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 4 82 78 24.35 0.92 2 4 83 79 24.84 0.32 3 5 9 4 286.97 0.38 4 5 56 51 38.41 0.37 5 5 75 70 34.36 0.34 6 5 78 73 29.98 0.30 7 5 79 74 28.38 0.35 8 6 9 3 295.44 3.68 9 6 10 4 289.16 0.40 10 6 75 69 35.79 0.32 11 7 10 3 298.62 0.96 12 7 11 4 289.16 0.40 13 7 30 23 66.93 0.31 14 7 31 24 66.89 0.30 15 7 75 68 36.68 0.50 16 8 11 3 291.66 0.87 17 8 12 4 289.14 0.39 18 9 12 3 304.07 0.34 19 9 13 4 292.79 2.09 20 9 56 47 40.63 1.02 21 10 13 3 296.00 3.70 22 10 14 4 292.41 2.29 23 10 30 20 67.23 0.17 24 10 31 21 67.22 0.17 25 10 75 65 41.02 0.58 26 11 14 3 292.81 2.08 27 11 15 4 288.36 0.24 28 11 26 15 67.36 0.20 29 11 30 19 67.06 0.26 30 12 15 3 292.81 2.08 31 12 16 4 288.37 0.24 32 13 16 3 295.95 0.79 33 13 52 39 42.30 0.39 34 14 17 3 298.01 1.94 35 14 18 4 288.03 0.07 36 14 34 20 66.86 0.35 37 14 35 21 66.83 0.35 38 15 18 3 291.95 2.03 39 15 19 4 274.64 0.40 40 16 55 39 42.69 0.41 41 17 40 23 66.56 0.17 42 17 48 31 56.10 1.40 43 21 24 3 333.37 1.03 44 25 29 4 255.88 10.81 45 26 30 4 230.09 1.84 46 29 32 3 324.73 2.08 47 30 34 4 279.22 0.27 48 31 34 3 288.69 3.40 49 31 71 40 96.92 1.83 50 31 72 41 96.92 1.82 51 33 36 3 295.38 0.43 52 33 37 4 257.60 2.46 53 34 37 3 290.82 1.14 54 34 38 4 274.83 4.33 55 34 71 37 113.30 0.18 56 35 38 3 293.16 0.03 57 35 40 5 190.96 1.33 58 35 45 10 177.38 0.29 59 35 68 33 113.49 0.24 60 35 69 34 113.48 0.24 61 35 70 35 113.38 0.20 62 35 71 36 113.32 0.20 63 35 74 39 113.45 0.24 64 40 45 5 224.37 4.21 65 41 44 3 291.56 0.74 66 41 45 4 286.88 0.79 67 42 45 3 296.04 1.17 68 42 46 4 271.07 3.74 69 42 66 24 131.41 0.46 70 42 67 25 131.34 0.42 71 42 68 26 131.34 0.42 72 43 46 3 292.57 0.56 73 44 48 4 290.50 1.07 74 45 48 3 290.51 1.08 75 45 49 4 289.39 0.53 76 45 65 20 132.22 0.78 77 45 68 23 132.59 0.60 78 46 49 3 299.06 0.51 79 46 50 4 289.40 0.52 80 46 66 20 132.12 0.74 81 47 50 3 294.64 2.32 82 47 51 4 293.81 2.73 83 48 51 3 305.18 0.37 84 48 52 4 284.22 2.08 85 49 52 3 284.22 2.08 86 49 53 4 284.22 2.08 87 50 53 3 302.73 2.29 88 50 54 4 289.67 0.64 89 50 62 12 133.02 0.52 90 51 54 3 292.44 0.29 91 52 55 3 304.49 2.19 92 52 56 4 301.52 2.89 93 52 78 26 132.88 0.48 94 53 56 3 290.89 0.04 95 53 57 4 289.19 0.88 96 53 59 6 244.22 0.61 97 53 60 7 177.03 0.20 98 53 61 8 177.03 0.20 99 56 78 22 133.01 0.51 100 58 78 20 133.07 0.52 101 58 81 23 132.92 0.47 102 58 82 24 132.81 0.50 103 58 85 27 132.66 0.43 104 61 64 3 298.20 0.45 105 61 65 4 265.87 9.30 106 61 77 16 133.26 0.63 107 61 81 20 132.93 0.54 108 62 66 4 253.44 3.09 109 63 66 3 289.90 0.13 110 63 67 4 287.31 1.42 111 64 67 3 291.18 0.51 112 64 68 4 278.19 0.05 113 64 77 13 145.72 0.79 114 65 68 3 281.55 1.73 115 65 74 9 159.70 5.69 116 65 77 12 145.65 0.68 117 68 73 5 223.81 0.20 118 68 74 6 197.99 7.82 119 70 73 3 293.63 1.11 120 71 74 3 293.63 1.10 121 71 75 4 293.62 1.10 122 72 75 3 293.63 1.10 123 72 76 4 294.22 0.81 124 73 76 3 295.98 1.68 125 73 77 4 288.83 1.89 126 74 77 3 289.04 1.79 127 74 78 4 289.03 1.79 128 75 78 3 303.91 4.72 129 75 79 4 284.81 0.14 130 76 79 3 290.26 0.61 131 76 80 4 284.82 0.14 132 77 80 3 294.81 2.12 133 77 81 4 284.74 0.10 134 78 81 3 286.01 0.19 135 78 82 4 282.18 1.34 136 79 82 3 296.46 0.47 137 79 83 4 289.47 1.54 138 80 83 3 290.64 0.95 139 80 84 4 282.70 1.64 140 81 85 4 282.57 1.70 141 82 85 3 277.85 2.08 142 82 86 4 277.43 1.86 143 83 86 3 293.89 2.52