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 2 115 113 64.20 8.32 2 2 124 122 61.77 8.07 3 2 125 123 61.44 7.96 4 2 126 124 61.42 7.96 5 2 130 128 61.47 7.94 6 3 127 124 61.49 7.93 7 3 130 127 61.51 7.93 8 4 124 120 63.47 8.70 9 4 125 121 61.66 7.88 10 4 127 123 61.52 7.94 11 5 110 105 62.79 8.49 12 5 124 119 63.48 8.70 13 5 125 120 63.50 8.69 14 6 110 104 63.52 8.64 15 6 121 115 91.58 1.38 16 6 122 116 91.58 1.38 17 6 123 117 87.73 0.74 18 6 124 118 63.50 8.70 19 6 125 119 63.48 8.70 20 7 110 103 63.52 8.64 21 7 111 104 63.52 8.65 22 7 112 105 65.69 7.59 23 7 120 113 99.23 0.11 24 7 121 114 99.23 0.11 25 7 122 115 97.81 0.61 26 7 125 118 85.06 2.08 27 8 11 3 359.61 3.60 28 8 109 101 63.55 8.66 29 8 110 102 65.69 7.59 30 8 122 114 99.92 0.23 31 9 14 5 339.50 4.18 32 9 122 113 100.11 0.14 33 10 13 3 366.66 0.08 34 10 14 4 339.65 4.09 35 11 14 3 359.95 3.14 36 11 15 4 349.92 1.04 37 11 39 28 115.20 2.19 38 11 42 31 115.12 2.21 39 11 46 35 114.23 2.67 40 11 109 98 101.33 0.64 41 11 111 100 109.08 2.12 42 11 120 109 114.20 2.67 43 12 15 3 356.38 1.21 44 12 16 4 349.91 1.04 45 12 39 27 115.18 2.21 46 13 16 3 356.25 1.28 47 13 17 4 349.92 1.06 48 14 17 3 360.06 2.78 49 14 18 4 348.70 1.67 50 14 109 95 115.20 2.21 51 15 18 3 414.14 3.56 52 15 19 4 352.88 0.42 53 15 38 23 309.46 1.56 54 15 39 24 210.08 36.59 55 15 42 27 136.73 0.03 56 15 61 46 136.92 0.01 57 15 105 90 115.20 2.21 58 16 19 3 371.40 4.38 59 16 20 4 523.34 1.59 60 16 35 19 337.06 4.04 61 16 36 20 333.49 2.27 62 16 39 23 294.82 0.81 63 18 104 86 137.07 0.04 64 18 105 87 137.08 0.04 65 18 106 88 137.10 0.04 66 18 107 89 137.08 0.04 67 18 109 91 137.15 0.07 68 19 38 19 360.99 1.29 69 19 101 82 137.15 0.07 70 19 105 86 137.15 0.06 71 22 67 45 143.19 1.14 72 22 91 69 143.02 1.15 73 22 95 73 143.03 1.14 74 22 99 77 143.05 1.15 75 22 100 78 143.06 1.14 76 22 101 79 143.07 1.14 77 22 104 82 143.06 1.14 78 25 90 65 143.08 1.14 79 25 91 66 143.07 1.15 80 26 67 41 143.19 1.14 81 26 101 75 143.29 1.08 82 30 67 37 143.31 1.08 83 30 68 38 143.31 1.08 84 33 64 31 145.16 0.78 85 33 65 32 144.16 0.73 86 33 66 33 144.71 0.56 87 33 67 34 143.40 1.11 88 33 101 68 143.44 1.12 89 34 38 4 532.18 4.06 90 35 38 3 365.05 0.74 91 35 39 4 355.62 1.37 92 36 39 3 367.40 0.86 93 36 40 4 355.06 1.65 94 37 40 3 358.36 0.03 95 37 41 4 357.81 0.27 96 37 64 27 145.45 0.80 97 38 41 3 361.80 1.69 98 38 42 4 348.42 3.46 99 38 61 23 145.40 0.81 100 38 64 26 145.45 0.80 101 38 65 27 145.38 0.83 102 38 101 63 145.43 0.79 103 39 42 3 358.38 0.03 104 39 43 4 344.79 5.38 105 39 46 7 344.42 5.17 106 40 43 3 366.56 0.44 107 40 44 4 356.75 0.60 108 41 44 3 371.40 1.95 109 41 60 19 148.19 0.14 110 41 61 20 148.06 0.20 111 41 64 23 148.10 0.18 112 42 45 3 425.81 2.79 113 42 46 4 372.32 1.49 114 42 58 16 148.15 0.18 115 42 61 19 148.14 0.18 116 42 111 69 300.87 2.60 117 42 139 97 148.15 0.18 118 43 46 3 371.41 1.94 119 43 47 4 368.54 0.51 120 44 47 3 370.19 0.33 121 44 48 4 367.94 0.21 122 44 57 13 222.08 36.76 123 45 48 3 363.58 2.98 124 45 53 8 287.84 5.75 125 45 58 13 222.05 36.75 126 46 111 65 341.30 6.95 127 46 112 66 343.58 6.05 128 46 113 67 353.55 1.10 129 46 120 74 374.90 1.88 130 47 113 66 380.04 0.39 131 48 52 4 557.93 2.10 132 48 53 5 542.04 13.20 133 48 57 9 442.40 36.30 134 48 113 65 398.26 3.36 135 49 113 64 400.25 2.57 136 50 112 62 399.56 2.73 137 50 113 63 400.25 2.57 138 50 114 64 412.06 3.27 139 50 115 65 415.96 5.22 140 50 126 76 419.84 0.22 141 50 134 84 409.41 2.49 142 50 135 85 398.76 3.10 143 51 126 75 441.54 2.06 144 51 133 82 422.21 1.25 145 51 134 83 413.45 0.47 146 52 133 81 444.41 0.23 147 53 133 80 569.80 1.98 148 53 134 81 443.78 0.26 149 53 135 82 425.44 0.34 150 53 138 85 420.07 0.13 151 54 138 84 420.08 0.13 152 55 138 83 421.11 0.42 153 55 141 86 416.83 0.88 154 55 142 87 415.35 1.44 155 58 138 80 429.81 0.42 156 58 139 81 424.11 1.58 157 58 142 84 421.05 0.57 158 59 142 83 422.29 0.71 159 62 142 80 424.14 1.58 160 62 143 81 423.95 1.58 161 62 146 84 415.06 1.55 162 66 146 80 423.93 1.59 163 66 150 84 412.50 1.58 164 69 147 78 423.98 1.58 165 69 150 81 413.57 1.38 166 71 152 81 412.51 1.57 167 71 153 82 412.17 1.43 168 71 188 117 270.39 1.33 169 72 152 80 414.04 0.81 170 72 153 81 408.69 0.03 171 72 154 82 397.76 2.01 172 72 156 84 396.68 2.51 173 74 147 73 425.79 1.52 174 74 151 77 412.56 1.54 175 74 155 81 343.79 3.29 176 74 156 82 340.46 4.96 177 75 147 72 426.88 2.02 178 75 156 81 332.00 9.08 179 75 157 82 331.99 9.08 180 75 158 83 331.99 9.08 181 75 193 118 263.44 3.49 182 76 147 71 426.87 2.00 183 76 148 72 425.68 1.43 184 76 151 75 420.29 1.14 185 76 155 79 351.18 0.40 186 76 156 80 332.10 9.10 187 76 157 81 331.86 9.11 188 76 158 82 331.87 9.11 189 76 174 98 272.18 0.71 190 76 178 102 272.16 0.71 191 76 182 106 272.00 0.75 192 77 157 80 331.86 9.11 193 77 158 81 331.81 9.10 194 78 158 80 331.81 9.10 195 78 159 81 331.52 9.10 196 78 160 82 331.42 9.14 197 78 169 91 272.61 0.65 198 78 172 94 272.41 0.62 199 78 173 95 272.36 0.62 200 78 174 96 272.12 0.71 201 79 160 81 330.89 9.02 202 79 163 84 308.11 16.75 203 79 169 90 272.78 0.61 204 80 158 78 331.72 9.12 205 83 158 75 331.95 9.06 206 83 195 112 262.56 3.59 207 83 234 151 58.38 7.37 208 83 237 154 54.93 5.75 209 83 238 155 52.32 4.88 210 84 158 74 331.85 9.12 211 86 237 151 52.34 4.88 212 87 158 71 332.05 9.05 213 87 193 106 263.49 3.50 214 87 231 144 124.26 22.11 215 87 233 146 59.52 6.99 216 87 234 147 57.78 7.08 217 87 237 150 52.34 4.88 218 94 156 62 359.59 3.06 219 94 193 99 263.54 3.51 220 95 147 52 425.29 1.31 221 96 147 51 423.93 1.59 222 97 143 46 430.47 0.21 223 97 144 47 425.85 1.55 224 97 147 50 415.56 1.46 225 100 147 47 420.22 0.88 226 102 143 41 424.08 1.57 227 102 146 44 421.06 0.77 228 102 147 45 415.48 1.40 229 102 150 48 412.51 1.58 230 128 137 9 424.37 0.54 231 131 134 3 452.12 2.02 232 132 141 9 416.62 1.02 233 133 138 5 420.32 0.03 234 134 137 3 435.10 2.23 235 134 138 4 424.80 1.21 236 135 138 3 432.19 0.53 237 135 139 4 424.84 1.19 238 136 139 3 425.71 1.56 239 136 140 4 424.99 1.15 240 137 140 3 427.25 1.76 241 137 141 4 425.00 1.14 242 138 141 3 424.96 1.12 243 138 142 4 424.93 1.10 244 139 142 3 424.93 1.10 245 139 143 4 424.90 1.09 246 140 143 3 424.93 1.10 247 140 144 4 420.54 1.03 248 140 173 33 271.98 0.69 249 141 144 3 424.43 1.37 250 141 145 4 420.13 1.21 251 141 173 32 271.99 0.69 252 141 177 36 271.88 0.69 253 142 145 3 422.12 0.21 254 142 146 4 413.35 1.19 255 143 146 3 413.34 1.19 256 143 147 4 412.59 1.54 257 144 147 3 412.57 1.54 258 144 148 4 412.52 1.56 259 144 173 29 272.04 0.70 260 144 177 33 271.99 0.69 261 144 178 34 271.89 0.68 262 145 148 3 419.48 1.92 263 145 149 4 412.29 1.47 264 145 177 32 272.00 0.68 265 145 181 36 271.41 0.89 266 146 149 3 409.28 0.04 267 146 150 4 408.09 0.62 268 147 150 3 408.99 0.18 269 147 151 4 408.09 0.62 270 148 151 3 408.08 0.63 271 148 178 30 272.04 0.70 272 148 181 33 271.57 0.86 273 148 182 34 271.19 0.99 274 149 181 32 271.86 0.75 275 149 183 34 270.77 1.20 276 149 186 37 270.36 1.31 277 150 186 36 270.39 1.33 278 151 155 4 369.96 1.24 279 151 186 35 270.44 1.31 280 152 186 34 270.37 1.32 281 152 187 35 270.29 1.29 282 153 186 33 270.43 1.30 283 153 187 34 270.31 1.31 284 153 188 35 270.28 1.30 285 153 189 36 270.26 1.31 286 154 188 34 270.25 1.30 287 154 189 35 268.84 1.73 288 155 182 27 272.07 0.75 289 155 187 32 270.29 1.30 290 155 189 34 268.30 1.51 291 155 190 35 263.66 3.54 292 155 191 36 263.66 3.54 293 156 191 35 263.57 3.52 294 156 193 37 263.49 3.50 295 157 174 17 272.43 0.64 296 157 190 33 263.67 3.54 297 157 191 34 263.54 3.52 298 157 192 35 263.43 3.50 299 157 193 36 263.43 3.50 300 158 193 35 263.37 3.53 301 158 195 37 262.88 3.65 302 158 234 76 61.73 7.83 303 159 167 8 272.93 0.65 304 159 168 9 272.93 0.65 305 159 192 33 263.48 3.52 306 159 193 34 263.37 3.53 307 159 194 35 263.09 3.56 308 159 195 36 263.07 3.56 309 159 211 52 252.99 0.06 310 159 214 55 253.21 0.17 311 160 163 3 360.69 1.36 312 160 167 7 272.92 0.65 313 160 195 35 263.09 3.56 314 161 167 6 272.92 0.66 315 161 194 33 263.32 3.52 316 161 195 34 263.21 3.56 317 161 196 35 263.09 3.55 318 161 202 41 253.05 0.03 319 161 203 42 253.00 0.03 320 161 204 43 252.12 0.33 321 162 196 34 263.11 3.54 322 162 197 35 263.10 3.54 323 162 201 39 253.19 0.09 324 162 203 41 252.99 0.02 325 163 166 3 356.71 4.85 326 163 203 40 253.18 0.09 327 164 203 39 253.19 0.09 328 166 203 37 253.20 0.10 329 166 204 38 252.99 0.01 330 166 210 44 253.19 0.11 331 167 194 27 263.16 3.56 332 167 204 37 252.94 0.03 333 167 210 43 253.16 0.12 334 167 211 44 253.02 0.06 335 168 174 6 285.19 2.54 336 168 175 7 285.18 2.54 337 168 179 11 284.70 2.32 338 168 210 42 253.02 0.05 339 168 211 43 253.00 0.06 340 168 213 45 253.24 0.16 341 168 214 46 253.22 0.16 342 168 217 49 253.23 0.15 343 169 172 3 364.03 0.09 344 169 175 6 309.50 7.74 345 170 175 5 309.50 7.74 346 170 213 43 253.23 0.16 347 171 175 4 317.97 6.57 348 171 176 5 310.01 7.70 349 172 175 3 358.26 1.17 350 172 176 4 333.43 1.16 351 173 176 3 361.85 0.94 352 173 177 4 313.37 6.08 353 173 178 5 310.12 7.71 354 174 178 4 310.12 7.71 355 174 179 5 313.69 6.78 356 174 180 6 314.43 6.42 357 174 214 40 253.09 0.11 358 175 179 4 336.48 2.64 359 175 180 5 342.42 0.33 360 175 217 42 252.69 0.07 361 176 180 4 359.44 1.78 362 177 180 3 372.58 3.04 363 177 181 4 360.48 1.26 364 178 181 3 361.54 1.09 365 178 182 4 358.01 2.50 366 179 182 3 365.12 1.06 367 179 214 35 252.92 0.18 368 179 217 38 252.68 0.06 369 179 218 39 252.62 0.07 370 179 221 42 252.16 0.18 371 180 217 37 252.68 0.06 372 182 187 5 306.94 10.97 373 182 190 8 273.44 0.79 374 182 223 41 245.78 2.18 375 183 186 3 370.74 5.25 376 183 187 4 358.30 0.62 377 184 187 3 361.52 0.94 378 184 221 37 247.11 1.63 379 184 222 38 246.98 1.65 380 184 223 39 245.78 2.15 381 187 190 3 474.87 1.97 382 187 223 36 245.78 2.17 383 188 224 36 245.75 2.16 384 189 224 35 245.75 2.16 385 190 218 28 252.46 0.01 386 190 223 33 247.00 1.67 387 190 224 34 245.84 2.12 388 190 225 35 245.59 2.13 389 190 226 36 244.66 2.22 390 191 226 35 241.40 0.93 391 191 228 37 230.51 3.11 392 192 211 19 252.68 0.10 393 192 214 22 252.81 0.14 394 192 218 26 252.71 0.09 395 192 225 33 245.89 2.12 396 192 226 34 245.49 2.06 397 192 227 35 226.75 0.76 398 192 228 36 219.36 1.27 399 193 228 35 204.62 1.01 400 193 231 38 124.12 22.04 401 193 234 41 63.29 7.51 402 194 204 10 252.17 0.01 403 194 205 11 246.03 2.16 404 194 206 12 245.88 2.10 405 194 211 17 252.95 0.07 406 194 227 33 241.48 0.89 407 194 228 34 213.52 0.82 408 194 229 35 194.09 3.81 409 194 230 36 177.93 0.42 410 195 230 35 173.18 2.48 411 195 231 36 173.18 2.48 412 195 234 39 62.23 8.04 413 195 235 40 62.22 8.04 414 195 238 43 59.57 7.92 415 196 202 6 253.14 0.09 416 196 204 8 253.00 0.05 417 196 205 9 252.15 0.32 418 196 229 33 203.86 0.92 419 196 230 34 193.72 3.92 420 196 235 39 62.24 8.04 421 196 238 42 59.60 7.92 422 197 200 3 322.67 13.93 423 197 201 4 322.66 13.93 424 198 235 37 121.11 20.53 425 198 238 40 59.61 7.92 426 198 239 41 59.56 7.92 427 198 242 44 59.57 7.92 428 198 245 47 59.52 7.92 429 198 247 49 59.49 7.92 430 198 248 50 59.50 7.92 431 199 245 46 59.52 7.92 432 199 247 48 59.49 7.92 433 202 205 3 450.91 2.25 434 205 229 24 253.24 12.42 435 206 228 22 494.06 1.11 436 206 229 23 311.44 4.07 437 228 231 3 375.87 1.99 438 230 235 5 343.12 1.24 439 231 234 3 366.54 2.19 440 231 235 4 343.32 1.27 441 232 235 3 359.82 0.43 442 232 236 4 343.72 1.07 443 233 236 3 362.45 1.78 444 233 237 4 352.10 2.01 445 234 237 3 356.88 4.38 446 234 238 4 351.73 2.19 447 235 238 3 363.32 0.52 448 235 239 4 343.49 1.20 449 236 239 3 346.61 0.75 450 236 240 4 559.77 2.75