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 8 4 655.18 3.52 2 4 9 5 643.36 0.95 3 4 12 8 614.03 8.67 4 4 50 46 96.49 0.62 5 4 53 49 96.49 0.62 6 4 55 51 96.47 0.63 7 5 8 3 673.07 2.10 8 5 9 4 659.50 1.92 9 6 9 3 674.19 1.54 10 6 10 4 659.51 1.91 11 7 10 3 661.53 1.06 12 7 11 4 659.51 1.91 13 7 37 30 138.23 0.25 14 7 38 31 138.43 0.24 15 7 46 39 116.70 1.30 16 8 11 3 663.75 2.30 17 8 12 4 656.18 0.27 18 8 46 38 116.69 1.29 19 8 49 41 116.62 1.27 20 8 50 42 116.62 1.27 21 8 53 45 115.37 0.71 22 9 12 3 662.00 3.18 23 9 13 4 656.13 0.24 24 9 16 7 652.08 2.06 25 10 13 3 661.07 2.23 26 10 14 4 654.62 0.99 27 10 35 25 138.47 0.26 28 11 14 3 662.75 1.65 29 11 15 4 656.14 0.20 30 11 31 20 138.26 0.27 31 11 35 24 138.50 0.24 32 11 37 26 138.47 0.26 33 11 46 35 116.92 1.29 34 11 47 36 116.83 1.32 35 11 50 39 116.81 1.33 36 12 15 3 674.84 3.58 37 12 16 4 657.86 0.66 38 12 50 38 116.66 1.26 39 12 55 43 110.13 0.43 40 12 56 44 110.08 0.46 41 12 68 56 86.86 1.10 42 13 16 3 679.75 3.93 43 13 17 4 656.13 0.20 44 13 91 78 47.33 0.60 45 14 17 3 679.80 3.90 46 14 18 4 656.08 0.17 47 14 31 17 138.44 0.24 48 14 34 20 138.68 0.23 49 14 35 21 138.66 0.24 50 15 18 3 680.77 3.41 51 15 19 4 661.58 3.46 52 15 26 11 146.13 1.62 53 15 31 16 139.31 0.56 54 15 47 32 134.97 1.01 55 15 50 35 120.95 2.40 56 15 66 51 88.29 1.40 57 15 68 53 86.92 1.08 58 16 19 3 670.71 1.11 59 16 20 4 659.33 0.03 60 16 68 52 87.14 1.16 61 16 91 75 53.29 1.12 62 17 20 3 670.70 1.10 63 17 21 4 659.32 0.03 64 17 87 70 52.48 0.67 65 17 90 73 52.66 0.82 66 17 91 74 52.77 0.85 67 18 21 3 669.14 1.89 68 18 22 4 659.32 0.03 69 18 23 5 646.28 6.49 70 18 24 6 607.78 3.76 71 18 25 7 402.41 5.99 72 18 26 8 169.43 3.60 73 18 30 12 155.53 3.35 74 18 64 46 92.81 0.35 75 19 22 3 670.32 1.30 76 19 23 4 628.96 1.26 77 19 24 5 602.32 4.45 78 19 25 6 407.86 3.27 79 19 68 49 88.23 1.41 80 20 87 67 53.50 1.02 81 21 85 64 53.80 0.91 82 21 86 65 53.79 0.91 83 21 87 66 53.36 1.08 84 24 64 40 92.81 0.34 85 25 64 39 92.79 0.35 86 25 66 41 91.83 0.33 87 26 30 4 651.06 2.17 88 26 31 5 651.05 2.18 89 26 64 38 92.79 0.35 90 26 66 40 92.41 0.49 91 27 30 3 664.59 0.14 92 27 31 4 660.28 2.40 93 27 63 36 92.80 0.35 94 27 64 37 92.48 0.50 95 28 31 3 666.04 3.90 96 28 32 4 652.96 1.26 97 28 40 12 259.13 52.63 98 28 43 15 257.73 53.31 99 28 44 16 257.72 53.30 100 28 47 19 257.67 53.31 101 28 58 30 110.00 0.48 102 28 66 38 92.33 0.57 103 29 32 3 667.88 0.74 104 29 33 4 660.28 2.41 105 29 40 11 371.49 3.52 106 30 33 3 683.29 3.12 107 30 34 4 660.28 2.41 108 30 64 34 92.80 0.35 109 31 34 3 685.99 1.79 110 31 35 4 652.20 1.55 111 31 37 6 621.49 2.69 112 31 43 12 257.75 53.30 113 31 47 16 257.72 53.27 114 32 35 3 680.61 4.48 115 32 36 4 646.54 0.00 116 32 37 5 605.58 10.63 117 32 39 7 381.31 1.18 118 32 40 8 381.10 1.28 119 32 43 11 265.00 56.91 120 33 36 3 657.04 0.77 121 37 42 5 643.08 2.37 122 37 43 6 631.14 3.43 123 37 46 9 615.32 0.70 124 38 42 4 660.49 2.04 125 39 42 3 666.46 0.81 126 39 43 4 667.81 2.28 127 40 43 3 667.81 2.29 128 40 44 4 668.53 1.92 129 41 44 3 668.55 1.92 130 41 45 4 666.38 0.83 131 42 45 3 671.73 1.15 132 42 46 4 667.13 0.46 133 43 46 3 677.10 2.14 134 43 47 4 664.49 0.12 135 44 47 3 669.90 1.83 136 44 48 4 661.88 1.38 137 45 48 3 667.08 0.42 138 45 49 4 656.82 1.11 139 46 49 3 662.26 2.83 140 46 50 4 654.95 0.17 141 47 50 3 659.37 1.38 142 47 51 4 652.88 0.85 143 47 56 9 479.20 50.63 144 47 58 11 237.53 64.31 145 47 66 19 88.14 1.38 146 48 51 3 659.38 1.38 147 48 52 4 652.01 1.29 148 48 58 10 261.60 52.62 149 49 52 3 655.44 3.35 150 49 53 4 648.13 0.73 151 50 53 3 653.63 1.24 152 50 54 4 648.00 0.68 153 50 55 5 624.81 4.16 154 50 56 6 585.68 2.60 155 51 54 3 644.35 2.48 156 51 56 5 490.62 44.93 157 51 58 7 267.01 49.95 158 54 69 15 82.75 0.14 159 54 70 16 82.74 0.14 160 55 68 13 86.91 1.07 161 55 69 14 82.75 0.13 162 56 66 10 88.23 1.42 163 56 67 11 87.58 1.18 164 56 68 12 86.91 1.07 165 56 69 13 84.17 0.57 166 57 66 9 88.24 1.42 167 57 67 10 87.90 1.34 168 57 69 12 87.13 1.17 169 58 65 7 88.32 1.41 170 59 65 6 88.33 1.41 171 59 67 8 88.31 1.41 172 62 65 3 672.30 3.97 173 68 71 3 712.67 1.33 174 73 97 24 572.31 0.16 175 74 99 25 572.16 0.14 176 75 98 23 572.29 0.17 177 75 99 24 572.16 0.14 178 75 100 25 572.11 0.17 179 75 102 27 572.04 0.13 180 76 97 21 572.40 0.18 181 76 98 22 572.34 0.16 182 76 100 24 572.28 0.17 183 76 102 26 572.13 0.15 184 76 109 33 571.55 0.24 185 76 110 34 571.49 0.23 186 76 111 35 571.48 0.24 187 76 112 36 571.46 0.24 188 77 94 17 572.72 0.13 189 77 96 19 572.53 0.17 190 77 97 20 572.40 0.18 191 77 110 33 571.57 0.26 192 77 111 34 571.48 0.24 193 77 112 35 571.48 0.24 194 78 94 16 572.75 0.14 195 78 95 17 572.68 0.14 196 78 96 18 572.63 0.14 197 78 98 20 572.51 0.17 198 78 112 34 571.49 0.24 199 78 113 35 571.49 0.24 200 78 114 36 571.48 0.24 201 78 130 52 304.70 0.40 202 79 82 3 758.58 0.23 203 79 88 9 572.95 0.13 204 79 89 10 572.91 0.12 205 79 93 14 572.82 0.11 206 79 94 15 572.81 0.10 207 79 111 32 571.60 0.26 208 79 112 33 571.54 0.26 209 79 113 34 571.50 0.24 210 79 114 35 571.49 0.24 211 80 93 13 572.89 0.11 212 80 95 15 572.81 0.12 213 80 114 34 571.51 0.24 214 81 93 12 572.95 0.13 215 82 88 6 573.15 0.12 216 82 93 11 572.96 0.13 217 82 148 66 315.00 0.56 218 82 153 71 314.54 0.33 219 83 86 3 668.09 2.91 220 83 92 9 573.15 0.12 221 83 93 10 573.08 0.12 222 83 148 65 315.24 0.54 223 84 148 64 315.25 0.55 224 84 151 67 315.21 0.53 225 85 151 66 315.23 0.53 226 86 90 4 607.77 5.23 227 86 92 6 594.32 1.51 228 86 93 7 588.20 4.57 229 86 148 62 315.19 0.54 230 87 90 3 659.56 5.00 231 87 93 6 594.32 1.51 232 87 148 61 314.91 0.56 233 88 93 5 599.77 1.22 234 88 111 23 571.75 0.24 235 88 146 58 313.28 0.64 236 88 148 60 314.83 0.54 237 88 153 65 314.86 0.55 238 88 189 101 303.14 0.57 239 89 94 5 602.13 2.40 240 89 111 22 571.62 0.25 241 90 93 3 669.48 1.31 242 90 94 4 654.23 6.29 243 91 94 3 667.86 0.52 244 94 97 3 799.67 1.70 245 95 114 19 571.51 0.24 246 98 112 14 571.49 0.24 247 98 130 32 304.67 0.39 248 100 104 4 677.24 5.69 249 100 105 5 677.23 5.68 250 100 196 96 255.83 6.99 251 101 104 3 677.23 5.69 252 102 105 3 689.73 2.64 253 102 108 6 573.14 0.01 254 102 109 7 571.60 0.24 255 103 108 5 573.21 0.01 256 105 108 3 682.23 1.46 257 105 109 4 651.62 4.90 258 105 132 27 304.26 0.48 259 105 193 88 289.86 1.12 260 105 194 89 289.86 1.12 261 105 195 90 289.86 1.12 262 105 196 91 289.84 1.11 263 107 134 27 304.24 0.46 264 107 191 84 303.19 0.74 265 107 193 86 290.61 1.21 266 108 134 26 304.23 0.47 267 109 132 23 304.25 0.47 268 109 133 24 303.93 0.62 269 109 134 25 303.78 0.70 270 109 193 84 290.25 1.16 271 110 133 23 304.30 0.43 272 110 134 24 303.78 0.69 273 110 135 25 303.76 0.69 274 111 132 21 304.39 0.41 275 111 133 22 304.30 0.44 276 111 135 24 304.05 0.56 277 112 130 18 304.72 0.41 278 112 131 19 304.47 0.42 279 112 132 20 304.39 0.42 280 112 196 84 267.79 1.46 281 113 130 17 304.86 0.43 282 113 131 18 304.57 0.44 283 113 133 20 304.46 0.42 284 113 146 33 304.50 0.43 285 113 153 40 313.78 0.57 286 113 155 42 305.44 0.03 287 114 128 14 313.22 0.65 288 114 129 15 305.80 0.41 289 114 130 16 304.87 0.43 290 115 125 10 314.25 0.18 291 115 126 11 314.25 0.18 292 115 127 12 314.25 0.18 293 115 128 13 314.19 0.21 294 115 129 14 310.57 1.97 295 115 131 16 305.28 0.64 296 116 127 11 318.60 0.20 297 117 127 10 318.62 0.20 298 118 121 3 654.08 3.02 299 118 126 8 333.88 2.54 300 118 127 9 321.06 0.42 301 118 171 53 342.69 2.69 302 118 174 56 342.62 2.73 303 119 156 37 342.33 2.71 304 119 169 50 342.34 2.71 305 119 170 51 342.55 2.65 306 119 171 52 342.72 2.71 307 119 174 55 342.53 2.69 308 120 123 3 681.64 0.17 309 120 124 4 652.14 2.59 310 120 125 5 574.78 0.42 311 120 144 24 342.37 2.69 312 120 155 35 342.36 2.72 313 120 156 36 342.39 2.71 314 120 157 37 342.48 2.68 315 120 168 48 342.62 2.69 316 120 169 49 342.55 2.66 317 120 170 50 342.66 2.71 318 121 124 3 654.37 3.02 319 121 125 4 601.48 11.68 320 121 126 5 574.71 0.47 321 121 170 49 343.01 2.60 322 121 171 50 343.05 2.62 323 122 170 48 343.04 2.62 324 122 171 49 343.08 2.62 325 123 144 21 342.89 2.65 326 123 157 34 343.07 2.61 327 123 170 47 343.10 2.62 328 124 197 73 290.49 1.15 329 125 129 4 619.24 7.18 330 125 131 6 369.69 2.79 331 125 195 70 290.48 1.15 332 126 129 3 665.45 2.96 333 126 197 71 284.71 3.00 334 129 195 66 296.61 7.21 335 129 196 67 294.85 8.07 336 129 197 68 256.15 6.94 337 130 195 65 296.18 7.43 338 130 196 66 287.93 11.54 339 130 198 68 256.00 6.98 340 131 146 15 345.94 2.28 341 131 155 24 345.84 2.32 342 131 192 61 344.44 2.02 343 131 194 63 336.88 2.67 344 131 195 64 280.12 0.59 345 132 192 60 344.66 2.09 346 132 193 61 344.30 2.05 347 132 194 62 336.90 2.66 348 133 146 13 346.07 2.27 349 133 190 57 346.04 2.25 350 133 191 58 345.20 2.00 351 133 192 59 344.77 2.04 352 133 193 60 344.47 2.01 353 134 190 56 346.07 2.27 354 134 191 57 345.45 2.03 355 134 193 59 345.16 2.02 356 135 189 54 347.00 1.82 357 135 190 55 346.42 2.10 358 136 139 3 735.45 3.96 359 136 188 52 347.63 1.97 360 136 190 54 346.97 1.82 361 136 191 55 346.97 1.82 362 137 188 51 347.63 1.97 363 139 143 4 658.35 2.19 364 139 145 6 367.73 7.69 365 139 158 19 357.35 2.69 366 139 188 49 348.05 1.89 367 139 191 52 347.77 1.92 368 140 143 3 677.32 1.55 369 140 158 18 357.42 2.67 370 141 158 17 357.47 2.69 371 141 159 18 357.29 2.69 372 141 160 19 357.07 2.58 373 142 157 15 357.79 2.58 374 142 158 16 357.76 2.57 375 143 157 14 357.82 2.56 376 143 158 15 357.80 2.58 377 143 191 48 348.82 1.93 378 144 155 11 359.34 2.73 379 144 156 12 358.26 2.65 380 144 157 13 357.93 2.55 381 144 191 47 348.82 1.93 382 144 192 48 348.81 1.93 383 145 155 10 359.38 2.75 384 145 156 11 358.81 2.90 385 145 158 13 358.36 2.69 386 145 188 43 351.98 2.10 387 145 190 45 349.66 2.21 388 145 191 46 348.82 1.93 389 146 153 7 360.55 2.71 390 146 154 8 360.39 2.75 391 146 155 9 359.42 2.73 392 146 188 42 352.27 1.96 393 146 189 43 350.97 2.12 394 146 190 44 349.97 2.35 395 147 153 6 364.20 4.54 396 147 154 7 360.49 2.71 397 147 167 20 359.22 2.81 398 147 186 39 353.73 2.15 399 147 187 40 352.88 1.75 400 147 188 41 352.30 1.95 401 148 151 3 669.00 1.34 402 148 152 4 499.24 0.31 403 148 153 5 364.68 4.30 404 148 186 38 353.73 2.15 405 148 187 39 353.69 2.15 406 148 189 41 352.70 1.81 407 149 152 3 657.19 0.43 408 149 154 5 591.41 5.26 409 149 167 18 360.62 2.65 410 149 179 30 357.95 2.51 411 149 184 35 356.17 2.05 412 149 185 36 355.37 2.38 413 149 186 37 354.25 1.89 414 150 184 34 356.18 2.06 415 150 185 35 355.37 2.38 416 154 167 13 486.87 2.62 417 156 167 11 496.59 0.59 418 156 168 12 497.36 0.30 419 156 169 13 497.41 0.30 420 156 177 21 497.27 0.34 421 157 167 10 497.40 0.32 422 157 168 11 497.40 0.29 423 157 170 13 497.54 0.34 424 158 165 7 497.46 0.33 425 158 167 9 497.44 0.31 426 158 186 28 356.55 0.50 427 158 188 30 351.31 2.27 428 159 165 6 497.48 0.32 429 159 166 7 497.48 0.32 430 159 168 9 497.57 0.32 431 160 165 5 497.48 0.32 432 161 164 3 636.45 2.44 433 161 166 5 497.73 0.40 434 163 180 17 497.68 0.37 435 163 181 18 497.60 0.36 436 163 182 19 497.50 0.32 437 164 178 14 497.80 0.38 438 164 179 15 497.70 0.37 439 164 180 16 497.68 0.37 440 164 181 17 497.66 0.36 441 164 182 18 497.68 0.37 442 165 178 13 497.84 0.39 443 165 179 14 497.75 0.38 444 165 181 16 497.71 0.38 445 165 186 21 357.76 1.10 446 166 177 11 497.95 0.35 447 166 178 12 497.84 0.39 448 167 176 9 498.01 0.34 449 167 177 10 498.00 0.34 450 167 179 12 497.99 0.34 451 167 186 19 356.86 0.65 452 168 176 8 498.05 0.32 453 169 174 5 498.39 0.34 454 169 175 6 498.31 0.31 455 169 176 7 498.13 0.32 456 171 174 3 667.81 6.24 457 179 184 5 498.88 0.39 458 179 186 7 427.26 35.85 459 180 183 3 680.63 1.83 460 180 184 4 623.53 9.08 461 181 186 5 430.70 34.47