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 6 4 451.62 4.31 2 2 34 32 33.51 3.04 3 2 35 33 32.77 3.41 4 2 38 36 31.00 3.43 5 2 57 55 24.70 2.90 6 3 6 3 464.23 2.46 7 3 31 28 36.79 1.91 8 3 35 32 33.57 3.06 9 5 45 40 34.58 2.53 10 5 53 48 34.56 2.53 11 5 57 52 34.58 2.53 12 6 10 4 447.49 1.98 13 6 11 5 445.87 1.17 14 6 31 25 67.36 0.01 15 6 34 28 65.28 0.07 16 6 57 51 35.34 2.19 17 6 226 220 37.07 1.30 18 7 10 3 460.13 0.02 19 7 11 4 452.30 0.42 20 7 31 24 67.51 0.07 21 8 11 3 466.30 3.10 22 8 12 4 452.50 0.30 23 8 31 23 67.37 0.01 24 8 32 24 69.41 1.02 25 9 12 3 470.42 1.05 26 9 13 4 463.66 1.86 27 10 13 3 466.30 3.10 28 10 14 4 460.24 3.57 29 10 225 215 67.78 0.07 30 10 226 216 67.78 0.07 31 11 14 3 468.45 3.13 32 11 15 4 463.15 2.12 33 11 18 7 441.18 1.30 34 11 30 19 79.50 0.50 35 11 31 20 79.36 0.48 36 11 34 23 79.00 0.29 37 11 151 140 79.41 0.47 38 12 15 3 468.45 3.13 39 12 16 4 447.85 2.03 40 12 18 6 441.18 1.30 41 13 16 3 466.81 3.95 42 13 221 208 79.40 0.50 43 13 225 212 79.42 0.50 44 14 61 47 277.98 99.77 45 14 221 207 79.39 0.49 46 14 222 208 79.39 0.49 47 14 225 211 79.43 0.50 48 14 226 212 79.44 0.50 49 15 18 3 485.00 1.31 50 15 65 50 277.79 99.66 51 15 84 69 273.20 97.37 52 15 222 207 79.46 0.49 53 16 77 61 547.65 2.87 54 16 81 65 433.09 22.30 55 17 20 3 481.65 1.76 56 17 23 6 433.17 22.26 57 17 76 59 608.23 5.49 58 17 77 60 594.15 2.19 59 17 81 64 466.91 7.93 60 17 82 65 433.09 22.30 61 18 23 5 433.18 22.26 62 18 26 8 433.26 22.21 63 18 29 11 624.12 3.65 64 18 30 12 639.42 3.90 65 18 83 65 433.13 22.30 66 18 84 66 433.09 22.30 67 19 26 7 433.26 22.21 68 19 27 8 621.36 3.12 69 20 23 3 497.38 0.34 70 20 26 6 649.83 1.39 71 20 82 62 636.83 6.74 72 24 86 62 614.43 11.02 73 24 87 63 568.09 1.74 74 24 88 64 549.01 3.91 75 24 90 66 488.84 0.55 76 25 87 62 639.16 1.35 77 28 144 116 319.03 0.10 78 28 145 117 318.95 0.07 79 28 146 118 318.81 0.08 80 28 147 119 317.86 0.15 81 29 115 86 434.19 1.92 82 29 116 87 434.19 1.91 83 29 151 122 317.67 0.25 84 30 151 121 317.83 0.20 85 33 147 114 318.93 0.07 86 33 148 115 318.47 0.04 87 33 151 118 317.88 0.22 88 34 151 117 317.87 0.23 89 36 148 112 318.93 0.06 90 37 148 111 318.93 0.07 91 37 151 114 318.28 0.12 92 37 152 115 317.83 0.21 93 37 155 118 317.26 0.33 94 38 155 117 317.55 0.18 95 40 152 112 318.51 0.07 96 41 132 91 333.19 0.65 97 41 152 111 318.62 0.04 98 41 155 114 317.81 0.21 99 41 156 115 317.75 0.24 100 41 159 118 315.62 0.15 101 42 159 117 317.14 0.28 102 43 159 116 315.78 0.14 103 43 169 126 235.86 0.21 104 44 155 111 317.56 0.18 105 44 158 114 315.86 0.18 106 44 159 115 315.37 0.20 107 47 169 122 235.94 0.18 108 47 173 126 235.66 0.19 109 47 175 128 235.54 0.14 110 51 228 177 203.03 0.28 111 52 172 120 235.74 0.15 112 52 173 121 235.57 0.11 113 54 226 172 204.38 0.94 114 54 227 173 204.38 0.94 115 54 228 174 204.17 0.89 116 55 172 117 235.60 0.09 117 55 219 164 204.36 0.94 118 55 223 168 204.37 0.94 119 55 228 173 204.35 0.95 120 55 229 174 204.28 0.96 121 55 230 175 203.17 1.05 122 55 231 176 201.43 0.26 123 56 158 102 313.99 0.53 124 56 169 113 235.78 0.18 125 56 172 116 235.53 0.12 126 57 226 169 204.44 0.97 127 58 219 161 204.28 0.98 128 58 222 164 204.41 0.97 129 58 223 165 204.40 0.97 130 58 226 168 204.43 0.97 131 59 158 99 303.17 0.12 132 59 172 113 235.53 0.12 133 59 191 132 204.31 1.02 134 59 194 135 204.09 1.08 135 59 219 160 204.28 0.98 136 60 154 94 317.06 0.27 137 60 155 95 315.79 0.14 138 60 158 98 290.57 0.30 139 61 222 161 204.38 0.98 140 62 191 129 204.27 1.03 141 62 215 153 203.53 1.21 142 62 218 156 204.06 1.09 143 62 219 157 204.08 1.08 144 62 222 160 204.38 0.97 145 63 158 95 297.04 2.94 146 63 191 128 204.13 1.10 147 63 194 131 203.83 1.17 148 63 195 132 202.53 1.45 149 63 198 135 201.74 1.25 150 63 215 152 203.47 1.24 151 64 116 52 434.19 1.91 152 64 117 53 434.13 1.90 153 64 154 90 315.74 0.14 154 65 218 153 204.03 1.10 155 65 222 157 204.34 0.99 156 66 211 145 202.03 1.41 157 66 214 148 202.39 1.40 158 66 215 149 203.10 1.05 159 66 218 152 203.75 0.93 160 67 116 49 434.18 1.91 161 67 117 50 434.12 1.89 162 67 118 51 434.02 1.93 163 67 198 131 200.65 0.72 164 67 215 148 203.20 1.10 165 68 115 47 434.18 1.92 166 68 116 48 434.14 1.90 167 68 118 50 434.05 1.91 168 69 214 145 199.04 0.09 169 69 218 149 202.87 1.04 170 79 218 139 164.33 0.01 171 80 214 134 164.28 0.00 172 80 217 137 164.28 0.00 173 80 218 138 164.28 0.01 174 80 221 141 164.28 0.01 175 81 218 137 164.28 0.01 176 81 221 140 164.27 0.00 177 82 218 136 164.28 0.00 178 83 218 135 162.88 0.29 179 84 116 32 434.12 1.90 180 84 151 67 317.56 0.19 181 87 114 27 434.13 1.96 182 87 115 28 434.12 1.94 183 87 118 31 434.09 1.91 184 87 144 57 318.81 0.07 185 88 112 24 434.19 1.98 186 88 113 25 434.18 1.98 187 88 114 26 434.16 1.96 188 88 118 30 434.11 1.91 189 88 144 56 318.95 0.07 190 89 92 3 491.32 3.05 191 89 96 7 434.56 2.13 192 89 112 23 434.20 1.98 193 89 113 24 434.19 1.98 194 89 118 29 434.13 1.90 195 92 96 4 502.26 0.35 196 92 110 18 435.32 1.59 197 92 112 20 434.38 1.92 198 93 110 17 435.36 1.59 199 94 110 16 435.36 1.59 200 95 109 14 435.38 1.59 201 95 110 15 435.35 1.59 202 95 111 16 435.34 1.59 203 96 111 15 435.34 1.58 204 96 112 16 435.35 1.60 205 96 120 24 434.66 1.70 206 96 121 25 434.56 1.68 207 96 122 26 434.63 1.67 208 97 111 14 435.39 1.60 209 97 122 25 434.68 1.67 210 98 122 24 434.69 1.67 211 98 123 25 434.68 1.67 212 100 122 22 434.84 1.63 213 103 122 19 434.84 1.63 214 103 123 20 434.79 1.65 215 103 126 23 434.12 1.85 216 103 127 24 434.21 1.81 217 103 130 27 399.69 1.09 218 103 137 34 328.01 1.94 219 104 137 33 328.00 1.94 220 105 111 6 435.44 1.59 221 105 122 17 434.79 1.65 222 106 109 3 467.11 4.08 223 106 111 5 449.00 4.97 224 106 137 31 327.94 1.93 225 106 138 32 327.88 1.94 226 109 138 29 327.86 1.95 227 109 140 31 326.86 2.06 228 110 114 4 558.54 0.31 229 110 140 30 325.84 1.64 230 111 114 3 616.00 1.20 231 111 120 9 434.62 1.67 232 111 121 10 434.59 1.66 233 111 122 11 434.57 1.64 234 111 125 14 393.12 0.90 235 111 137 26 327.86 1.95 236 111 140 29 319.68 0.12 237 112 119 7 434.86 1.57 238 112 125 13 411.41 10.04 239 113 118 5 434.83 1.55 240 113 119 6 434.82 1.56 241 113 120 7 434.72 1.59 242 114 118 4 434.82 1.54 243 114 119 5 434.82 1.54 244 114 125 11 411.45 10.07 245 114 140 26 319.66 0.12 246 114 141 27 319.45 0.12 247 114 143 29 319.34 0.11 248 114 144 30 319.16 0.17 249 115 118 3 454.86 0.24 250 115 143 28 319.33 0.12 251 116 150 34 317.68 0.21 252 116 151 35 317.57 0.18 253 116 154 38 315.70 0.12 254 117 154 37 315.73 0.13 255 117 157 40 297.01 2.91 256 119 124 5 452.51 2.35 257 119 125 6 441.17 3.30 258 119 128 9 437.59 1.53 259 119 143 24 319.39 0.13 260 119 153 34 317.36 0.27 261 119 156 37 315.83 0.17 262 120 124 4 452.51 2.35 263 120 125 5 452.54 2.32 264 121 124 3 468.22 1.12 265 121 125 4 455.49 3.79 266 122 125 3 469.63 0.41 267 122 126 4 455.49 3.79 268 122 137 15 327.88 1.94 269 123 127 4 457.58 3.29 270 124 127 3 494.20 0.73 271 124 128 4 456.67 3.74 272 124 156 32 317.36 0.26 273 125 128 3 464.25 7.52 274 125 129 4 456.12 3.46 275 125 136 11 327.95 1.93 276 125 137 12 327.88 1.94 277 125 140 15 325.67 1.62 278 125 143 18 319.54 0.11 279 126 129 3 468.45 5.42 280 126 130 4 464.23 7.52 281 126 137 11 327.97 1.94 282 127 130 3 467.03 8.85 283 127 131 4 464.22 7.53 284 127 156 29 317.62 0.18 285 128 131 3 471.72 6.50 286 128 132 4 452.93 1.79 287 128 136 8 328.02 1.92 288 128 153 25 317.72 0.19 289 128 156 28 317.20 0.20 290 129 132 3 463.59 4.29 291 129 133 4 448.26 2.43 292 129 134 5 437.75 1.38 293 129 136 7 328.02 1.92 294 130 133 3 466.31 0.72 295 131 156 25 317.67 0.21 296 132 136 4 507.63 0.14 297 132 149 17 319.34 0.12 298 132 152 20 318.25 0.22 299 132 153 21 318.22 0.22 300 134 142 8 327.42 2.14 301 135 138 3 494.49 0.67 302 135 139 4 461.68 1.90 303 136 139 3 463.03 1.23 304 136 140 4 340.38 4.03 305 136 142 6 340.37 4.04 306 136 143 7 326.94 1.09 307 136 149 13 319.22 0.18 308 136 153 17 317.77 0.22 309 137 140 3 481.37 1.94 310 139 142 3 494.58 2.32 311 140 143 3 487.97 0.99 312 141 144 3 474.15 5.91 313 141 145 4 455.36 0.96 314 142 145 3 466.88 2.27 315 142 146 4 441.50 3.73 316 142 149 7 318.56 0.12 317 143 149 6 317.87 0.16 318 143 150 7 317.76 0.23 319 143 153 10 317.11 0.24 320 146 149 3 469.00 3.93 321 146 150 4 457.00 4.07 322 147 150 3 457.00 4.07 323 147 151 4 460.11 5.55 324 148 151 3 468.56 1.32 325 148 152 4 460.12 5.55 326 149 152 3 460.09 5.58 327 149 153 4 462.87 4.19 328 150 153 3 470.92 2.50 329 150 154 4 462.89 4.20 330 151 154 3 468.60 1.34 331 151 155 4 462.89 4.20 332 152 155 3 467.37 3.09 333 152 156 4 462.88 4.20 334 153 156 3 464.00 4.77 335 153 157 4 459.91 5.58 336 154 157 3 477.20 1.83 337 154 158 4 459.84 5.62 338 155 158 3 475.96 2.45 339 155 159 4 460.95 5.05 340 156 159 3 461.00 5.03 341 156 160 4 460.95 5.05 342 157 160 3 491.48 3.96 343 157 162 5 458.14 3.65 344 157 198 41 198.07 0.57 345 158 167 9 235.83 0.21 346 158 168 10 235.80 0.20 347 158 169 11 235.77 0.21 348 158 172 14 235.69 0.14 349 158 194 36 201.83 0.17 350 159 167 8 235.84 0.20 351 159 169 10 235.81 0.21 352 160 167 7 235.86 0.21 353 161 165 4 445.44 1.57 354 161 166 5 235.88 0.19 355 161 167 6 235.85 0.20 356 162 165 3 472.43 2.60 357 162 197 35 202.27 0.38 358 164 243 79 54.04 2.08 359 165 197 32 201.81 0.15 360 165 242 77 54.68 1.79 361 166 170 4 476.15 4.62 362 166 171 5 452.41 0.10 363 166 176 10 225.15 2.26 364 166 197 31 201.86 0.17 365 166 242 76 76.24 12.57 366 167 170 3 482.25 1.57 367 167 171 4 477.43 3.98 368 167 197 30 201.84 0.18 369 168 171 3 487.88 1.24 370 168 172 4 477.43 3.98 371 168 194 26 202.18 0.34 372 168 197 29 201.84 0.17 373 169 172 3 487.88 1.24 374 169 173 4 462.69 2.07 375 170 173 3 481.10 2.16 376 170 174 4 461.99 2.42 377 170 175 5 282.28 26.14 378 170 176 6 221.25 0.47 379 171 174 3 467.42 4.43 380 171 176 5 277.57 28.48 381 171 190 19 203.24 0.41 382 171 193 22 202.91 0.28 383 171 194 23 202.91 0.28 384 171 197 26 202.91 0.28 385 172 194 22 203.06 0.35 386 176 182 6 417.62 21.82 387 176 187 11 204.34 0.86 388 176 189 13 203.55 0.51 389 176 193 17 203.53 0.52 390 178 182 4 392.92 26.89 391 178 183 5 393.12 26.90 392 178 187 9 204.34 0.85 393 178 188 10 204.34 0.85 394 178 189 11 204.19 0.77 395 179 182 3 464.18 1.11 396 179 183 4 417.64 22.34 397 180 183 3 463.80 3.31 398 180 184 4 400.36 30.45 399 181 184 3 461.15 4.10 400 181 185 4 456.23 2.52 401 182 185 3 463.89 6.36 402 182 186 4 453.28 4.00 403 182 187 5 321.10 59.19 404 182 242 60 143.28 0.76 405 183 186 3 455.61 2.83 406 185 239 54 160.84 7.23 407 185 240 55 160.44 7.12 408 186 239 53 160.73 7.28 409 187 193 6 204.01 0.73 410 187 196 9 203.99 0.73 411 187 239 52 160.41 7.13 412 187 240 53 146.12 0.01 413 187 241 54 145.56 0.12 414 187 242 55 130.18 0.43 415 188 193 5 348.56 49.82 416 188 233 45 200.52 1.69 417 189 233 44 200.59 1.73 418 190 193 3 489.17 1.50 419 190 194 4 479.06 1.61 420 190 232 42 205.88 0.67 421 190 233 43 200.80 1.88 422 191 194 3 484.25 0.89 423 191 195 4 479.05 1.61 424 191 215 24 206.47 0.57 425 191 216 25 206.39 0.56 426 191 219 28 206.50 0.56 427 191 233 42 206.03 0.70 428 191 234 43 200.37 2.05 429 192 195 3 481.00 2.59 430 192 196 4 459.18 0.51 431 192 233 41 206.28 0.60 432 192 234 42 200.78 1.90 433 192 235 43 199.61 2.23 434 192 236 44 191.47 6.27 435 192 239 47 174.18 14.69 436 193 196 3 463.60 2.71 437 193 197 4 459.34 0.58 438 193 239 46 171.33 16.10 439 193 242 49 96.88 1.98 440 194 197 3 460.26 1.05 441 194 198 4 455.09 2.48 442 195 198 3 473.53 2.45 443 195 199 4 448.59 0.98 444 195 200 5 445.41 0.25 445 195 203 8 206.91 0.59 446 195 204 9 206.84 0.59 447 195 212 17 206.84 0.57 448 195 215 20 206.88 0.57 449 195 236 41 205.99 0.68 450 196 199 3 460.50 1.25 451 196 200 4 394.09 25.90 452 196 204 8 206.05 0.71 453 196 236 40 205.99 0.69 454 196 239 43 167.34 18.14 455 196 240 44 167.29 18.14 456 196 241 45 67.67 8.28 457 196 242 46 54.77 1.83 458 197 242 45 54.71 1.80 459 198 215 17 474.92 4.77 460 199 202 3 489.99 6.48 461 199 203 4 453.84 4.29 462 199 215 16 533.74 7.49 463 200 203 3 460.39 1.03 464 200 204 4 337.28 62.56 465 200 241 41 130.88 36.27 466 201 241 40 149.77 26.90 467 204 239 35 445.64 0.22 468 204 241 37 149.73 26.89 469 205 237 32 515.73 0.04 470 205 238 33 473.09 0.43 471 205 239 34 441.83 2.40 472 236 239 3 487.54 1.79