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 57.44 1.03 2 16 140 119 58.85 0.36 3 16 142 121 57.59 1.09 4 16 143 122 62.27 1.73 5 16 144 123 63.69 1.02 6 16 156 135 60.59 1.06 7 16 157 136 60.59 1.06 8 16 158 137 59.23 0.28 9 16 189 170 60.52 0.41 10 16 190 171 57.20 0.94 11 16 194 175 57.34 1.01 12 17 143 121 63.69 1.02 13 17 144 122 63.69 1.02 14 17 145 123 67.16 0.65 15 17 146 124 68.59 0.05 16 17 188 167 64.00 0.88 17 17 188 168 63.93 0.90 18 17 189 169 63.63 1.02 19 17 191 171 63.62 1.03 20 17 220 195 63.91 0.90 21 17 221 196 63.91 0.89 22 18 188 166 64.00 0.88 23 18 188 167 63.93 0.90 24 19 157 133 69.33 0.13 25 19 158 134 64.27 0.73 26 20 137 112 83.55 0.09 27 20 156 131 92.03 4.34 28 20 157 132 74.22 0.07 29 20 158 133 130.55 23.59 30 20 159 134 269.56 7.04 31 21 71 47 142.38 0.46 32 21 154 128 148.87 3.79 33 21 155 129 156.24 0.57 34 21 156 130 115.56 1.09 35 22 26 4 168.42 0.37 36 22 27 5 159.63 0.84 37 22 71 46 144.38 0.61 38 22 139 112 138.62 0.08 39 22 155 128 167.50 0.80 40 22 156 129 209.84 4.89 41 23 26 3 174.28 0.96 42 23 71 45 151.25 0.73 43 24 71 44 151.25 0.73 44 24 79 52 151.98 0.74 45 25 28 3 175.76 0.36 46 25 69 41 149.63 0.11 47 25 79 51 151.99 0.74 48 25 117 89 144.38 0.45 49 27 30 3 181.00 2.36 50 27 137 105 144.77 0.43 51 27 139 107 150.49 0.73 52 27 157 125 253.53 9.05 53 28 116 85 151.89 0.78 54 28 117 86 151.88 0.78 55 28 118 87 151.16 0.55 56 28 119 88 151.02 0.62 57 29 45 14 150.73 0.53 58 29 46 15 150.06 0.71 59 29 119 87 151.25 0.56 60 29 120 88 150.97 0.61 61 29 121 89 149.88 0.80 62 29 198 166 151.53 0.74 63 29 200 168 151.56 0.72 64 30 43 11 152.01 0.74 65 30 44 12 151.85 0.73 66 30 139 104 151.98 0.73 67 30 140 105 152.15 0.81 68 30 141 106 155.75 0.09 69 30 155 120 174.12 2.54 70 30 198 165 151.58 0.72 71 31 43 10 152.27 0.77 72 31 44 11 152.00 0.74 73 31 45 12 152.00 0.74 74 31 46 13 151.99 0.73 75 31 52 19 152.01 0.74 76 31 65 32 155.84 0.04 77 31 65 33 155.76 0.07 78 31 66 34 155.40 0.09 79 31 141 105 155.99 0.20 80 32 40 6 157.05 0.37 81 32 42 8 155.81 0.06 82 32 43 9 155.24 0.18 83 32 65 31 156.09 0.15 84 32 65 32 155.85 0.04 85 32 73 38 156.56 0.32 86 32 141 104 155.77 0.10 87 33 40 5 157.25 0.36 88 33 41 6 157.09 0.35 89 33 42 7 156.25 0.09 90 33 43 8 155.85 0.05 91 33 52 17 156.05 0.14 92 33 54 19 156.09 0.16 93 33 58 23 157.08 0.35 94 33 63 28 156.91 0.27 95 33 64 29 156.61 0.20 96 33 65 30 156.12 0.18 97 33 104 68 156.88 0.34 98 33 106 70 156.08 0.17 99 34 39 3 165.33 1.85 100 34 40 4 157.25 0.36 101 34 41 5 157.24 0.36 102 34 63 27 157.07 0.33 103 34 64 28 156.71 0.15 104 34 65 30 156.57 0.22 105 37 41 4 166.88 0.28 106 37 60 23 161.99 0.28 107 45 121 75 222.55 1.56 108 46 121 74 261.26 3.08 109 47 121 73 281.22 0.90 110 47 123 75 197.25 1.92 111 47 238 186 45.55 0.02 112 47 242 190 32.10 1.09 113 48 242 189 32.10 1.09 114 51 242 186 30.57 0.34 115 51 245 189 22.09 0.42 116 71 153 80 152.75 0.98 117 71 154 81 151.97 0.74 118 71 155 82 151.65 0.82 119 72 153 79 152.37 0.86 120 72 154 80 151.98 0.74 121 73 152 77 153.36 0.80 122 73 153 78 152.38 0.87 123 74 153 77 152.81 1.06 124 87 245 154 25.91 1.50 125 89 237 144 76.23 1.24 126 89 241 148 34.34 0.03 127 89 245 152 22.50 0.21 128 91 234 139 106.69 0.20 129 91 237 142 78.80 0.03 130 92 237 141 95.59 2.13 131 98 180 80 154.80 0.18 132 99 180 79 154.03 0.41 133 100 177 75 151.30 0.46 134 100 179 77 152.63 0.24 135 100 180 78 153.25 0.07 136 101 179 76 152.56 0.28 137 101 234 129 108.39 0.37 138 102 229 123 153.22 0.51 139 103 229 122 152.19 0.01 140 103 234 127 102.86 1.51 141 103 237 130 75.45 1.23 142 103 238 131 55.52 5.04 143 105 237 128 72.54 2.50 144 105 238 129 44.36 0.02 145 105 241 132 32.12 1.09 146 105 242 133 30.59 0.34 147 107 245 134 22.08 0.42 148 123 204 81 280.62 3.69 149 123 231 104 146.93 3.67 150 123 235 108 74.96 0.58 151 123 238 111 52.73 3.60 152 124 204 80 182.84 0.16 153 124 209 81 171.28 1.33 154 124 210 82 167.02 0.39 155 124 231 103 182.10 1.91 156 124 232 104 107.49 0.09 157 124 235 107 79.75 0.30 158 125 204 79 189.09 2.96 159 127 210 80 158.72 0.21 160 128 210 79 154.68 0.12 161 129 134 4 166.28 0.31 162 129 162 32 137.84 0.29 163 129 210 78 154.74 0.12 164 130 134 3 182.21 0.23 165 130 162 31 140.69 0.89 166 132 162 30 140.81 0.95 167 132 163 31 142.06 0.38 168 132 164 32 142.18 0.32 169 133 162 29 142.06 0.38 170 134 161 27 142.09 0.40 171 134 162 28 142.28 0.47 172 135 159 24 141.16 0.79 173 135 160 25 142.09 0.40 174 135 161 26 142.11 0.39 175 136 159 23 140.99 0.87 176 136 160 24 142.03 0.35 177 136 162 26 144.83 0.48 178 137 157 20 139.93 0.57 179 137 158 21 140.83 0.83 180 137 159 22 140.97 0.87 181 138 157 19 138.54 0.06 182 138 158 20 138.64 0.07 183 138 160 22 144.52 0.55 184 138 183 45 155.35 0.14 185 138 228 88 154.91 0.19 186 139 155 16 144.10 0.54 187 139 156 17 140.63 0.73 188 139 157 18 138.61 0.08 189 140 155 15 143.68 0.76 190 140 156 16 141.03 0.79 191 141 152 11 151.75 0.68 192 141 153 12 151.69 0.65 193 141 154 13 151.16 0.77 194 141 155 14 144.08 0.57 195 142 152 10 151.75 0.68 196 142 194 54 285.19 2.83 197 143 148 5 163.11 0.08 198 143 149 6 154.99 0.01 199 143 150 7 154.97 0.01 200 143 191 50 195.56 0.43 201 144 150 6 155.44 0.24 202 144 152 8 154.75 0.07 203 144 156 12 144.08 0.57 204 145 148 3 179.62 3.12 205 145 149 4 157.11 0.42 206 145 150 5 156.61 0.68 207 146 220 71 153.59 0.61 208 146 221 72 152.94 0.27 209 152 156 4 171.13 0.79 210 158 188 32 143.14 0.96 211 158 189 33 143.13 0.97 212 159 184 26 165.35 0.59 213 160 183 23 173.65 1.21 214 160 184 24 165.35 0.59 215 160 184 25 164.69 0.88 216 161 183 22 180.66 1.75 217 161 184 23 168.89 1.16 218 161 184 24 168.92 1.12 219 162 181 19 281.68 4.86 220 162 182 20 259.05 6.28 221 162 183 21 180.68 1.76 222 162 201 41 150.34 0.57 223 163 182 19 270.41 0.77 224 163 183 20 239.26 16.17 225 163 184 21 208.96 1.02 226 163 185 23 180.62 1.73 227 163 225 60 150.72 0.73 228 171 223 50 154.49 0.20 229 171 225 52 154.83 0.21 230 172 215 41 155.09 0.10 231 172 216 42 155.02 0.12 232 172 217 43 155.05 0.10 233 172 224 50 154.99 0.15 234 172 225 51 154.99 0.15 235 172 227 53 154.75 0.15 236 175 215 38 155.19 0.14 237 176 215 37 155.18 0.17 238 176 227 49 154.91 0.18 239 178 230 50 154.78 0.23 240 178 233 53 151.69 0.69 241 179 229 48 154.82 0.21 242 179 230 49 154.69 0.18 243 179 233 52 151.11 0.51 244 179 234 53 149.31 0.20 245 180 215 33 155.15 0.15 246 180 227 45 154.92 0.18 247 180 228 46 154.84 0.21 248 180 230 48 153.50 0.70 249 181 227 44 154.91 0.18 250 181 228 45 154.83 0.20 251 181 230 47 152.09 0.66 252 182 225 41 154.91 0.20 253 182 226 42 154.91 0.19 254 182 227 43 154.41 0.31 255 183 199 18 155.23 0.18 256 183 226 41 154.91 0.18 257 183 228 43 154.76 0.16 258 184 188 5 250.56 2.25 259 185 222 34 155.24 0.20 260 185 223 35 155.16 0.21 261 185 225 37 155.12 0.21 262 186 222 33 155.24 0.20 263 187 221 30 155.56 0.11 264 187 221 31 155.55 0.11 265 187 222 32 155.20 0.21 266 188 221 29 155.63 0.07 267 188 221 28 157.81 1.12 268 189 221 27 187.18 13.51 269 189 226 33 154.90 0.20 270 190 228 34 154.81 0.21 271 199 228 25 154.91 0.17 272 209 231 22 127.50 4.01 273 210 230 20 154.77 0.12 274 210 231 21 142.99 5.62 275 210 232 22 110.42 0.26 276 211 228 17 154.84 0.14 277 211 229 18 154.75 0.13 278 211 231 20 115.28 0.38 279 212 228 16 154.72 0.12 280 212 229 17 154.68 0.12 281 212 231 19 112.77 0.91 282 213 228 15 154.69 0.11 283 214 227 13 154.93 0.15 284 214 228 14 154.83 0.15 285 214 229 15 154.71 0.12 286 215 226 11 155.06 0.19 287 215 227 12 154.94 0.15 288 216 226 10 155.03 0.19 289 216 227 11 155.03 0.19 290 217 224 7 196.49 5.93 291 221 224 3 274.60 0.79 292 231 235 4 267.76 0.20 293 231 238 7 55.48 4.99 294 232 235 3 83.30 0.22 295 234 237 3 70.97 0.32 296 234 238 4 69.28 1.14 297 235 238 3 55.58 5.02 298 235 239 4 46.47 0.48 299 236 239 3 58.21 6.33 300 236 240 4 45.55 0.03 301 237 240 3 43.56 0.23 302 237 241 4 43.28 0.36 303 238 241 3 34.34 0.02 304 238 242 4 32.22 1.03 305 239 242 3 33.41 0.45 306 239 243 4 32.23 1.03 307 240 243 3 49.60 8.53 308 240 244 4 30.77 0.30 309 241 244 3 30.78 0.39 310 241 245 4 30.21 0.12 311 242 245 3 48.37 9.19