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 50.05 1.39 2 16 140 119 53.99 3.35 3 16 142 121 54.02 3.31 4 16 143 122 60.56 0.77 5 16 144 123 61.08 1.01 6 16 156 134 57.48 2.17 7 16 158 136 60.26 0.61 8 16 189 169 60.27 0.74 9 16 190 170 50.07 1.40 10 16 194 174 44.58 1.35 11 17 143 121 61.51 0.80 12 17 144 122 61.51 0.80 13 17 145 123 61.65 0.80 14 17 158 135 61.63 0.73 15 17 188 166 61.72 0.82 16 17 188 167 61.58 0.76 17 17 189 168 60.48 0.72 18 17 191 170 60.58 0.76 19 17 220 194 61.41 0.80 20 17 221 195 61.54 0.78 21 18 158 134 61.70 0.76 22 18 188 165 61.72 0.82 23 18 188 166 61.65 0.80 24 19 157 132 61.77 0.77 25 19 158 133 61.69 0.77 26 20 156 130 119.64 15.83 27 20 157 131 69.25 1.25 28 20 158 132 68.14 1.07 29 21 71 47 141.38 0.48 30 21 154 127 151.36 0.58 31 21 155 128 151.91 0.30 32 21 156 129 132.25 9.53 33 22 26 4 181.80 6.63 34 22 27 5 168.03 0.98 35 22 71 46 141.38 0.48 36 22 139 112 139.62 0.79 37 22 155 127 156.91 0.07 38 22 156 128 193.51 1.56 39 23 26 3 202.75 1.34 40 24 71 44 145.12 0.90 41 25 28 3 187.47 0.54 42 25 69 41 143.22 0.07 43 25 71 43 149.02 0.88 44 25 77 49 150.35 0.59 45 25 79 51 149.75 0.79 46 25 117 89 142.21 0.10 47 27 30 3 242.35 10.71 48 27 137 105 142.53 0.27 49 27 139 107 142.72 0.21 50 27 157 124 281.64 0.38 51 28 117 86 149.81 0.59 52 28 118 87 147.12 0.56 53 28 119 88 145.25 0.76 54 29 45 14 143.26 0.06 55 29 46 15 143.24 0.07 56 29 119 87 148.39 1.19 57 29 120 88 145.79 1.02 58 29 121 89 143.26 0.06 59 29 198 165 148.92 1.21 60 29 200 167 149.32 0.58 61 30 43 11 150.17 0.70 62 30 44 12 149.94 0.65 63 30 139 104 150.11 0.67 64 30 140 105 150.56 0.69 65 30 141 106 152.30 0.24 66 30 155 119 254.50 4.49 67 30 198 164 149.81 0.77 68 31 43 10 151.29 0.47 69 31 44 11 150.04 0.66 70 31 45 12 150.08 0.67 71 31 46 13 150.06 0.67 72 31 52 19 150.08 0.67 73 31 65 32 152.30 0.31 74 31 66 33 152.28 0.31 75 31 67 34 151.47 0.55 76 31 141 105 152.32 0.24 77 32 40 6 152.90 0.13 78 32 42 8 152.38 0.28 79 32 43 9 151.90 0.27 80 32 65 31 152.40 0.28 81 32 66 32 152.31 0.30 82 32 73 38 152.85 0.11 83 32 141 104 152.31 0.24 84 33 40 5 152.99 0.12 85 33 41 6 152.94 0.11 86 33 42 7 152.38 0.28 87 33 43 8 152.36 0.27 88 33 52 17 152.38 0.28 89 33 54 19 152.38 0.27 90 33 58 23 152.67 0.32 91 33 63 28 152.94 0.20 92 33 64 29 152.93 0.20 93 33 65 30 152.56 0.26 94 33 104 68 152.43 0.24 95 33 106 70 152.49 0.23 96 34 39 3 182.84 0.08 97 34 40 4 153.11 0.07 98 34 41 5 153.10 0.06 99 34 63 27 154.10 0.33 100 34 64 28 153.03 0.15 101 34 66 30 152.97 0.18 102 37 41 4 219.17 4.62 103 37 60 23 262.10 3.75 104 37 63 26 154.13 0.35 105 40 43 3 283.50 0.00 106 40 73 32 283.23 0.12 107 40 193 151 283.50 0.00 108 41 193 150 283.50 0.00 109 45 121 75 232.19 3.54 110 46 119 72 283.50 0.00 111 46 120 73 279.62 1.81 112 46 121 74 275.44 3.41 113 47 120 72 283.32 0.03 114 47 121 73 279.26 1.51 115 47 123 75 200.69 0.83 116 47 242 189 29.36 0.27 117 48 120 71 283.38 0.00 118 48 242 188 29.36 0.27 119 51 241 184 42.00 2.31 120 51 242 185 29.32 0.29 121 53 103 49 283.50 0.00 122 53 238 179 51.52 0.33 123 69 79 10 283.50 0.00 124 70 141 69 283.50 0.00 125 71 141 68 283.50 0.00 126 71 153 79 150.05 0.63 127 71 154 80 149.54 0.64 128 71 155 81 147.68 1.21 129 72 153 78 150.00 0.65 130 72 154 79 149.55 0.64 131 73 153 77 149.99 0.67 132 74 153 76 150.06 0.65 133 76 80 4 283.50 0.00 134 79 117 38 283.50 0.00 135 81 112 31 283.50 0.00 136 81 113 32 283.50 0.00 137 81 118 37 283.50 0.00 138 83 109 26 283.50 0.00 139 84 109 25 283.50 0.00 140 85 109 24 283.50 0.00 141 86 109 23 283.50 0.00 142 87 245 153 24.63 0.74 143 89 237 143 73.09 0.74 144 89 241 147 41.87 2.45 145 90 237 142 75.86 0.64 146 91 234 138 104.21 0.61 147 91 237 141 73.09 0.74 148 92 237 140 89.50 1.02 149 98 180 79 232.53 11.34 150 99 180 78 185.84 11.93 151 99 214 110 283.50 0.00 152 100 177 74 185.75 11.95 153 100 179 76 185.77 11.96 154 100 180 77 185.76 11.96 155 101 179 75 185.69 11.98 156 101 234 128 125.34 6.94 157 102 229 122 150.78 0.76 158 103 231 123 149.47 1.16 159 103 234 126 94.19 0.36 160 103 237 129 73.08 0.74 161 103 238 130 71.06 0.57 162 104 237 128 73.05 0.73 163 105 237 127 73.04 0.72 164 105 238 128 63.29 0.12 165 105 241 131 30.28 0.61 166 105 242 132 29.32 0.29 167 107 245 133 20.04 1.05 168 121 200 78 283.44 0.03 169 121 204 82 283.44 0.03 170 121 209 83 283.41 0.05 171 122 203 80 283.48 0.01 172 122 204 81 282.85 0.27 173 122 209 82 274.90 3.66 174 123 209 81 195.43 2.75 175 123 231 103 197.41 22.73 176 123 235 107 74.53 0.90 177 123 238 110 65.61 1.91 178 123 239 111 62.80 3.28 179 123 242 114 32.40 0.34 180 124 204 79 188.68 6.12 181 124 209 80 169.18 2.31 182 124 210 81 166.26 1.75 183 124 231 102 276.29 0.50 184 124 232 103 105.91 0.38 185 124 235 106 75.84 0.32 186 125 204 78 193.72 3.60 187 127 210 79 156.88 1.72 188 127 232 101 283.50 0.00 189 128 210 78 151.34 0.48 190 129 134 4 161.88 0.76 191 129 162 31 139.65 0.15 192 129 210 77 151.49 0.47 193 130 134 3 175.59 0.93 194 130 162 30 141.26 0.52 195 132 162 29 141.29 0.51 196 132 163 30 141.62 0.59 197 132 164 31 141.66 0.61 198 133 162 28 141.63 0.60 199 134 161 26 141.62 0.61 200 134 162 27 141.69 0.60 201 134 201 68 283.49 0.00 202 135 159 23 141.58 0.62 203 135 160 24 141.66 0.61 204 135 161 25 141.68 0.60 205 136 159 22 141.58 0.61 206 136 160 23 141.65 0.62 207 136 162 25 142.55 0.27 208 136 199 64 283.50 0.00 209 137 157 19 138.69 0.30 210 137 158 20 140.98 0.50 211 137 159 21 141.47 0.65 212 138 157 18 138.69 0.33 213 138 158 19 140.56 0.32 214 138 160 21 141.72 0.61 215 138 190 53 283.28 0.12 216 138 228 87 151.62 0.42 217 139 155 15 141.69 0.62 218 139 156 16 141.23 0.59 219 139 157 17 138.69 0.32 220 140 155 14 141.69 0.62 221 140 156 15 141.33 0.49 222 141 152 10 147.67 0.09 223 141 153 11 147.33 0.26 224 141 154 12 145.68 0.97 225 141 155 13 141.64 0.58 226 142 152 9 149.24 0.68 227 142 192 51 283.50 0.01 228 142 193 52 283.49 0.01 229 142 194 53 283.32 0.09 230 143 191 49 257.87 5.59 231 143 192 50 283.30 0.08 232 144 150 5 152.09 0.33 233 144 151 6 150.96 0.12 234 144 152 7 150.43 0.39 235 144 156 11 142.91 1.23 236 145 220 71 154.65 1.30 237 145 221 72 154.64 1.29 238 147 150 3 163.55 0.27 239 150 156 6 152.08 0.24 240 151 154 3 168.50 0.91 241 151 156 5 152.25 0.30 242 158 188 32 141.31 0.57 243 158 189 33 141.04 0.69 244 159 184 26 170.63 0.36 245 160 183 23 185.99 5.64 246 160 184 24 167.91 1.08 247 160 184 25 167.91 1.08 248 160 199 41 141.68 0.61 249 160 228 66 141.41 0.64 250 161 183 22 213.22 3.43 251 161 184 23 185.98 5.64 252 161 184 24 177.16 1.24 253 162 181 19 283.01 0.17 254 162 182 20 274.60 0.03 255 162 183 21 224.41 6.02 256 162 201 41 142.57 0.26 257 163 167 4 283.48 0.01 258 163 182 19 278.37 0.69 259 163 183 20 264.34 5.08 260 163 184 21 274.61 0.07 261 163 185 23 226.28 1.66 262 163 225 60 147.51 0.25 263 164 168 4 283.49 0.01 264 165 168 3 283.49 0.01 265 165 169 4 283.49 0.01 266 167 171 4 283.50 0.00 267 167 185 19 283.29 0.05 268 168 171 3 283.50 0.00 269 168 172 4 283.50 0.00 270 170 173 3 283.50 0.00 271 171 185 15 283.48 0.01 272 171 223 50 151.50 0.48 273 171 225 52 151.37 0.47 274 172 215 41 162.94 0.42 275 172 216 42 156.24 2.85 276 172 217 43 156.22 2.83 277 172 224 50 151.52 0.48 278 172 225 51 151.52 0.48 279 172 227 53 150.97 0.67 280 175 215 38 156.36 2.89 281 176 215 37 156.35 2.88 282 176 227 49 151.47 0.47 283 178 230 50 151.04 0.64 284 178 233 53 150.40 0.61 285 179 229 48 151.20 0.57 286 179 230 49 150.94 0.67 287 179 233 52 148.77 0.24 288 179 234 53 143.52 0.19 289 180 215 33 185.69 11.85 290 180 227 45 151.44 0.47 291 180 228 46 151.03 0.65 292 180 230 48 150.88 0.69 293 181 199 20 151.88 0.45 294 181 210 27 151.25 0.53 295 181 211 28 151.37 0.48 296 181 227 44 151.41 0.46 297 181 228 45 150.98 0.67 298 181 229 46 150.97 0.66 299 181 230 47 150.84 0.69 300 182 225 41 151.47 0.48 301 182 226 42 151.42 0.46 302 182 227 43 150.91 0.68 303 183 225 40 151.53 0.47 304 183 226 41 151.50 0.49 305 183 228 43 151.34 0.49 306 184 187 3 283.20 0.14 307 184 188 5 281.98 0.27 308 185 222 34 153.23 1.09 309 185 223 35 151.82 0.48 310 185 225 37 151.74 0.48 311 186 222 33 153.27 1.10 312 187 221 30 155.49 2.02 313 187 221 31 155.41 2.03 314 187 222 32 153.34 1.14 315 188 221 29 155.52 2.02 316 188 221 28 205.91 27.21 317 189 220 26 283.23 0.01 318 189 221 27 256.33 2.00 319 189 226 33 151.12 0.62 320 190 228 34 150.97 0.71 321 194 197 3 283.50 0.00 322 195 214 15 283.50 0.00 323 199 211 8 283.49 0.01 324 199 228 25 151.61 0.43 325 209 231 22 110.75 0.35 326 210 230 20 151.48 0.47 327 210 231 21 118.28 3.41 328 210 232 22 104.79 0.19 329 211 228 17 151.58 0.45 330 211 229 18 151.48 0.47 331 211 231 20 121.98 5.26 332 212 228 16 151.24 0.59 333 212 229 17 150.87 0.67 334 212 231 19 122.81 1.72 335 213 228 15 150.91 0.69 336 214 227 13 151.59 0.43 337 214 228 14 151.15 0.64 338 214 229 15 150.92 0.69 339 215 226 11 151.72 0.45 340 215 227 12 151.48 0.48 341 217 224 7 173.19 3.49 342 221 224 3 281.88 0.72 343 230 233 3 283.41 0.04 344 230 234 4 281.62 0.28 345 231 234 3 281.60 0.27 346 231 235 4 251.31 15.42 347 231 238 7 70.92 0.64 348 232 235 3 83.56 0.04 349 234 237 3 71.75 0.49 350 234 238 4 71.28 0.70 351 235 238 3 71.17 0.76 352 235 239 4 70.61 0.48 353 236 239 3 71.23 0.73 354 236 240 4 70.79 0.74 355 237 240 3 58.10 3.62 356 237 241 4 51.45 0.34 357 238 241 3 34.26 1.35 358 238 242 4 30.27 0.60 359 239 242 3 32.59 0.44 360 239 243 4 31.52 0.01 361 240 243 3 70.23 1.60 362 240 244 4 29.49 0.21 363 241 244 3 29.55 0.33