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 3 7 4 36.52 0.34 2 4 7 3 45.65 0.84 3 4 16 12 31.39 0.24 4 4 103 99 31.38 0.24 5 4 108 104 31.36 0.25 6 4 109 105 31.36 0.24 7 4 110 106 31.38 0.24 8 5 104 99 31.44 0.27 9 5 105 100 31.43 0.26 10 5 106 101 31.39 0.24 11 5 107 102 31.36 0.24 12 5 108 103 31.36 0.25 13 6 104 98 31.45 0.27 14 7 103 96 33.07 1.04 15 8 16 8 142.44 0.10 16 8 103 95 40.48 0.21 17 9 14 5 165.59 3.31 18 9 16 7 165.38 3.29 19 9 111 102 165.32 3.33 20 11 14 3 168.56 1.86 21 15 183 168 168.81 1.76 22 15 186 171 166.65 2.80 23 15 188 173 252.21 1.28 24 16 183 167 165.61 3.31 25 16 184 168 165.58 3.32 26 16 185 169 165.52 3.31 27 17 181 164 175.72 0.83 28 17 182 165 165.59 3.31 29 17 183 166 165.55 3.31 30 17 184 167 165.44 3.27 31 17 191 174 168.42 1.90 32 18 181 163 165.62 3.31 33 18 182 164 165.59 3.32 34 18 184 166 146.21 1.19 35 19 179 160 185.92 1.38 36 19 180 161 165.60 3.31 37 19 181 162 165.56 3.31 38 20 179 159 165.63 3.31 39 20 180 160 165.58 3.31 40 21 177 156 183.93 0.40 41 21 178 157 165.62 3.31 42 21 179 158 165.56 3.31 43 22 153 131 165.55 3.31 44 22 177 155 165.61 3.31 45 22 178 156 165.57 3.31 46 22 214 192 122.61 0.18 47 22 215 193 122.18 0.14 48 23 175 152 177.88 2.59 49 23 176 153 165.62 3.31 50 23 177 154 165.53 3.31 51 23 215 192 122.61 0.18 52 24 175 151 165.60 3.31 53 24 176 152 165.53 3.31 54 24 214 190 122.72 0.17 55 24 215 191 122.63 0.17 56 25 130 105 168.44 1.94 57 25 172 147 168.60 1.92 58 25 174 149 165.61 3.31 59 25 175 150 165.46 3.27 60 26 173 147 165.61 3.31 61 26 174 148 165.41 3.31 62 27 31 4 122.83 0.15 63 27 34 7 122.78 0.15 64 27 70 43 168.75 1.79 65 27 171 144 165.62 3.31 66 27 173 146 165.50 3.29 67 28 31 3 122.81 0.14 68 28 169 141 165.27 3.47 69 28 170 142 165.32 3.45 70 28 171 143 165.29 3.42 71 28 172 144 165.21 3.44 72 28 173 145 165.00 3.47 73 29 173 144 165.38 3.29 74 31 171 140 122.82 0.14 75 34 68 34 122.78 0.16 76 34 69 35 122.74 0.17 77 34 135 101 122.86 0.14 78 35 68 33 122.74 0.17 79 35 89 54 121.95 0.06 80 36 67 31 122.77 0.15 81 36 68 32 122.69 0.17 82 36 136 100 122.75 0.14 83 36 137 101 122.73 0.14 84 36 138 102 122.61 0.17 85 36 139 103 122.06 0.20 86 37 67 30 122.70 0.16 87 37 68 31 122.62 0.15 88 37 87 50 118.86 0.61 89 37 88 51 119.90 0.33 90 37 89 52 120.58 0.19 91 37 94 57 120.12 0.42 92 37 139 102 121.51 0.04 93 37 141 104 121.83 0.12 94 38 66 28 122.71 0.15 95 38 67 29 122.62 0.15 96 38 87 49 113.74 2.92 97 38 139 101 121.31 0.05 98 38 140 102 120.95 0.04 99 38 141 103 119.67 0.41 100 39 66 27 122.76 0.15 101 39 67 28 122.71 0.15 102 39 135 96 122.68 0.16 103 39 136 97 122.67 0.16 104 39 137 98 122.28 0.34 105 39 139 100 120.69 0.08 106 40 64 24 122.97 0.16 107 40 65 25 122.81 0.14 108 40 66 26 122.77 0.15 109 41 64 23 122.97 0.16 110 41 65 24 122.81 0.14 111 41 85 44 119.84 0.32 112 41 224 183 229.02 6.02 113 42 62 20 167.37 2.48 114 42 63 21 163.84 2.96 115 42 64 22 122.98 0.15 116 43 61 18 169.49 2.89 117 43 62 19 167.38 2.48 118 43 63 20 164.88 3.48 119 43 81 38 120.99 0.01 120 44 61 17 169.59 2.87 121 44 62 18 168.00 2.21 122 45 59 14 169.84 2.93 123 45 60 15 169.82 2.92 124 45 61 16 169.59 2.86 125 46 52 6 252.85 0.70 126 46 54 8 251.13 0.05 127 46 59 13 169.84 2.93 128 46 60 14 169.83 2.93 129 46 62 16 169.80 2.94 130 47 52 5 252.84 0.71 131 47 53 6 251.52 0.13 132 47 54 7 251.41 0.09 133 58 77 19 122.44 0.07 134 58 78 20 122.41 0.06 135 60 76 16 240.63 1.81 136 60 77 17 189.27 11.65 137 61 76 15 249.96 2.41 138 85 222 137 87.50 0.18 139 85 223 138 73.33 0.21 140 86 220 134 114.42 2.84 141 86 221 135 108.89 0.52 142 86 222 136 85.14 0.99 143 86 223 137 78.55 1.35 144 87 220 133 116.19 1.96 145 87 221 134 114.13 2.89 146 87 223 136 108.90 0.52 147 88 215 127 122.76 0.17 148 88 216 128 122.70 0.15 149 88 219 131 120.80 0.12 150 88 220 132 119.64 0.32 151 90 219 129 122.51 0.23 152 95 215 120 122.69 0.16 153 96 220 124 109.85 0.57 154 97 153 56 168.58 1.87 155 97 215 118 122.48 0.22 156 97 217 120 120.66 0.19 157 97 220 123 109.68 0.59 158 100 184 84 147.98 1.41 159 101 184 83 163.48 3.72 160 102 184 82 161.97 2.96 161 103 184 81 165.47 3.33 162 103 185 82 165.28 3.29 163 109 184 75 165.54 3.33 164 124 181 57 245.03 0.88 165 140 223 83 121.01 0.01 166 140 224 84 119.70 0.39 167 141 221 80 121.50 0.04 168 141 222 81 119.98 0.38 169 141 224 83 116.20 1.96 170 142 222 80 118.84 0.64 171 142 223 81 116.21 1.96 172 142 224 82 114.38 2.82 173 146 220 74 116.19 1.96 174 146 221 75 109.56 0.69 175 146 222 76 87.53 0.21 176 149 184 35 157.75 1.10 177 150 184 34 157.77 1.11 178 151 182 31 167.76 2.21 179 151 184 33 145.43 1.81 180 153 210 57 122.72 0.16 181 153 211 58 122.52 0.23 182 153 212 59 122.41 0.21 183 154 187 33 252.55 0.13 184 154 210 56 122.65 0.17 185 154 212 58 122.42 0.21 186 155 208 53 122.73 0.17 187 155 209 54 122.72 0.17 188 155 210 55 122.50 0.24 189 158 206 48 122.83 0.14 190 176 214 38 122.70 0.18 191 177 214 37 122.64 0.17 192 178 211 33 122.72 0.17 193 178 214 36 122.42 0.23 194 194 209 15 122.74 0.17 195 194 211 17 122.69 0.17 196 196 206 10 122.85 0.14 197 197 205 8 122.97 0.14 198 197 206 9 122.83 0.14 199 198 204 6 155.00 2.19 200 198 205 7 129.35 3.05 201 199 202 3 252.09 0.03 202 199 203 4 167.09 2.43 203 199 204 5 155.00 2.19 204 200 203 3 206.56 8.01 205 211 214 3 201.99 7.79 206 215 220 5 208.49 2.15 207 216 219 3 250.37 0.96 208 217 220 3 239.38 0.61