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 1 127 131 4 227.25 0.84 2 128 131 3 228.12 1.28 3 128 132 4 223.69 2.62 4 129 132 3 231.75 0.05 5 131 135 4 228.86 2.55 6 132 135 3 228.86 2.55 7 133 136 3 239.12 0.10 8 133 137 4 231.77 1.08 9 134 137 3 231.78 1.08 10 134 138 4 231.77 1.08 11 135 138 3 245.95 0.33 12 135 139 4 231.78 1.07 13 136 139 3 231.74 1.07 14 136 140 4 228.90 1.55 15 136 174 38 89.11 2.24 16 136 175 39 89.11 2.24 17 136 178 42 88.83 2.31 18 137 140 3 229.06 1.54 19 137 141 4 229.06 1.54 20 138 141 3 230.12 0.38 21 138 142 4 224.46 0.66 22 139 142 3 225.88 0.04 23 139 143 4 223.47 1.15 24 139 167 28 92.29 1.54 25 139 171 32 89.45 2.27 26 139 175 36 89.39 2.29 27 140 143 3 226.61 0.69 28 140 144 4 220.63 0.79 29 140 175 35 89.40 2.30 30 140 178 38 88.94 2.27 31 140 179 39 88.83 2.30 32 140 182 42 88.27 2.06 33 141 144 3 220.64 0.79 34 141 145 4 220.60 0.79 35 142 145 3 232.03 1.74 36 142 146 4 223.87 0.85 37 142 165 23 95.63 0.61 38 142 167 25 95.62 0.61 39 143 146 3 229.01 1.86 40 143 147 4 222.79 2.87 41 143 161 18 95.17 0.40 42 143 165 22 95.70 0.59 43 143 172 29 89.68 2.30 44 143 175 32 89.59 2.32 45 143 176 33 89.59 2.33 46 144 147 3 231.81 1.64 47 144 148 4 224.28 0.65 48 144 179 35 89.14 2.17 49 144 184 40 79.82 0.17 50 144 197 53 56.38 0.76 51 145 148 3 230.34 2.38 52 145 149 4 224.28 0.66 53 146 149 3 222.02 1.64 54 146 150 4 215.25 1.75 55 146 156 10 96.16 0.77 56 146 161 15 96.08 0.74 57 146 164 18 96.12 0.76 58 146 165 19 96.04 0.72 59 147 150 3 224.16 2.71 60 147 156 9 96.10 0.80 61 147 161 14 96.08 0.74 62 147 176 29 94.34 0.01 63 147 185 38 78.96 0.26 64 147 195 48 59.15 1.48 65 147 196 49 57.20 0.82 66 147 197 50 56.80 0.92 67 148 197 49 56.91 0.96 68 149 164 15 101.96 0.10 69 150 154 4 216.90 2.33 70 150 156 6 119.81 4.55 71 151 154 3 250.02 1.40 72 152 199 47 56.93 0.96 73 153 196 43 59.71 1.44 74 155 188 33 72.78 2.48 75 155 194 39 59.72 1.45 76 155 195 40 59.68 1.45 77 155 196 41 59.42 1.41 78 156 160 4 217.76 2.58 79 156 161 5 218.06 2.43 80 156 194 38 59.66 1.44 81 156 195 39 59.65 1.44 82 157 160 3 225.90 0.90 83 157 161 4 220.09 3.22 84 157 192 35 59.81 1.49 85 157 193 36 59.73 1.45 86 157 194 37 59.52 1.38 87 157 195 38 59.52 1.38 88 158 161 3 227.62 0.04 89 158 162 4 227.13 0.28 90 158 169 11 133.36 1.32 91 158 172 14 129.28 0.64 92 158 173 15 129.25 0.65 93 158 176 18 123.60 2.19 94 158 195 37 59.52 1.38 95 159 162 3 231.36 1.82 96 159 163 4 227.15 0.28 97 159 169 10 133.41 1.30 98 160 163 3 227.15 0.28 99 160 164 4 227.09 0.26 100 161 164 3 232.46 2.42 101 161 165 4 223.18 1.69 102 161 172 11 129.38 0.68 103 161 176 15 129.30 0.66 104 162 165 3 231.31 2.41 105 162 166 4 183.52 0.88 106 162 167 5 168.53 5.54 107 162 168 6 148.02 5.74 108 162 169 7 147.78 5.85 109 162 172 10 129.96 0.40 110 163 166 3 221.16 0.62 111 165 172 7 187.69 7.08 112 167 171 4 202.66 2.32 113 167 172 5 199.94 0.96 114 168 171 3 231.93 0.12 115 168 172 4 215.33 2.16 116 169 172 3 215.75 2.37 117 169 173 4 202.67 2.31 118 170 174 4 220.99 1.57 119 171 174 3 223.06 0.54 120 171 175 4 221.01 1.56 121 172 175 3 226.58 2.31 122 172 176 4 220.38 1.17 123 173 176 3 220.39 1.17 124 173 177 4 220.38 1.16 125 174 177 3 237.52 3.17 126 174 178 4 221.11 0.76 127 175 178 3 224.54 0.96 128 175 179 4 220.34 1.14 129 176 179 3 232.20 2.54 130 176 180 4 224.61 3.27 131 176 195 19 59.08 1.42 132 177 180 3 227.73 4.88 133 177 181 4 222.60 2.44 134 177 195 18 59.52 1.49 135 178 181 3 228.94 1.10 136 178 182 4 222.32 2.59 137 179 182 3 224.23 3.45 138 179 183 4 222.31 2.59 139 179 184 5 194.90 1.59 140 179 185 6 137.21 0.07 141 180 183 3 229.41 0.76 142 180 185 5 137.22 0.07 143 180 195 15 59.52 1.49 144 184 197 13 58.00 1.06 145 184 198 14 56.50 0.79 146 185 195 10 59.54 1.50 147 185 196 11 59.12 1.40 148 185 197 12 57.58 1.27 149 185 198 13 56.70 0.84 150 186 195 9 81.14 12.26 151 186 196 10 59.41 1.54 152 186 197 11 59.12 1.40 153 186 198 12 56.72 0.84 154 187 193 6 103.07 1.35 155 187 194 7 103.00 1.34 156 187 195 8 81.14 12.26 157 188 193 5 103.08 1.35 158 188 194 6 103.03 1.35 159 188 196 8 102.98 1.34 160 190 193 3 229.84 4.08