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 5 499.56 2.48 2 2 10 8 492.38 0.23 3 2 130 128 39.99 0.80 4 2 133 131 33.21 0.97 5 2 134 132 31.91 0.62 6 2 137 135 31.91 0.63 7 3 6 3 514.74 4.87 8 3 7 4 520.17 2.16 9 4 7 3 520.17 2.16 10 4 8 4 514.17 0.84 11 4 79 75 51.08 2.77 12 5 8 3 520.62 1.58 13 5 9 4 519.77 1.96 14 6 9 3 525.17 0.74 15 6 10 4 519.00 2.34 16 6 130 124 62.27 2.68 17 6 133 127 62.27 2.68 18 7 10 3 508.75 1.89 19 7 11 4 517.57 2.54 20 7 76 69 62.29 2.68 21 7 79 72 62.29 2.68 22 7 80 73 62.30 2.69 23 7 134 127 62.30 2.69 24 7 137 130 62.30 2.69 25 8 11 3 524.24 0.79 26 8 12 4 515.66 3.49 27 9 12 3 524.38 0.86 28 9 13 4 515.68 3.48 29 9 126 117 78.53 0.10 30 9 127 118 77.47 0.49 31 9 130 121 77.43 0.48 32 10 13 3 532.36 0.66 33 10 14 4 515.99 3.33 34 10 76 66 77.17 0.73 35 10 130 120 77.53 0.51 36 10 131 121 77.05 0.67 37 10 134 124 77.05 0.67 38 11 14 3 518.89 1.79 39 11 15 4 515.89 3.28 40 11 76 65 77.65 0.56 41 11 77 66 77.66 0.57 42 11 79 68 77.67 0.56 43 12 15 3 520.94 2.73 44 12 16 4 518.93 1.74 45 13 16 3 521.07 2.69 46 13 17 4 514.92 3.73 47 13 115 102 87.81 1.81 48 13 119 106 96.15 2.03 49 13 122 109 88.23 1.93 50 13 123 110 87.82 1.81 51 13 131 118 83.90 0.15 52 14 17 3 511.60 2.19 53 14 18 4 506.51 0.36 54 14 69 55 131.21 23.51 55 14 72 58 86.81 1.55 56 14 73 59 83.95 0.12 57 14 76 62 83.90 0.15 58 14 77 63 85.79 1.05 59 14 131 117 87.06 1.44 60 15 18 3 529.21 0.14 61 15 19 4 522.54 3.48 62 16 19 3 529.21 0.14 63 16 24 8 469.95 3.85 64 16 119 103 96.33 2.06 65 16 122 106 96.29 2.05 66 17 20 3 529.53 0.01 67 17 21 4 489.42 1.58 68 17 24 7 415.14 31.25 69 17 69 52 139.25 19.50 70 17 115 98 96.27 2.06 71 18 77 59 96.21 2.04 72 20 23 3 523.12 1.76 73 20 24 4 518.21 0.38 74 21 24 3 518.22 0.38 75 21 25 4 513.35 3.73 76 21 66 45 152.20 14.41 77 21 69 48 152.12 14.44 78 22 25 3 519.89 0.47 79 22 26 4 519.23 0.79 80 22 62 40 157.47 12.40 81 22 66 44 153.72 13.65 82 23 26 3 521.60 1.31 83 23 27 4 517.56 0.05 84 23 118 95 170.33 0.78 85 24 27 3 525.38 0.58 86 24 28 4 513.57 0.61 87 24 69 45 159.27 10.88 88 24 118 94 170.34 0.78 89 24 119 95 170.34 0.78 90 25 28 3 519.75 3.40 91 25 29 4 513.75 0.57 92 25 65 40 159.27 10.88 93 25 69 44 159.26 10.88 94 26 29 3 521.51 1.96 95 26 30 4 517.47 1.29 96 26 56 30 212.96 0.98 97 26 62 36 178.65 2.53 98 27 30 3 526.53 0.45 99 27 31 4 517.48 1.29 100 27 114 87 173.33 0.23 101 27 118 91 172.81 0.10 102 28 31 3 517.52 1.32 103 28 32 4 517.37 1.34 104 28 69 41 178.33 2.14 105 28 107 79 173.66 0.20 106 28 110 82 173.45 0.22 107 28 111 83 173.43 0.23 108 28 114 86 173.34 0.22 109 29 32 3 521.68 0.81 110 29 33 4 517.35 1.35 111 29 43 14 287.81 7.81 112 29 61 32 192.36 1.89 113 29 64 35 183.66 0.06 114 29 65 36 178.97 2.34 115 29 68 39 182.03 0.81 116 30 33 3 524.90 0.81 117 30 34 4 517.25 1.31 118 30 52 22 220.75 1.04 119 30 55 25 219.74 0.85 120 30 56 26 219.81 0.85 121 31 34 3 521.71 0.79 122 31 35 4 517.22 1.32 123 31 110 79 173.49 0.21 124 31 113 82 173.41 0.18 125 31 114 83 173.39 0.19 126 32 35 3 524.86 0.82 127 32 36 4 505.77 1.26 128 32 39 7 355.91 3.78 129 32 106 74 173.84 0.11 130 32 107 75 173.68 0.20 131 32 110 78 173.48 0.23 132 33 36 3 517.29 0.82 133 33 37 4 487.50 6.19 134 33 39 6 426.57 8.14 135 33 40 7 346.24 8.61 136 33 43 10 331.21 16.09 137 33 55 22 222.68 0.13 138 33 61 28 221.69 0.61 139 34 37 3 523.52 2.31 140 34 52 18 223.21 0.39 141 34 55 21 225.07 0.55 142 36 39 3 537.48 1.24 143 36 106 70 174.06 0.11 144 36 109 73 174.02 0.11 145 37 40 3 532.29 2.84 146 38 41 3 525.76 0.42 147 38 103 65 174.65 0.12 148 38 106 68 174.40 0.01 149 39 42 3 535.60 0.29 150 39 43 4 530.82 2.10 151 39 103 64 174.38 0.01 152 39 106 67 174.34 0.02 153 40 43 3 530.91 2.06 154 40 46 6 419.94 0.46 155 40 47 7 260.34 1.05 156 40 49 9 260.35 1.05 157 40 55 15 246.91 6.51 158 41 47 6 277.88 2.23 159 42 97 55 175.31 0.06 160 42 98 56 175.31 0.06 161 42 99 57 175.31 0.06 162 42 100 58 175.33 0.04 163 42 103 61 174.85 0.11 164 43 46 3 522.25 0.74 165 43 47 4 475.54 9.15 166 44 47 3 533.53 2.84 167 45 48 3 597.66 0.90 168 45 60 15 227.83 0.34 169 45 64 19 225.68 0.30 170 46 49 3 535.25 4.50 171 46 60 14 227.46 0.52 172 46 61 15 225.62 0.33 173 46 64 18 225.65 0.30 174 49 54 5 485.31 4.03 175 49 55 6 442.97 8.25 176 49 58 9 334.74 14.13 177 49 61 12 251.74 2.29 178 50 54 4 502.45 0.03 179 51 54 3 522.57 3.93 180 51 55 4 503.11 0.32 181 52 55 3 509.94 3.23 182 52 56 4 503.11 0.32 183 53 56 3 515.32 0.54 184 53 57 4 498.11 2.18 185 54 57 3 508.06 3.09 186 54 58 4 498.06 2.18 187 55 58 3 526.36 3.25 188 55 61 6 422.81 5.74 189 58 61 3 521.70 0.06 190 58 62 4 516.24 1.84 191 59 62 3 517.06 2.25 192 59 63 4 517.06 2.25 193 60 63 3 517.07 2.25 194 60 64 4 517.05 2.25 195 61 64 3 510.17 5.70 196 61 65 4 510.17 5.70 197 62 65 3 515.39 3.09 198 62 66 4 509.37 5.30 199 63 66 3 511.63 3.04 200 63 67 4 507.19 5.26 201 64 67 3 513.36 2.18 202 64 68 4 499.24 0.01 203 65 68 3 517.29 1.01 204 65 69 4 500.26 0.53 205 66 69 3 521.15 1.58 206 66 70 4 503.63 2.21 207 67 70 3 522.63 0.84 208 67 71 4 518.54 2.87 209 68 71 3 518.57 2.88 210 68 72 4 518.55 2.87 211 68 107 39 174.95 0.21 212 69 72 3 518.56 2.87 213 69 73 4 516.79 3.75 214 70 73 3 516.81 3.74 215 70 74 4 516.83 3.73 216 71 74 3 525.29 2.60 217 71 75 4 514.74 2.69 218 72 75 3 514.80 2.66 219 72 76 4 514.74 2.69 220 72 111 39 174.94 0.22 221 72 135 63 171.78 0.21 222 73 76 3 517.15 1.47 223 73 77 4 511.66 1.16 224 74 77 3 516.00 0.89 225 74 78 4 514.61 2.58 226 75 78 3 520.85 0.55 227 75 79 4 514.61 2.57 228 75 82 7 262.01 8.01 229 75 85 10 223.46 4.58 230 75 86 11 239.32 3.34 231 75 89 14 239.31 3.34 232 75 138 63 170.28 0.52 233 76 79 3 522.00 1.12 234 76 131 55 172.58 0.21 235 76 134 58 172.00 0.21 236 78 81 3 509.49 1.17 237 78 82 4 442.57 11.79 238 78 85 7 345.33 13.36 239 80 137 57 172.18 0.04 240 82 85 3 521.88 1.33 241 82 86 4 526.39 0.93 242 82 137 55 172.16 0.04 243 82 138 56 171.94 0.04 244 82 141 59 169.37 0.81 245 83 86 3 528.60 2.03 246 83 87 4 526.40 0.93 247 83 145 62 165.49 0.04 248 84 87 3 533.50 0.59 249 84 88 4 531.69 0.49 250 85 88 3 559.17 1.20 251 85 89 4 523.26 0.64 252 86 89 3 527.34 1.40 253 86 90 4 514.02 2.42 254 86 138 52 170.93 0.18 255 86 141 55 167.69 0.03 256 86 142 56 166.93 0.14 257 87 90 3 532.99 2.31 258 87 91 4 510.07 0.46 259 87 145 58 164.49 0.14 260 88 91 3 518.00 0.43 261 88 92 4 511.89 0.96 262 89 92 3 520.39 1.59 263 89 93 4 509.96 1.94 264 89 138 49 171.21 0.04 265 89 142 53 166.87 0.11 266 90 93 3 518.69 2.43 267 90 94 4 496.68 4.70 268 90 142 52 166.80 0.14 269 90 145 55 158.09 0.62 270 90 146 56 153.05 0.14 271 90 149 59 138.19 0.97 272 91 94 3 521.78 0.89 273 91 95 4 495.18 5.42 274 91 149 58 145.68 1.56 275 92 95 3 521.19 1.18 276 92 96 4 482.90 6.33 277 92 97 5 469.39 0.42 278 93 97 4 466.98 0.79 279 93 98 5 359.78 9.22 280 93 99 6 353.94 6.32 281 93 146 53 153.05 0.15 282 94 98 4 423.36 22.59 283 94 146 52 153.03 0.15 284 94 149 55 132.08 1.18 285 94 151 57 87.58 4.84 286 95 98 3 520.56 0.85 287 98 151 53 92.30 7.11 288 99 103 4 500.75 3.02 289 99 104 5 500.88 3.09 290 99 146 47 153.03 0.15 291 99 151 52 88.62 5.27 292 100 103 3 522.83 2.44 293 100 104 4 512.50 2.72 294 100 151 51 92.68 7.40 295 100 153 53 19.79 1.14 296 101 104 3 519.41 0.72 297 101 105 4 512.51 2.71 298 101 139 38 167.64 0.01 299 101 142 41 165.84 0.60 300 101 143 42 161.32 0.28 301 101 146 45 153.03 0.15 302 101 153 52 15.62 0.95 303 102 105 3 512.51 2.71 304 102 106 4 512.51 2.71 305 103 106 3 512.50 2.73 306 103 107 4 516.68 0.64 307 104 107 3 518.94 0.53 308 104 108 4 516.19 0.39 309 104 139 35 167.15 0.24 310 104 142 38 164.78 0.17 311 104 146 42 153.03 0.15 312 105 108 3 518.46 0.76 313 105 109 4 523.84 4.21 314 105 139 34 167.21 0.21 315 106 109 3 526.12 3.07 316 106 110 4 523.84 4.21 317 107 110 3 523.83 4.21 318 107 111 4 514.73 0.34 319 108 111 3 521.17 5.54 320 108 112 4 505.84 4.12 321 108 135 27 171.53 0.10 322 108 139 31 167.15 0.23 323 109 112 3 511.61 2.54 324 109 113 4 510.62 1.75 325 110 113 3 524.36 1.15 326 110 114 4 510.62 1.75 327 111 114 3 524.36 1.15 328 111 115 4 512.36 0.90 329 111 135 24 171.53 0.10 330 112 115 3 516.21 1.03 331 112 116 4 512.15 1.01 332 112 123 11 252.94 5.94 333 112 128 16 172.25 0.28 334 112 131 19 172.17 0.35 335 112 132 20 172.13 0.34 336 112 135 23 171.59 0.13 337 113 116 3 521.40 5.41 338 113 117 4 521.40 5.41 339 114 117 3 524.89 3.67 340 114 118 4 521.40 5.41 341 115 118 3 521.67 0.71 342 115 119 4 470.85 4.88 343 115 123 8 266.37 0.79 344 115 131 16 172.20 0.36 345 116 120 4 497.39 8.39 346 116 123 7 257.12 3.85 347 116 128 12 224.07 8.48 348 117 120 3 547.25 1.64 349 119 122 3 519.11 0.58 350 119 123 4 465.76 14.45 351 120 123 3 487.80 9.38 352 122 127 5 465.45 4.22 353 123 127 4 468.17 2.87 354 123 128 5 468.19 2.85 355 123 131 8 438.33 9.34 356 124 127 3 511.59 4.75 357 124 128 4 498.65 1.76 358 125 128 3 518.07 1.51 359 125 129 4 498.64 1.75 360 126 129 3 509.37 0.70 361 126 130 4 502.90 3.87 362 127 130 3 521.76 5.72 363 127 131 4 502.37 3.60 364 128 131 3 503.71 4.13 365 128 132 4 502.34 3.61 366 129 132 3 507.61 1.71 367 129 133 4 496.76 0.92 368 130 133 3 505.24 1.21 369 130 134 4 497.71 1.40 370 131 134 3 502.15 3.63 371 131 135 4 497.42 1.54 372 132 135 3 519.15 3.65 373 132 136 4 498.66 2.18 374 133 136 3 507.47 2.21 375 133 137 4 498.69 2.19 376 134 137 3 517.84 0.58 377 134 138 4 507.48 2.20 378 135 138 3 510.22 0.83 379 135 139 4 502.37 0.47 380 136 139 3 503.15 0.08 381 136 140 4 499.79 1.76 382 137 140 3 505.52 1.10 383 137 141 4 505.51 1.10 384 138 141 3 524.77 3.41 385 138 142 4 509.48 0.88 386 139 142 3 514.74 1.74 387 139 143 4 509.40 0.91 388 140 143 3 514.92 1.82 389 140 144 4 509.48 0.87 390 141 144 3 513.08 2.75 391 141 145 4 509.40 0.91 392 142 145 3 509.49 0.95 393 142 146 4 499.56 1.52 394 143 146 3 507.84 1.77 395 143 147 4 510.60 4.01 396 144 147 3 518.46 0.09 397 144 148 4 503.44 0.43 398 145 148 3 511.19 3.54 399 145 149 4 503.25 0.42 400 146 149 3 507.01 2.63 401 146 150 4 502.93 0.58 402 146 151 5 443.10 5.91 403 146 153 7 267.61 0.09 404 147 150 3 502.93 0.59 405 147 151 4 491.19 3.06 406 147 152 5 475.84 10.50