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 30 53 20 22.18 0.21 2 31 53 19 22.25 0.18 3 31 56 22 39.05 0.33 4 31 57 23 42.76 0.30 5 33 56 20 45.87 1.09 6 33 57 21 48.23 0.09 7 34 56 19 48.65 0.30 8 35 38 3 733.41 5.57 9 35 39 4 713.70 0.64 10 35 56 18 56.90 0.57 11 36 39 3 723.99 0.17 12 36 40 4 717.94 2.75 13 37 40 3 723.39 0.12 14 37 41 4 717.95 2.75 15 38 41 3 722.58 0.43 16 38 42 4 713.72 0.64 17 38 56 15 75.50 0.52 18 38 64 23 90.69 1.38 19 38 73 32 86.48 1.54 20 39 42 3 737.76 3.54 21 39 43 4 713.70 0.65 22 40 43 3 724.64 1.66 23 41 61 17 91.08 1.22 24 41 62 18 91.25 1.14 25 41 63 19 91.25 1.14 26 42 45 3 725.45 2.66 27 42 46 4 720.41 3.79 28 42 54 9 86.92 0.03 29 42 56 11 89.85 1.27 30 42 60 15 91.12 1.20 31 42 61 16 91.14 1.19 32 43 46 3 736.79 4.24 33 43 47 4 720.41 3.79 34 45 54 6 90.73 1.08 35 45 271 223 91.12 1.20 36 45 273 225 90.79 1.06 37 46 54 5 90.80 1.05 38 51 216 165 91.66 0.95 39 51 274 223 92.95 1.54 40 51 275 224 90.87 1.08 41 51 276 225 90.49 0.91 42 52 113 61 97.03 0.42 43 52 115 63 98.74 0.08 44 52 273 221 97.06 0.43 45 52 274 222 93.71 1.92 46 52 275 223 91.66 0.95 47 53 273 220 98.42 0.06 48 53 274 221 95.58 0.99 49 54 59 5 726.14 2.12 50 54 271 217 117.12 1.15 51 54 272 218 98.62 0.01 52 54 273 219 98.43 0.06 53 55 58 3 751.42 9.37 54 55 59 4 722.68 0.39 55 55 109 54 110.94 1.98 56 55 272 217 100.63 1.01 57 55 273 218 98.60 0.02 58 55 274 219 98.58 0.03 59 56 59 3 734.60 2.10 60 56 74 18 143.25 1.05 61 57 74 17 143.20 1.04 62 58 75 17 143.38 1.14 63 58 103 45 141.69 0.34 64 58 105 47 143.13 1.04 65 58 106 48 141.69 0.34 66 58 107 49 134.33 0.80 67 58 109 51 133.99 0.46 68 58 272 214 130.94 1.00 69 59 75 16 143.41 1.14 70 59 270 211 137.28 1.28 71 59 271 212 135.69 1.05 72 59 272 213 134.25 0.33 73 60 65 5 676.83 1.95 74 60 72 12 143.52 1.11 75 60 75 15 143.47 1.11 76 60 88 28 149.98 2.13 77 60 101 41 143.47 1.11 78 60 267 207 143.06 1.30 79 60 269 209 143.05 1.30 80 60 270 210 143.03 1.30 81 60 271 211 143.03 1.30 82 61 65 4 676.84 1.96 83 61 268 207 143.06 1.30 84 61 269 208 143.06 1.30 85 61 271 210 143.06 1.30 86 62 65 3 715.96 5.01 87 62 85 23 167.41 0.34 88 62 268 206 143.09 1.31 89 63 85 22 167.60 0.28 90 64 85 21 167.60 0.28 91 65 72 7 167.73 0.32 92 65 73 8 167.78 0.29 93 65 84 19 167.87 0.30 94 65 85 20 167.78 0.32 95 65 87 22 167.60 0.28 96 65 88 23 167.77 0.28 97 65 268 203 167.37 0.34 98 66 70 4 675.86 4.08 99 66 71 5 649.61 0.56 100 66 72 6 167.74 0.32 101 66 83 17 167.97 0.26 102 66 84 18 167.87 0.30 103 66 85 19 167.85 0.30 104 67 70 3 724.15 2.79 105 67 71 4 676.97 0.10 106 67 73 6 167.83 0.32 107 70 83 13 192.66 1.45 108 72 75 3 713.71 0.96 109 72 83 11 197.10 1.41 110 72 88 16 195.56 0.70 111 74 103 29 197.74 1.84 112 74 104 30 197.74 1.85 113 75 101 26 198.07 1.86 114 75 102 27 197.92 1.88 115 75 103 28 197.74 1.84 116 75 104 29 197.75 1.85 117 75 252 177 197.82 1.83 118 75 253 178 197.97 1.85 119 75 270 195 197.72 1.78 120 76 101 25 198.16 1.85 121 76 102 26 198.06 1.86 122 76 104 28 198.03 1.84 123 77 81 4 688.02 2.82 124 77 83 6 547.56 50.16 125 77 100 23 199.21 1.89 126 77 101 24 198.16 1.85 127 78 81 3 750.32 0.14 128 78 99 21 222.50 0.26 129 78 100 22 202.15 0.69 130 78 141 63 211.03 1.83 131 79 98 19 233.98 1.75 132 79 99 20 232.55 1.21 133 80 90 10 234.04 1.75 134 80 92 12 234.46 1.64 135 80 97 17 234.02 1.76 136 80 98 18 234.01 1.76 137 80 99 19 233.99 1.75 138 81 88 7 234.44 1.62 139 81 89 8 234.41 1.62 140 81 90 9 234.03 1.75 141 81 99 18 234.02 1.76 142 81 100 19 234.02 1.75 143 81 101 20 234.02 1.75 144 82 88 6 234.45 1.62 145 82 89 7 234.44 1.62 146 83 87 4 705.65 8.47 147 83 88 5 234.45 1.62 148 84 87 3 739.16 5.11 149 87 266 179 260.07 1.35 150 87 267 180 242.94 0.33 151 87 268 181 235.36 1.46 152 88 101 13 258.76 2.05 153 88 266 178 260.18 1.36 154 88 267 179 255.65 0.85 155 89 92 3 754.34 0.52 156 89 264 175 260.80 1.37 157 89 265 176 260.47 1.51 158 89 266 177 260.19 1.36 159 90 99 9 260.56 1.39 160 90 100 10 260.53 1.38 161 90 101 11 260.47 1.35 162 90 254 164 260.38 1.36 163 90 255 165 260.42 1.38 164 90 256 166 260.52 1.38 165 90 265 175 260.80 1.37 166 90 267 177 260.67 1.41 167 91 97 6 261.13 1.32 168 91 256 165 260.72 1.40 169 91 257 166 260.81 1.44 170 91 258 167 261.10 1.30 171 91 263 172 261.37 1.24 172 91 264 173 261.02 1.36 173 91 265 174 260.86 1.40 174 92 97 5 664.34 3.97 175 92 258 166 263.77 0.07 176 92 263 171 261.40 1.25 177 92 264 172 261.09 1.34 178 93 262 169 277.95 1.12 179 93 263 170 263.74 1.27 180 93 264 171 261.40 1.25 181 94 97 3 754.43 1.99 182 94 258 164 310.60 1.20 183 94 262 168 305.73 0.78 184 95 258 163 315.84 0.82 185 95 259 164 316.57 0.58 186 95 260 165 316.03 0.85 187 95 262 167 314.70 0.62 188 96 258 162 316.61 0.56 189 96 259 163 316.80 0.51 190 97 257 160 317.50 0.40 191 97 258 161 317.16 0.57 192 98 142 44 318.03 0.36 193 98 143 45 318.00 0.35 194 98 144 46 317.98 0.35 195 98 147 49 317.72 0.37 196 98 256 158 317.72 0.37 197 98 257 159 317.55 0.39 198 99 255 156 317.81 0.36 199 99 256 157 317.76 0.38 200 100 140 40 318.25 0.36 201 100 141 41 318.20 0.35 202 100 254 154 317.82 0.36 203 100 255 155 317.82 0.35 204 101 253 152 317.89 0.34 205 101 254 153 317.87 0.34 206 102 134 32 318.05 0.28 207 102 136 34 323.24 0.98 208 102 138 36 323.53 1.10 209 102 139 37 321.56 0.47 210 102 140 38 321.18 0.28 211 102 141 39 321.18 0.28 212 102 148 46 318.87 0.64 213 102 251 149 319.75 0.42 214 102 252 150 318.12 0.32 215 102 253 151 317.91 0.35 216 103 139 36 323.51 1.10 217 103 251 148 320.24 1.34 218 103 252 149 318.19 0.35 219 104 139 35 323.57 1.10 220 104 251 147 323.57 1.10 221 105 251 146 323.57 1.10 222 106 137 31 325.07 1.41 223 106 249 143 325.25 1.31 224 106 250 144 325.01 1.41 225 106 251 145 323.59 1.10 226 107 249 142 328.72 2.98 227 107 250 143 325.24 1.31 228 107 252 145 324.51 1.15 229 108 248 140 347.20 2.54 230 108 249 141 328.73 2.98 231 109 112 3 768.37 2.65 232 109 272 163 316.49 0.68 233 109 274 165 314.87 0.83 234 110 215 105 430.30 0.91 235 111 215 104 430.28 0.92 236 111 216 105 430.30 0.92 237 111 217 106 430.30 0.92 238 111 274 163 314.94 0.79 239 111 275 164 313.69 0.85 240 112 135 23 429.01 0.98 241 112 213 101 430.72 0.77 242 112 214 102 430.39 0.93 243 112 215 103 430.35 0.92 244 112 220 108 430.37 0.92 245 112 246 134 430.25 0.91 246 112 252 140 426.89 1.06 247 112 273 161 315.56 0.52 248 112 274 162 313.83 0.78 249 112 275 163 313.42 0.74 250 113 212 99 430.78 0.77 251 113 213 100 430.65 0.81 252 113 214 101 430.39 0.93 253 113 272 159 316.13 0.78 254 113 273 160 315.30 0.64 255 113 275 162 314.06 0.75 256 114 133 19 429.27 1.02 257 114 212 98 430.92 0.71 258 114 213 99 430.74 0.77 259 114 252 138 429.49 0.92 260 114 270 156 317.37 0.80 261 114 271 157 316.53 0.58 262 114 272 158 315.56 0.52 263 115 210 95 431.50 0.71 264 115 211 96 431.23 0.82 265 115 212 97 430.93 0.70 266 115 235 120 431.72 0.73 267 115 270 155 317.38 0.80 268 115 271 156 316.75 0.53 269 115 273 158 316.07 0.56 270 116 133 17 429.97 0.95 271 116 210 94 431.50 0.71 272 116 211 95 431.32 0.79 273 116 254 138 429.89 0.96 274 116 267 151 328.12 1.00 275 116 269 153 319.44 0.42 276 116 270 154 318.52 0.23 277 117 208 91 432.23 0.84 278 117 209 92 432.05 0.87 279 117 210 93 431.74 0.72 280 117 267 150 328.13 1.01 281 117 268 151 323.43 0.62 282 117 269 152 321.06 0.01 283 118 131 13 430.50 0.84 284 118 159 41 430.98 0.83 285 118 202 84 432.10 0.86 286 118 208 90 432.23 0.84 287 118 209 91 432.06 0.86 288 118 211 93 432.05 0.87 289 118 266 148 329.93 1.29 290 118 267 149 328.13 1.01 291 118 268 150 328.13 1.01 292 119 208 89 432.26 0.83 293 119 265 146 330.72 1.60 294 119 266 147 330.06 1.32 295 119 268 149 329.39 1.02 296 120 202 82 432.32 0.92 297 120 203 83 432.14 0.86 298 120 204 84 432.58 0.86 299 120 263 143 352.26 6.08 300 120 264 144 349.50 6.67 301 120 265 145 330.70 1.60 302 121 204 83 432.59 0.86 303 121 263 142 352.87 6.38 304 121 264 143 352.18 6.12 305 122 203 81 451.13 6.99 306 122 204 82 458.42 3.35 307 122 263 141 352.88 6.38 308 124 203 79 517.85 1.23 309 124 204 80 517.57 1.37 310 125 203 78 520.87 0.28 311 126 162 36 537.22 0.28 312 126 203 77 531.57 0.83 313 126 261 135 426.95 1.02 314 127 161 34 537.25 0.34 315 127 162 35 537.29 0.29 316 127 203 76 534.39 0.57 317 127 261 134 419.49 1.34 318 127 263 136 383.46 1.45 319 128 161 33 537.36 0.30 320 128 162 34 537.36 0.29 321 128 258 130 430.32 0.94 322 128 259 131 430.09 1.04 323 128 261 133 415.01 0.87 324 128 262 134 383.89 1.23 325 128 263 135 366.47 1.35 326 128 265 137 364.46 0.74 327 129 146 17 537.67 0.35 328 129 160 31 537.44 0.29 329 129 161 32 537.45 0.29 330 129 162 33 537.44 0.29 331 129 186 57 537.51 0.27 332 129 257 128 430.48 0.94 333 129 258 129 430.32 0.94 334 129 259 130 429.61 1.10 335 130 146 16 537.81 0.29 336 130 159 29 537.44 0.30 337 130 161 31 537.50 0.27 338 130 256 126 430.82 0.82 339 130 257 127 430.51 0.97 340 130 265 135 342.29 4.23 341 131 146 15 537.87 0.28 342 131 158 27 537.59 0.29 343 131 159 28 537.51 0.27 344 131 254 123 431.39 0.84 345 131 255 124 431.16 0.82 346 131 256 125 430.50 0.96 347 131 265 134 330.13 1.32 348 132 146 14 537.91 0.29 349 132 157 25 537.67 0.34 350 132 158 26 537.60 0.30 351 132 254 122 431.33 0.87 352 132 255 123 431.24 0.86 353 133 156 23 537.98 0.27 354 133 157 24 537.76 0.33 355 133 159 26 537.96 0.26 356 133 211 78 537.83 0.30 357 133 213 80 537.49 0.33 358 133 253 120 431.40 0.85 359 133 254 121 431.32 0.88 360 133 270 137 316.26 0.71 361 134 145 11 538.32 0.29 362 134 148 14 538.35 0.28 363 134 152 18 538.34 0.28 364 134 155 21 538.00 0.28 365 134 156 22 537.99 0.27 366 134 158 24 538.01 0.27 367 134 252 118 431.48 0.84 368 134 253 119 431.41 0.84 369 134 254 120 431.41 0.85 370 134 255 121 431.35 0.88 371 135 154 19 538.28 0.27 372 135 155 20 538.23 0.29 373 135 246 111 453.50 2.10 374 135 247 112 453.48 2.10 375 135 248 113 451.87 1.30 376 135 249 114 451.15 1.20 377 135 250 115 434.86 0.40 378 135 251 116 431.54 0.84 379 135 252 117 431.49 0.84 380 136 152 16 538.34 0.28 381 136 153 17 538.31 0.27 382 136 154 18 538.28 0.27 383 136 155 19 538.29 0.28 384 136 250 114 435.20 0.23 385 136 251 115 433.97 0.03 386 137 153 16 538.33 0.27 387 137 247 110 453.48 2.12 388 137 249 112 451.69 1.32 389 137 250 113 435.91 0.10 390 137 251 114 435.25 0.23 391 138 251 113 435.23 0.22 392 139 251 112 432.93 0.67 393 140 148 8 639.35 1.42 394 140 149 9 538.51 0.29 395 142 147 5 654.73 5.19 396 142 148 6 646.30 1.05 397 142 149 7 646.30 1.05 398 143 147 4 678.31 4.35 399 143 148 5 654.66 5.23 400 143 149 6 646.32 1.06 401 144 148 4 690.19 6.50 402 144 150 6 654.76 5.21 403 145 148 3 704.71 1.85 404 145 149 4 690.14 6.47 405 145 150 5 688.61 2.17 406 145 152 7 654.77 5.21 407 145 158 13 540.98 0.58 408 145 184 39 543.42 0.57 409 146 158 12 540.56 0.77 410 146 160 14 540.67 0.73 411 146 184 38 551.78 0.41 412 146 255 109 431.33 0.88 413 146 256 110 431.03 0.77 414 146 257 111 430.50 0.95 415 147 255 108 431.40 0.84 416 147 256 109 431.25 0.83 417 147 257 110 431.15 0.82 418 148 255 107 431.43 0.83 419 149 152 3 771.80 0.01 420 150 182 32 622.37 2.48 421 150 183 33 620.81 2.48 422 150 184 34 612.41 0.27 423 151 178 27 629.36 0.60 424 151 180 29 623.85 2.76 425 151 182 31 621.75 2.17 426 151 183 32 621.73 2.16 427 152 155 3 859.97 2.93 428 152 156 4 766.29 2.63 429 152 158 6 763.02 0.99 430 152 176 24 631.18 0.86 431 152 178 26 629.36 0.61 432 152 179 27 629.35 0.61 433 152 180 28 627.41 0.97 434 152 184 32 622.87 2.55 435 153 178 25 629.81 0.46 436 153 179 26 629.35 0.62 437 153 180 27 629.26 0.62 438 153 247 94 451.92 1.30 439 154 177 23 630.62 0.79 440 154 178 24 630.31 0.65 441 154 247 93 451.90 1.29 442 155 175 20 632.09 0.88 443 155 176 21 631.69 0.98 444 155 177 22 630.38 0.65 445 155 220 65 546.09 2.12 446 155 244 89 506.03 1.80 447 155 246 91 453.50 2.10 448 156 175 19 632.08 0.86 449 156 176 20 631.86 0.95 450 157 173 16 633.49 0.59 451 157 174 17 633.25 0.64 452 157 175 18 632.08 0.86 453 157 213 56 549.25 3.24 454 157 222 65 549.30 3.24 455 158 172 14 633.62 0.60 456 158 173 15 633.45 0.61 457 158 174 16 633.33 0.61 458 158 176 18 632.94 0.52 459 158 184 26 630.81 0.72 460 159 172 13 633.63 0.60 461 159 173 14 633.50 0.59 462 159 202 43 623.46 2.29 463 159 211 52 621.38 2.81 464 159 224 65 622.53 2.64 465 160 170 10 633.94 0.59 466 160 171 11 633.88 0.60 467 160 172 12 633.77 0.58 468 160 174 14 633.57 0.57 469 160 189 29 625.01 1.88 470 160 202 42 623.97 2.33 471 161 170 9 633.95 0.59 472 161 171 10 633.89 0.61 473 161 202 41 623.97 2.33 474 161 203 42 623.99 2.33 475 162 170 8 634.04 0.58 476 162 189 27 630.58 0.61 477 162 261 99 417.01 0.10 478 163 166 3 729.60 2.23 479 163 167 4 715.16 0.97 480 163 168 5 661.55 11.69 481 163 169 6 645.20 6.13 482 163 170 7 634.04 0.58 483 163 189 26 631.00 0.65 484 164 186 22 631.13 0.70 485 164 187 23 631.12 0.70 486 164 189 25 631.00 0.65 487 165 187 22 631.14 0.70 488 165 188 23 631.12 0.70 489 165 189 24 631.13 0.70 490 169 172 3 806.25 5.33 491 169 199 30 623.79 2.27 492 170 189 19 630.59 0.60 493 171 199 28 623.47 2.29 494 171 200 29 623.72 2.24 495 171 201 30 623.76 2.25 496 171 202 31 623.98 2.33 497 171 203 32 624.00 2.33 498 172 198 26 622.44 2.59 499 172 199 27 622.56 2.66 500 172 202 30 623.98 2.33 501 173 197 24 622.44 2.59 502 173 198 25 621.40 2.92 503 173 200 27 622.85 2.53 504 173 222 49 608.40 0.58 505 173 224 51 622.56 2.66 506 173 238 65 618.43 2.04 507 174 194 20 623.09 2.48 508 174 196 22 622.58 2.66 509 174 197 23 620.64 3.15 510 175 194 19 622.98 2.52 511 175 195 20 622.59 2.65 512 175 196 21 621.43 2.94 513 175 220 45 549.12 3.20 514 175 222 47 553.15 2.23 515 175 241 66 549.01 3.21 516 176 193 17 622.99 2.52 517 176 194 18 622.43 2.60 518 177 182 5 708.09 0.71 519 177 195 18 621.45 2.94 520 177 244 67 502.28 3.61 521 178 181 3 772.71 3.21 522 178 182 4 705.83 1.84 523 182 193 11 636.09 0.18 524 183 193 10 637.59 0.47 525 184 189 5 712.36 1.40 526 184 190 6 669.83 1.13 527 184 193 9 639.50 0.28 528 185 188 3 735.31 5.78 529 185 189 4 712.38 1.41 530 185 190 5 671.29 0.40 531 185 192 7 652.36 3.20 532 185 193 8 639.56 0.26 533 186 189 3 724.24 0.52 534 188 191 3 737.72 0.21 535 190 193 3 730.08 3.66 536 190 194 4 697.40 0.10 537 191 194 3 729.25 4.41 538 195 241 46 548.23 3.21 539 195 244 49 523.29 10.41 540 196 239 43 636.91 1.65 541 196 240 44 554.96 0.63 542 196 241 45 552.38 1.55 543 197 239 42 687.63 2.52 544 203 263 60 353.25 6.19 545 208 268 60 328.62 1.04 546 214 275 61 313.75 0.92 547 215 246 31 766.87 4.83 548 216 275 59 313.75 0.92 549 216 277 61 313.60 0.98 550 217 277 60 312.94 0.73 551 220 244 24 879.36 12.02 552 241 244 3 753.45 5.30 553 252 270 18 316.63 0.58 554 252 272 20 315.11 0.73 555 254 267 13 321.62 0.26 556 254 270 16 315.61 0.76 557 256 265 9 333.07 2.79 558 257 265 8 349.71 7.00 559 258 261 3 770.97 0.24 560 258 262 4 659.63 12.41 561 258 263 5 548.52 55.25 562 258 265 7 354.12 5.15