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 17 20 3 287.39 0.50 2 17 63 46 56.47 0.76 3 18 63 45 56.48 0.75 4 19 22 3 281.82 6.38 5 19 63 44 56.48 0.76 6 19 67 48 56.47 0.76 7 19 71 52 56.45 0.76 8 22 64 42 75.60 1.18 9 24 28 4 212.70 0.11 10 24 29 5 204.42 1.24 11 24 32 8 197.58 2.18 12 24 60 36 94.77 0.51 13 24 64 40 90.33 1.66 14 24 68 44 88.00 1.13 15 25 28 3 229.78 0.46 16 25 29 4 216.77 1.80 17 26 29 3 240.72 0.24 18 26 30 4 216.87 1.84 19 27 30 3 229.21 0.18 20 27 31 4 221.24 0.94 21 28 31 3 224.06 0.48 22 28 32 4 226.24 1.56 23 28 58 30 118.17 1.18 24 28 60 32 117.50 1.47 25 29 32 3 241.74 1.38 26 29 33 4 225.09 0.03 27 29 68 39 110.58 0.70 28 30 33 3 229.62 2.23 29 30 34 4 225.09 0.03 30 31 34 3 241.60 0.21 31 31 35 4 228.38 2.62 32 31 54 23 120.25 1.85 33 31 57 26 120.27 1.86 34 31 58 27 120.03 1.89 35 32 35 3 226.50 1.72 36 32 36 4 226.48 1.73 37 32 54 22 120.27 1.85 38 32 60 28 120.14 1.83 39 32 65 33 117.03 1.64 40 32 68 36 116.81 1.53 41 33 36 3 239.22 1.40 42 33 37 4 226.37 1.79 43 33 41 8 190.81 2.34 44 33 68 35 118.79 2.33 45 34 37 3 231.84 0.64 46 34 38 4 226.16 1.88 47 35 38 3 225.27 1.44 48 35 39 4 222.67 0.22 49 35 50 15 120.39 1.82 50 35 51 16 120.30 1.84 51 35 54 19 120.33 1.83 52 35 65 30 119.88 1.92 53 36 39 3 229.53 2.37 54 36 40 4 213.03 3.27 55 36 41 5 184.05 9.06 56 36 68 32 119.87 1.94 57 36 69 33 116.81 1.53 58 37 41 4 222.32 0.05 59 39 42 3 241.84 1.05 60 39 43 4 217.22 2.50 61 39 47 8 129.64 1.31 62 39 51 12 121.94 2.50 63 39 65 26 120.25 1.87 64 41 68 27 119.94 1.92 65 41 69 28 118.95 1.68 66 41 72 31 114.14 0.23 67 41 73 32 107.13 2.23 68 42 69 27 119.94 1.92 69 43 51 8 157.69 6.90 70 43 65 22 120.25 1.88 71 43 66 23 120.12 1.83 72 43 69 26 120.14 1.82 73 44 47 3 236.94 0.49 74 44 48 4 224.46 0.58 75 45 48 3 235.96 0.01 76 46 49 3 260.56 0.78 77 47 50 3 236.34 1.79 78 47 51 4 224.49 0.58 79 48 51 3 234.06 2.94 80 48 52 4 223.97 0.69 81 49 53 4 220.15 2.69 82 50 53 3 232.15 1.88 83 50 54 4 223.68 0.93 84 51 54 3 237.72 0.91 85 51 55 4 230.56 1.09 86 51 62 11 128.19 1.50 87 51 65 14 121.25 1.38 88 52 55 3 233.97 0.61 89 52 56 4 233.97 0.61 90 53 56 3 233.97 0.61 91 53 57 4 233.97 0.61 92 54 57 3 235.43 0.12 93 54 58 4 232.42 1.38 94 54 60 6 219.00 1.28 95 54 65 11 154.13 0.01 96 55 58 3 232.43 1.38 97 55 59 4 217.56 2.27 98 55 60 5 206.55 0.63 99 55 62 7 163.89 3.41 100 60 64 4 226.43 0.12 101 60 65 5 226.39 0.13 102 61 64 3 229.34 1.57 103 61 65 4 226.63 0.21 104 62 65 3 226.63 0.21 105 62 66 4 226.64 0.23 106 63 66 3 238.34 0.86 107 63 67 4 234.95 0.11 108 64 67 3 237.68 0.53 109 64 68 4 227.81 0.35 110 65 68 3 236.97 0.89 111 65 69 4 236.96 0.89 112 66 69 3 236.97 0.88 113 66 70 4 234.97 0.11 114 67 70 3 233.46 0.10 115 67 71 4 230.79 1.22 116 68 71 3 233.03 1.09 117 68 72 4 228.41 1.21 118 69 72 3 235.93 1.72 119 69 73 4 226.32 0.24 120 70 73 3 239.06 0.14 121 72 75 3 270.00 0.40 122 72 76 4 196.94 9.31