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 2 5 3 465.48 11.23 2 4 9 5 293.76 4.76 3 4 10 6 293.76 4.76 4 5 9 4 329.89 3.60 5 11 88 77 73.75 0.21 6 11 92 81 73.54 0.32 7 11 152 141 62.55 0.82 8 13 17 4 545.61 0.29 9 13 18 5 545.57 0.30 10 13 21 8 527.34 2.04 11 13 85 72 79.05 0.24 12 13 88 75 74.42 0.50 13 13 89 76 79.77 0.21 14 13 145 132 84.81 0.51 15 13 148 135 78.13 0.24 16 13 149 136 78.10 0.24 17 14 17 3 566.41 0.74 18 14 18 4 547.75 1.36 19 14 89 75 87.29 1.08 20 15 18 3 567.82 1.45 21 15 19 4 547.74 1.37 22 15 89 74 92.35 1.44 23 16 19 3 558.15 2.19 24 16 20 4 545.67 0.30 25 17 20 3 567.61 2.54 26 17 21 4 547.79 1.35 27 17 145 128 97.16 0.16 28 17 148 131 97.37 0.21 29 18 21 3 564.68 4.00 30 18 22 4 546.45 2.97 31 18 86 68 98.05 0.11 32 18 89 71 99.60 0.54 33 19 22 3 560.48 0.12 34 19 23 4 553.56 6.66 35 20 23 3 573.15 2.96 36 20 24 4 553.34 6.77 37 20 141 121 115.77 1.05 38 20 142 122 115.68 1.02 39 20 145 125 115.66 1.02 40 21 24 3 570.24 0.18 41 21 25 4 556.60 5.13 42 21 82 61 115.64 1.02 43 21 85 64 115.64 1.02 44 21 145 124 115.68 1.02 45 21 146 125 115.67 1.02 46 22 25 3 566.77 0.05 47 22 26 4 556.11 5.38 48 22 82 60 117.98 0.13 49 23 26 3 553.21 6.83 50 23 27 4 562.35 2.25 51 23 137 114 133.49 0.62 52 23 142 119 131.97 0.42 53 24 27 3 563.46 1.57 54 24 28 4 562.22 2.19 55 24 129 105 132.86 0.81 56 24 133 109 133.49 0.61 57 24 137 113 133.50 0.61 58 24 142 118 132.87 0.88 59 24 146 122 131.59 0.61 60 25 28 3 562.22 2.19 61 25 29 4 555.50 1.18 62 25 35 10 456.24 12.00 63 25 75 50 133.09 0.80 64 25 78 53 131.60 0.61 65 25 79 54 131.59 0.61 66 25 82 57 131.59 0.61 67 25 146 121 132.88 0.88 68 26 29 3 570.75 2.08 69 26 30 4 559.76 0.98 70 27 30 3 570.98 1.97 71 27 134 107 144.80 3.11 72 27 137 110 140.16 0.81 73 28 31 3 569.82 0.67 74 28 32 4 559.08 0.63 75 28 35 7 456.56 13.97 76 28 78 50 133.62 0.56 77 28 129 101 133.85 0.67 78 28 132 104 138.60 1.48 79 28 133 105 140.16 0.81 80 28 146 118 133.90 0.70 81 29 32 3 559.27 0.73 82 31 34 3 568.99 0.96 83 31 35 4 563.54 1.74 84 32 35 3 573.32 1.05 85 32 36 4 564.66 0.93 86 32 75 43 150.12 1.05 87 33 36 3 578.57 1.57 88 33 37 4 564.68 0.93 89 34 37 3 567.81 0.64 90 34 38 4 560.38 4.33 91 35 38 3 568.76 1.99 92 35 39 4 560.53 4.26 93 35 78 43 222.81 1.21 94 35 128 93 196.16 12.34 95 35 132 97 193.56 1.91 96 36 39 3 566.57 3.08 97 36 40 4 561.27 3.90 98 36 71 35 223.91 0.84 99 36 74 38 222.80 1.20 100 36 75 39 222.81 1.22 101 37 40 3 571.78 0.48 102 37 41 4 553.75 1.01 103 37 65 28 225.59 1.40 104 38 41 3 567.73 1.07 105 38 42 4 558.07 4.42 106 38 128 90 219.42 0.71 107 38 131 93 219.33 0.75 108 38 132 94 219.30 0.77 109 39 42 3 569.73 4.64 110 39 43 4 558.09 4.42 111 39 74 35 223.96 0.83 112 39 77 38 223.97 0.84 113 39 78 39 223.94 0.83 114 39 121 82 219.88 0.64 115 39 124 85 219.83 0.61 116 39 125 86 219.81 0.61 117 39 128 89 219.44 0.70 118 40 43 3 565.81 0.56 119 40 44 4 547.64 0.81 120 40 54 14 285.16 5.07 121 40 70 30 224.53 0.96 122 40 73 33 224.16 0.80 123 40 74 34 224.02 0.82 124 41 44 3 565.81 0.57 125 41 45 4 547.65 0.80 126 41 64 23 227.32 0.99 127 41 65 24 227.30 0.98 128 42 45 3 564.95 0.78 129 42 46 4 545.96 0.60 130 42 124 82 219.83 0.61 131 42 127 85 219.75 0.58 132 43 46 3 563.11 1.70 133 43 47 4 549.75 1.84 134 43 50 7 480.09 2.08 135 43 51 8 444.42 0.16 136 43 120 77 219.93 0.62 137 43 121 78 219.91 0.64 138 43 124 81 219.84 0.62 139 44 47 3 561.74 2.73 140 44 48 4 474.67 13.92 141 44 51 7 416.28 28.74 142 44 64 20 231.27 0.89 143 46 120 74 220.22 0.64 144 46 123 77 220.19 0.63 145 47 50 3 571.86 2.29 146 47 51 4 568.50 0.61 147 47 120 73 220.25 0.63 148 48 51 3 572.07 2.19 149 48 52 4 566.16 0.55 150 49 52 3 566.63 0.31 151 49 53 4 566.63 0.31 152 50 53 3 578.88 3.91 153 50 117 67 220.27 0.64 154 51 54 3 578.88 3.90 155 52 55 3 567.60 1.74 156 53 111 58 220.62 0.63 157 53 112 59 220.59 0.60 158 53 113 60 220.57 0.59 159 53 117 64 220.36 0.67 160 54 67 13 261.24 4.62 161 54 69 15 243.13 4.38 162 54 70 16 243.03 4.44 163 54 73 19 241.76 5.06 164 55 67 12 261.25 4.62 165 56 60 4 322.11 6.29 166 56 61 5 285.70 2.98 167 56 62 6 284.85 2.85 168 56 67 11 271.14 9.56 169 57 60 3 402.53 4.44 170 59 68 9 304.31 0.20 171 61 66 5 374.35 25.87 172 61 67 6 321.19 1.07 173 61 68 7 321.19 1.07 174 63 66 3 556.16 5.70 175 63 67 4 543.58 1.48 176 64 67 3 555.69 4.58 177 64 70 6 506.01 1.51 178 65 71 6 538.78 4.84 179 66 71 5 551.43 1.48 180 67 70 3 575.03 4.75 181 67 71 4 552.26 1.06 182 68 71 3 570.94 6.80 183 68 72 4 552.26 1.06 184 69 72 3 558.38 0.52 185 69 73 4 551.43 1.48 186 70 73 3 553.64 2.08 187 70 74 4 551.43 1.47 188 71 74 3 555.96 0.93 189 71 75 4 553.01 2.27 190 72 75 3 565.30 0.32 191 72 76 4 551.36 1.47 192 73 76 3 557.02 0.39 193 73 77 4 547.09 1.51 194 74 77 3 563.77 2.98 195 74 78 4 556.90 6.41 196 75 78 3 565.21 5.33 197 75 79 4 546.15 1.04 198 76 79 3 566.10 5.76 199 76 80 4 546.50 0.33 200 77 80 3 566.60 1.56 201 77 81 4 546.51 0.32 202 77 121 44 220.14 0.61 203 77 150 73 217.74 0.51 204 78 81 3 558.63 0.54 205 78 82 4 542.77 2.19 206 78 125 47 219.97 0.60 207 78 128 50 220.00 0.59 208 78 129 51 219.93 0.62 209 78 146 68 218.81 0.62 210 79 82 3 555.00 0.76 211 79 83 4 550.32 1.58 212 80 83 3 551.68 1.12 213 80 84 4 550.51 1.70 214 80 96 16 267.07 6.00 215 80 100 20 221.58 0.76 216 80 104 24 220.75 0.63 217 80 153 73 203.17 1.35 218 81 84 3 553.57 2.06 219 81 85 4 552.40 2.65 220 81 125 44 220.16 0.60 221 81 146 65 218.82 0.62 222 81 149 68 218.15 0.33 223 81 150 69 217.74 0.51 224 81 153 72 204.62 0.14 225 82 85 3 568.52 5.42 226 82 86 4 550.49 1.72 227 82 146 64 218.83 0.62 228 83 86 3 552.96 2.37 229 83 87 4 550.46 1.73 230 84 87 3 557.29 0.10 231 84 88 4 550.42 1.72 232 84 94 10 313.58 2.52 233 84 149 65 218.30 0.36 234 84 153 69 216.95 0.41 235 85 88 3 563.01 0.96 236 85 89 4 550.41 1.72 237 85 149 64 218.30 0.36 238 86 89 3 568.63 5.51 239 86 90 4 555.72 0.94 240 87 90 3 555.73 0.94 241 87 91 4 517.26 0.48 242 87 92 5 507.75 4.25 243 87 93 6 389.07 11.31 244 87 94 7 321.62 1.44 245 87 95 8 321.57 1.43 246 87 96 9 321.57 1.43 247 88 92 4 450.78 22.09 248 88 93 5 358.31 19.75 249 88 94 6 338.39 9.79 250 88 148 60 219.00 0.56 251 88 149 61 218.97 0.56 252 88 152 64 218.32 0.27 253 91 95 4 547.98 2.08 254 94 152 58 218.15 0.32 255 94 153 59 218.12 0.33 256 94 156 62 207.50 0.86 257 96 100 4 552.58 1.94 258 96 101 5 533.07 6.04 259 96 153 57 218.11 0.33 260 97 100 3 561.82 0.29 261 97 101 4 555.09 0.69 262 98 101 3 563.71 0.65 263 98 102 4 555.10 0.69 264 99 102 3 563.74 0.64 265 99 103 4 559.47 1.50 266 100 103 3 559.82 1.32 267 100 104 4 559.47 1.51 268 101 104 3 567.48 2.50 269 101 105 4 558.41 2.02 270 101 156 55 203.12 1.35 271 101 157 56 193.78 0.78 272 101 160 59 192.03 0.60 273 102 105 3 561.92 0.29 274 102 106 4 558.40 2.02 275 102 160 58 192.38 0.41 276 103 106 3 563.89 1.27 277 103 107 4 554.59 0.11 278 104 107 3 560.40 3.02 279 104 108 4 554.77 0.00 280 104 157 53 192.85 0.46 281 105 108 3 568.71 0.28 282 105 109 4 551.21 1.47 283 105 157 52 192.86 0.46 284 105 160 55 188.90 0.09 285 105 161 56 184.42 1.11 286 106 109 3 565.75 0.33 287 106 110 4 549.14 2.49 288 107 110 3 563.85 1.28 289 107 111 4 549.11 2.51 290 108 111 3 556.88 0.71 291 108 112 4 542.38 0.83 292 108 113 5 457.05 12.04 293 108 118 10 416.20 8.38 294 108 157 49 192.80 0.43 295 108 161 53 183.05 1.18 296 109 112 3 557.31 0.49 297 109 161 52 182.19 1.45 298 112 117 5 546.37 2.43 299 113 117 4 546.36 2.43 300 113 118 5 546.36 2.43 301 113 161 48 182.88 1.10 302 114 117 3 568.28 3.50 303 114 118 4 553.18 0.98 304 115 118 3 568.35 3.46 305 115 119 4 552.65 1.26 306 115 158 43 192.19 0.28 307 116 119 3 565.47 4.54 308 116 120 4 552.65 1.26 309 117 120 3 568.50 3.02 310 117 121 4 552.66 1.26 311 118 121 3 558.99 1.91 312 118 122 4 543.89 1.69 313 118 150 32 217.74 0.51 314 118 154 36 198.75 0.83 315 118 157 39 192.71 0.38 316 118 158 40 191.90 0.74 317 118 161 43 182.90 1.10 318 119 122 3 548.34 0.53 319 119 123 4 544.41 1.43 320 120 123 3 549.84 1.23 321 120 124 4 547.33 0.03 322 121 124 3 561.58 7.04 323 121 125 4 545.31 3.14 324 121 150 29 217.74 0.52 325 122 125 3 552.02 0.22 326 122 126 4 545.32 3.14 327 122 147 25 218.16 0.44 328 122 150 28 217.70 0.52 329 122 151 29 217.68 0.52 330 123 126 3 570.09 2.19 331 123 127 4 545.34 3.14 332 124 127 3 556.95 3.20 333 124 128 4 549.81 0.90 334 125 128 3 572.41 2.12 335 125 129 4 556.09 3.63 336 125 146 21 218.49 0.58 337 125 150 25 217.71 0.52 338 126 129 3 562.51 2.83 339 126 130 4 556.08 3.63 340 126 138 12 317.87 4.38 341 126 143 17 218.50 0.57 342 126 146 20 218.50 0.57 343 126 147 21 218.16 0.45 344 127 130 3 566.94 1.80 345 127 131 4 549.99 0.29 346 128 131 3 566.94 1.80 347 128 132 4 548.78 0.33 348 129 132 3 567.79 3.34 349 129 133 4 548.78 0.33 350 129 138 9 331.84 2.09 351 129 146 17 254.48 1.82 352 130 133 3 575.14 3.17 353 130 138 8 305.62 5.53 354 133 137 4 545.51 1.86 355 133 138 5 451.13 12.67 356 133 142 9 383.80 2.44 357 134 137 3 570.04 1.26 358 134 138 4 545.52 1.86 359 135 138 3 574.01 2.64 360 137 142 5 549.22 0.82 361 138 142 4 551.54 1.56 362 138 143 5 549.65 0.60 363 139 142 3 563.19 0.06 364 139 143 4 551.56 1.54 365 140 143 3 557.22 2.93 366 140 144 4 552.20 1.38 367 141 144 3 561.39 0.86 368 141 145 4 553.65 0.67 369 142 145 3 554.77 1.23 370 142 146 4 555.53 1.61 371 143 146 3 570.29 2.41 372 143 147 4 562.13 1.68 373 144 147 3 562.14 1.68 374 144 148 4 562.13 1.68 375 145 148 3 581.63 2.85 376 145 149 4 562.13 1.69 377 146 149 3 569.32 1.90 378 146 150 4 562.11 1.69 379 147 150 3 562.11 1.68 380 147 151 4 553.81 1.33 381 148 151 3 563.06 5.03 382 148 152 4 553.80 1.33 383 149 152 3 580.18 3.58 384 149 153 4 554.45 1.02 385 150 153 3 575.29 1.14 386 150 154 4 554.66 1.12 387 151 154 3 561.19 2.12 388 151 155 4 554.72 1.11 389 152 155 3 557.43 2.35 390 152 156 4 554.84 1.05 391 153 156 3 561.24 2.15 392 153 157 4 554.84 1.05 393 154 157 3 561.21 0.78 394 154 158 4 554.40 1.21 395 155 158 3 558.33 2.75 396 155 159 4 554.88 0.96 397 156 159 3 564.56 0.36 398 156 160 4 564.78 0.48 399 157 160 3 572.38 1.21 400 157 161 4 564.78 0.48 401 158 161 3 561.25 2.24 402 158 162 4 561.25 2.24 403 159 162 3 579.48 1.75