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 52.80 1.11 2 16 140 119 52.23 1.41 3 16 142 121 55.02 0.01 4 16 143 122 59.69 1.18 5 16 144 123 60.30 1.15 6 16 156 135 56.85 0.71 7 16 157 136 56.16 0.45 8 16 158 137 56.69 0.71 9 16 189 170 58.66 1.22 10 16 190 171 49.57 2.72 11 16 194 175 49.57 2.71 12 17 143 121 60.53 1.03 13 17 144 122 60.33 1.13 14 17 145 123 61.55 0.53 15 17 146 124 61.64 0.48 16 17 188 167 65.06 1.17 17 17 188 168 61.38 0.59 18 17 189 169 59.97 1.29 19 17 191 171 60.25 1.15 20 17 220 195 61.23 0.67 21 17 221 196 61.61 0.49 22 18 158 135 62.71 0.14 23 18 188 166 65.08 1.16 24 18 188 167 61.63 0.48 25 19 157 133 62.11 0.43 26 19 158 134 62.71 0.14 27 20 137 112 85.29 1.70 28 20 156 131 119.54 17.29 29 20 157 132 77.00 0.34 30 20 158 133 195.41 1.57 31 20 159 134 280.89 1.54 32 21 154 128 149.49 2.31 33 21 155 129 157.94 1.91 34 21 156 130 133.31 10.40 35 22 26 4 173.66 0.12 36 22 27 5 148.13 6.41 37 22 139 112 142.49 0.55 38 22 155 128 167.29 0.26 39 22 156 129 200.47 2.73 40 23 26 3 189.78 6.55 41 24 71 44 143.83 0.65 42 24 117 90 146.28 0.47 43 25 28 3 174.33 0.18 44 25 69 41 145.68 0.18 45 25 79 51 153.18 2.80 46 25 117 89 145.33 0.01 47 27 30 3 196.47 5.48 48 27 137 105 144.56 0.58 49 27 139 107 151.63 2.28 50 28 116 85 153.10 2.78 51 28 117 86 153.09 2.77 52 28 118 87 152.02 2.49 53 28 119 88 149.00 1.01 54 29 45 14 147.29 0.23 55 29 46 15 146.50 0.36 56 29 119 87 152.11 2.46 57 29 120 88 148.46 0.73 58 29 121 89 146.49 0.36 59 29 137 103 153.80 2.66 60 29 198 166 153.47 2.66 61 29 200 168 153.61 2.68 62 30 43 11 155.05 2.04 63 30 44 12 153.78 2.63 64 30 139 104 153.83 2.66 65 30 140 105 156.13 1.86 66 30 141 106 157.08 1.81 67 30 155 120 232.88 16.39 68 30 198 165 153.73 2.66 69 31 43 10 156.14 1.54 70 31 44 11 153.82 2.65 71 31 45 12 153.80 2.64 72 31 46 13 153.80 2.64 73 31 52 19 153.80 2.64 74 31 65 32 157.41 1.98 75 31 66 33 157.25 1.92 76 31 67 34 156.91 1.95 77 31 141 105 157.10 1.82 78 32 40 6 158.03 1.92 79 32 42 8 157.12 1.82 80 32 43 9 156.62 1.73 81 32 65 31 157.44 1.97 82 32 66 32 157.41 1.98 83 32 73 38 157.99 1.95 84 32 141 104 157.11 1.82 85 33 40 5 159.00 1.54 86 33 41 6 157.99 1.95 87 33 42 7 157.91 1.91 88 33 43 8 157.10 1.81 89 33 52 17 157.10 1.80 90 33 54 19 157.10 1.80 91 33 58 23 158.08 1.97 92 33 63 28 158.11 1.95 93 33 64 29 158.02 1.91 94 33 65 30 157.44 1.97 95 33 106 70 157.34 1.92 96 34 39 3 168.66 0.80 97 34 40 4 159.01 1.54 98 34 41 5 159.03 1.55 99 34 63 27 158.15 1.96 100 34 64 28 158.05 1.92 101 34 66 30 158.06 1.93 102 35 41 4 172.88 0.58 103 35 60 23 172.41 0.82 104 35 62 25 167.74 1.24 105 45 121 75 213.01 0.76 106 46 120 73 255.56 5.36 107 46 121 74 231.83 1.42 108 47 120 72 285.11 0.51 109 47 121 73 249.58 4.13 110 47 123 75 195.28 1.11 111 47 238 186 67.42 0.46 112 47 242 190 29.34 0.21 113 48 242 189 29.80 0.43 114 51 242 186 29.21 0.27 115 51 245 189 21.09 0.36 116 69 118 49 288.39 0.74 117 71 153 80 154.39 3.04 118 71 154 81 153.02 2.54 119 71 155 82 151.93 2.36 120 72 153 79 154.38 3.04 121 72 154 80 154.19 3.01 122 73 153 78 154.38 3.04 123 74 153 77 155.05 2.71 124 87 245 154 20.84 0.75 125 89 237 144 78.98 1.88 126 89 241 148 31.44 0.32 127 89 245 152 22.07 0.14 128 91 234 139 105.72 0.03 129 91 237 142 81.54 0.60 130 92 237 141 101.36 0.35 131 98 180 80 209.92 16.55 132 99 180 79 209.90 16.55 133 100 177 75 175.76 0.42 134 100 179 77 175.84 0.44 135 100 180 78 175.84 0.45 136 101 179 76 175.67 0.48 137 101 234 129 119.25 1.46 138 102 229 123 153.54 2.25 139 103 229 122 153.54 2.25 140 103 234 127 103.62 1.04 141 103 237 130 78.65 2.04 142 103 238 131 72.56 0.48 143 104 237 129 78.65 2.04 144 105 237 128 74.47 0.42 145 105 238 129 67.47 0.42 146 105 241 132 30.21 0.24 147 107 245 134 20.73 0.47 148 122 204 82 281.10 2.44 149 122 209 83 249.34 0.49 150 123 204 81 227.84 4.30 151 123 209 82 191.94 1.42 152 123 231 104 208.20 29.02 153 123 235 108 73.53 0.06 154 123 238 111 69.00 1.08 155 123 239 112 67.34 0.42 156 124 204 80 195.99 0.99 157 124 209 81 165.33 1.57 158 124 210 82 159.65 2.53 159 124 232 104 105.19 0.41 160 124 235 107 78.06 0.29 161 127 210 80 154.43 2.36 162 128 210 79 153.32 1.99 163 129 162 32 143.05 0.83 164 129 201 73 149.60 0.11 165 129 210 78 154.14 2.38 166 131 134 3 184.47 0.18 167 131 162 31 143.53 0.72 168 132 162 30 143.51 0.73 169 132 163 31 143.61 0.73 170 132 164 32 143.69 0.70 171 133 161 28 143.54 0.71 172 133 162 29 143.68 0.70 173 134 161 27 143.66 0.69 174 134 162 28 143.70 0.70 175 135 159 24 143.56 0.71 176 135 160 25 143.66 0.69 177 135 161 26 143.68 0.70 178 136 159 23 143.62 0.68 179 136 160 24 143.63 0.67 180 136 162 26 146.22 0.47 181 137 157 20 143.25 0.84 182 137 158 21 143.53 0.71 183 137 159 22 143.57 0.70 184 138 157 19 138.83 1.19 185 138 158 20 143.18 0.90 186 138 160 22 144.07 0.82 187 138 183 45 156.56 2.09 188 138 228 88 154.25 2.33 189 139 155 16 143.76 0.72 190 139 156 17 143.56 0.71 191 139 157 18 142.53 0.53 192 140 155 15 143.72 0.70 193 140 156 16 143.53 0.72 194 141 151 10 156.53 1.69 195 141 152 11 153.84 2.69 196 141 153 12 153.75 2.66 197 141 154 13 151.97 2.00 198 141 155 14 143.72 0.70 199 142 151 9 156.55 1.69 200 142 152 10 156.53 1.69 201 143 148 5 162.39 0.03 202 143 149 6 157.00 1.84 203 143 150 7 156.81 1.78 204 143 151 8 156.55 1.69 205 143 191 50 235.20 8.68 206 144 150 6 157.00 1.84 207 144 152 8 156.80 1.76 208 144 156 12 143.62 0.76 209 145 148 3 173.84 2.02 210 145 150 5 157.12 1.77 211 146 220 71 155.06 2.48 212 146 221 72 155.05 2.49 213 146 221 73 154.84 2.41 214 151 192 43 156.59 1.72 215 151 193 44 156.56 1.69 216 152 156 4 168.26 1.41 217 158 188 32 143.58 0.74 218 158 189 33 143.29 0.86 219 159 184 26 143.74 0.73 220 160 184 24 143.57 0.74 221 160 184 25 143.71 0.71 222 161 183 22 172.18 13.54 223 161 184 23 143.69 0.70 224 161 184 24 143.88 0.70 225 162 181 19 239.58 9.30 226 162 182 20 228.13 3.64 227 162 183 21 172.18 13.55 228 162 201 41 148.34 1.31 229 163 182 19 228.19 3.61 230 163 183 20 191.49 4.19 231 163 184 21 191.46 4.17 232 163 185 23 179.19 10.09 233 163 225 60 149.53 0.56 234 165 230 63 143.75 0.71 235 167 185 19 269.54 8.97 236 171 223 50 154.74 2.44 237 171 224 51 154.59 2.49 238 171 225 52 154.72 2.43 239 172 215 41 174.18 0.09 240 172 216 42 172.66 0.32 241 172 217 43 163.84 0.17 242 172 224 50 154.75 2.44 243 172 225 51 154.75 2.44 244 172 227 53 154.24 2.42 245 175 215 38 175.03 0.46 246 176 215 37 175.12 0.46 247 176 227 49 154.68 2.46 248 178 230 50 154.35 2.39 249 178 233 53 153.38 2.33 250 179 229 48 154.41 2.43 251 179 230 49 154.10 2.48 252 179 233 52 148.81 0.90 253 179 234 53 147.48 0.24 254 180 215 33 175.28 0.37 255 180 227 45 154.68 2.44 256 180 228 46 154.42 2.44 257 180 230 48 154.08 2.50 258 181 199 20 156.62 2.03 259 181 210 27 155.52 2.23 260 181 211 28 156.09 1.94 261 181 227 44 154.53 2.42 262 181 228 45 154.28 2.42 263 181 229 46 154.26 2.43 264 181 230 47 154.03 2.48 265 182 225 41 154.78 2.44 266 182 226 42 154.67 2.49 267 182 227 43 154.15 2.46 268 183 225 40 154.83 2.47 269 183 226 41 154.71 2.48 270 183 228 43 154.45 2.42 271 184 225 39 154.84 2.46 272 184 188 5 288.26 0.43 273 185 222 34 159.77 1.43 274 185 223 35 155.91 2.38 275 185 225 37 155.62 2.25 276 186 222 33 159.85 1.39 277 187 221 30 168.13 0.64 278 187 221 31 165.97 1.56 279 187 222 32 159.78 1.43 280 188 221 29 171.58 1.00 281 188 221 28 183.00 4.95 282 189 221 27 225.15 17.36 283 189 226 33 154.20 2.42 284 190 228 34 153.71 2.18 285 199 228 25 154.34 2.37 286 209 231 22 135.66 6.61 287 210 230 20 153.52 2.07 288 210 231 21 132.47 8.21 289 210 232 22 127.72 10.45 290 211 228 17 154.37 2.39 291 211 229 18 153.74 2.19 292 211 231 20 108.88 0.05 293 212 228 16 154.19 2.41 294 212 229 17 153.18 2.05 295 212 231 19 131.62 8.60 296 213 228 15 153.38 2.15 297 214 227 13 154.30 2.43 298 214 228 14 154.00 2.46 299 214 229 15 153.35 2.16 300 215 226 11 154.59 2.51 301 215 227 12 154.18 2.39 302 216 227 11 154.09 2.44 303 217 224 7 235.08 19.92 304 221 224 3 287.32 1.32 305 229 234 5 286.18 2.23 306 230 234 4 287.85 1.49 307 231 235 4 262.35 9.95 308 231 238 7 71.72 0.20 309 232 235 3 85.55 1.05 310 234 237 3 78.12 2.24 311 234 238 4 72.84 0.37 312 235 238 3 72.85 0.38 313 235 239 4 71.65 0.21 314 236 239 3 72.70 0.40 315 236 240 4 71.53 0.15 316 237 240 3 67.42 0.46 317 237 241 4 67.35 0.46 318 238 241 3 54.28 4.26 319 238 242 4 30.22 0.24 320 239 242 3 46.28 8.27 321 239 243 4 30.23 0.24 322 240 243 3 31.37 0.81 323 240 244 4 30.23 0.24 324 241 244 3 47.07 9.09 325 241 245 4 28.64 0.06 326 242 245 3 47.54 8.86