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 16 139 118 49.00 1.91 2 16 140 119 48.98 1.89 3 16 142 121 49.03 1.91 4 16 143 122 60.25 2.83 5 16 144 123 60.65 2.66 6 16 156 135 56.00 1.54 7 16 157 136 50.48 1.96 8 16 158 137 49.73 1.59 9 16 189 170 59.97 2.70 10 16 190 171 45.31 0.24 11 16 194 175 45.32 0.24 12 17 143 121 61.49 2.33 13 17 144 122 61.33 2.35 14 17 145 123 67.50 0.49 15 17 146 124 68.59 0.05 16 17 188 167 61.55 2.44 17 17 188 168 61.18 2.49 18 17 189 169 60.44 2.67 19 17 191 171 60.66 2.64 20 17 220 195 61.37 2.39 21 17 221 196 61.33 2.35 22 18 158 135 66.77 1.41 23 18 188 166 61.55 2.44 24 18 188 167 61.42 2.38 25 19 157 133 70.50 0.46 26 19 158 134 66.76 1.41 27 20 137 112 82.85 0.18 28 20 156 131 92.25 4.23 29 20 157 132 72.54 1.12 30 20 158 133 130.16 27.77 31 20 159 134 281.12 3.71 32 21 71 47 137.53 0.21 33 21 154 128 144.46 3.58 34 21 155 129 152.61 0.33 35 21 156 130 130.85 10.85 36 22 26 4 166.53 0.01 37 22 27 5 157.68 0.12 38 22 71 46 137.77 0.21 39 22 139 112 137.19 0.06 40 22 155 128 164.74 2.39 41 22 156 129 219.93 3.90 42 23 26 3 173.38 3.04 43 24 71 44 143.83 0.39 44 25 28 3 172.94 1.05 45 25 79 51 149.25 0.82 46 25 117 89 138.46 0.49 47 27 30 3 222.63 18.89 48 27 137 105 138.53 0.50 49 27 139 107 142.16 0.48 50 28 116 85 149.28 0.83 51 28 117 86 149.21 0.81 52 28 118 87 148.59 0.94 53 28 119 88 144.38 0.45 54 29 45 14 144.13 0.32 55 29 46 15 144.05 0.28 56 29 119 87 148.86 0.81 57 29 120 88 144.39 0.44 58 29 121 89 144.05 0.28 59 29 137 103 149.33 0.80 60 29 198 166 148.62 0.69 61 29 200 168 148.31 0.78 62 30 43 11 149.46 0.72 63 30 44 12 149.22 0.81 64 30 139 104 149.41 0.81 65 30 140 105 149.54 0.80 66 30 141 106 153.07 0.09 67 30 155 120 175.75 1.85 68 30 198 165 148.79 0.60 69 31 43 10 151.80 0.28 70 31 44 11 149.41 0.83 71 31 45 12 149.41 0.83 72 31 46 13 149.39 0.82 73 31 52 19 149.37 0.80 74 31 66 32 153.06 0.14 75 31 67 33 153.03 0.15 76 31 68 34 152.66 0.15 77 31 141 105 153.10 0.10 78 32 40 6 153.88 0.23 79 32 42 8 153.12 0.12 80 32 43 9 152.78 0.20 81 32 66 31 153.42 0.12 82 32 67 32 153.10 0.17 83 32 73 38 153.80 0.17 84 32 141 104 153.12 0.10 85 33 40 5 155.06 0.81 86 33 41 6 153.88 0.24 87 33 42 7 153.31 0.04 88 33 43 8 153.21 0.07 89 33 54 19 153.14 0.10 90 33 58 23 153.78 0.23 91 33 63 28 153.85 0.21 92 33 64 29 153.87 0.21 93 33 66 30 153.53 0.10 94 33 104 68 153.38 0.03 95 33 106 70 153.43 0.09 96 34 39 3 174.27 0.78 97 34 40 4 155.06 0.81 98 34 41 5 155.06 0.81 99 34 63 27 153.91 0.21 100 34 64 28 153.88 0.22 101 34 67 30 153.87 0.21 102 37 41 4 166.53 1.43 103 37 60 23 161.63 0.10 104 45 121 75 218.44 0.61 105 46 120 73 282.64 3.03 106 46 121 74 250.14 1.32 107 47 121 73 282.33 2.98 108 47 123 75 198.46 0.53 109 47 238 186 59.20 1.20 110 47 242 190 32.59 0.84 111 48 242 189 32.60 0.84 112 51 242 186 31.09 0.09 113 51 245 189 22.09 0.42 114 71 153 80 149.60 0.82 115 71 154 81 149.03 0.77 116 71 155 82 148.31 1.08 117 72 153 79 149.57 0.80 118 72 154 80 149.54 0.81 119 73 153 78 149.58 0.83 120 74 153 77 149.58 0.83 121 87 245 154 25.92 1.49 122 89 237 144 76.20 0.89 123 89 241 148 45.03 7.06 124 89 245 152 22.52 0.22 125 91 234 139 106.03 0.26 126 91 237 142 78.64 0.04 127 92 237 141 95.59 2.14 128 98 175 75 149.71 0.69 129 98 180 80 152.66 0.29 130 99 180 79 151.88 0.10 131 100 177 75 149.81 0.71 132 100 179 77 151.44 0.06 133 100 180 78 151.81 0.24 134 101 179 76 151.06 0.04 135 101 234 129 114.12 3.24 136 102 229 123 152.13 0.40 137 103 229 122 152.16 0.39 138 103 234 127 103.40 1.44 139 103 237 130 74.98 1.30 140 103 238 131 67.67 1.14 141 105 237 128 73.93 1.80 142 105 238 129 59.67 1.43 143 105 241 132 32.61 0.84 144 105 242 133 31.09 0.09 145 107 245 134 22.09 0.42 146 122 209 83 282.92 2.83 147 123 231 104 151.55 0.21 148 123 235 108 71.27 0.28 149 123 238 111 60.63 1.79 150 123 239 112 59.02 1.29 151 124 204 80 185.37 0.66 152 124 209 81 170.03 0.42 153 124 210 82 168.31 0.26 154 124 231 103 272.20 5.08 155 124 232 104 107.25 0.04 156 124 235 107 76.77 0.32 157 125 204 79 187.34 0.34 158 127 210 80 158.72 0.21 159 128 210 79 152.56 0.35 160 129 134 4 164.44 0.68 161 129 162 32 137.19 0.07 162 129 210 78 152.87 0.41 163 130 134 3 182.91 0.12 164 130 162 31 137.53 0.14 165 132 162 30 137.55 0.15 166 132 163 31 137.63 0.18 167 132 164 32 137.75 0.19 168 133 162 29 137.68 0.17 169 134 161 27 137.69 0.17 170 134 162 28 137.77 0.14 171 135 159 24 137.58 0.14 172 135 160 25 137.74 0.14 173 135 161 26 137.75 0.14 174 136 159 23 137.57 0.14 175 136 160 24 137.59 0.14 176 136 162 26 138.50 0.48 177 137 157 20 137.52 0.12 178 137 158 21 137.56 0.14 179 137 159 22 137.58 0.14 180 138 157 19 137.17 0.05 181 138 158 20 137.21 0.04 182 138 160 22 137.92 0.19 183 138 183 45 153.40 0.07 184 138 228 88 152.99 0.37 185 139 155 16 137.89 0.20 186 139 156 17 137.53 0.13 187 139 157 18 137.20 0.04 188 140 155 15 137.84 0.22 189 140 156 16 137.61 0.17 190 141 152 11 148.97 0.71 191 141 153 12 148.75 0.67 192 141 154 13 143.41 0.60 193 141 155 14 137.84 0.22 194 142 152 10 149.31 0.83 195 143 148 5 157.87 0.03 196 143 149 6 152.91 0.01 197 143 150 7 152.55 0.08 198 143 191 50 200.12 0.88 199 144 150 6 152.91 0.02 200 144 152 8 152.47 0.09 201 144 156 12 137.82 0.23 202 145 148 3 173.65 1.19 203 145 149 4 157.83 0.01 204 145 150 5 152.99 0.00 205 146 220 71 151.46 0.70 206 146 221 72 151.47 0.70 207 152 156 4 165.28 0.51 208 158 188 32 137.81 0.21 209 158 189 33 137.74 0.23 210 159 184 26 170.12 2.96 211 160 183 23 171.03 2.53 212 160 184 24 162.85 0.81 213 160 184 25 162.75 0.72 214 161 183 22 178.52 2.91 215 161 184 23 171.03 2.52 216 161 184 24 171.02 2.52 217 162 181 19 281.70 0.61 218 162 182 20 256.40 13.26 219 162 183 21 186.18 0.95 220 163 182 19 277.29 2.88 221 163 183 20 205.30 2.51 222 163 184 21 205.24 2.52 223 163 185 23 186.17 0.95 224 163 225 60 140.97 0.13 225 167 185 19 284.93 1.03 226 171 223 50 152.66 0.20 227 171 225 52 152.72 0.25 228 172 215 41 153.16 0.01 229 174 215 39 153.15 0.01 230 176 215 37 153.19 0.04 231 176 227 49 152.79 0.24 232 178 230 50 152.74 0.24 233 178 233 53 149.98 0.65 234 179 229 48 152.78 0.24 235 179 230 49 152.46 0.29 236 179 233 52 148.91 0.95 237 179 234 53 148.38 0.86 238 180 215 33 153.09 0.14 239 180 227 45 152.81 0.24 240 180 228 46 152.78 0.24 241 180 229 47 152.34 0.23 242 180 230 48 151.77 0.08 243 181 227 44 152.75 0.25 244 181 228 45 152.62 0.23 245 181 230 47 150.03 0.68 246 182 225 41 152.81 0.24 247 182 226 42 152.77 0.25 248 182 227 43 152.18 0.29 249 183 199 18 153.06 0.10 250 183 226 41 152.81 0.24 251 183 228 43 152.52 0.20 252 184 188 5 275.39 4.33 253 185 222 34 153.43 0.10 254 185 223 35 153.09 0.24 255 185 225 37 152.84 0.21 256 186 222 33 153.44 0.11 257 187 221 30 153.61 0.09 258 187 221 31 153.52 0.12 259 187 222 32 153.44 0.12 260 188 221 29 153.80 0.18 261 188 221 28 153.83 0.21 262 189 221 27 170.13 8.36 263 189 226 33 152.78 0.41 264 190 228 34 152.78 0.39 265 199 228 25 153.00 0.36 266 209 231 22 150.15 0.73 267 210 230 20 152.87 0.41 268 210 231 21 151.03 0.41 269 210 232 22 112.22 0.64 270 211 228 17 152.97 0.36 271 211 229 18 152.81 0.39 272 211 231 20 110.85 0.04 273 212 228 16 152.66 0.31 274 212 229 17 152.43 0.41 275 212 231 19 112.22 0.64 276 213 228 15 152.44 0.42 277 214 227 13 152.97 0.35 278 214 228 14 152.80 0.39 279 214 229 15 152.45 0.41 280 215 226 11 152.99 0.35 281 215 227 12 152.93 0.34 282 217 224 7 172.17 6.23 283 221 224 3 285.21 2.06 284 231 235 4 279.58 5.05 285 231 238 7 61.51 1.94 286 232 235 3 81.94 0.02 287 234 237 3 71.30 0.43 288 234 238 4 69.39 1.20 289 235 238 3 69.57 1.10 290 235 239 4 68.65 1.56 291 236 239 3 71.33 0.22 292 236 240 4 60.79 2.00 293 237 240 3 59.61 2.06 294 237 241 4 57.44 1.66 295 238 241 3 46.93 6.80 296 238 242 4 32.61 0.84 297 239 242 3 32.61 0.84 298 239 243 4 32.60 0.84 299 240 243 3 48.95 8.86 300 240 244 4 31.11 0.10 301 241 244 3 31.13 0.07 302 241 245 4 29.54 0.21 303 242 245 3 48.87 8.94