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 17 189 169 29.93 1.04 2 18 158 135 44.08 0.27 3 18 188 167 29.31 0.90 4 18 189 168 29.97 1.02 5 19 157 133 53.38 4.15 6 19 158 134 44.08 0.27 7 19 188 166 57.61 2.37 8 20 137 112 73.48 0.07 9 20 149 124 132.59 0.72 10 20 156 131 77.61 2.13 11 20 157 132 68.51 2.33 12 20 158 133 120.15 28.19 13 20 159 134 259.74 3.83 14 20 188 165 78.41 1.34 15 21 149 123 132.61 0.71 16 21 150 124 132.56 0.71 17 21 154 128 145.99 0.38 18 21 155 129 146.01 0.39 19 21 156 130 146.21 0.24 20 22 26 4 160.13 0.55 21 22 27 5 153.08 0.72 22 22 155 128 159.55 2.43 23 22 156 129 181.22 1.08 24 23 26 3 167.32 1.94 25 24 71 44 132.93 0.56 26 25 28 3 160.47 0.58 27 25 69 41 133.09 0.48 28 25 79 51 138.31 0.84 29 25 117 89 132.89 0.57 30 27 30 3 202.51 14.02 31 27 137 105 133.12 0.48 32 27 139 107 133.53 0.42 33 28 116 85 138.22 0.92 34 28 117 86 138.13 0.90 35 28 118 87 135.67 0.64 36 28 119 88 133.61 0.38 37 29 45 14 133.81 0.29 38 29 46 15 133.59 0.37 39 29 119 87 135.77 0.60 40 29 120 88 133.86 0.51 41 29 121 89 133.18 0.50 42 29 137 103 138.25 0.82 43 29 198 166 137.40 0.42 44 29 200 168 137.04 0.24 45 30 43 11 138.38 0.85 46 30 44 12 138.34 0.86 47 30 139 104 138.31 0.83 48 30 141 106 145.81 0.48 49 30 155 120 203.12 20.93 50 30 198 165 138.21 0.82 51 31 43 10 144.92 0.12 52 31 44 11 138.37 0.85 53 31 45 12 138.38 0.85 54 31 46 13 138.35 0.86 55 31 52 19 138.41 0.83 56 31 65 32 146.12 0.45 57 31 65 33 146.05 0.40 58 31 66 34 145.56 0.45 59 31 141 105 146.24 0.46 60 32 40 6 146.43 0.40 61 32 42 8 146.23 0.47 62 32 43 9 145.72 0.45 63 32 65 31 146.19 0.43 64 32 65 32 146.17 0.43 65 32 70 35 146.32 0.36 66 32 73 38 146.43 0.38 67 32 141 104 146.25 0.46 68 33 40 5 146.53 0.42 69 33 41 6 146.43 0.41 70 33 42 7 146.25 0.47 71 33 43 8 146.24 0.46 72 33 52 17 146.18 0.43 73 33 54 19 146.16 0.43 74 33 58 23 146.35 0.48 75 33 63 28 146.41 0.41 76 33 64 29 146.41 0.40 77 33 65 30 146.33 0.36 78 34 39 3 156.66 1.37 79 34 40 4 146.55 0.42 80 34 41 5 146.62 0.47 81 34 63 27 146.52 0.46 82 34 64 28 146.41 0.41 83 34 65 30 146.41 0.39 84 37 41 4 157.75 0.75 85 37 60 23 148.30 1.28 86 37 62 25 148.29 1.28 87 45 121 75 205.68 0.70 88 46 120 73 237.88 5.67 89 46 121 74 218.52 0.51 90 47 120 72 275.46 0.43 91 47 121 73 252.50 1.65 92 47 123 75 197.41 0.41 93 47 238 186 55.08 0.01 94 47 242 190 37.39 0.71 95 48 120 71 276.20 0.79 96 48 242 189 37.69 0.86 97 51 242 186 37.38 0.71 98 51 245 189 27.48 1.68 99 71 153 80 139.00 1.12 100 71 154 81 137.24 1.04 101 71 155 82 133.94 0.27 102 72 153 79 139.00 1.13 103 72 154 80 138.48 0.92 104 73 152 77 140.15 1.67 105 73 153 78 139.02 1.13 106 74 153 77 140.13 1.66 107 87 245 154 35.25 0.02 108 89 237 144 66.19 0.81 109 89 241 148 47.42 0.99 110 89 245 152 35.29 0.06 111 91 234 139 93.98 0.87 112 91 237 142 68.84 0.49 113 92 237 141 85.53 0.39 114 98 180 80 199.17 27.15 115 99 180 79 145.74 0.51 116 100 177 75 143.83 1.22 117 100 179 77 144.13 1.30 118 100 180 78 145.72 0.51 119 101 179 76 144.06 1.33 120 101 234 129 107.64 2.21 121 102 229 123 142.20 1.15 122 103 229 122 141.59 0.87 123 103 234 127 88.92 0.09 124 103 237 130 65.86 0.74 125 103 238 131 56.97 0.36 126 105 237 128 65.86 0.74 127 105 238 129 54.94 0.07 128 105 241 132 39.52 0.34 129 105 242 133 37.38 0.69 130 107 245 134 24.48 0.99 131 122 204 82 265.25 7.82 132 122 209 83 254.46 2.61 133 123 204 81 222.65 2.69 134 123 209 82 188.34 4.33 135 123 231 104 261.87 4.50 136 123 235 108 65.20 1.08 137 123 238 111 55.65 0.10 138 123 239 112 55.48 0.18 139 124 204 80 177.68 0.32 140 124 209 81 171.38 3.46 141 124 210 82 163.12 0.40 142 124 231 103 274.69 1.90 143 124 232 104 196.06 27.67 144 124 235 107 67.14 0.18 145 127 210 80 153.52 1.22 146 128 210 79 143.58 0.46 147 129 134 4 160.29 0.47 148 129 162 32 131.30 0.82 149 129 210 78 147.17 1.35 150 130 134 3 171.46 0.41 151 130 162 31 132.23 0.67 152 132 162 30 132.25 0.68 153 132 163 31 132.26 0.68 154 132 164 32 132.42 0.71 155 133 161 28 132.24 0.68 156 133 162 29 132.34 0.70 157 134 161 27 132.35 0.68 158 134 162 28 132.41 0.70 159 135 160 25 132.34 0.69 160 135 161 26 132.38 0.68 161 136 159 23 132.31 0.69 162 136 160 24 132.34 0.69 163 136 162 26 133.13 0.48 164 137 157 20 131.60 0.36 165 137 158 21 132.25 0.65 166 137 159 22 132.33 0.69 167 138 157 19 128.62 0.96 168 138 158 20 131.97 0.54 169 138 160 22 133.09 0.48 170 138 183 45 146.38 0.34 171 138 228 88 147.02 0.73 172 139 155 16 132.70 0.67 173 139 156 17 132.33 0.70 174 139 157 18 131.03 0.07 175 140 155 15 132.70 0.67 176 140 156 16 132.53 0.67 177 141 152 11 134.12 0.63 178 141 153 12 134.60 0.39 179 141 154 13 133.59 0.40 180 141 155 14 132.70 0.67 181 142 152 10 133.62 0.39 182 142 156 14 132.71 0.67 183 143 190 49 235.79 9.22 184 143 191 50 184.83 1.08 185 143 192 51 271.68 0.33 186 144 191 49 174.00 0.86 187 145 148 3 200.74 1.27 188 146 150 4 159.18 0.07 189 146 151 5 145.44 0.59 190 146 152 6 144.25 1.15 191 147 151 4 153.38 0.20 192 150 154 4 149.31 1.05 193 150 156 6 146.28 0.39 194 151 154 3 153.12 0.85 195 151 156 5 151.03 0.19 196 152 156 4 162.38 1.64 197 158 184 27 155.78 0.30 198 158 188 32 133.12 0.47 199 158 189 33 132.77 0.65 200 158 190 34 132.69 0.68 201 159 184 26 159.00 0.14 202 160 183 23 169.63 1.16 203 160 184 24 159.00 0.14 204 160 184 25 159.00 0.14 205 161 183 22 170.27 1.20 206 161 184 23 167.88 2.31 207 161 184 24 166.56 2.68 208 162 181 19 223.86 1.07 209 162 182 20 174.40 0.29 210 162 183 21 170.29 1.19 211 162 201 41 133.56 0.36 212 163 182 19 196.06 4.44 213 163 183 20 173.94 0.54 214 163 184 21 173.52 0.32 215 163 185 23 170.28 1.19 216 167 185 19 250.13 7.15 217 171 225 52 145.39 0.21 218 172 215 41 146.28 0.35 219 172 216 42 146.26 0.35 220 172 217 43 146.27 0.35 221 172 224 50 145.68 0.20 222 172 225 51 145.67 0.20 223 172 227 53 145.35 0.23 224 175 215 38 146.23 0.36 225 176 215 37 146.22 0.36 226 176 227 49 145.63 0.22 227 178 230 50 145.23 0.17 228 178 233 53 140.64 0.37 229 179 229 48 145.23 0.17 230 179 230 49 144.65 0.06 231 179 233 52 136.62 0.21 232 179 234 53 135.17 0.02 233 180 215 33 146.15 0.34 234 180 227 45 145.46 0.22 235 180 228 46 145.24 0.16 236 180 230 48 144.56 0.02 237 181 199 20 146.30 0.38 238 181 210 27 145.83 0.46 239 181 211 28 145.87 0.47 240 181 227 44 145.40 0.21 241 181 228 45 145.15 0.12 242 181 229 46 144.73 0.01 243 181 230 47 143.58 0.51 244 182 225 41 145.53 0.21 245 182 226 42 145.40 0.20 246 182 227 43 144.63 0.05 247 182 228 44 144.63 0.06 248 183 225 40 145.58 0.19 249 183 226 41 145.41 0.18 250 183 228 43 145.00 0.07 251 184 188 4 272.76 4.20 252 184 188 5 248.03 16.57 253 185 222 34 146.31 0.25 254 185 223 35 146.17 0.24 255 185 225 37 146.10 0.28 256 186 222 33 146.31 0.25 257 186 223 34 146.27 0.25 258 187 222 32 146.31 0.25 259 189 226 33 142.36 1.27 260 199 228 25 147.06 1.19 261 209 231 22 127.34 6.70 262 210 229 19 153.08 1.66 263 210 230 20 144.59 0.95 264 210 231 21 127.33 6.71 265 210 232 22 96.31 0.16 266 211 228 17 145.68 1.42 267 211 229 18 143.82 0.53 268 211 231 20 108.29 0.64 269 212 228 16 144.65 0.93 270 212 229 17 143.59 0.43 271 212 231 19 107.94 0.82 272 213 228 15 143.83 0.53 273 214 227 13 146.24 0.91 274 214 228 14 144.39 0.80 275 214 229 15 143.82 0.52 276 215 226 11 146.56 0.50 277 215 227 12 144.48 0.82 278 216 225 9 146.99 0.57 279 216 226 10 145.88 0.30 280 216 227 11 145.70 0.22 281 217 224 7 163.75 7.81 282 231 238 7 57.16 0.85 283 232 235 3 74.89 1.95 284 234 237 3 61.56 0.36 285 234 238 4 57.91 0.82 286 235 238 3 59.00 0.10 287 235 239 4 58.99 0.10 288 236 239 3 60.64 0.20 289 236 240 4 56.59 0.57 290 237 240 3 56.02 0.47 291 237 241 4 54.77 0.04 292 238 241 3 52.25 2.35 293 238 242 4 38.41 1.20 294 239 242 3 41.37 0.28 295 239 243 4 39.15 0.14 296 240 243 3 48.15 3.68 297 240 244 4 39.13 0.14 298 241 244 3 47.14 4.18 299 241 245 4 38.82 0.02 300 242 245 3 43.04 1.65