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 4 8 4 263.47 1.04 2 5 8 3 271.25 1.78 3 5 9 4 260.34 0.58 4 6 9 3 268.67 1.42 5 6 10 4 268.65 1.43 6 6 53 47 75.26 0.33 7 6 77 71 39.47 0.07 8 6 78 72 39.23 0.18 9 6 81 75 26.68 1.69 10 7 10 3 273.09 0.78 11 7 11 4 268.74 1.43 12 7 74 67 40.31 0.37 13 8 11 3 272.93 0.34 14 8 12 4 268.74 1.43 15 9 12 3 270.91 0.34 16 9 13 4 268.74 1.43 17 9 53 44 84.64 2.98 18 10 13 3 272.93 0.34 19 10 14 4 269.50 1.04 20 10 49 39 84.64 2.96 21 10 53 43 84.84 2.88 22 10 73 63 48.31 0.33 23 10 74 64 48.31 0.33 24 10 77 67 48.30 0.33 25 11 14 3 272.55 0.62 26 11 15 4 269.72 0.80 27 11 23 12 143.36 0.25 28 11 24 13 135.50 3.65 29 11 27 16 132.07 2.00 30 11 74 63 49.17 0.04 31 12 15 3 280.93 2.88 32 12 16 4 271.27 2.06 33 13 16 3 277.56 4.57 34 13 17 4 271.27 2.06 35 13 45 32 84.48 2.88 36 13 48 35 84.92 2.85 37 13 53 40 85.05 2.96 38 14 17 3 271.27 2.06 39 14 18 4 271.27 2.06 40 14 23 9 143.41 0.25 41 14 70 56 53.58 1.34 42 15 18 3 272.19 1.59 43 15 19 4 264.95 1.57 44 15 20 5 222.21 0.65 45 15 23 8 161.30 3.66 46 15 24 9 143.41 0.23 47 16 19 3 264.59 1.73 48 17 37 20 84.36 2.85 49 17 41 24 84.68 2.77 50 17 42 25 84.86 2.86 51 17 45 28 84.93 2.85 52 18 23 5 213.59 1.70 53 18 31 13 124.56 1.64 54 18 36 18 84.23 2.81 55 20 23 3 311.31 0.93 56 21 24 3 268.31 0.63 57 22 25 3 281.44 0.38 58 22 26 4 260.31 4.50 59 22 29 7 161.75 1.57 60 22 36 14 127.84 1.71 61 23 26 3 269.68 1.26 62 23 29 6 168.75 1.93 63 23 31 8 155.60 1.50 64 23 70 47 87.16 1.84 65 26 29 3 277.28 3.59 66 26 70 44 90.45 0.62 67 27 70 43 90.45 0.63 68 27 71 44 90.25 0.58 69 27 74 47 90.44 0.64 70 28 69 41 90.84 0.54 71 28 70 42 90.88 0.56 72 29 34 5 221.88 3.48 73 29 36 7 169.30 0.89 74 29 69 40 100.95 0.89 75 29 70 41 100.34 0.91 76 30 33 3 264.19 0.94 77 30 34 4 226.16 1.33 78 30 68 38 101.03 0.90 79 30 69 39 101.04 0.88 80 31 36 5 199.63 14.59 81 31 37 6 162.22 1.37 82 31 67 36 101.36 0.77 83 31 68 37 101.28 0.81 84 31 69 38 101.28 0.81 85 31 70 39 101.28 0.81 86 31 73 42 101.28 0.81 87 32 35 3 254.50 2.52 88 32 64 32 101.41 0.77 89 32 67 35 101.41 0.78 90 32 68 36 101.33 0.81 91 37 41 4 252.24 0.68 92 37 42 5 258.48 1.26 93 39 42 3 275.38 2.21 94 39 43 4 272.18 3.81 95 40 43 3 273.25 1.10 96 40 44 4 268.23 1.39 97 41 44 3 275.42 2.19 98 41 45 4 266.87 1.17 99 42 45 3 270.01 2.73 100 42 46 4 266.87 1.16 101 42 62 20 107.31 0.28 102 43 46 3 269.31 0.07 103 43 47 4 262.80 0.34 104 44 47 3 267.47 1.67 105 44 48 4 268.03 2.93 106 45 48 3 276.27 3.67 107 45 49 4 262.97 0.76 108 45 73 28 104.36 1.19 109 46 49 3 263.34 0.58 110 46 50 4 263.33 0.58 111 46 55 9 180.09 2.43 112 46 57 11 159.38 1.95 113 46 58 12 159.12 2.08 114 46 59 13 145.28 1.96 115 47 50 3 274.94 4.33 116 47 51 4 263.37 0.56 117 48 51 3 269.56 2.54 118 48 52 4 263.36 0.56 119 48 53 5 259.68 2.38 120 49 53 4 257.42 3.08 121 49 54 5 244.19 3.52 122 49 55 6 185.35 2.10 123 49 67 18 108.27 0.15 124 49 73 24 107.20 0.24 125 49 77 28 104.36 1.19 126 50 54 4 205.31 2.96 127 50 55 5 200.38 5.41 128 51 54 3 262.54 0.99 129 53 77 24 104.38 1.19 130 53 81 28 102.70 1.62 131 55 76 21 104.48 1.12 132 55 77 22 104.41 1.16 133 55 80 25 102.73 1.61 134 57 67 10 125.45 3.71 135 58 62 4 181.84 2.69 136 59 62 3 263.48 1.14 137 62 67 5 251.38 2.50 138 63 66 3 277.03 6.08 139 63 67 4 251.39 2.50 140 64 67 3 258.51 0.85 141 64 68 4 251.37 2.50 142 65 68 3 258.52 0.85 143 65 72 7 207.65 0.40 144 66 72 6 186.83 0.61 145 66 73 7 186.81 0.62 146 66 76 10 186.68 0.55 147 67 73 6 186.81 0.60 148 67 76 9 186.66 0.53 149 69 72 3 269.49 3.52 150 69 73 4 263.31 0.23 151 70 73 3 271.64 2.44 152 70 74 4 263.38 0.20 153 71 74 3 272.96 1.79 154 71 75 4 263.49 0.23 155 72 75 3 272.36 2.80 156 72 76 4 263.50 0.23 157 73 76 3 261.12 1.12 158 73 77 4 270.69 3.64 159 74 77 3 273.30 2.36 160 74 78 4 270.90 3.56 161 75 78 3 273.30 2.36 162 75 79 4 270.74 3.64 163 76 79 3 273.30 2.36 164 76 80 4 273.30 2.36 165 77 80 3 273.23 2.40 166 77 81 4 270.74 3.64