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 5 486.93 5.31 2 2 10 8 466.43 4.50 3 2 130 128 39.54 0.28 4 2 133 131 25.82 0.21 5 2 134 132 25.57 0.14 6 2 137 135 25.57 0.14 7 3 6 3 507.26 3.01 8 3 7 4 496.02 2.60 9 4 7 3 510.34 4.31 10 4 8 4 498.44 0.40 11 5 8 3 521.42 3.19 12 5 9 4 500.24 0.50 13 6 9 3 518.77 4.51 14 6 10 4 497.38 2.08 15 6 130 124 63.52 1.49 16 6 133 127 63.52 1.49 17 7 10 3 498.93 2.84 18 7 11 4 497.38 2.08 19 7 76 69 63.57 1.46 20 7 79 72 63.55 1.48 21 7 80 73 63.55 1.48 22 7 134 127 63.54 1.48 23 7 137 130 63.55 1.48 24 8 11 3 510.92 1.59 25 8 12 4 496.89 2.31 26 9 12 3 507.74 4.21 27 9 13 4 499.63 0.13 28 9 126 117 75.59 1.07 29 9 127 118 75.50 1.10 30 9 130 121 75.39 1.08 31 10 13 3 500.44 0.54 32 10 14 4 499.64 0.13 33 10 76 66 75.44 1.09 34 10 130 120 75.45 1.08 35 10 131 121 75.36 1.08 36 10 134 124 75.36 1.08 37 11 14 3 499.65 0.13 38 11 15 4 499.65 0.13 39 11 76 65 75.45 1.09 40 11 77 66 75.44 1.09 41 11 79 68 75.45 1.09 42 12 15 3 523.76 2.27 43 13 16 3 529.30 0.53 44 13 17 4 515.82 1.22 45 13 115 102 82.48 0.82 46 13 123 110 83.90 0.12 47 13 127 114 79.09 2.52 48 13 131 118 78.97 2.52 49 14 17 3 515.82 1.22 50 14 18 4 505.88 6.19 51 14 69 55 121.47 23.77 52 14 72 58 79.00 2.54 53 14 73 59 78.98 2.54 54 14 76 62 78.93 2.55 55 14 77 63 78.98 2.54 56 14 131 117 79.05 2.53 57 15 18 3 513.53 2.35 58 15 19 4 505.88 6.18 59 16 19 3 515.96 1.28 60 16 24 8 423.60 4.67 61 16 119 103 100.73 1.49 62 16 122 106 100.74 1.48 63 17 20 3 520.03 1.01 64 17 21 4 471.38 4.92 65 17 24 7 323.22 1.81 66 17 69 52 141.62 22.65 67 17 115 98 96.73 0.64 68 18 77 59 130.36 16.46 69 20 23 3 513.89 2.04 70 20 24 4 497.69 10.48 71 21 24 3 506.15 6.26 72 21 25 4 497.69 10.48 73 21 66 45 165.10 19.37 74 21 69 48 157.37 23.22 75 21 70 49 157.36 23.23 76 22 25 3 506.13 6.27 77 22 26 4 505.78 6.44 78 22 62 40 166.77 18.93 79 22 66 44 165.11 19.37 80 23 26 3 514.92 1.88 81 23 27 4 505.83 6.42 82 24 27 3 505.66 5.11 83 24 28 4 499.63 2.97 84 24 69 45 166.91 18.70 85 24 114 90 150.56 6.17 86 24 115 91 152.81 4.95 87 24 118 94 152.66 3.81 88 24 119 95 153.16 3.65 89 25 28 3 509.00 0.40 90 25 29 4 499.68 2.94 91 25 65 40 167.77 18.33 92 25 69 44 166.91 18.70 93 26 29 3 513.70 0.01 94 26 30 4 499.66 2.93 95 26 56 30 183.20 17.57 96 26 61 35 175.00 14.95 97 26 62 36 174.75 15.05 98 26 65 39 173.32 15.65 99 27 30 3 509.59 2.04 100 27 31 4 506.36 3.65 101 27 114 87 154.42 4.25 102 27 118 91 154.34 3.10 103 28 31 3 512.07 0.81 104 28 32 4 509.16 2.25 105 28 69 41 174.78 14.83 106 28 107 79 154.16 4.57 107 28 110 82 154.52 4.30 108 28 111 83 154.43 4.27 109 28 114 86 155.35 3.78 110 29 32 3 509.18 2.25 111 29 33 4 506.23 3.71 112 29 61 32 176.65 14.28 113 29 64 35 176.47 14.21 114 29 65 36 176.27 14.23 115 29 107 78 154.60 4.34 116 30 33 3 509.67 2.02 117 30 34 4 503.58 5.05 118 30 52 22 192.43 21.80 119 30 55 25 191.90 21.65 120 30 56 26 191.90 21.65 121 30 61 31 178.53 15.16 122 31 34 3 517.01 1.83 123 31 35 4 492.31 0.57 124 31 110 79 154.79 4.19 125 31 113 82 155.66 3.74 126 31 114 83 155.65 3.73 127 32 35 3 507.91 0.73 128 32 36 4 491.89 0.78 129 32 39 7 402.07 1.99 130 32 106 74 154.87 4.24 131 32 107 75 154.87 4.23 132 33 36 3 513.72 0.18 133 33 37 4 476.75 1.56 134 33 39 6 397.26 4.44 135 33 40 7 251.43 22.64 136 33 43 10 237.66 29.53 137 33 46 13 199.84 25.50 138 33 55 22 192.86 22.02 139 33 61 28 192.62 21.96 140 34 37 3 525.66 2.06 141 34 52 18 192.88 22.00 142 34 55 21 192.88 22.00 143 36 39 3 530.39 2.88 144 36 106 70 154.94 4.22 145 37 40 3 519.81 2.42 146 38 41 3 514.07 5.29 147 38 103 65 156.30 4.25 148 38 106 68 155.94 3.86 149 39 42 3 519.26 2.69 150 39 43 4 515.06 4.25 151 39 103 64 154.96 4.25 152 39 106 67 155.84 3.81 153 40 43 3 519.32 2.11 154 40 46 6 337.36 8.24 155 40 47 7 233.27 31.59 156 40 49 9 225.53 27.73 157 40 55 15 198.68 24.59 158 41 47 6 316.85 5.25 159 42 97 55 155.79 4.64 160 42 98 56 155.77 4.65 161 42 99 57 155.72 4.64 162 42 100 58 156.25 4.38 163 42 103 61 156.52 4.15 164 43 46 3 516.80 2.31 165 43 47 4 494.75 0.68 166 43 64 21 194.30 22.50 167 44 47 3 524.21 0.56 168 45 48 3 561.24 0.18 169 45 60 15 195.52 23.00 170 45 64 19 195.47 23.00 171 46 49 3 521.64 0.12 172 46 60 14 196.47 23.48 173 46 61 15 195.47 23.01 174 46 64 18 194.61 22.58 175 48 54 6 447.41 9.31 176 49 54 5 447.06 9.18 177 49 55 6 386.88 15.95 178 49 58 9 249.29 37.60 179 49 61 12 222.83 29.14 180 50 54 4 499.97 1.16 181 51 54 3 507.05 0.79 182 51 55 4 499.99 1.15 183 52 55 3 499.98 1.14 184 52 56 4 499.99 1.14 185 53 56 3 508.92 0.15 186 53 57 4 500.00 1.14 187 54 57 3 495.76 0.98 188 54 58 4 492.04 2.83 189 55 58 3 505.56 1.81 190 55 61 6 425.04 6.06 191 58 61 3 509.22 0.19 192 58 62 4 500.16 4.26 193 59 62 3 505.77 1.46 194 59 63 4 500.16 4.27 195 60 63 3 498.31 5.20 196 60 64 4 507.44 0.64 197 61 64 3 515.02 2.88 198 61 65 4 492.06 7.05 199 62 65 3 507.41 0.52 200 62 66 4 492.29 6.94 201 63 66 3 513.85 2.10 202 63 67 4 492.31 6.94 203 64 67 3 501.02 2.56 204 64 68 4 499.07 3.61 205 65 68 3 517.67 1.67 206 65 69 4 510.86 2.27 207 66 69 3 516.50 0.42 208 66 70 4 501.19 2.21 209 67 70 3 516.77 0.68 210 67 71 4 510.86 2.27 211 68 71 3 514.49 1.85 212 68 72 4 505.96 0.18 213 68 107 39 161.32 0.96 214 69 72 3 508.58 0.84 215 69 73 4 505.20 2.41 216 69 111 42 161.57 0.70 217 70 73 3 514.21 0.71 218 70 74 4 514.15 0.69 219 71 74 3 512.50 1.56 220 71 75 4 512.46 1.54 221 71 89 18 163.08 1.56 222 72 75 3 522.54 2.92 223 72 76 4 512.49 1.55 224 72 111 39 191.73 14.38 225 72 135 63 161.55 1.72 226 72 138 66 159.10 0.70 227 73 76 3 523.37 2.51 228 73 77 4 511.33 2.13 229 74 77 3 524.83 1.78 230 74 78 4 524.83 1.78 231 75 78 3 514.83 3.23 232 75 82 7 208.27 23.80 233 75 85 10 163.68 1.52 234 75 86 11 163.66 1.51 235 75 89 14 163.66 1.51 236 75 138 63 189.10 15.70 237 76 79 3 519.15 2.92 238 76 131 55 189.85 15.59 239 76 134 58 189.40 15.61 240 78 81 3 504.72 2.01 241 78 82 4 345.58 5.67 242 78 85 7 346.70 5.11 243 80 137 57 220.98 31.39 244 82 85 3 506.53 1.38 245 82 86 4 480.00 4.78 246 82 137 55 233.12 37.41 247 82 141 59 230.06 36.29 248 83 86 3 510.67 3.45 249 83 87 4 496.67 3.56 250 83 145 62 228.94 36.84 251 84 88 4 517.38 1.00 252 85 88 3 545.07 1.56 253 85 89 4 517.38 1.00 254 86 89 3 518.31 1.47 255 86 90 4 505.08 0.68 256 86 138 52 233.38 37.84 257 86 141 55 233.12 37.94 258 86 142 56 232.15 38.26 259 86 145 59 229.49 39.59 260 87 90 3 519.47 0.04 261 87 91 4 506.93 0.25 262 87 145 58 229.49 39.59 263 88 91 3 512.92 3.31 264 88 92 4 506.87 0.28 265 89 92 3 518.34 0.48 266 89 93 4 505.38 0.47 267 90 93 3 522.17 3.97 268 90 94 4 506.48 0.09 269 90 142 52 230.26 39.40 270 90 145 55 229.30 39.68 271 90 146 56 229.37 39.73 272 91 94 3 522.12 3.99 273 91 95 4 493.50 1.06 274 91 149 58 227.99 39.97 275 92 95 3 517.72 1.73 276 92 96 4 453.45 2.12 277 92 97 5 452.38 1.61 278 93 97 4 370.78 3.05 279 93 98 5 403.03 13.09 280 93 99 6 323.16 5.26 281 93 146 53 229.36 39.87 282 94 98 4 370.75 3.04 283 94 146 52 229.33 39.87 284 94 149 55 221.60 43.33 285 94 151 57 179.55 63.13 286 95 98 3 531.78 4.42 287 95 149 54 227.44 40.41 288 98 151 53 187.47 60.25 289 99 103 4 507.73 1.14 290 99 104 5 504.36 2.81 291 99 146 47 229.72 40.06 292 99 151 52 187.21 60.37 293 100 103 3 521.45 1.90 294 100 104 4 517.63 3.81 295 100 146 46 229.75 40.09 296 100 151 51 187.21 60.37 297 101 104 3 518.25 3.50 298 101 105 4 517.62 3.81 299 101 139 38 233.91 38.24 300 101 142 41 230.44 39.98 301 101 143 42 230.16 39.88 302 101 146 45 229.75 40.09 303 102 105 3 511.12 0.07 304 102 106 4 512.41 1.21 305 103 106 3 517.85 3.71 306 103 107 4 512.40 1.22 307 104 107 3 514.49 1.31 308 104 108 4 508.68 0.88 309 104 138 34 234.34 38.12 310 104 139 35 233.90 38.33 311 104 142 38 230.47 40.02 312 104 146 42 230.03 40.23 313 105 108 3 517.12 2.64 314 105 109 4 508.49 0.79 315 105 139 34 233.90 38.30 316 106 109 3 515.62 1.88 317 106 110 4 508.48 0.79 318 107 110 3 508.48 0.79 319 107 111 4 508.48 0.79 320 108 111 3 509.44 0.96 321 108 112 4 508.80 0.62 322 108 135 27 234.44 38.12 323 108 139 31 233.97 38.36 324 109 112 3 507.68 0.05 325 109 113 4 500.01 5.55 326 110 113 3 505.65 2.73 327 110 114 4 499.60 5.76 328 111 114 3 514.28 2.59 329 111 115 4 499.56 5.78 330 111 135 24 234.78 38.25 331 112 115 3 514.01 1.35 332 112 116 4 505.09 3.02 333 112 123 11 289.66 11.44 334 112 128 16 235.21 38.16 335 112 131 19 235.12 38.12 336 112 132 20 235.01 38.16 337 112 135 23 234.86 38.23 338 113 116 3 519.21 1.04 339 113 117 4 505.08 3.02 340 114 117 3 502.92 1.94 341 114 118 4 495.36 5.71 342 115 118 3 522.09 1.00 343 115 119 4 504.00 0.57 344 115 123 8 289.73 11.45 345 115 131 16 235.44 38.30 346 116 119 3 511.98 0.95 347 116 120 4 467.13 2.39 348 116 123 7 289.81 11.48 349 116 128 12 287.50 12.51 350 117 120 3 516.78 0.13 351 119 122 3 494.97 2.79 352 119 123 4 446.74 5.61 353 123 127 4 500.88 2.16 354 123 128 5 488.74 8.22 355 123 131 8 453.53 5.20 356 124 127 3 504.45 0.38 357 124 128 4 503.06 1.08 358 125 128 3 514.68 1.15 359 125 129 4 506.63 0.70 360 126 129 3 506.65 0.70 361 126 130 4 506.63 0.70 362 127 130 3 507.79 0.12 363 127 131 4 504.54 0.34 364 128 131 3 507.26 0.39 365 128 132 4 504.50 0.32 366 129 132 3 507.14 0.14 367 129 133 4 504.49 0.33 368 130 133 3 510.97 1.78 369 130 134 4 503.98 0.04 370 131 134 3 509.36 0.97 371 131 135 4 502.50 0.56 372 132 135 3 508.37 2.38 373 132 136 4 502.49 0.56 374 133 136 3 508.37 2.38 375 133 137 4 503.92 0.15 376 134 137 3 505.36 3.88 377 134 138 4 502.31 0.96 378 135 138 3 504.75 0.26 379 135 139 4 504.74 0.26 380 136 139 3 502.75 0.76 381 136 140 4 495.13 4.54 382 137 140 3 507.41 1.59 383 137 141 4 502.26 0.98 384 138 141 3 518.47 2.99 385 138 142 4 503.19 0.50 386 139 142 3 518.48 2.99 387 139 143 4 502.02 0.09 388 140 143 3 513.40 1.71 389 140 144 4 501.31 0.28 390 141 144 3 509.87 0.74 391 141 145 4 505.75 1.31 392 142 145 3 507.90 2.94 393 142 146 4 502.60 0.27 394 143 146 3 506.93 1.90 395 143 147 4 502.60 0.27 396 144 147 3 512.26 0.77 397 144 148 4 505.13 1.37 398 145 148 3 509.83 0.45 399 145 149 4 500.76 0.82 400 146 149 3 509.28 0.70 401 146 150 4 492.28 5.05 402 146 151 5 345.69 3.16 403 147 150 3 491.36 5.52