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 26.16 1.16 2 4 83 79 26.16 1.16 3 5 9 4 283.34 0.62 4 5 56 51 37.71 1.28 5 5 75 70 36.05 0.59 6 5 79 74 27.55 0.50 7 5 82 77 27.55 0.49 8 6 9 3 292.98 1.28 9 6 10 4 297.18 2.31 10 6 75 69 36.46 0.76 11 7 10 3 297.18 2.31 12 7 11 4 287.33 2.62 13 7 30 23 59.27 1.59 14 7 31 24 59.24 1.57 15 7 75 68 36.80 0.59 16 8 11 3 291.50 0.54 17 8 12 4 292.63 0.04 18 9 12 3 297.18 2.30 19 9 13 4 292.63 0.04 20 9 56 47 41.65 0.82 21 10 13 3 293.36 0.39 22 10 14 4 286.83 2.83 23 10 31 21 59.46 1.68 24 10 75 65 38.22 0.44 25 11 14 3 294.63 1.11 26 11 15 4 290.30 0.10 27 11 26 15 97.81 17.82 28 11 30 19 59.55 1.63 29 12 15 3 293.68 1.59 30 12 16 4 292.48 2.19 31 13 16 3 293.58 1.64 32 13 17 4 293.58 1.64 33 13 48 35 43.05 1.48 34 13 52 39 43.01 1.47 35 14 17 3 302.32 0.20 36 14 34 20 59.37 1.53 37 14 35 21 59.37 1.53 38 15 18 3 287.62 0.24 39 15 19 4 287.62 0.24 40 17 40 23 63.22 0.04 41 17 48 31 50.60 2.27 42 18 21 3 363.03 2.10 43 24 34 10 157.18 0.57 44 26 30 4 230.16 2.79 45 30 34 4 239.03 15.22 46 31 71 40 102.23 0.38 47 31 72 41 96.95 0.51 48 32 71 39 104.92 0.40 49 33 36 3 286.22 0.50 50 33 37 4 274.16 2.35 51 33 71 38 105.24 0.31 52 34 37 3 300.37 1.32 53 34 71 37 105.25 0.32 54 35 40 5 177.75 0.09 55 35 45 10 167.77 2.06 56 35 68 33 105.37 0.28 57 35 69 34 105.35 0.28 58 35 71 36 105.33 0.28 59 35 74 39 105.34 0.28 60 40 44 4 259.74 7.41 61 40 45 5 230.62 4.47 62 41 45 4 291.20 1.51 63 42 45 3 297.32 3.02 64 42 46 4 271.00 2.62 65 42 66 24 115.50 2.27 66 43 46 3 284.03 3.16 67 44 48 4 293.12 0.78 68 45 48 3 293.12 0.78 69 45 49 4 286.49 0.51 70 45 65 20 116.02 2.17 71 45 68 23 116.05 2.18 72 46 49 3 294.11 0.80 73 46 50 4 290.64 0.33 74 47 50 3 292.64 0.67 75 47 51 4 290.64 0.33 76 48 51 3 299.73 2.48 77 48 52 4 287.70 1.14 78 49 52 3 296.44 2.58 79 49 53 4 288.81 1.21 80 50 53 3 292.67 0.64 81 50 54 4 290.88 1.44 82 51 54 3 299.10 4.64 83 51 55 4 291.29 1.23 84 52 55 3 294.24 2.21 85 52 56 4 290.26 1.74 86 53 56 3 294.69 0.47 87 53 57 4 290.24 1.74 88 53 58 5 262.76 6.46 89 53 59 6 241.12 4.36 90 53 60 7 203.43 0.88 91 53 61 8 203.18 1.00 92 54 57 3 280.56 2.14 93 56 78 22 117.06 1.78 94 56 82 26 116.96 1.75 95 58 78 20 116.92 1.85 96 58 81 23 116.75 1.78 97 61 64 3 305.10 1.52 98 61 65 4 229.06 1.18 99 61 77 16 121.39 0.28 100 62 66 4 253.36 13.32 101 63 66 3 290.54 1.40 102 63 67 4 282.39 1.18 103 64 67 3 292.80 0.40 104 64 68 4 275.55 2.24 105 64 77 13 141.09 0.18 106 65 68 3 283.18 0.79 107 65 77 12 149.35 0.51 108 68 73 5 258.80 2.63 109 68 74 6 235.43 12.38 110 70 73 3 293.84 1.01 111 71 74 3 293.05 1.78 112 71 75 4 292.62 1.65 113 72 75 3 292.66 1.64 114 72 76 4 289.92 0.28 115 73 76 3 292.65 1.64 116 73 77 4 289.42 0.03 117 74 77 3 290.39 0.51 118 74 78 4 289.41 0.03 119 75 78 3 302.87 1.01 120 75 79 4 283.69 1.13 121 76 79 3 288.62 0.39 122 76 80 4 283.69 1.15 123 77 80 3 287.05 0.27 124 77 81 4 287.05 0.27 125 78 81 3 295.65 2.61 126 78 82 4 287.05 0.27 127 79 82 3 289.54 0.38 128 79 83 4 288.25 1.02 129 80 83 3 293.37 1.84 130 80 84 4 288.52 0.89 131 81 84 3 300.92 0.83 132 81 85 4 285.97 0.14 133 82 85 3 289.50 0.67 134 82 86 4 285.39 0.42 135 83 86 3 292.22 1.53