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 1 138 137 19.63 2.67 2 1 141 140 18.79 3.08 3 2 134 132 39.27 0.09 4 3 7 4 521.71 2.09 5 3 8 5 507.31 5.16 6 3 11 8 491.06 0.56 7 3 131 128 48.00 0.01 8 3 134 131 40.01 0.28 9 3 135 132 39.27 0.09 10 3 138 135 39.27 0.09 11 4 7 3 523.88 1.17 12 4 8 4 522.27 1.81 13 5 8 3 522.44 1.89 14 5 9 4 522.27 1.80 15 5 80 75 64.34 3.46 16 6 9 3 522.28 1.81 17 6 10 4 522.27 1.80 18 7 10 3 515.75 1.45 19 7 11 4 510.69 3.54 20 7 131 124 74.78 0.93 21 7 134 127 74.78 0.93 22 8 11 3 516.22 1.73 23 8 12 4 515.48 0.64 24 8 77 69 74.85 0.96 25 8 80 72 74.85 0.96 26 8 81 73 74.86 0.96 27 8 135 127 74.83 0.95 28 8 138 130 74.85 0.96 29 9 12 3 522.73 1.52 30 9 13 4 516.38 1.64 31 10 13 3 533.12 0.41 32 10 14 4 516.60 1.53 33 10 127 117 91.44 0.40 34 10 128 118 91.33 0.38 35 10 131 121 91.27 0.35 36 11 14 3 533.12 0.41 37 11 15 4 522.67 1.51 38 11 77 66 91.34 0.36 39 11 131 120 91.35 0.36 40 11 132 121 91.31 0.38 41 11 135 124 91.25 0.35 42 12 15 3 532.80 2.02 43 12 16 4 523.76 1.00 44 12 77 65 91.40 0.38 45 12 78 66 91.41 0.37 46 12 80 68 91.39 0.36 47 13 16 3 533.29 1.78 48 13 17 4 527.71 1.01 49 13 123 110 101.48 0.07 50 14 17 3 533.29 1.78 51 14 18 4 524.66 2.35 52 14 120 106 101.95 0.14 53 14 123 109 101.46 0.06 54 14 124 110 100.66 0.33 55 14 132 118 99.20 0.42 56 15 18 3 524.65 2.35 57 15 19 4 524.65 2.35 58 15 70 55 100.64 0.30 59 15 73 58 99.97 0.63 60 15 74 59 99.04 0.58 61 15 77 62 98.96 0.57 62 15 78 63 99.03 0.59 63 15 132 117 100.58 0.33 64 16 19 3 525.55 1.91 65 16 20 4 527.54 0.91 66 17 20 3 531.53 2.90 67 17 120 103 106.49 1.69 68 17 123 106 101.94 0.09 69 18 21 3 535.78 0.78 70 18 22 4 513.60 2.81 71 18 25 7 414.57 6.70 72 18 70 52 176.24 0.32 73 18 116 98 102.03 0.06 74 18 120 102 107.66 1.41 75 19 22 3 520.62 0.55 76 19 78 59 139.18 18.84 77 21 24 3 545.82 4.71 78 21 25 4 520.15 0.09 79 21 119 98 146.75 1.60 80 22 25 3 520.15 0.09 81 22 26 4 512.69 3.65 82 22 67 45 180.26 0.89 83 22 70 48 179.83 0.70 84 23 26 3 523.44 1.56 85 23 27 4 512.72 3.63 86 23 63 40 181.50 1.03 87 23 67 44 180.40 0.95 88 24 27 3 528.62 0.37 89 24 28 4 510.21 2.35 90 24 119 95 173.46 0.28 91 25 28 3 524.79 2.10 92 25 29 4 510.38 2.26 93 25 70 45 180.40 0.96 94 25 115 90 174.50 0.47 95 25 119 94 173.47 0.29 96 25 120 95 173.47 0.29 97 26 29 3 526.76 3.74 98 26 30 4 517.05 1.11 99 26 66 40 180.46 0.95 100 26 70 44 180.40 0.96 101 27 30 3 532.12 1.06 102 27 31 4 516.14 5.15 103 27 57 30 212.80 7.08 104 27 62 35 181.96 0.85 105 27 63 36 181.96 0.85 106 28 31 3 530.27 1.91 107 28 32 4 516.85 4.79 108 28 115 87 174.54 0.49 109 28 119 91 173.50 0.28 110 29 32 3 516.86 4.79 111 29 33 4 516.14 5.15 112 29 70 41 181.43 0.78 113 29 108 79 174.92 0.54 114 29 111 82 174.79 0.56 115 29 112 83 174.74 0.56 116 29 115 86 174.54 0.49 117 30 33 3 527.96 0.76 118 30 34 4 516.39 5.02 119 30 62 32 187.53 1.21 120 30 65 35 182.42 1.06 121 30 66 36 181.69 0.73 122 30 108 78 174.93 0.54 123 31 34 3 520.24 2.45 124 31 35 4 503.07 2.10 125 31 53 22 229.19 0.54 126 31 56 25 224.08 1.61 127 31 57 26 228.71 0.78 128 32 35 3 524.74 2.33 129 32 36 4 502.62 1.88 130 32 111 79 174.81 0.56 131 32 114 82 174.75 0.58 132 32 115 83 174.77 0.58 133 33 36 3 521.87 1.12 134 33 37 4 501.81 2.27 135 33 40 7 348.32 3.52 136 33 107 74 175.03 0.53 137 33 108 75 175.00 0.53 138 33 111 78 174.84 0.58 139 34 38 4 476.70 12.23 140 34 40 6 363.68 12.88 141 34 41 7 325.00 0.26 142 34 44 10 317.57 3.46 143 34 56 22 231.78 0.70 144 34 62 28 231.77 0.71 145 35 38 3 527.95 1.23 146 35 53 18 234.06 0.44 147 37 40 3 534.02 0.01 148 37 107 70 175.35 0.60 149 37 110 73 175.35 0.60 150 38 41 3 523.17 2.04 151 39 42 3 531.04 1.02 152 39 104 65 175.93 0.45 153 39 107 68 175.82 0.47 154 40 43 3 533.11 2.96 155 40 44 4 527.43 0.12 156 40 104 64 175.74 0.48 157 40 107 67 175.53 0.58 158 41 44 3 537.24 0.90 159 41 47 6 345.74 16.31 160 41 48 7 290.41 6.15 161 41 50 9 284.31 3.12 162 41 56 15 242.09 1.74 163 42 48 6 296.31 3.15 164 43 98 55 176.61 0.32 165 43 99 56 176.59 0.30 166 43 100 57 176.56 0.30 167 43 104 61 176.38 0.24 168 44 47 3 522.97 1.72 169 44 48 4 488.01 8.95 170 44 65 21 239.50 0.48 171 45 48 3 539.38 1.52 172 46 49 3 608.62 1.79 173 46 61 15 239.69 0.54 174 46 65 19 239.65 0.53 175 47 50 3 534.88 0.73 176 47 61 14 239.69 0.54 177 47 62 15 239.66 0.54 178 47 65 18 239.61 0.53 179 50 55 5 492.41 10.03 180 50 56 6 406.87 21.80 181 50 59 9 304.69 1.32 182 50 62 12 284.56 3.23 183 51 55 4 522.13 4.79 184 52 55 3 522.97 4.37 185 52 56 4 514.70 0.16 186 53 56 3 522.70 3.84 187 53 57 4 514.70 0.16 188 54 57 3 523.40 2.17 189 54 58 4 514.70 0.16 190 55 58 3 529.59 0.92 191 55 59 4 514.69 0.15 192 56 59 3 525.47 3.14 193 56 62 6 440.41 10.06 194 59 62 3 525.52 0.35 195 59 63 4 519.27 3.48 196 60 63 3 525.52 0.35 197 60 64 4 519.27 3.48 198 61 64 3 525.65 0.29 199 61 65 4 525.04 0.59 200 62 65 3 525.65 0.29 201 62 66 4 514.09 1.41 202 63 66 3 525.62 0.28 203 63 67 4 513.11 1.90 204 64 67 3 528.36 2.44 205 64 68 4 516.40 3.54 206 65 68 3 517.80 2.84 207 65 69 4 505.91 1.71 208 66 69 3 517.38 1.24 209 66 70 4 508.10 2.76 210 67 70 3 533.16 0.74 211 67 71 4 507.63 2.52 212 68 71 3 534.14 0.26 213 68 72 4 524.49 3.59 214 69 72 3 525.49 4.08 215 69 73 4 522.16 4.75 216 69 108 39 174.88 0.52 217 70 73 3 525.10 3.29 218 70 74 4 506.66 2.06 219 71 74 3 523.00 4.33 220 71 75 4 517.51 3.37 221 72 75 3 528.32 6.99 222 72 76 4 518.15 3.05 223 73 76 3 519.30 2.48 224 73 77 4 518.45 2.91 225 73 112 39 174.68 0.51 226 73 136 63 171.70 0.67 227 74 77 3 527.07 1.40 228 74 78 4 518.46 2.90 229 75 78 3 528.50 2.93 230 75 79 4 517.64 2.49 231 76 79 3 519.53 1.55 232 76 83 7 260.10 0.33 233 76 86 10 242.38 0.09 234 76 87 11 242.16 0.20 235 76 90 14 216.85 12.84 236 76 139 63 170.05 0.91 237 77 80 3 527.82 1.62 238 77 135 58 172.05 0.69 239 79 82 3 528.84 3.18 240 79 83 4 359.32 4.67 241 79 86 7 325.47 0.81 242 81 138 57 171.88 0.68 243 83 86 3 526.97 2.22 244 83 87 4 523.49 3.94 245 83 138 55 171.86 0.67 246 83 142 59 168.86 0.53 247 84 87 3 535.27 1.74 248 84 88 4 530.70 3.52 249 85 88 3 544.79 1.79 250 85 89 4 536.51 2.35 251 86 89 3 554.91 2.33 252 86 90 4 528.25 1.57 253 87 90 3 531.41 3.16 254 87 91 4 525.65 0.99 255 87 139 52 171.08 0.41 256 87 142 55 168.56 0.41 257 87 143 56 167.69 0.70 258 87 146 59 163.87 1.93 259 88 91 3 532.54 0.58 260 88 92 4 525.09 1.27 261 89 92 3 531.89 0.90 262 89 93 4 520.69 3.46 263 90 93 3 531.90 0.90 264 90 94 4 520.58 3.48 265 90 139 49 171.58 0.66 266 90 143 53 167.31 0.52 267 91 94 3 521.14 4.02 268 91 95 4 511.51 0.61 269 91 143 52 167.20 0.57 270 91 146 55 160.02 0.59 271 91 147 56 159.30 0.40 272 91 150 59 148.12 0.83 273 92 95 3 531.69 4.76 274 92 96 4 503.93 3.18 275 92 150 58 146.01 0.63 276 93 97 4 406.93 8.45 277 93 98 5 356.08 1.06 278 94 98 4 338.14 4.19 279 94 99 5 294.89 0.98 280 94 100 6 285.42 1.66 281 94 147 53 156.16 1.14 282 95 99 4 294.88 0.97 283 95 147 52 156.16 1.14 284 95 152 57 89.27 4.24 285 96 99 3 525.41 4.30 286 99 152 53 78.84 1.37 287 100 104 4 518.40 3.74 288 100 105 5 516.91 4.49 289 100 147 47 156.15 1.14 290 100 152 52 87.48 3.15 291 101 104 3 525.56 0.18 292 101 105 4 521.48 2.21 293 101 152 51 94.30 6.59 294 101 154 53 25.07 1.44 295 102 105 3 528.22 1.16 296 102 106 4 516.96 4.47 297 102 143 41 167.12 0.56 298 102 144 42 161.20 0.58 299 102 147 45 156.05 1.18 300 102 154 52 25.06 1.44 301 103 106 3 524.71 3.88 302 103 107 4 519.98 2.96 303 104 107 3 519.96 2.94 304 104 108 4 519.95 2.94 305 105 108 3 530.08 1.20 306 105 109 4 507.97 0.03 307 105 140 35 167.27 0.60 308 105 143 38 165.19 0.18 309 106 109 3 521.46 3.40 310 106 110 4 520.51 3.60 311 106 140 34 167.25 0.61 312 107 110 3 525.54 1.09 313 107 111 4 512.10 0.61 314 108 111 3 510.68 1.32 315 108 112 4 508.42 3.10 316 109 112 3 523.29 0.07 317 109 113 4 515.75 0.56 318 109 136 27 171.31 0.52 319 109 140 31 167.25 0.62 320 110 113 3 523.29 0.07 321 110 114 4 515.74 0.56 322 111 114 3 527.46 2.02 323 111 115 4 524.20 3.64 324 112 115 3 531.60 0.05 325 112 116 4 524.21 3.64 326 112 136 24 171.33 0.53 327 113 116 3 531.10 4.01 328 113 117 4 515.75 0.58 329 113 124 11 270.51 6.09 330 113 129 16 172.09 0.72 331 113 132 19 172.03 0.69 332 113 133 20 171.98 0.67 333 113 136 23 171.51 0.46 334 114 117 3 522.50 0.29 335 114 118 4 515.75 0.58 336 115 118 3 524.08 0.49 337 115 119 4 509.75 2.42 338 116 119 3 525.89 1.40 339 116 120 4 491.24 6.83 340 116 124 8 277.82 2.44 341 116 132 16 199.22 0.23 342 117 121 4 446.39 9.26 343 117 124 7 277.79 2.46 344 118 121 3 537.87 0.62 345 120 123 3 517.42 2.23 346 120 124 4 440.60 2.27 347 121 124 3 510.70 1.13 348 123 128 5 481.78 3.21 349 124 128 4 481.78 3.21 350 124 129 5 473.12 7.54 351 124 132 8 436.82 3.35 352 125 128 3 516.63 0.91 353 125 129 4 505.57 0.70 354 126 129 3 515.79 1.32 355 126 130 4 505.58 0.69 356 127 130 3 513.03 1.71 357 127 131 4 502.79 5.07 358 128 131 3 524.33 3.92 359 128 132 4 501.20 5.85 360 129 132 3 528.80 1.68 361 129 133 4 501.21 5.85 362 130 133 3 512.50 2.02 363 130 134 4 501.20 5.84 364 131 134 3 520.78 1.44 365 131 135 4 511.96 0.43 366 132 135 3 511.95 0.43 367 132 136 4 511.95 0.43 368 133 136 3 514.51 0.84 369 133 137 4 492.25 1.56 370 134 137 3 514.66 1.80 371 134 138 4 492.27 1.57 372 135 138 3 514.66 1.80 373 135 139 4 498.40 0.76 374 136 139 3 501.31 0.69 375 136 140 4 500.56 1.07 376 137 140 3 506.78 1.04 377 137 141 4 507.90 2.58 378 138 141 3 511.49 3.39 379 138 142 4 507.90 2.58 380 139 142 3 514.51 0.65 381 139 143 4 511.56 0.81 382 140 143 3 511.59 0.82 383 140 144 4 516.51 3.28 384 141 144 3 520.16 1.46 385 141 145 4 519.54 1.78 386 142 145 3 519.60 1.75 387 142 146 4 519.55 1.77 388 143 146 3 520.75 1.75 389 143 147 4 519.59 1.75 390 144 147 3 519.59 1.75 391 144 148 4 519.59 1.75 392 144 153 9 259.60 4.32 393 145 148 3 518.60 1.78 394 145 149 4 500.25 8.67 395 146 149 3 500.25 8.67 396 146 150 4 500.25 8.67 397 147 150 3 514.50 1.54 398 147 151 4 500.26 8.67 399 147 152 5 403.62 1.83 400 147 153 6 346.97 30.16 401 147 154 7 361.47 22.91 402 148 151 3 500.26 8.67 403 148 153 5 347.06 30.11