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 3 249.41 2.31 2 2 6 4 247.51 3.25 3 3 6 3 255.78 0.65 4 3 8 5 225.11 3.71 5 4 7 3 260.62 3.06 6 4 8 4 218.14 0.22 7 4 10 6 211.95 3.31 8 7 11 4 179.55 3.52 9 7 12 5 207.17 2.73 10 8 50 42 73.88 5.76 11 9 12 3 252.47 1.45 12 9 13 4 247.73 1.71 13 9 50 41 81.33 2.04 14 9 53 44 73.99 5.70 15 10 13 3 256.50 2.30 16 10 14 4 247.74 1.71 17 11 14 3 252.12 0.48 18 11 15 4 247.93 1.61 19 12 15 3 252.15 0.49 20 12 16 4 247.93 1.61 21 12 43 31 101.85 1.02 22 12 46 34 95.96 2.05 23 12 50 38 86.55 0.75 24 12 54 42 81.45 2.07 25 13 16 3 252.15 0.48 26 13 17 4 247.94 1.62 27 13 53 40 81.54 2.04 28 13 54 41 81.43 2.08 29 13 58 45 81.32 2.08 30 13 59 46 81.32 2.08 31 13 62 49 72.54 4.12 32 14 17 3 252.15 0.48 33 14 18 4 246.34 2.42 34 15 18 3 249.68 0.76 35 15 19 4 243.39 0.07 36 15 41 26 102.20 0.89 37 15 43 28 102.23 0.87 38 16 19 3 249.68 0.76 39 16 20 4 243.43 0.10 40 16 37 21 102.18 0.89 41 16 41 25 102.20 0.89 42 16 43 27 102.22 0.86 43 16 54 38 86.58 0.76 44 16 59 43 81.38 2.05 45 17 20 3 254.77 1.90 46 17 21 4 246.65 1.52 47 17 62 45 74.70 5.19 48 17 64 47 66.74 1.33 49 18 21 3 255.07 1.75 50 18 22 4 248.20 2.29 51 19 22 3 252.88 0.04 52 19 23 4 247.21 0.35 53 19 32 13 129.94 4.00 54 19 37 18 102.44 0.82 55 19 40 21 102.41 0.83 56 19 41 22 102.36 0.84 57 20 23 3 252.38 0.21 58 20 24 4 243.72 0.48 59 20 37 17 102.43 0.82 60 20 72 52 68.44 0.09 61 20 73 53 64.28 0.04 62 20 74 54 63.23 0.40 63 21 24 3 252.38 0.21 64 21 25 4 244.07 0.57 65 21 74 53 63.22 0.44 66 22 25 3 250.84 0.93 67 22 26 4 250.50 1.09 68 23 26 3 251.33 1.36 69 23 27 4 245.61 1.36 70 23 28 5 227.50 2.08 71 23 30 7 223.80 3.00 72 23 32 9 168.56 0.90 73 23 40 17 102.64 0.83 74 24 27 3 252.43 1.85 75 24 28 4 236.29 3.25 76 24 29 5 204.07 0.58 77 24 74 50 63.44 0.45 78 24 76 52 63.21 0.42 79 31 68 37 69.42 0.04 80 31 71 40 69.10 0.26 81 31 72 41 69.00 0.29 82 31 73 42 68.91 0.29 83 32 36 4 243.09 0.62 84 32 37 5 237.96 1.93 85 32 71 39 69.08 0.27 86 32 72 40 69.00 0.29 87 33 36 3 251.84 1.73 88 33 37 4 246.09 0.84 89 33 71 38 69.01 0.30 90 34 37 3 257.08 0.89 91 34 38 4 246.20 0.79 92 34 51 17 102.94 0.84 93 34 54 20 102.86 0.88 94 34 55 21 102.70 0.95 95 34 59 25 101.50 0.49 96 34 72 38 68.96 0.33 97 35 38 3 250.75 1.48 98 35 39 4 246.75 0.51 99 35 51 16 110.25 1.10 100 36 39 3 263.56 3.91 101 37 40 3 260.42 1.52 102 37 41 4 246.12 0.84 103 37 59 22 101.37 0.54 104 37 72 35 68.97 0.30 105 38 41 3 253.05 0.32 106 38 42 4 240.81 3.50 107 38 43 5 183.48 1.11 108 38 44 6 148.91 1.68 109 38 46 8 144.40 0.53 110 38 51 13 141.23 2.06 111 38 54 16 110.00 1.19 112 39 42 3 249.14 0.68 113 39 44 5 205.99 12.37 114 43 46 3 229.19 2.04 115 46 50 4 241.67 1.97 116 46 51 5 241.67 1.97 117 46 54 8 222.62 7.00 118 47 50 3 251.93 1.45 119 47 51 4 241.72 1.98 120 48 51 3 249.77 0.36 121 48 52 4 248.26 1.10 122 49 52 3 253.52 1.52 123 49 53 4 253.50 1.52 124 50 53 3 254.50 1.73 125 50 54 4 253.51 1.52 126 51 54 3 253.50 1.52 127 51 55 4 248.21 4.16 128 52 55 3 253.41 1.56 129 52 56 4 253.41 1.56 130 53 56 3 254.46 1.03 131 53 57 4 238.36 0.24 132 53 58 5 225.22 5.82 133 54 58 4 215.78 3.70 134 54 59 5 205.37 2.00 135 55 60 5 205.70 1.89 136 55 72 17 91.06 11.51 137 56 60 4 225.52 8.03 138 57 60 3 247.83 0.62 139 57 61 4 229.63 4.22 140 58 61 3 253.66 2.93 141 58 62 4 222.52 6.54 142 59 65 6 125.66 5.44 143 59 67 8 122.27 4.08 144 59 72 13 90.89 11.60 145 60 67 7 122.25 4.08 146 62 65 3 244.77 2.02 147 63 75 12 89.61 13.13 148 64 74 10 115.16 1.08 149 64 75 11 89.58 13.16 150 64 77 13 88.70 12.76 151 65 72 7 133.49 1.27 152 65 73 8 132.81 1.29 153 65 74 9 121.23 1.63 154 65 75 10 90.31 13.50 155 66 72 6 134.02 1.53 156 66 73 7 132.82 1.29 157 66 75 9 121.87 1.33 158 67 70 3 262.16 2.23 159 67 71 4 210.66 0.06 160 67 72 5 134.28 1.41 161 68 71 3 252.10 1.57 162 68 73 5 163.87 8.71 163 78 81 3 336.16 4.92