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 7 5 487.79 9.46 2 2 10 8 471.19 1.38 3 2 130 128 48.04 0.44 4 2 133 131 30.77 0.18 5 2 134 132 29.98 0.19 6 2 137 135 30.99 0.70 7 3 6 3 520.54 1.36 8 3 7 4 516.47 3.40 9 4 7 3 520.52 1.35 10 4 8 4 507.74 0.97 11 4 79 75 56.56 2.00 12 5 8 3 527.21 1.99 13 5 9 4 514.45 2.23 14 6 9 3 526.16 3.63 15 6 10 4 513.08 2.91 16 6 130 124 71.81 0.70 17 6 133 127 71.84 0.72 18 7 10 3 509.51 0.10 19 7 11 4 503.65 3.10 20 7 76 69 71.89 0.74 21 7 79 72 71.86 0.72 22 7 80 73 71.92 0.73 23 7 134 127 71.88 0.71 24 7 137 130 71.91 0.72 25 8 11 3 522.74 2.56 26 8 12 4 516.38 0.61 27 9 12 3 538.53 5.34 28 9 13 4 516.39 0.61 29 9 126 117 84.79 0.42 30 9 127 118 84.67 0.46 31 9 130 121 84.63 0.45 32 10 13 3 535.32 2.04 33 10 14 4 514.32 1.66 34 10 76 66 84.66 0.43 35 10 130 120 84.67 0.45 36 10 131 121 84.62 0.45 37 10 134 124 84.62 0.45 38 11 14 3 531.86 3.77 39 11 15 4 514.44 1.59 40 11 76 65 84.77 0.40 41 11 77 66 84.78 0.41 42 11 79 68 84.80 0.41 43 12 15 3 535.26 2.08 44 12 16 4 529.31 0.90 45 13 16 3 530.40 0.37 46 13 17 4 524.87 3.12 47 13 115 102 88.94 0.84 48 13 119 106 89.36 0.88 49 13 122 109 89.23 0.85 50 13 123 110 88.75 1.09 51 13 131 118 88.36 1.12 52 14 17 3 524.88 3.12 53 14 18 4 524.87 3.12 54 14 69 55 137.23 23.16 55 14 72 58 88.48 1.07 56 14 73 59 88.36 1.12 57 14 76 62 88.36 1.13 58 14 77 63 88.36 1.12 59 15 18 3 523.36 2.37 60 15 19 4 516.66 0.07 61 16 19 3 517.14 0.18 62 16 24 8 455.00 5.04 63 16 119 103 104.72 0.78 64 16 122 106 99.53 1.76 65 17 20 3 535.18 1.27 66 17 21 4 491.20 3.44 67 17 24 7 449.84 2.47 68 17 69 52 187.70 3.12 69 17 115 98 99.47 1.77 70 18 21 3 517.70 0.46 71 18 77 59 97.82 0.97 72 20 23 3 519.82 0.86 73 20 24 4 515.66 1.22 74 20 118 98 152.49 5.41 75 21 24 3 521.12 0.82 76 21 25 4 515.66 1.22 77 21 66 45 188.49 3.12 78 21 69 48 188.35 3.19 79 22 25 3 515.69 1.22 80 22 26 4 515.66 1.22 81 22 62 40 189.49 3.55 82 22 66 44 188.59 3.17 83 23 26 3 523.62 3.98 84 23 27 4 515.67 1.24 85 23 118 95 167.75 0.42 86 24 27 3 533.04 0.73 87 24 28 4 515.65 1.24 88 24 69 45 188.62 3.15 89 24 114 90 167.47 0.11 90 24 115 91 167.46 0.12 91 24 118 94 168.10 0.59 92 24 119 95 168.10 0.58 93 25 28 3 519.75 0.80 94 25 29 4 514.32 1.85 95 25 65 40 188.64 3.15 96 25 69 44 188.58 3.18 97 26 29 3 524.05 2.95 98 26 30 4 513.03 2.48 99 26 55 29 222.52 4.69 100 26 56 30 222.44 4.66 101 26 58 32 221.91 4.90 102 26 62 36 190.53 3.96 103 27 30 3 517.13 0.53 104 27 31 4 507.98 1.17 105 27 114 87 169.32 1.03 106 27 118 91 169.23 1.05 107 28 31 3 517.13 0.53 108 28 32 4 510.09 0.11 109 28 69 41 189.47 3.56 110 28 107 79 170.13 0.85 111 28 110 82 169.96 0.87 112 28 111 83 169.94 0.86 113 28 114 86 169.35 1.05 114 29 32 3 522.66 0.42 115 29 33 4 503.20 1.20 116 29 61 32 207.94 0.35 117 29 64 35 192.80 4.10 118 29 65 36 190.56 3.96 119 29 107 78 170.31 0.94 120 30 33 3 519.57 0.39 121 30 34 4 509.43 0.52 122 30 52 22 231.71 0.46 123 30 55 25 231.33 0.37 124 30 56 26 231.37 0.39 125 31 34 3 520.98 5.25 126 31 35 4 509.44 0.52 127 31 110 79 169.96 0.87 128 31 113 82 169.74 0.88 129 32 35 3 524.97 3.26 130 32 36 4 509.43 0.53 131 32 39 7 385.63 8.33 132 32 106 74 170.44 0.98 133 32 107 75 170.33 0.93 134 32 110 78 169.97 0.87 135 33 36 3 528.67 2.02 136 33 37 4 487.29 10.54 137 33 39 6 385.64 8.32 138 33 40 7 356.20 3.00 139 33 43 10 314.18 6.88 140 33 46 13 262.25 2.77 141 33 55 22 232.11 0.42 142 33 61 28 231.80 0.53 143 34 37 3 525.58 3.99 144 34 52 18 232.61 0.15 145 34 55 21 232.13 0.42 146 36 39 3 526.00 4.74 147 36 106 70 170.55 0.97 148 37 40 3 527.73 3.95 149 37 41 4 520.39 6.15 150 38 41 3 528.84 1.92 151 38 103 65 170.75 0.97 152 38 106 68 170.73 0.97 153 39 42 3 526.47 3.10 154 39 43 4 526.47 3.11 155 39 103 64 170.71 0.97 156 39 106 67 170.64 0.99 157 40 43 3 525.51 1.96 158 40 46 6 313.62 0.34 159 40 47 7 284.98 2.30 160 40 49 9 275.42 0.69 161 40 55 15 242.62 1.81 162 41 47 6 296.26 9.00 163 42 97 55 171.19 1.10 164 42 98 56 171.19 1.10 165 42 99 57 171.10 1.12 166 42 100 58 171.15 1.09 167 42 103 61 170.81 0.99 168 43 46 3 525.47 5.13 169 43 47 4 494.88 4.95 170 43 64 21 233.81 1.39 171 44 47 3 524.38 1.55 172 45 48 3 592.76 1.68 173 45 60 15 234.38 1.13 174 45 64 19 234.37 1.12 175 46 49 3 537.79 0.70 176 46 60 14 234.39 1.13 177 46 61 15 234.35 1.13 178 46 64 18 234.36 1.14 179 47 50 3 627.83 1.95 180 49 54 5 454.00 8.54 181 49 55 6 390.28 19.79 182 49 58 9 284.21 3.35 183 49 61 12 259.67 3.46 184 50 54 4 500.34 2.46 185 51 54 3 517.47 6.09 186 51 55 4 500.49 2.39 187 52 55 3 519.62 4.79 188 52 56 4 500.36 2.46 189 53 56 3 517.47 6.10 190 53 57 4 500.36 2.46 191 54 57 3 503.53 4.04 192 54 58 4 500.32 2.44 193 55 58 3 528.00 4.10 194 55 61 6 400.79 1.70 195 58 61 3 521.15 2.21 196 58 62 4 513.66 5.23 197 59 62 3 516.24 3.75 198 59 63 4 502.95 2.59 199 60 63 3 507.90 4.12 200 60 64 4 502.96 2.58 201 61 64 3 519.97 1.91 202 61 65 4 515.60 4.10 203 62 65 3 519.98 1.92 204 62 66 4 515.60 4.10 205 63 66 3 520.45 1.69 206 63 67 4 515.60 4.10 207 64 67 3 510.31 1.46 208 64 68 4 507.84 2.71 209 65 68 3 520.40 3.56 210 65 69 4 509.17 2.05 211 66 69 3 526.49 3.39 212 66 70 4 509.65 1.81 213 67 70 3 526.13 3.57 214 67 71 4 509.66 1.80 215 68 71 3 524.71 0.48 216 68 72 4 510.13 1.25 217 68 107 39 170.53 1.03 218 69 72 3 518.60 2.54 219 69 73 4 510.81 1.59 220 70 73 3 526.12 0.04 221 70 74 4 516.21 3.81 222 71 74 3 529.05 2.60 223 71 75 4 516.23 3.81 224 72 75 3 525.02 0.58 225 72 76 4 516.22 3.81 226 72 111 39 170.50 1.03 227 72 135 63 167.50 1.60 228 72 138 66 166.85 1.89 229 73 76 3 520.90 1.48 230 73 77 4 522.44 6.59 231 74 77 3 535.31 0.15 232 74 78 4 524.71 5.46 233 75 78 3 535.31 0.15 234 75 79 4 528.93 3.34 235 75 82 7 246.50 5.18 236 75 85 10 189.58 10.11 237 75 89 14 171.48 1.06 238 75 138 63 167.06 1.79 239 76 79 3 535.79 0.10 240 76 131 55 168.15 1.53 241 76 134 58 167.79 1.61 242 78 81 3 520.33 5.54 243 78 82 4 414.51 14.15 244 78 85 7 380.06 32.62 245 80 137 57 167.80 1.62 246 82 85 3 527.37 2.67 247 82 86 4 519.08 0.57 248 82 137 55 167.79 1.62 249 82 141 59 167.09 1.81 250 83 86 3 526.50 3.10 251 83 87 4 519.08 0.57 252 84 87 3 536.30 2.46 253 84 88 4 531.37 0.01 254 85 88 3 554.76 2.22 255 85 89 4 526.50 2.44 256 86 89 3 531.36 0.01 257 86 90 4 526.29 2.54 258 86 138 52 167.22 1.81 259 86 141 55 166.85 1.93 260 86 142 56 165.55 1.92 261 86 145 59 159.07 0.28 262 87 90 3 529.94 0.71 263 87 91 4 516.78 2.22 264 87 145 58 159.48 0.07 265 88 91 3 520.99 0.44 266 88 92 4 514.03 0.87 267 89 92 3 519.23 3.46 268 89 93 4 515.74 1.73 269 89 138 49 167.18 1.83 270 89 142 53 163.54 1.24 271 90 93 3 515.23 1.99 272 90 94 4 512.51 0.62 273 90 142 52 162.84 1.01 274 90 145 55 157.53 0.28 275 90 146 56 156.81 0.07 276 91 94 3 526.07 1.21 277 91 95 4 511.16 1.28 278 91 149 58 153.02 0.62 279 92 95 3 532.97 2.25 280 92 96 4 476.59 12.39 281 92 97 5 454.04 6.12 282 93 97 4 416.52 12.64 283 93 98 5 416.49 12.63 284 93 99 6 279.21 3.54 285 93 146 53 156.49 0.03 286 94 98 4 382.86 29.45 287 94 146 52 155.72 0.33 288 94 149 55 146.55 2.48 289 94 151 57 92.05 10.03 290 95 149 54 151.88 0.05 291 95 151 56 117.99 2.79 292 99 103 4 517.57 3.71 293 99 104 5 509.75 2.67 294 99 146 47 155.58 0.29 295 99 152 53 55.98 2.38 296 100 103 3 523.76 0.97 297 100 104 4 519.58 2.71 298 100 152 52 51.02 2.13 299 101 104 3 525.37 0.17 300 101 105 4 515.41 4.79 301 101 142 41 163.18 1.18 302 101 143 42 157.76 0.03 303 101 146 45 154.77 0.09 304 101 152 51 46.25 1.03 305 102 105 3 525.35 0.18 306 102 106 4 523.21 0.89 307 103 106 3 520.42 2.64 308 103 107 4 514.26 0.44 309 104 107 3 523.40 0.80 310 104 108 4 512.64 0.37 311 104 138 34 166.71 1.76 312 104 139 35 165.97 2.10 313 104 142 38 159.58 0.06 314 104 146 42 156.34 0.07 315 105 108 3 521.12 0.35 316 105 109 4 512.72 0.33 317 105 139 34 166.15 2.02 318 106 109 3 517.73 2.17 319 106 110 4 508.13 1.99 320 107 110 3 513.12 4.48 321 107 111 4 514.28 5.06 322 108 111 3 524.42 0.01 323 108 112 4 508.09 1.99 324 108 135 27 167.25 1.51 325 109 112 3 521.06 1.69 326 109 113 4 514.26 5.08 327 110 113 3 524.43 0.00 328 110 114 4 512.76 5.83 329 111 114 3 521.05 1.69 330 111 115 4 506.88 2.96 331 111 135 24 167.44 1.60 332 112 115 3 507.45 2.69 333 112 116 4 506.90 2.96 334 112 123 11 273.89 4.01 335 112 128 16 168.05 1.50 336 112 131 19 167.56 1.56 337 112 132 20 167.55 1.56 338 112 135 23 167.47 1.58 339 113 116 3 516.56 0.09 340 113 117 4 509.06 1.91 341 114 117 3 519.74 2.48 342 114 118 4 509.74 1.56 343 115 118 3 520.77 2.21 344 115 119 4 499.77 0.52 345 115 123 8 284.74 9.43 346 115 131 16 209.81 4.12 347 116 119 3 528.59 1.12 348 116 120 4 500.06 3.27 349 116 123 7 279.16 6.64 350 117 120 3 542.66 2.57 351 119 122 3 516.07 4.57 352 119 123 4 489.54 0.36 353 120 123 3 521.71 3.23 354 120 124 4 490.06 0.61 355 122 127 5 470.85 5.74 356 123 127 4 479.13 9.88 357 123 128 5 490.48 4.08 358 123 131 8 419.98 12.70 359 124 127 3 524.28 0.68 360 124 128 4 505.84 0.26 361 125 128 3 513.98 0.20 362 125 129 4 502.02 1.66 363 126 129 3 505.85 0.26 364 126 130 4 508.78 1.73 365 127 130 3 512.58 0.18 366 127 131 4 508.77 1.72 367 128 131 3 517.02 0.86 368 128 132 4 512.60 0.16 369 129 132 3 521.64 1.44 370 129 133 4 513.79 0.76 371 130 133 3 521.64 1.44 372 130 134 4 513.79 0.76 373 131 134 3 521.99 2.60 374 131 135 4 506.40 4.46 375 132 135 3 512.89 0.30 376 132 136 4 503.34 5.07 377 132 139 7 492.28 0.45 378 133 136 3 509.47 2.00 379 133 137 4 503.32 5.07 380 134 137 3 519.51 4.22 381 134 138 4 501.55 2.02 382 135 138 3 505.54 0.03 383 135 139 4 500.29 3.56 384 136 139 3 512.10 2.34 385 136 140 4 499.38 3.10 386 137 140 3 512.76 0.20 387 137 141 4 499.42 3.10 388 138 141 3 520.85 3.18 389 138 142 4 502.86 1.70 390 139 142 3 519.39 3.91 391 139 143 4 502.90 1.68 392 140 143 3 522.16 1.89 393 140 144 4 510.55 0.52 394 141 144 3 520.46 3.18 395 141 145 4 511.49 0.98 396 142 145 3 524.00 1.40 397 142 146 4 511.49 0.98 398 143 146 3 515.24 1.89 399 143 147 4 511.05 0.76 400 144 147 3 523.39 2.19 401 144 148 4 509.25 1.65 402 145 148 3 512.33 3.18 403 145 149 4 509.26 1.65 404 146 149 3 519.32 1.51 405 146 150 4 508.35 2.10 406 146 151 5 363.54 6.08 407 146 152 6 353.29 11.21 408 147 150 3 484.94 3.72 409 147 151 4 482.18 3.00 410 147 153 6 265.81 1.25