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 98 148 50 150.03 4.12 2 98 151 53 154.12 2.08 3 98 152 54 180.83 7.80 4 98 155 57 188.34 8.34 5 98 165 67 150.12 4.16 6 99 102 3 687.38 8.21 7 99 148 49 163.20 2.10 8 99 152 53 197.22 13.35 9 100 103 3 765.89 0.91 10 101 106 5 639.84 4.94 11 101 145 44 197.97 13.03 12 101 278 177 33.29 1.75 13 102 144 42 197.97 13.03 14 102 145 43 195.04 14.50 15 102 148 46 197.97 13.03 16 102 149 47 204.33 16.16 17 102 152 50 211.41 16.82 18 103 106 3 702.99 8.16 19 103 107 4 661.98 0.82 20 103 145 42 208.24 17.18 21 103 149 46 209.39 17.75 22 103 152 49 211.47 16.83 23 104 107 3 679.11 0.93 24 104 117 13 209.88 17.96 25 104 120 16 209.91 17.95 26 104 121 17 209.93 17.95 27 104 124 20 212.30 16.77 28 104 146 42 209.78 17.89 29 104 149 45 210.90 17.34 30 104 150 46 211.77 17.00 31 104 153 49 212.43 16.70 32 105 274 169 35.91 1.12 33 106 145 39 214.03 15.80 34 106 274 168 35.78 1.06 35 106 278 172 35.16 1.33 36 107 113 6 634.54 12.96 37 107 117 10 216.06 15.30 38 107 142 35 214.03 15.80 39 107 145 38 214.03 15.80 40 107 146 39 214.05 15.81 41 107 260 153 169.53 3.51 42 108 113 5 660.56 0.04 43 108 267 159 105.94 2.79 44 108 270 162 48.27 4.42 45 108 271 163 45.79 3.73 46 108 274 166 45.80 3.74 47 109 113 4 660.55 0.04 48 109 114 5 411.44 98.58 49 109 117 8 231.58 8.65 50 109 267 158 111.91 0.10 51 110 113 3 684.12 8.83 52 110 114 4 634.52 12.96 53 110 267 157 112.38 0.14 54 111 264 153 160.55 1.16 55 111 267 156 124.41 0.61 56 112 260 148 170.09 3.73 57 112 261 149 168.96 3.24 58 113 116 3 689.56 3.74 59 113 117 4 659.21 0.58 60 113 260 147 170.08 3.73 61 114 117 3 684.70 5.07 62 114 118 4 667.59 3.49 63 115 118 3 676.67 3.46 64 115 119 4 660.48 0.07 65 115 258 143 172.03 3.24 66 116 119 3 675.85 0.68 67 116 120 4 660.76 0.23 68 116 135 19 238.47 6.21 69 116 146 30 242.99 4.58 70 116 258 142 171.92 3.30 71 116 260 144 170.03 3.77 72 117 120 3 661.40 0.39 73 117 121 4 660.52 0.06 74 117 146 29 243.08 4.62 75 118 121 3 705.97 17.18 76 118 122 4 662.00 0.14 77 119 122 3 670.35 3.98 78 119 123 4 662.00 0.14 79 119 133 14 243.06 4.62 80 119 256 137 173.03 3.39 81 119 258 139 172.43 3.20 82 120 123 3 702.44 9.68 83 120 124 4 666.71 2.45 84 120 133 13 248.04 4.45 85 120 135 15 244.50 3.91 86 120 146 26 247.22 4.90 87 120 150 30 249.44 4.84 88 121 124 3 676.43 2.62 89 121 125 4 671.42 0.11 90 122 125 3 671.43 0.11 91 122 126 4 666.75 2.23 92 122 130 8 253.91 6.70 93 123 126 3 675.37 2.08 94 123 127 4 657.73 1.15 95 123 130 7 252.03 5.87 96 123 133 10 251.22 5.75 97 123 150 27 252.15 5.83 98 123 229 106 252.04 5.87 99 123 231 108 251.56 5.91 100 123 256 133 173.21 3.48 101 124 127 3 667.93 1.85 102 124 150 26 251.72 5.92 103 124 153 29 264.09 0.06 104 124 154 30 252.25 5.85 105 125 153 28 294.04 5.29 106 126 129 3 708.44 13.54 107 127 229 102 282.71 11.96 108 128 131 3 728.50 3.50 109 128 227 99 412.92 0.44 110 128 229 101 289.88 15.51 111 130 229 99 413.11 0.46 112 130 256 126 183.49 4.08 113 131 224 93 413.16 0.47 114 131 228 97 413.19 0.47 115 131 229 98 413.12 0.46 116 131 230 99 413.10 0.46 117 131 254 123 193.56 8.37 118 131 255 124 192.25 8.46 119 132 220 88 413.12 0.47 120 132 229 97 413.14 0.46 121 132 230 98 413.10 0.46 122 132 251 119 195.81 7.92 123 132 254 122 193.48 8.34 124 132 255 123 185.77 5.22 125 132 256 124 178.68 6.07 126 133 150 17 413.30 0.46 127 133 229 96 413.26 0.45 128 133 230 97 413.14 0.45 129 133 231 98 413.10 0.47 130 133 232 99 413.10 0.46 131 133 256 123 173.03 3.39 132 134 232 98 413.10 0.47 133 134 234 100 413.09 0.47 134 134 236 102 411.54 0.18 135 134 237 103 310.35 10.88 136 134 238 104 309.47 11.29 137 134 241 107 309.54 11.27 138 134 252 118 193.66 8.38 139 134 256 122 173.03 3.38 140 134 257 123 172.94 3.38 141 134 258 124 172.87 3.41 142 135 143 8 413.14 0.45 143 135 146 11 413.29 0.45 144 135 232 97 413.13 0.45 145 135 233 98 413.10 0.47 146 135 234 99 413.10 0.47 147 135 258 123 172.38 3.35 148 135 260 125 171.06 3.73 149 136 143 7 413.24 0.46 150 136 234 98 413.10 0.47 151 136 236 100 412.79 0.35 152 136 237 101 358.64 9.96 153 136 257 121 172.97 3.39 154 136 258 122 172.90 3.37 155 136 259 123 171.94 3.31 156 136 260 124 171.03 3.75 157 137 141 4 655.81 0.01 158 137 143 6 414.49 0.42 159 137 234 97 413.13 0.46 160 137 235 98 413.07 0.46 161 137 260 123 170.93 3.81 162 138 141 3 755.53 1.13 163 138 143 5 668.65 3.50 164 139 143 4 723.54 8.06 165 139 298 159 96.74 0.55 166 140 298 158 54.71 8.10 167 140 299 159 34.19 2.15 168 140 300 160 34.14 2.16 169 141 260 119 170.87 3.78 170 141 261 120 170.03 3.77 171 141 262 121 166.06 2.21 172 141 263 122 161.40 3.31 173 142 145 3 674.28 1.42 174 142 146 4 658.86 0.00 175 142 260 118 170.82 3.77 176 143 146 3 694.36 11.46 177 143 147 4 662.38 1.36 178 143 233 90 413.51 0.44 179 143 234 91 413.51 0.44 180 143 235 92 413.40 0.47 181 143 260 117 170.05 3.78 182 144 147 3 679.50 0.20 183 144 148 4 663.16 1.03 184 144 165 21 413.94 0.43 185 144 201 57 413.53 0.45 186 145 148 3 711.19 5.70 187 145 149 4 664.37 1.64 188 146 149 3 688.61 5.59 189 146 150 4 683.86 5.92 190 146 260 114 170.05 3.77 191 147 150 3 718.21 11.25 192 147 151 4 683.86 5.92 193 147 165 18 414.05 0.42 194 147 199 52 414.05 0.42 195 147 200 53 414.03 0.42 196 147 201 54 413.64 0.43 197 147 231 84 414.05 0.42 198 147 233 86 413.62 0.44 199 148 151 3 674.66 5.91 200 148 152 4 671.01 4.08 201 148 165 17 414.04 0.41 202 149 152 3 682.35 6.67 203 149 153 4 662.88 0.04 204 150 153 3 692.73 5.49 205 150 154 4 679.86 0.23 206 150 199 49 414.17 0.43 207 150 231 81 414.14 0.45 208 151 154 3 710.13 14.91 209 151 155 4 681.02 0.36 210 151 163 12 414.25 0.39 211 151 199 48 414.10 0.41 212 152 155 3 681.03 0.36 213 152 156 4 670.41 5.67 214 153 156 3 686.64 2.21 215 153 157 4 676.93 0.54 216 154 157 3 676.93 0.55 217 154 158 4 652.07 3.50 218 154 161 7 414.39 0.42 219 154 163 9 414.30 0.40 220 155 159 4 647.86 4.99 221 155 163 8 414.31 0.40 222 156 159 3 669.78 4.60 223 158 161 3 722.25 2.19 224 161 196 35 609.38 11.12 225 162 194 32 609.47 11.12 226 162 195 33 609.44 11.12 227 162 196 34 609.39 11.12 228 162 197 35 609.38 11.12 229 163 197 34 609.38 11.12 230 163 199 36 609.38 11.12 231 164 190 26 609.56 11.12 232 164 191 27 609.54 11.11 233 164 195 31 609.50 11.13 234 164 197 33 609.44 11.12 235 164 198 34 609.38 11.12 236 164 199 35 609.38 11.12 237 165 199 34 609.38 11.12 238 165 201 36 609.38 11.12 239 166 170 4 700.53 12.49 240 166 191 25 609.62 11.10 241 166 198 32 609.48 11.12 242 166 199 33 609.41 11.11 243 166 200 34 609.38 11.12 244 166 201 35 609.38 11.12 245 167 170 3 700.56 12.48 246 167 171 4 700.53 12.49 247 167 201 34 609.37 11.12 248 168 171 3 701.28 12.85 249 168 172 4 669.73 5.84 250 168 200 32 609.45 11.12 251 168 201 33 609.41 11.11 252 168 202 34 609.38 11.12 253 168 203 35 609.28 11.13 254 168 205 37 594.88 12.52 255 168 206 38 552.19 0.21 256 169 172 3 677.08 2.17 257 169 173 4 671.32 5.04 258 169 205 36 597.81 11.09 259 170 173 3 668.38 3.58 260 170 174 4 667.00 4.25 261 170 191 21 610.01 11.09 262 171 175 4 666.20 0.35 263 171 187 16 610.06 11.12 264 171 191 20 609.98 11.08 265 171 212 41 483.43 0.78 266 171 215 44 483.36 0.80 267 171 216 45 483.09 0.74 268 171 219 48 482.96 0.66 269 172 175 3 697.40 3.13 270 172 176 4 667.11 0.10 271 172 205 33 603.75 9.71 272 172 209 37 515.50 5.71 273 172 212 40 483.44 0.78 274 173 176 3 691.73 5.96 275 173 177 4 667.12 0.10 276 174 177 3 692.83 5.42 277 174 178 4 667.38 0.24 278 174 187 13 610.25 11.19 279 174 190 16 610.25 11.19 280 174 191 17 610.25 11.19 281 175 178 3 667.38 0.24 282 175 179 4 667.37 0.24 283 175 184 9 610.33 11.19 284 175 187 12 610.25 11.18 285 175 212 37 483.39 0.80 286 175 215 40 483.34 0.82 287 176 179 3 675.64 0.94 288 176 180 4 664.38 1.47 289 177 180 3 664.65 1.60 290 177 181 4 661.65 1.73 291 178 182 4 614.16 12.63 292 178 183 5 610.38 11.16 293 178 184 6 610.33 11.19 294 178 187 9 610.27 11.20 295 179 182 3 638.86 1.79 296 183 186 3 729.95 2.25 297 183 187 4 674.26 2.46 298 184 187 3 697.76 8.00 299 184 188 4 674.23 2.44 300 185 188 3 687.41 4.12 301 185 189 4 663.33 2.99 302 186 189 3 714.35 20.14 303 186 190 4 663.31 2.99 304 187 190 3 674.70 0.11 305 187 191 4 661.91 3.67 306 187 215 28 483.18 0.77 307 188 191 3 677.39 0.04 308 188 192 4 659.23 2.33 309 188 193 5 656.38 3.75 310 188 215 27 483.06 0.70 311 189 192 3 718.15 8.82 312 189 193 4 642.14 3.27 313 189 194 5 642.08 3.28 314 190 195 5 624.34 15.21 315 191 195 4 650.38 2.19 316 191 219 28 482.70 0.63 317 191 223 32 482.56 0.65 318 192 195 3 689.59 3.89 319 192 215 23 483.14 0.75 320 192 218 26 482.75 0.60 321 192 219 27 482.70 0.62 322 192 222 30 482.62 0.66 323 192 223 31 482.56 0.65 324 195 198 3 746.93 0.23 325 195 223 28 481.97 0.36 326 195 228 33 480.44 0.05 327 196 228 32 480.42 0.07 328 196 229 33 480.42 0.07 329 197 229 32 480.27 0.09 330 198 223 25 480.87 0.12 331 198 229 31 480.40 0.04 332 198 230 32 480.25 0.07 333 198 231 33 480.24 0.07 334 199 231 32 480.19 0.06 335 200 216 16 482.89 0.65 336 200 230 30 480.41 0.03 337 200 231 31 480.29 0.01 338 200 232 32 480.16 0.04 339 200 233 33 480.14 0.04 340 201 233 32 480.11 0.02 341 202 205 3 754.26 0.16 342 202 233 31 480.28 0.01 343 203 206 3 735.76 5.80 344 203 216 13 483.43 0.77 345 203 232 29 480.36 0.01 346 203 233 30 480.30 0.01 347 203 234 31 480.25 0.01 348 203 241 38 309.78 11.37 349 203 244 41 309.28 11.18 350 203 252 49 194.36 8.54 351 204 207 3 716.78 10.64 352 204 234 30 480.30 0.01 353 204 235 31 480.29 0.01 354 204 241 37 309.79 11.37 355 205 209 4 717.10 10.49 356 206 209 3 679.44 6.59 357 206 212 6 645.17 12.70 358 206 213 7 494.51 4.76 359 206 216 10 483.49 0.74 360 206 244 38 309.28 11.19 361 207 213 6 664.90 3.04 362 207 241 34 309.78 11.37 363 207 242 35 309.56 11.27 364 207 243 36 309.32 11.20 365 207 244 37 309.29 11.19 366 208 213 5 675.83 0.60 367 208 243 35 309.32 11.20 368 209 212 3 717.61 10.72 369 209 213 4 675.84 0.60 370 210 213 3 700.56 11.75 371 210 214 4 675.84 0.60 372 210 245 35 308.72 11.01 373 211 214 3 720.07 9.50 374 211 215 4 679.43 1.20 375 212 215 3 700.52 11.75 376 212 216 4 679.46 1.23 377 213 216 3 683.75 0.92 378 213 217 4 676.26 2.83 379 213 243 30 309.31 11.19 380 213 244 31 308.50 10.98 381 213 245 32 304.54 9.02 382 213 248 35 264.05 3.07 383 214 217 3 682.99 0.52 384 214 218 4 703.88 13.74 385 214 245 31 298.97 10.19 386 214 247 33 278.95 0.18 387 215 218 3 711.99 9.69 388 215 219 4 676.11 2.98 389 216 219 3 676.15 2.97 390 216 220 4 676.09 3.00 391 216 248 32 222.80 11.00 392 217 220 3 722.22 4.57 393 217 221 4 700.71 15.32 394 217 247 30 232.96 12.03 395 217 248 31 203.25 5.15 396 217 251 34 200.88 6.45 397 218 221 3 676.00 3.04 398 218 222 4 674.71 3.68 399 219 222 3 714.83 1.67 400 219 223 4 679.32 7.74 401 220 223 3 700.13 9.01 402 220 224 4 657.79 5.17 403 220 230 10 480.74 0.12 404 220 232 12 480.70 0.10 405 220 251 31 197.19 7.99 406 220 254 34 195.89 8.19 407 221 224 3 684.36 5.21 408 221 225 4 657.83 5.15 409 221 251 30 200.58 6.30 410 222 225 3 711.17 0.96 411 222 226 4 660.50 6.49 412 223 226 3 690.43 2.56 413 223 227 4 657.83 5.16 414 223 228 5 480.80 0.11 415 223 230 7 480.79 0.11 416 224 227 3 669.29 0.59 417 224 230 6 480.80 0.10 418 224 254 30 194.47 8.69 419 232 252 20 193.75 8.42 420 234 241 7 309.56 11.28 421 236 240 4 598.19 41.77 422 236 241 5 309.62 11.29 423 237 240 3 684.60 6.46 424 237 241 4 585.85 26.95 425 238 241 3 689.58 3.97 426 238 249 11 196.21 8.05 427 238 252 14 195.78 7.84 428 238 253 15 195.69 7.88 429 238 257 19 182.05 7.63 430 239 249 10 257.91 1.19 431 239 253 14 209.81 12.62 432 241 244 3 741.69 2.17 433 241 252 11 263.23 3.12 434 244 248 4 680.58 4.40 435 244 249 5 607.71 34.53 436 244 252 8 584.48 27.46 437 245 248 3 700.08 14.16 438 245 249 4 663.68 6.55 439 246 249 3 668.01 4.48 440 246 250 4 667.91 4.44 441 247 250 3 689.18 0.06 442 247 251 4 685.35 2.00 443 248 251 3 685.36 2.00 444 248 252 4 689.21 0.08 445 249 252 3 689.21 0.07 446 249 253 4 689.21 0.07 447 250 253 3 689.20 0.07 448 250 254 4 685.34 2.00 449 251 254 3 692.81 0.92 450 253 257 4 561.20 20.55 451 263 267 4 663.69 3.74 452 263 268 5 583.42 29.14 453 263 271 8 604.11 26.05 454 263 299 36 595.96 21.95 455 264 267 3 699.11 13.96 456 264 268 4 674.81 1.82 457 265 268 3 705.02 13.80 458 265 269 4 717.57 1.28 459 265 293 28 659.40 5.87 460 266 269 3 729.47 0.55 461 266 270 4 722.45 2.89 462 267 270 3 729.47 0.55 463 267 271 4 723.38 3.31 464 268 271 3 723.56 3.37 465 268 272 4 723.68 3.40 466 268 292 24 725.35 4.25 467 268 293 25 725.69 4.21 468 268 295 27 725.79 4.16 469 268 296 28 725.68 4.23 470 268 299 31 723.68 3.23 471 268 302 34 723.68 3.24 472 269 272 3 723.74 3.43 473 269 273 4 725.74 3.45 474 269 288 19 725.36 4.25 475 269 289 20 725.46 4.29 476 269 292 23 725.49 4.19 477 269 293 24 725.74 4.19 478 270 273 3 725.89 3.51 479 270 274 4 725.95 3.54 480 271 274 3 725.99 3.52 481 271 275 4 725.96 3.54 482 271 299 28 726.50 3.83 483 271 302 31 726.51 3.82 484 272 275 3 726.00 3.54 485 272 276 4 726.74 3.90 486 272 288 16 727.03 3.82 487 272 292 20 726.78 3.71 488 272 302 30 726.51 3.82 489 272 306 34 724.55 2.85 490 273 276 3 728.25 3.24 491 273 277 4 728.42 3.29 492 273 288 15 727.10 3.82 493 274 277 3 728.44 3.29 494 274 278 4 728.44 3.29 495 275 278 3 728.44 3.29 496 275 279 4 728.44 3.29 497 275 302 27 728.16 3.34 498 275 303 28 727.95 3.45 499 275 306 31 728.25 3.38 500 276 279 3 732.34 1.34 501 276 280 4 822.59 6.00 502 276 281 5 880.91 3.49 503 276 282 6 903.26 1.28 504 276 283 7 903.31 1.30 505 276 306 30 728.45 3.29 506 276 310 34 723.49 1.40 507 277 280 3 909.49 0.87 508 279 310 31 724.38 1.84 509 281 310 29 799.29 3.26 510 282 313 31 711.88 0.17 511 283 313 30 744.11 1.08 512 283 320 37 72.06 1.01 513 284 319 35 78.45 2.08 514 284 320 36 72.09 1.00 515 287 320 33 72.03 0.99 516 287 322 35 66.27 0.92 517 287 325 38 66.22 0.91 518 290 322 32 66.38 0.90 519 290 326 36 64.66 1.62 520 291 329 38 63.54 1.21 521 294 333 39 42.48 1.20 522 295 332 37 50.91 4.62 523 295 333 38 42.69 1.09 524 301 331 30 56.09 2.50 525 301 332 31 54.83 3.02 526 301 335 34 50.84 4.65 527 304 332 28 56.01 2.46 528 305 329 24 63.55 1.20 529 305 332 27 54.85 3.00 530 306 310 4 868.97 4.88 531 307 310 3 723.36 1.33 532 307 311 4 723.27 1.29 533 308 311 3 723.27 1.29 534 308 312 4 723.27 1.29 535 308 328 20 64.67 1.61 536 308 329 21 64.38 1.49 537 308 332 24 61.33 0.08 538 309 312 3 716.45 2.10 539 309 313 4 711.76 4.44 540 309 320 11 73.25 0.44 541 309 325 16 66.34 0.95 542 309 328 19 66.16 0.88 543 309 329 20 66.13 0.88 544 310 313 3 697.59 1.13 545 310 314 4 691.82 0.79 546 311 314 3 689.29 0.48 547 311 315 4 685.00 2.62 548 312 315 3 702.16 12.45 549 312 316 4 677.12 1.70 550 312 318 6 662.54 4.25 551 312 319 7 190.02 38.29 552 312 320 8 84.78 0.44 553 312 324 12 73.47 0.42 554 312 328 16 69.03 0.24 555 313 316 3 710.22 8.42 556 313 319 6 85.48 3.14 557 313 320 7 83.28 0.30 558 316 319 3 745.19 2.08 559 318 324 6 660.69 2.56 560 319 324 5 660.69 2.56 561 320 325 5 589.62 24.16 562 321 324 3 663.46 3.94 563 321 325 4 675.93 4.34 564 322 325 3 686.15 0.76 565 322 326 4 681.52 1.55 566 323 326 3 682.56 1.04 567 323 327 4 681.52 1.56 568 324 327 3 686.18 0.77 569 324 328 4 670.13 7.25 570 325 328 3 678.35 4.69 571 325 329 4 649.27 3.44 572 326 329 3 679.86 3.93 573 326 330 4 649.25 3.45 574 327 330 3 681.43 3.81 575 329 332 3 681.36 3.37 576 329 333 4 676.96 0.99 577 330 333 3 735.68 2.62 578 331 335 4 180.56 40.56