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 5 33 28 101.46 9.80 2 5 34 29 100.02 10.52 3 5 35 30 100.01 10.52 4 5 36 31 100.00 10.52 5 5 98 93 100.01 10.52 6 5 99 94 100.00 10.53 7 5 100 95 85.70 3.52 8 6 32 26 101.45 9.80 9 6 33 27 101.48 9.79 10 6 98 92 100.00 10.52 11 7 30 23 101.67 9.72 12 7 31 24 101.58 9.76 13 7 32 25 101.48 9.79 14 7 95 88 101.56 9.77 15 7 96 89 101.53 9.76 16 7 97 90 100.39 10.33 17 7 98 91 100.94 10.06 18 8 30 22 101.68 9.72 19 8 31 23 101.66 9.72 20 8 33 25 101.66 9.72 21 8 34 26 101.66 9.72 22 9 28 19 102.00 9.62 23 9 29 20 101.89 9.64 24 9 30 21 101.72 9.72 25 10 28 18 102.09 9.59 26 10 29 19 102.00 9.62 27 10 31 21 101.94 9.64 28 11 26 15 102.23 9.52 29 11 27 16 102.22 9.53 30 11 28 17 102.10 9.59 31 12 17 5 120.01 0.86 32 12 26 14 102.27 9.53 33 12 27 15 102.26 9.52 34 12 29 17 102.18 9.54 35 13 16 3 130.68 0.44 36 13 26 13 102.30 9.51 37 14 17 3 124.30 1.27 38 14 21 7 106.66 7.45 39 14 22 8 106.62 7.46 40 14 23 9 106.32 7.56 41 14 25 11 104.34 8.54 42 14 27 13 102.30 9.52 43 15 18 3 134.41 0.46 44 15 21 6 108.66 6.46 45 15 22 7 106.62 7.46 46 17 27 10 102.85 9.29 47 17 29 12 102.41 9.44 48 17 93 76 102.31 9.54 49 19 90 71 104.14 8.65 50 19 93 74 103.37 9.00 51 21 80 59 134.34 0.99 52 21 90 69 124.36 2.14 53 22 82 60 122.77 0.21 54 22 83 61 162.80 1.93 55 23 80 57 118.00 1.82 56 23 81 58 118.03 1.83 57 23 82 59 118.03 1.83 58 23 83 60 123.00 0.32 59 25 80 55 109.45 6.05 60 25 81 56 112.73 4.44 61 27 78 51 102.62 9.43 62 27 79 52 103.08 9.21 63 27 80 53 103.22 9.15 64 28 78 50 102.50 9.50 65 30 76 46 102.29 9.52 66 32 70 38 101.57 9.77 67 32 71 39 101.61 9.75 68 32 72 40 101.70 9.72 69 33 70 37 101.58 9.76 70 34 70 36 101.58 9.76 71 36 39 3 237.47 0.35 72 36 67 31 101.66 9.72 73 36 68 32 101.58 9.76 74 36 69 33 101.50 9.79 75 36 70 34 101.04 10.01 76 37 67 30 101.64 9.74 77 39 68 29 101.58 9.77 78 39 100 61 186.91 18.64 79 40 44 4 236.56 1.23 80 40 45 5 236.53 1.23 81 40 48 8 193.10 2.55 82 40 66 26 101.68 9.72 83 40 67 27 101.56 9.75 84 40 68 28 101.57 9.77 85 44 66 22 101.61 9.74 86 44 67 23 101.58 9.76 87 44 68 24 101.61 9.74 88 47 56 9 117.53 1.97 89 47 64 17 102.19 9.54 90 47 65 18 102.17 9.54 91 47 66 19 101.58 9.76 92 48 66 18 101.61 9.77 93 50 55 5 212.37 3.98 94 50 56 6 175.97 19.71 95 51 56 5 197.00 10.05 96 51 63 12 102.31 9.52 97 51 64 13 102.25 9.52 98 51 66 15 102.06 9.60 99 59 64 5 152.41 18.77 100 65 69 4 234.97 0.75 101 68 100 32 100.02 10.52 102 69 99 30 101.53 9.78 103 69 100 31 99.98 10.51 104 70 98 28 101.47 9.80 105 70 99 29 100.02 10.52 106 71 98 27 101.50 9.79 107 71 99 28 101.46 9.80 108 72 75 3 222.69 2.02 109 72 95 23 101.67 9.72 110 72 97 25 101.58 9.76 111 72 98 26 101.55 9.78 112 73 97 24 101.67 9.72 113 73 98 25 101.62 9.75 114 73 99 26 101.61 9.75 115 74 95 21 102.00 9.61 116 74 96 22 101.81 9.68 117 74 97 23 101.71 9.72 118 75 92 17 101.75 9.77 119 75 94 19 102.11 9.56 120 75 95 20 102.06 9.59 121 75 96 21 101.98 9.61 122 76 92 16 101.80 9.76 123 76 93 17 102.14 9.59 124 76 94 18 102.12 9.56 125 76 96 20 102.12 9.57 126 77 89 12 102.12 9.63 127 77 90 13 102.00 9.70 128 77 91 14 101.91 9.73 129 77 92 15 102.00 9.68 130 78 89 11 102.14 9.63 131 78 90 12 102.02 9.69 132 78 93 15 102.30 9.54 133 78 94 16 102.31 9.52 134 79 87 8 113.61 3.90 135 79 88 9 108.96 6.23 136 79 89 10 102.14 9.63 137 80 87 7 113.62 3.90 138 80 88 8 112.58 4.42 139 80 90 10 112.31 4.59 140 81 86 5 113.64 3.89 141 81 87 6 113.63 3.90 142 81 88 7 113.64 3.91 143 82 85 3 132.21 1.40 144 82 86 4 118.59 1.42 145 82 88 6 113.66 3.91 146 90 93 3 168.78 0.00