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 16 146 130 47.42 0.80 2 16 148 132 47.08 0.06 3 16 149 133 52.24 0.34 4 16 150 134 52.72 0.42 5 16 161 145 48.55 0.30 6 16 162 146 48.55 0.29 7 16 163 147 48.86 0.45 8 16 197 181 49.27 0.24 9 16 198 182 45.87 0.28 10 16 202 186 42.77 1.28 11 17 149 132 52.91 0.33 12 17 150 133 52.74 0.41 13 17 151 134 52.92 0.33 14 17 152 135 52.95 0.34 15 17 195 178 52.75 0.42 16 17 196 179 52.69 0.44 17 17 197 180 52.32 0.33 18 17 199 182 52.16 0.39 19 17 229 212 52.41 0.29 20 17 230 213 52.70 0.42 21 18 195 177 52.73 0.42 22 18 196 178 52.73 0.42 23 19 162 143 52.74 0.42 24 19 163 144 52.73 0.42 25 20 161 141 59.29 0.72 26 20 162 142 57.52 0.10 27 21 75 54 153.24 29.91 28 21 159 138 74.38 5.13 29 21 160 139 65.23 1.36 30 21 161 140 64.77 1.48 31 22 26 4 429.54 9.17 32 22 27 5 404.50 9.06 33 22 75 53 153.94 29.59 34 22 160 138 66.09 0.98 35 22 162 140 65.56 1.19 36 23 26 3 432.04 7.92 37 24 75 51 205.15 4.08 38 24 81 57 209.49 1.95 39 25 28 3 445.78 6.38 40 25 122 97 204.66 3.88 41 25 123 98 204.59 3.92 42 27 30 3 441.12 0.43 43 27 143 116 156.97 7.61 44 27 145 118 137.54 0.14 45 27 162 135 153.44 5.09 46 27 208 181 170.44 0.87 47 27 215 188 183.06 0.28 48 28 122 94 205.22 4.05 49 28 123 95 205.21 4.05 50 28 124 96 205.12 4.01 51 28 125 97 205.05 4.02 52 29 48 19 279.18 0.66 53 29 49 20 270.19 1.02 54 29 125 96 205.06 4.01 55 29 126 97 205.06 4.01 56 29 127 98 205.00 4.03 57 30 46 16 286.76 1.36 58 30 47 17 286.38 1.54 59 30 145 115 187.38 1.08 60 30 147 117 194.28 0.21 61 30 160 130 194.19 0.18 62 30 206 176 180.00 0.30 63 31 46 15 286.78 1.36 64 31 47 16 286.48 1.51 65 31 48 17 286.42 1.54 66 31 49 18 286.36 1.55 67 31 55 24 286.33 1.54 68 31 70 39 326.25 0.34 69 31 71 40 326.25 0.34 70 31 72 41 326.19 0.32 71 31 147 116 194.39 0.18 72 32 43 11 315.90 0.14 73 32 45 13 287.62 1.43 74 32 70 38 326.26 0.34 75 32 71 39 326.25 0.35 76 32 74 42 326.47 0.35 77 32 77 45 326.89 0.49 78 32 147 115 195.62 0.83 79 33 43 10 321.22 1.10 80 33 44 11 307.97 2.96 81 33 45 12 300.79 5.15 82 33 57 24 287.22 1.37 83 33 61 28 307.63 3.08 84 33 62 29 317.29 0.83 85 33 68 35 326.39 0.33 86 33 69 36 326.28 0.34 87 33 70 37 326.28 0.34 88 33 112 79 286.88 1.31 89 34 41 7 326.19 0.37 90 34 42 8 326.09 0.37 91 34 43 9 323.59 0.09 92 34 44 10 317.31 0.82 93 34 68 34 326.39 0.33 94 34 69 35 326.37 0.32 95 34 71 37 326.46 0.35 96 34 77 43 327.35 0.66 97 35 41 6 326.23 0.35 98 35 42 7 326.21 0.35 99 35 44 9 325.55 0.09 100 35 66 31 326.41 0.35 101 35 67 32 326.44 0.35 102 35 68 33 326.39 0.33 103 36 39 3 480.47 0.34 104 36 40 4 404.29 5.62 105 36 41 5 326.25 0.37 106 36 67 31 326.45 0.35 107 37 40 3 431.79 1.90 108 41 67 26 328.73 0.53 109 41 68 27 328.68 0.52 110 41 69 28 328.44 0.56 111 43 77 34 331.77 0.80 112 43 147 104 196.02 0.78 113 43 156 113 196.27 0.76 114 43 201 158 178.49 0.38 115 44 68 24 328.89 0.48 116 44 201 157 178.49 0.38 117 45 201 156 178.17 0.27 118 45 203 158 179.28 0.46 119 46 203 157 179.22 0.43 120 46 204 158 179.58 0.59 121 46 205 159 180.53 1.06 122 47 204 157 179.23 0.42 123 47 205 158 179.59 0.59 124 47 206 159 185.36 0.17 125 48 127 79 206.22 3.56 126 48 206 158 184.66 0.07 127 48 217 169 185.63 0.21 128 49 72 23 366.00 1.83 129 49 114 65 370.55 0.34 130 49 118 69 211.81 3.87 131 49 120 71 210.66 3.46 132 49 124 75 207.20 3.73 133 49 125 76 207.16 3.73 134 49 126 77 206.88 3.68 135 49 127 78 206.86 3.68 136 50 111 61 371.39 0.41 137 50 126 76 207.05 3.75 138 50 129 79 206.66 3.77 139 50 248 198 76.31 0.51 140 50 252 202 35.91 2.11 141 51 126 75 207.21 3.71 142 51 252 201 35.91 2.11 143 52 114 62 370.71 0.27 144 52 117 65 211.83 3.86 145 52 118 66 211.83 3.86 146 52 120 68 211.81 3.87 147 52 126 74 207.25 3.70 148 53 113 60 370.78 0.30 149 53 114 61 370.48 0.37 150 53 117 64 215.19 5.51 151 54 111 57 371.31 0.46 152 54 112 58 371.06 0.44 153 54 113 59 370.61 0.33 154 54 114 60 370.45 0.38 155 54 251 197 47.23 1.62 156 54 252 198 35.90 2.12 157 54 255 201 21.06 0.11 158 55 70 15 366.81 2.01 159 55 111 56 371.19 0.41 160 55 112 57 370.71 0.28 161 55 114 59 370.45 0.38 162 56 109 53 371.48 0.41 163 56 110 54 371.30 0.46 164 56 111 55 371.06 0.46 165 56 129 73 206.29 3.60 166 56 217 161 186.16 0.36 167 56 220 164 185.31 0.20 168 56 241 185 117.89 1.02 169 56 248 192 76.35 0.50 170 57 109 52 371.41 0.42 171 57 110 53 371.20 0.42 172 57 112 55 370.98 0.47 173 57 204 147 179.27 0.44 174 57 220 163 185.50 0.19 175 58 108 50 371.53 0.41 176 58 109 51 371.44 0.41 177 58 110 52 371.39 0.42 178 58 204 146 183.20 0.01 179 58 220 162 185.63 0.22 180 58 221 163 185.52 0.18 181 59 94 35 371.35 0.45 182 59 98 39 371.73 0.46 183 59 108 49 371.56 0.42 184 59 109 50 371.45 0.41 185 59 110 51 371.24 0.41 186 60 98 38 371.72 0.46 187 60 108 48 371.55 0.42 188 60 203 143 185.40 0.15 189 60 222 162 185.62 0.21 190 61 68 7 370.96 0.83 191 61 203 142 184.78 0.12 192 61 204 143 185.40 0.15 193 62 68 6 371.13 0.74 194 62 92 30 369.51 0.39 195 62 94 32 371.42 0.42 196 62 110 48 371.20 0.42 197 62 112 50 371.14 0.42 198 63 98 35 371.87 0.44 199 63 100 37 371.88 0.45 200 64 68 4 517.34 5.29 201 68 89 21 371.87 0.44 202 68 92 24 371.93 0.46 203 69 86 17 372.80 0.43 204 69 87 18 372.70 0.43 205 69 88 19 372.23 0.24 206 69 89 20 371.88 0.43 207 70 86 16 372.81 0.43 208 70 87 17 372.74 0.42 209 70 89 19 372.51 0.36 210 70 112 42 371.98 0.42 211 70 114 44 371.86 0.43 212 71 74 3 464.58 4.54 213 71 84 13 372.99 0.40 214 71 85 14 372.87 0.42 215 71 86 15 372.81 0.43 216 72 84 12 373.00 0.39 217 72 85 13 372.88 0.42 218 72 118 46 371.51 0.42 219 72 124 52 207.06 3.75 220 73 83 10 373.05 0.36 221 73 84 11 373.00 0.39 222 73 123 50 207.06 3.73 223 73 124 51 207.04 3.73 224 74 77 3 473.49 3.48 225 74 81 7 373.48 0.36 226 74 84 10 373.06 0.36 227 74 147 73 195.68 0.84 228 75 81 6 373.53 0.35 229 75 147 72 195.75 0.85 230 75 158 83 195.98 0.78 231 75 159 84 195.52 0.92 232 75 160 85 194.33 1.49 233 76 79 3 431.34 5.04 234 76 81 5 373.87 0.21 235 76 158 82 195.81 0.87 236 76 159 83 195.56 0.92 237 77 147 70 195.99 0.79 238 77 157 80 196.03 0.78 239 77 158 81 195.99 0.78 240 78 158 80 196.03 0.78 241 80 84 4 415.70 2.20 242 81 84 3 459.74 3.45 243 83 123 40 208.05 4.22 244 85 118 33 371.60 0.40 245 85 119 34 371.59 0.40 246 85 121 36 371.21 0.26 247 85 124 39 208.59 4.36 248 87 114 27 371.97 0.41 249 87 115 28 371.82 0.35 250 87 116 29 371.67 0.40 251 87 118 31 371.36 0.32 252 88 114 26 371.97 0.41 253 88 115 27 371.92 0.42 254 89 92 3 504.48 1.76 255 89 112 23 372.20 0.34 256 89 113 24 372.12 0.36 257 89 114 25 372.05 0.36 258 90 113 23 372.12 0.36 259 90 114 24 372.07 0.36 260 90 115 25 371.92 0.43 261 91 112 21 373.98 0.18 262 91 113 22 372.28 0.42 263 91 255 164 21.05 0.11 264 92 111 19 488.50 2.54 265 92 112 20 378.88 0.58 266 93 111 18 539.57 5.81 267 93 247 154 87.66 1.82 268 93 251 158 62.54 0.58 269 93 255 162 27.04 3.10 270 94 247 153 87.71 1.85 271 95 244 149 115.42 0.77 272 95 247 152 88.76 1.41 273 96 247 151 103.16 2.40 274 103 187 84 194.45 0.40 275 103 222 119 186.16 0.38 276 103 223 120 186.16 0.38 277 104 182 78 192.01 0.32 278 104 184 80 193.79 0.10 279 104 187 83 194.44 0.40 280 106 187 81 193.01 0.19 281 107 244 137 115.99 1.02 282 108 222 114 185.50 0.18 283 108 239 131 125.48 0.30 284 109 220 111 185.62 0.23 285 109 239 130 125.37 0.31 286 109 244 135 111.08 0.33 287 109 247 138 87.71 1.85 288 109 248 139 84.71 0.96 289 110 247 137 86.00 1.00 290 111 247 136 85.41 1.28 291 111 248 137 77.58 0.10 292 111 251 140 37.14 1.83 293 113 255 142 21.06 0.11 294 114 118 4 437.10 4.33 295 118 124 6 377.63 0.90 296 119 124 5 377.67 0.89 297 120 124 4 377.67 0.88 298 120 125 5 377.62 0.90 299 120 126 6 377.63 0.89 300 121 124 3 431.38 1.53 301 121 125 4 408.51 5.20 302 128 214 86 186.16 0.35 303 128 215 87 185.94 0.37 304 128 216 88 185.53 0.17 305 128 217 89 185.52 0.19 306 129 241 112 118.09 1.10 307 129 245 116 86.51 1.41 308 129 248 119 78.72 0.11 309 130 134 4 413.69 1.87 310 130 217 87 185.68 0.23 311 130 218 88 185.63 0.21 312 130 241 111 118.16 1.08 313 130 242 112 116.32 0.86 314 130 245 115 92.52 0.92 315 131 134 3 436.14 1.62 316 131 242 111 118.09 1.11 317 132 242 110 118.10 1.11 318 132 245 113 104.41 2.79 319 133 240 107 125.37 0.31 320 133 242 109 118.36 1.19 321 134 218 84 316.82 37.70 322 134 242 108 121.56 0.41 323 135 240 105 125.34 0.32 324 136 140 4 431.44 0.22 325 136 142 6 427.15 1.68 326 136 167 31 431.68 0.52 327 136 209 73 425.09 2.68 328 136 211 75 428.45 2.88 329 136 218 82 336.20 39.20 330 137 140 3 446.64 7.07 331 137 167 30 432.95 0.23 332 138 167 29 433.01 0.26 333 138 168 30 433.01 0.26 334 138 169 31 432.83 0.35 335 138 172 34 433.29 0.40 336 139 166 27 437.59 2.02 337 139 167 28 433.19 0.34 338 140 166 26 453.16 2.55 339 140 167 27 440.48 3.29 340 142 165 23 605.35 4.71 341 142 167 25 521.73 19.45 342 142 207 65 494.76 1.01 343 142 208 66 583.75 8.77 344 143 207 64 547.75 0.53 345 144 198 54 336.57 39.10 346 144 206 62 566.02 0.36 347 144 221 77 476.74 0.22 348 144 236 92 133.32 0.74 349 144 238 94 125.70 0.40 350 145 206 61 564.89 10.48 351 146 202 56 459.97 4.42 352 147 202 55 470.16 0.41 353 148 200 52 469.91 0.52 354 148 201 53 470.00 0.48 355 148 202 54 470.16 0.41 356 149 199 50 460.19 4.37 357 149 200 51 470.00 0.48 358 151 199 48 474.05 1.36 359 152 199 47 475.27 0.76 360 152 228 76 461.37 3.88 361 152 229 77 469.86 0.43 362 156 201 45 473.89 1.45 363 163 196 33 431.20 8.38 364 164 196 32 431.25 8.37 365 165 196 31 394.74 25.19 366 165 197 32 372.50 32.26 367 165 236 71 133.68 0.67 368 165 238 73 133.40 0.79 369 168 235 67 133.79 0.70 370 173 235 62 136.81 0.01 371 177 233 56 185.41 15.99 372 177 234 57 185.14 16.12 373 178 233 55 183.43 16.96 374 178 234 56 183.39 16.97 375 178 235 57 183.39 16.97 376 179 234 55 183.41 16.98 377 179 235 56 183.40 16.98 378 179 237 58 180.27 18.41 379 183 237 54 133.90 0.70 380 185 240 55 133.62 0.70 381 186 239 53 133.61 0.70 382 186 240 54 133.50 0.68 383 186 243 57 125.14 0.15 384 186 244 58 125.14 0.16 385 187 237 50 133.74 0.67 386 187 238 51 133.69 0.66 387 187 240 53 132.05 0.99 388 188 237 49 133.71 0.66 389 188 238 50 133.65 0.66 390 188 240 52 128.81 1.98 391 189 235 46 133.84 0.71 392 189 236 47 133.73 0.67 393 189 237 48 133.57 0.70 394 190 235 45 133.80 0.70 395 190 236 46 133.70 0.66 396 190 238 48 133.41 0.79 397 191 235 44 133.73 0.67 398 192 231 39 185.46 16.00 399 192 232 40 184.84 16.25 400 192 233 41 180.39 18.43 401 192 234 42 179.72 18.50 402 192 235 43 133.75 0.69 403 193 232 39 185.15 16.14 404 194 230 36 228.34 3.68 405 194 231 37 197.06 19.30 406 194 232 38 184.99 16.18 407 195 230 35 465.14 12.80 408 196 230 34 522.50 30.45 409 197 230 33 498.36 18.38 410 197 236 39 133.55 0.68 411 198 202 4 578.33 6.62 412 198 236 38 133.37 0.77 413 199 202 3 478.31 0.20 414 199 224 25 613.38 0.70 415 202 205 3 473.72 1.29 416 207 219 12 611.48 1.74 417 207 238 31 125.45 0.29 418 209 218 9 604.12 4.10 419 217 241 24 118.09 1.10 420 218 240 22 124.00 0.64 421 218 241 23 118.09 1.10 422 219 238 19 125.44 0.29 423 219 239 20 125.31 0.29 424 219 241 22 118.08 1.10 425 220 238 18 125.44 0.29 426 220 239 19 125.35 0.31 427 220 241 21 118.09 1.10 428 221 236 15 133.41 0.79 429 221 238 17 125.45 0.29 430 222 237 15 133.17 0.67 431 222 238 16 129.15 0.87 432 222 239 17 127.41 1.11 433 223 236 13 133.83 0.73 434 223 237 14 133.38 0.77 435 224 229 5 469.62 0.61 436 224 236 12 133.79 0.71 437 225 231 6 455.31 6.39 438 225 234 9 178.35 19.50 439 227 231 4 613.04 0.74 440 231 234 3 425.39 2.46 441 239 244 5 418.58 2.72 442 240 243 3 439.67 6.02 443 240 244 4 429.29 4.30 444 241 244 3 432.83 2.60 445 241 245 4 418.92 2.55 446 241 248 7 382.39 3.69 447 242 245 3 437.62 0.21 448 244 247 3 437.22 0.04 449 244 248 4 416.20 1.51 450 245 248 3 428.11 1.14 451 245 249 4 422.75 1.55 452 246 249 3 441.28 5.45 453 246 250 4 422.75 1.54 454 247 250 3 428.97 4.65 455 247 251 4 411.08 7.46 456 248 251 3 434.84 1.72 457 248 252 4 422.84 1.58 458 249 252 3 431.89 2.94 459 249 253 4 422.71 1.64 460 250 253 3 424.76 2.54 461 250 254 4 413.39 2.96 462 251 254 3 414.47 2.68 463 251 255 4 408.54 1.00 464 252 255 3 438.11 0.82