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 10 105 95 32.05 0.10 2 10 106 96 28.36 0.12 3 10 107 97 25.57 0.10 4 11 104 93 43.73 0.28 5 11 105 94 31.64 0.30 6 12 33 21 66.29 0.13 7 12 34 22 65.78 0.35 8 12 35 23 65.66 0.33 9 12 36 24 55.18 0.23 10 12 37 25 55.18 0.23 11 12 38 26 65.67 0.32 12 12 76 64 53.42 0.66 13 12 103 91 53.18 1.22 14 12 104 92 47.28 1.19 15 13 33 20 66.29 0.13 16 13 34 21 66.25 0.12 17 13 101 88 69.34 0.04 18 13 103 90 55.26 0.43 19 14 31 17 64.33 0.20 20 14 32 18 66.11 0.21 21 14 33 19 68.06 0.76 22 14 101 87 77.52 0.27 23 14 102 88 65.95 0.14 24 14 103 89 65.11 0.04 25 14 104 90 64.77 0.12 26 15 31 16 68.06 0.76 27 15 32 17 70.42 0.82 28 15 33 18 70.52 0.77 29 15 98 83 82.38 0.75 30 15 100 85 81.17 0.53 31 15 101 86 80.28 0.46 32 16 29 13 71.55 1.05 33 16 31 15 75.14 0.84 34 16 97 81 82.33 0.79 35 16 98 82 82.31 0.78 36 16 99 83 82.31 0.78 37 16 100 84 81.78 0.54 38 16 102 86 80.58 0.34 39 17 30 13 82.33 0.71 40 17 98 81 82.38 0.75 41 18 29 11 120.48 18.34 42 18 30 12 82.33 0.71 43 19 27 8 185.19 50.59 44 19 28 9 185.16 50.60 45 19 29 10 120.48 18.34 46 19 30 11 120.64 18.38 47 19 92 73 82.50 0.76 48 20 27 7 238.60 24.57 49 20 28 8 185.19 50.59 50 21 26 5 309.94 7.90 51 21 27 6 238.61 24.57 52 21 82 61 153.84 3.03 53 21 93 72 125.42 10.17 54 22 26 4 508.79 0.85 55 22 27 5 244.26 24.29 56 22 28 6 244.08 24.20 57 22 79 57 169.59 3.77 58 22 162 140 81.83 0.46 59 23 26 3 673.90 27.25 60 23 160 137 81.81 0.46 61 23 162 139 81.83 0.47 62 24 160 136 81.83 0.47 63 25 81 56 170.09 3.71 64 25 82 57 169.88 3.79 65 25 83 58 169.74 3.75 66 25 160 135 81.84 0.46 67 26 79 53 171.49 3.85 68 26 80 54 170.89 3.58 69 26 81 55 170.09 3.71 70 26 82 56 170.09 3.71 71 26 128 102 81.75 0.42 72 27 78 51 173.72 4.20 73 27 79 52 172.19 3.52 74 27 80 53 171.57 3.80 75 27 82 55 170.78 3.64 76 27 92 65 169.84 3.73 77 28 77 49 173.77 4.21 78 28 78 50 173.75 4.21 79 28 79 51 172.28 3.48 80 29 76 47 174.56 4.54 81 29 77 48 173.80 4.20 82 29 78 49 173.77 4.21 83 29 92 63 170.75 3.59 84 29 96 67 164.26 5.12 85 29 102 73 159.19 5.17 86 30 76 46 174.78 4.43 87 30 77 47 174.52 4.55 88 31 37 6 296.57 2.34 89 31 53 22 226.09 5.99 90 31 76 45 177.06 4.68 91 31 102 71 159.33 5.11 92 32 37 5 298.30 2.48 93 32 38 6 244.62 23.64 94 32 74 42 221.55 9.29 95 32 75 43 181.47 4.83 96 33 38 5 384.25 45.86 97 33 101 68 160.09 5.08 98 34 37 3 871.57 2.83 99 34 38 4 493.57 8.54 100 35 40 5 292.57 0.35 101 35 41 6 279.70 6.08 102 36 40 4 593.59 51.21 103 36 41 5 288.62 2.32 104 36 51 15 250.25 8.56 105 37 41 4 386.13 44.91 106 37 51 14 250.56 8.55 107 37 66 29 250.52 8.53 108 37 68 31 250.50 8.52 109 37 74 37 250.53 8.54 110 37 75 38 250.49 8.53 111 37 76 39 250.34 8.54 112 37 104 67 158.98 5.28 113 38 73 35 253.84 10.11 114 38 74 36 250.55 8.54 115 38 75 37 250.53 8.53 116 39 73 34 253.84 10.11 117 39 74 35 250.61 8.55 118 40 73 33 270.04 6.46 119 41 46 5 877.36 1.48 120 41 49 8 303.44 4.84 121 41 68 27 273.60 8.11 122 41 73 32 273.79 8.01 123 41 74 33 267.01 6.32 124 42 72 30 273.82 8.03 125 42 73 31 273.79 8.01 126 43 46 3 908.20 0.03 127 43 68 25 273.92 8.09 128 43 69 26 274.21 8.13 129 43 70 27 274.23 8.12 130 43 71 28 274.22 8.12 131 43 72 29 274.18 8.11 132 43 73 30 274.17 8.11 133 43 74 31 274.13 8.12 134 44 70 26 274.22 8.12 135 44 71 27 274.29 8.10 136 45 69 24 274.28 8.10 137 45 70 25 274.28 8.10 138 45 135 90 133.05 1.84 139 45 138 93 133.36 1.85 140 45 139 94 133.28 1.90 141 46 49 3 842.15 2.81 142 46 136 90 133.18 1.85 143 46 139 93 133.47 1.85 144 47 110 63 152.36 5.80 145 47 136 89 133.17 1.85 146 47 139 92 133.57 1.91 147 48 65 17 274.94 8.23 148 48 110 62 143.69 5.12 149 48 132 84 132.56 1.88 150 48 136 88 133.31 1.85 151 49 65 16 274.95 8.23 152 49 66 17 274.93 8.24 153 49 108 59 155.04 5.66 154 49 109 60 146.72 3.92 155 50 63 13 277.11 7.80 156 50 64 14 276.73 7.98 157 50 65 15 274.95 8.23 158 50 66 16 274.95 8.23 159 50 106 56 157.51 4.75 160 50 108 58 153.67 6.21 161 50 109 59 143.65 5.12 162 50 110 60 143.28 5.29 163 51 63 12 277.11 7.80 164 51 64 13 277.07 7.82 165 51 66 15 276.23 7.82 166 51 104 53 158.44 5.01 167 51 105 54 157.96 4.79 168 51 106 55 155.53 5.66 169 51 107 56 156.63 5.12 170 51 108 57 153.80 5.30 171 52 62 10 277.27 7.80 172 52 63 11 277.11 7.80 173 52 105 53 157.96 4.78 174 52 106 54 157.00 5.25 175 53 61 8 282.81 5.56 176 53 62 9 277.82 8.01 177 53 102 49 159.35 5.06 178 53 103 50 158.99 5.16 179 53 104 51 157.97 4.82 180 53 105 52 157.96 4.79 181 54 57 3 653.25 23.51 182 54 58 4 431.83 31.02 183 54 59 5 404.74 44.55 184 54 60 6 312.38 2.87 185 54 61 7 291.53 1.31 186 54 102 48 159.13 5.15 187 55 58 3 877.88 4.46 188 55 61 6 291.55 1.31 189 55 88 33 200.72 4.92 190 55 91 36 200.44 4.88 191 55 92 37 200.34 4.83 192 55 95 40 199.60 5.07 193 55 96 41 195.44 6.83 194 55 102 47 159.13 5.14 195 56 91 35 200.72 4.92 196 56 95 39 199.27 5.22 197 56 100 44 176.62 4.62 198 58 91 33 200.73 4.92 199 61 88 27 200.78 4.94 200 64 78 14 274.87 8.27 201 64 79 15 274.84 8.26 202 64 80 16 274.74 8.28 203 64 129 65 125.23 4.41 204 65 110 45 142.47 5.07 205 65 132 67 130.91 1.94 206 66 76 10 275.24 8.26 207 66 77 11 274.96 8.31 208 67 76 9 275.33 8.27 209 67 77 10 275.07 8.28 210 67 132 65 132.25 1.99 211 67 135 68 132.83 1.84 212 68 71 3 941.50 3.42 213 68 74 6 275.43 8.29 214 68 75 7 275.38 8.29 215 68 76 8 275.38 8.29 216 68 77 9 275.37 8.29 217 76 104 28 158.83 5.22 218 78 92 14 241.41 13.49 219 79 128 49 81.77 0.45 220 79 129 50 81.73 0.46 221 79 130 51 81.89 0.42 222 79 131 52 81.89 0.42 223 80 88 8 285.94 4.27 224 80 92 12 241.65 13.43 225 81 127 46 81.77 0.42 226 81 155 74 81.84 0.44 227 81 156 75 81.85 0.44 228 81 161 80 81.92 0.42 229 81 246 165 81.62 0.36 230 81 247 166 81.64 0.35 231 81 248 167 81.64 0.36 232 82 89 7 283.27 5.59 233 82 92 10 243.44 14.30 234 83 86 3 734.08 4.20 235 83 89 6 307.58 0.65 236 84 89 5 427.48 31.47 237 85 89 4 720.00 1.83 238 85 90 5 604.60 1.26 239 86 90 4 715.77 2.53 240 87 91 4 776.23 26.89 241 88 91 3 789.99 26.39 242 88 92 4 776.71 26.59 243 89 92 3 776.77 26.62 244 89 93 4 782.15 25.05 245 90 93 3 834.31 1.02 246 90 94 4 776.75 26.62 247 91 94 3 785.88 22.05 248 91 95 4 776.68 26.62 249 91 96 5 776.68 26.62 250 92 96 4 493.01 57.20 251 92 97 5 493.02 57.20 252 93 97 4 607.01 0.19 253 95 100 5 489.13 10.30 254 110 243 133 353.91 2.89 255 111 114 3 925.07 2.54 256 111 243 132 353.92 2.89 257 112 123 11 354.88 2.62 258 112 215 103 354.57 2.64 259 112 216 104 353.91 2.89 260 112 241 129 354.52 2.59 261 112 243 131 353.92 2.89 262 113 123 10 355.09 2.72 263 113 136 23 355.61 2.87 264 113 137 24 355.60 2.87 265 113 140 27 517.55 7.23 266 113 215 102 355.09 2.72 267 113 241 128 355.39 2.82 268 114 213 99 355.48 2.83 269 114 215 101 355.43 2.81 270 114 241 127 355.44 2.82 271 115 121 6 355.63 2.86 272 115 140 25 536.91 2.33 273 115 145 30 566.93 1.71 274 115 215 100 355.61 2.85 275 116 119 3 878.62 2.14 276 116 121 5 662.75 24.13 277 116 213 97 367.97 1.92 278 116 239 123 367.95 1.92 279 117 121 4 897.41 0.35 280 117 145 28 587.89 0.20 281 118 144 26 588.29 0.17 282 118 147 29 588.12 0.21 283 119 147 28 588.26 0.15 284 119 148 29 588.19 0.20 285 119 213 94 461.42 0.57 286 120 148 28 588.19 0.19 287 120 150 30 588.34 0.12 288 121 140 19 588.66 0.10 289 121 145 24 588.56 0.09 290 121 147 26 588.46 0.12 291 121 148 27 588.40 0.12 292 121 149 28 588.38 0.13 293 121 150 29 588.35 0.12 294 121 213 92 461.88 0.35 295 121 215 94 461.99 0.35 296 122 150 28 588.38 0.12 297 122 152 30 588.43 0.11 298 122 178 56 588.28 0.18 299 122 209 87 462.23 0.40 300 122 210 88 462.12 0.39 301 122 213 91 462.04 0.35 302 122 214 92 462.00 0.35 303 122 215 93 462.00 0.35 304 123 133 10 589.02 0.00 305 123 137 14 588.70 0.10 306 123 150 27 588.42 0.13 307 123 151 28 588.39 0.12 308 123 152 29 588.49 0.08 309 123 215 92 462.00 0.35 310 123 216 93 462.08 0.33 311 123 217 94 462.13 0.29 312 124 152 28 588.49 0.08 313 124 193 69 485.73 7.92 314 124 215 91 462.13 0.34 315 124 216 92 462.11 0.32 316 124 217 93 462.15 0.30 317 125 130 5 589.14 0.01 318 125 133 8 589.21 0.04 319 125 152 27 588.59 0.11 320 125 153 28 588.64 0.09 321 125 154 29 589.12 0.09 322 125 217 92 462.15 0.30 323 126 154 28 589.16 0.07 324 126 155 29 589.25 0.04 325 126 217 91 462.25 0.30 326 126 218 92 462.18 0.29 327 126 219 93 462.22 0.29 328 126 245 119 461.79 0.46 329 126 246 120 461.48 0.58 330 126 249 123 426.65 0.16 331 126 250 124 426.60 0.15 332 127 130 3 878.56 0.71 333 127 153 26 589.25 0.05 334 127 154 27 589.27 0.06 335 127 155 28 589.27 0.04 336 127 161 34 589.50 0.09 337 127 246 119 461.49 0.58 338 127 249 122 426.67 0.17 339 128 131 3 874.41 2.69 340 128 161 33 589.59 0.11 341 128 246 118 461.81 0.46 342 129 132 3 892.88 3.96 343 129 245 116 461.88 0.45 344 129 246 117 461.58 0.52 345 130 133 3 735.16 1.25 346 130 134 4 721.07 2.35 347 130 153 23 589.61 0.10 348 130 167 37 589.62 0.12 349 130 245 115 461.82 0.46 350 131 134 3 838.28 5.37 351 131 135 4 780.12 23.71 352 132 135 3 822.06 2.75 353 132 136 4 776.75 25.40 354 133 136 3 834.38 3.42 355 133 137 4 775.58 24.82 356 133 217 84 462.16 0.30 357 134 137 3 826.72 0.41 358 134 138 4 825.65 0.12 359 134 163 29 589.90 0.20 360 135 138 3 845.61 0.60 361 135 139 4 839.10 3.35 362 136 139 3 839.11 3.35 363 136 140 4 839.10 3.35 364 137 140 3 845.21 0.40 365 137 141 4 839.16 3.39 366 137 151 14 589.70 0.14 367 137 170 33 589.99 0.14 368 138 141 3 836.49 4.74 369 138 142 4 821.36 2.05 370 138 170 32 589.84 0.21 371 139 142 3 837.29 4.36 372 139 143 4 769.51 27.89 373 140 143 3 837.57 4.19 374 140 144 4 820.68 2.18 375 140 145 5 590.67 0.01 376 140 149 9 590.36 0.01 377 141 145 4 599.87 4.59 378 141 149 8 590.34 0.00 379 141 170 29 590.35 0.01 380 141 175 34 590.60 0.01 381 141 177 36 590.38 0.01 382 142 175 33 612.63 7.95 383 145 149 4 707.90 1.55 384 146 175 29 695.25 1.62 385 146 176 30 695.33 1.59 386 147 175 28 695.34 1.59 387 147 176 29 695.34 1.59 388 148 176 28 695.33 1.59 389 149 176 27 695.42 1.57 390 149 177 28 695.37 1.58 391 149 178 29 695.37 1.58 392 150 176 26 695.57 1.58 393 150 177 27 695.40 1.58 394 150 178 28 695.36 1.58 395 151 167 16 695.57 1.60 396 151 171 20 695.59 1.57 397 151 177 26 695.57 1.58 398 151 178 27 695.43 1.57 399 151 179 28 695.38 1.58 400 151 180 29 695.36 1.58 401 152 178 26 695.57 1.58 402 152 180 28 695.36 1.58 403 152 201 49 462.49 0.41 404 153 161 8 696.26 1.57 405 153 162 9 696.06 1.50 406 153 164 11 695.62 1.65 407 153 167 14 695.64 1.60 408 153 180 27 695.48 1.58 409 153 182 29 695.33 1.59 410 154 182 28 695.34 1.58 411 154 249 95 426.66 0.16 412 155 161 6 696.36 1.54 413 155 182 27 695.49 1.59 414 155 183 28 695.37 1.57 415 155 190 35 486.06 7.83 416 155 249 94 426.66 0.17 417 156 160 4 782.24 24.66 418 156 161 5 696.44 1.52 419 156 183 27 695.47 1.58 420 156 186 30 664.25 2.23 421 156 187 31 624.39 1.98 422 156 188 32 535.98 31.90 423 157 183 26 695.51 1.58 424 157 186 29 692.94 2.31 425 157 187 30 642.69 3.36 426 158 161 3 717.95 3.56 427 158 162 4 700.12 3.35 428 158 183 25 695.56 1.57 429 163 166 3 825.67 1.21 430 163 167 4 825.66 1.21 431 164 167 3 840.87 3.81 432 164 168 4 779.28 24.39 433 165 168 3 786.42 20.83 434 165 169 4 773.63 21.57 435 166 169 3 832.75 2.93 436 166 170 4 774.16 21.81 437 167 170 3 820.51 1.36 438 167 171 4 774.16 21.80 439 167 179 12 695.70 1.49 440 168 171 3 788.04 16.93 441 168 172 4 773.76 21.61 442 168 179 11 695.73 1.51 443 169 172 3 773.76 21.61 444 169 173 4 773.75 21.61 445 170 173 3 830.85 2.88 446 170 174 4 777.71 29.45 447 170 175 5 767.88 24.54 448 170 177 7 695.92 1.51 449 171 177 6 695.90 1.52 450 171 178 7 695.89 1.52 451 171 179 8 695.84 1.50 452 174 177 3 874.43 5.23 453 180 193 13 485.84 7.95 454 180 194 14 485.75 7.91 455 181 194 13 485.81 7.92 456 182 193 11 485.84 7.95 457 182 194 12 485.75 7.91 458 183 186 3 883.47 3.33 459 183 193 10 485.85 7.94 460 183 194 11 485.81 7.92 461 184 190 6 491.50 5.20 462 184 193 9 485.99 7.91 463 184 194 10 485.93 7.89 464 184 195 11 485.87 7.86 465 186 190 4 514.48 6.08 466 189 248 59 458.17 1.72 467 190 193 3 916.33 0.93 468 190 194 4 879.58 3.23 469 190 196 6 536.91 28.71 470 190 248 58 446.57 3.06 471 190 249 59 435.96 2.96 472 191 219 28 462.30 0.29 473 191 248 57 439.20 1.29 474 191 249 58 431.41 0.69 475 191 250 59 430.97 0.87 476 192 249 57 429.00 0.10 477 192 250 58 426.69 0.16 478 192 251 59 426.62 0.14 479 193 198 5 468.31 1.66 480 193 201 8 468.28 1.65 481 193 250 57 426.64 0.14 482 193 251 58 426.62 0.14 483 196 199 3 874.05 4.58 484 197 202 5 825.24 2.48 485 198 201 3 832.53 1.17 486 198 202 4 825.18 2.51 487 198 225 27 462.74 0.48 488 198 229 31 463.32 0.45 489 198 251 53 426.57 0.14 490 199 202 3 833.71 5.07 491 199 203 4 827.34 1.44 492 200 203 3 854.39 2.36 493 200 204 4 827.34 1.43 494 201 204 3 840.21 5.00 495 201 205 4 825.86 0.69 496 201 210 9 464.55 0.38 497 201 229 28 463.41 0.47 498 202 205 3 850.23 4.45 499 202 206 4 823.55 0.46 500 202 229 27 463.28 0.42 501 202 233 31 464.47 0.48 502 203 206 3 829.97 3.88 503 203 207 4 821.20 0.51 504 204 207 3 819.22 2.29 505 204 208 4 817.35 1.36 506 205 229 24 464.48 0.48 507 205 230 25 464.59 0.44 508 205 233 28 464.68 0.45 509 205 235 30 464.62 0.42 510 206 233 27 464.68 0.45 511 210 214 4 478.07 5.01 512 210 235 25 812.19 0.90 513 211 214 3 843.12 3.73 514 211 235 24 812.19 0.90 515 211 236 25 812.18 0.90 516 211 237 26 812.11 0.91 517 211 238 27 812.14 0.90 518 211 240 29 786.18 1.14 519 212 238 26 812.14 0.90 520 212 239 27 812.10 0.91 521 212 240 28 812.10 0.91 522 213 239 26 812.10 0.91 523 213 240 27 812.12 0.90 524 214 239 25 812.16 0.90 525 214 240 26 812.13 0.89 526 214 241 27 812.13 0.89 527 214 242 28 812.12 0.90 528 215 239 24 812.22 0.89 529 215 241 26 812.13 0.89 530 216 222 6 812.25 0.95 531 216 226 10 812.25 0.88 532 216 241 25 812.16 0.90 533 216 242 26 812.13 0.89 534 216 243 27 812.12 0.90 535 216 251 35 426.34 0.21 536 217 222 5 817.44 2.39 537 217 243 26 812.13 0.89 538 217 245 28 812.08 0.89 539 217 250 33 426.61 0.15 540 218 222 4 819.98 1.84 541 218 243 25 812.18 0.89 542 218 244 26 812.12 0.90 543 218 245 27 812.08 0.89 544 218 246 28 812.03 0.88 545 218 250 32 426.61 0.15 546 219 222 3 866.35 3.39 547 219 245 26 812.12 0.90 548 219 246 27 812.10 0.91 549 219 247 28 795.27 0.85 550 219 248 29 726.36 3.44 551 219 249 30 655.04 22.48 552 219 250 31 426.69 0.16 553 220 223 3 822.59 0.18 554 220 224 4 822.59 0.18 555 220 244 24 812.18 0.89 556 221 224 3 822.60 0.18 557 221 225 4 818.23 2.00 558 221 251 30 426.70 0.17 559 222 226 4 813.81 0.70 560 222 243 21 812.30 0.85 561 222 244 22 812.23 0.88 562 222 250 28 426.64 0.14 563 222 251 29 426.34 0.21 564 223 227 4 815.01 0.62 565 223 242 19 812.32 0.85 566 223 243 20 812.32 0.85 567 223 244 21 812.29 0.84 568 224 227 3 845.52 5.71 569 224 228 4 815.09 0.66 570 225 228 3 816.38 1.31 571 225 229 4 815.19 0.70 572 225 251 26 426.62 0.15 573 226 229 3 839.39 0.27 574 226 230 4 815.22 0.68 575 226 251 25 426.39 0.23 576 227 230 3 834.64 2.12 577 227 231 4 815.22 0.68 578 227 242 15 812.37 0.84 579 228 231 3 838.10 0.39 580 228 232 4 815.31 0.60 581 229 232 3 815.28 0.59 582 229 233 4 815.03 0.47 583 230 233 3 823.14 3.04 584 230 234 4 814.62 0.53 585 230 235 5 812.94 0.93 586 237 240 3 833.94 9.32