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 58.65 0.59 2 16 140 119 58.64 0.59 3 16 142 121 58.95 0.69 4 16 143 122 61.91 0.55 5 16 144 123 62.25 0.39 6 16 156 135 60.22 1.30 7 16 157 136 59.06 0.73 8 16 158 137 58.97 0.69 9 16 189 170 61.11 0.91 10 16 190 171 58.42 0.51 11 16 194 175 58.43 0.51 12 17 143 121 62.26 0.38 13 17 144 122 62.26 0.38 14 17 145 123 64.30 0.70 15 17 146 124 68.93 1.61 16 17 188 167 62.41 0.30 17 17 188 168 62.30 0.35 18 17 189 169 62.12 0.42 19 17 191 171 62.25 0.38 20 17 220 195 62.27 0.37 21 17 221 196 62.38 0.31 22 18 158 135 65.69 0.74 23 18 188 166 62.43 0.30 24 18 188 167 62.38 0.32 25 19 157 133 65.91 0.66 26 19 158 134 65.60 0.79 27 20 137 112 86.17 1.80 28 20 156 131 123.19 16.59 29 20 157 132 73.76 0.43 30 20 158 133 178.19 4.24 31 20 159 134 267.54 1.94 32 21 71 47 138.73 0.85 33 21 154 128 156.43 0.04 34 21 155 129 157.00 0.32 35 21 156 130 157.20 0.27 36 22 26 4 172.03 1.66 37 22 27 5 160.84 1.33 38 22 71 46 138.75 0.85 39 22 139 112 138.19 0.83 40 22 155 128 162.78 0.89 41 22 156 129 186.74 2.31 42 23 26 3 182.60 1.34 43 24 71 44 142.43 0.61 44 25 28 3 233.06 26.71 45 25 69 41 142.44 0.61 46 25 117 89 139.74 0.54 47 27 30 3 181.43 1.91 48 27 137 105 142.37 0.62 49 27 139 107 147.50 1.94 50 28 116 85 150.77 1.02 51 28 117 86 150.56 1.07 52 28 118 87 149.72 0.89 53 28 119 88 147.56 1.94 54 29 45 14 147.55 1.94 55 29 46 15 144.75 0.54 56 29 119 87 150.09 0.88 57 29 120 88 147.58 1.95 58 29 121 89 144.74 0.54 59 29 198 166 149.88 1.26 60 29 200 168 150.34 1.02 61 30 43 11 150.71 1.03 62 30 44 12 150.69 1.04 63 30 139 104 150.77 1.02 64 30 140 105 150.83 1.03 65 30 141 106 157.30 0.30 66 30 155 120 244.50 21.54 67 30 198 165 150.38 1.01 68 31 43 10 150.81 1.02 69 31 44 11 150.71 1.03 70 31 45 12 150.76 1.02 71 31 46 13 150.81 1.02 72 31 52 19 150.77 1.01 73 31 65 32 157.22 0.30 74 31 66 33 157.20 0.31 75 31 67 34 154.56 0.18 76 31 141 105 157.35 0.32 77 32 40 6 157.70 0.41 78 32 42 8 157.30 0.31 79 32 65 31 157.38 0.29 80 32 66 32 157.25 0.30 81 32 73 38 157.56 0.34 82 32 141 104 157.35 0.32 83 33 40 5 157.88 0.40 84 33 41 6 157.86 0.40 85 33 42 7 157.32 0.32 86 33 43 8 157.33 0.32 87 33 52 17 157.33 0.29 88 33 54 19 157.30 0.30 89 33 63 28 157.75 0.42 90 33 64 29 157.75 0.42 91 33 65 30 157.41 0.29 92 33 104 68 157.71 0.42 93 33 106 70 157.37 0.29 94 34 39 3 167.38 2.17 95 34 40 4 157.88 0.40 96 34 41 5 157.89 0.40 97 34 63 27 157.76 0.42 98 34 64 28 157.75 0.42 99 34 66 30 157.74 0.42 100 37 41 4 178.77 1.75 101 37 60 23 262.70 8.12 102 37 62 25 179.29 1.93 103 40 73 32 288.31 0.09 104 45 121 75 217.96 4.08 105 46 120 73 261.46 2.44 106 46 121 74 243.69 4.02 107 47 120 72 284.26 0.57 108 47 121 73 270.17 1.91 109 47 123 75 202.09 2.36 110 47 238 186 43.69 0.21 111 47 242 190 29.79 0.03 112 48 120 71 287.62 0.70 113 48 242 189 29.79 0.03 114 49 120 70 287.94 0.53 115 51 242 186 29.78 0.03 116 51 245 189 21.18 0.34 117 71 153 80 151.40 1.17 118 71 154 81 150.99 0.98 119 71 155 82 150.37 0.97 120 72 153 79 151.28 1.12 121 72 154 80 151.25 1.11 122 73 153 78 151.28 1.12 123 74 153 77 151.28 1.14 124 87 245 154 21.18 0.58 125 89 237 144 74.58 0.04 126 89 241 148 32.73 1.48 127 89 245 152 22.30 0.03 128 91 234 139 102.81 0.01 129 91 237 142 76.20 0.85 130 92 237 141 97.16 0.65 131 98 180 80 250.78 0.24 132 99 180 79 162.06 4.65 133 99 215 112 288.37 0.18 134 100 177 75 161.38 4.98 135 100 179 77 161.42 4.94 136 100 180 78 161.94 4.69 137 101 179 76 161.41 4.93 138 101 234 129 107.61 1.04 139 102 229 123 151.12 0.52 140 103 229 122 150.24 0.95 141 103 234 127 101.48 0.42 142 103 237 130 72.38 1.41 143 103 238 131 66.77 0.63 144 105 237 128 70.53 0.81 145 105 238 129 43.87 0.39 146 105 241 132 29.82 0.03 147 105 242 133 29.80 0.03 148 107 245 134 19.91 0.07 149 121 209 84 287.16 0.71 150 122 203 81 288.00 0.43 151 122 204 82 283.49 1.25 152 122 209 83 269.91 8.03 153 123 209 82 193.18 3.26 154 123 231 104 284.88 1.33 155 123 235 108 75.23 0.82 156 123 238 111 51.77 3.36 157 124 204 80 184.03 1.77 158 124 209 81 166.33 2.02 159 124 210 82 163.69 1.22 160 124 231 103 286.74 0.42 161 124 232 104 192.18 43.41 162 124 235 107 77.52 0.80 163 125 204 79 180.50 0.22 164 127 210 80 161.54 2.29 165 128 210 79 153.17 0.94 166 129 134 4 166.15 0.86 167 129 162 32 135.94 0.54 168 129 210 78 155.51 0.64 169 130 134 3 182.80 0.97 170 130 162 31 138.57 0.90 171 132 162 30 138.59 0.90 172 132 164 32 138.69 0.86 173 133 161 28 138.59 0.90 174 133 162 29 138.69 0.85 175 134 161 27 138.70 0.86 176 134 162 28 138.73 0.85 177 135 159 24 138.65 0.88 178 135 160 25 138.69 0.86 179 135 161 26 138.72 0.85 180 136 159 23 138.66 0.88 181 136 160 24 138.69 0.86 182 136 162 26 144.63 0.51 183 137 157 20 138.35 0.96 184 137 158 21 138.59 0.90 185 137 159 22 138.60 0.91 186 138 157 19 138.06 0.90 187 138 158 20 138.27 0.86 188 138 160 22 139.50 0.48 189 138 183 45 156.95 0.56 190 138 228 88 158.52 0.79 191 139 155 16 138.78 0.83 192 139 156 17 138.59 0.91 193 139 157 18 138.19 0.83 194 140 155 15 138.76 0.83 195 140 156 16 138.68 0.86 196 141 152 11 150.66 1.05 197 141 153 12 150.66 1.05 198 141 154 13 147.56 1.94 199 141 155 14 138.77 0.83 200 142 151 9 154.18 1.54 201 142 152 10 152.08 0.49 202 142 194 54 288.38 0.29 203 143 148 5 163.54 2.12 204 143 149 6 157.34 0.35 205 143 150 7 156.63 0.42 206 143 151 8 154.81 1.23 207 143 191 50 217.18 0.26 208 143 192 51 288.00 0.42 209 144 150 6 156.91 0.56 210 144 152 8 156.52 0.48 211 144 156 12 138.58 0.89 212 145 148 3 173.16 1.56 213 145 149 4 157.62 0.30 214 145 150 5 157.38 0.35 215 151 192 43 154.35 0.78 216 152 156 4 166.81 1.11 217 158 184 27 150.65 5.09 218 158 188 32 138.72 0.83 219 158 189 33 138.30 0.91 220 159 184 26 150.67 5.09 221 160 183 23 178.41 1.86 222 160 184 24 150.62 5.12 223 160 184 25 150.66 5.09 224 161 183 22 179.51 1.64 225 161 184 23 150.82 5.20 226 161 184 24 150.86 5.19 227 162 181 19 272.43 1.86 228 162 182 20 198.03 0.48 229 162 183 21 181.30 0.75 230 162 201 41 144.60 0.53 231 163 182 19 269.83 3.14 232 163 183 20 198.03 0.48 233 163 184 21 198.02 0.47 234 163 185 23 180.02 1.42 235 163 225 60 147.56 1.97 236 167 185 19 283.72 1.27 237 171 185 15 287.31 0.82 238 171 223 50 155.53 0.62 239 171 224 51 155.80 0.61 240 171 225 52 155.78 0.60 241 172 215 41 163.59 3.81 242 172 216 42 163.37 3.71 243 172 217 43 163.35 3.70 244 172 224 50 155.86 0.61 245 172 225 51 155.87 0.60 246 172 227 53 155.66 0.65 247 175 215 38 163.62 3.85 248 176 215 37 163.62 3.85 249 176 227 49 155.68 0.69 250 178 230 50 155.40 0.72 251 178 233 53 150.39 0.86 252 179 229 48 155.40 0.72 253 179 230 49 153.09 0.02 254 179 233 52 150.19 0.96 255 179 234 53 147.37 0.45 256 180 215 33 163.55 3.84 257 180 227 45 155.70 0.64 258 180 228 46 155.58 0.64 259 180 230 48 152.03 0.37 260 181 210 27 155.87 0.61 261 181 227 44 155.62 0.62 262 181 228 45 155.31 0.76 263 181 230 47 150.69 1.02 264 182 225 41 155.69 0.68 265 182 226 42 155.60 0.63 266 182 227 43 152.90 0.30 267 183 199 18 156.62 0.70 268 183 226 41 155.69 0.66 269 183 228 43 155.35 0.74 270 184 225 39 155.87 0.60 271 184 188 5 286.56 0.47 272 185 222 34 156.93 0.71 273 185 223 35 156.12 0.65 274 185 225 37 155.91 0.60 275 186 222 33 156.94 0.71 276 187 221 30 162.82 3.46 277 187 221 31 159.24 1.70 278 187 222 32 157.82 1.16 279 188 221 29 162.84 3.45 280 188 221 28 177.59 3.77 281 189 220 26 288.01 0.20 282 189 221 27 223.81 17.98 283 189 226 33 155.33 0.76 284 190 228 34 153.75 1.54 285 199 228 25 155.72 0.61 286 209 231 22 113.62 0.98 287 210 229 19 155.81 0.56 288 210 230 20 153.18 0.94 289 210 231 21 117.12 0.22 290 210 232 22 109.75 0.03 291 211 228 17 155.62 0.63 292 211 229 18 153.66 1.04 293 211 231 20 116.28 0.35 294 212 228 16 153.69 0.98 295 212 229 17 152.54 1.23 296 212 231 19 117.92 0.61 297 213 228 15 153.33 1.01 298 214 227 13 155.65 0.65 299 214 228 14 155.02 0.34 300 214 229 15 152.99 1.16 301 215 226 11 155.90 0.58 302 215 227 12 155.63 0.63 303 217 224 7 183.62 2.54 304 221 224 3 283.05 2.15 305 229 234 5 288.26 0.09 306 230 233 3 288.48 0.01 307 230 234 4 288.48 0.01 308 231 234 3 288.48 0.01 309 231 238 7 66.62 0.71 310 232 235 3 84.98 1.48 311 234 237 3 72.21 1.45 312 234 238 4 66.87 0.59 313 235 238 3 70.40 2.35 314 235 239 4 66.87 0.59 315 236 239 3 70.40 2.35 316 236 240 4 66.61 0.71 317 237 240 3 54.52 5.16 318 237 241 4 41.79 0.14 319 238 241 3 56.03 4.41 320 238 242 4 30.25 0.24 321 239 242 3 53.13 10.04 322 239 243 4 30.24 0.24 323 240 243 3 38.54 2.73 324 240 244 4 29.80 0.03 325 241 244 3 70.17 1.52 326 241 245 4 29.30 0.24 327 242 245 3 48.59 9.29