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 10 13 3 78.14 0.82 2 10 14 4 78.06 0.85 3 11 14 3 86.83 1.28 4 11 121 110 58.15 1.24 5 11 127 116 57.93 1.35 6 12 122 110 58.27 1.23 7 12 123 111 58.23 1.22 8 12 125 113 57.92 1.36 9 12 126 114 57.92 1.35 10 12 127 115 57.93 1.35 11 13 122 109 58.27 1.23 12 14 121 107 59.20 0.78 13 14 122 108 59.16 0.80 14 15 121 106 70.84 0.45 15 16 129 113 168.08 0.76 16 18 21 3 182.78 0.94 17 19 22 3 245.90 1.88 18 22 201 179 185.75 0.22 19 23 201 178 173.31 0.20 20 23 202 179 173.28 0.21 21 24 199 175 196.50 1.52 22 24 200 176 173.34 0.18 23 24 201 177 172.97 0.07 24 24 209 185 270.60 7.12 25 25 199 174 173.60 0.25 26 25 200 175 173.31 0.20 27 25 202 177 94.45 1.75 28 26 197 171 203.12 0.75 29 26 199 173 172.99 0.10 30 27 167 140 243.97 17.42 31 27 169 142 242.71 16.86 32 27 171 144 200.30 2.08 33 27 197 170 176.98 0.39 34 27 198 171 173.34 0.18 35 28 196 168 178.96 0.60 36 28 197 169 172.98 0.10 37 29 171 142 177.10 0.10 38 29 195 166 178.78 0.75 39 29 196 167 173.08 0.06 40 29 229 200 162.27 0.10 41 29 232 203 162.20 0.12 42 29 233 204 162.09 0.09 43 30 193 163 193.08 1.02 44 30 194 164 178.78 0.75 45 31 193 162 173.66 0.30 46 31 194 163 173.17 0.09 47 31 232 201 162.23 0.10 48 31 233 202 162.15 0.10 49 32 148 116 226.02 2.69 50 32 190 158 196.72 1.41 51 32 192 160 177.33 1.54 52 32 193 161 172.97 0.09 53 33 190 157 176.97 1.65 54 33 191 158 173.42 0.16 55 33 192 159 172.88 0.10 56 34 38 4 162.28 0.11 57 34 39 5 162.28 0.11 58 34 41 7 162.19 0.12 59 34 88 54 196.59 1.18 60 35 38 3 162.28 0.11 61 35 191 156 162.27 0.14 62 38 189 151 162.21 0.14 63 41 86 45 162.21 0.13 64 41 87 46 162.21 0.13 65 42 107 65 161.84 0.10 66 43 85 42 162.06 0.10 67 43 86 43 162.07 0.10 68 43 154 111 162.21 0.12 69 43 155 112 162.22 0.12 70 43 157 114 162.02 0.09 71 44 85 41 161.88 0.18 72 44 86 42 161.87 0.18 73 44 105 61 154.00 0.20 74 44 106 62 160.37 0.18 75 44 107 63 161.69 0.08 76 44 112 68 158.84 0.25 77 44 157 113 162.01 0.10 78 45 85 40 161.88 0.18 79 45 105 60 151.55 1.02 80 45 157 112 161.85 0.06 81 45 158 113 161.06 0.32 82 45 159 114 160.78 0.25 83 46 84 38 162.03 0.10 84 46 85 39 162.03 0.10 85 46 153 107 162.06 0.10 86 46 155 109 161.90 0.10 87 46 156 110 161.88 0.09 88 46 157 111 159.80 0.54 89 47 82 35 162.04 0.10 90 47 83 36 162.03 0.10 91 47 84 37 162.05 0.10 92 48 81 33 162.03 0.09 93 48 82 34 162.04 0.09 94 48 83 35 162.04 0.10 95 48 242 194 285.05 1.41 96 49 81 32 162.05 0.10 97 49 82 33 162.06 0.10 98 50 80 30 162.06 0.10 99 50 81 31 162.06 0.10 100 51 79 28 162.12 0.12 101 51 80 29 162.07 0.10 102 52 78 26 162.13 0.12 103 52 79 27 162.13 0.12 104 53 77 24 162.17 0.11 105 53 78 25 162.19 0.12 106 54 61 7 286.94 0.53 107 54 62 8 286.94 0.53 108 54 77 23 162.21 0.12 109 55 77 22 162.22 0.13 110 55 79 24 162.25 0.14 111 61 77 16 162.24 0.14 112 75 96 21 287.90 0.30 113 76 96 20 287.90 0.30 114 98 199 101 186.66 0.23 115 102 165 63 243.62 17.33 116 103 240 137 122.58 1.56 117 103 241 138 100.73 1.28 118 104 164 60 243.62 17.33 119 104 238 134 155.00 0.66 120 104 239 135 150.22 0.47 121 104 240 136 129.85 2.85 122 104 241 137 115.57 0.69 123 105 238 133 156.02 0.86 124 105 239 134 153.55 0.06 125 105 241 136 141.40 2.15 126 106 237 131 161.87 0.07 127 106 238 132 159.61 0.55 128 113 233 120 162.22 0.10 129 114 238 124 153.58 0.07 130 115 171 56 188.53 1.00 131 115 233 118 162.21 0.12 132 115 235 120 161.85 0.07 133 115 238 123 150.36 0.56 134 117 167 50 243.96 17.43 135 118 167 49 244.00 17.41 136 118 202 84 90.81 0.01 137 119 165 46 244.08 17.41 138 119 166 47 244.06 17.42 139 119 202 83 167.82 0.90 140 120 166 46 278.63 0.13 141 120 167 47 244.01 17.41 142 120 168 48 278.62 0.10 143 120 202 82 167.82 0.90 144 121 202 81 172.69 0.04 145 123 165 42 259.82 9.54 146 125 165 40 261.19 8.86 147 139 199 60 287.97 0.06 148 158 241 83 161.03 0.12 149 158 242 84 160.78 0.24 150 159 239 80 161.93 0.04 151 159 240 81 160.79 0.24 152 159 241 82 160.70 0.24 153 159 242 83 160.00 0.58 154 160 240 80 160.75 0.24 155 160 242 82 156.41 0.05 156 162 240 78 158.30 0.24 157 164 238 74 159.43 0.57 158 167 202 35 287.05 0.33 159 168 202 34 287.05 0.33 160 171 229 58 162.09 0.10 161 171 230 59 161.88 0.02 162 172 230 58 161.89 0.01 163 173 227 54 162.13 0.09 164 173 228 55 161.92 0.01 165 194 232 38 162.15 0.10 166 196 229 33 162.13 0.10 167 196 232 36 161.96 0.13 168 212 226 14 162.15 0.09 169 212 227 15 162.15 0.09 170 212 229 17 162.06 0.09 171 214 225 11 162.28 0.12 172 215 223 8 162.44 0.09 173 215 224 9 162.33 0.11 174 216 221 5 180.72 1.68 175 216 222 6 165.83 1.57 176 216 223 7 162.44 0.10 177 217 220 3 287.30 0.24 178 217 221 4 180.72 1.69 179 217 222 5 165.83 1.57 180 218 221 3 208.41 5.40 181 229 232 3 230.55 6.12 182 234 237 3 281.12 0.01 183 234 238 4 279.29 0.06 184 235 238 3 280.85 0.14