 272.17 0.99 144 73 76 3 283.51 0.93 145 73 77 4 272.16 0.99 146 74 77 3 271.82 1.17 147 74 78 4 271.81 1.17 148 75 78 3 277.59 1.72 149 75 79 4 275.80 0.83 150 76 79 3 280.62 1.57 151 76 80 4 282.39 0.68 152 77 80 3 286.81 0.68 153 77 81 4 242.44 7.57