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 1 226 225 42.03 3.32 2 1 227 226 42.02 3.33 3 1 228 227 41.23 3.22 4 2 242 240 29.61 0.52 5 3 6 3 568.00 2.03 6 3 7 4 565.51 1.28 7 3 228 225 47.01 2.26 8 3 230 227 43.09 2.79 9 3 235 232 41.36 3.29 10 3 238 235 32.02 0.45 11 3 239 236 29.88 0.62 12 3 242 239 29.77 0.58 13 4 7 3 570.57 1.25 14 4 8 4 565.50 1.28 15 4 242 238 29.94 0.49 16 5 8 3 570.82 1.38 17 5 9 4 566.73 0.67 18 5 226 221 68.75 1.54 19 6 9 3 572.66 2.91 20 6 10 4 564.87 0.27 21 6 185 179 68.79 1.53 22 6 211 205 68.79 1.53 23 6 226 220 68.79 1.53 24 6 228 222 68.56 1.61 25 6 235 229 52.69 0.72 26 6 239 233 42.82 0.30 27 7 10 3 568.81 1.71 28 7 11 4 564.86 0.27 29 7 239 232 44.13 0.31 30 7 242 235 41.36 0.48 31 7 244 237 32.69 0.65 32 8 11 3 571.47 0.10 33 8 12 4 565.55 0.65 34 9 12 3 574.98 1.78 35 9 13 4 564.85 0.29 36 9 183 174 239.08 2.16 37 9 209 200 81.95 0.51 38 9 211 202 72.55 0.84 39 9 225 216 76.39 1.89 40 9 226 217 72.69 0.80 41 10 13 3 577.11 2.85 42 10 16 6 295.03 29.44 43 10 86 76 347.22 3.34 44 10 91 81 342.36 5.77 45 10 92 82 295.06 29.44 46 10 183 173 243.39 4.05 47 10 185 175 239.26 2.06 48 11 91 80 364.78 2.89 49 13 16 3 599.47 5.45 50 13 182 169 298.50 2.43 51 13 183 170 265.23 0.64 52 14 180 166 306.96 0.47 53 14 182 168 306.75 0.46 54 15 93 78 477.36 0.30 55 15 180 165 306.96 0.47 56 15 181 166 306.83 0.47 57 15 182 167 306.81 0.48 58 15 183 168 306.76 0.46 59 16 91 75 477.56 0.36 60 16 92 76 477.48 0.35 61 16 93 77 477.46 0.35 62 16 183 167 306.76 0.46 63 16 185 169 306.76 0.46 64 17 92 75 477.56 0.36 65 17 93 76 477.50 0.34 66 17 94 77 477.45 0.35 67 17 96 79 477.45 0.35 68 17 177 160 307.19 0.52 69 17 178 161 307.01 0.48 70 17 181 164 306.98 0.47 71 17 183 166 306.88 0.47 72 17 184 167 306.81 0.48 73 17 185 168 306.80 0.48 74 18 83 65 477.59 0.39 75 18 92 74 477.69 0.36 76 18 94 76 477.57 0.38 77 18 95 77 477.48 0.34 78 18 96 78 477.48 0.34 79 18 185 167 306.81 0.48 80 18 187 169 306.75 0.46 81 19 96 77 477.50 0.33 82 19 98 79 477.64 0.38 83 19 115 96 477.22 0.21 84 19 184 165 306.95 0.46 85 19 185 166 306.88 0.46 86 19 186 167 306.79 0.47 87 19 187 168 306.78 0.47 88 19 191 172 252.50 2.28 89 19 196 177 201.86 0.53 90 19 199 180 201.38 0.57 91 19 200 181 201.36 0.56 92 20 24 4 539.44 12.59 93 20 83 63 478.06 0.30 94 20 95 75 477.72 0.38 95 20 96 76 477.63 0.37 96 20 97 77 477.52 0.33 97 20 98 78 477.64 0.38 98 20 104 84 477.67 0.38 99 20 187 167 306.78 0.47 100 21 24 3 596.81 0.13 101 21 98 77 477.65 0.38 102 21 99 78 477.64 0.38 103 21 187 166 306.88 0.46 104 21 188 167 306.76 0.46 105 21 189 168 300.80 1.92 106 22 25 3 606.28 3.69 107 22 99 77 477.68 0.39 108 22 188 166 306.86 0.46 109 23 188 165 306.85 0.46 110 23 232 209 116.87 1.43 111 24 83 59 583.28 4.78 112 24 99 75 504.87 0.51 113 24 104 80 504.41 0.67 114 24 187 163 306.89 0.46 115 24 188 164 306.81 0.46 116 24 232 208 112.89 0.49 117 25 99 74 504.88 0.52 118 25 101 76 504.89 0.52 119 25 103 78 504.75 0.55 120 27 232 205 115.04 0.51 121 27 233 206 113.03 0.48 122 28 103 75 504.81 0.57 123 30 101 71 504.93 0.54 124 30 103 73 504.91 0.54 125 34 190 156 306.98 0.48 126 34 192 158 306.91 0.48 127 34 193 159 306.89 0.48 128 40 162 122 418.43 0.86 129 45 162 117 418.44 0.85 130 48 159 111 419.31 0.69 131 48 161 113 418.44 0.86 132 48 162 114 418.43 0.86 133 49 161 112 418.56 0.81 134 49 162 113 418.43 0.86 135 50 156 106 433.56 1.57 136 50 161 111 418.98 0.71 137 50 162 112 418.84 0.75 138 50 163 113 418.43 0.86 139 50 164 114 418.37 0.90 140 53 154 101 434.12 1.37 141 53 155 102 434.12 1.37 142 53 156 103 433.42 1.42 143 53 157 104 432.30 1.84 144 53 161 108 419.01 0.81 145 54 125 71 498.87 0.42 146 54 154 100 434.12 1.37 147 54 156 102 434.04 1.39 148 57 145 88 498.84 0.42 149 57 154 97 434.11 1.38 150 58 144 86 498.84 0.42 151 58 145 87 498.84 0.42 152 60 157 97 429.74 0.75 153 60 159 99 422.56 0.35 154 60 161 101 418.94 0.79 155 61 122 61 498.88 0.42 156 61 136 75 498.84 0.43 157 61 140 79 498.80 0.42 158 61 144 83 498.80 0.43 159 61 146 85 498.45 0.36 160 61 154 93 434.10 1.38 161 61 155 94 433.74 1.27 162 61 156 95 429.81 0.79 163 61 157 96 428.74 0.32 164 65 140 75 498.65 0.39 165 68 100 32 504.98 0.53 166 68 119 51 498.44 0.38 167 68 159 91 418.42 0.86 168 69 122 53 498.26 0.46 169 69 133 64 498.14 0.52 170 69 136 67 498.14 0.53 171 69 137 68 498.12 0.54 172 69 140 71 498.58 0.40 173 71 100 29 504.98 0.53 174 71 101 30 504.94 0.54 175 71 119 48 498.04 0.54 176 72 119 47 497.98 0.54 177 72 120 48 496.57 0.09 178 72 133 61 496.53 0.10 179 72 137 65 496.76 0.18 180 74 103 29 504.90 0.54 181 74 106 32 504.76 0.56 182 75 103 28 504.89 0.54 183 75 106 31 504.71 0.55 184 76 103 27 504.81 0.57 185 76 106 30 503.98 0.84 186 76 107 31 503.71 0.90 187 77 233 156 111.83 0.58 188 78 233 155 111.83 0.58 189 78 236 158 110.05 0.28 190 78 237 159 109.83 0.38 191 78 240 162 102.51 1.67 192 79 82 3 585.99 6.13 193 79 83 4 570.47 0.66 194 79 232 153 112.50 0.60 195 79 236 157 109.62 0.29 196 80 83 3 576.89 1.58 197 80 84 4 569.83 0.60 198 80 103 23 504.81 0.57 199 80 104 24 504.63 0.61 200 80 107 27 502.67 0.57 201 81 84 3 572.40 0.68 202 81 85 4 572.38 0.67 203 81 107 26 502.81 0.61 204 81 240 159 94.53 2.29 205 82 85 3 581.84 4.06 206 82 86 4 569.72 0.60 207 82 235 153 110.24 0.19 208 82 236 154 108.70 0.01 209 82 239 157 92.45 1.45 210 82 240 158 89.05 0.23 211 82 245 163 42.74 0.21 212 83 86 3 574.40 2.84 213 83 87 4 569.70 0.70 214 83 92 9 505.76 0.61 215 83 95 12 505.22 0.48 216 83 104 21 504.80 0.56 217 83 187 104 306.81 0.47 218 84 87 3 576.55 1.00 219 84 88 4 569.69 0.70 220 84 107 23 503.80 0.76 221 84 108 24 502.86 0.63 222 84 109 25 502.62 0.57 223 85 88 3 579.79 0.62 224 85 89 4 558.85 3.87 225 85 245 160 41.59 0.41 226 86 89 3 573.15 2.70 227 86 90 4 556.20 5.19 228 86 91 5 508.97 0.96 229 86 92 6 505.80 0.62 230 86 244 158 41.66 0.38 231 86 245 159 41.45 0.41 232 87 90 3 561.93 4.34 233 87 92 5 505.79 0.62 234 87 109 22 503.05 0.54 235 87 110 23 502.86 0.63 236 87 111 24 502.82 0.64 237 89 245 156 41.59 0.42 238 89 246 157 41.59 0.42 239 91 244 153 41.59 0.42 240 92 185 93 306.81 0.48 241 93 111 18 502.66 0.57 242 93 177 84 307.08 0.51 243 94 111 17 501.60 0.06 244 94 113 19 501.55 0.04 245 94 177 83 307.13 0.51 246 95 104 9 504.98 0.51 247 95 111 16 501.61 0.07 248 95 112 17 501.40 0.02 249 95 113 18 501.40 0.02 250 96 113 17 501.02 0.14 251 96 115 19 500.62 0.31 252 96 174 78 307.38 0.50 253 96 178 82 307.29 0.52 254 96 184 88 306.98 0.47 255 96 199 103 201.41 0.58 256 97 104 7 505.01 0.52 257 97 112 15 501.39 0.03 258 97 113 16 500.90 0.20 259 97 114 17 500.52 0.36 260 97 115 18 500.50 0.35 261 98 116 18 498.97 0.42 262 98 189 91 306.39 0.47 263 98 196 98 201.87 0.52 264 100 116 16 498.89 0.44 265 100 117 17 498.84 0.43 266 100 118 18 496.42 0.01 267 100 119 19 496.37 0.01 268 100 159 59 377.11 3.97 269 101 119 18 496.23 0.05 270 102 105 3 575.93 2.46 271 102 106 4 551.09 4.59 272 102 114 12 499.16 0.36 273 102 118 16 496.23 0.06 274 102 119 17 496.19 0.04 275 102 120 18 495.91 0.10 276 103 106 3 580.93 8.04 277 103 107 4 551.11 4.59 278 104 107 3 564.89 0.22 279 104 108 4 551.11 4.59 280 104 109 5 526.32 0.03 281 104 112 8 505.73 0.35 282 105 108 3 556.45 4.45 283 105 109 4 537.40 11.40 284 105 112 7 506.55 0.06 285 105 114 9 506.54 0.05 286 109 112 3 609.97 1.55 287 111 173 62 307.32 0.53 288 111 177 66 307.23 0.54 289 113 170 57 307.38 0.51 290 113 173 60 307.38 0.51 291 113 174 61 307.30 0.53 292 113 177 64 307.25 0.55 293 114 117 3 570.76 5.46 294 114 118 4 559.93 0.24 295 114 167 53 307.80 0.52 296 114 170 56 307.60 0.54 297 115 160 45 362.65 0.33 298 115 166 51 307.88 0.55 299 115 167 52 307.85 0.54 300 115 170 55 307.73 0.51 301 115 171 56 307.71 0.52 302 115 174 59 307.69 0.51 303 115 196 81 201.87 0.52 304 115 199 84 201.88 0.51 305 116 159 43 364.89 0.76 306 116 160 44 362.61 0.35 307 117 158 41 377.05 3.91 308 117 159 42 365.56 0.61 309 117 160 43 365.10 0.85 310 118 121 3 615.31 1.29 311 118 158 40 386.25 0.59 312 118 159 41 377.03 3.92 313 121 157 36 418.57 0.92 314 121 158 37 418.39 0.88 315 122 155 33 475.64 26.19 316 122 156 34 419.35 0.73 317 122 157 35 418.45 0.86 318 122 158 36 418.42 0.88 319 123 155 32 475.68 26.16 320 123 156 33 420.42 1.24 321 123 158 35 419.19 0.90 322 124 151 27 687.85 5.80 323 124 153 29 540.10 3.59 324 124 154 30 530.60 1.16 325 124 155 31 475.69 26.16 326 125 154 29 533.44 0.23 327 125 156 31 527.81 0.18 328 126 153 27 588.72 3.15 329 131 155 24 530.17 1.08 330 136 155 19 601.67 36.74 331 139 155 16 611.38 31.91 332 145 154 9 631.39 21.88 333 146 154 8 560.82 7.20 334 146 155 9 536.88 1.48 335 147 153 6 588.54 0.43 336 147 154 7 543.65 1.91 337 147 155 8 536.86 1.48 338 148 152 4 567.64 1.47 339 148 153 5 553.35 0.43 340 148 155 7 533.42 0.24 341 156 161 5 590.24 4.24 342 156 164 8 533.78 0.19 343 157 161 4 613.12 1.05 344 159 164 5 569.81 7.05 345 160 164 4 565.34 9.29 346 160 165 5 540.13 3.31 347 160 166 6 421.62 56.26 348 160 167 7 308.00 0.55 349 161 164 3 581.42 3.70 350 162 193 31 258.23 5.14 351 166 171 5 536.59 0.47 352 166 195 29 212.09 4.70 353 167 170 3 572.91 5.55 354 167 171 4 553.98 2.94 355 168 171 3 574.33 0.94 356 168 172 4 568.99 3.60 357 169 172 3 572.38 1.90 358 169 173 4 564.60 2.38 359 170 173 3 572.79 1.68 360 170 174 4 566.32 3.23 361 171 174 3 572.37 1.47 362 171 175 4 564.61 4.09 363 171 195 24 201.92 0.54 364 172 175 3 575.04 2.81 365 172 176 4 564.59 4.08 366 173 176 3 584.38 1.86 367 173 177 4 564.59 4.09 368 174 177 3 572.66 5.67 369 174 178 4 564.11 4.33 370 174 199 25 201.40 0.58 371 175 178 3 576.27 0.45 372 175 179 4 555.32 0.07 373 175 199 24 201.41 0.57 374 175 202 27 200.74 0.62 375 176 179 3 577.69 1.70 376 176 180 4 555.32 0.07 377 177 180 3 567.87 4.65 378 177 181 4 554.71 0.35 379 178 181 3 558.39 1.93 380 178 184 6 307.65 0.84 381 178 199 21 201.37 0.58 382 178 202 24 200.59 0.55 383 178 203 25 199.05 0.10 384 179 202 23 200.59 0.55 385 179 206 27 198.65 0.16 386 181 203 22 199.05 0.09 387 181 208 27 198.62 0.17 388 182 208 26 198.62 0.18 389 182 209 27 198.60 0.17 390 183 209 26 198.59 0.18 391 183 211 28 198.55 0.16 392 184 199 15 201.38 0.57 393 184 200 16 201.25 0.54 394 184 203 19 199.11 0.10 395 184 209 25 198.65 0.17 396 184 210 26 198.55 0.17 397 184 211 27 198.53 0.17 398 185 211 26 198.47 0.15 399 185 213 28 198.41 0.17 400 186 189 3 601.02 0.81 401 186 191 5 540.45 3.62 402 186 200 14 201.30 0.55 403 186 210 24 198.68 0.15 404 186 211 25 198.56 0.15 405 186 212 26 198.44 0.16 406 186 213 27 198.42 0.17 407 187 213 26 198.34 0.14 408 187 232 45 112.67 0.54 409 187 235 48 111.83 0.11 410 188 213 25 198.46 0.15 411 188 214 26 198.22 0.17 412 189 214 25 198.46 0.15 413 189 218 29 160.93 2.02 414 190 218 28 153.48 3.09 415 190 219 29 153.49 3.09 416 191 197 6 201.94 0.51 417 191 200 9 201.94 0.51 418 191 212 21 198.77 0.17 419 191 218 27 153.48 3.09 420 191 219 28 153.47 3.10 421 191 220 29 153.41 3.07 422 192 197 5 559.14 0.94 423 193 196 3 609.43 3.78 424 193 197 4 577.49 1.36 425 194 197 3 588.32 1.90 426 194 198 4 581.46 0.57 427 194 220 26 153.47 3.10 428 195 198 3 585.63 0.58 429 195 199 4 584.86 0.17 430 196 199 3 586.36 0.21 431 196 200 4 589.96 1.04 432 197 200 3 602.90 0.96 433 197 220 23 152.90 2.94 434 198 201 3 586.03 0.76 435 198 202 4 572.00 0.92 436 199 202 3 572.16 0.84 437 199 203 4 571.62 0.57 438 200 203 3 569.53 0.48 439 200 204 4 561.99 0.45 440 200 210 10 199.88 0.75 441 200 220 20 144.88 0.30 442 201 204 3 562.55 0.17 443 201 205 4 561.99 0.45 444 201 220 19 144.88 0.30 445 201 223 22 144.64 0.33 446 202 205 3 562.35 0.62 447 202 206 4 558.37 1.36 448 203 206 3 572.03 1.30 449 203 207 4 549.90 2.50 450 203 208 5 436.87 47.98 451 203 209 6 436.87 47.98 452 204 207 3 575.28 2.93 453 204 208 4 543.82 5.46 454 204 210 6 317.30 2.02 455 204 223 19 144.56 0.34 456 209 225 16 144.46 0.34 457 210 220 10 144.87 0.29 458 210 223 13 144.60 0.31 459 210 224 14 144.47 0.34 460 210 225 15 144.47 0.34 461 210 226 16 144.47 0.34 462 211 226 15 144.46 0.34 463 211 228 17 144.34 0.32 464 212 218 6 153.31 3.03 465 212 220 8 145.72 0.13 466 212 221 9 144.81 0.31 467 212 224 12 144.58 0.29 468 212 226 14 144.47 0.34 469 212 227 15 144.37 0.34 470 212 228 16 144.34 0.32 471 213 228 15 144.37 0.29 472 213 230 17 142.54 0.30 473 213 232 19 112.67 0.54 474 213 235 22 110.48 0.41 475 214 218 4 581.53 1.01 476 214 227 13 144.46 0.33 477 214 228 14 144.44 0.34 478 214 229 15 144.31 0.27 479 214 230 16 144.27 0.29 480 215 229 14 144.44 0.33 481 215 230 15 144.41 0.32 482 215 231 16 144.27 0.29 483 216 227 11 144.69 0.30 484 216 229 13 144.45 0.34 485 217 221 4 546.25 4.51 486 217 227 10 144.66 0.29 487 218 221 3 584.14 0.50 488 220 223 3 576.78 0.86 489 220 224 4 554.32 1.22 490 221 224 3 553.82 0.89 491 221 227 6 144.50 0.34 492 224 227 3 593.09 0.96 493 228 235 7 336.72 7.82 494 230 234 4 556.35 0.18 495 230 235 5 537.29 1.94 496 230 238 8 443.72 44.41 497 231 234 3 570.32 6.80 498 231 235 4 555.88 0.42 499 232 235 3 567.41 4.21 500 232 236 4 550.69 2.19 501 233 236 3 556.34 0.18 502 233 237 4 559.51 2.96 503 234 237 3 561.06 2.19 504 234 238 4 560.40 2.52 505 235 238 3 574.28 4.41 506 235 239 4 564.46 0.49 507 236 239 3 566.80 1.66 508 236 240 4 564.48 0.50 509 237 240 3 569.87 1.14 510 237 241 4 559.52 2.98 511 238 241 3 561.71 1.89 512 238 242 4 559.50 2.99 513 239 242 3 574.25 3.29 514 239 243 4 545.23 5.68 515 239 244 5 428.37 51.10 516 240 243 3 574.25 3.29 517 240 245 5 321.99 1.96 518 243 246 3 575.60 5.83