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 16 134 116 62.74 0.57 2 16 135 117 62.76 0.58 3 16 137 119 62.80 0.60 4 16 138 120 67.05 0.31 5 16 139 121 67.22 0.23 6 16 151 133 63.01 0.52 7 16 152 134 62.90 0.57 8 16 153 135 62.80 0.60 9 16 186 168 65.55 0.39 10 16 187 169 52.82 5.11 11 16 188 170 61.82 0.60 12 16 191 173 52.82 5.11 13 17 138 119 67.23 0.24 14 17 139 120 67.23 0.24 15 17 140 121 67.34 0.27 16 17 141 122 67.34 0.27 17 17 184 165 67.37 0.26 18 17 185 166 67.33 0.27 19 17 186 167 67.11 0.29 20 17 188 169 67.22 0.24 21 17 212 193 67.28 0.26 22 17 213 194 67.30 0.27 23 18 153 133 68.18 0.52 24 18 184 164 67.38 0.26 25 18 185 165 67.34 0.27 26 19 152 131 70.10 0.17 27 19 153 132 67.50 0.18 28 20 132 110 83.67 0.88 29 20 151 129 160.82 0.52 30 20 152 130 117.55 21.09 31 20 153 131 198.52 0.27 32 20 154 132 284.80 0.89 33 21 149 126 160.84 0.54 34 21 150 127 160.87 0.54 35 21 151 128 161.81 1.01 36 22 26 4 166.70 0.65 37 22 27 5 163.19 1.11 38 22 134 110 140.68 0.97 39 22 150 126 166.15 0.87 40 22 151 127 202.16 0.84 41 23 26 3 199.44 8.55 42 24 68 44 143.75 0.58 43 25 28 3 168.85 0.43 44 27 30 3 170.56 0.13 45 27 132 103 143.91 0.65 46 27 134 105 150.69 0.24 47 27 152 123 287.03 1.03 48 28 115 85 146.30 0.49 49 28 116 86 146.27 0.48 50 29 42 13 158.52 0.79 51 29 43 14 145.93 0.33 52 29 44 15 145.89 0.34 53 29 116 85 150.22 1.07 54 29 117 86 146.25 0.48 55 29 118 87 145.89 0.34 56 29 132 101 158.18 1.00 57 29 195 164 157.12 0.95 58 29 197 166 157.53 0.99 59 30 41 11 158.85 0.82 60 30 42 12 158.76 0.81 61 30 134 102 158.60 0.88 62 30 135 103 158.91 0.79 63 30 136 104 160.80 0.51 64 30 150 118 167.97 0.01 65 30 195 163 157.96 0.75 66 31 41 10 158.96 0.81 67 31 42 11 158.80 0.79 68 31 43 12 158.84 0.82 69 31 44 13 158.79 0.79 70 31 50 19 158.82 0.78 71 31 63 32 161.99 1.12 72 31 64 33 162.08 1.16 73 31 65 34 161.30 1.48 74 31 136 103 160.84 0.53 75 32 38 6 162.72 1.08 76 32 40 8 161.22 0.40 77 32 41 9 160.31 0.35 78 32 63 31 162.15 1.16 79 32 64 32 162.12 1.17 80 32 70 38 162.38 1.27 81 32 136 102 160.85 0.52 82 33 38 5 162.75 1.08 83 33 39 6 162.66 1.04 84 33 40 7 162.28 0.90 85 33 41 8 160.91 0.54 86 33 50 17 161.81 0.99 87 33 52 19 161.69 0.94 88 33 56 23 162.64 1.03 89 33 61 28 162.75 1.10 90 33 62 29 162.70 1.11 91 33 63 30 162.58 1.06 92 33 101 68 162.62 1.04 93 33 103 70 162.59 1.05 94 34 37 3 167.65 0.80 95 34 38 4 162.76 1.08 96 34 39 5 162.75 1.07 97 34 61 27 162.76 1.10 98 34 62 28 162.71 1.11 99 34 64 30 162.69 1.10 100 35 39 4 170.38 0.74 101 35 58 23 168.55 0.18 102 38 190 150 286.63 0.28 103 43 118 73 214.37 0.57 104 44 117 71 240.34 1.88 105 44 118 72 240.18 1.81 106 45 117 70 269.27 2.55 107 45 118 71 240.25 1.83 108 45 120 73 194.99 0.07 109 45 231 184 50.91 2.21 110 45 235 188 31.82 0.32 111 46 117 69 287.00 0.21 112 46 235 187 31.86 0.30 113 49 235 184 31.77 0.29 114 49 238 187 21.82 0.57 115 51 231 178 48.39 2.48 116 66 115 47 286.14 0.16 117 68 148 78 160.71 1.40 118 68 149 79 158.63 0.71 119 68 150 80 157.36 0.75 120 69 148 77 160.67 1.40 121 69 149 78 158.93 0.84 122 70 148 76 160.70 1.41 123 71 148 75 160.69 1.41 124 84 238 152 23.35 0.20 125 86 230 142 76.52 0.15 126 86 234 146 41.55 2.54 127 86 238 150 23.78 0.41 128 88 227 137 105.89 0.96 129 88 230 140 80.35 0.32 130 89 230 139 95.47 0.33 131 95 175 78 218.98 26.39 132 96 175 77 167.06 0.52 133 97 172 73 167.00 0.51 134 97 174 75 167.00 0.50 135 97 175 76 167.00 0.51 136 98 174 74 166.91 0.53 137 98 227 127 107.44 1.10 138 99 222 121 156.69 1.45 139 100 222 120 156.55 1.39 140 100 227 125 97.92 1.61 141 100 230 128 75.28 0.69 142 100 231 129 52.65 1.38 143 102 230 126 74.03 0.37 144 102 231 127 48.39 2.49 145 102 234 130 31.96 0.30 146 102 235 131 31.85 0.30 147 104 238 132 21.23 0.31 148 118 202 84 285.32 2.06 149 119 201 82 265.06 8.07 150 119 202 83 251.43 3.67 151 120 201 81 239.29 9.73 152 120 202 82 189.56 1.44 153 120 224 104 273.32 7.56 154 120 228 108 75.78 0.42 155 120 231 111 53.11 1.61 156 121 201 80 187.14 2.07 157 121 202 81 174.20 0.91 158 121 203 82 161.27 0.56 159 121 224 103 287.23 0.62 160 121 225 104 106.92 0.86 161 121 228 107 78.25 0.58 162 123 203 80 157.61 1.23 163 124 203 79 155.87 1.90 164 125 129 4 163.74 1.36 165 125 157 32 142.21 0.46 166 125 203 78 157.25 1.39 167 126 129 3 180.97 1.05 168 126 157 31 143.53 0.58 169 127 157 30 143.54 0.58 170 127 158 31 143.62 0.58 171 127 159 32 143.63 0.58 172 128 156 28 143.55 0.59 173 128 157 29 143.62 0.58 174 129 156 27 143.63 0.58 175 129 157 28 143.66 0.59 176 130 154 24 143.59 0.58 177 130 155 25 143.63 0.58 178 130 156 26 143.65 0.58 179 131 153 22 143.59 0.58 180 131 154 23 143.59 0.58 181 131 155 24 143.64 0.58 182 131 157 26 143.91 0.65 183 132 152 20 142.71 0.79 184 132 153 21 143.52 0.59 185 132 154 22 143.56 0.60 186 133 152 19 140.66 0.96 187 133 153 20 142.78 0.82 188 133 155 22 143.77 0.58 189 133 178 45 160.68 0.70 190 133 221 88 157.28 1.39 191 134 150 16 143.68 0.59 192 134 151 17 143.53 0.59 193 134 152 18 140.67 0.98 194 135 150 15 143.63 0.58 195 135 151 16 143.45 0.66 196 136 146 10 159.13 0.86 197 136 147 11 158.50 0.89 198 136 148 12 158.12 0.89 199 136 149 13 151.25 0.49 200 136 150 14 143.63 0.59 201 137 146 9 159.13 0.86 202 137 147 10 159.12 0.87 203 137 189 52 287.09 0.04 204 137 191 54 286.48 0.21 205 138 143 5 164.28 0.14 206 138 144 6 159.76 0.70 207 138 145 7 159.36 0.85 208 138 146 8 159.13 0.86 209 138 188 50 212.85 2.09 210 138 189 51 286.48 0.21 211 139 145 6 159.45 0.85 212 139 147 8 159.23 0.87 213 139 151 12 143.62 0.60 214 140 143 3 169.92 1.21 215 140 144 4 161.11 0.56 216 140 145 5 160.22 0.48 217 141 212 71 158.22 1.10 218 141 213 72 158.34 1.15 219 141 214 73 158.24 1.09 220 146 189 43 159.21 0.88 221 147 151 4 164.38 0.39 222 153 180 27 143.59 0.60 223 153 185 32 143.40 0.67 224 153 186 33 143.28 0.61 225 153 187 34 142.99 0.65 226 154 180 26 143.77 0.58 227 155 179 24 143.34 0.67 228 155 180 25 143.71 0.60 229 156 178 22 156.28 6.96 230 156 179 23 156.30 6.94 231 156 180 24 156.41 6.88 232 157 176 19 230.69 8.03 233 157 177 20 210.36 2.08 234 157 178 21 175.55 2.07 235 157 198 41 143.94 0.65 236 158 177 19 215.38 0.39 237 158 178 20 210.32 2.10 238 158 179 21 191.46 7.33 239 158 181 23 179.49 4.04 240 158 218 60 149.97 0.14 241 162 181 19 277.22 3.87 242 166 216 50 158.66 1.05 243 166 217 51 158.56 1.09 244 166 218 52 158.47 1.14 245 167 208 41 165.72 0.11 246 167 209 42 163.86 0.49 247 167 210 43 163.79 0.53 248 167 217 50 158.68 1.04 249 167 218 51 158.66 1.05 250 167 220 53 158.16 0.98 251 170 208 38 166.63 0.28 252 171 208 37 166.73 0.37 253 171 220 49 158.59 1.07 254 173 223 50 157.84 1.29 255 173 226 53 156.62 1.47 256 174 222 48 157.89 1.32 257 174 223 49 157.55 1.26 258 174 226 52 151.74 1.87 259 174 227 53 149.43 1.07 260 175 208 33 166.88 0.47 261 175 220 45 158.24 1.26 262 175 221 46 157.70 1.22 263 175 223 48 157.28 1.39 264 176 196 20 160.55 0.66 265 176 203 27 159.88 0.58 266 176 204 28 159.24 0.93 267 176 220 44 157.76 1.25 268 176 221 45 157.66 1.22 269 176 222 46 157.57 1.26 270 176 223 47 157.26 1.39 271 177 218 41 158.15 1.29 272 177 219 42 157.74 1.24 273 177 220 43 157.53 1.27 274 178 218 40 158.41 1.17 275 178 219 41 157.90 1.32 276 178 221 43 157.59 1.26 277 180 185 5 236.12 4.58 278 181 215 34 161.17 0.53 279 181 216 35 160.02 0.55 280 181 218 37 159.16 0.79 281 182 215 33 161.18 0.53 282 183 213 30 161.88 0.52 283 183 214 31 161.53 0.55 284 183 215 32 161.19 0.53 285 184 213 29 161.91 0.52 286 185 213 28 164.41 0.20 287 186 212 26 287.18 0.30 288 186 213 27 253.38 2.66 289 186 219 33 156.80 1.60 290 187 221 34 157.12 1.33 291 196 221 25 157.28 1.39 292 202 224 22 115.39 0.93 293 203 222 19 157.57 1.25 294 203 223 20 155.58 0.98 295 203 224 21 115.41 0.92 296 203 225 22 112.85 2.00 297 204 221 17 157.28 1.38 298 204 222 18 156.74 1.48 299 204 224 20 113.57 1.84 300 205 221 16 157.16 1.33 301 205 222 17 156.40 1.64 302 205 224 19 113.56 1.70 303 206 221 15 156.68 1.50 304 207 220 13 157.55 1.28 305 207 221 14 157.13 1.31 306 207 222 15 156.74 1.49 307 208 219 11 157.81 1.29 308 208 220 12 157.56 1.28 309 210 217 7 166.26 2.58 310 214 217 3 279.12 0.78 311 224 231 7 50.59 2.87 312 225 228 3 81.30 0.58 313 227 230 3 73.77 0.07 314 227 231 4 53.14 1.61 315 228 231 3 56.16 0.10 316 228 232 4 50.94 2.63 317 229 232 3 72.43 0.89 318 229 233 4 51.01 2.66 319 230 233 3 48.56 2.58 320 230 234 4 47.12 1.95 321 231 234 3 38.66 3.06 322 231 235 4 31.86 0.30 323 232 235 3 31.89 0.32 324 232 236 4 31.86 0.30 325 233 236 3 32.72 0.10 326 233 237 4 31.85 0.30 327 234 237 3 31.73 0.27 328 234 238 4 30.55 0.02 329 235 238 3 26.79 1.91