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 45.00 0.27 2 16 140 119 45.06 0.30 3 16 142 121 45.57 0.48 4 16 143 122 53.16 0.97 5 16 144 123 55.66 0.14 6 16 156 135 46.73 0.36 7 16 157 136 46.98 0.21 8 16 158 137 45.99 0.75 9 16 189 170 51.63 0.58 10 16 190 171 44.80 0.29 11 16 194 175 44.80 0.29 12 17 143 121 55.86 0.12 13 17 144 122 55.80 0.15 14 17 145 123 56.41 0.29 15 17 146 124 57.37 0.77 16 17 188 167 56.40 0.29 17 17 188 168 56.04 0.19 18 17 189 169 55.66 0.11 19 17 191 171 55.62 0.14 20 17 220 195 56.27 0.33 21 17 221 196 56.29 0.33 22 18 158 135 57.18 0.05 23 18 188 166 56.40 0.30 24 18 188 167 56.35 0.32 25 19 157 133 58.97 0.45 26 19 158 134 56.75 0.09 27 20 137 112 84.98 0.79 28 20 156 131 85.39 0.99 29 20 157 132 72.47 1.17 30 20 158 133 202.41 6.70 31 20 159 134 271.33 9.06 32 21 154 128 136.69 0.38 33 21 155 129 135.72 0.07 34 21 156 130 120.01 1.44 35 22 26 4 167.10 0.29 36 22 27 5 146.68 5.58 37 22 139 112 135.40 0.29 38 22 155 128 172.47 2.28 39 22 156 129 194.69 1.61 40 23 26 3 182.84 1.47 41 24 71 44 140.59 0.57 42 25 69 41 143.68 0.53 43 25 79 51 155.18 1.82 44 25 117 89 140.59 0.44 45 27 30 3 220.22 19.71 46 27 137 105 140.66 0.54 47 27 139 107 145.12 1.02 48 27 157 125 286.55 0.14 49 28 116 85 154.98 1.72 50 28 117 86 154.96 1.72 51 28 118 87 153.84 1.92 52 28 119 88 150.50 0.51 53 29 45 14 149.28 1.02 54 29 46 15 145.75 0.01 55 29 119 87 153.83 1.91 56 29 120 88 150.15 0.12 57 29 121 89 145.41 0.91 58 29 137 103 155.34 1.75 59 29 198 166 155.06 1.60 60 29 200 168 154.85 1.73 61 30 43 11 155.37 1.75 62 30 44 12 155.34 1.75 63 30 139 104 155.37 1.75 64 30 140 105 155.49 1.74 65 30 141 106 157.21 1.16 66 30 155 120 173.56 2.94 67 30 198 165 155.06 1.60 68 31 43 10 156.46 1.23 69 31 44 11 155.37 1.75 70 31 45 12 155.36 1.75 71 31 46 13 155.35 1.75 72 31 52 19 155.38 1.76 73 31 65 32 157.10 1.24 74 31 66 33 157.11 1.25 75 31 67 34 156.78 1.40 76 31 141 105 157.24 1.15 77 32 40 6 157.77 1.19 78 32 42 8 157.25 1.16 79 32 65 31 157.25 1.19 80 32 66 32 157.18 1.23 81 32 70 35 157.30 1.30 82 32 73 38 157.72 1.24 83 32 141 104 157.24 1.15 84 33 40 5 157.77 1.18 85 33 41 6 157.76 1.18 86 33 42 7 157.27 1.15 87 33 43 8 157.24 1.15 88 33 54 19 157.27 1.17 89 33 58 23 157.72 1.21 90 33 63 28 157.78 1.23 91 33 64 29 157.78 1.23 92 33 65 30 157.31 1.17 93 33 104 68 157.46 1.10 94 33 106 70 157.25 1.19 95 34 39 3 169.94 2.62 96 34 40 4 157.78 1.18 97 34 41 5 157.77 1.18 98 34 63 27 157.80 1.23 99 34 64 28 157.78 1.23 100 34 66 30 157.78 1.23 101 37 41 4 171.09 2.04 102 37 60 23 169.91 4.41 103 37 62 25 164.81 1.86 104 40 73 32 285.81 2.58 105 45 121 75 220.34 0.01 106 46 120 73 254.09 3.08 107 46 121 74 238.11 2.60 108 47 121 73 264.06 2.61 109 47 123 75 197.11 2.50 110 47 238 186 65.16 0.83 111 47 242 190 32.18 0.57 112 48 242 189 32.18 0.57 113 51 242 186 32.16 0.57 114 51 245 189 23.02 0.06 115 53 238 180 65.02 0.91 116 71 153 80 155.61 1.86 117 71 154 81 154.97 1.75 118 71 155 82 154.80 1.67 119 72 153 79 155.46 1.94 120 72 154 80 155.38 1.91 121 73 153 78 155.72 1.80 122 74 153 77 155.72 1.80 123 87 245 154 22.14 0.38 124 89 237 144 80.67 0.96 125 89 241 148 48.30 6.89 126 89 245 152 20.22 0.62 127 91 234 139 108.57 0.99 128 91 237 142 80.56 0.74 129 92 237 141 99.34 3.35 130 98 180 80 210.25 17.36 131 99 180 79 201.91 21.48 132 100 177 75 169.26 5.45 133 100 179 77 201.65 21.60 134 100 180 78 201.80 21.52 135 101 179 76 169.17 5.41 136 101 234 129 122.79 6.07 137 102 229 123 155.84 1.30 138 103 229 122 155.84 1.30 139 103 234 127 102.60 1.84 140 103 237 130 76.23 1.24 141 103 238 131 69.55 1.01 142 105 237 128 75.47 1.23 143 105 238 129 65.55 0.64 144 105 241 132 32.41 0.47 145 105 242 133 32.18 0.56 146 107 245 134 20.01 0.61 147 122 204 82 281.33 4.41 148 122 209 83 255.55 1.84 149 123 204 81 241.96 0.84 150 123 209 82 193.56 1.27 151 123 231 104 212.06 38.21 152 123 235 108 73.66 1.37 153 123 238 111 67.04 0.06 154 124 204 80 191.63 0.94 155 124 209 81 181.28 0.62 156 124 210 82 166.94 1.90 157 124 232 104 109.19 0.73 158 124 235 107 78.38 0.99 159 125 204 79 207.19 2.87 160 127 210 80 159.26 2.37 161 128 210 79 153.84 0.12 162 129 134 4 165.33 0.68 163 129 162 32 136.59 0.33 164 129 210 78 156.49 1.07 165 130 134 3 181.37 0.65 166 130 162 31 137.00 0.43 167 132 162 30 137.00 0.43 168 132 163 31 137.14 0.48 169 132 164 32 137.20 0.48 170 133 161 28 137.02 0.42 171 133 162 29 137.09 0.46 172 134 161 27 137.09 0.46 173 134 162 28 137.26 0.52 174 135 159 24 137.02 0.42 175 135 160 25 137.10 0.46 176 135 161 26 137.12 0.46 177 136 159 23 137.02 0.42 178 136 160 24 137.10 0.46 179 136 162 26 144.09 0.43 180 137 157 20 136.41 0.14 181 137 158 21 137.00 0.42 182 137 159 22 137.04 0.43 183 138 157 19 135.01 0.45 184 138 158 20 135.49 0.33 185 138 160 22 137.52 0.43 186 138 228 88 156.78 1.15 187 139 155 16 137.31 0.52 188 139 156 17 137.01 0.43 189 139 157 18 135.40 0.29 190 140 155 15 137.31 0.52 191 140 156 16 137.03 0.44 192 141 151 10 155.87 1.67 193 141 152 11 155.40 1.75 194 141 153 12 155.38 1.75 195 141 154 13 146.97 0.83 196 141 155 14 137.28 0.50 197 142 151 9 156.69 1.28 198 142 152 10 155.99 1.61 199 142 194 54 286.91 0.48 200 143 148 5 157.50 1.10 201 143 149 6 157.09 1.17 202 143 150 7 156.98 1.18 203 143 151 8 156.88 1.19 204 143 191 50 201.12 1.71 205 144 150 6 157.06 1.17 206 144 152 8 156.96 1.19 207 144 156 12 137.27 0.51 208 145 148 3 173.06 1.38 209 145 149 4 157.48 1.31 210 145 150 5 157.14 1.15 211 146 220 71 156.80 1.25 212 146 221 72 156.79 1.26 213 146 221 73 156.78 1.25 214 151 192 43 156.94 1.19 215 152 156 4 164.38 0.53 216 158 184 27 137.42 0.48 217 158 188 32 137.23 0.49 218 158 189 33 137.21 0.49 219 159 184 26 137.52 0.45 220 160 184 24 137.14 0.48 221 160 184 25 137.50 0.45 222 161 183 22 151.91 6.82 223 161 184 23 137.28 0.51 224 161 184 24 140.59 0.59 225 162 181 19 213.11 3.73 226 162 182 20 189.03 1.65 227 162 183 21 151.92 6.82 228 162 201 41 146.40 0.34 229 163 182 19 199.02 3.33 230 163 183 20 165.31 13.46 231 163 184 21 170.50 10.85 232 163 185 23 157.77 3.96 233 163 225 60 152.44 1.30 234 171 223 50 156.94 1.20 235 171 224 51 156.94 1.20 236 171 225 52 156.94 1.20 237 172 215 41 169.55 5.01 238 172 216 42 168.06 4.29 239 172 217 43 168.03 4.28 240 172 224 50 156.97 1.21 241 172 225 51 156.96 1.21 242 172 227 53 156.61 1.23 243 175 215 38 169.75 5.11 244 176 215 37 169.83 5.16 245 176 227 49 156.81 1.28 246 178 230 50 156.65 1.21 247 178 233 53 154.88 1.74 248 179 229 48 156.66 1.21 249 179 230 49 156.50 1.24 250 179 233 52 151.38 0.84 251 179 234 53 148.16 0.76 252 180 215 33 169.87 5.16 253 180 227 45 156.81 1.22 254 180 228 46 156.66 1.21 255 180 230 48 156.09 1.32 256 181 199 20 157.33 1.16 257 181 210 27 157.05 1.24 258 181 211 28 157.06 1.25 259 181 227 44 156.74 1.19 260 181 228 45 156.61 1.24 261 181 229 46 156.52 1.28 262 181 230 47 155.84 1.43 263 182 225 41 156.91 1.19 264 182 226 42 156.74 1.19 265 182 227 43 156.56 1.26 266 183 225 40 156.94 1.19 267 183 226 41 156.90 1.20 268 183 228 43 156.60 1.24 269 184 188 5 279.79 0.60 270 185 222 34 159.55 0.08 271 185 223 35 157.22 1.12 272 185 225 37 157.03 1.22 273 186 222 33 161.54 0.90 274 187 221 30 169.52 4.79 275 187 221 31 164.88 2.48 276 187 222 32 161.55 0.90 277 188 221 29 170.03 5.05 278 188 221 28 202.30 21.18 279 189 221 27 215.38 23.73 280 189 226 33 156.11 1.06 281 190 228 34 156.02 1.16 282 199 228 25 156.78 1.13 283 209 231 22 118.74 0.45 284 210 229 19 156.80 1.14 285 210 230 20 154.08 0.18 286 210 231 21 120.48 0.06 287 210 232 22 113.38 1.35 288 211 228 17 156.73 1.12 289 211 229 18 156.13 1.22 290 211 231 20 118.25 0.61 291 212 228 16 156.12 1.23 292 212 229 17 156.02 1.21 293 212 231 19 116.48 0.19 294 213 228 15 156.10 1.22 295 214 227 13 156.78 1.15 296 214 228 14 156.22 1.17 297 214 229 15 156.12 1.22 298 215 226 11 156.97 1.21 299 215 227 12 156.66 1.21 300 216 227 11 156.53 1.27 301 217 224 7 166.37 5.73 302 231 235 4 284.82 0.68 303 231 238 7 69.52 1.05 304 232 235 3 82.98 0.51 305 234 237 3 71.88 0.78 306 234 238 4 69.72 1.05 307 235 238 3 71.25 0.19 308 235 239 4 69.50 1.04 309 236 239 3 69.53 1.06 310 236 240 4 69.24 1.16 311 237 240 3 66.88 0.03 312 237 241 4 64.83 0.98 313 238 241 3 67.34 1.85 314 238 242 4 32.27 0.52 315 239 242 3 68.89 1.07 316 239 243 4 32.27 0.53 317 240 243 3 52.19 9.43 318 240 244 4 32.27 0.53 319 241 244 3 32.13 0.45 320 241 245 4 31.02 0.03 321 242 245 3 22.28 0.42