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 59.36 0.27 2 16 140 119 59.29 0.30 3 16 142 121 59.41 0.24 4 16 143 122 64.69 0.23 5 16 144 123 65.16 0.07 6 16 156 135 64.08 0.17 7 16 157 136 60.06 0.09 8 16 158 137 58.01 0.84 9 16 189 170 62.22 0.86 10 16 190 171 52.34 3.17 11 16 194 175 52.36 3.17 12 17 143 121 65.19 0.08 13 17 144 122 65.17 0.07 14 17 145 123 65.25 0.07 15 17 146 124 65.28 0.05 16 17 188 167 65.28 0.05 17 17 188 168 65.12 0.03 18 17 189 169 65.08 0.06 19 17 191 171 65.09 0.06 20 17 220 195 65.15 0.04 21 17 221 196 65.15 0.04 22 18 158 135 65.88 0.24 23 18 188 166 65.32 0.03 24 18 188 167 65.15 0.04 25 19 157 133 65.88 0.24 26 19 158 134 65.88 0.24 27 20 137 112 81.62 0.07 28 20 156 131 86.67 0.18 29 20 157 132 76.27 1.17 30 20 158 133 202.99 4.22 31 20 159 134 257.75 0.14 32 21 154 128 148.03 5.08 33 21 155 129 147.94 5.13 34 21 156 130 136.87 10.66 35 22 26 4 170.07 0.05 36 22 27 5 135.62 0.76 37 22 139 112 136.30 0.59 38 22 155 128 166.84 2.00 39 22 156 129 203.59 0.88 40 23 26 3 174.40 0.83 41 24 71 44 140.12 0.07 42 25 28 3 176.59 2.88 43 25 69 41 140.67 0.24 44 25 79 51 157.76 1.24 45 25 117 89 140.56 0.25 46 27 30 3 174.02 0.12 47 27 137 105 143.34 1.52 48 27 139 107 151.40 1.26 49 28 116 85 157.47 1.16 50 28 117 86 157.10 1.38 51 28 118 87 155.23 1.85 52 28 119 88 150.22 0.56 53 29 45 14 148.62 0.12 54 29 46 15 148.22 0.01 55 29 119 87 156.10 1.41 56 29 120 88 148.66 0.22 57 29 121 89 146.41 0.70 58 29 137 103 158.16 1.28 59 29 198 166 157.24 1.23 60 29 200 168 157.46 1.11 61 30 43 11 158.16 1.27 62 30 44 12 157.90 1.30 63 30 139 104 158.28 1.32 64 30 140 105 158.93 1.30 65 30 141 106 160.30 0.92 66 30 155 120 172.21 0.71 67 30 198 165 157.54 1.22 68 31 43 10 159.66 0.96 69 31 44 11 158.06 1.22 70 31 45 12 158.06 1.22 71 31 46 13 158.06 1.22 72 31 52 19 158.06 1.22 73 31 65 32 160.15 0.82 74 31 65 33 160.14 0.82 75 31 66 34 159.88 0.78 76 31 141 105 160.34 0.91 77 32 40 6 160.91 1.01 78 32 42 8 160.49 0.95 79 32 43 9 159.97 0.90 80 32 65 31 160.47 0.97 81 32 65 32 160.35 0.91 82 32 73 38 160.91 0.94 83 32 141 104 160.34 0.91 84 33 40 5 161.01 0.96 85 33 41 6 160.90 1.01 86 33 42 7 160.52 0.95 87 33 43 8 160.47 0.96 88 33 52 17 160.47 0.97 89 33 54 19 160.43 0.95 90 33 58 23 161.02 0.97 91 33 63 28 161.01 0.98 92 33 64 29 160.94 0.96 93 33 65 30 160.52 0.95 94 33 104 68 160.78 1.06 95 33 106 70 160.52 0.96 96 34 39 3 170.13 0.96 97 34 40 4 161.03 0.96 98 34 41 5 161.05 0.96 99 34 63 27 161.03 0.98 100 34 64 28 160.97 0.97 101 34 65 30 160.93 0.97 102 37 41 4 175.94 1.46 103 37 60 23 169.43 0.59 104 37 62 25 161.09 0.97 105 40 73 32 287.76 0.17 106 45 121 75 212.44 0.26 107 46 120 73 242.38 0.01 108 46 121 74 239.19 1.57 109 47 120 72 286.51 1.38 110 47 121 73 262.80 10.23 111 47 123 75 202.77 1.69 112 47 238 186 51.83 1.84 113 47 242 190 31.45 0.48 114 48 242 189 31.46 0.48 115 51 242 186 31.39 0.51 116 51 245 189 20.98 0.04 117 71 153 80 158.56 1.31 118 71 154 81 157.27 1.51 119 71 155 82 155.06 0.48 120 72 153 79 158.56 1.31 121 72 154 80 158.12 1.29 122 73 153 78 158.56 1.31 123 74 153 77 159.02 1.09 124 87 245 154 21.77 0.44 125 89 237 144 76.59 2.14 126 89 241 148 32.42 0.10 127 89 245 152 21.98 0.51 128 91 234 139 104.92 0.64 129 91 237 142 82.59 0.79 130 92 237 141 100.06 0.42 131 98 180 80 171.99 0.01 132 99 180 79 171.96 0.01 133 100 177 75 171.88 0.02 134 100 179 77 171.90 0.01 135 100 180 78 171.91 0.01 136 101 179 76 171.79 0.06 137 101 234 129 118.94 2.12 138 102 229 123 157.08 1.51 139 103 229 122 157.01 1.54 140 103 234 127 99.25 0.09 141 103 237 130 72.02 0.36 142 103 238 131 69.18 0.21 143 105 237 128 71.25 0.29 144 105 238 129 48.66 1.91 145 105 241 132 32.74 0.16 146 105 242 133 31.39 0.51 147 107 245 134 16.19 0.18 148 122 204 82 286.96 0.25 149 122 209 83 265.94 8.70 150 123 204 81 250.60 1.03 151 123 209 82 201.41 2.31 152 123 231 104 258.62 11.65 153 123 235 108 71.16 0.36 154 123 238 111 57.74 4.79 155 124 204 80 187.08 0.18 156 124 209 81 177.62 3.79 157 124 210 82 160.03 0.74 158 124 231 103 287.35 0.27 159 124 232 104 174.90 32.64 160 124 235 107 80.89 0.05 161 127 210 80 159.53 0.88 162 128 210 79 155.72 1.57 163 129 134 4 163.06 1.40 164 129 162 32 137.31 0.40 165 129 210 78 157.92 1.28 166 130 134 3 178.69 0.86 167 130 162 31 137.54 0.29 168 132 162 30 137.55 0.29 169 132 163 31 137.84 0.22 170 132 164 32 137.91 0.24 171 133 161 28 137.56 0.31 172 133 162 29 137.83 0.23 173 134 161 27 137.87 0.26 174 134 162 28 137.91 0.26 175 135 160 25 137.88 0.26 176 135 161 26 137.89 0.26 177 136 159 23 137.66 0.30 178 136 160 24 137.84 0.28 179 136 162 26 147.35 0.36 180 137 157 20 137.41 0.35 181 137 158 21 137.60 0.29 182 137 159 22 137.66 0.30 183 138 157 19 136.11 0.51 184 138 158 20 137.25 0.23 185 138 160 22 138.11 0.27 186 138 183 45 160.36 1.02 187 138 228 88 158.81 0.96 188 139 155 16 137.96 0.24 189 139 156 17 137.62 0.30 190 139 157 18 136.41 0.53 191 140 155 15 137.96 0.23 192 140 156 16 137.65 0.23 193 141 151 10 159.66 0.95 194 141 152 11 158.25 1.31 195 141 153 12 158.16 1.28 196 141 154 13 152.90 1.55 197 141 155 14 138.12 0.32 198 142 151 9 159.69 0.93 199 142 152 10 159.66 0.94 200 142 194 54 287.64 0.27 201 143 148 5 160.74 0.88 202 143 149 6 160.01 0.99 203 143 150 7 159.87 0.98 204 143 151 8 159.72 0.93 205 143 191 50 193.16 1.10 206 143 192 51 286.29 0.38 207 144 150 6 160.02 0.99 208 144 152 8 159.72 0.91 209 144 156 12 139.06 0.17 210 145 148 3 168.13 0.92 211 145 149 4 160.84 0.93 212 145 150 5 160.34 0.85 213 146 220 71 159.68 0.96 214 146 221 72 159.67 0.95 215 146 221 73 159.66 0.94 216 151 192 43 159.77 0.92 217 152 156 4 169.55 0.57 218 158 184 27 137.85 0.22 219 158 188 32 137.81 0.20 220 158 189 33 137.47 0.11 221 159 184 26 137.93 0.24 222 160 184 24 137.81 0.21 223 160 184 25 137.91 0.24 224 161 183 22 137.84 0.21 225 161 184 23 137.92 0.24 226 161 184 24 139.35 0.46 227 162 181 19 235.11 11.85 228 162 182 20 194.58 8.56 229 162 183 21 174.19 0.32 230 162 201 41 148.07 0.03 231 163 182 19 230.49 14.04 232 163 183 20 179.35 0.97 233 163 184 21 179.38 0.99 234 163 185 23 177.40 1.57 235 163 225 60 153.49 2.73 236 171 223 50 159.79 0.86 237 171 224 51 159.78 0.86 238 171 225 52 159.78 0.86 239 172 215 41 170.74 0.03 240 172 216 42 167.09 1.01 241 172 217 43 164.66 0.21 242 172 224 50 159.82 0.86 243 172 225 51 159.80 0.86 244 172 227 53 159.47 0.74 245 175 215 38 171.40 0.19 246 176 215 37 171.42 0.20 247 176 227 49 159.68 0.92 248 178 230 50 158.21 1.35 249 178 233 53 157.10 1.58 250 179 229 48 158.71 1.10 251 179 230 49 158.14 1.39 252 179 233 52 153.84 0.83 253 179 234 53 148.39 0.31 254 180 215 33 171.87 0.04 255 180 227 45 159.69 0.90 256 180 228 46 159.47 0.91 257 180 230 48 158.07 1.35 258 181 199 20 160.38 0.96 259 181 210 27 159.88 0.93 260 181 211 28 159.89 0.94 261 181 227 44 159.68 0.90 262 181 228 45 158.95 0.98 263 181 229 46 158.24 1.33 264 181 230 47 157.75 1.47 265 182 225 41 159.69 0.91 266 182 226 42 159.68 0.90 267 182 227 43 158.20 1.32 268 183 225 40 159.72 0.90 269 183 226 41 159.68 0.91 270 183 228 43 158.44 1.45 271 184 188 5 261.69 0.09 272 185 222 34 160.54 0.90 273 185 223 35 160.08 0.90 274 185 225 37 159.84 0.98 275 186 222 33 160.56 0.90 276 187 221 30 168.31 0.85 277 187 221 31 167.42 0.48 278 187 222 32 160.56 0.90 279 188 221 29 170.30 0.17 280 188 221 28 170.88 0.12 281 189 221 27 200.05 0.87 282 189 226 33 157.97 1.36 283 190 228 34 157.03 1.59 284 199 228 25 159.03 1.09 285 209 231 22 122.28 0.45 286 210 229 19 159.58 0.89 287 210 230 20 155.83 1.62 288 210 231 21 122.53 0.57 289 210 232 22 112.83 0.67 290 211 228 17 158.90 0.96 291 211 229 18 157.02 1.58 292 211 231 20 114.71 0.26 293 212 228 16 157.97 1.30 294 212 229 17 156.27 1.70 295 212 231 19 126.97 5.87 296 213 228 15 157.56 1.10 297 214 227 13 158.92 0.98 298 214 228 14 157.91 1.28 299 214 229 15 157.46 1.36 300 215 226 11 159.77 0.85 301 215 227 12 159.35 0.77 302 216 226 10 159.44 0.73 303 217 224 7 190.44 3.12 304 221 224 3 286.56 0.17 305 231 235 4 281.25 2.17 306 231 238 7 68.98 0.07 307 232 235 3 87.59 2.44 308 234 237 3 72.04 0.15 309 234 238 4 69.39 0.12 310 235 238 3 71.63 0.36 311 235 239 4 56.67 5.33 312 236 239 3 70.47 0.10 313 236 240 4 56.03 5.58 314 237 240 3 69.44 0.42 315 237 241 4 47.84 1.91 316 238 241 3 65.11 2.58 317 238 242 4 32.76 0.15 318 239 242 3 38.84 2.58 319 239 243 4 31.46 0.48 320 240 243 3 31.84 0.30 321 240 244 4 31.47 0.48 322 241 244 3 33.26 0.61 323 241 245 4 30.78 0.21 324 242 245 3 33.13 0.68