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 38 36 180.11 1.13 2 3 37 34 180.02 1.11 3 3 38 35 180.12 1.13 4 3 39 36 180.11 1.13 5 3 40 37 180.00 1.11 6 3 44 41 179.96 1.16 7 4 37 33 180.26 1.07 8 5 37 32 180.28 1.07 9 5 40 35 180.28 1.07 10 6 10 4 252.31 3.35 11 6 11 5 239.63 1.95 12 6 37 31 180.63 1.14 13 6 93 87 28.62 0.60 14 6 94 88 20.81 0.56 15 7 10 3 258.23 0.39 16 7 11 4 252.31 3.35 17 7 94 87 21.21 0.76 18 7 95 88 20.70 0.61 19 8 11 3 259.87 0.42 20 8 12 4 253.00 3.00 21 8 50 42 180.05 1.11 22 8 51 43 180.00 1.13 23 8 54 46 172.54 0.24 24 9 12 3 266.43 1.69 25 9 13 4 252.99 3.00 26 9 54 45 172.58 0.22 27 9 58 49 163.13 1.16 28 10 13 3 250.80 1.79 29 10 14 4 246.91 0.70 30 10 91 81 29.51 0.24 31 10 92 82 30.14 0.56 32 10 93 83 29.50 0.24 33 10 94 84 27.64 0.14 34 11 14 3 257.32 0.93 35 11 15 4 246.80 0.76 36 11 29 18 180.30 1.07 37 11 33 22 180.62 1.01 38 11 37 26 181.84 1.05 39 11 51 40 180.06 1.11 40 12 15 3 253.72 0.23 41 12 16 4 247.50 0.40 42 12 29 17 180.40 1.02 43 12 51 39 180.19 1.05 44 12 54 42 176.50 0.10 45 12 55 43 172.53 0.24 46 12 58 46 166.38 0.25 47 12 61 49 132.12 3.23 48 13 16 3 250.75 0.64 49 13 17 4 245.37 0.67 50 13 61 48 134.02 4.19 51 13 87 74 42.73 1.24 52 13 88 75 41.16 0.45 53 13 91 78 32.66 0.89 54 14 17 3 250.94 1.72 55 14 18 4 247.24 0.27 56 14 32 18 181.65 1.03 57 14 36 22 182.28 1.28 58 14 91 77 32.67 0.90 59 14 92 78 31.82 1.18 60 15 18 3 250.72 0.62 61 15 19 4 245.37 0.67 62 15 29 14 180.89 1.07 63 15 32 17 181.26 1.22 64 16 19 3 245.72 0.49 65 16 22 6 182.37 0.84 66 16 23 7 182.35 0.84 67 16 24 8 182.12 0.78 68 16 77 61 101.79 0.71 69 16 78 62 101.65 0.69 70 16 79 63 101.07 0.71 71 16 84 68 57.08 0.36 72 17 84 67 57.08 0.38 73 17 88 71 52.54 1.37 74 17 92 75 41.70 0.23 75 18 32 14 182.23 1.31 76 18 92 74 41.69 0.23 77 19 22 3 260.17 1.97 78 19 24 5 207.63 1.57 79 21 24 3 329.66 3.02 80 22 78 56 101.79 0.71 81 22 79 57 101.67 0.74 82 22 84 62 64.09 1.04 83 23 76 53 101.87 0.70 84 23 78 55 101.73 0.71 85 24 28 4 240.62 5.65 86 24 76 52 101.84 0.71 87 24 77 53 101.80 0.71 88 24 78 54 101.73 0.71 89 25 28 3 255.02 1.55 90 25 76 51 101.81 0.72 91 25 77 52 101.81 0.72 92 26 29 3 264.92 0.18 93 26 30 4 257.59 0.78 94 26 51 25 228.87 2.71 95 26 52 26 193.56 0.95 96 26 77 51 101.77 0.72 97 27 30 3 257.58 0.78 98 27 31 4 371.14 3.69 99 29 51 22 365.05 1.30 100 29 55 26 223.72 5.29 101 51 54 3 250.25 1.05 102 51 55 4 246.50 0.83 103 52 55 3 249.75 1.69 104 53 56 3 256.57 0.32 105 53 57 4 251.63 0.79 106 54 57 3 251.64 0.80 107 54 58 4 249.05 0.49 108 55 58 3 261.13 0.54 109 55 61 6 220.97 4.17 110 55 77 22 101.76 0.72 111 56 59 3 258.19 0.75 112 56 77 21 101.81 0.72 113 58 61 3 280.76 0.15 114 59 63 4 257.16 1.28 115 60 80 20 101.67 0.77 116 60 83 23 57.05 0.44 117 60 86 26 57.16 0.38 118 60 87 27 57.13 0.39 119 61 78 17 101.81 0.74 120 61 79 18 101.70 0.78 121 61 87 26 57.13 0.39 122 62 76 14 102.14 0.66 123 62 78 16 101.81 0.74 124 62 79 17 101.81 0.74 125 62 80 18 101.77 0.74 126 63 76 13 102.14 0.66 127 63 77 14 102.06 0.64 128 64 75 11 102.27 0.63 129 64 76 12 102.20 0.66 130 64 78 14 102.12 0.67 131 65 74 9 102.31 0.64 132 65 75 10 102.27 0.63 133 66 74 8 102.31 0.64 134 69 72 3 215.48 9.20 135 79 84 5 153.05 15.19 136 79 87 8 149.09 17.18 137 80 83 3 234.42 3.68 138 80 84 4 208.63 8.35 139 83 86 3 252.88 0.35 140 83 87 4 251.39 1.09 141 84 87 3 254.91 0.68 142 84 88 4 248.14 0.54 143 85 88 3 253.08 0.43 144 85 89 4 248.15 0.54 145 86 89 3 255.19 2.21 146 86 90 4 251.52 0.35 147 87 90 3 250.28 0.28 148 87 91 4 245.38 2.62 149 88 91 3 245.38 2.62 150 88 92 4 241.44 0.85 151 89 93 4 241.38 0.83 152 90 93 3 254.34 0.01