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 15 221 191 28.75 0.12 2 18 158 130 52.40 2.19 3 18 188 161 46.01 1.33 4 18 188 162 28.77 0.12 5 19 157 128 54.08 3.04 6 19 158 129 52.40 2.19 7 20 137 112 79.64 0.31 8 20 156 126 113.20 13.97 9 20 157 127 68.36 0.69 10 20 158 128 108.08 19.16 11 20 159 129 262.38 3.93 12 21 71 47 127.93 0.86 13 21 154 123 133.75 4.11 14 21 155 124 142.75 0.03 15 21 156 125 142.40 0.05 16 22 27 5 250.02 3.74 17 22 71 46 128.83 0.87 18 22 139 112 126.81 0.66 19 22 155 123 149.27 0.88 20 22 156 124 167.91 0.73 21 24 71 44 129.85 0.55 22 25 117 89 129.28 0.68 23 27 137 105 129.34 0.81 24 27 139 107 130.00 0.83 25 28 116 85 137.89 0.35 26 28 117 86 137.86 0.34 27 28 118 87 137.22 0.55 28 28 119 88 134.21 0.42 29 29 45 14 131.53 0.51 30 29 46 15 131.53 0.51 31 29 119 87 137.70 0.35 32 29 120 88 134.21 0.42 33 29 121 89 131.41 0.57 34 29 137 103 137.78 0.33 35 29 198 161 136.77 0.21 36 29 200 163 137.39 0.18 37 30 43 11 137.87 0.34 38 30 44 12 137.78 0.35 39 30 139 104 137.84 0.34 40 30 140 105 138.60 0.58 41 30 141 106 143.90 0.41 42 30 198 160 137.66 0.32 43 31 43 10 138.49 0.05 44 31 44 11 137.87 0.34 45 31 45 12 137.88 0.34 46 31 46 13 137.88 0.35 47 31 52 19 137.88 0.35 48 31 66 32 143.78 0.48 49 31 67 33 143.85 0.47 50 31 68 34 143.31 0.65 51 31 141 105 143.93 0.41 52 32 40 6 157.69 1.07 53 32 42 8 149.28 0.84 54 32 66 31 144.37 0.36 55 32 67 32 143.97 0.46 56 32 73 38 147.71 0.98 57 32 141 104 143.94 0.41 58 33 40 5 165.87 2.74 59 33 41 6 157.69 1.07 60 33 42 7 149.48 0.76 61 33 43 8 147.14 1.20 62 33 54 19 148.72 0.38 63 33 58 23 152.15 1.78 64 33 63 28 149.60 0.78 65 33 64 29 149.56 0.77 66 33 66 30 146.52 0.41 67 33 106 70 149.51 0.77 68 34 39 3 267.09 2.27 69 34 40 4 200.75 14.70 70 34 41 5 172.42 0.54 71 34 63 27 150.62 1.23 72 34 64 28 149.60 0.78 73 34 67 30 149.59 0.79 74 37 60 23 268.12 0.09 75 37 62 25 262.70 0.98 76 45 121 75 262.87 1.77 77 46 121 74 268.24 1.36 78 47 123 75 232.99 0.70 79 47 238 181 55.38 0.07 80 47 242 185 40.46 0.91 81 48 242 184 40.51 0.93 82 51 242 181 38.66 0.46 83 51 245 184 32.38 0.10 84 53 238 175 55.38 0.07 85 71 153 75 140.17 1.02 86 71 154 76 138.12 0.50 87 71 155 77 136.91 0.12 88 72 152 73 140.17 1.02 89 72 153 74 140.16 1.02 90 72 154 75 139.74 1.22 91 73 153 73 140.18 1.02 92 74 149 68 143.52 1.12 93 74 151 70 142.29 1.32 94 74 153 72 140.19 1.03 95 87 245 149 34.83 0.84 96 89 237 139 70.42 0.82 97 89 241 143 48.11 1.01 98 89 245 147 37.02 0.02 99 90 237 138 70.42 0.82 100 91 234 134 98.47 1.31 101 91 237 137 70.42 0.82 102 92 237 136 88.28 1.92 103 98 180 75 150.54 2.15 104 99 180 74 148.92 2.94 105 100 177 70 146.50 4.16 106 100 179 72 148.06 3.33 107 100 180 73 148.09 3.32 108 101 179 71 146.59 4.02 109 101 234 124 108.48 2.48 110 102 229 118 140.02 0.17 111 103 229 117 140.08 0.12 112 103 234 122 92.61 0.42 113 103 237 125 67.32 0.70 114 103 238 126 61.80 2.10 115 105 237 123 66.18 1.17 116 105 238 124 55.43 0.07 117 105 241 127 47.39 1.36 118 105 242 128 39.33 0.12 119 107 245 129 28.12 0.83 120 121 209 79 268.84 1.21 121 122 204 77 264.84 2.69 122 122 209 78 258.77 0.31 123 123 204 76 239.59 0.15 124 123 231 99 260.56 1.23 125 123 235 103 64.86 0.75 126 123 238 106 56.54 0.63 127 123 239 107 55.38 0.07 128 124 204 75 159.15 0.30 129 124 209 76 148.05 2.17 130 124 210 77 147.68 2.08 131 124 231 98 265.28 3.04 132 124 232 99 94.48 0.18 133 124 235 102 69.20 0.82 134 125 204 74 161.97 1.03 135 127 210 75 144.10 0.65 136 128 210 74 141.32 0.26 137 129 134 4 154.66 0.07 138 129 162 27 127.83 0.67 139 129 210 73 143.59 0.43 140 130 134 3 163.05 0.58 141 130 162 26 128.11 0.77 142 132 162 25 128.10 0.76 143 132 163 26 128.23 0.81 144 132 164 27 128.60 0.62 145 133 161 23 128.13 0.76 146 133 162 24 128.24 0.81 147 134 161 22 128.23 0.81 148 134 162 23 128.26 0.81 149 135 159 19 128.22 0.81 150 135 160 20 128.25 0.81 151 135 161 21 128.26 0.81 152 136 159 18 128.13 0.82 153 136 160 19 128.19 0.83 154 136 162 21 129.75 0.96 155 137 157 15 127.54 1.01 156 137 158 16 128.06 0.79 157 137 159 17 128.18 0.83 158 138 157 14 125.84 0.18 159 138 158 15 127.58 1.03 160 138 160 17 129.16 0.73 161 138 183 40 144.06 0.44 162 138 190 49 268.91 0.43 163 138 228 83 143.84 0.55 164 139 155 11 128.38 0.73 165 139 156 12 127.92 0.86 166 139 157 13 126.81 0.66 167 140 155 10 128.38 0.73 168 140 156 11 127.86 0.90 169 141 153 7 132.68 0.57 170 141 154 8 129.28 0.79 171 141 155 9 128.38 0.72 172 158 188 32 127.77 0.96 173 158 189 33 127.75 0.96 174 159 184 26 213.16 1.72 175 160 183 23 268.72 1.41 176 160 184 24 185.78 0.51 177 160 184 25 201.69 7.46 178 161 184 23 264.45 3.53 179 161 184 24 264.44 3.53 180 162 199 39 134.89 0.82 181 162 201 41 131.75 0.74 182 163 225 60 134.74 0.42 183 171 223 50 143.56 0.45 184 171 224 51 143.62 0.43 185 171 225 52 143.79 0.51 186 172 215 41 150.70 2.84 187 172 216 42 150.62 2.81 188 172 217 43 150.40 2.71 189 172 224 50 143.84 0.53 190 172 225 51 143.88 0.53 191 172 227 53 143.22 0.66 192 175 215 38 151.05 2.62 193 175 217 40 151.05 2.62 194 176 215 37 150.65 2.83 195 176 227 49 143.59 0.56 196 178 230 50 141.38 0.04 197 178 233 53 137.77 0.28 198 179 229 48 142.82 0.29 199 179 230 49 140.62 0.34 200 179 233 52 136.95 0.42 201 179 234 53 136.41 0.42 202 180 215 33 149.78 2.47 203 180 227 45 143.70 0.55 204 180 228 46 143.03 0.36 205 180 230 48 140.00 0.14 206 181 227 44 143.59 0.49 207 181 228 45 142.90 0.21 208 181 230 47 139.53 0.35 209 182 225 41 143.71 0.47 210 182 226 42 143.64 0.50 211 182 227 43 142.36 0.48 212 183 199 18 144.05 0.44 213 183 226 41 143.73 0.48 214 183 228 43 141.91 0.06 215 184 225 39 143.87 0.52 216 184 188 5 266.25 2.27 217 184 225 38 143.94 0.50 218 185 222 34 144.24 0.59 219 185 223 35 144.02 0.52 220 185 225 37 143.94 0.49 221 186 222 33 144.24 0.59 222 187 221 30 149.72 2.12 223 187 221 31 149.67 2.11 224 187 222 32 149.65 2.11 225 188 221 29 149.97 2.19 226 188 221 28 201.56 27.98 227 189 220 26 267.95 0.76 228 189 221 27 259.87 1.16 229 189 226 33 141.66 0.93 230 190 228 34 141.88 0.78 231 199 228 25 143.87 0.56 232 209 231 22 120.56 9.09 233 210 230 20 142.38 0.54 234 210 231 21 120.81 9.21 235 211 228 17 143.84 0.54 236 211 229 18 143.50 0.48 237 211 231 20 99.73 1.33 238 212 228 16 143.51 0.48 239 212 229 17 140.38 0.14 240 212 231 19 105.41 1.50 241 213 228 15 141.09 0.13 242 214 227 13 143.93 0.61 243 214 228 14 143.50 0.49 244 214 229 15 141.19 0.00 245 215 226 11 144.09 0.65 246 215 227 12 143.86 0.66 247 217 224 7 144.27 0.66 248 221 224 3 264.15 1.14 249 229 234 5 246.24 2.54 250 230 234 4 264.67 1.15 251 231 234 3 265.45 1.54 252 231 235 4 238.96 1.01 253 231 238 7 60.56 0.79 254 232 235 3 76.91 0.82 255 234 237 3 64.94 0.70 256 234 238 4 62.66 0.20 257 235 238 3 64.72 0.90 258 235 239 4 60.77 0.74 259 236 239 3 62.75 0.22 260 236 240 4 57.17 0.82 261 237 240 3 55.65 0.06 262 237 241 4 55.31 0.07 263 238 241 3 47.59 1.46 264 238 242 4 41.87 1.40 265 239 242 3 51.73 3.54 266 239 243 4 40.73 0.83 267 240 243 3 44.48 2.33 268 240 244 4 40.73 0.83 269 241 244 3 39.51 0.22 270 241 245 4 39.12 0.03 271 242 245 3 47.18 7.30