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 42.13 0.59 2 16 140 119 42.19 0.63 3 16 142 121 44.59 0.41 4 16 143 122 56.27 3.70 5 16 144 123 58.66 2.71 6 16 156 135 54.09 4.42 7 16 158 137 43.06 0.24 8 16 189 170 56.23 3.21 9 16 190 171 42.13 0.60 10 16 191 172 46.81 0.83 11 16 194 175 42.13 0.60 12 17 143 121 58.93 2.60 13 17 144 122 58.90 2.59 14 17 145 123 60.05 2.44 15 17 146 124 65.03 0.13 16 17 188 167 59.62 2.21 17 17 188 168 58.82 2.58 18 17 189 169 58.44 2.62 19 17 191 171 58.58 2.70 20 17 220 195 58.91 2.59 21 17 221 196 58.88 2.58 22 18 158 135 62.08 1.01 23 18 188 166 59.59 2.23 24 18 188 167 59.19 2.41 25 19 157 133 64.91 0.70 26 19 158 134 62.08 1.01 27 20 137 112 85.05 1.09 28 20 156 131 121.96 15.60 29 20 157 132 77.23 0.12 30 20 158 133 204.10 0.87 31 20 159 134 277.44 2.65 32 21 154 128 146.66 4.04 33 21 155 129 148.84 5.42 34 21 156 130 134.59 10.07 35 22 26 4 168.00 0.63 36 22 27 5 162.20 0.24 37 22 139 112 137.96 0.04 38 22 155 128 166.37 1.08 39 22 156 129 193.97 1.08 40 23 26 3 202.15 12.00 41 24 71 44 141.84 0.05 42 25 69 41 141.25 0.66 43 25 79 51 152.88 0.76 44 25 117 89 139.94 0.26 45 27 30 3 218.40 9.04 46 27 137 105 140.13 0.17 47 27 139 107 148.13 0.14 48 28 116 85 152.78 0.78 49 28 117 86 152.76 0.76 50 28 118 87 152.41 0.60 51 28 119 88 149.31 0.77 52 29 45 14 149.14 0.69 53 29 46 15 146.94 0.37 54 29 119 87 152.42 0.60 55 29 120 88 149.31 0.77 56 29 121 89 146.95 0.37 57 29 137 103 152.86 0.76 58 29 198 166 152.82 0.76 59 29 200 168 152.81 0.76 60 30 43 11 153.13 0.68 61 30 44 12 152.91 0.78 62 30 139 104 152.94 0.76 63 30 140 105 153.25 0.74 64 30 141 106 155.47 0.43 65 30 155 120 275.88 4.12 66 30 198 165 152.84 0.75 67 31 43 10 153.76 0.82 68 31 44 11 153.12 0.68 69 31 45 12 152.94 0.76 70 31 46 13 152.93 0.76 71 31 52 19 152.94 0.76 72 31 65 32 155.49 0.48 73 31 66 33 155.46 0.46 74 31 67 34 154.27 0.53 75 31 141 105 155.58 0.42 76 32 40 6 155.99 0.60 77 32 42 8 155.58 0.43 78 32 65 31 155.55 0.47 79 32 66 32 155.52 0.46 80 32 73 38 155.72 0.49 81 32 141 104 155.58 0.42 82 33 40 5 156.06 0.58 83 33 41 6 155.90 0.55 84 33 42 7 155.82 0.55 85 33 43 8 155.59 0.43 86 33 52 17 155.55 0.46 87 33 54 19 155.59 0.44 88 33 58 23 155.98 0.55 89 33 63 28 156.00 0.54 90 33 64 29 155.97 0.54 91 33 65 30 155.56 0.46 92 33 104 68 155.94 0.53 93 33 106 70 155.60 0.45 94 34 39 3 166.03 0.39 95 34 40 4 156.08 0.59 96 34 41 5 156.63 0.32 97 34 63 27 156.00 0.54 98 34 64 28 156.00 0.55 99 34 66 30 155.91 0.57 100 37 41 4 166.55 0.85 101 37 60 23 166.69 0.59 102 45 121 75 205.43 0.26 103 46 120 73 231.37 5.45 104 46 121 74 216.09 0.12 105 47 120 72 279.14 1.96 106 47 121 73 231.90 7.54 107 47 123 75 194.94 0.38 108 47 238 186 67.97 0.33 109 48 242 189 31.62 0.13 110 51 242 186 31.62 0.13 111 51 245 189 20.09 0.17 112 53 238 180 62.66 2.99 113 71 153 80 153.34 0.79 114 71 154 81 152.82 0.77 115 71 155 82 152.49 0.64 116 72 153 79 153.33 0.79 117 72 154 80 153.17 0.81 118 73 153 78 153.34 0.79 119 74 153 77 153.59 0.73 120 87 245 154 21.00 1.37 121 89 237 144 76.78 1.26 122 89 241 148 50.44 0.83 123 89 245 152 23.39 0.04 124 91 234 139 105.87 0.12 125 91 237 142 81.41 1.02 126 92 237 141 95.31 1.88 127 98 180 80 169.05 1.17 128 99 180 79 169.02 1.18 129 100 177 75 168.94 1.16 130 100 179 77 168.94 1.17 131 100 180 78 168.94 1.17 132 101 179 76 168.86 1.18 133 101 234 129 110.44 0.25 134 102 229 123 151.58 1.25 135 103 229 122 151.55 1.26 136 103 234 127 101.42 0.20 137 103 237 130 75.69 0.74 138 103 238 131 71.91 0.28 139 104 237 129 76.70 1.25 140 105 237 128 74.91 0.39 141 105 238 129 69.17 0.93 142 105 241 132 40.01 4.28 143 105 242 133 31.62 0.13 144 107 245 134 18.25 0.01 145 121 209 84 285.30 0.18 146 122 204 82 263.84 3.48 147 122 209 83 230.59 7.44 148 123 204 81 215.60 0.06 149 123 209 82 198.05 3.16 150 123 231 104 273.66 2.37 151 123 235 108 74.36 0.49 152 123 238 111 68.61 0.01 153 123 239 112 62.69 2.96 154 124 204 80 189.69 1.25 155 124 209 81 176.71 0.04 156 124 210 82 167.31 1.54 157 124 232 104 259.30 3.89 158 124 235 107 77.97 0.69 159 127 210 80 156.12 0.03 160 128 210 79 152.56 0.30 161 129 134 4 166.16 0.64 162 129 162 32 137.86 0.01 163 129 201 73 156.08 0.12 164 129 210 78 153.93 0.78 165 130 134 3 180.69 0.15 166 130 162 31 138.72 0.04 167 132 162 30 138.75 0.03 168 132 163 31 139.09 0.15 169 132 164 32 139.17 0.15 170 133 162 29 139.15 0.14 171 134 161 27 139.18 0.14 172 134 162 28 139.19 0.14 173 135 159 24 139.14 0.15 174 135 160 25 139.18 0.14 175 135 161 26 139.19 0.14 176 136 158 22 139.15 0.14 177 136 159 23 139.14 0.14 178 136 160 24 139.19 0.14 179 136 162 26 141.37 0.45 180 137 157 20 138.34 0.20 181 137 158 21 139.12 0.14 182 137 159 22 139.15 0.14 183 138 157 19 137.70 0.41 184 138 158 20 138.52 0.01 185 138 160 22 139.45 0.18 186 138 183 45 155.62 0.54 187 138 228 88 154.28 0.81 188 139 155 16 139.30 0.12 189 139 156 17 138.94 0.17 190 139 157 18 137.79 0.11 191 140 155 15 139.29 0.14 192 140 156 16 139.06 0.11 193 141 152 11 152.98 0.72 194 141 153 12 152.84 0.74 195 141 154 13 147.69 0.12 196 141 155 14 139.25 0.12 197 142 151 9 153.88 0.69 198 142 152 10 153.67 0.78 199 143 148 5 158.25 0.28 200 143 149 6 155.28 0.55 201 143 150 7 155.19 0.58 202 143 151 8 154.55 0.36 203 143 191 50 195.53 1.28 204 143 192 51 283.59 0.83 205 144 150 6 155.25 0.57 206 144 152 8 154.66 0.42 207 144 156 12 139.21 0.12 208 145 148 3 177.79 0.09 209 145 149 4 156.17 0.76 210 146 220 71 154.05 0.77 211 146 221 72 153.97 0.71 212 151 192 43 154.67 0.42 213 152 156 4 169.75 0.82 214 158 188 32 139.06 0.21 215 158 189 33 138.88 0.12 216 159 184 26 139.33 0.16 217 160 184 24 139.03 0.20 218 160 184 25 139.30 0.17 219 161 183 22 161.90 11.55 220 161 184 23 156.51 8.83 221 161 184 24 156.67 8.75 222 162 181 19 233.93 1.35 223 162 182 20 196.77 3.32 224 162 183 21 162.00 11.60 225 162 201 41 145.38 0.56 226 163 182 19 215.53 10.55 227 163 183 20 187.37 1.02 228 163 184 21 187.33 1.03 229 163 185 23 181.69 1.77 230 163 225 60 149.86 1.08 231 167 185 19 264.75 10.29 232 171 223 50 154.74 0.54 233 171 224 51 154.72 0.54 234 171 225 52 154.72 0.54 235 172 215 41 168.72 1.23 236 172 216 42 168.63 1.23 237 172 217 43 168.60 1.22 238 172 224 50 154.78 0.54 239 172 225 51 154.75 0.53 240 172 227 53 153.96 0.58 241 175 215 38 168.87 1.11 242 176 215 37 168.93 1.14 243 176 227 49 154.59 0.47 244 178 230 50 153.92 0.77 245 178 233 53 152.18 0.48 246 179 229 48 153.93 0.77 247 179 230 49 153.40 0.67 248 179 233 52 149.69 1.02 249 179 234 53 149.28 1.18 250 180 215 33 168.90 1.16 251 180 227 45 154.30 0.71 252 180 228 46 154.02 0.72 253 180 230 48 153.25 0.64 254 181 199 20 155.34 0.58 255 181 210 27 154.67 0.51 256 181 211 28 154.83 0.43 257 181 227 44 154.31 0.72 258 181 228 45 153.93 0.74 259 181 229 46 153.62 0.61 260 181 230 47 153.09 0.64 261 182 225 41 154.44 0.70 262 182 226 42 154.37 0.70 263 182 227 43 153.63 0.59 264 183 225 40 154.48 0.70 265 183 226 41 154.32 0.68 266 183 228 43 153.62 0.61 267 184 188 5 259.26 10.83 268 185 222 34 163.47 3.46 269 185 223 35 155.62 0.82 270 185 225 37 155.01 0.57 271 186 222 33 163.49 3.46 272 186 223 34 163.47 3.46 273 187 221 30 167.88 1.30 274 187 221 31 166.24 2.11 275 187 222 32 165.99 2.20 276 188 221 29 168.15 1.36 277 188 221 28 168.24 1.38 278 189 221 27 212.26 0.90 279 189 226 33 152.85 0.49 280 190 228 34 152.85 0.51 281 199 228 25 156.08 0.09 282 209 231 22 118.23 1.57 283 210 230 20 153.78 0.91 284 210 231 21 132.56 5.59 285 210 232 22 112.31 0.52 286 211 228 17 154.16 0.84 287 211 229 18 153.92 0.78 288 211 231 20 114.99 0.12 289 212 228 16 153.21 0.42 290 212 229 17 152.69 0.40 291 212 231 19 114.45 0.39 292 213 228 15 152.91 0.48 293 214 227 13 154.55 0.66 294 214 228 14 152.87 0.45 295 214 229 15 152.77 0.41 296 215 226 11 154.90 0.51 297 215 227 12 153.94 0.76 298 216 227 11 154.19 0.33 299 217 224 7 175.84 9.96 300 221 224 3 286.63 1.12 301 231 235 4 282.82 0.21 302 231 238 7 71.20 0.45 303 232 235 3 85.86 1.19 304 234 237 3 74.97 0.17 305 234 238 4 73.17 1.07 306 235 238 3 71.44 0.45 307 235 239 4 71.10 0.40 308 236 239 3 71.32 0.51 309 236 240 4 68.61 0.01 310 237 240 3 67.97 0.33 311 237 241 4 62.15 3.23 312 238 241 3 43.30 2.63 313 238 242 4 31.64 0.14 314 239 242 3 39.99 4.29 315 239 243 4 31.64 0.14 316 240 243 3 52.17 10.40 317 240 244 4 31.64 0.14 318 241 244 3 32.84 0.74 319 241 245 4 31.04 0.10 320 242 245 3 34.43 4.11