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 5 474.72 3.51 2 2 10 8 453.07 7.32 3 2 130 128 40.28 1.55 4 2 133 131 32.12 0.50 5 2 134 132 30.75 0.29 6 2 137 135 30.55 0.23 7 3 6 3 515.70 1.24 8 3 7 4 492.95 5.23 9 4 7 3 510.21 3.98 10 4 8 4 491.36 3.12 11 4 79 75 55.79 1.62 12 5 8 3 514.12 1.94 13 5 9 4 494.13 3.93 14 6 9 3 512.75 2.71 15 6 10 4 494.13 3.92 16 6 130 124 67.81 0.56 17 6 133 127 67.86 0.58 18 7 10 3 495.37 3.31 19 7 11 4 493.01 3.35 20 7 76 69 67.97 0.53 21 7 79 72 67.97 0.53 22 7 80 73 67.97 0.53 23 7 134 127 67.96 0.53 24 7 137 130 67.97 0.54 25 8 11 3 525.36 3.25 26 8 12 4 494.20 3.85 27 9 12 3 514.01 4.64 28 9 13 4 506.44 1.53 29 9 126 117 75.17 0.81 30 9 127 118 74.95 0.89 31 9 130 121 73.96 1.35 32 10 13 3 514.46 0.37 33 10 14 4 512.88 1.16 34 10 76 66 74.34 1.19 35 10 130 120 74.01 1.36 36 10 131 121 73.98 1.36 37 10 134 124 73.95 1.36 38 11 14 3 516.40 0.60 39 11 15 4 512.88 1.17 40 11 77 66 74.39 1.20 41 11 79 68 74.98 0.91 42 12 15 3 522.17 3.48 43 12 16 4 521.36 3.08 44 13 16 3 522.44 3.62 45 13 17 4 524.14 1.68 46 13 115 102 88.34 1.20 47 13 123 110 88.03 1.35 48 13 127 114 85.27 0.60 49 13 131 118 83.68 0.84 50 14 17 3 524.15 1.68 51 14 18 4 519.71 0.54 52 14 69 55 128.58 21.03 53 14 72 58 128.21 21.21 54 14 73 59 83.67 0.83 55 14 76 62 83.67 0.84 56 14 77 63 84.67 0.34 57 14 131 117 85.27 0.60 58 15 18 3 519.71 0.55 59 15 19 4 515.64 2.58 60 16 19 3 519.71 0.55 61 16 24 8 433.39 10.11 62 16 119 103 91.97 2.13 63 16 122 106 91.95 2.12 64 17 20 3 519.70 0.55 65 17 21 4 489.85 3.68 66 17 24 7 418.48 10.12 67 17 69 52 176.80 0.55 68 17 115 98 91.86 2.11 69 18 21 3 516.19 1.21 70 18 77 59 130.62 20.00 71 20 23 3 520.77 1.35 72 20 24 4 506.80 3.91 73 21 24 3 515.15 1.46 74 21 25 4 513.41 0.60 75 21 66 45 177.40 0.69 76 21 69 48 177.40 0.69 77 22 25 3 516.36 0.85 78 22 26 4 514.65 0.01 79 22 66 44 177.43 0.69 80 23 26 3 514.66 0.01 81 23 27 4 514.65 0.00 82 24 27 3 514.66 0.01 83 24 28 4 514.64 0.00 84 24 69 45 177.47 0.70 85 24 114 90 162.41 3.24 86 24 115 91 163.16 2.87 87 24 118 94 165.29 0.95 88 24 119 95 165.35 0.97 89 25 28 3 512.44 1.09 90 25 29 4 502.15 1.15 91 25 65 40 177.50 0.70 92 25 69 44 177.47 0.70 93 26 29 3 514.40 0.10 94 26 30 4 507.34 3.27 95 26 56 30 224.22 3.62 96 26 61 35 182.68 1.02 97 26 62 36 182.47 1.12 98 27 30 3 514.25 4.36 99 27 31 4 507.35 3.28 100 27 56 29 224.25 3.61 101 27 114 87 167.37 0.76 102 27 118 91 166.80 0.54 103 28 31 3 509.74 2.10 104 28 32 4 507.35 3.28 105 28 107 79 167.93 0.77 106 28 110 82 167.70 0.79 107 28 111 83 167.59 0.77 108 28 114 86 167.37 0.76 109 29 32 3 506.98 3.45 110 29 33 4 506.72 3.58 111 29 61 32 204.41 2.65 112 29 64 35 188.91 3.35 113 29 65 36 183.32 0.70 114 29 107 78 167.94 0.77 115 30 33 3 520.10 0.99 116 30 34 4 494.73 2.66 117 30 52 22 225.81 3.56 118 30 55 25 224.60 3.58 119 30 56 26 225.77 3.55 120 30 61 31 211.29 0.78 121 31 34 3 516.40 0.85 122 31 35 4 499.28 0.58 123 31 110 79 167.77 0.79 124 31 113 82 167.69 0.76 125 31 114 83 167.53 0.84 126 32 35 3 511.29 0.54 127 32 36 4 500.47 0.01 128 32 39 7 406.53 17.45 129 32 106 74 167.94 0.77 130 32 107 75 167.94 0.77 131 32 110 78 167.76 0.79 132 33 36 3 515.40 1.52 133 33 37 4 492.55 3.70 134 33 39 6 406.54 17.45 135 33 40 7 352.56 5.46 136 33 43 10 315.97 11.32 137 33 46 13 253.01 1.98 138 33 55 22 225.89 3.54 139 33 61 28 225.06 3.82 140 34 37 3 515.42 1.51 141 34 52 18 225.84 3.58 142 34 55 21 225.95 3.52 143 36 39 3 513.23 0.42 144 36 106 70 168.03 0.74 145 37 40 3 513.20 0.43 146 37 41 4 511.69 1.19 147 38 41 3 520.88 4.27 148 38 103 65 168.43 0.77 149 38 106 68 168.40 0.76 150 39 42 3 522.76 4.96 151 39 103 64 168.30 0.73 152 39 106 67 168.31 0.72 153 40 43 3 522.42 1.59 154 40 46 6 351.17 25.54 155 40 47 7 271.72 4.12 156 40 49 9 252.28 1.62 157 42 97 55 169.28 0.61 158 42 98 56 169.28 0.61 159 42 99 57 169.14 0.68 160 42 100 58 169.24 0.64 161 42 103 61 169.00 0.65 162 43 46 3 520.54 2.67 163 43 47 4 500.19 6.43 164 43 64 21 227.22 3.11 165 44 47 3 528.73 0.36 166 45 48 3 565.65 1.40 167 45 60 15 227.47 3.15 168 45 64 19 227.41 3.12 169 46 49 3 528.70 0.38 170 46 60 14 230.30 1.73 171 46 61 15 227.45 3.15 172 46 64 18 227.45 3.15 173 49 54 5 440.26 0.36 174 49 55 6 354.91 9.76 175 49 58 9 261.53 1.65 176 49 61 12 257.00 0.12 177 50 54 4 503.09 1.57 178 51 54 3 513.44 1.68 179 51 55 4 491.60 0.73 180 52 55 3 500.65 0.63 181 52 56 4 488.57 0.78 182 53 56 3 496.25 2.25 183 53 57 4 488.58 0.79 184 54 57 3 501.06 2.03 185 54 58 4 495.44 2.65 186 55 58 3 504.48 1.40 187 55 61 6 430.96 6.90 188 58 61 3 534.14 2.29 189 58 62 4 512.17 0.29 190 59 62 3 521.07 1.33 191 59 63 4 512.17 0.29 192 60 63 3 518.27 2.76 193 60 64 4 506.93 2.92 194 61 64 3 518.27 2.75 195 61 65 4 506.92 2.92 196 62 65 3 507.29 2.05 197 62 66 4 509.60 1.87 198 63 66 3 509.71 1.81 199 63 67 4 511.19 1.07 200 64 67 3 512.97 0.18 201 64 68 4 511.22 1.06 202 65 68 3 514.62 2.76 203 65 69 4 511.20 1.05 204 66 69 3 522.07 1.18 205 66 70 4 509.66 1.80 206 67 70 3 515.22 2.25 207 67 71 4 512.01 0.64 208 68 71 3 518.59 0.14 209 68 72 4 512.92 0.18 210 68 107 39 168.52 0.48 211 69 72 3 513.03 0.17 212 69 73 4 509.99 1.29 213 69 111 42 168.38 0.47 214 70 73 3 531.70 0.76 215 70 74 4 511.37 0.60 216 71 74 3 519.54 2.15 217 71 75 4 511.37 0.60 218 71 89 18 169.76 0.36 219 72 75 3 513.96 3.98 220 72 76 4 505.62 2.27 221 72 111 39 168.43 0.44 222 72 135 63 165.83 0.31 223 72 138 66 164.34 0.32 224 73 76 3 511.70 0.77 225 73 77 4 511.70 0.78 226 74 77 3 513.34 0.03 227 74 78 4 513.33 0.03 228 75 78 3 524.83 5.38 229 75 82 7 247.26 3.03 230 75 85 10 185.12 1.15 231 75 86 11 181.96 0.43 232 75 89 14 176.34 2.38 233 75 138 63 164.91 0.06 234 76 79 3 524.83 5.38 235 76 134 58 166.12 0.33 236 78 81 3 503.78 1.95 237 78 82 4 439.02 30.43 238 78 85 7 282.08 1.13 239 80 137 57 166.08 0.29 240 82 85 3 520.84 0.59 241 82 86 4 491.29 3.64 242 82 137 55 166.09 0.29 243 82 141 59 164.32 0.30 244 83 86 3 516.21 0.54 245 83 87 4 506.04 0.33 246 84 88 4 518.19 3.51 247 85 88 3 532.18 1.58 248 85 89 4 512.26 0.55 249 86 89 3 512.26 0.55 250 86 90 4 510.93 1.21 251 86 138 52 164.19 0.34 252 86 141 55 162.93 0.35 253 86 142 56 162.03 0.07 254 87 90 3 511.90 1.70 255 87 91 4 513.12 2.31 256 88 91 3 512.40 2.68 257 88 92 4 513.16 2.29 258 89 92 3 514.97 2.38 259 89 93 4 513.16 2.29 260 90 93 3 514.14 2.79 261 90 94 4 513.16 2.29 262 90 142 52 159.69 0.69 263 90 145 55 148.97 0.28 264 90 146 56 148.88 0.32 265 91 94 3 524.93 2.37 266 91 95 4 507.04 0.76 267 91 149 58 148.20 0.44 268 92 95 3 524.93 2.37 269 92 96 4 478.09 2.91 270 92 97 5 446.17 13.04 271 93 97 4 423.61 24.32 272 93 98 5 405.56 33.34 273 93 99 6 277.54 0.11 274 93 146 53 148.95 0.27 275 94 98 4 383.26 44.48 276 94 146 52 148.85 0.31 277 94 149 55 145.45 1.58 278 94 151 57 63.78 3.68 279 95 149 54 148.18 0.45 280 98 151 53 82.59 2.01 281 99 103 4 512.79 0.69 282 99 104 5 508.17 1.62 283 99 146 47 148.76 0.34 284 99 151 52 71.23 0.05 285 100 103 3 528.10 1.73 286 100 104 4 515.19 0.52 287 100 146 46 148.49 0.46 288 100 151 51 55.61 0.03 289 100 153 53 15.70 1.17 290 101 104 3 516.42 0.10 291 101 105 4 508.19 1.61 292 101 139 38 162.34 0.21 293 101 142 41 156.63 0.40 294 101 143 42 153.26 0.58 295 101 146 45 148.35 0.47 296 102 105 3 508.75 1.33 297 102 106 4 508.18 1.61 298 103 106 3 508.18 1.63 299 103 107 4 508.62 1.17 300 104 107 3 525.07 0.30 301 104 108 4 508.61 1.17 302 104 138 34 163.93 0.10 303 104 139 35 161.71 0.05 304 104 142 38 156.62 0.40 305 104 146 42 148.37 0.48 306 105 108 3 514.16 1.61 307 105 109 4 508.61 1.17 308 105 139 34 162.09 0.13 309 106 109 3 508.14 0.04 310 106 110 4 504.00 0.14 311 107 110 3 507.24 0.41 312 107 111 4 503.98 0.14 313 108 111 3 520.08 2.16 314 108 112 4 506.23 0.99 315 108 135 27 164.70 0.23 316 108 139 31 161.70 0.05 317 109 112 3 509.99 1.03 318 109 113 4 503.96 0.13 319 110 113 3 507.74 0.06 320 110 114 4 500.47 1.88 321 111 114 3 512.19 0.31 322 111 115 4 499.74 2.23 323 111 135 24 164.88 0.30 324 112 115 3 518.49 0.97 325 112 116 4 503.42 4.08 326 112 123 11 260.30 0.58 327 112 128 16 165.90 0.42 328 112 131 19 165.75 0.48 329 112 132 20 165.57 0.55 330 112 135 23 164.96 0.35 331 113 116 3 517.18 1.62 332 113 117 4 505.62 0.71 333 114 117 3 506.16 1.47 334 114 118 4 501.53 2.75 335 115 118 3 516.20 0.08 336 115 119 4 494.79 0.56 337 115 123 8 267.90 4.38 338 115 131 16 212.16 5.32 339 116 119 3 504.39 0.20 340 116 120 4 450.83 9.92 341 116 123 7 260.30 0.58 342 116 128 12 240.21 2.36 343 117 120 3 509.92 2.83 344 119 122 3 524.28 8.67 345 119 123 4 461.81 4.04 346 123 127 4 500.61 3.82 347 123 128 5 482.78 5.09 348 123 131 8 442.40 3.44 349 124 127 3 500.66 3.79 350 124 128 4 501.28 3.48 351 125 128 3 511.85 3.26 352 125 129 4 501.30 3.49 353 126 129 3 509.33 0.52 354 126 130 4 504.87 1.71 355 127 130 3 515.13 2.39 356 127 131 4 504.88 1.71 357 128 131 3 511.66 0.63 358 128 132 4 508.37 3.46 359 129 132 3 516.56 0.62 360 129 133 4 510.27 2.52 361 130 133 3 526.34 4.07 362 130 134 4 513.10 1.11 363 131 134 3 516.76 0.72 364 131 135 4 511.56 1.88 365 132 135 3 516.76 0.72 366 132 136 4 506.69 0.55 367 133 136 3 508.24 1.31 368 133 137 4 506.69 0.55 369 134 137 3 506.67 0.53 370 134 138 4 503.33 1.14 371 135 138 3 505.26 0.34 372 135 139 4 505.32 1.04 373 136 139 3 511.47 2.03 374 136 140 4 504.63 0.67 375 137 140 3 511.91 2.23 376 137 141 4 504.64 0.67 377 138 141 3 517.39 0.93 378 138 142 4 505.88 0.79 379 139 142 3 510.56 1.41 380 139 143 4 505.87 0.79 381 140 143 3 512.59 1.52 382 140 144 4 506.92 1.30 383 141 144 3 515.97 3.21 384 141 145 4 508.73 0.41 385 142 145 3 514.46 1.49 386 142 146 4 506.56 1.47 387 143 146 3 508.94 1.27 388 143 147 4 504.93 0.66 389 144 147 3 507.37 0.57 390 144 148 4 504.70 0.55 391 145 148 3 514.67 0.99 392 145 149 4 505.15 0.77 393 146 149 3 512.45 0.12 394 146 150 4 503.16 0.51 395 146 151 5 353.70 1.17 396 147 150 3 500.66 1.85