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 14 10 188.43 3.73 2 4 40 36 59.63 1.21 3 5 9 4 293.50 1.17 4 5 43 38 59.62 1.20 5 5 44 39 59.61 1.21 6 6 9 3 293.50 1.17 7 6 10 4 293.50 1.17 8 6 44 38 59.62 1.20 9 7 10 3 293.39 1.11 10 7 44 37 60.40 0.81 11 7 72 65 59.65 1.20 12 7 76 69 59.58 1.22 13 7 82 75 36.08 0.21 14 7 83 76 35.85 0.19 15 7 84 77 35.38 0.24 16 8 82 74 36.09 0.21 17 8 83 75 35.80 0.15 18 8 84 76 35.46 0.21 19 8 85 77 34.38 0.23 20 9 85 76 34.86 0.04 21 10 14 4 279.29 1.16 22 10 15 5 276.38 0.29 23 10 18 8 265.14 4.80 24 10 40 30 89.30 2.08 25 10 44 34 80.11 0.62 26 10 84 74 35.80 0.13 27 10 85 75 34.93 0.06 28 11 14 3 285.62 2.00 29 11 15 4 285.60 1.99 30 11 84 73 35.83 0.14 31 11 85 74 35.46 0.21 32 11 86 75 34.94 0.06 33 11 87 76 33.24 0.83 34 12 15 3 288.28 3.33 35 12 16 4 285.60 2.00 36 12 69 57 80.14 0.61 37 12 70 58 80.16 0.61 38 12 73 61 79.83 0.46 39 12 84 72 35.92 0.15 40 12 87 75 34.94 0.06 41 13 16 3 290.97 5.21 42 13 17 4 281.82 0.70 43 14 17 3 291.14 5.13 44 14 18 4 283.23 0.00 45 14 85 71 35.78 0.13 46 15 18 3 286.42 1.59 47 15 19 4 283.23 0.00 48 15 41 26 93.54 0.82 49 15 44 29 93.12 0.71 50 15 45 30 93.05 0.73 51 15 69 54 92.91 0.78 52 15 84 69 35.83 0.13 53 16 19 3 283.23 0.00 54 16 20 4 283.22 0.00 55 16 65 49 92.94 0.79 56 16 66 50 92.94 0.79 57 16 69 53 92.94 0.79 58 17 20 3 283.45 0.28 59 17 21 4 286.22 1.50 60 18 21 3 294.74 4.40 61 18 22 4 280.45 0.66 62 18 40 22 94.63 1.31 63 19 22 3 282.54 1.70 64 19 23 4 280.43 0.65 65 19 41 22 93.61 0.84 66 19 54 35 93.57 0.82 67 19 65 46 93.49 0.79 68 19 68 49 93.53 0.81 69 19 69 50 93.49 0.79 70 20 23 3 286.59 0.33 71 20 24 4 281.62 0.76 72 20 65 45 93.49 0.79 73 21 24 3 281.91 0.88 74 21 25 4 281.64 0.77 75 21 37 16 95.14 1.09 76 22 25 3 295.37 0.54 77 22 26 4 281.64 0.77 78 22 34 12 95.27 1.08 79 22 37 15 95.14 1.09 80 22 38 16 95.14 1.09 81 22 41 19 95.11 1.10 82 22 54 32 95.02 1.08 83 23 26 3 296.40 1.05 84 23 27 4 288.73 2.79 85 23 65 42 93.91 0.67 86 24 27 3 298.68 0.07 87 24 28 4 288.63 2.83 88 25 28 3 284.48 0.78 89 25 33 8 95.44 1.08 90 25 34 9 95.41 1.08 91 25 37 12 95.41 1.08 92 26 34 8 95.44 1.08 93 26 55 29 95.30 1.09 94 31 34 3 284.07 0.97 95 31 35 4 281.64 0.22 96 32 35 3 292.06 2.49 97 32 36 4 284.60 1.22 98 33 36 3 289.20 1.07 99 33 37 4 286.78 0.14 100 34 37 3 288.31 0.62 101 34 38 4 284.57 1.25 102 35 38 3 286.78 0.14 103 35 39 4 286.99 0.04 104 36 39 3 290.50 1.71 105 36 40 4 284.55 1.26 106 37 40 3 284.14 0.79 107 37 41 4 283.82 0.94 108 38 41 3 289.06 1.67 109 38 42 4 283.81 0.95 110 38 51 13 152.10 1.38 111 38 54 16 152.16 1.35 112 38 55 17 152.12 1.37 113 39 42 3 285.85 2.25 114 39 43 4 281.61 0.15 115 40 43 3 284.69 0.00 116 40 44 4 279.69 0.21 117 41 44 3 296.81 0.79 118 41 45 4 282.02 0.95 119 41 50 9 153.09 0.98 120 41 51 10 152.38 1.33 121 41 53 12 152.37 1.33 122 41 54 13 152.34 1.34 123 41 68 27 149.79 1.39 124 42 45 3 285.56 0.71 125 42 46 4 282.03 1.05 126 42 50 8 152.36 1.32 127 42 51 9 152.38 1.32 128 43 46 3 289.18 0.10 129 44 76 32 149.58 1.39 130 45 72 27 149.65 1.35 131 45 76 31 149.56 1.39 132 46 75 29 149.66 1.35 133 46 76 30 149.58 1.39 134 46 81 35 113.52 0.20 135 47 50 3 287.11 0.14 136 47 53 6 250.72 0.67 137 47 71 24 149.78 1.40 138 47 72 25 149.72 1.38 139 47 75 28 149.63 1.35 140 48 75 27 149.75 1.39 141 49 52 3 294.98 1.39 142 49 53 4 283.56 1.68 143 50 53 3 297.80 1.04 144 51 54 3 293.64 0.39 145 51 55 4 292.31 1.04 146 52 55 3 290.87 1.78 147 52 56 4 261.56 2.27 148 53 61 8 157.88 4.03 149 53 68 15 149.93 1.38 150 53 71 18 149.90 1.39 151 53 72 19 149.87 1.39 152 54 63 9 150.00 1.40 153 54 68 14 149.91 1.38 154 57 61 4 234.07 4.83 155 57 62 5 169.56 4.44 156 57 63 6 155.69 1.24 157 58 61 3 271.45 0.33 158 61 67 6 219.76 12.37 159 61 68 7 193.13 3.41 160 61 71 10 163.94 2.19 161 62 67 5 228.88 7.81 162 63 68 5 261.82 1.62 163 64 67 3 270.39 1.89 164 64 68 4 271.97 6.20 165 65 68 3 289.75 2.23 166 65 69 4 271.98 6.19 167 66 69 3 283.63 0.36 168 66 70 4 276.96 4.66 169 67 70 3 284.28 1.01 170 67 71 4 281.01 2.63 171 68 71 3 284.29 1.01 172 68 72 4 281.02 2.64 173 69 72 3 282.42 1.94 174 69 73 4 279.62 3.38 175 69 84 15 66.72 15.14 176 70 73 3 287.38 0.51 177 70 74 4 287.39 0.50 178 71 74 3 290.66 0.04 179 71 75 4 286.92 1.91 180 72 75 3 289.20 0.78 181 72 76 4 286.92 1.91 182 72 84 12 66.75 15.14 183 73 76 3 296.48 2.87 184 73 77 4 285.79 0.10 185 73 84 11 68.94 16.24 186 74 77 3 288.22 1.20 187 74 78 4 284.56 0.71 188 75 78 3 289.08 0.77 189 75 79 4 280.09 1.53 190 75 81 6 268.84 1.79 191 76 79 3 285.32 1.09 192 76 80 4 280.08 1.53 193 76 81 5 249.19 11.60 194 76 82 6 233.05 3.54 195 77 80 3 286.71 2.00