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 5 3 287.32 0.27 2 2 6 4 262.01 2.29 3 2 9 7 265.49 0.48 4 3 6 3 284.68 1.59 5 3 70 67 42.26 1.25 6 4 7 3 275.33 0.84 7 4 8 4 271.86 3.60 8 4 47 43 85.36 0.64 9 4 69 65 42.55 1.11 10 4 70 66 43.45 0.66 11 4 73 69 42.19 1.28 12 5 8 3 269.16 2.08 13 5 9 4 265.86 0.42 14 5 20 15 133.10 5.50 15 5 24 19 95.90 1.20 16 6 9 3 273.51 0.09 17 6 10 4 272.08 3.50 18 7 10 3 274.43 2.33 19 7 11 4 268.39 1.64 20 7 47 40 85.36 0.64 21 7 51 44 84.92 0.63 22 8 11 3 276.38 1.35 23 8 12 4 268.39 1.64 24 8 23 15 115.51 10.39 25 8 29 21 95.67 1.32 26 8 47 39 87.00 1.31 27 8 63 55 64.51 0.51 28 8 69 61 48.04 0.14 29 9 12 3 274.76 1.16 30 9 13 4 261.25 2.14 31 9 20 11 133.10 5.50 32 10 13 3 267.96 2.26 33 10 14 4 261.26 2.14 34 11 14 3 272.79 0.17 35 11 15 4 260.62 1.81 36 11 43 32 88.02 0.92 37 11 44 33 88.02 0.92 38 11 46 35 88.02 0.92 39 11 47 36 87.92 0.91 40 12 15 3 269.81 1.31 41 12 16 4 254.72 4.76 42 12 17 5 232.16 1.65 43 12 18 6 220.65 2.33 44 12 20 8 174.44 2.66 45 12 23 11 142.43 0.83 46 12 43 31 88.03 0.92 47 13 17 4 207.89 8.71 48 15 42 27 90.17 0.85 49 15 43 28 90.11 0.83 50 16 39 23 90.70 0.66 51 16 43 27 90.28 0.77 52 19 22 3 285.12 0.90 53 20 23 3 265.54 0.71 54 20 24 4 257.69 2.73 55 22 25 3 285.31 0.23 56 22 33 11 123.52 2.30 57 23 29 6 152.19 1.32 58 23 33 10 129.57 0.77 59 23 40 17 99.02 3.50 60 24 66 42 62.14 2.04 61 25 32 7 162.30 0.29 62 26 66 40 63.05 2.44 63 27 32 5 222.28 8.03 64 27 64 37 66.35 1.34 65 27 65 38 66.22 1.39 66 28 31 3 268.96 0.69 67 28 32 4 222.26 8.04 68 28 33 5 222.27 8.04 69 28 64 36 66.34 1.34 70 29 33 4 257.57 2.91 71 29 40 11 149.17 1.30 72 29 63 34 66.61 1.22 73 29 64 35 66.33 1.34 74 30 36 6 164.60 2.65 75 30 37 7 158.25 0.90 76 30 40 10 153.03 0.34 77 33 40 7 257.11 0.85 78 35 40 5 261.56 0.06 79 36 39 3 267.77 0.39 80 36 40 4 261.75 0.07 81 37 40 3 275.37 0.84 82 37 41 4 268.52 2.57 83 38 41 3 271.19 1.24 84 38 42 4 268.79 2.44 85 39 42 3 272.32 0.67 86 39 43 4 268.80 2.43 87 40 43 3 277.28 1.11 88 40 44 4 268.75 2.42 89 41 44 3 272.30 0.68 90 41 45 4 269.64 1.98 91 42 45 3 274.87 0.56 92 42 46 4 272.35 0.70 93 43 46 3 272.35 0.70 94 43 47 4 269.75 2.00 95 44 47 3 271.56 1.09 96 44 48 4 269.75 2.00 97 44 59 15 112.69 1.72 98 44 60 16 112.75 1.69 99 44 63 19 112.58 1.69 100 45 48 3 276.04 0.27 101 45 49 4 265.57 0.09 102 46 49 3 265.62 0.10 103 46 50 4 265.59 0.10 104 47 50 3 274.26 0.74 105 47 51 4 265.56 0.12 106 47 63 16 116.34 3.35 107 47 72 25 86.60 14.72 108 48 51 3 264.07 0.87 109 48 52 4 260.56 0.88 110 48 53 5 232.72 3.37 111 48 55 7 151.03 4.23 112 48 59 11 119.09 4.69 113 48 63 15 119.05 4.71 114 48 72 24 86.58 14.71 115 49 52 3 272.23 3.40 116 51 73 22 81.95 17.02 117 51 77 26 78.27 18.43 118 53 76 23 81.39 17.29 119 55 58 3 283.51 0.49 120 55 59 4 259.41 2.27 121 55 62 7 249.05 0.36 122 55 72 17 119.94 1.91 123 55 76 21 82.32 16.83 124 56 59 3 283.51 0.49 125 57 61 4 269.20 0.39 126 58 61 3 265.16 1.51 127 58 62 4 265.26 1.68 128 59 62 3 269.56 0.19 129 59 63 4 261.70 3.23 130 60 63 3 277.31 0.69 131 60 64 4 270.89 1.14 132 61 64 3 280.87 0.64 133 62 65 3 278.22 0.38 134 62 68 6 172.02 4.75 135 62 69 7 172.02 4.75 136 62 72 10 172.00 4.75 137 63 69 6 172.00 4.75 138 63 72 9 172.00 4.75 139 65 68 3 276.56 0.58 140 65 69 4 260.56 3.52 141 66 69 3 275.99 0.76 142 66 70 4 261.39 3.93 143 67 70 3 278.55 0.52 144 67 71 4 266.79 1.51 145 68 71 3 273.65 1.92 146 68 72 4 266.51 1.37 147 69 72 3 273.65 1.92 148 69 73 4 267.44 0.91 149 70 73 3 276.95 0.27 150 70 74 4 263.01 1.30 151 71 74 3 276.97 0.28 152 71 75 4 263.01 1.30 153 72 75 3 276.43 0.00 154 72 76 4 268.68 0.19 155 73 76 3 272.75 1.84 156 73 77 4 259.63 0.32 157 74 77 3 274.41 0.16