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 11 136 125 50.38 0.91 2 12 132 120 51.02 1.06 3 12 133 121 51.09 1.03 4 12 134 122 51.08 1.03 5 12 135 123 50.79 1.01 6 12 136 124 50.79 1.01 7 13 17 4 637.81 2.79 8 13 131 118 50.97 1.04 9 14 17 3 694.82 1.12 10 14 133 119 53.70 0.26 11 15 133 118 54.73 0.26 12 16 19 3 702.60 0.33 13 17 20 3 698.13 4.26 14 17 21 4 669.37 2.81 15 17 67 50 70.34 0.64 16 18 21 3 669.71 2.43 17 18 22 4 636.88 0.09 18 18 23 5 636.87 0.09 19 18 25 7 625.03 4.16 20 18 26 8 619.83 4.52 21 18 65 47 74.73 0.74 22 18 96 78 74.86 0.68 23 18 99 81 78.28 0.04 24 19 23 4 637.73 0.54 25 19 26 7 619.98 4.57 26 19 28 9 619.82 4.52 27 20 23 3 711.62 2.48 28 21 67 46 74.86 0.69 29 21 94 73 74.88 0.68 30 22 25 3 685.41 2.83 31 22 26 4 667.46 3.00 32 22 36 14 78.06 0.14 33 23 26 3 688.91 0.96 34 23 27 4 681.66 4.58 35 23 28 5 639.56 0.99 36 23 29 6 637.08 0.48 37 23 30 7 622.41 4.53 38 23 31 8 622.44 4.52 39 23 34 11 333.47 121.52 40 24 27 3 682.84 4.12 41 24 28 4 656.39 4.86 42 24 30 6 633.73 1.12 43 25 99 74 78.94 0.38 44 30 34 4 683.35 4.52 45 31 34 3 722.84 0.11 46 33 85 52 205.43 0.61 47 34 85 51 205.66 0.65 48 35 83 48 205.63 0.65 49 35 92 57 189.98 3.01 50 35 94 59 189.92 3.00 51 36 93 57 189.98 3.01 52 36 94 58 189.94 3.00 53 36 95 59 189.94 3.00 54 36 96 60 189.94 3.00 55 37 94 57 189.99 3.01 56 37 95 58 189.98 3.00 57 37 105 68 189.96 2.99 58 37 106 69 189.96 2.99 59 37 107 70 194.12 0.96 60 38 107 69 194.12 0.96 61 39 70 31 205.67 0.65 62 39 72 33 205.71 0.64 63 39 89 50 205.92 0.62 64 39 90 51 205.84 0.62 65 39 91 52 205.77 0.64 66 39 92 53 205.74 0.62 67 39 93 54 205.66 0.65 68 39 106 67 205.74 0.63 69 39 107 68 205.74 0.62 70 39 108 69 205.72 0.63 71 40 44 4 653.51 4.66 72 40 48 8 205.90 0.62 73 40 88 48 206.58 0.46 74 40 89 49 205.92 0.63 75 40 107 67 205.88 0.63 76 40 108 68 205.84 0.61 77 40 109 69 205.84 0.61 78 41 44 3 673.57 4.00 79 41 48 7 444.69 74.75 80 41 85 44 227.38 2.38 81 41 86 45 225.61 1.48 82 41 87 46 225.43 1.41 83 41 88 47 211.69 2.08 84 42 48 6 582.29 5.96 85 43 88 45 230.63 3.97 86 44 48 4 677.15 5.78 87 44 88 44 230.63 3.97 88 44 89 45 230.62 3.97 89 44 109 65 229.16 1.68 90 45 75 30 267.50 2.22 91 45 109 64 267.40 0.69 92 46 75 29 267.50 2.22 93 46 109 63 271.72 1.47 94 47 109 62 290.96 0.89 95 47 110 63 289.70 0.32 96 47 181 134 290.91 0.89 97 48 108 60 291.06 0.88 98 48 109 61 290.97 0.89 99 48 180 132 290.96 0.89 100 49 107 58 291.17 0.91 101 49 108 59 291.07 0.88 102 49 109 60 291.06 0.88 103 49 110 61 291.05 0.88 104 49 145 96 290.98 0.89 105 49 180 131 290.98 0.89 106 49 181 132 290.93 0.89 107 49 183 134 290.91 0.89 108 50 105 55 291.45 0.83 109 50 106 56 291.24 0.90 110 50 107 57 291.19 0.91 111 50 177 127 290.98 0.89 112 50 180 130 291.03 0.89 113 50 181 131 290.97 0.89 114 50 182 132 290.92 0.88 115 50 183 133 290.93 0.88 116 51 104 53 291.53 0.82 117 51 105 54 291.46 0.83 118 51 106 55 291.25 0.90 119 51 108 57 291.26 0.89 120 51 126 75 291.06 0.88 121 51 143 92 291.04 0.87 122 51 145 94 291.06 0.88 123 51 183 132 290.94 0.89 124 52 103 51 291.73 0.88 125 52 104 52 291.50 0.83 126 52 105 53 291.46 0.83 127 52 177 125 291.09 0.87 128 52 182 130 291.04 0.89 129 52 183 131 290.97 0.89 130 52 184 132 290.93 0.89 131 52 185 133 290.92 0.89 132 53 103 50 292.04 0.76 133 53 104 51 291.72 0.88 134 53 184 131 290.95 0.89 135 53 185 132 290.93 0.89 136 53 186 133 290.91 0.89 137 54 62 8 293.74 0.47 138 54 101 47 293.35 0.56 139 54 102 48 292.63 0.83 140 54 103 49 292.25 0.66 141 54 104 50 292.25 0.66 142 54 184 130 291.04 0.89 143 54 186 132 290.92 0.89 144 54 187 133 290.92 0.89 145 55 62 7 293.83 0.43 146 55 63 8 293.38 0.49 147 55 66 11 292.56 0.82 148 55 97 42 292.70 0.83 149 55 104 49 292.69 0.83 150 55 130 75 291.51 0.80 151 55 187 132 290.92 0.90 152 55 189 134 290.88 0.90 153 56 60 4 617.35 9.00 154 56 61 5 432.01 69.41 155 56 62 6 431.91 69.44 156 56 63 7 293.82 0.42 157 56 186 130 291.02 0.89 158 56 187 131 290.96 0.89 159 56 188 132 290.89 0.89 160 56 189 133 290.89 0.89 161 57 60 3 691.56 3.25 162 57 61 4 617.32 9.00 163 57 63 6 431.94 69.45 164 58 190 132 290.81 0.93 165 62 101 39 563.83 0.72 166 62 102 40 559.11 2.00 167 63 66 3 703.83 1.19 168 63 97 34 564.13 0.83 169 63 132 69 465.30 1.18 170 63 189 126 290.91 0.90 171 64 97 33 564.13 0.83 172 64 98 34 565.46 0.24 173 64 99 35 564.28 0.82 174 64 100 36 565.50 0.22 175 64 102 38 563.69 0.66 176 65 97 32 566.35 0.07 177 65 132 67 466.42 1.70 178 65 133 68 466.41 1.70 179 66 96 30 566.84 0.01 180 66 97 31 566.38 0.07 181 66 130 64 466.63 1.65 182 66 131 65 466.62 1.65 183 66 132 66 466.50 1.67 184 67 94 27 567.22 0.04 185 67 95 28 567.16 0.03 186 67 96 29 566.87 0.01 187 67 130 63 466.66 1.65 188 67 131 64 466.62 1.65 189 68 94 26 567.22 0.04 190 68 95 27 567.17 0.04 191 68 96 28 567.15 0.05 192 68 97 29 567.18 0.04 193 68 104 36 566.98 0.10 194 68 128 60 466.88 1.69 195 68 129 61 466.84 1.69 196 68 130 62 466.72 1.68 197 68 187 119 290.97 0.89 198 69 92 23 568.15 0.17 199 69 93 24 567.63 0.15 200 69 94 25 567.23 0.04 201 69 128 59 466.92 1.69 202 69 129 60 466.84 1.69 203 69 131 62 466.81 1.69 204 70 92 22 568.15 0.16 205 70 93 23 567.80 0.10 206 70 106 36 566.99 0.10 207 70 126 56 467.42 1.66 208 70 127 57 467.25 1.66 209 70 128 58 466.94 1.68 210 71 79 8 570.31 0.04 211 71 81 10 570.01 0.07 212 71 91 20 568.32 0.14 213 71 92 21 568.21 0.17 214 71 126 55 467.44 1.66 215 71 127 56 467.27 1.67 216 72 79 7 570.33 0.03 217 72 89 17 569.35 0.12 218 72 91 19 568.33 0.14 219 72 108 36 567.01 0.11 220 72 109 37 566.95 0.08 221 72 111 39 560.33 2.37 222 72 126 54 467.45 1.66 223 73 77 4 617.03 9.33 224 73 78 5 603.08 9.33 225 73 79 6 570.31 0.01 226 73 89 16 569.35 0.12 227 73 111 38 560.39 2.33 228 73 112 39 560.36 2.35 229 73 114 41 560.07 2.48 230 74 77 3 676.58 4.08 231 74 78 4 610.07 5.84 232 74 80 6 603.91 8.91 233 74 89 15 569.26 0.09 234 74 111 37 563.69 0.71 235 74 112 38 560.43 2.33 236 75 109 34 567.02 0.12 237 75 110 35 566.93 0.08 238 75 112 37 560.77 2.16 239 77 112 35 560.33 2.36 240 77 113 36 560.33 2.36 241 77 114 37 560.31 2.37 242 79 91 12 569.08 0.07 243 79 114 35 560.31 2.37 244 79 127 48 467.64 1.66 245 80 89 9 569.51 0.07 246 80 91 11 569.08 0.07 247 82 87 5 661.24 6.25 248 83 90 7 569.52 0.09 249 83 92 9 569.47 0.08 250 84 87 3 677.32 4.66 251 84 90 6 569.57 0.07 252 87 90 3 713.93 4.96 253 89 108 19 566.91 0.03 254 89 109 20 566.86 0.01 255 95 104 9 567.43 0.03 256 95 105 10 567.42 0.03 257 95 106 11 566.98 0.19 258 96 104 8 567.43 0.03 259 97 102 5 567.58 0.01 260 97 103 6 567.56 0.02 261 97 104 7 567.50 0.00 262 98 101 3 676.09 2.77 263 98 102 4 567.66 0.05 264 98 103 5 567.59 0.01 265 103 184 81 291.04 0.89 266 104 185 81 290.94 0.89 267 108 126 18 467.44 1.65 268 110 145 35 465.80 1.78 269 110 147 37 456.56 0.65 270 110 148 38 434.75 1.99 271 110 183 73 291.01 0.89 272 111 124 13 467.62 1.62 273 111 125 14 467.60 1.61 274 111 126 15 467.59 1.61 275 111 145 34 465.87 1.75 276 113 121 8 469.01 1.30 277 113 122 9 468.84 1.32 278 113 124 11 467.70 1.65 279 114 121 7 469.10 1.30 280 114 122 8 468.92 1.30 281 114 125 11 468.39 1.53 282 115 119 4 626.98 11.50 283 115 120 5 537.00 31.97 284 115 121 6 469.71 1.61 285 115 122 7 469.20 1.36 286 116 119 3 673.40 3.74 287 116 120 4 626.99 11.49 288 116 122 6 469.84 1.62 289 116 156 40 399.57 3.06 290 120 156 36 399.60 3.06 291 121 156 35 399.59 3.06 292 122 125 3 800.89 5.01 293 122 142 20 466.61 1.68 294 122 155 33 399.50 3.05 295 122 156 34 399.50 3.06 296 122 157 35 399.42 3.02 297 123 144 21 466.22 1.77 298 123 151 28 399.84 3.21 299 123 152 29 402.02 2.11 300 123 155 32 399.50 3.06 301 124 144 20 466.17 1.77 302 124 145 21 466.13 1.76 303 124 148 24 444.00 1.42 304 124 151 27 399.84 3.21 305 125 142 17 466.24 1.76 306 125 143 18 466.19 1.76 307 125 144 19 466.03 1.71 308 125 145 20 466.03 1.71 309 126 142 16 466.22 1.76 310 126 143 17 466.09 1.74 311 126 145 19 466.03 1.71 312 127 141 14 466.30 1.73 313 127 142 15 465.92 1.77 314 128 140 12 466.31 1.72 315 128 141 13 466.16 1.78 316 128 143 15 465.86 1.77 317 128 185 57 291.06 0.89 318 128 187 59 290.94 0.89 319 129 138 9 466.41 1.69 320 129 139 10 466.31 1.72 321 129 140 11 466.24 1.73 322 130 135 5 658.34 2.50 323 130 138 8 466.38 1.69 324 130 139 9 466.29 1.72 325 130 187 57 291.01 0.90 326 130 189 59 290.79 0.95 327 131 135 4 662.48 4.58 328 131 138 7 466.30 1.73 329 132 135 3 690.99 0.84 330 135 138 3 715.63 2.80 331 135 139 4 690.25 4.31 332 135 189 54 291.04 0.89 333 139 189 50 290.93 0.88 334 139 197 58 148.19 0.32 335 140 197 57 147.69 0.57 336 140 198 58 145.27 1.77 337 140 200 60 145.03 1.70 338 141 170 29 345.84 0.29 339 141 185 44 291.11 0.89 340 141 187 46 290.95 0.89 341 141 195 54 164.40 0.27 342 141 196 55 160.57 0.19 343 141 197 56 147.66 0.58 344 141 198 57 145.27 1.78 345 142 157 15 390.85 1.27 346 142 170 28 345.84 0.29 347 142 185 43 291.09 0.89 348 142 198 56 147.66 0.58 349 143 170 27 345.92 0.32 350 143 172 29 345.68 0.36 351 143 185 42 291.03 0.90 352 144 152 8 399.81 3.19 353 144 155 11 399.51 3.04 354 144 157 13 397.88 2.25 355 144 158 14 397.66 2.32 356 144 170 26 345.95 0.33 357 144 171 27 345.86 0.30 358 144 172 28 345.86 0.30 359 145 148 3 687.10 1.05 360 145 152 7 610.83 1.86 361 145 171 26 345.95 0.33 362 145 172 27 345.88 0.32 363 145 183 38 291.07 0.88 364 146 171 25 345.98 0.32 365 146 172 26 345.96 0.32 366 146 173 27 345.88 0.32 367 146 174 28 345.78 0.34 368 147 174 27 345.84 0.34 369 147 183 36 291.10 0.88 370 148 151 3 682.34 0.30 371 148 152 4 677.21 0.99 372 149 152 3 679.68 2.04 373 149 153 4 679.50 2.14 374 150 153 3 687.30 1.92 375 150 154 4 685.55 1.06 376 151 154 3 688.50 0.01 377 151 155 4 685.54 1.06 378 152 155 3 693.20 4.72 379 152 158 6 647.55 3.02 380 153 159 6 661.34 3.87 381 154 159 5 663.26 2.92 382 155 158 3 682.07 0.09 383 155 159 4 670.06 0.48 384 156 159 3 677.04 2.94 385 156 160 4 670.08 0.48 386 157 160 3 690.98 4.76 387 157 198 41 160.08 0.24 388 158 161 3 696.93 1.79 389 158 167 9 346.40 0.34 390 158 170 12 346.41 0.34 391 159 167 8 529.63 24.55 392 161 166 5 660.75 4.99 393 161 167 6 618.72 12.61 394 161 170 9 588.31 6.04 395 161 196 35 164.75 0.26 396 161 198 37 164.69 0.23 397 163 166 3 687.78 2.60 398 163 167 4 677.77 0.48 399 164 167 3 682.04 2.62 400 164 168 4 677.79 0.48 401 165 168 3 706.14 7.16 402 166 169 3 687.54 1.48 403 166 194 28 166.83 0.28 404 166 195 29 165.55 0.29 405 166 196 30 164.94 0.36 406 167 170 3 702.21 3.19 407 167 171 4 678.26 0.71 408 168 171 3 677.20 0.23 409 169 185 16 291.13 0.88 410 169 193 24 166.23 0.56 411 169 194 25 165.32 0.18 412 169 195 26 164.55 0.21 413 169 196 27 164.46 0.26 414 170 185 15 291.08 0.88 415 170 195 25 164.46 0.26 416 170 196 26 164.39 0.29 417 170 198 28 164.19 0.20 418 172 183 11 291.12 0.89 419 172 184 12 291.07 0.88 420 172 185 13 290.92 0.89 421 173 183 10 291.12 0.89 422 173 184 11 291.10 0.87 423 174 181 7 320.86 13.87 424 174 182 8 291.17 0.90 425 174 183 9 291.08 0.86 426 175 181 6 437.01 69.74 427 175 182 7 320.73 13.89 428 176 179 3 687.95 3.23 429 176 180 4 484.37 67.71 430 176 181 5 437.01 69.74 431 176 182 6 320.83 13.86 432 177 180 3 664.31 3.12 433 177 182 5 471.12 61.09 434 187 195 8 164.38 0.26 435 187 197 10 164.19 0.12 436 188 192 4 685.11 3.76 437 188 193 5 605.27 2.82 438 188 194 6 256.06 45.86 439 188 195 7 164.45 0.25 440 189 194 5 479.19 65.86 441 189 197 8 255.87 45.96 442 190 194 4 621.72 4.85 443 191 194 3 663.56 1.60