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 2 225 223 52.71 0.53 2 2 226 224 37.87 1.60 3 2 227 225 33.09 0.75 4 3 204 201 127.89 1.41 5 3 225 222 54.55 1.45 6 4 202 198 131.33 0.98 7 4 204 200 126.73 0.83 8 4 225 221 73.94 0.62 9 5 184 179 132.48 1.03 10 5 185 180 133.88 1.63 11 5 186 181 133.88 1.63 12 5 203 198 131.99 1.28 13 5 204 199 130.72 0.70 14 6 201 195 134.93 1.14 15 6 202 196 132.57 0.98 16 6 222 216 77.64 2.07 17 6 225 219 76.93 2.10 18 7 194 187 135.31 1.26 19 7 201 194 134.99 1.17 20 7 202 195 134.16 1.49 21 8 199 191 136.41 1.40 22 8 200 192 135.56 1.40 23 8 201 193 135.38 1.32 24 8 222 214 78.98 1.47 25 9 200 191 136.08 1.56 26 9 222 213 78.98 1.47 27 10 200 190 136.47 1.44 28 10 220 210 99.59 4.76 29 10 221 211 89.34 0.32 30 10 222 212 83.92 1.00 31 11 220 209 99.59 4.76 32 11 221 210 89.33 0.32 33 11 223 212 89.03 0.42 34 11 243 232 23.74 1.71 35 12 177 165 177.86 3.56 36 12 219 207 103.56 2.83 37 12 220 208 100.74 4.21 38 13 177 164 189.59 5.68 39 13 217 204 122.92 0.12 40 13 219 206 111.45 3.37 41 13 240 227 38.41 1.00 42 13 243 230 35.98 2.20 43 14 156 142 191.16 4.93 44 14 157 143 189.66 5.65 45 14 177 163 189.62 5.70 46 14 218 204 115.87 3.55 47 15 156 141 191.62 5.10 48 15 157 142 191.62 5.10 49 15 215 200 123.55 0.04 50 15 216 201 123.50 0.06 51 15 217 202 122.92 0.11 52 16 159 143 191.77 5.16 53 16 212 196 134.82 1.23 54 16 213 197 131.80 1.35 55 16 214 198 128.00 2.03 56 16 215 199 123.58 0.06 57 16 216 200 123.50 0.07 58 16 218 202 116.09 3.40 59 17 152 135 192.06 5.12 60 17 156 139 191.88 5.18 61 17 157 140 191.84 5.16 62 17 158 141 191.80 5.14 63 17 159 142 191.81 5.17 64 18 159 141 191.87 5.17 65 18 209 191 152.38 0.85 66 18 212 194 135.86 1.70 67 18 213 195 132.56 0.96 68 18 214 196 128.00 2.04 69 19 149 130 192.09 5.13 70 19 158 139 191.93 5.17 71 19 159 140 191.91 5.17 72 19 160 141 191.87 5.17 73 19 163 144 191.89 5.16 74 21 139 118 205.16 2.67 75 24 135 111 198.51 5.92 76 24 139 115 208.19 4.49 77 24 142 118 209.10 4.29 78 24 144 120 208.71 4.32 79 26 101 75 209.19 4.27 80 26 102 76 209.12 4.30 81 26 105 79 209.12 4.30 82 26 138 112 209.10 4.29 83 27 99 72 209.42 4.32 84 27 102 75 209.28 4.25 85 27 142 115 209.29 4.27 86 28 102 74 209.34 4.28 87 29 99 70 223.46 4.91 88 31 35 4 796.61 9.54 89 31 36 5 799.75 6.02 90 31 39 8 738.23 8.38 91 31 97 66 359.33 5.17 92 31 99 68 349.12 0.85 93 32 35 3 862.47 1.47 94 32 36 4 808.70 3.49 95 33 36 3 852.57 2.07 96 35 38 3 854.88 2.31 97 35 39 4 854.37 2.05 98 36 39 3 854.37 2.05 99 36 40 4 854.37 2.05 100 36 93 57 432.69 0.77 101 36 94 58 434.19 0.13 102 37 40 3 864.32 2.27 103 37 41 4 854.35 2.05 104 38 41 3 856.53 3.14 105 38 42 4 852.01 1.01 106 39 42 3 852.02 1.02 107 39 43 4 841.27 2.61 108 39 93 54 445.03 1.53 109 39 99 60 435.80 0.88 110 39 100 61 434.26 0.10 111 40 43 3 854.17 2.08 112 40 44 4 812.25 4.25 113 40 94 54 453.62 3.28 114 41 44 3 821.25 6.15 115 41 45 4 803.63 3.85 116 41 46 5 817.99 3.37 117 42 46 4 818.00 3.38 118 43 46 3 822.00 5.38 119 43 47 4 833.74 0.34 120 43 86 43 459.63 0.64 121 43 89 46 459.51 0.66 122 43 100 57 453.10 3.49 123 44 47 3 860.73 7.16 124 44 48 4 854.45 0.18 125 45 48 3 864.93 5.06 126 45 49 4 849.73 2.54 127 46 49 3 857.15 3.70 128 46 50 4 838.90 2.87 129 47 50 3 856.41 0.80 130 47 51 4 838.87 2.85 131 47 80 33 464.48 2.45 132 47 81 34 469.57 0.30 133 47 86 39 476.73 0.88 134 48 51 3 859.88 7.62 135 48 52 4 838.80 2.81 136 49 52 3 859.77 7.67 137 49 53 4 838.80 2.81 138 50 53 3 834.77 2.66 139 50 54 4 836.88 3.71 140 50 80 30 480.23 0.91 141 50 137 87 471.54 0.67 142 50 140 90 470.14 0.03 143 51 55 4 830.77 0.19 144 51 80 29 480.24 0.92 145 52 55 3 847.21 1.46 146 52 56 4 837.98 3.41 147 53 56 3 858.24 0.07 148 53 57 4 837.48 3.54 149 53 140 87 480.15 1.03 150 53 146 93 478.53 1.02 151 54 57 3 855.14 5.29 152 54 58 4 837.93 3.39 153 54 77 23 481.20 1.24 154 54 80 26 481.14 1.25 155 54 133 79 480.42 1.10 156 55 58 3 853.45 4.14 157 55 59 4 853.43 4.13 158 55 77 22 481.23 1.26 159 56 59 3 883.56 1.56 160 56 60 4 853.20 4.25 161 57 60 3 855.51 3.10 162 57 61 4 853.20 4.25 163 57 166 109 480.49 1.33 164 57 169 112 480.49 1.33 165 57 170 113 480.44 1.30 166 58 61 3 867.16 8.25 167 58 62 4 856.19 2.75 168 58 70 12 489.05 2.29 169 58 73 15 481.80 1.33 170 58 74 16 481.79 1.33 171 58 77 19 481.79 1.34 172 59 62 3 849.07 5.01 173 59 63 4 845.05 3.01 174 59 70 11 489.14 2.33 175 60 63 3 839.00 4.28 176 60 64 4 836.86 3.59 177 60 150 90 480.48 1.31 178 60 169 109 480.50 1.33 179 60 170 110 480.49 1.33 180 61 64 3 838.98 4.27 181 61 65 4 829.00 0.34 182 61 66 5 812.03 3.80 183 61 70 9 501.68 2.25 184 61 73 12 495.41 0.88 185 61 169 108 480.50 1.33 186 62 66 4 749.30 3.46 187 62 67 5 619.99 6.57 188 62 70 8 495.36 5.42 189 64 169 105 480.57 1.30 190 64 173 109 480.38 1.33 191 65 69 4 838.37 2.58 192 65 168 103 480.73 1.27 193 65 169 104 480.68 1.25 194 65 173 108 480.44 1.30 195 66 69 3 885.57 5.74 196 66 70 4 845.69 1.07 197 67 70 3 846.71 1.48 198 67 71 4 853.47 4.95 199 69 72 3 866.30 0.20 200 69 73 4 856.11 3.64 201 70 73 3 856.34 3.52 202 70 74 4 855.10 3.12 203 71 74 3 856.12 3.64 204 71 75 4 856.12 3.63 205 72 75 3 874.38 0.57 206 72 76 4 857.91 4.50 207 73 76 3 861.45 2.73 208 73 77 4 857.91 4.50 209 73 165 92 480.68 1.26 210 73 166 93 480.63 1.27 211 73 169 96 480.59 1.29 212 74 77 3 873.26 3.73 213 74 78 4 857.94 4.48 214 75 78 3 860.53 0.60 215 75 79 4 855.33 3.20 216 76 79 3 867.42 0.81 217 76 80 4 853.56 4.01 218 76 126 50 483.68 0.94 219 76 133 57 482.37 1.14 220 77 80 3 857.94 1.80 221 77 81 4 852.83 4.35 222 78 81 3 840.82 1.49 223 78 82 4 831.07 2.66 224 79 82 3 843.72 0.66 225 79 85 6 800.87 0.04 226 79 130 51 483.65 0.95 227 79 133 54 483.57 0.98 228 80 133 53 483.55 0.99 229 80 137 57 482.94 1.04 230 82 85 3 854.08 1.60 231 82 86 4 829.86 3.60 232 83 86 3 863.30 3.01 233 83 87 4 845.24 1.17 234 84 87 3 853.75 0.18 235 84 88 4 849.22 0.83 236 85 89 4 840.91 4.98 237 85 107 22 490.89 0.35 238 86 89 3 858.90 4.02 239 86 90 4 840.91 4.98 240 87 90 3 856.51 2.83 241 87 91 4 840.90 4.98 242 88 91 3 867.36 0.64 243 88 92 4 853.93 6.04 244 88 107 19 501.38 4.35 245 89 92 3 867.62 0.51 246 89 93 4 854.23 6.20 247 89 104 15 503.28 4.84 248 89 107 18 502.99 4.96 249 90 93 3 867.62 0.51 250 90 94 4 846.12 9.97 251 91 94 3 851.19 7.41 252 91 95 4 830.05 1.95 253 92 95 3 840.98 3.21 254 92 96 4 812.81 5.50 255 92 97 5 812.73 5.54 256 92 98 6 694.12 10.77 257 92 103 11 549.18 12.81 258 92 106 14 549.51 13.01 259 92 107 15 544.99 10.75 260 93 97 4 768.02 16.80 261 93 98 5 731.22 35.21 262 93 100 7 658.88 29.16 263 93 103 10 565.16 17.66 264 94 97 3 857.09 4.77 265 98 102 4 826.84 5.34 266 98 103 5 816.09 1.07 267 98 106 8 799.13 7.40 268 99 102 3 854.22 2.78 269 99 103 4 851.25 4.26 270 100 103 3 854.95 2.42 271 100 104 4 840.06 1.34 272 100 141 41 491.26 0.03 273 101 104 3 855.25 2.27 274 101 105 4 851.26 4.25 275 101 138 37 491.31 0.00 276 101 141 40 491.26 0.03 277 101 142 41 491.25 0.03 278 102 105 3 848.93 0.90 279 102 106 4 844.95 1.10 280 103 106 3 873.27 5.86 281 103 107 4 873.29 5.85 282 104 107 3 876.68 4.16 283 104 108 4 844.91 1.11 284 104 137 33 491.38 0.01 285 104 141 37 491.25 0.03 286 105 108 3 854.94 3.33 287 105 109 4 839.95 1.34 288 106 109 3 848.23 0.84 289 106 110 4 853.03 3.17 290 107 110 3 861.58 1.88 291 107 111 4 853.03 3.17 292 108 111 3 849.31 0.29 293 108 112 4 842.38 2.16 294 108 131 23 491.50 0.01 295 108 134 26 491.45 0.01 296 109 113 4 837.45 0.14 297 110 113 3 850.98 6.62 298 110 114 4 835.35 3.58 299 111 114 3 855.10 0.46 300 111 115 4 840.19 1.18 301 111 130 19 491.68 0.01 302 112 115 3 852.95 0.18 303 112 116 4 845.40 1.42 304 112 127 15 492.07 0.18 305 112 131 19 492.05 0.18 306 113 116 3 852.02 0.64 307 113 117 4 849.30 0.73 308 114 117 3 864.98 7.10 309 115 118 3 867.49 8.36 310 115 123 8 492.37 0.17 311 115 126 11 492.32 0.17 312 115 127 12 492.19 0.15 313 115 130 15 492.22 0.14 314 116 124 8 492.34 0.17 315 116 127 11 492.24 0.14 316 118 123 5 772.75 17.36 317 120 123 3 846.77 2.30 318 120 124 4 836.88 0.79 319 121 124 3 841.08 0.54 320 121 125 4 838.04 1.36 321 122 125 3 869.56 5.44 322 122 126 4 845.38 1.62 323 123 126 3 845.38 1.62 324 123 127 4 845.38 1.62 325 124 127 3 866.31 3.81 326 124 128 4 851.05 3.83 327 125 128 3 866.89 3.52 328 125 129 4 845.35 1.65 329 126 129 3 845.21 1.58 330 126 130 4 845.21 1.58 331 127 130 3 852.06 2.07 332 127 131 4 842.81 0.51 333 128 131 3 856.82 2.71 334 128 132 4 842.82 0.51 335 129 132 3 850.71 3.44 336 129 133 4 856.76 0.41 337 130 133 3 856.76 0.40 338 130 134 4 852.06 1.95 339 131 134 3 850.70 3.44 340 131 135 4 846.01 1.09 341 132 135 3 856.17 0.10 342 132 136 4 844.95 1.62 343 132 164 32 480.78 1.30 344 133 136 3 853.73 1.12 345 133 137 4 844.94 1.62 346 134 137 3 846.82 2.56 347 134 138 4 854.62 6.56 348 135 138 3 854.63 6.56 349 135 139 4 854.63 6.56 350 136 139 3 854.63 6.56 351 136 140 4 854.63 6.56 352 136 166 30 480.81 1.32 353 137 140 3 862.49 2.62 354 137 141 4 853.60 7.07 355 138 141 3 856.65 1.25 356 138 142 4 843.95 2.29 357 139 143 4 843.47 2.51 358 139 144 5 558.62 15.83 359 139 147 8 547.11 11.03 360 140 143 3 817.46 10.50 361 148 151 3 886.58 4.11 362 149 152 3 904.57 2.14 363 149 163 14 482.62 1.95 364 149 167 18 482.56 1.99 365 149 171 22 482.39 2.03 366 149 172 23 501.65 11.65 367 150 170 20 482.54 1.99 368 150 172 22 500.85 11.28 369 152 156 4 864.09 1.84 370 152 172 20 553.56 37.51 371 152 175 23 554.04 37.91 372 153 175 22 554.13 37.90 373 155 175 20 554.09 37.95 374 155 177 22 553.97 38.04 375 156 177 21 553.96 38.05 376 157 177 20 553.85 38.12 377 157 180 23 524.75 52.64 378 157 218 61 114.52 3.48 379 158 163 5 869.20 1.08 380 158 171 13 554.50 37.84 381 158 178 20 552.79 38.64 382 158 179 21 521.94 54.05 383 158 180 22 521.85 54.09 384 159 180 21 515.13 57.45 385 159 208 49 272.58 0.55 386 159 209 50 261.30 0.66 387 159 218 59 115.37 3.04 388 160 163 3 915.66 0.21 389 160 180 20 515.14 57.45 390 160 181 21 503.36 63.34 391 160 182 22 503.36 63.34 392 160 209 49 255.26 1.14 393 161 181 20 503.37 63.34 394 161 182 21 503.35 63.34 395 161 209 48 256.48 1.76 396 162 181 19 500.37 64.86 397 162 183 21 478.68 75.68 398 163 167 4 812.56 8.37 399 163 168 5 801.15 2.63 400 163 181 18 503.38 63.37 401 164 167 3 860.74 3.01 402 164 168 4 834.81 2.69 403 165 168 3 844.22 5.25 404 165 169 4 813.87 7.79 405 165 189 24 327.55 0.69 406 166 169 3 854.53 0.10 407 166 170 4 844.22 5.25 408 167 170 3 862.39 3.75 409 167 171 4 813.86 7.79 410 168 171 3 846.90 2.98 411 168 189 21 328.69 1.23 412 168 193 25 329.83 1.88 413 171 176 5 839.54 0.75 414 171 179 8 626.77 2.77 415 171 193 22 333.39 3.65 416 172 175 3 886.70 8.02 417 172 176 4 840.52 0.26 418 173 176 3 861.78 4.54 419 173 179 6 820.14 10.43 420 173 193 20 333.91 3.87 421 173 197 24 333.78 3.95 422 176 179 3 1018.85 2.93 423 179 190 11 334.25 3.85 424 179 193 14 334.26 3.85 425 179 199 20 333.69 4.08 426 179 201 22 333.46 4.09 427 179 202 23 333.49 4.12 428 180 202 22 333.49 4.12 429 180 205 25 333.35 4.12 430 180 227 47 77.15 2.19 431 181 190 9 436.10 47.06 432 181 202 21 333.58 4.17 433 181 203 22 333.44 4.13 434 181 204 23 333.44 4.13 435 181 205 24 333.28 4.16 436 182 203 21 333.56 4.17 437 182 205 23 333.28 4.16 438 182 206 24 331.95 4.63 439 182 209 27 279.99 1.33 440 183 188 5 620.85 5.83 441 183 190 7 581.38 25.57 442 183 203 20 333.56 4.18 443 183 204 21 333.52 4.19 444 184 204 20 333.50 4.19 445 185 188 3 825.66 17.64 446 187 191 4 819.14 6.11 447 188 191 3 835.88 2.23 448 188 192 4 837.00 2.79 449 188 203 15 333.59 4.20 450 189 192 3 865.04 2.69 451 189 193 4 851.12 4.26 452 190 193 3 859.87 2.94 453 190 194 4 850.12 4.76 454 190 203 13 333.64 4.22 455 191 194 3 850.12 4.76 456 191 195 4 847.74 3.71 457 191 203 12 333.62 4.21 458 192 195 3 857.03 0.94 459 192 196 4 847.72 3.72 460 193 196 3 857.03 0.94 461 193 197 4 847.71 3.72 462 194 197 3 847.71 3.73 463 194 198 4 781.72 12.61 464 194 199 5 731.81 3.72 465 194 201 7 437.94 43.15 466 195 198 3 847.35 12.70 467 200 222 22 78.98 1.47 468 201 220 19 88.79 0.34 469 202 205 3 905.75 1.55 470 202 220 18 86.14 0.42 471 202 227 25 77.11 2.19 472 205 208 3 861.05 0.96 473 207 210 3 837.80 2.31 474 207 211 4 829.53 6.42 475 208 211 3 847.14 2.38 476 208 212 4 828.14 7.12 477 212 216 4 815.96 7.40 478 212 218 6 553.63 17.98 479 212 229 17 77.20 2.23 480 213 216 3 850.23 1.50 481 216 229 13 77.25 2.23 482 217 230 13 77.21 2.23 483 218 227 9 77.41 2.23 484 218 228 10 77.39 2.22 485 218 229 11 77.21 2.23 486 219 227 8 77.41 2.23 487 219 228 9 77.36 2.23 488 219 231 12 77.11 2.19 489 219 236 17 51.20 0.42 490 219 239 20 44.89 1.58 491 220 227 7 77.38 2.23 492 221 226 5 147.54 37.29 493 221 228 7 77.33 2.23 494 221 239 18 35.64 2.20 495 228 231 3 870.45 3.62 496 231 235 4 819.41 9.71 497 231 236 5 808.36 10.76 498 232 235 3 859.15 6.42 499 232 236 4 832.76 3.03 500 233 236 3 842.17 1.36 501 233 237 4 813.79 8.10 502 234 238 4 836.85 3.44 503 235 238 3 860.46 8.37 504 235 239 4 836.85 3.45 505 236 239 3 851.84 3.85 506 236 240 4 836.83 3.45 507 237 240 3 854.45 5.67 508 237 241 4 838.31 2.72 509 238 241 3 862.24 1.78 510 238 242 4 851.22 3.73 511 239 242 3 852.50 3.09 512 239 243 4 828.61 0.45 513 240 243 3 857.33 0.68 514 240 244 4 828.62 0.45 515 241 244 3 865.55 4.79 516 241 245 4 830.11 0.30 517 242 245 3 844.38 5.54 518 242 246 4 838.80 2.75 519 243 246 3 854.76 0.35 520 243 247 4 838.81 2.74 521 244 247 3 847.92 3.99 522 244 248 4 841.42 1.44 523 245 248 3 868.76 2.76 524 245 249 4 841.09 1.28 525 246 249 3 843.30 0.13