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 15 142 120 50.45 1.72 2 15 143 121 50.45 1.72 3 15 156 126 51.88 1.94 4 15 188 160 50.50 1.74 5 15 189 161 49.72 1.97 6 15 190 162 49.73 1.98 7 15 191 163 49.75 1.98 8 15 194 166 49.77 1.98 9 18 158 127 50.90 1.82 10 18 188 158 50.92 1.80 11 18 188 159 50.51 1.75 12 19 157 125 52.81 1.48 13 19 158 126 50.81 1.85 14 20 137 112 77.29 0.16 15 20 156 123 88.01 2.31 16 20 157 124 68.02 0.40 17 20 158 125 67.22 0.80 18 20 159 126 76.23 0.42 19 21 71 47 130.41 0.18 20 21 154 120 129.28 0.04 21 21 155 121 129.24 0.07 22 21 156 122 98.05 0.66 23 22 26 4 239.11 5.21 24 22 27 5 177.94 24.29 25 22 71 46 131.68 0.66 26 22 139 112 129.29 0.07 27 22 155 120 140.81 0.71 28 22 156 121 166.19 0.71 29 23 26 3 250.86 0.67 30 24 71 44 136.38 0.07 31 25 28 3 239.24 5.15 32 25 69 41 135.30 0.42 33 25 117 89 134.36 0.01 34 27 30 3 247.75 0.24 35 27 137 105 134.35 0.04 36 27 139 107 139.12 0.85 37 28 116 85 142.63 0.07 38 28 117 86 142.35 0.05 39 28 118 87 141.25 0.01 40 28 119 88 137.41 0.59 41 29 45 14 137.37 0.60 42 29 46 15 136.48 1.03 43 29 119 87 142.08 0.14 44 29 120 88 137.41 0.58 45 29 121 89 136.05 0.14 46 29 137 103 142.58 0.04 47 29 198 158 142.05 0.18 48 29 200 160 142.14 0.04 49 30 43 11 143.64 0.42 50 30 44 12 142.60 0.05 51 30 139 104 142.62 0.03 52 30 140 105 143.82 0.39 53 30 155 112 253.70 0.83 54 30 198 157 142.43 0.01 55 31 43 10 158.75 0.43 56 31 44 11 142.63 0.04 57 31 45 12 142.65 0.04 58 31 46 13 142.84 0.14 59 31 52 19 142.65 0.04 60 31 66 32 233.05 6.44 61 31 67 33 221.62 0.84 62 31 68 34 160.08 2.41 63 32 67 32 234.89 4.84 64 40 193 144 253.75 0.38 65 45 121 75 246.69 3.82 66 46 120 73 252.89 0.81 67 46 121 74 252.83 0.83 68 47 120 72 252.93 0.79 69 47 121 73 252.86 0.82 70 47 123 75 240.19 3.65 71 47 238 178 58.66 0.24 72 47 242 182 31.85 0.43 73 48 120 71 254.19 0.15 74 48 242 181 31.86 0.43 75 51 242 178 31.85 0.43 76 51 245 181 21.62 2.39 77 71 153 72 151.02 2.06 78 71 154 73 142.22 0.20 79 71 155 74 141.77 0.03 80 72 153 71 148.16 2.21 81 72 154 72 146.50 1.99 82 73 152 69 191.18 9.67 83 73 153 70 148.95 1.03 84 74 152 68 212.36 2.31 85 74 153 69 154.23 0.45 86 87 245 146 23.38 1.29 87 89 237 136 70.70 1.23 88 89 241 140 33.66 0.76 89 89 245 144 21.58 2.37 90 90 237 135 73.65 0.10 91 91 234 131 95.58 0.39 92 91 237 134 73.65 0.10 93 92 237 133 83.96 0.75 94 99 180 71 254.46 0.77 95 100 177 67 254.47 0.77 96 100 179 69 254.43 0.79 97 100 180 70 254.44 0.78 98 101 179 68 254.42 0.79 99 101 234 121 105.88 2.02 100 102 229 115 143.90 0.03 101 103 229 114 143.62 0.17 102 103 234 119 86.80 0.65 103 103 237 122 68.27 0.29 104 103 238 123 63.30 0.53 105 105 237 120 68.25 0.30 106 105 238 121 59.80 0.31 107 105 241 124 32.45 0.15 108 105 242 125 31.77 0.48 109 107 245 126 21.40 2.28 110 122 204 74 253.00 0.75 111 122 209 75 246.81 3.85 112 123 204 73 246.12 4.11 113 123 209 74 205.91 4.77 114 123 231 96 136.85 3.48 115 123 235 100 67.43 0.46 116 123 238 103 60.98 1.06 117 123 239 104 58.26 0.45 118 124 204 72 180.37 6.73 119 124 209 73 158.83 3.53 120 124 210 74 150.11 0.83 121 124 231 95 196.36 24.89 122 124 232 96 98.02 0.92 123 124 235 99 71.25 1.79 124 125 204 71 170.68 1.67 125 127 210 72 147.58 0.42 126 128 210 71 143.88 0.01 127 129 134 4 147.45 0.37 128 129 162 24 129.28 0.06 129 129 210 70 146.85 0.23 130 130 134 3 155.76 0.60 131 130 162 23 129.52 0.14 132 132 162 22 129.63 0.19 133 132 163 23 130.23 0.08 134 132 164 24 130.42 0.00 135 133 161 20 129.99 0.02 136 133 162 21 130.25 0.09 137 134 161 19 130.25 0.09 138 134 162 20 130.27 0.09 139 135 159 16 130.24 0.08 140 135 160 17 130.26 0.09 141 135 161 18 130.27 0.09 142 136 159 15 130.23 0.09 143 136 160 16 130.25 0.09 144 136 162 18 134.40 0.04 145 137 157 12 129.55 0.19 146 137 158 13 130.18 0.09 147 137 159 14 130.22 0.08 148 138 157 11 129.28 0.06 149 138 158 12 129.31 0.06 150 138 160 14 132.47 0.98 151 138 183 37 149.30 0.79 152 138 228 80 147.02 0.20 153 139 155 8 131.38 0.61 154 139 156 9 130.21 0.09 155 139 157 10 129.27 0.06 156 140 155 7 131.38 0.60 157 140 156 8 130.18 0.07 158 141 152 3 142.08 0.12 159 141 153 4 142.08 0.12 160 141 154 5 136.15 0.19 161 141 155 6 130.37 0.10 162 142 192 44 253.69 0.35 163 142 194 46 240.84 6.09 164 143 191 42 148.94 3.15 165 143 192 43 247.22 0.49 166 158 188 32 129.97 0.12 167 158 189 33 129.28 0.07 168 162 199 39 135.97 0.73 169 162 201 41 137.77 1.71 170 163 225 60 140.22 0.48 171 171 223 50 147.38 0.39 172 171 224 51 147.29 0.44 173 171 225 52 147.22 0.48 174 172 224 50 147.43 0.39 175 172 225 51 147.43 0.39 176 172 227 53 147.08 0.42 177 176 227 49 147.22 0.46 178 178 230 50 146.33 0.70 179 178 233 53 142.45 0.02 180 179 229 48 147.00 0.36 181 179 230 49 146.09 0.60 182 179 233 52 141.56 0.12 183 179 234 53 140.46 0.65 184 180 215 33 254.06 0.86 185 180 227 45 147.23 0.46 186 180 228 46 147.00 0.36 187 180 230 48 145.59 0.85 188 181 227 44 147.09 0.42 189 181 228 45 146.29 0.71 190 181 230 47 143.19 0.33 191 182 225 41 147.26 0.46 192 182 226 42 147.20 0.47 193 182 227 43 145.81 0.76 194 183 199 18 149.00 0.74 195 183 226 41 147.22 0.48 196 183 228 43 146.49 0.58 197 184 225 39 147.40 0.39 198 184 188 5 254.40 0.38 199 184 225 38 147.52 0.45 200 185 222 34 148.90 0.63 201 185 223 35 148.25 0.77 202 185 225 37 147.57 0.47 203 186 222 33 148.91 0.63 204 187 221 30 149.41 0.83 205 187 221 31 149.38 0.82 206 187 222 32 148.94 0.64 207 188 221 29 149.45 0.81 208 188 221 28 151.69 0.29 209 189 221 27 192.81 15.76 210 189 226 33 144.48 0.24 211 190 228 34 143.82 0.02 212 199 228 25 147.25 0.29 213 209 231 22 112.92 1.22 214 210 230 20 143.90 0.02 215 210 231 21 114.17 0.29 216 211 228 17 147.14 0.26 217 211 229 18 144.28 0.17 218 211 231 20 105.67 0.15 219 212 228 16 144.22 0.14 220 212 229 17 143.88 0.01 221 212 231 19 108.45 0.73 222 213 228 15 143.90 0.01 223 214 227 13 147.39 0.39 224 214 228 14 145.58 0.84 225 214 229 15 143.90 0.01 226 215 226 11 147.44 0.39 227 215 227 12 147.31 0.45 228 217 224 7 174.45 2.85 229 221 224 3 254.30 0.76 230 231 235 4 253.19 1.21 231 231 238 7 62.52 0.24 232 232 235 3 75.05 0.27 233 234 237 3 67.31 0.13 234 234 238 4 64.90 0.86 235 235 238 3 65.47 0.57 236 235 239 4 61.73 0.17 237 236 239 3 65.47 0.57 238 236 240 4 60.80 0.01 239 237 240 3 59.79 0.32 240 237 241 4 57.19 0.97 241 238 241 3 45.45 4.93 242 238 242 4 32.45 0.15 243 239 242 3 44.18 5.63 244 239 243 4 32.83 0.05 245 240 243 3 32.84 0.05 246 240 244 4 31.87 0.43 247 241 244 3 51.58 9.43 248 241 245 4 31.28 0.59 249 242 245 3 43.09 8.20