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 30 26 585.10 1.34 2 4 49 45 507.05 1.77 3 5 29 24 585.19 1.36 4 5 30 25 585.19 1.36 5 5 49 44 507.10 1.77 6 5 120 115 242.29 1.16 7 6 30 24 585.19 1.37 8 6 31 25 585.18 1.38 9 6 32 26 585.15 1.36 10 6 49 43 507.12 1.78 11 6 50 44 507.10 1.78 12 6 51 45 507.10 1.78 13 6 120 114 251.25 0.10 14 7 24 17 585.27 1.33 15 7 29 22 585.27 1.34 16 7 30 23 585.26 1.34 17 7 31 24 585.18 1.38 18 7 32 25 585.17 1.37 19 7 51 44 507.11 1.78 20 7 53 46 507.08 1.78 21 7 116 109 255.25 0.72 22 7 120 113 251.40 0.14 23 8 32 24 585.18 1.37 24 8 34 26 585.14 1.36 25 8 40 32 507.56 1.72 26 8 44 36 507.38 1.79 27 8 48 40 507.30 1.78 28 8 50 42 507.20 1.79 29 8 51 43 507.15 1.79 30 8 52 44 507.10 1.78 31 8 53 45 507.10 1.78 32 8 77 69 417.63 0.48 33 9 17 8 585.45 1.24 34 9 20 11 585.44 1.26 35 9 24 15 585.36 1.31 36 9 31 22 585.31 1.34 37 9 32 23 585.28 1.33 38 9 33 24 585.15 1.36 39 9 34 25 585.15 1.36 40 9 53 44 507.10 1.78 41 10 34 24 585.16 1.37 42 10 37 27 536.54 3.06 43 10 40 30 507.80 1.79 44 10 52 42 507.20 1.79 45 10 53 43 507.12 1.79 46 10 54 44 507.10 1.78 47 10 55 45 507.07 1.78 48 10 58 48 497.22 1.27 49 11 16 5 611.48 4.33 50 11 17 6 587.99 1.88 51 11 34 23 585.24 1.36 52 11 35 24 585.18 1.38 53 11 55 44 507.10 1.78 54 11 58 47 499.31 0.22 55 11 82 71 417.19 0.51 56 11 105 94 323.89 0.55 57 12 17 5 612.31 4.68 58 12 35 23 585.13 1.41 59 12 55 43 507.13 1.78 60 12 57 45 507.04 1.79 61 12 58 46 491.74 1.47 62 12 59 47 491.72 1.46 63 13 16 3 632.33 3.56 64 13 17 4 615.44 3.13 65 14 17 3 629.23 2.02 66 14 18 4 615.47 3.15 67 15 18 3 623.67 7.24 68 15 19 4 612.35 4.71 69 16 19 3 630.81 1.29 70 16 20 4 617.25 4.78 71 16 82 66 417.14 0.49 72 16 105 89 320.00 1.85 73 17 20 3 638.09 4.38 74 17 21 4 617.26 4.78 75 17 33 16 585.35 1.34 76 17 34 17 585.34 1.34 77 17 35 18 585.21 1.39 78 18 21 3 628.75 7.44 79 18 22 4 618.13 4.34 80 19 22 3 620.71 5.60 81 19 23 4 618.11 4.33 82 20 23 3 630.59 1.85 83 20 24 4 618.11 4.33 84 20 53 33 507.15 1.79 85 20 107 87 284.61 1.96 86 20 112 92 256.59 0.93 87 21 24 3 633.33 0.48 88 21 25 4 618.16 4.60 89 21 31 10 585.43 1.33 90 21 33 12 585.40 1.33 91 22 25 3 633.62 0.34 92 22 26 4 609.31 0.15 93 23 26 3 625.61 0.36 94 23 27 4 619.10 3.62 95 23 109 86 256.59 0.91 96 23 112 89 256.61 0.92 97 23 113 90 256.55 0.91 98 24 27 3 622.85 1.02 99 24 28 4 614.93 2.94 100 24 29 5 589.41 0.46 101 24 31 7 586.20 1.19 102 24 113 89 256.35 0.83 103 24 116 92 255.78 0.79 104 25 28 3 634.39 2.16 105 25 29 4 596.49 1.38 106 25 30 5 591.18 0.56 107 25 31 6 587.50 1.45 108 27 113 86 256.37 0.84 109 29 116 87 255.51 0.84 110 29 120 91 251.47 0.16 111 34 39 5 507.76 1.81 112 34 40 6 507.76 1.80 113 34 43 9 507.75 1.80 114 37 40 3 625.81 5.06 115 37 41 4 602.04 1.23 116 37 58 21 504.60 1.15 117 37 61 24 420.63 0.03 118 37 66 29 420.23 0.12 119 38 41 3 611.71 2.83 120 38 42 4 596.35 1.62 121 38 61 23 420.63 0.03 122 39 42 3 622.55 1.94 123 39 43 4 609.12 4.77 124 40 43 3 625.69 0.37 125 40 44 4 622.54 1.94 126 40 52 12 507.19 1.79 127 40 66 26 420.28 0.09 128 40 70 30 419.95 0.01 129 41 44 3 627.04 2.47 130 41 61 20 421.08 0.16 131 41 66 25 420.24 0.11 132 41 69 28 419.94 0.01 133 41 70 29 419.94 0.01 134 41 73 32 418.54 0.36 135 44 48 4 631.10 0.85 136 44 70 26 419.91 0.00 137 44 75 31 417.88 0.43 138 44 77 33 417.74 0.43 139 45 48 3 627.35 1.02 140 46 75 29 417.63 0.46 141 47 127 80 205.96 5.05 142 49 120 71 251.43 0.12 143 49 123 74 233.38 4.90 144 49 124 75 230.95 4.17 145 49 127 78 205.97 5.07 146 50 77 27 417.26 0.47 147 50 78 28 417.23 0.47 148 50 120 70 251.40 0.14 149 50 123 73 232.86 5.16 150 51 77 26 417.32 0.48 151 51 78 27 417.22 0.47 152 51 80 29 417.14 0.49 153 51 116 65 255.59 0.90 154 51 119 68 251.51 0.17 155 51 120 69 251.40 0.14 156 52 66 14 419.86 0.27 157 52 70 18 419.21 0.18 158 52 77 25 417.62 0.48 159 52 78 26 417.41 0.51 160 52 79 27 417.16 0.48 161 52 80 28 417.15 0.48 162 53 80 27 417.15 0.49 163 53 82 29 417.13 0.48 164 53 112 59 256.50 0.95 165 53 116 63 256.09 0.96 166 54 58 4 679.82 2.07 167 54 63 9 420.51 0.01 168 54 66 12 420.50 0.02 169 54 79 25 417.62 0.48 170 54 80 26 417.31 0.47 171 54 81 27 417.14 0.48 172 54 82 28 417.14 0.48 173 55 58 3 677.34 3.31 174 55 63 8 420.61 0.01 175 55 82 27 417.14 0.48 176 55 105 50 323.98 0.57 177 56 62 6 421.01 0.13 178 56 63 7 420.97 0.15 179 56 64 8 420.99 0.14 180 56 81 25 417.57 0.46 181 56 82 26 417.32 0.55 182 56 83 27 417.19 0.51 183 56 102 46 326.01 0.42 184 57 85 28 417.17 0.51 185 57 88 31 395.26 2.69 186 58 61 3 654.57 0.40 187 58 62 4 462.92 20.80 188 58 63 5 554.03 21.13 189 61 65 4 608.18 4.22 190 61 66 5 556.40 22.07 191 61 69 8 509.89 1.42 192 62 65 3 614.69 0.99 193 62 66 4 621.04 1.83 194 63 66 3 626.11 0.70 195 63 67 4 621.07 1.83 196 63 81 18 417.64 0.47 197 64 67 3 621.77 2.19 198 64 68 4 622.25 1.26 199 64 81 17 417.76 0.46 200 64 94 30 326.44 0.49 201 65 68 3 623.00 1.64 202 65 69 4 622.27 1.25 203 66 69 3 630.88 5.55 204 66 70 4 622.27 1.25 205 67 70 3 626.13 0.73 206 67 71 4 616.12 1.83 207 67 79 12 417.97 0.48 208 67 81 14 417.74 0.47 209 67 94 27 326.38 0.47 210 67 97 30 326.29 0.48 211 68 71 3 621.02 4.28 212 68 72 4 620.42 0.33 213 69 72 3 625.34 2.12 214 69 73 4 610.88 5.12 215 70 73 3 629.35 0.68 216 70 74 4 608.25 6.42 217 70 75 5 421.01 1.00 218 70 77 7 418.05 0.47 219 70 79 9 418.00 0.47 220 71 74 3 623.45 1.18 221 71 97 26 326.25 0.47 222 76 126 50 228.95 3.20 223 76 130 54 206.06 5.01 224 77 123 46 249.68 0.36 225 78 98 20 326.09 0.46 226 78 100 22 325.93 0.47 227 78 119 41 251.54 0.16 228 78 122 44 251.37 0.12 229 78 123 45 250.19 0.30 230 79 98 19 326.18 0.50 231 79 99 20 326.03 0.45 232 79 100 21 326.00 0.43 233 80 100 20 326.01 0.43 234 80 101 21 325.74 0.47 235 80 103 23 324.07 0.56 236 80 112 32 256.50 0.95 237 80 115 35 256.29 0.88 238 80 116 36 256.15 0.96 239 81 90 9 326.48 0.52 240 81 99 18 326.19 0.50 241 81 101 20 326.01 0.43 242 81 102 21 325.68 0.49 243 81 103 22 324.58 0.69 244 82 103 21 324.05 0.57 245 82 105 23 323.95 0.56 246 82 107 25 317.73 1.35 247 83 86 3 642.84 4.07 248 83 102 19 326.01 0.42 249 83 103 20 325.78 0.52 250 83 104 21 324.07 0.56 251 83 105 22 324.00 0.56 252 84 105 21 324.04 0.57 253 85 88 3 643.07 4.22 254 88 102 14 326.42 0.55 255 89 102 13 326.42 0.55 256 90 94 4 607.44 3.94 257 90 95 5 598.72 0.32 258 90 99 9 326.72 0.55 259 90 102 12 326.37 0.56 260 91 94 3 620.39 2.54 261 91 95 4 608.06 3.62 262 92 95 3 618.38 1.54 263 92 96 4 611.72 5.44 264 93 96 3 628.50 0.59 265 93 97 4 625.93 1.66 266 94 97 3 630.48 0.61 267 94 99 5 556.41 21.50 268 95 98 3 649.73 0.26 269 95 99 4 472.04 20.68 270 100 115 15 256.36 0.91 271 100 118 18 255.91 0.86 272 100 119 19 255.51 0.90 273 100 122 22 253.62 1.19 274 101 115 14 256.38 0.91 275 103 111 8 256.68 0.93 276 103 112 9 256.64 0.93 277 103 115 12 256.59 0.96 278 104 107 3 648.02 1.50 279 107 112 5 602.33 1.55 280 108 111 3 645.09 5.99 281 108 112 4 616.66 7.32 282 109 112 3 644.18 6.44 283 109 113 4 626.47 2.40 284 110 113 3 629.62 0.83 285 110 114 4 613.63 4.10 286 111 114 3 620.25 0.92 287 111 115 4 613.84 4.11 288 112 115 3 626.62 2.28 289 112 116 4 613.86 4.11 290 113 116 3 614.93 3.57 291 113 117 4 613.86 4.11 292 114 117 3 626.72 2.33 293 114 118 4 613.85 4.11 294 115 118 3 630.82 0.89 295 115 119 4 617.73 2.14 296 116 119 3 621.26 3.89 297 116 120 4 617.69 2.10 298 117 120 3 632.14 0.70 299 117 121 4 611.28 1.47 300 118 121 3 632.14 0.70 301 118 122 4 617.81 2.19 302 119 122 3 632.16 0.72 303 119 123 4 612.13 5.03 304 120 123 3 615.01 3.62 305 120 124 4 617.88 2.16 306 121 124 3 620.54 0.85 307 121 125 4 618.45 1.90 308 122 125 3 627.48 2.62 309 122 126 4 618.45 1.90 310 123 126 3 618.46 1.89 311 123 127 4 618.44 1.89 312 124 127 3 624.92 5.12 313 124 128 4 620.54 2.94 314 125 128 3 624.92 5.12 315 125 129 4 620.24 3.10 316 126 129 3 625.86 5.62 317 126 130 4 620.52 2.96 318 127 130 3 620.18 3.13 319 127 131 4 620.18 3.13 320 128 131 3 620.16 3.13 321 128 132 4 620.15 3.12 322 129 132 3 620.34 3.15 323 129 133 4 617.56 1.88 324 130 133 3 629.16 1.32 325 130 134 4 615.30 3.85 326 131 134 3 622.22 0.39 327 131 135 4 615.31 3.84 328 132 135 3 641.25 1.23 329 132 136 4 605.82 0.90 330 133 136 3 623.29 1.71 331 133 137 4 612.11 0.60 332 134 137 3 638.62 0.64 333 134 138 4 620.03 3.34 334 135 138 3 630.22 1.76 335 135 139 4 612.13 0.62 336 136 139 3 612.15 0.61 337 136 140 4 612.13 0.62 338 136 196 60 30.46 1.90 339 136 199 63 28.07 3.08 340 136 200 64 23.27 0.85 341 137 140 3 615.63 1.12 342 137 141 4 615.62 1.12 343 137 200 63 28.07 3.08 344 138 141 3 617.00 4.52 345 138 142 4 618.64 2.68 346 139 142 3 630.20 3.08 347 139 143 4 618.66 2.68 348 139 184 45 67.44 1.08 349 139 185 46 49.83 3.17 350 140 143 3 633.20 1.46 351 140 151 11 130.09 1.16 352 140 185 45 67.38 1.05 353 140 196 56 45.75 0.56 354 140 197 57 39.12 0.14 355 140 200 60 37.26 0.59 356 142 184 42 69.38 0.69 357 143 147 4 528.42 42.90 358 143 151 8 427.17 0.23 359 143 181 38 73.22 2.58 360 143 184 41 69.41 0.68 361 143 185 42 69.41 0.68 362 144 147 3 616.92 1.34 363 144 148 4 603.05 5.59 364 144 184 40 94.80 0.40 365 145 148 3 606.38 3.93 366 145 149 4 610.57 1.84 367 146 149 3 610.59 1.83 368 146 150 4 610.57 1.83 369 146 177 31 104.11 3.94 370 147 150 3 614.62 0.19 371 147 151 4 611.00 2.05 372 147 177 30 104.06 3.92 373 147 180 33 103.96 3.87 374 147 181 34 103.94 3.87 375 147 184 37 103.78 3.84 376 148 151 3 617.07 0.31 377 148 152 4 615.05 0.03 378 149 152 3 624.74 2.79 379 149 153 4 622.62 1.65 380 149 167 18 347.87 39.17 381 150 153 3 629.52 0.40 382 150 154 4 622.57 1.67 383 150 163 13 167.48 1.88 384 150 167 17 427.67 0.07 385 150 169 19 305.11 61.35 386 150 174 24 104.24 3.96 387 150 177 27 104.23 3.96 388 150 178 28 104.22 3.95 389 150 181 31 104.15 3.91 390 151 154 3 626.20 0.14 391 151 155 4 616.57 1.36 392 151 181 30 104.00 3.87 393 151 185 34 103.75 3.83 394 151 193 42 86.63 1.30 395 151 197 46 83.56 0.29 396 152 155 3 639.47 1.57 397 152 156 4 629.88 1.98 398 153 156 3 639.47 1.57 399 153 157 4 632.79 0.53 400 153 158 5 485.71 17.58 401 153 163 10 433.93 3.05 402 153 166 13 480.63 20.26 403 153 167 14 480.43 20.16 404 154 157 3 637.97 2.06 405 154 163 9 437.39 1.38 406 154 178 24 109.53 1.34 407 154 190 36 86.89 1.37 408 154 193 39 86.75 1.30 409 155 193 38 86.73 1.31 410 155 194 39 86.62 1.29 411 155 197 42 84.95 0.88 412 158 178 20 624.07 0.10 413 159 178 19 624.08 0.10 414 160 178 18 624.08 0.10 415 163 178 15 690.51 12.36 416 174 178 4 714.70 7.62 417 175 178 3 633.57 0.73 418 175 179 4 624.08 0.10 419 176 179 3 635.19 1.60 420 176 180 4 624.09 0.10 421 177 180 3 631.87 3.26 422 177 181 4 624.08 0.10 423 178 181 3 623.73 0.08 424 178 182 4 621.09 1.40 425 179 182 3 626.57 1.87 426 179 183 4 617.78 3.18 427 180 183 3 623.48 0.33 428 180 184 4 611.66 0.10 429 181 184 3 614.88 1.71 430 181 185 4 611.64 0.10 431 181 193 12 113.80 0.84 432 182 185 3 626.29 0.70 433 182 186 4 517.44 0.45 434 182 187 5 131.66 0.09 435 182 188 6 128.39 1.72 436 182 189 7 127.59 2.12 437 182 190 8 117.75 2.78 438 182 193 11 113.83 0.83 439 183 186 3 597.63 0.01 440 185 193 8 113.88 0.83 441 185 196 11 113.82 0.82 442 187 192 5 205.89 27.21 443 187 193 6 122.89 0.57 444 187 196 9 122.89 0.57 445 189 192 3 615.79 4.01 446 189 193 4 605.72 9.44 447 190 193 3 605.72 9.44 448 190 194 4 592.27 2.73 449 191 194 3 631.23 3.31 450 191 195 4 616.10 4.26 451 192 195 3 627.52 2.46 452 192 196 4 574.41 25.11 453 193 196 3 623.72 0.55 454 193 197 4 623.62 0.51 455 194 197 3 617.84 3.49 456 194 198 4 607.19 8.72 457 195 198 3 617.90 3.52 458 195 199 4 572.45 26.09 459 196 199 3 598.71 4.26 460 196 200 4 559.10 19.41 461 197 200 3 625.25 7.33