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 4 62 58 18.52 1.46 2 7 10 3 796.25 1.32 3 7 61 54 86.80 0.04 4 7 62 55 86.98 0.05 5 7 79 72 86.81 0.05 6 8 11 3 806.42 0.29 7 8 202 194 87.21 0.35 8 9 12 3 772.74 5.36 9 9 13 4 748.54 5.51 10 9 201 192 87.95 0.01 11 9 202 193 87.22 0.35 12 9 205 196 86.56 0.02 13 10 13 3 754.45 3.77 14 10 14 4 736.49 1.27 15 10 61 51 89.95 0.93 16 11 14 3 764.49 1.20 17 11 15 4 752.92 6.93 18 12 15 3 757.09 4.86 19 12 16 4 753.06 6.87 20 12 205 193 92.31 0.09 21 12 206 194 90.31 0.91 22 12 209 197 88.28 0.06 23 13 16 3 772.73 2.96 24 13 17 4 755.15 5.82 25 13 57 44 95.87 0.83 26 13 60 47 96.11 0.90 27 13 61 48 97.81 0.12 28 13 79 66 98.08 0.05 29 13 205 192 95.58 0.85 30 14 17 3 745.97 1.23 31 14 18 4 751.56 1.47 32 14 61 47 100.82 0.27 33 15 18 3 765.16 3.48 34 15 19 4 748.52 0.05 35 15 209 194 95.94 0.83 36 16 19 3 761.99 0.18 37 16 20 4 745.62 1.52 38 16 57 41 101.86 0.68 39 16 209 193 95.94 0.83 40 16 213 197 95.92 0.82 41 17 20 3 753.52 0.49 42 17 21 4 748.79 0.07 43 17 57 40 101.85 0.68 44 17 58 41 102.48 0.38 45 18 21 3 763.29 0.17 46 18 22 4 749.85 0.76 47 19 22 3 774.47 4.40 48 19 23 4 749.86 0.77 49 19 209 190 101.07 0.32 50 19 213 194 100.38 0.14 51 20 23 3 774.48 4.39 52 20 24 4 766.43 8.42 53 20 50 30 102.53 0.47 54 20 53 33 102.58 0.46 55 20 54 34 102.61 0.45 56 20 57 37 102.64 0.42 57 20 212 192 101.07 0.32 58 20 213 193 101.01 0.32 59 20 216 196 100.81 0.19 60 20 217 197 99.27 0.23 61 21 24 3 774.90 4.21 62 21 25 4 770.34 6.49 63 21 54 33 102.61 0.44 64 22 25 3 771.66 5.83 65 22 26 4 770.34 6.49 66 23 26 3 772.48 5.42 67 23 27 4 770.34 6.49 68 23 217 194 99.74 0.04 69 24 27 3 773.13 5.08 70 24 28 4 752.79 1.61 71 24 47 23 102.64 0.50 72 24 50 26 102.63 0.49 73 24 51 27 102.68 0.47 74 25 28 3 766.67 8.54 75 25 29 4 758.86 1.43 76 26 29 3 763.68 0.09 77 26 30 4 758.86 1.43 78 26 225 199 63.85 0.01 79 27 30 3 764.01 1.08 80 27 31 4 758.85 1.43 81 27 43 16 102.74 0.53 82 27 47 20 102.77 0.52 83 27 50 23 102.78 0.49 84 27 217 190 101.70 0.09 85 27 221 194 89.03 3.31 86 27 224 197 65.59 0.82 87 28 31 3 778.82 2.19 88 28 32 4 766.39 2.35 89 28 47 19 102.77 0.52 90 29 32 3 766.39 2.35 91 30 43 13 102.80 0.54 92 31 34 3 816.20 5.12 93 31 43 12 102.79 0.54 94 34 37 3 814.38 1.41 95 34 40 6 620.71 0.42 96 36 39 3 755.16 3.61 97 36 40 4 715.18 7.52 98 36 230 194 52.60 1.57 99 36 231 195 47.66 0.01 100 37 40 3 735.62 0.21 101 37 41 4 739.94 4.59 102 38 41 3 768.40 0.78 103 38 42 4 765.15 2.41 104 38 230 192 55.53 0.10 105 39 42 3 765.15 2.41 106 39 43 4 760.59 4.70 107 39 229 190 49.43 0.01 108 39 230 191 48.54 0.45 109 40 43 3 760.59 4.70 110 40 44 4 751.47 0.81 111 41 44 3 766.88 1.55 112 41 45 4 765.02 0.62 113 41 99 58 197.91 46.62 114 42 45 3 765.02 0.62 115 42 46 4 765.02 0.62 116 42 96 54 197.61 46.48 117 42 99 57 197.92 46.62 118 42 100 58 197.71 46.54 119 42 229 187 48.53 0.45 120 43 46 3 767.27 1.71 121 43 47 4 759.31 3.48 122 43 224 181 69.06 0.72 123 43 229 186 48.53 0.44 124 44 47 3 768.32 2.23 125 44 48 4 762.98 1.65 126 45 48 3 767.73 1.94 127 45 49 4 765.06 0.60 128 45 92 47 199.45 46.02 129 45 96 51 198.09 46.70 130 46 49 3 766.32 2.64 131 46 50 4 763.77 1.36 132 46 220 174 100.64 0.92 133 46 224 178 66.31 0.47 134 47 50 3 785.62 0.73 135 47 51 4 758.89 0.42 136 48 51 3 772.60 5.78 137 48 52 4 757.61 0.23 138 48 92 44 199.86 45.91 139 49 52 3 781.90 1.12 140 49 53 4 758.88 0.86 141 49 89 40 199.69 45.98 142 49 92 43 199.84 45.91 143 49 93 44 199.69 45.98 144 49 216 167 103.44 0.64 145 50 53 3 763.03 1.21 146 50 54 4 760.33 1.60 147 51 54 3 763.89 0.18 148 51 55 4 760.34 1.60 149 52 55 3 768.71 2.23 150 52 56 4 760.25 1.64 151 52 85 33 201.25 45.25 152 52 88 36 201.28 45.26 153 52 89 37 201.21 45.29 154 53 56 3 771.16 6.66 155 53 57 4 760.24 1.64 156 53 85 32 201.27 45.25 157 53 216 163 106.14 2.10 158 54 57 3 763.68 3.36 159 54 58 4 760.13 1.59 160 55 58 3 770.82 0.21 161 55 59 4 761.97 0.69 162 56 59 3 773.87 4.37 163 56 60 4 760.12 1.62 164 56 84 28 204.29 43.86 165 56 85 29 201.50 45.26 166 57 60 3 773.69 4.46 167 57 61 4 760.12 1.63 168 57 209 152 107.70 1.61 169 57 212 155 106.45 2.24 170 58 61 3 771.22 5.70 171 58 62 4 756.09 3.65 172 59 62 3 776.24 4.04 173 59 63 4 741.56 0.78 174 59 64 5 463.90 7.38 175 59 65 6 463.90 7.38 176 60 64 4 659.78 41.67 177 60 65 5 434.84 11.86 178 60 79 19 213.56 39.70 179 60 81 21 211.33 40.82 180 60 82 22 211.34 40.83 181 64 80 16 226.04 35.47 182 65 78 13 243.16 42.88 183 65 79 14 233.30 39.05 184 65 80 15 225.22 35.14 185 65 81 16 223.25 35.18 186 66 77 11 250.11 39.79 187 66 78 12 243.16 42.88 188 66 79 13 233.69 39.16 189 66 80 14 233.69 39.16 190 67 77 10 261.41 37.17 191 67 78 11 250.01 39.71 192 67 80 13 243.53 42.73 193 68 75 7 378.20 5.98 194 68 76 8 378.13 6.00 195 69 76 7 389.18 0.49 196 69 78 9 300.75 44.64 197 69 126 57 274.36 30.80 198 69 127 58 274.42 30.82 199 69 129 60 280.00 31.09 200 70 74 4 626.98 16.34 201 70 75 5 396.46 2.96 202 70 76 6 396.27 3.05 203 70 129 59 280.19 31.16 204 71 74 3 774.21 4.15 205 71 76 5 433.26 9.13 206 71 78 7 443.29 6.50 207 71 129 58 280.19 31.16 208 71 130 59 280.20 31.17 209 71 131 60 280.20 31.16 210 71 134 63 280.21 31.16 211 71 194 123 253.89 18.00 212 71 195 124 253.84 17.98 213 72 131 59 280.23 31.16 214 76 194 118 293.24 1.78 215 77 194 117 293.42 1.89 216 77 201 124 227.91 34.55 217 78 83 5 769.32 1.21 218 78 194 116 290.99 3.12 219 79 82 3 804.51 0.60 220 80 83 3 769.05 1.35 221 80 84 4 752.02 1.99 222 80 127 47 353.16 15.81 223 81 84 3 778.23 3.06 224 81 85 4 758.56 1.28 225 82 85 3 774.22 5.06 226 82 86 4 758.55 1.28 227 82 208 126 209.40 52.29 228 83 87 4 758.51 1.30 229 83 119 36 353.25 15.78 230 83 123 40 353.25 15.78 231 83 126 43 353.45 15.78 232 83 189 106 306.29 7.51 233 84 87 3 762.62 0.74 234 84 88 4 768.40 3.64 235 85 88 3 779.00 1.65 236 85 89 4 756.84 0.30 237 85 216 131 210.43 54.06 238 86 89 3 768.38 3.65 239 86 90 4 744.93 2.54 240 86 208 122 213.37 53.54 241 86 212 126 211.19 54.33 242 86 216 130 210.43 54.06 243 87 90 3 780.62 0.17 244 87 91 4 756.85 0.29 245 87 119 32 353.94 15.58 246 88 91 3 784.76 3.83 247 88 92 4 759.10 1.89 248 89 92 3 760.71 2.69 249 89 93 4 753.00 1.01 250 89 216 127 211.03 54.37 251 90 93 3 753.15 1.08 252 90 94 4 750.75 0.14 253 90 182 92 307.66 7.42 254 91 94 3 759.12 4.04 255 91 95 4 750.60 0.22 256 91 112 21 354.41 15.48 257 92 95 3 759.13 4.04 258 92 96 4 755.14 0.09 259 93 96 3 757.81 1.25 260 93 97 4 757.80 1.25 261 93 182 89 308.03 7.55 262 93 219 126 211.11 54.47 263 94 97 3 774.28 0.93 264 94 98 4 754.17 0.40 265 94 111 17 354.88 15.31 266 94 115 21 354.79 15.36 267 94 148 54 354.76 15.35 268 94 152 58 354.80 15.27 269 94 182 88 308.17 7.49 270 95 98 3 780.31 2.09 271 95 99 4 760.54 2.79 272 96 99 3 775.32 4.58 273 96 100 4 758.01 4.06 274 96 219 123 211.58 54.65 275 96 223 127 196.93 60.80 276 97 100 3 775.32 4.59 277 97 101 4 758.00 4.05 278 97 152 55 355.13 15.16 279 97 174 77 309.19 7.53 280 97 219 122 211.78 54.58 281 98 101 3 777.06 2.30 282 98 102 4 738.12 5.82 283 98 103 5 632.07 14.63 284 98 108 10 355.46 15.04 285 98 156 58 357.18 14.12 286 99 102 3 748.56 0.60 287 100 170 70 311.91 8.38 288 100 171 71 311.87 8.39 289 100 174 74 311.84 8.39 290 100 223 123 210.15 54.81 291 100 228 128 157.52 49.73 292 101 156 55 357.23 14.11 293 101 159 58 356.95 13.81 294 101 160 59 356.45 13.71 295 101 171 70 311.88 8.39 296 102 159 57 362.63 11.17 297 103 107 4 744.97 4.75 298 103 156 53 357.40 14.04 299 104 107 3 764.52 0.77 300 104 108 4 734.72 0.38 301 105 108 3 769.13 1.54 302 105 109 4 734.72 0.38 303 106 109 3 745.00 4.76 304 106 110 4 745.00 4.75 305 107 110 3 770.26 2.46 306 107 111 4 755.35 0.42 307 108 111 3 765.68 4.75 308 108 112 4 750.78 2.71 309 109 112 3 769.29 5.58 310 109 113 4 750.80 2.71 311 110 113 3 770.44 0.56 312 110 114 4 750.79 2.71 313 111 114 3 757.08 0.42 314 111 115 4 757.07 0.42 315 111 148 37 369.65 8.15 316 111 156 45 369.63 8.14 317 112 115 3 769.84 5.87 318 112 116 4 751.78 3.17 319 113 116 3 757.22 0.45 320 113 117 4 758.75 0.30 321 114 117 3 774.63 3.44 322 114 118 4 751.78 3.19 323 114 144 30 370.39 8.26 324 115 118 3 750.45 3.85 325 115 119 4 757.07 0.54 326 115 148 33 370.34 8.21 327 116 119 3 780.40 2.28 328 116 120 4 757.02 0.53 329 117 120 3 760.28 1.50 330 117 121 4 755.32 0.33 331 118 121 3 774.39 2.39 332 118 122 4 755.32 0.33 333 118 141 23 370.58 8.24 334 118 144 26 370.55 8.22 335 118 145 27 370.55 8.22 336 118 148 30 370.62 8.18 337 119 122 3 755.96 0.66 338 119 123 4 750.01 2.32 339 120 123 3 765.07 2.28 340 120 124 4 751.59 6.38 341 121 124 3 760.91 1.72 342 121 125 4 760.97 1.69 343 121 140 19 370.83 8.21 344 121 141 20 370.81 8.21 345 122 125 3 766.42 0.78 346 122 126 4 761.23 1.81 347 122 141 19 370.83 8.21 348 123 126 3 772.62 3.88 349 123 127 4 758.59 0.49 350 124 127 3 783.16 6.97 351 124 128 4 743.47 1.04 352 125 128 3 755.50 8.65 353 125 134 9 371.20 8.36 354 125 137 12 371.18 8.34 355 126 134 8 417.23 3.33 356 126 189 63 323.42 15.49 357 128 133 5 717.26 5.50 358 128 134 6 484.49 3.91 359 128 137 9 487.65 24.58 360 129 134 5 720.73 3.93 361 130 133 3 784.72 2.44 362 130 134 4 742.97 6.97 363 131 134 3 759.38 0.13 364 131 135 4 757.63 0.36 365 131 195 64 312.39 11.38 366 132 135 3 775.71 3.76 367 132 136 4 759.11 0.37 368 133 136 3 764.97 2.71 369 133 137 4 750.99 3.69 370 134 137 3 768.51 0.94 371 134 138 4 736.47 5.73 372 134 189 55 323.89 15.64 373 134 194 60 317.89 14.04 374 134 195 61 312.38 11.38 375 135 138 3 755.27 0.71 376 135 139 4 743.91 0.14 377 135 190 55 323.78 15.60 378 135 195 60 312.38 11.37 379 135 196 61 312.37 11.38 380 136 139 3 771.83 3.90 381 136 140 4 762.89 3.09 382 137 140 3 770.68 0.80 383 137 141 4 757.72 0.52 384 138 141 3 772.11 1.52 385 138 142 4 759.12 0.18 386 138 186 48 323.98 15.61 387 138 189 51 323.93 15.63 388 138 190 52 323.78 15.64 389 139 142 3 780.13 5.53 390 139 143 4 759.12 0.18 391 140 143 3 768.78 0.31 392 140 144 4 759.14 0.18 393 141 144 3 759.36 0.29 394 141 145 4 759.17 0.20 395 142 145 3 762.62 1.53 396 142 146 4 755.75 2.02 397 143 146 3 772.25 1.41 398 143 147 4 762.75 1.46 399 144 147 3 762.77 1.47 400 144 148 4 762.78 1.46 401 145 148 3 767.58 0.94 402 145 149 4 762.78 1.46 403 145 182 37 324.39 15.61 404 145 183 38 324.38 15.62 405 145 186 41 324.20 15.64 406 146 149 3 764.08 0.82 407 146 150 4 764.04 0.81 408 147 150 3 767.40 0.88 409 147 151 4 762.75 1.45 410 148 151 3 766.96 0.65 411 148 152 4 762.51 1.41 412 149 152 3 766.76 0.74 413 149 153 4 762.48 1.40 414 149 178 29 325.03 15.45 415 149 179 30 324.86 15.45 416 150 153 3 784.28 2.23 417 150 154 4 746.16 6.75 418 150 155 5 714.71 0.20 419 151 155 4 636.22 8.61 420 151 156 5 636.22 8.61 421 152 156 4 636.21 8.60 422 152 157 5 636.23 8.60 423 152 178 26 325.16 15.45 424 153 157 4 636.23 8.60 425 153 175 22 325.26 15.40 426 153 179 26 325.25 15.40 427 154 158 4 710.68 7.41 428 155 158 3 765.22 3.04 429 155 159 4 721.89 2.23 430 156 159 3 741.57 12.03 431 156 160 4 714.46 2.72 432 156 171 15 326.18 15.50 433 157 160 3 717.69 4.33 434 157 161 4 735.03 4.34 435 157 171 14 326.17 15.46 436 157 175 18 325.50 15.31 437 160 168 8 326.33 15.42 438 160 171 11 326.21 15.48 439 162 167 5 626.43 23.14 440 164 167 3 759.79 2.89 441 164 168 4 728.32 9.13 442 165 168 3 768.23 7.95 443 165 169 4 728.37 9.11 444 166 169 3 753.08 0.64 445 166 170 4 756.67 1.32 446 166 227 61 209.63 54.11 447 167 170 3 766.06 3.38 448 167 171 4 756.69 1.30 449 167 228 61 189.59 62.82 450 168 171 3 766.07 3.38 451 168 172 4 756.63 1.28 452 169 172 3 757.98 1.96 453 169 173 4 757.98 1.95 454 170 173 3 779.00 3.04 455 170 174 4 767.39 2.75 456 170 226 56 194.03 61.70 457 170 228 58 174.28 56.46 458 171 174 3 767.39 2.75 459 171 175 4 767.39 2.75 460 172 175 3 784.58 4.20 461 172 176 4 755.71 1.38 462 173 176 3 767.33 4.42 463 173 177 4 765.97 3.47 464 174 177 3 770.84 2.68 465 174 178 4 755.99 1.52 466 174 219 45 211.94 54.63 467 174 223 49 211.05 54.45 468 175 178 3 760.63 0.80 469 175 179 4 755.99 1.52 470 176 179 3 760.63 0.80 471 176 180 4 757.02 1.01 472 177 180 3 764.74 0.59 473 177 181 4 757.00 0.98 474 178 181 3 778.03 6.09 475 178 182 4 757.02 0.78 476 178 219 41 212.09 54.64 477 179 182 3 775.90 7.16 478 179 183 4 759.41 0.21 479 180 183 3 775.66 7.28 480 180 184 4 759.42 0.21 481 181 184 3 769.74 4.24 482 181 185 4 759.17 0.33 483 181 211 30 214.66 54.52 484 181 214 33 214.21 54.72 485 181 215 34 214.05 54.79 486 182 185 3 771.25 1.29 487 182 186 4 768.65 0.45 488 183 186 3 792.72 1.24 489 183 187 4 768.22 0.23 490 184 187 3 782.06 4.09 491 184 188 4 755.03 0.90 492 184 211 27 215.11 54.43 493 185 188 3 775.91 1.02 494 185 189 4 747.23 0.55 495 185 208 23 215.41 54.52 496 185 211 26 214.99 54.48 497 185 212 27 215.00 54.48 498 185 215 30 215.01 54.46 499 186 189 3 778.95 0.75 500 186 190 4 755.48 4.84 501 187 190 3 777.71 0.13 502 187 191 4 755.39 4.88 503 188 191 3 778.06 0.06 504 188 192 4 714.25 2.67 505 188 204 16 233.86 62.02 506 188 207 19 232.13 62.76 507 188 211 23 215.54 54.47 508 189 192 3 758.63 0.77 509 189 193 4 713.59 3.00 510 189 208 19 215.93 54.28 511 190 196 6 405.55 9.12 512 191 196 5 414.70 4.54 513 191 197 6 405.55 9.12 514 191 198 7 323.87 31.71 515 191 199 8 276.80 51.25 516 192 199 7 265.97 53.70 517 193 197 4 600.95 38.64 518 193 204 11 247.81 59.44 519 194 201 7 390.54 3.25 520 199 203 4 729.26 5.29 521 199 204 5 698.48 10.07 522 199 207 8 698.42 10.03 523 200 203 3 767.54 2.66 524 200 204 4 698.52 10.08 525 201 204 3 738.35 6.74 526 201 205 4 713.04 2.83 527 202 205 3 765.99 3.85 528 202 206 4 736.50 8.90 529 203 206 3 756.29 0.99 530 203 207 4 744.93 4.70 531 204 207 3 765.89 0.42 532 204 208 4 748.97 2.68 533 205 208 3 749.36 2.87 534 205 209 4 745.09 4.62 535 206 209 3 768.93 2.81 536 206 210 4 755.10 9.59 537 207 210 3 776.56 1.15 538 207 211 4 776.56 1.15 539 208 211 3 776.56 1.15 540 208 212 4 766.61 6.12 541 209 212 3 752.19 1.09 542 209 213 4 745.14 4.62 543 210 213 3 770.14 2.58 544 210 214 4 735.06 0.41 545 211 214 3 769.64 2.33 546 211 215 4 734.72 0.24 547 212 215 3 769.64 2.33 548 212 216 4 721.21 7.00 549 213 217 4 652.73 13.20 550 213 218 5 587.29 37.02 551 214 218 4 587.07 37.12 552 214 219 5 595.36 32.98 553 215 219 4 655.52 2.91 554 216 220 4 710.52 16.51 555 217 220 3 756.52 4.52 556 217 221 4 725.62 8.96 557 218 221 3 759.87 6.43 558 218 222 4 745.00 0.72 559 219 222 3 784.82 3.99 560 219 223 4 718.37 1.71 561 220 223 3 764.35 4.19 562 220 224 4 720.13 0.83 563 221 224 3 795.21 0.09 564 221 225 4 721.60 0.32 565 222 225 3 765.67 5.62 566 222 226 4 707.48 6.74 567 223 226 3 734.86 6.91 568 223 228 5 590.35 43.47 569 223 229 6 511.84 8.66 570 224 229 5 490.84 1.83 571 226 229 3 794.05 3.13 572 227 230 3 708.09 0.51