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 1 137 145 8 59.26 11.07 2 137 146 9 58.83 10.86 3 138 144 6 169.94 1.31 4 138 145 7 120.52 20.17 5 138 147 9 80.78 0.31 6 138 173 35 36.55 0.35 7 139 143 4 275.80 1.83 8 139 144 5 169.94 1.30 9 140 143 3 338.73 2.02 10 140 145 5 286.04 6.95 11 140 152 12 78.81 0.58 12 140 212 72 38.27 0.42 13 140 221 81 37.11 0.14 14 140 232 92 37.12 0.14 15 140 235 95 13.47 0.22 16 141 221 80 37.89 0.48 17 141 235 94 16.43 0.30 18 142 153 11 78.78 0.58 19 142 154 12 78.53 0.49 20 142 155 13 78.23 0.64 21 142 214 72 41.37 0.29 22 143 152 9 78.84 0.57 23 143 153 10 78.78 0.58 24 143 154 11 78.55 0.48 25 143 159 16 77.86 0.58 26 143 211 68 52.84 3.75 27 143 212 69 40.52 0.72 28 144 152 8 78.85 0.57 29 144 153 9 78.79 0.59 30 144 156 12 78.53 0.48 31 145 151 6 198.73 19.11 32 145 152 7 78.84 0.56 33 145 161 16 77.80 0.58 34 145 166 21 66.56 0.06 35 145 169 24 58.23 1.37 36 145 173 28 56.75 1.95 37 146 149 3 348.53 1.58 38 146 150 4 287.83 11.71 39 146 151 5 198.74 19.11 40 147 166 19 69.59 1.47 41 147 170 23 58.38 1.34 42 147 173 26 58.38 1.34 43 150 163 13 77.53 0.72 44 150 166 16 66.12 0.28 45 150 193 43 83.52 1.92 46 152 158 6 236.36 1.06 47 152 159 7 200.44 18.99 48 152 161 9 77.83 0.58 49 152 169 17 65.42 0.54 50 152 211 59 68.77 1.60 51 152 212 60 64.55 0.04 52 153 156 3 324.95 2.44 53 153 157 4 265.87 4.96 54 153 158 5 236.36 1.05 55 153 159 6 236.34 1.05 56 154 157 3 338.11 4.21 57 154 159 5 265.56 5.12 58 159 211 52 110.48 0.08 59 161 165 4 323.55 0.93 60 161 166 5 316.62 2.52 61 161 169 8 307.83 6.19 62 161 208 47 117.91 0.90 63 161 211 50 117.91 0.92 64 162 165 3 343.57 0.73 65 162 166 4 337.78 2.17 66 162 198 36 151.25 0.54 67 163 166 3 342.61 0.24 68 163 167 4 339.92 1.09 69 163 193 30 152.12 0.38 70 163 194 31 151.94 0.43 71 163 195 32 151.44 0.43 72 163 198 35 151.56 0.48 73 164 167 3 346.04 1.82 74 164 168 4 339.97 1.07 75 164 195 31 151.73 0.53 76 164 198 34 151.56 0.48 77 164 204 40 146.13 0.46 78 165 168 3 342.25 0.07 79 165 169 4 330.45 3.69 80 165 204 39 150.34 0.21 81 165 208 43 144.75 0.99 82 165 211 46 147.62 0.71 83 166 169 3 336.61 2.89 84 166 170 4 331.06 3.43 85 167 170 3 342.89 0.12 86 167 171 4 334.72 1.59 87 167 189 22 152.35 0.48 88 167 195 28 152.40 0.40 89 168 171 3 340.53 1.30 90 168 172 4 337.99 0.04 91 168 185 17 152.47 0.54 92 168 189 21 152.42 0.49 93 168 201 33 152.03 0.35 94 168 204 36 152.04 0.35 95 168 205 37 151.90 0.41 96 168 208 40 151.88 0.42 97 169 172 3 337.39 0.34 98 169 173 4 337.39 0.34 99 169 208 39 151.88 0.42 100 169 222 53 151.68 0.48 101 170 173 3 337.39 0.35 102 170 174 4 337.36 0.36 103 171 174 3 340.56 1.19 104 171 175 4 337.91 0.10 105 171 180 9 235.61 1.25 106 171 185 14 152.56 0.55 107 171 188 17 152.56 0.55 108 172 175 3 340.53 1.21 109 172 176 4 337.91 0.10 110 172 180 8 235.55 1.28 111 172 185 13 153.44 0.11 112 172 205 33 152.12 0.35 113 172 222 50 151.78 0.44 114 172 230 58 151.84 0.42 115 172 231 59 151.59 0.50 116 172 232 60 151.46 0.48 117 173 176 3 343.06 0.06 118 173 232 59 151.56 0.52 119 175 178 3 337.82 0.07 120 175 180 5 320.45 2.23 121 175 188 13 178.53 12.64 122 176 232 56 151.61 0.49 123 176 234 58 151.40 0.43 124 177 231 54 151.85 0.42 125 177 232 55 151.79 0.45 126 177 233 56 151.65 0.48 127 177 234 57 151.62 0.49 128 178 231 53 152.03 0.34 129 179 225 46 152.12 0.30 130 179 228 49 152.19 0.30 131 179 230 51 152.10 0.32 132 179 231 52 151.85 0.41 133 180 184 4 325.26 0.23 134 180 185 5 319.17 2.27 135 180 188 8 307.58 1.95 136 180 229 49 152.10 0.33 137 180 230 50 152.09 0.32 138 181 184 3 335.49 3.79 139 181 185 4 325.32 0.24 140 181 228 47 152.30 0.33 141 181 229 48 152.09 0.33 142 182 185 3 331.58 1.85 143 182 186 4 325.37 0.26 144 182 201 19 152.90 0.29 145 182 202 20 152.91 0.29 146 183 186 3 347.56 1.22 147 183 187 4 342.33 0.37 148 184 187 3 349.29 2.08 149 184 188 4 337.80 4.42 150 185 188 3 343.03 1.81 151 185 189 4 335.28 3.16 152 185 201 16 152.91 0.29 153 185 230 45 152.02 0.34 154 186 189 3 343.03 1.81 155 186 190 4 337.80 4.42 156 186 196 10 153.96 0.49 157 186 201 15 152.91 0.29 158 187 190 3 342.12 2.26 159 189 195 6 154.11 0.52 160 189 196 7 154.08 0.54 161 190 196 6 154.11 0.53 162 194 197 3 355.39 1.97 163 194 198 4 329.33 3.49 164 195 198 3 341.62 0.20 165 198 204 6 329.39 0.48 166 199 203 4 330.70 0.12 167 199 204 5 329.45 0.46 168 200 203 3 345.61 1.97 169 200 204 4 333.68 1.61 170 201 204 3 334.00 1.77 171 201 205 4 333.67 1.61 172 201 230 29 207.81 5.20 173 202 205 3 338.94 1.37 174 202 206 4 331.55 0.55 175 202 230 28 207.90 5.25 176 203 206 3 337.48 0.29 177 203 207 4 332.89 1.45 178 204 207 3 333.11 1.34 179 204 208 4 332.90 1.44 180 205 208 3 333.94 1.76 181 205 209 4 331.93 2.15 182 205 222 17 220.99 1.65 183 205 230 25 207.94 5.24 184 206 209 3 339.46 3.60 185 206 210 4 333.31 1.46 186 207 210 3 343.31 1.68 187 207 211 4 337.18 4.75 188 208 211 3 341.29 2.69 189 208 212 4 331.94 2.13 190 208 222 14 222.16 2.08 191 209 212 3 337.31 0.58 192 209 213 4 320.86 1.79 193 209 216 7 231.00 5.42 194 209 219 10 230.97 5.40 195 209 222 13 221.88 1.94 196 209 223 14 221.88 1.94 197 209 224 15 221.88 1.94 198 209 230 21 210.06 5.03 199 210 216 6 232.41 4.84 200 212 221 9 231.06 5.39 201 212 222 10 231.03 5.38 202 213 216 3 333.04 4.00 203 213 219 6 231.19 5.45 204 213 220 7 231.19 5.45 205 213 221 8 231.08 5.40 206 213 222 9 231.06 5.39 207 215 218 3 336.92 2.31 208 215 219 4 324.32 8.60 209 216 219 3 332.05 4.74 210 219 222 3 352.28 0.79 211 219 223 4 319.55 6.16 212 220 223 3 357.63 0.96 213 220 233 13 209.88 4.96 214 220 234 14 209.83 4.94 215 220 235 15 209.77 4.92 216 221 231 10 210.05 5.03 217 221 232 11 209.84 4.93 218 221 233 12 209.74 4.91 219 221 235 14 209.68 4.90 220 222 231 9 209.88 4.96 221 223 230 7 210.06 5.03 222 223 231 8 209.95 4.98 223 223 233 10 209.83 4.92 224 224 229 5 243.68 1.28 225 224 230 6 210.06 5.03 226 225 228 3 338.00 3.06 227 225 229 4 250.25 4.43 228 225 231 6 234.67 7.28