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 50 48 21.48 1.12 2 7 13 6 225.74 1.94 3 7 47 40 46.45 0.14 4 8 12 4 231.75 3.15 5 8 13 5 225.74 1.94 6 8 47 39 48.05 0.73 7 9 12 3 239.72 1.74 8 9 13 4 229.31 1.53 9 9 47 38 53.68 1.74 10 10 13 3 240.97 1.38 11 10 14 4 231.04 0.67 12 10 47 37 59.42 1.08 13 10 63 53 47.98 0.70 14 10 66 56 48.00 0.70 15 11 14 3 238.19 2.51 16 11 15 4 231.05 0.67 17 11 66 55 48.01 0.71 18 11 70 59 55.58 0.45 19 12 15 3 242.06 2.60 20 12 16 4 231.03 0.66 21 12 70 58 60.86 1.03 22 13 16 3 234.06 2.18 23 13 17 4 231.01 0.66 24 13 18 5 229.97 0.14 25 13 43 30 60.83 1.00 26 13 47 34 60.98 1.03 27 14 17 3 246.02 4.53 28 14 18 4 226.00 1.61 29 14 19 5 225.99 1.62 30 14 40 26 60.85 1.00 31 14 43 29 60.94 1.05 32 14 63 49 60.98 1.04 33 14 66 52 60.97 1.04 34 14 67 53 60.89 1.02 35 14 72 58 60.77 0.96 36 15 19 4 212.37 2.81 37 15 20 5 212.93 3.09 38 15 22 7 212.21 2.88 39 15 70 55 60.95 1.02 40 15 72 57 60.87 1.00 41 16 19 3 235.60 0.66 42 16 20 4 212.81 3.04 43 17 20 3 235.62 0.68 44 17 43 26 60.99 1.03 45 18 33 15 60.89 1.00 46 18 35 17 60.71 0.94 47 18 39 21 60.90 1.02 48 18 43 25 61.01 1.04 49 18 72 54 60.92 1.02 50 19 33 14 60.89 1.01 51 19 72 53 60.89 1.01 52 20 23 3 269.99 1.02 53 22 25 3 238.14 1.28 54 24 27 3 239.06 2.77 55 24 32 8 60.87 0.93 56 27 32 5 190.18 16.95 57 30 70 40 115.49 0.29 58 30 71 41 115.28 0.29 59 31 70 39 115.62 0.26 60 31 71 40 115.30 0.30 61 31 73 42 114.22 0.27 62 32 71 39 115.66 0.23 63 33 71 38 115.84 0.27 64 33 72 39 115.83 0.26 65 33 73 40 115.70 0.21 66 34 73 39 115.71 0.20 67 34 75 41 115.67 0.21 68 35 39 4 238.75 2.86 69 35 40 5 238.74 2.87 70 35 72 37 116.10 0.22 71 35 73 38 116.03 0.25 72 35 74 39 115.81 0.15 73 35 75 40 115.70 0.21 74 36 39 3 249.97 1.60 75 36 74 38 116.03 0.25 76 36 75 39 115.78 0.18 77 36 76 40 115.70 0.21 78 37 40 3 246.61 0.08 79 37 41 4 231.72 0.66 80 37 60 23 116.33 0.34 81 37 74 37 116.08 0.24 82 37 75 38 116.06 0.24 83 38 41 3 243.50 1.01 84 38 42 4 238.77 2.86 85 39 42 3 247.08 0.17 86 39 43 4 233.26 0.04 87 40 43 3 236.80 1.66 88 40 44 4 230.82 1.26 89 40 60 20 116.43 0.35 90 40 63 23 116.41 0.30 91 40 74 34 116.08 0.23 92 41 44 3 243.27 1.57 93 41 45 4 234.03 0.12 94 42 45 3 234.66 0.20 95 42 46 4 235.90 0.42 96 43 46 3 242.59 3.46 97 43 47 4 237.85 1.40 98 44 47 3 246.15 0.93 99 44 48 4 234.01 0.52 100 44 59 15 117.88 0.29 101 44 63 19 116.59 0.29 102 45 48 3 237.85 1.40 103 45 49 4 242.41 0.42 104 46 49 3 263.75 0.47 105 47 51 4 226.71 2.70 106 48 51 3 237.16 1.11 107 48 53 5 158.55 2.38 108 48 55 7 139.75 2.28 109 48 56 8 134.53 0.32 110 48 59 11 130.57 1.53 111 51 63 12 131.55 1.25 112 53 59 6 146.65 0.21 113 54 58 4 229.58 1.30 114 55 58 3 236.86 1.22 115 55 59 4 238.50 0.41 116 56 59 3 241.54 0.58 117 56 60 4 242.18 0.90 118 57 60 3 242.19 0.90 119 57 61 4 243.36 0.30 120 58 61 3 243.37 0.31 121 58 62 4 243.37 0.31 122 59 62 3 245.02 0.51 123 59 63 4 235.36 0.21 124 60 63 3 238.75 1.91 125 60 64 4 235.35 0.21 126 61 64 3 242.91 0.54 127 61 65 4 238.59 1.41 128 62 66 4 236.56 2.43 129 63 66 3 244.93 2.33 130 63 67 4 242.54 0.83 131 64 67 3 243.03 1.07 132 64 68 4 243.03 1.07 133 64 74 10 121.67 0.69 134 65 68 3 245.25 2.19 135 65 69 4 243.03 1.08 136 66 69 3 243.03 1.08 137 67 70 3 250.81 0.59 138 67 71 4 237.66 1.28 139 67 72 5 141.15 0.62 140 67 74 7 141.49 0.51