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 31.21 0.20 2 16 140 119 45.00 6.75 3 16 142 121 31.25 0.22 4 16 143 122 56.55 3.76 5 16 144 123 59.01 2.64 6 16 156 135 54.20 3.13 7 16 158 137 53.37 2.78 8 16 189 170 58.04 2.57 9 16 190 171 30.25 0.28 10 16 194 175 30.25 0.28 11 17 143 121 59.02 2.64 12 17 144 122 59.02 2.64 13 17 145 123 60.41 2.44 14 17 146 124 62.34 1.48 15 17 188 167 59.98 2.19 16 17 188 168 59.77 2.29 17 17 189 169 58.95 2.62 18 17 191 171 59.01 2.64 19 17 220 195 59.59 2.34 20 17 221 196 59.76 2.27 21 18 158 135 65.06 0.62 22 18 188 166 60.19 2.19 23 18 188 167 59.91 2.23 24 19 157 133 66.70 0.20 25 19 158 134 65.06 0.62 26 20 137 112 88.26 0.57 27 20 156 131 96.09 1.08 28 20 157 132 76.89 0.25 29 20 158 133 196.02 10.33 30 20 159 134 261.06 5.54 31 21 154 128 147.25 4.30 32 21 155 129 146.94 4.47 33 21 156 130 133.19 11.04 34 22 26 4 165.09 2.31 35 22 27 5 147.95 6.31 36 22 139 112 136.97 0.26 37 22 155 128 165.16 1.69 38 22 156 129 201.43 0.68 39 23 26 3 177.88 0.14 40 24 71 44 139.51 0.10 41 25 69 41 141.66 0.46 42 25 79 51 151.49 0.14 43 25 117 89 139.68 0.40 44 27 30 3 248.92 6.21 45 27 137 105 139.26 0.01 46 27 139 107 147.17 0.33 47 27 157 125 286.12 0.83 48 28 116 85 151.65 0.21 49 28 117 86 151.64 0.21 50 28 118 87 150.05 0.24 51 28 119 88 148.62 0.41 52 29 45 14 149.13 0.69 53 29 46 15 146.95 0.38 54 29 119 87 150.46 0.04 55 29 120 88 148.61 0.40 56 29 121 89 146.99 0.36 57 29 137 103 151.78 0.23 58 29 198 166 151.62 0.20 59 29 200 168 151.75 0.24 60 30 43 11 154.18 0.32 61 30 44 12 152.06 0.09 62 30 139 104 152.18 0.09 63 30 140 105 153.71 0.07 64 30 141 106 155.80 0.10 65 30 155 120 275.06 3.71 66 30 198 165 152.06 0.08 67 31 43 10 155.00 0.20 68 31 44 11 152.85 0.48 69 31 45 12 152.85 0.48 70 31 46 13 152.31 0.11 71 31 52 19 152.84 0.47 72 31 65 32 155.62 0.10 73 31 66 33 155.59 0.08 74 31 67 34 155.26 0.10 75 31 141 105 155.83 0.10 76 32 40 6 156.22 0.05 77 32 42 8 155.85 0.09 78 32 65 31 155.88 0.07 79 32 66 32 155.66 0.10 80 32 73 38 156.19 0.04 81 32 141 104 155.83 0.10 82 33 40 5 156.34 0.01 83 33 41 6 156.21 0.06 84 33 42 7 156.06 0.01 85 33 43 8 155.88 0.09 86 33 52 17 155.88 0.07 87 33 54 19 155.87 0.08 88 33 58 23 156.28 0.02 89 33 63 28 156.24 0.06 90 33 64 29 156.22 0.06 91 33 65 30 155.88 0.07 92 33 106 70 155.87 0.08 93 34 39 3 165.71 1.64 94 34 40 4 156.36 0.01 95 34 41 5 157.30 0.48 96 34 63 27 156.25 0.05 97 34 64 28 156.22 0.07 98 34 66 30 156.24 0.05 99 37 41 4 170.21 3.55 100 37 60 23 165.17 1.35 101 37 62 25 164.61 1.08 102 45 121 75 214.10 0.87 103 46 120 73 251.22 1.70 104 46 121 74 222.86 2.28 105 47 120 72 281.25 4.28 106 47 121 73 240.75 3.49 107 47 123 75 199.79 0.12 108 47 238 186 58.90 1.58 109 47 242 190 46.38 1.53 110 48 242 189 46.62 1.65 111 51 242 186 46.02 1.71 112 51 245 189 27.54 3.56 113 53 238 180 57.89 1.34 114 71 153 80 153.88 0.43 115 71 154 81 152.69 0.73 116 71 155 82 151.25 0.14 117 72 153 79 153.84 0.41 118 72 154 80 153.46 0.57 119 73 153 78 153.84 0.43 120 74 153 77 154.53 0.09 121 87 245 154 43.36 2.75 122 89 237 144 78.48 2.15 123 89 241 148 51.59 0.24 124 89 245 152 43.45 2.71 125 91 234 139 105.86 0.12 126 91 237 142 81.59 0.92 127 92 237 141 95.32 1.87 128 98 180 80 210.11 27.50 129 99 180 79 163.94 4.42 130 100 177 75 163.42 4.65 131 100 179 77 163.88 4.42 132 100 180 78 163.87 4.41 133 101 179 76 163.85 4.41 134 101 234 129 113.96 1.51 135 102 229 123 153.62 0.57 136 103 229 122 153.56 0.60 137 103 234 127 103.56 1.27 138 103 237 130 76.67 1.26 139 103 238 131 69.88 0.66 140 105 237 128 73.31 0.92 141 105 238 129 61.91 3.33 142 105 241 132 47.16 1.68 143 105 242 133 46.70 1.60 144 107 245 134 26.50 4.08 145 122 204 82 280.70 2.49 146 122 209 83 257.92 6.45 147 123 204 81 237.74 2.64 148 123 209 82 201.62 1.36 149 123 231 104 246.16 4.05 150 123 235 108 73.27 0.95 151 123 238 111 68.19 0.61 152 124 204 80 191.45 0.41 153 124 209 81 181.91 1.55 154 124 210 82 164.77 2.81 155 124 232 104 111.46 0.09 156 124 235 107 79.36 1.38 157 127 210 80 156.57 0.67 158 128 210 79 153.68 0.61 159 129 134 4 169.66 1.07 160 129 162 32 138.01 0.03 161 129 201 73 155.62 0.35 162 129 210 78 154.44 0.23 163 130 134 3 181.57 1.19 164 130 162 31 138.59 0.04 165 132 162 30 138.74 0.05 166 132 163 31 138.75 0.04 167 132 164 32 138.77 0.04 168 133 161 28 138.74 0.05 169 133 162 29 138.84 0.07 170 134 161 27 138.87 0.07 171 134 162 28 138.93 0.09 172 135 159 24 138.79 0.05 173 135 160 25 138.84 0.06 174 135 161 26 138.91 0.09 175 136 159 23 138.80 0.04 176 136 160 24 138.82 0.04 177 136 162 26 140.14 0.17 178 137 157 20 138.40 0.14 179 137 158 21 138.75 0.04 180 137 159 22 138.81 0.04 181 138 157 19 135.71 0.42 182 138 158 20 138.06 0.26 183 138 160 22 139.00 0.12 184 138 183 45 155.77 0.15 185 138 228 88 154.48 0.25 186 139 155 16 138.98 0.12 187 139 156 17 138.72 0.07 188 139 157 18 136.24 0.62 189 140 155 15 138.98 0.12 190 140 156 16 138.84 0.06 191 141 151 10 154.91 0.21 192 141 152 11 152.22 0.11 193 141 153 12 151.75 0.24 194 141 154 13 144.58 1.15 195 141 155 14 138.99 0.11 196 142 151 9 154.99 0.24 197 142 152 10 154.91 0.21 198 143 148 5 156.25 0.04 199 143 149 6 155.53 0.09 200 143 150 7 155.33 0.10 201 143 151 8 155.00 0.24 202 143 191 50 195.98 2.39 203 143 192 51 285.88 2.55 204 144 150 6 155.48 0.07 205 144 152 8 155.02 0.24 206 144 156 12 139.00 0.11 207 145 148 3 169.94 0.84 208 145 149 4 156.24 0.04 209 145 191 48 180.97 2.13 210 146 220 71 154.93 0.18 211 146 221 72 154.91 0.19 212 151 192 43 155.31 0.10 213 152 156 4 169.81 0.80 214 158 188 32 138.94 0.10 215 158 189 33 138.87 0.12 216 159 184 26 139.03 0.12 217 160 184 24 138.87 0.12 218 160 184 25 139.02 0.12 219 161 183 22 179.41 2.90 220 161 184 23 138.93 0.09 221 161 184 24 139.50 0.14 222 162 181 19 228.68 3.98 223 162 182 20 191.85 0.59 224 162 183 21 179.49 2.94 225 162 201 41 144.96 1.03 226 163 182 19 225.06 9.56 227 163 183 20 188.27 1.20 228 163 184 21 191.80 0.60 229 163 185 23 179.27 2.98 230 163 225 60 150.38 0.68 231 167 185 19 281.87 0.59 232 171 223 50 154.99 0.15 233 171 224 51 154.93 0.12 234 171 225 52 154.92 0.12 235 172 215 41 163.16 4.03 236 172 216 42 160.75 2.99 237 172 217 43 160.77 2.97 238 172 224 50 154.99 0.15 239 172 225 51 155.00 0.14 240 172 227 53 154.71 0.07 241 175 215 38 163.20 4.00 242 176 215 37 163.43 4.12 243 176 227 49 154.95 0.13 244 178 230 50 154.66 0.12 245 178 233 53 152.03 0.28 246 179 229 48 154.75 0.17 247 179 230 49 154.38 0.21 248 179 233 52 150.87 0.50 249 179 234 53 149.41 1.11 250 180 215 33 163.45 4.12 251 180 227 45 154.97 0.14 252 180 228 46 154.83 0.12 253 180 230 48 153.63 0.54 254 181 199 20 155.81 0.11 255 181 210 27 155.32 0.10 256 181 211 28 155.33 0.10 257 181 227 44 154.90 0.17 258 181 228 45 154.78 0.12 259 181 229 46 154.44 0.24 260 181 230 47 153.38 0.49 261 182 225 41 154.97 0.14 262 182 226 42 154.90 0.13 263 182 227 43 154.43 0.23 264 183 225 40 155.00 0.15 265 183 226 41 154.91 0.16 266 183 228 43 154.72 0.09 267 184 188 5 274.43 5.49 268 185 222 34 156.31 0.01 269 185 223 35 155.69 0.23 270 185 225 37 155.02 0.11 271 186 222 33 156.33 0.01 272 187 221 30 158.61 1.06 273 187 221 31 158.60 1.05 274 187 222 32 156.46 0.00 275 188 221 29 162.62 1.88 276 188 221 28 167.03 0.96 277 189 221 27 184.53 1.15 278 189 226 33 154.01 0.04 279 190 228 34 153.35 0.52 280 199 228 25 154.19 0.45 281 209 231 22 120.42 0.64 282 210 230 20 153.69 0.61 283 210 231 21 137.32 7.82 284 210 232 22 112.58 0.42 285 211 228 17 153.79 0.61 286 211 229 18 153.69 0.61 287 211 231 20 111.81 0.93 288 212 228 16 153.72 0.60 289 212 229 17 153.03 0.30 290 212 231 19 126.49 5.88 291 213 228 15 153.69 0.60 292 214 227 13 154.63 0.21 293 214 228 14 153.32 0.39 294 214 229 15 153.02 0.30 295 215 226 11 154.78 0.16 296 215 227 12 154.36 0.27 297 216 227 11 154.40 0.21 298 217 224 7 168.91 6.80 299 221 224 3 285.72 0.43 300 231 235 4 284.48 1.04 301 231 238 7 68.59 0.45 302 232 235 3 83.61 0.05 303 234 237 3 74.47 0.35 304 234 238 4 69.81 0.61 305 235 238 3 69.40 0.21 306 235 239 4 65.27 1.44 307 236 239 3 69.14 0.28 308 236 240 4 65.26 1.44 309 237 240 3 61.27 3.00 310 237 241 4 57.37 1.47 311 238 241 3 47.59 1.47 312 238 242 4 46.83 1.66 313 239 242 3 56.08 6.14 314 239 243 4 46.73 1.61 315 240 243 3 47.19 1.70 316 240 244 4 46.65 1.65 317 241 244 3 46.37 1.89 318 241 245 4 44.94 2.33 319 242 245 3 43.85 3.28