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 49.45 1.63 2 16 140 119 49.48 1.65 3 16 142 121 49.70 1.57 4 16 143 122 58.33 1.89 5 16 144 123 58.96 1.65 6 16 156 135 56.79 1.22 7 16 157 136 56.03 1.59 8 16 158 137 56.02 1.60 9 16 189 170 58.09 1.76 10 16 190 171 45.12 0.09 11 16 194 175 45.07 0.07 12 17 143 121 58.97 1.64 13 17 144 122 58.97 1.64 14 17 145 123 60.75 1.41 15 17 146 124 61.72 1.89 16 17 188 167 59.40 1.47 17 17 188 168 59.38 1.47 18 17 189 169 58.95 1.65 19 17 191 171 58.94 1.64 20 17 220 195 59.00 1.67 21 17 221 196 58.98 1.64 22 18 158 135 60.73 2.06 23 18 188 166 59.40 1.47 24 18 188 167 59.40 1.47 25 19 157 133 66.86 1.01 26 19 158 134 59.72 1.64 27 20 137 112 82.64 0.37 28 20 156 131 90.41 1.12 29 20 157 132 72.58 1.10 30 20 158 133 180.14 2.77 31 20 159 134 272.66 0.52 32 21 71 47 138.07 1.30 33 21 154 128 137.06 1.37 34 21 155 129 145.78 3.42 35 21 156 130 112.63 0.64 36 22 26 4 166.93 0.20 37 22 27 5 152.35 6.46 38 22 71 46 138.25 1.24 39 22 139 112 136.80 1.32 40 22 155 128 166.05 2.56 41 22 156 129 209.35 9.19 42 23 26 3 177.47 5.10 43 24 71 44 144.40 0.61 44 25 28 3 173.54 1.47 45 25 69 41 143.88 0.36 46 25 79 51 149.11 0.70 47 25 117 89 139.11 0.83 48 27 30 3 185.29 0.21 49 27 137 105 138.87 1.03 50 27 139 107 143.79 0.07 51 27 157 125 280.80 4.12 52 28 116 85 149.03 0.70 53 28 117 86 149.01 0.71 54 28 118 87 148.06 0.42 55 28 119 88 146.50 1.07 56 29 45 14 145.78 0.93 57 29 46 15 145.91 1.36 58 29 119 87 148.13 0.45 59 29 120 88 147.68 0.48 60 29 121 89 145.41 1.11 61 29 137 103 149.10 0.69 62 29 198 166 148.26 0.36 63 29 200 168 148.13 0.28 64 30 43 11 149.19 0.68 65 30 44 12 149.11 0.69 66 30 139 104 149.21 0.66 67 30 140 105 149.28 0.67 68 30 141 106 153.35 0.04 69 30 155 120 172.63 2.21 70 30 198 165 148.80 0.59 71 31 43 10 149.93 0.66 72 31 44 11 149.13 0.69 73 31 45 12 149.19 0.65 74 31 46 13 149.16 0.70 75 31 52 19 149.13 0.70 76 31 66 32 153.78 0.01 77 31 67 33 153.47 0.01 78 31 68 34 153.05 0.00 79 31 141 105 153.42 0.04 80 32 40 6 154.18 0.03 81 32 42 8 153.49 0.00 82 32 43 9 153.21 0.01 83 32 66 31 153.96 0.07 84 32 67 32 153.94 0.07 85 32 73 38 154.28 0.05 86 32 141 104 153.41 0.03 87 33 40 5 154.27 0.05 88 33 41 6 154.12 0.01 89 33 42 7 153.78 0.01 90 33 43 8 153.49 0.00 91 33 54 19 153.52 0.01 92 33 58 23 153.79 0.01 93 33 63 28 154.24 0.01 94 33 64 29 154.24 0.01 95 33 66 30 154.16 0.04 96 33 104 68 153.78 0.01 97 33 106 70 153.96 0.07 98 34 39 3 168.67 3.53 99 34 40 4 154.28 0.05 100 34 41 5 154.29 0.04 101 34 63 27 154.25 0.01 102 34 64 28 154.25 0.01 103 34 67 30 154.30 0.04 104 37 41 4 166.05 0.87 105 37 60 23 161.96 0.27 106 45 121 75 219.52 0.77 107 46 120 73 283.16 2.80 108 46 121 74 247.06 1.87 109 47 121 73 282.43 2.79 110 47 123 75 195.78 2.79 111 47 238 186 60.46 2.04 112 47 242 190 32.41 0.94 113 48 242 189 32.41 0.94 114 51 242 186 30.88 0.19 115 51 245 189 24.73 0.89 116 71 153 80 150.75 0.03 117 71 154 81 149.00 0.69 118 71 155 82 148.25 0.88 119 72 153 79 150.62 0.01 120 72 154 80 149.19 0.66 121 73 152 77 152.38 0.44 122 73 153 78 151.01 0.19 123 74 153 77 152.12 0.44 124 87 245 154 25.93 1.49 125 89 237 144 76.56 1.07 126 89 241 148 44.99 7.08 127 89 245 152 23.27 0.17 128 91 234 139 106.03 0.25 129 91 237 142 77.52 0.80 130 92 237 141 95.90 2.29 131 98 180 80 152.91 0.38 132 99 180 79 152.81 0.34 133 100 177 75 151.19 0.02 134 100 179 77 151.41 0.07 135 100 180 78 151.50 0.06 136 101 179 76 150.00 0.57 137 101 234 129 107.25 0.03 138 102 229 123 153.72 1.04 139 103 229 122 153.74 1.07 140 103 234 127 103.42 1.43 141 103 237 130 74.23 1.68 142 103 238 131 68.74 0.60 143 105 237 128 72.55 2.50 144 105 238 129 59.30 2.03 145 105 241 132 32.56 0.86 146 105 242 133 30.91 0.18 147 107 245 134 22.09 0.42 148 122 204 82 283.04 2.90 149 122 209 83 272.97 2.08 150 123 231 104 246.49 1.52 151 123 235 108 72.11 0.70 152 123 238 111 60.51 2.04 153 123 239 112 60.47 2.04 154 124 204 80 181.07 0.56 155 124 209 81 174.80 3.52 156 124 210 82 165.87 1.38 157 124 231 103 284.50 0.27 158 124 232 104 131.51 12.10 159 124 235 107 78.14 0.17 160 125 204 79 184.95 1.25 161 127 210 80 160.94 0.79 162 128 210 79 156.12 0.70 163 129 134 4 167.64 0.99 164 129 162 32 136.79 1.29 165 129 210 78 156.60 0.69 166 130 134 3 189.12 0.44 167 130 162 31 137.60 1.59 168 132 162 30 137.60 1.59 169 132 163 31 137.73 1.54 170 132 164 32 137.79 1.53 171 133 162 29 137.77 1.51 172 134 161 27 137.77 1.54 173 134 162 28 137.79 1.53 174 135 160 25 137.77 1.54 175 135 161 26 137.78 1.54 176 136 159 23 137.72 1.54 177 136 160 24 137.75 1.54 178 136 162 26 140.09 1.56 179 137 157 20 136.87 1.28 180 137 158 21 137.56 1.61 181 137 159 22 137.72 1.54 182 138 157 19 136.60 1.23 183 138 158 20 136.84 1.30 184 138 160 22 138.24 1.34 185 138 183 45 154.34 0.09 186 138 228 88 156.37 0.77 187 139 155 16 138.24 1.34 188 139 156 17 137.56 1.61 189 139 157 18 136.80 1.32 190 140 155 15 138.21 1.33 191 140 156 16 137.72 1.55 192 141 152 11 149.00 0.73 193 141 153 12 148.26 0.42 194 141 154 13 146.50 1.07 195 141 155 14 138.20 1.32 196 142 152 10 148.97 0.77 197 143 148 5 154.06 0.04 198 143 149 6 153.16 0.10 199 143 150 7 152.50 0.30 200 143 191 50 195.56 0.43 201 144 150 6 153.15 0.09 202 144 152 8 151.39 0.06 203 144 156 12 138.16 1.33 204 145 148 3 173.25 1.47 205 145 149 4 153.83 0.14 206 145 150 5 153.58 0.03 207 146 220 71 149.49 0.95 208 146 221 72 149.62 0.90 209 152 156 4 165.88 0.20 210 158 188 32 137.92 1.45 211 158 189 33 137.88 1.46 212 159 184 26 164.97 0.49 213 160 183 23 166.83 0.40 214 160 184 24 164.96 0.49 215 160 184 25 164.97 0.49 216 161 183 22 167.31 0.64 217 161 184 23 166.35 0.17 218 161 184 24 166.34 0.17 219 162 181 19 269.04 0.59 220 162 182 20 184.62 5.87 221 162 183 21 170.81 1.00 222 163 182 19 228.08 13.89 223 163 183 20 180.25 3.70 224 163 184 21 184.60 5.88 225 163 185 23 170.83 0.99 226 163 225 60 145.19 0.21 227 167 185 19 233.59 0.27 228 168 185 18 254.13 0.97 229 168 225 55 153.72 0.17 230 171 223 50 154.22 0.23 231 172 223 49 154.36 0.16 232 172 224 50 154.06 0.21 233 173 217 42 154.24 0.13 234 173 224 49 154.41 0.14 235 174 215 39 156.87 1.41 236 174 217 41 154.26 0.12 237 174 224 48 154.41 0.14 238 174 225 49 154.41 0.14 239 174 227 51 153.98 0.24 240 175 215 38 156.87 1.41 241 176 215 37 154.20 0.12 242 176 227 49 153.97 0.24 243 178 230 50 153.75 0.14 244 178 233 53 151.96 0.06 245 179 229 48 153.59 0.06 246 179 230 49 153.05 0.10 247 179 233 52 148.39 0.85 248 179 234 53 148.18 0.76 249 180 215 33 154.10 0.17 250 180 227 45 153.94 0.14 251 180 228 46 153.43 0.02 252 180 229 47 152.88 0.08 253 180 230 48 152.46 0.29 254 181 227 44 153.85 0.15 255 181 228 45 153.38 0.01 256 181 230 47 151.65 0.11 257 182 225 41 154.06 0.16 258 182 226 42 153.88 0.14 259 182 227 43 153.16 0.04 260 183 199 18 154.02 0.10 261 183 226 41 153.94 0.14 262 183 228 43 153.34 0.07 263 184 225 39 154.12 0.17 264 184 188 5 280.72 4.57 265 185 222 34 154.96 0.26 266 185 223 35 154.47 0.09 267 185 225 37 153.94 0.20 268 186 222 33 155.05 0.34 269 187 221 30 156.42 0.61 270 187 221 31 155.58 0.52 271 187 222 32 155.11 0.31 272 188 221 29 156.67 0.61 273 188 221 28 171.40 7.96 274 189 221 27 224.18 8.38 275 189 226 33 154.75 0.16 276 190 228 34 155.39 0.48 277 199 228 25 156.33 0.74 278 209 231 22 152.34 1.75 279 210 230 20 156.28 0.72 280 210 231 21 155.15 0.35 281 210 232 22 133.22 11.14 282 211 228 17 156.33 0.74 283 211 229 18 156.28 0.72 284 211 231 20 133.90 10.79 285 212 228 16 156.16 0.67 286 212 229 17 155.84 0.59 287 212 231 19 143.94 5.80 288 213 228 15 155.83 0.61 289 214 227 13 156.47 0.72 290 214 228 14 156.18 0.70 291 214 229 15 156.18 0.70 292 215 226 11 156.53 0.70 293 215 227 12 156.48 0.71 294 216 227 11 156.49 0.72 295 217 224 7 182.10 1.26 296 221 224 3 286.33 1.59 297 231 238 7 69.28 1.14 298 232 235 3 82.38 0.24 299 234 237 3 76.07 1.97 300 234 238 4 69.48 1.06 301 235 238 3 71.31 2.06 302 235 239 4 64.81 1.01 303 236 239 3 71.27 0.20 304 236 240 4 63.69 0.45 305 237 240 3 59.56 2.08 306 237 241 4 58.58 2.38 307 238 241 3 48.40 7.62 308 238 242 4 47.23 8.20 309 239 242 3 32.60 0.85 310 239 243 4 32.52 0.88 311 240 243 3 48.79 8.94 312 240 244 4 31.03 0.14 313 241 244 3 33.16 1.33 314 241 245 4 30.34 0.19 315 242 245 3 48.87 8.94