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 24 125 101 46.68 0.37 2 25 45 20 99.84 4.25 3 25 77 52 90.28 1.00 4 25 78 53 90.22 0.97 5 25 79 54 90.06 0.98 6 25 80 55 90.03 0.99 7 25 81 56 90.02 0.99 8 26 42 16 99.93 4.35 9 26 44 18 99.81 4.29 10 26 45 19 100.05 4.17 11 26 81 55 90.03 0.99 12 26 83 57 90.03 0.99 13 27 45 18 100.20 4.12 14 27 46 19 100.16 4.10 15 27 63 36 100.35 3.99 16 27 74 47 90.30 0.99 17 27 77 50 90.34 0.99 18 27 79 52 90.28 0.99 19 27 81 54 90.09 0.99 20 27 82 55 90.06 0.98 21 27 83 56 90.06 0.98 22 28 33 5 165.00 14.12 23 28 34 6 100.48 4.46 24 28 37 9 100.45 4.42 25 28 44 16 100.39 4.09 26 28 46 18 100.38 4.04 27 28 47 19 100.32 4.02 28 28 48 20 100.36 4.00 29 28 83 55 90.07 0.98 30 29 48 19 100.36 4.00 31 29 63 34 100.53 3.95 32 29 64 35 100.47 3.94 33 29 69 40 91.03 0.76 34 29 74 45 90.83 0.90 35 29 82 53 90.30 0.99 36 29 83 54 90.13 0.97 37 29 84 55 90.08 0.98 38 29 89 60 90.11 0.98 39 29 94 65 90.26 0.97 40 30 33 3 410.05 1.81 41 30 34 4 410.05 1.81 42 30 48 18 100.50 4.04 43 30 85 55 90.09 0.97 44 31 34 3 439.23 10.77 45 31 35 4 413.87 0.10 46 31 48 17 100.62 3.98 47 31 49 18 100.59 4.00 48 31 50 19 100.45 4.06 49 31 51 20 100.39 4.06 50 31 246 215 89.98 0.98 51 32 35 3 415.97 0.86 52 32 36 4 413.87 0.10 53 32 246 214 89.98 0.98 54 32 247 215 90.02 0.98 55 32 248 216 90.01 0.98 56 33 36 3 415.88 0.90 57 33 37 4 408.31 2.88 58 33 83 50 90.57 0.99 59 33 84 51 90.48 0.95 60 33 85 52 90.46 0.95 61 33 107 74 90.29 0.99 62 34 37 3 436.95 9.34 63 34 38 4 413.13 2.57 64 34 47 13 100.89 3.94 65 34 51 17 100.86 3.98 66 34 53 19 110.59 1.94 67 34 57 23 111.59 1.45 68 35 38 3 433.31 7.40 69 35 39 4 413.25 2.63 70 35 53 18 111.74 2.50 71 35 246 211 90.12 0.97 72 35 248 213 90.13 0.97 73 35 250 215 90.12 0.97 74 36 39 3 413.26 2.63 75 36 40 4 405.28 1.36 76 36 107 71 90.80 0.92 77 36 115 79 90.28 0.99 78 36 118 82 90.66 0.98 79 36 119 83 90.56 1.02 80 36 122 86 90.95 1.02 81 36 248 212 90.14 0.98 82 36 249 213 90.13 0.97 83 37 40 3 436.74 9.11 84 37 41 4 410.85 1.43 85 37 42 5 345.51 13.29 86 37 44 7 170.84 19.09 87 37 83 46 91.16 0.97 88 37 122 85 90.97 1.02 89 38 41 3 413.24 2.64 90 38 42 4 354.18 8.96 91 38 43 5 354.16 8.96 92 38 44 6 345.52 13.29 93 38 54 16 170.58 18.73 94 38 56 18 171.09 18.89 95 38 57 19 171.03 18.91 96 38 60 22 266.84 25.41 97 38 131 93 90.92 1.08 98 39 119 80 90.86 1.10 99 39 131 92 90.86 1.10 100 39 135 96 90.35 1.04 101 39 249 210 90.15 0.97 102 40 119 79 90.78 1.05 103 40 122 82 91.19 1.05 104 40 126 86 91.42 0.94 105 40 128 88 91.41 0.94 106 40 131 91 90.87 1.10 107 40 132 92 90.76 1.06 108 41 126 85 91.42 0.95 109 41 127 86 91.45 0.94 110 41 128 87 91.34 0.97 111 41 131 90 90.89 1.10 112 42 122 80 91.30 0.99 113 42 125 83 91.44 0.96 114 42 126 84 91.41 0.95 115 42 127 85 91.44 0.96 116 44 47 3 528.24 0.24 117 45 77 32 91.88 1.19 118 46 63 17 550.16 0.94 119 46 77 31 92.10 1.30 120 48 64 16 561.66 3.29 121 50 246 196 90.08 1.02 122 52 242 190 90.05 1.00 123 52 246 194 90.16 0.98 124 53 246 193 90.20 0.96 125 53 250 197 90.11 0.98 126 61 73 12 92.58 1.57 127 61 77 16 92.59 1.55 128 63 69 6 92.68 1.59 129 63 70 7 92.56 1.65 130 63 73 10 92.64 1.60 131 63 74 11 92.56 1.57 132 63 77 14 92.58 1.57 133 64 68 4 393.47 2.02 134 64 69 5 92.67 1.59 135 65 68 3 400.02 5.30 136 68 93 25 92.20 1.69 137 69 74 5 405.38 1.34 138 69 89 20 91.71 1.49 139 69 93 24 92.80 1.96 140 69 94 25 92.78 1.95 141 70 73 3 462.03 21.38 142 70 74 4 432.81 11.18 143 71 74 3 432.81 11.17 144 71 75 4 431.67 11.73 145 71 93 22 107.31 9.20 146 71 96 25 177.97 18.37 147 71 97 26 177.97 18.37 148 72 75 3 487.22 15.49 149 72 76 4 407.75 0.15 150 73 76 3 432.47 8.93 151 73 77 4 404.10 1.68 152 74 77 3 440.86 4.74 153 74 78 4 432.46 8.93 154 74 79 5 396.16 2.60 155 74 82 8 229.28 39.62 156 74 97 23 242.43 43.75 157 75 78 3 464.61 19.00 158 75 79 4 411.00 1.80 159 75 97 22 242.34 43.74 160 75 100 25 260.91 45.95 161 75 102 27 247.42 43.45 162 79 82 3 528.20 4.87 163 79 102 23 279.62 45.21 164 80 103 23 279.71 45.20 165 80 125 45 191.49 2.96 166 81 103 22 279.71 45.20 167 81 104 23 279.72 45.21 168 81 105 24 279.71 45.21 169 81 122 41 194.06 2.60 170 81 125 44 192.03 3.19 171 82 97 15 279.87 45.15 172 82 102 20 279.86 45.15 173 82 103 21 279.79 45.18 174 82 104 22 279.75 45.21 175 82 105 23 279.73 45.21 176 83 105 22 279.75 45.22 177 83 107 24 279.71 45.21 178 83 122 39 194.53 2.62 179 84 89 5 279.98 45.16 180 84 94 10 279.94 45.16 181 84 104 20 279.86 45.17 182 84 105 21 279.81 45.20 183 84 106 22 279.73 45.21 184 84 107 23 279.73 45.21 185 85 88 3 466.24 19.22 186 85 89 4 280.00 45.18 187 85 106 21 279.79 45.20 188 85 107 22 279.75 45.21 189 85 108 23 279.73 45.21 190 86 106 20 279.89 45.16 191 86 108 22 279.75 45.21 192 89 94 5 404.06 1.43 193 90 93 3 447.50 3.35 194 90 94 4 413.69 3.57 195 91 94 3 417.93 1.45 196 91 95 4 407.45 0.45 197 91 106 15 280.04 45.13 198 92 95 3 423.66 1.42 199 92 96 4 407.52 0.48 200 93 96 3 423.65 1.42 201 93 97 4 419.90 0.45 202 94 97 3 460.31 19.75 203 94 98 4 461.31 26.41 204 94 104 10 280.20 45.09 205 94 106 12 280.11 45.13 206 95 98 3 467.48 23.34 207 95 99 4 407.49 0.48 208 96 99 3 467.48 23.34 209 96 100 4 413.72 2.64 210 97 100 3 459.38 27.39 211 97 101 4 405.49 0.44 212 97 102 5 336.55 17.82 213 97 104 7 280.20 45.09 214 98 101 3 413.48 4.44 215 98 102 4 386.23 7.38 216 103 125 22 234.81 17.53 217 105 121 16 234.87 17.55 218 105 122 17 234.87 17.54 219 105 125 20 235.13 17.57 220 107 118 11 234.84 17.53 221 109 114 5 325.46 27.79 222 109 115 6 235.59 17.15 223 109 247 138 234.66 17.52 224 110 114 4 398.75 2.18 225 110 173 63 234.59 17.53 226 110 174 64 234.59 17.53 227 110 175 65 234.67 17.51 228 111 114 3 411.69 3.69 229 111 115 4 401.20 3.40 230 111 175 64 234.77 17.53 231 111 178 67 234.74 17.55 232 112 115 3 409.31 0.66 233 112 116 4 404.00 2.00 234 112 139 27 235.02 17.61 235 112 140 28 235.12 17.55 236 112 143 31 234.88 17.54 237 112 175 63 234.88 17.53 238 112 178 66 234.89 17.54 239 112 179 67 234.86 17.53 240 112 251 139 234.85 17.53 241 113 116 3 408.62 0.32 242 113 117 4 409.52 0.77 243 113 140 27 235.15 17.56 244 113 178 65 235.16 17.54 245 114 117 3 413.86 1.41 246 114 118 4 403.55 2.21 247 115 118 3 410.39 2.96 248 115 119 4 406.16 0.91 249 115 139 24 235.87 17.46 250 115 175 60 235.58 17.46 251 115 247 132 235.66 17.54 252 115 248 133 235.84 17.46 253 115 249 134 235.86 17.45 254 115 251 136 235.84 17.46 255 116 119 3 424.95 6.95 256 116 120 4 408.19 1.43 257 116 136 20 235.88 17.46 258 116 139 23 235.87 17.46 259 116 140 24 235.86 17.46 260 117 120 3 425.80 6.53 261 117 121 4 409.21 1.85 262 118 121 3 412.31 0.30 263 118 122 4 415.71 1.61 264 119 122 3 461.31 22.35 265 119 123 4 459.59 23.21 266 119 132 13 236.06 17.51 267 119 135 16 236.05 17.51 268 119 136 17 236.05 17.51 269 119 249 130 235.99 17.48 270 120 123 3 510.65 2.06 271 120 124 4 514.60 0.08 272 120 136 16 236.06 17.51 273 120 137 17 236.06 17.51 274 120 140 20 236.06 17.51 275 121 124 3 529.16 0.39 276 121 125 4 472.68 16.93 277 122 125 3 470.43 17.78 278 122 126 4 414.43 0.62 279 123 126 3 435.12 10.10 280 123 129 6 236.15 17.51 281 123 132 9 236.12 17.50 282 123 133 10 236.13 17.50 283 126 129 3 405.13 5.12 284 128 131 3 462.89 23.38 285 128 132 4 432.05 12.29 286 129 132 3 432.13 12.24 287 129 133 4 430.69 12.96 288 130 133 3 431.20 12.70 289 130 134 4 404.38 0.42 290 131 134 3 408.92 0.73 291 131 135 4 406.81 1.64 292 132 135 3 408.65 1.51 293 132 136 4 406.81 1.64 294 133 136 3 407.41 2.13 295 133 137 4 397.61 3.80 296 134 137 3 408.13 1.97 297 134 138 4 388.91 0.55 298 135 138 3 431.82 9.88 299 135 139 4 427.38 12.07 300 136 139 3 435.91 11.50 301 136 140 4 431.80 9.87 302 137 140 3 431.82 9.88 303 137 141 4 400.49 5.78 304 138 141 3 405.63 3.23 305 138 142 4 395.80 3.74 306 139 142 3 442.75 9.01 307 139 143 4 395.78 3.76 308 139 249 110 311.24 18.01 309 139 251 112 311.25 18.01 310 139 252 113 311.25 18.01 311 140 143 3 412.89 5.07 312 140 144 4 400.32 1.42 313 141 144 3 408.86 2.85 314 141 145 4 396.48 3.34 315 142 145 3 483.31 15.79 316 142 146 4 395.96 1.83 317 142 252 110 321.74 20.50 318 143 146 3 434.43 13.61 319 143 147 4 394.73 2.44 320 143 178 35 322.07 20.62 321 143 182 39 321.91 20.55 322 143 252 109 321.88 20.55 323 144 147 3 412.93 0.15 324 144 148 4 405.97 3.17 325 145 148 3 418.13 2.46 326 145 149 4 398.25 0.69 327 146 149 3 408.58 2.32 328 146 150 4 406.42 3.40 329 146 252 106 322.48 20.69 330 146 255 109 322.44 20.71 331 146 256 110 322.44 20.71 332 146 259 113 322.44 20.71 333 147 150 3 461.69 22.31 334 147 151 4 378.77 0.88 335 147 182 35 322.48 20.73 336 148 151 3 453.20 26.56 337 150 153 3 491.53 6.16 338 150 182 32 322.78 20.64 339 150 183 33 322.64 20.70 340 150 256 106 322.68 20.68 341 150 259 109 322.62 20.69 342 150 260 110 322.63 20.69 343 153 263 110 322.98 20.54 344 155 184 29 336.55 18.54 345 155 186 31 433.25 0.34 346 156 184 28 380.55 22.54 347 156 185 29 428.11 1.24 348 156 186 30 439.81 1.50 349 156 210 54 498.69 1.51 350 156 262 106 338.82 19.67 351 156 263 107 336.94 18.73 352 156 265 109 324.12 20.46 353 157 186 29 440.01 1.58 354 157 188 31 455.38 5.23 355 157 207 50 498.69 1.51 356 157 208 51 498.69 1.51 357 157 209 52 498.69 1.51 358 157 210 53 498.92 1.40 359 157 211 54 498.98 1.37 360 158 180 22 454.12 5.29 361 158 185 27 446.38 1.41 362 158 186 28 453.62 5.01 363 158 187 29 454.70 5.55 364 158 188 30 455.98 4.95 365 158 211 53 498.98 1.37 366 158 213 55 499.31 1.20 367 158 262 104 393.85 1.82 368 159 169 10 457.00 4.92 369 159 188 29 456.29 4.95 370 159 189 30 456.51 4.89 371 159 199 40 497.56 1.65 372 159 204 45 498.84 1.40 373 159 209 50 499.26 1.27 374 159 211 52 499.41 1.19 375 159 212 53 499.38 1.18 376 159 213 54 499.39 1.18 377 159 228 69 500.08 0.98 378 160 169 9 457.00 4.92 379 160 170 10 456.98 4.92 380 160 176 16 456.27 4.95 381 160 177 17 456.34 4.92 382 160 180 20 456.00 4.95 383 160 187 27 456.38 4.95 384 160 213 53 499.46 1.15 385 160 244 84 495.76 2.17 386 161 167 6 497.49 1.70 387 161 168 7 497.44 1.71 388 161 212 51 499.54 1.14 389 161 213 52 499.50 1.15 390 161 214 53 499.48 1.15 391 161 224 63 499.56 1.14 392 161 227 66 500.32 0.96 393 161 228 67 500.32 0.96 394 162 168 6 497.56 1.74 395 162 169 7 497.42 1.70 396 162 176 14 465.59 3.90 397 162 196 34 497.56 1.65 398 162 215 53 499.50 1.15 399 162 244 82 498.35 1.23 400 162 245 83 498.10 1.12 401 164 167 3 498.86 1.41 402 164 223 59 500.17 0.97 403 164 224 60 500.22 0.96 404 164 227 63 500.43 1.02 405 166 198 32 506.90 3.08 406 167 198 31 507.00 3.12 407 167 199 32 506.90 3.08 408 167 227 60 503.16 1.45 409 168 196 28 507.82 2.96 410 168 197 29 507.80 2.96 411 168 198 30 507.42 2.91 412 169 189 20 499.06 1.19 413 169 196 27 508.03 2.88 414 169 197 28 507.81 2.96 415 169 199 30 507.80 2.96 416 170 174 4 498.06 0.32 417 170 187 17 496.63 0.28 418 170 189 19 499.53 0.98 419 170 195 25 508.08 2.87 420 170 196 26 508.07 2.86 421 171 177 6 499.56 0.94 422 171 187 16 499.05 1.20 423 171 189 18 500.01 0.90 424 171 192 21 506.92 2.52 425 171 195 24 508.08 2.87 426 171 197 26 508.19 2.85 427 172 177 5 499.58 0.94 428 172 190 18 501.42 0.24 429 174 177 3 506.13 1.86 430 174 178 4 506.13 1.86 431 174 196 22 656.04 4.36 432 175 178 3 506.95 2.27 433 175 179 4 506.65 2.12 434 175 247 72 507.07 2.57 435 175 251 76 505.71 1.92 436 176 179 3 508.72 1.34 437 176 180 4 507.63 2.60 438 176 244 68 507.17 2.64 439 176 245 69 507.59 2.61 440 177 180 3 507.63 2.60 441 177 181 4 507.69 2.58 442 177 187 10 534.63 2.61 443 178 181 3 509.73 1.62 444 178 182 4 507.68 2.57 445 179 182 3 507.88 2.67 446 179 183 4 507.65 2.58 447 179 244 65 629.45 14.59 448 179 251 72 556.56 3.02 449 179 255 76 507.32 2.54 450 179 258 79 507.32 2.54 451 180 183 3 511.35 0.92 452 180 258 78 507.62 2.70 453 180 262 82 432.17 16.21 454 183 262 79 487.04 9.95 455 184 262 78 471.66 3.54 456 185 262 77 513.71 58.11 457 210 265 55 404.12 60.42 458 210 266 56 404.03 60.41 459 211 265 54 404.84 60.06 460 235 265 30 595.31 35.18 461 237 265 28 635.75 14.96 462 258 262 4 585.51 1.32 463 259 262 3 499.88 3.53 464 259 263 4 487.04 9.95 465 260 263 3 502.12 4.65 466 260 264 4 487.05 9.95 467 261 264 3 493.05 12.95 468 261 265 4 487.05 9.95 469 262 265 3 465.65 20.82