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 63 143 78 81.92 0.28 2 63 144 79 73.61 0.65 3 65 92 27 258.15 36.70 4 65 165 98 177.18 0.25 5 65 169 102 163.97 0.70 6 66 92 26 258.14 36.69 7 66 94 28 258.17 36.65 8 66 144 76 177.97 0.09 9 66 165 97 177.87 0.07 10 67 90 23 259.15 37.09 11 67 91 24 259.17 37.09 12 67 92 25 258.91 36.97 13 67 93 26 258.48 36.76 14 67 94 27 258.27 36.64 15 67 144 75 178.81 0.34 16 67 146 77 177.83 0.05 17 67 148 79 177.87 0.07 18 67 165 96 178.16 0.07 19 67 218 149 177.84 0.06 20 68 95 27 258.50 36.75 21 68 97 29 259.56 36.65 22 68 142 72 180.15 0.28 23 68 144 74 179.85 0.11 24 68 146 76 179.01 0.27 25 68 147 77 177.94 0.10 26 68 148 78 178.83 0.34 27 69 87 18 259.15 37.11 28 69 93 24 259.66 36.79 29 69 95 26 259.31 36.54 30 69 96 27 259.22 36.52 31 69 97 28 259.62 36.63 32 69 148 77 178.88 0.34 33 69 149 78 178.92 0.33 34 69 150 79 180.93 0.26 35 70 97 27 259.89 36.67 36 70 139 67 181.19 0.22 37 70 142 70 181.82 0.15 38 70 147 75 180.82 0.31 39 70 148 76 180.76 0.32 40 70 149 77 179.96 0.18 41 70 150 78 180.96 0.27 42 70 224 152 180.26 0.32 43 71 80 9 260.24 36.76 44 71 84 13 259.96 36.90 45 71 97 26 260.05 36.66 46 71 98 27 260.06 36.66 47 71 99 28 260.25 36.75 48 71 150 77 181.00 0.26 49 71 152 79 184.35 0.06 50 72 99 27 260.25 36.75 51 72 132 58 205.96 10.27 52 72 135 61 181.54 0.02 53 72 152 78 184.56 0.01 54 73 80 7 260.18 36.80 55 73 98 25 260.31 36.73 56 73 99 26 260.30 36.74 57 73 100 27 260.28 36.75 58 73 101 28 260.45 36.83 59 73 132 57 209.44 11.38 60 73 152 77 184.58 0.01 61 74 101 27 260.45 36.83 62 74 132 56 210.02 11.64 63 74 152 76 185.12 0.20 64 75 101 26 260.49 36.83 65 76 79 3 698.29 0.40 66 76 80 4 688.67 4.00 67 76 152 74 185.66 0.42 68 77 80 3 708.73 4.04 69 77 81 4 697.49 0.00 70 77 111 32 262.16 36.02 71 78 81 3 727.31 2.74 72 78 82 4 706.86 4.91 73 79 82 3 713.61 5.63 74 79 83 4 706.87 4.90 75 79 152 71 185.89 0.55 76 79 273 192 185.38 0.35 77 80 83 3 717.47 2.33 78 80 84 4 706.88 4.88 79 80 98 18 262.74 35.78 80 80 108 26 262.87 35.80 81 81 84 3 700.29 0.30 82 81 85 4 691.73 2.71 83 81 111 28 263.10 35.70 84 81 112 29 263.09 35.70 85 82 85 3 706.90 4.88 86 82 86 4 700.04 5.54 87 82 273 189 187.34 1.37 88 83 86 3 707.32 1.90 89 83 87 4 700.04 5.54 90 83 152 67 187.74 1.57 91 83 153 68 188.18 1.76 92 83 154 69 188.17 1.75 93 83 155 70 186.85 1.09 94 83 273 188 187.72 1.59 95 84 87 3 717.57 3.23 96 84 88 4 715.78 2.33 97 84 96 12 265.22 34.63 98 84 98 14 263.30 35.58 99 84 112 26 268.19 33.16 100 84 122 36 267.58 33.45 101 84 124 38 266.79 33.84 102 85 88 3 723.34 2.32 103 85 112 25 268.53 33.29 104 86 89 3 733.66 1.72 105 86 90 4 716.16 3.93 106 86 155 67 193.77 4.57 107 86 156 68 193.77 4.58 108 86 157 69 193.77 4.58 109 86 158 70 193.78 4.61 110 87 90 3 714.39 3.04 111 87 93 6 414.73 56.08 112 87 150 61 193.45 4.70 113 87 154 65 193.88 4.62 114 87 155 66 193.85 4.63 115 87 156 67 193.74 4.60 116 87 161 72 192.97 5.09 117 88 93 5 594.85 33.98 118 88 112 22 374.22 79.01 119 88 118 28 409.87 61.18 120 88 119 29 298.10 18.71 121 88 120 30 269.44 33.04 122 90 93 3 718.85 4.25 123 90 158 66 191.88 5.72 124 90 161 69 191.88 5.72 125 90 162 70 191.93 5.74 126 91 162 69 191.92 5.75 127 92 165 71 191.53 5.96 128 93 96 3 833.75 1.09 129 93 120 25 606.98 37.88 130 94 120 24 606.98 37.88 131 94 121 25 606.98 37.88 132 94 143 47 191.62 5.99 133 94 144 48 191.54 5.99 134 95 120 23 606.99 37.88 135 95 121 24 606.98 37.88 136 95 123 26 606.98 37.88 137 95 141 44 192.33 6.00 138 95 143 46 192.28 6.32 139 96 120 22 607.02 37.88 140 96 121 23 607.00 37.88 141 96 122 24 606.98 37.88 142 96 123 25 606.98 37.88 143 97 123 24 606.98 37.88 144 97 125 26 606.97 37.88 145 97 139 40 192.56 6.21 146 97 141 42 193.34 5.92 147 97 142 43 192.96 6.11 148 98 122 22 607.04 37.88 149 98 123 23 606.99 37.88 150 98 124 24 606.97 37.88 151 98 125 25 606.97 37.88 152 99 125 24 606.97 37.88 153 99 127 26 606.94 37.89 154 99 132 31 416.97 61.27 155 99 139 38 193.59 5.82 156 100 106 4 700.33 0.18 157 100 107 5 607.15 37.90 158 100 108 6 607.13 37.90 159 100 124 22 607.03 37.88 160 100 125 23 606.99 37.88 161 100 126 24 606.97 37.88 162 100 127 25 606.96 37.88 163 100 132 30 443.98 71.92 164 101 127 24 606.97 37.88 165 101 132 29 459.50 64.25 166 102 126 22 607.00 37.88 167 102 127 23 606.99 37.88 168 106 110 4 726.80 0.45 169 108 111 3 721.77 1.64 170 108 112 4 700.11 0.10 171 108 124 16 607.14 37.84 172 109 112 3 700.14 0.09 173 109 113 4 700.12 0.10 174 109 124 15 607.12 37.84 175 110 113 3 706.51 1.64 176 110 114 4 702.85 0.94 177 111 114 3 714.22 1.49 178 111 115 4 705.65 0.47 179 112 115 3 723.25 0.93 180 112 116 4 705.65 0.47 181 112 118 6 700.68 0.14 182 112 122 10 607.21 37.86 183 112 124 12 607.20 37.86 184 113 116 3 719.12 1.14 185 123 141 18 192.89 6.13 186 125 139 14 192.61 6.23 187 125 141 16 198.18 7.48 188 127 131 4 701.47 0.03 189 127 132 5 690.93 1.89 190 127 137 10 391.55 59.91 191 127 139 12 200.50 7.38 192 128 131 3 733.38 0.90 193 128 132 4 701.48 0.03 194 129 132 3 703.77 0.88 195 129 133 4 701.77 0.12 196 130 133 3 721.48 2.60 197 131 134 3 718.16 4.26 198 131 137 6 689.00 2.93 199 132 137 5 695.88 1.40 200 134 137 3 748.50 2.62 201 135 149 14 199.50 7.22 202 135 151 16 199.53 7.25 203 135 214 79 199.34 7.20 204 135 215 80 199.37 7.21 205 135 245 110 191.50 10.94 206 135 246 111 191.69 10.85 207 136 214 78 199.41 7.19 208 136 224 88 199.37 7.21 209 136 227 91 199.19 7.27 210 136 228 92 199.31 7.24 211 136 245 109 191.45 10.99 212 136 249 113 199.10 7.25 213 137 224 87 199.42 7.20 214 138 224 86 199.44 7.19 215 138 225 87 199.44 7.20 216 138 228 90 199.41 7.20 217 139 142 3 733.86 3.61 218 142 147 5 408.37 60.75 219 142 221 79 212.49 11.80 220 144 221 77 221.47 13.77 221 145 168 23 227.61 15.76 222 145 220 75 226.06 15.98 223 145 221 76 221.47 13.77 224 146 165 19 227.83 15.78 225 146 168 22 227.60 15.75 226 146 219 73 226.52 15.79 227 146 220 74 226.46 15.79 228 147 218 71 227.75 15.81 229 147 219 72 227.59 15.75 230 147 221 74 226.94 15.98 231 148 161 13 228.06 15.79 232 148 217 69 227.80 15.80 233 148 218 70 227.76 15.81 234 149 214 65 227.86 15.78 235 149 215 66 227.94 15.79 236 149 216 67 228.01 15.79 237 149 217 68 227.94 15.79 238 149 219 70 228.02 15.79 239 150 154 4 679.22 13.36 240 150 156 6 249.90 18.73 241 150 216 66 228.04 15.79 242 151 154 3 705.84 0.65 243 153 272 119 276.64 21.95 244 153 273 120 269.45 25.29 245 154 270 116 277.19 22.04 246 154 271 117 277.18 22.04 247 154 272 118 276.78 22.01 248 155 270 115 277.20 22.04 249 155 271 116 277.19 22.05 250 155 273 118 277.17 22.04 251 156 160 4 693.66 0.14 252 156 161 5 690.53 0.79 253 156 178 22 277.19 22.04 254 156 216 60 276.70 21.98 255 156 269 113 284.69 25.18 256 156 270 114 277.20 22.05 257 157 160 3 708.47 0.86 258 157 161 4 708.38 7.22 259 157 269 112 289.92 22.57 260 158 161 3 725.01 1.09 261 158 162 4 714.78 4.02 262 159 162 3 715.00 3.93 263 159 163 4 714.79 4.03 264 159 321 149 24.05 1.64 265 160 163 3 714.79 4.03 266 160 164 4 690.53 0.78 267 160 178 18 358.97 2.12 268 160 267 107 360.32 1.46 269 160 268 108 360.91 1.75 270 160 269 109 362.40 0.95 271 161 164 3 714.79 4.03 272 161 165 4 690.24 0.90 273 161 178 17 360.63 1.83 274 161 218 57 359.05 2.10 275 162 165 3 716.73 4.90 276 162 166 4 694.06 0.03 277 163 166 3 707.42 0.51 278 163 167 4 700.22 3.04 279 163 265 102 363.89 1.18 280 163 316 140 42.10 1.07 281 163 317 141 41.82 1.01 282 163 318 142 33.37 2.18 283 164 167 3 720.79 2.40 284 164 168 4 700.21 3.04 285 164 176 12 363.89 1.19 286 164 178 14 363.91 1.19 287 164 218 54 363.89 1.19 288 165 168 3 706.38 0.04 289 165 169 4 700.46 3.15 290 165 218 53 364.51 0.89 291 166 169 3 706.62 0.08 292 166 170 4 702.64 1.88 293 167 170 3 706.20 0.28 294 167 171 4 706.01 0.19 295 167 176 9 382.01 0.03 296 167 265 98 382.02 0.04 297 167 316 136 41.91 0.98 298 168 171 3 706.01 0.19 299 168 172 4 691.05 1.55 300 168 174 6 617.02 21.49 301 168 176 8 382.02 0.03 302 168 218 50 382.13 0.01 303 168 219 51 382.14 0.01 304 168 220 52 382.16 0.01 305 169 172 3 698.94 4.88 306 171 174 3 713.98 2.96 307 171 176 5 602.26 39.69 308 171 263 92 433.61 3.23 309 172 220 48 433.77 0.91 310 173 223 50 433.79 0.92 311 173 253 80 434.30 0.73 312 173 257 84 435.37 1.04 313 173 259 86 437.14 1.53 314 174 253 79 435.65 1.20 315 174 259 85 437.21 1.55 316 174 260 86 437.26 1.59 317 174 261 87 437.16 1.67 318 174 262 88 437.19 1.66 319 174 263 89 438.88 1.02 320 175 212 37 437.23 1.64 321 175 214 39 437.28 1.66 322 175 217 42 440.62 0.06 323 175 218 43 440.60 0.08 324 175 219 44 439.31 0.25 325 175 249 74 435.74 0.89 326 175 250 75 435.67 0.90 327 175 253 78 436.23 1.08 328 175 261 86 437.29 1.61 329 175 262 87 437.29 1.61 330 175 263 88 450.42 2.28 331 176 217 41 440.64 0.07 332 176 218 42 440.61 0.07 333 176 263 87 461.20 3.10 334 176 265 89 485.22 3.44 335 177 212 35 440.81 0.10 336 177 216 39 445.60 0.15 337 177 217 40 440.64 0.07 338 177 263 86 478.42 0.20 339 177 264 87 485.04 3.48 340 177 265 88 490.07 2.68 341 178 216 38 473.08 0.91 342 178 264 86 490.13 2.65 343 178 265 87 491.54 3.02 344 178 267 89 488.88 4.36 345 178 270 92 479.20 1.12 346 179 212 33 489.32 1.40 347 179 213 34 489.15 1.35 348 179 216 37 477.69 0.12 349 179 270 91 488.88 4.35 350 180 209 29 519.71 14.18 351 180 211 31 494.90 2.71 352 180 212 32 490.19 1.82 353 180 264 84 493.45 3.52 354 181 193 12 558.58 32.66 355 181 194 13 558.51 32.69 356 181 195 14 558.48 32.69 357 181 209 28 519.73 14.18 358 181 210 29 519.72 14.18 359 181 211 30 495.94 2.37 360 181 213 32 494.59 2.88 361 181 288 94 439.46 0.66 362 182 193 11 558.61 32.65 363 182 194 12 558.54 32.69 364 182 195 13 558.54 32.69 365 182 196 14 558.57 32.70 366 182 198 16 558.44 32.80 367 182 199 17 558.44 32.84 368 182 200 18 558.28 32.92 369 182 201 19 558.27 32.93 370 182 207 25 557.74 33.08 371 182 208 26 539.99 24.23 372 182 209 27 519.78 14.16 373 182 210 28 519.73 14.18 374 182 211 29 519.70 14.18 375 182 311 116 88.07 0.15 376 183 191 8 558.62 32.63 377 183 192 9 558.62 32.65 378 183 193 10 558.62 32.65 379 183 201 18 558.28 32.93 380 183 210 27 540.00 24.24 381 183 211 28 531.79 20.14 382 183 297 101 435.68 1.81 383 183 307 111 172.52 37.43 384 183 309 113 88.76 0.06 385 183 311 115 88.23 0.15 386 184 191 7 558.63 32.64 387 184 192 8 558.63 32.65 388 184 198 14 558.59 32.77 389 184 199 15 558.48 32.83 390 184 201 17 558.28 32.94 391 184 311 114 88.84 0.04 392 185 190 5 558.66 32.62 393 185 191 6 558.63 32.63 394 187 190 3 710.63 4.61 395 190 298 95 436.69 1.42 396 191 297 93 436.87 1.48 397 191 298 94 436.59 1.36 398 191 301 97 430.28 2.96 399 191 307 103 275.13 25.50 400 192 294 89 438.09 1.01 401 193 198 5 706.85 4.41 402 193 211 18 557.94 33.21 403 193 213 20 557.96 33.23 404 193 247 54 439.72 0.48 405 193 288 82 439.77 0.53 406 193 290 84 438.64 0.96 407 193 293 87 438.41 1.01 408 193 294 88 438.07 1.01 409 193 297 91 436.26 1.78 410 194 198 4 695.68 10.00 411 194 290 83 438.66 0.96 412 195 198 3 732.92 2.76 413 196 207 11 557.93 33.29 414 200 206 6 558.28 33.23 415 200 207 7 558.25 33.23 416 200 208 8 558.12 33.30 417 201 208 7 558.25 33.23 418 201 311 97 88.38 0.11 419 202 208 6 558.25 33.24 420 203 208 5 683.13 16.29 421 207 313 93 87.06 0.26 422 208 311 90 87.99 0.17 423 208 312 91 87.08 0.25 424 208 313 92 84.72 0.59 425 209 212 3 805.49 3.13 426 209 262 53 556.26 34.91 427 209 263 54 556.36 34.94 428 209 264 55 556.36 34.94 429 209 311 89 87.08 0.24 430 209 312 90 86.70 0.26 431 209 313 91 84.38 0.26 432 209 314 92 83.70 0.08 433 210 261 51 556.19 34.94 434 210 309 86 88.23 0.16 435 210 310 87 88.16 0.15 436 210 311 88 86.86 0.30 437 211 247 36 439.19 0.74 438 211 250 39 439.57 0.58 439 211 261 50 556.19 34.94 440 211 297 73 435.57 1.82 441 211 309 85 88.21 0.17 442 212 217 5 619.63 13.67 443 212 250 38 439.57 0.58 444 212 262 50 556.27 34.96 445 212 263 51 556.34 34.97 446 212 264 52 556.33 34.97 447 213 217 4 631.99 19.84 448 213 246 33 438.63 0.95 449 213 288 62 521.84 40.54 450 213 293 67 438.54 0.99 451 214 217 3 641.90 23.57 452 214 219 5 618.63 13.18 453 214 246 32 438.48 0.97 454 214 249 35 439.53 0.55 455 216 270 54 556.39 35.04 456 219 224 5 712.38 1.99 457 219 249 30 556.07 35.18 458 220 223 3 715.33 2.10 459 221 224 3 713.79 1.29 460 221 225 4 713.80 1.28 461 222 225 3 713.79 1.28 462 222 226 4 699.46 5.88 463 223 226 3 708.54 1.33 464 223 227 4 699.47 5.88 465 223 249 26 558.06 35.80 466 223 252 29 558.47 35.95 467 223 253 30 558.45 35.66 468 223 256 33 559.78 36.20 469 223 257 34 559.85 36.20 470 224 227 3 709.25 0.99 471 224 228 4 715.65 2.21 472 225 228 3 732.42 1.02 473 225 229 4 715.64 2.22 474 226 229 3 720.51 0.21 475 226 230 4 715.64 2.22 476 226 252 26 559.59 36.23 477 226 256 30 559.85 36.20 478 227 230 3 714.41 2.84 479 227 234 7 624.38 22.57 480 227 235 8 624.15 22.69 481 227 238 11 605.94 14.62 482 227 248 21 559.35 36.34 483 227 252 25 559.66 36.26 484 228 235 7 624.27 22.63 485 230 234 4 634.43 20.77 486 230 235 5 634.43 20.77 487 230 252 22 559.84 36.20 488 230 304 61 397.69 1.26 489 231 234 3 715.84 1.77 490 231 235 4 658.22 18.18 491 231 304 60 398.00 1.34 492 232 235 3 702.43 3.93 493 232 236 4 639.41 18.28 494 233 236 3 711.14 2.83 495 233 237 4 699.91 8.45 496 233 303 57 403.32 0.90 497 234 237 3 710.52 2.54 498 234 238 4 642.91 20.05 499 234 248 14 559.73 36.24 500 234 300 53 403.94 0.64 501 234 303 56 398.15 1.41 502 234 304 57 398.14 1.41 503 235 238 3 710.54 2.53 504 235 239 4 642.94 20.04 505 236 239 3 711.36 2.11 506 236 240 4 639.28 18.26 507 237 240 3 710.53 2.52 508 237 241 4 642.69 16.54 509 237 295 45 573.01 29.48 510 237 296 46 559.52 36.22 511 237 299 49 538.67 44.08 512 237 300 50 471.74 32.44 513 237 303 53 403.83 0.64 514 238 241 3 713.12 1.65 515 238 244 6 576.98 27.62 516 238 245 7 560.90 36.80 517 238 248 10 560.00 36.24 518 241 244 3 749.54 1.34 519 241 295 41 728.53 1.91 520 241 296 42 690.45 8.29 521 247 300 40 768.34 3.16 522 248 300 39 854.50 22.03 523 250 309 46 88.17 0.17 524 251 300 36 900.73 1.07 525 251 301 37 854.52 22.03 526 251 304 40 705.72 0.93 527 251 308 44 88.27 0.15 528 251 309 45 88.17 0.17 529 254 308 41 300.32 106.20 530 254 309 42 88.20 0.17 531 254 310 43 88.16 0.17 532 255 304 36 740.97 1.97 533 255 308 40 300.33 106.20 534 258 310 39 300.30 106.22 535 259 310 38 88.12 0.14 536 260 310 37 88.04 0.15 537 260 311 38 88.00 0.16 538 260 312 39 83.31 0.73 539 263 314 38 44.73 1.71 540 263 316 40 42.16 1.08 541 264 314 37 44.97 1.59 542 264 315 38 42.18 1.09 543 264 316 39 42.16 1.09 544 265 316 38 42.14 1.09 545 266 315 36 42.22 1.08 546 266 316 37 42.16 1.09 547 266 317 38 42.13 1.08 548 268 321 40 29.07 1.53 549 268 322 41 24.88 1.25 550 295 299 4 854.07 4.10 551 296 299 3 720.91 2.39 552 296 300 4 719.96 2.86 553 297 300 3 732.10 6.21 554 297 301 4 719.54 2.65 555 298 301 3 722.58 1.45 556 298 302 4 719.53 2.65 557 299 302 3 719.53 2.66 558 299 303 4 719.50 2.65 559 300 303 3 715.59 0.74 560 300 304 4 703.52 3.57 561 301 304 3 715.57 0.76 562 301 305 4 649.98 20.21 563 301 306 5 633.38 20.08 564 301 307 6 380.86 57.59 565 302 305 3 702.79 3.81 566 318 321 3 694.88 1.26 567 318 325 7 34.36 5.61 568 319 326 7 22.41 0.12 569 320 323 3 642.20 23.62 570 320 325 5 45.45 0.07 571 321 325 4 663.03 13.54 572 322 325 3 702.23 4.09 573 324 327 3 728.98 3.73