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 9 47 38 25.62 1.60 2 9 48 39 22.02 1.18 3 11 16 5 151.78 5.25 4 11 17 6 114.01 2.44 5 11 20 9 122.40 4.62 6 11 47 36 40.76 0.29 7 11 48 37 37.77 0.52 8 11 50 39 37.94 0.44 9 11 51 40 37.63 0.59 10 13 16 3 198.68 1.07 11 13 17 4 196.50 0.28 12 14 17 3 203.93 1.94 13 14 18 4 197.99 1.02 14 14 57 43 48.16 0.70 15 15 18 3 199.71 0.17 16 15 19 4 197.38 0.94 17 16 19 3 199.71 0.17 18 16 20 4 198.47 0.45 19 17 20 3 199.61 1.02 20 17 21 4 198.47 0.45 21 17 51 34 67.68 0.09 22 17 52 35 66.18 0.66 23 18 21 3 200.99 0.82 24 18 22 4 196.94 0.30 25 18 52 34 74.34 0.19 26 18 61 43 59.29 2.75 27 19 22 3 201.19 0.71 28 19 23 4 196.94 0.30 29 20 23 3 203.72 1.85 30 20 24 4 196.30 0.03 31 20 48 28 77.95 0.90 32 20 51 31 76.34 0.19 33 21 24 3 203.72 1.85 34 21 25 4 199.65 0.18 35 21 36 15 80.63 2.21 36 21 43 22 78.20 0.99 37 21 49 28 77.98 0.89 38 21 51 30 77.76 0.89 39 21 52 31 77.34 0.69 40 21 58 37 75.14 0.06 41 21 61 40 74.92 0.01 42 21 62 41 74.89 0.03 43 22 25 3 202.75 1.50 44 22 26 4 199.64 0.17 45 22 61 39 74.91 0.01 46 22 64 42 74.89 0.03 47 22 65 43 74.63 0.07 48 22 68 46 62.97 0.28 49 23 26 3 198.69 0.65 50 23 27 4 198.58 0.70 51 23 48 25 79.08 0.46 52 24 27 3 205.27 1.28 53 24 28 4 196.68 0.14 54 24 43 19 79.27 0.47 55 24 46 22 79.25 0.46 56 24 48 24 79.06 0.47 57 24 49 25 78.96 0.42 58 25 28 3 196.57 0.18 59 25 29 4 194.70 0.72 60 25 30 5 167.19 2.93 61 25 39 14 79.11 0.64 62 25 43 18 79.27 0.47 63 25 62 37 75.53 0.23 64 25 65 40 74.89 0.02 65 26 29 3 200.25 0.74 66 26 65 39 74.91 0.03 67 26 68 42 69.56 0.14 68 27 48 21 79.25 0.46 69 28 42 14 79.71 0.43 70 28 43 15 79.47 0.56 71 28 46 18 79.31 0.47 72 29 65 36 76.95 0.58 73 30 34 4 175.52 0.12 74 30 39 9 80.75 0.88 75 30 42 12 82.07 0.68 76 30 43 13 82.07 0.68 77 30 62 32 77.00 0.61 78 30 65 35 76.95 0.58 79 31 34 3 200.83 0.52 80 31 66 35 76.90 0.62 81 32 66 34 76.90 0.62 82 32 69 37 72.67 0.47 83 32 70 38 64.36 0.39 84 33 66 33 77.04 0.60 85 34 38 4 181.71 3.93 86 34 39 5 178.43 2.30 87 34 62 28 78.84 0.25 88 34 66 32 77.06 0.59 89 35 38 3 209.22 0.27 90 35 39 4 189.66 1.54 91 35 62 27 78.97 0.22 92 36 39 3 201.09 0.71 93 36 40 4 192.40 0.17 94 36 43 7 189.74 1.50 95 36 49 13 111.94 1.81 96 36 55 19 82.17 1.23 97 36 58 22 79.10 0.27 98 36 59 23 79.00 0.23 99 36 62 26 78.95 0.21 100 37 40 3 203.46 0.40 101 37 41 4 192.45 0.17 102 38 41 3 206.64 1.20 103 38 42 4 196.99 2.44 104 39 42 3 205.23 1.68 105 39 43 4 190.94 0.93 106 39 62 23 76.91 0.64 107 40 43 3 207.63 0.47 108 40 44 4 190.90 0.92 109 40 49 9 107.76 0.52 110 40 55 15 85.41 2.86 111 41 44 3 196.47 0.34 112 41 45 4 190.79 0.96 113 43 46 3 202.27 2.20 114 43 49 6 111.50 1.35 115 44 49 5 111.50 1.34 116 46 49 3 209.82 0.01 117 47 50 3 211.61 1.57 118 48 51 3 209.31 2.72 119 49 52 3 215.47 0.67 120 49 55 6 143.08 5.43 121 49 58 9 109.99 2.66 122 52 57 5 187.37 1.02 123 52 58 6 148.56 3.06 124 52 61 9 139.45 7.62 125 53 57 4 205.18 0.83 126 54 57 3 207.47 1.11 127 54 58 4 202.13 0.69 128 55 58 3 202.13 0.69 129 55 59 4 202.13 0.69 130 56 59 3 204.78 0.64 131 56 60 4 202.12 0.68 132 57 60 3 204.63 0.70 133 57 61 4 201.34 0.94 134 58 61 3 204.63 0.71 135 58 62 4 201.21 1.00 136 59 62 3 202.22 0.41 137 59 63 4 198.46 0.10 138 60 63 3 197.60 0.34 139 60 64 4 195.27 1.50 140 61 64 3 199.59 0.41 141 61 65 4 197.05 0.10 142 62 65 3 195.82 0.57 143 62 66 4 195.85 0.56 144 63 66 3 199.63 1.30 145 63 67 4 195.94 0.53 146 64 67 3 196.27 0.37 147 64 68 4 195.93 0.53 148 65 68 3 204.63 1.21 149 65 69 4 200.95 3.04 150 66 69 3 204.63 1.21 151 66 70 4 193.37 0.73 152 67 70 3 205.06 3.41