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 3 6 3 535.70 4.34 2 3 7 4 525.25 0.42 3 3 109 106 43.18 1.39 4 3 141 138 47.94 0.96 5 4 7 3 526.56 0.24 6 4 8 4 525.22 0.43 7 4 32 28 53.50 0.88 8 4 144 140 51.05 0.62 9 5 8 3 525.33 0.49 10 5 9 4 520.89 1.74 11 6 9 3 525.45 0.27 12 6 10 4 515.70 4.34 13 6 109 103 53.86 0.74 14 6 110 104 53.77 0.78 15 6 113 107 53.66 0.80 16 7 10 3 527.07 1.34 17 7 11 4 522.13 1.12 18 7 32 25 55.64 0.46 19 7 63 56 53.76 0.79 20 7 144 137 53.76 0.79 21 7 147 140 53.48 0.89 22 7 148 141 53.46 0.89 23 8 11 3 533.93 2.09 24 8 12 4 522.13 1.12 25 8 28 20 55.68 0.48 26 8 29 21 55.78 0.43 27 8 32 24 55.71 0.46 28 9 12 3 528.56 0.59 29 9 13 4 525.43 0.56 30 10 13 3 526.73 0.09 31 10 14 4 528.54 0.59 32 10 113 103 54.08 0.82 33 10 148 138 53.68 0.98 34 10 151 141 53.29 0.84 35 10 152 142 52.68 0.72 36 11 14 3 536.35 3.27 37 11 15 4 527.30 0.29 38 11 28 17 55.86 0.40 39 11 60 49 53.95 0.88 40 11 63 52 54.09 0.81 41 11 147 136 54.06 0.82 42 11 151 140 53.67 0.98 43 12 15 3 526.90 0.49 44 12 21 9 79.61 1.96 45 12 24 12 55.90 0.41 46 12 25 13 55.93 0.42 47 12 28 16 55.88 0.40 48 13 155 142 38.81 0.32 49 14 56 42 53.94 0.89 50 14 59 45 54.04 0.84 51 14 151 137 53.97 0.86 52 14 154 140 51.21 0.68 53 14 155 141 44.41 0.56 54 15 21 6 376.26 42.45 55 15 24 9 86.09 0.97 56 15 56 41 54.00 0.85 57 16 21 5 509.07 2.00 58 17 21 4 515.76 1.26 59 18 21 3 531.14 0.58 60 18 22 4 521.90 0.86 61 19 22 3 529.90 0.04 62 19 23 4 521.68 4.15 63 20 23 3 526.01 1.98 64 20 24 4 521.67 4.15 65 20 45 25 78.12 1.72 66 20 49 29 65.06 1.45 67 20 50 30 65.17 1.40 68 20 52 32 63.33 0.60 69 21 24 3 520.24 0.75 70 21 25 4 520.59 0.74 71 22 25 3 526.59 0.21 72 22 26 4 520.70 0.74 73 23 26 3 529.82 2.23 74 23 27 4 520.70 0.73 75 23 45 22 78.22 1.76 76 24 27 3 524.20 1.01 77 24 28 4 520.71 0.73 78 24 45 21 78.27 1.78 79 24 52 28 66.78 0.34 80 24 60 36 66.13 0.74 81 25 28 3 537.09 0.30 82 25 29 4 516.76 1.24 83 26 29 3 525.42 0.57 84 26 30 4 518.63 2.18 85 27 30 3 523.75 0.80 86 27 31 4 518.48 2.26 87 27 42 15 80.34 0.76 88 27 45 18 80.35 0.74 89 28 31 3 523.53 0.58 90 28 32 4 511.68 1.14 91 28 60 32 77.76 1.97 92 28 63 35 77.89 1.94 93 28 64 36 78.41 1.70 94 29 32 3 530.90 3.70 95 29 33 4 517.00 1.52 96 30 33 3 523.26 0.12 97 30 34 4 518.49 2.26 98 30 35 5 352.16 38.11 99 31 34 3 530.89 3.71 100 31 37 6 86.44 0.03 101 31 42 11 86.18 0.16 102 31 64 33 80.29 0.78 103 31 67 36 80.31 0.79 104 31 68 37 80.33 0.79 105 32 63 31 80.30 0.78 106 32 67 35 80.31 0.79 107 32 144 112 79.23 1.29 108 36 68 32 164.08 2.44 109 37 42 5 519.11 2.22 110 37 68 31 166.78 1.32 111 37 70 33 174.59 0.79 112 38 41 3 523.64 0.24 113 38 42 4 519.75 1.99 114 39 42 3 524.22 0.24 115 39 43 4 519.66 1.95 116 39 64 25 174.51 0.78 117 39 65 26 174.56 0.77 118 39 68 29 176.34 0.24 119 39 70 31 178.33 0.05 120 39 71 32 178.92 0.01 121 39 74 35 180.50 0.39 122 40 43 3 527.20 0.86 123 40 44 4 526.13 1.29 124 40 74 34 180.52 0.38 125 40 77 37 180.50 0.39 126 41 44 3 532.45 2.78 127 41 45 4 524.73 1.99 128 42 45 3 534.94 2.57 129 42 46 4 520.77 3.97 130 42 64 22 180.72 0.28 131 43 46 3 524.71 3.02 132 43 47 4 513.84 0.50 133 43 61 18 180.75 0.29 134 43 65 22 180.83 0.26 135 43 77 34 181.25 0.27 136 43 79 36 181.06 0.35 137 43 80 37 181.02 0.34 138 44 47 3 522.75 0.99 139 44 48 4 513.35 0.28 140 45 48 3 531.05 5.17 141 45 49 4 514.26 3.22 142 46 49 3 534.52 1.51 143 46 52 6 371.33 29.16 144 46 57 11 181.22 0.23 145 46 60 14 181.22 0.24 146 46 61 15 181.25 0.24 147 46 64 18 181.27 0.24 148 46 79 33 181.35 0.24 149 47 57 10 181.25 0.24 150 47 79 32 181.30 0.24 151 49 52 3 546.50 3.77 152 49 57 8 206.53 9.56 153 52 56 4 505.86 0.80 154 52 57 5 500.25 2.04 155 52 60 8 474.45 3.82 156 53 56 3 527.60 7.81 157 53 57 4 505.88 0.78 158 54 57 3 537.54 2.84 159 54 58 4 518.94 7.22 160 54 83 29 210.26 2.45 161 55 58 3 538.31 2.46 162 55 59 4 523.11 5.13 163 55 83 28 210.34 2.44 164 55 84 29 210.31 2.46 165 55 125 70 210.11 2.50 166 55 154 99 194.77 2.67 167 56 59 3 528.04 2.68 168 56 60 4 518.94 7.22 169 57 60 3 537.70 2.15 170 57 61 4 508.24 1.92 171 57 79 22 219.58 0.86 172 58 61 3 530.24 5.88 173 58 62 4 510.56 3.10 174 58 80 22 219.34 0.92 175 58 83 25 219.10 0.88 176 58 84 26 218.99 0.88 177 59 62 3 532.09 4.96 178 59 63 4 518.73 0.98 179 59 84 25 219.32 0.92 180 59 128 69 219.28 0.94 181 59 147 88 218.68 0.90 182 59 150 91 218.48 0.80 183 59 151 92 218.67 0.91 184 59 154 95 211.14 1.75 185 60 63 3 524.91 2.12 186 60 64 4 514.81 1.00 187 61 64 3 524.91 2.12 188 61 65 4 511.48 2.68 189 61 80 19 219.96 0.94 190 62 65 3 528.81 5.16 191 62 66 4 511.48 2.68 192 62 80 18 220.03 0.94 193 62 84 22 219.99 0.95 194 62 128 66 219.93 0.94 195 62 131 69 220.03 0.94 196 62 132 70 220.03 0.94 197 62 135 73 220.16 0.99 198 62 143 81 220.06 0.97 199 62 147 85 219.80 0.95 200 63 66 3 523.79 2.19 201 63 67 4 512.07 2.98 202 63 144 81 219.91 0.95 203 63 147 84 219.91 0.95 204 64 67 3 531.23 1.18 205 64 68 4 512.07 2.97 206 65 132 67 220.25 0.98 207 65 135 70 220.28 0.97 208 66 69 3 540.52 0.71 209 66 135 69 220.28 0.97 210 66 140 74 220.24 0.95 211 66 143 77 220.21 0.96 212 66 144 78 220.19 0.95 213 67 144 77 220.24 0.95 214 71 74 3 492.91 4.76 215 76 81 5 512.64 1.34 216 76 132 56 223.12 0.74 217 76 133 57 223.28 0.69 218 77 80 3 526.60 1.69 219 77 81 4 520.76 1.24 220 77 132 55 223.45 0.60 221 78 81 3 536.15 1.52 222 78 82 4 519.69 1.77 223 79 82 3 542.40 0.26 224 79 83 4 519.78 1.79 225 80 83 3 537.51 2.20 226 80 84 4 519.82 1.79 227 80 132 52 224.28 0.47 228 81 84 3 534.82 0.80 229 81 85 4 519.79 1.79 230 81 132 51 224.31 0.45 231 81 133 52 224.34 0.45 232 82 85 3 528.30 2.46 233 82 86 4 519.78 1.79 234 82 87 5 486.94 4.24 235 83 86 3 528.29 2.46 236 84 125 41 223.90 0.52 237 84 126 42 223.99 0.50 238 84 128 44 223.99 0.50 239 84 129 45 224.00 0.51 240 84 132 48 224.33 0.46 241 85 88 3 571.94 0.49 242 85 129 44 224.00 0.51 243 89 92 3 551.74 1.16 244 89 93 4 517.71 4.66 245 91 94 3 527.91 0.45 246 91 95 4 512.02 2.87 247 92 95 3 524.16 4.51 248 92 96 4 510.63 3.58 249 92 120 28 313.73 2.21 250 92 122 30 313.73 2.21 251 92 123 31 313.62 2.17 252 93 96 3 519.50 0.85 253 93 97 4 526.94 1.50 254 93 126 33 331.50 0.48 255 93 130 37 342.38 0.16 256 94 97 3 537.94 2.77 257 94 98 4 530.46 0.98 258 95 98 3 530.92 0.75 259 95 99 4 519.69 0.71 260 95 119 24 342.01 0.03 261 95 123 28 342.17 0.06 262 96 99 3 528.52 0.01 263 96 100 4 519.71 0.70 264 96 123 27 342.21 0.04 265 96 126 30 342.23 0.05 266 96 127 31 342.20 0.04 267 96 130 34 351.83 2.19 268 97 100 3 520.95 0.07 269 97 101 4 519.72 0.70 270 97 130 33 352.01 2.23 271 98 101 3 521.14 0.02 272 98 102 4 521.14 0.02 273 99 102 3 519.09 1.05 274 99 103 4 515.67 0.70 275 99 116 17 352.02 2.22 276 99 119 20 352.00 2.22 277 99 124 25 352.04 2.21 278 99 127 28 352.20 2.22 279 99 146 47 352.19 2.21 280 100 103 3 534.17 0.26 281 100 104 4 516.08 0.51 282 100 127 27 354.39 3.21 283 100 130 30 357.47 3.00 284 100 131 31 357.48 3.00 285 100 137 37 377.93 0.14 286 101 104 3 531.90 0.24 287 101 105 4 525.11 3.64 288 102 105 3 530.79 1.05 289 102 106 4 524.58 2.21 290 102 115 13 358.78 3.19 291 102 119 17 358.78 3.19 292 103 106 3 520.24 1.82 293 103 112 9 359.11 3.03 294 103 115 12 359.13 3.02 295 103 116 13 359.12 3.03 296 103 127 24 359.12 3.02 297 103 138 35 385.35 2.19 298 103 142 39 365.18 6.28 299 103 146 43 358.79 3.20 300 104 138 34 384.24 2.77 301 106 111 5 427.56 3.75 302 106 112 6 403.33 0.69 303 106 115 9 403.38 0.68 304 106 142 36 416.52 0.93 305 107 139 32 418.40 0.90 306 107 141 34 418.47 0.95 307 107 142 35 418.38 0.96 308 108 111 3 539.10 2.94 309 108 112 4 521.23 5.99 310 108 141 33 418.53 0.96 311 108 142 34 418.46 0.93 312 109 112 3 531.58 0.82 313 109 113 4 521.25 5.98 314 109 141 32 418.55 0.96 315 109 144 35 418.51 0.96 316 109 145 36 418.44 0.94 317 109 148 39 418.51 0.96 318 110 113 3 522.56 5.16 319 110 114 4 514.89 0.60 320 111 114 3 538.92 3.02 321 111 115 4 534.29 0.71 322 112 115 3 532.82 1.46 323 112 116 4 520.50 2.19 324 112 142 30 419.39 0.75 325 112 145 33 419.39 0.76 326 113 116 3 534.28 0.71 327 113 117 4 524.30 4.47 328 113 145 32 419.41 0.76 329 113 148 35 419.39 0.75 330 113 149 36 419.35 0.78 331 113 152 39 419.41 0.76 332 114 117 3 534.72 0.47 333 115 118 3 538.21 0.01 334 115 119 4 536.95 0.64 335 116 119 3 538.52 0.15 336 116 124 8 419.76 0.81 337 116 146 30 419.77 0.81 338 116 149 33 419.75 0.80 339 117 149 32 419.76 0.81 340 117 152 35 419.76 0.81 341 117 153 36 419.76 0.81 342 119 123 4 509.45 3.80 343 119 124 5 500.10 0.01 344 119 153 34 419.81 0.78 345 120 123 3 530.86 0.71 346 120 124 4 507.09 2.61 347 121 124 3 519.65 1.30 348 121 125 4 515.14 1.43 349 121 153 32 419.84 0.78 350 121 154 33 419.81 0.78 351 122 125 3 519.66 1.30 352 122 126 4 519.65 1.30 353 123 126 3 518.01 2.12 354 123 127 4 525.14 3.50 355 124 127 3 525.15 3.50 356 124 128 4 525.18 3.48 357 124 146 22 420.00 0.77 358 124 149 25 419.92 0.79 359 124 150 26 419.87 0.79 360 124 153 29 419.89 0.80 361 125 128 3 525.19 3.48 362 125 129 4 525.19 3.48 363 125 150 25 419.97 0.77 364 126 129 3 525.29 3.42 365 126 130 4 525.29 3.42 366 127 130 3 519.33 0.44 367 127 131 4 515.66 1.47 368 127 146 19 420.06 0.77 369 128 131 3 519.62 3.44 370 128 132 4 515.66 1.47 371 128 146 18 420.09 0.76 372 128 147 19 420.06 0.76 373 128 150 22 420.01 0.77 374 129 132 3 523.63 0.96 375 129 133 4 515.67 1.47 376 130 133 3 532.63 0.27 377 130 134 4 520.17 0.78 378 131 134 3 522.99 0.63 379 131 135 4 498.99 0.38 380 131 138 7 420.56 0.73 381 131 146 15 420.28 0.78 382 132 135 3 515.67 1.48 383 134 137 3 528.67 0.60 384 135 138 3 561.41 0.27 385 135 143 8 420.47 0.78 386 138 142 4 496.74 1.16 387 138 143 5 493.32 2.83 388 139 142 3 523.66 0.10 389 139 143 4 513.50 1.84 390 140 143 3 527.76 1.95 391 140 144 4 513.49 1.84 392 141 144 3 531.19 0.24 393 141 145 4 513.38 1.79 394 142 145 3 525.60 3.04 395 142 146 4 514.68 2.44 396 143 146 3 526.35 3.35 397 143 147 4 514.67 2.46 398 144 147 3 521.28 0.82 399 144 148 4 510.87 4.36 400 145 148 3 528.77 0.26 401 145 149 4 513.49 3.05 402 146 149 3 517.60 0.99 403 146 150 4 510.87 4.36 404 147 150 3 527.79 2.95 405 147 151 4 510.79 4.33 406 148 151 3 510.79 4.33 407 148 152 4 510.25 4.56 408 149 152 3 513.63 6.25 409 149 153 4 510.19 4.53 410 150 153 3 530.88 1.50 411 150 154 4 517.01 3.97 412 151 154 3 524.62 0.77 413 151 155 4 517.03 3.98 414 152 155 3 534.88 0.95 415 152 156 4 519.80 3.10 416 153 156 3 530.08 2.46 417 153 157 4 525.49 0.26 418 154 157 3 526.65 0.84 419 154 158 4 526.65 0.84 420 155 158 3 530.11 2.05