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 1 136 135 22.50 0.28 2 2 136 134 23.37 0.04 3 3 7 4 478.04 2.67 4 3 75 72 24.91 0.60 5 3 78 75 24.94 0.59 6 3 79 76 24.96 0.58 7 3 133 130 25.05 0.67 8 3 136 133 24.51 0.40 9 3 137 134 24.89 0.59 10 4 7 3 518.19 6.99 11 4 8 4 500.31 1.96 12 4 79 75 30.48 1.05 13 5 8 3 506.35 1.06 14 5 9 4 500.19 1.90 15 5 79 74 39.63 2.14 16 6 9 3 504.38 0.08 17 6 10 4 500.18 1.90 18 7 10 3 506.99 0.91 19 7 11 4 504.47 0.04 20 7 129 122 49.38 1.29 21 7 132 125 46.50 0.14 22 7 133 126 45.84 0.33 23 7 136 129 45.87 0.34 24 8 11 3 504.91 0.13 25 8 12 4 504.47 0.04 26 8 76 68 45.85 0.33 27 8 79 71 45.85 0.34 28 9 12 3 505.16 0.31 29 9 13 4 504.47 0.04 30 10 13 3 505.47 0.47 31 10 14 4 505.45 0.46 32 10 129 119 65.96 0.37 33 10 130 120 65.86 0.39 34 11 14 3 517.00 1.35 35 11 15 4 505.00 0.69 36 11 72 61 65.69 0.42 37 11 75 64 65.69 0.42 38 11 130 119 65.96 0.38 39 11 133 122 65.84 0.38 40 11 134 123 65.70 0.41 41 12 15 3 507.32 0.45 42 12 16 4 505.02 0.69 43 12 72 60 65.81 0.40 44 13 16 3 508.96 0.36 45 13 17 4 505.04 0.69 46 14 17 3 507.76 0.96 47 14 18 4 504.24 0.29 48 14 118 104 71.56 0.84 49 14 122 108 78.86 2.40 50 14 130 116 71.68 0.80 51 14 134 120 71.55 0.83 52 15 18 3 504.84 0.01 53 15 19 4 504.25 0.29 54 15 69 54 71.55 0.82 55 15 72 57 71.52 0.83 56 15 134 119 71.64 0.82 57 16 19 3 504.82 0.01 58 16 20 4 504.24 0.29 59 17 20 3 515.50 2.88 60 17 25 8 421.45 10.58 61 17 121 104 97.52 0.04 62 17 122 105 97.52 0.04 63 17 125 108 97.53 0.04 64 18 21 3 541.69 3.48 65 18 22 4 514.24 2.25 66 18 25 7 405.58 18.50 67 18 26 8 431.57 5.50 68 18 65 47 96.83 0.36 69 18 68 50 95.55 0.76 70 18 117 99 97.51 0.04 71 18 118 100 97.50 0.04 72 18 121 103 97.52 0.04 73 19 22 3 515.62 2.82 74 21 24 3 517.61 1.80 75 21 25 4 498.26 3.22 76 22 25 3 517.61 1.80 77 22 26 4 498.25 3.23 78 22 61 39 113.85 0.06 79 22 65 43 104.29 1.17 80 23 26 3 520.63 0.58 81 23 27 4 504.66 0.06 82 23 55 32 128.37 1.07 83 23 61 38 118.87 0.04 84 24 27 3 516.34 2.73 85 24 28 4 504.66 0.06 86 25 28 3 498.44 3.18 87 25 29 4 491.79 6.51 88 25 117 92 124.34 0.66 89 25 121 96 129.06 0.19 90 26 29 3 505.19 0.18 91 26 30 4 505.79 0.49 92 26 60 34 136.07 0.48 93 26 61 35 130.81 1.72 94 26 64 38 124.34 0.69 95 26 65 39 124.38 0.70 96 27 30 3 520.97 3.29 97 27 31 4 505.79 0.49 98 27 53 26 138.83 0.00 99 27 54 27 138.81 0.01 100 27 55 28 138.74 0.04 101 27 60 33 137.85 0.09 102 28 31 3 505.79 0.49 103 28 32 4 492.45 2.58 104 28 120 92 138.56 0.12 105 29 32 3 505.93 0.42 106 29 33 4 500.00 1.20 107 29 64 35 138.44 0.16 108 29 68 39 138.00 0.04 109 29 110 81 137.77 0.03 110 29 113 84 137.83 0.05 111 29 114 85 137.80 0.01 112 29 117 88 138.44 0.11 113 30 33 3 505.06 0.01 114 30 34 4 501.32 1.85 115 30 44 14 139.12 0.01 116 30 46 16 139.12 0.00 117 30 47 17 139.12 0.00 118 30 53 23 139.00 0.03 119 30 60 30 138.77 0.04 120 30 64 34 138.58 0.10 121 31 34 3 514.06 1.89 122 31 35 4 510.12 3.85 123 31 53 22 139.00 0.03 124 32 35 3 507.59 0.56 125 32 36 4 504.17 0.01 126 32 113 81 138.28 0.15 127 32 116 84 138.56 0.12 128 32 117 85 138.56 0.12 129 33 36 3 512.59 3.42 130 33 37 4 504.62 0.21 131 33 40 7 370.76 5.29 132 33 109 76 138.28 0.15 133 33 113 80 138.47 0.11 134 34 37 3 504.62 0.21 135 34 38 4 420.85 2.52 136 34 40 6 375.91 7.86 137 34 41 7 304.62 2.48 138 34 47 13 139.24 0.01 139 34 53 19 139.14 0.03 140 36 109 73 138.44 0.12 141 36 112 76 138.51 0.13 142 36 113 77 138.55 0.12 143 36 116 80 138.63 0.12 144 37 40 3 516.20 0.30 145 37 109 72 138.45 0.12 146 38 41 3 525.91 2.54 147 39 42 3 533.98 0.83 148 40 43 3 522.23 0.70 149 40 44 4 513.59 0.70 150 41 44 3 516.88 0.94 151 41 47 6 290.78 3.15 152 41 48 7 262.48 0.38 153 41 49 8 267.65 2.96 154 41 50 9 262.48 0.38 155 41 51 10 201.87 30.68 156 42 48 6 262.48 0.38 157 43 100 57 133.10 1.44 158 43 101 58 133.35 1.56 159 43 106 63 138.22 0.14 160 44 47 3 510.01 3.88 161 44 48 4 474.46 1.14 162 45 48 3 530.91 0.09 163 46 54 8 139.97 0.19 164 46 59 13 139.44 0.13 165 46 60 14 139.43 0.12 166 46 63 17 139.43 0.12 167 47 50 3 516.37 2.11 168 47 53 6 139.93 0.17 169 47 54 7 139.91 0.18 170 47 60 13 139.31 0.18 171 50 54 4 519.25 1.93 172 53 60 7 427.61 0.53 173 54 57 3 515.73 1.05 174 54 60 6 461.55 3.06 175 55 61 6 477.56 1.26 176 56 61 5 484.62 2.57 177 57 60 3 509.52 3.39 178 57 61 4 487.85 1.29 179 58 61 3 499.38 1.68 180 58 62 4 490.16 0.20 181 59 62 3 516.11 2.19 182 59 63 4 487.51 1.12 183 60 63 3 517.71 1.39 184 60 64 4 502.88 8.79 185 61 64 3 510.36 6.70 186 61 65 4 487.87 1.29 187 62 65 3 499.58 1.57 188 62 66 4 491.49 2.47 189 63 66 3 511.59 4.44 190 63 67 4 491.70 2.37 191 64 67 3 507.17 3.88 192 64 68 4 507.90 2.92 193 65 68 3 518.97 2.62 194 65 69 4 507.90 2.91 195 66 69 3 514.32 0.29 196 66 70 4 507.94 2.89 197 67 70 3 511.32 4.58 198 67 71 4 507.94 2.90 199 67 114 47 188.03 0.54 200 68 71 3 508.70 2.50 201 68 72 4 501.66 0.24 202 68 114 46 186.69 0.01 203 68 117 49 188.97 0.58 204 68 118 50 189.59 0.33 205 69 72 3 507.95 2.90 206 69 73 4 501.65 0.24 207 70 73 3 506.21 1.47 208 70 74 4 501.60 0.26 209 70 90 20 185.19 0.65 210 70 93 23 185.17 0.66 211 70 141 71 185.33 0.69 212 71 74 3 501.34 0.08 213 71 75 4 495.94 2.58 214 71 114 43 189.18 0.12 215 71 134 63 189.71 0.36 216 71 137 66 188.98 0.12 217 71 138 67 185.37 0.68 218 71 141 70 185.34 0.69 219 72 75 3 495.31 1.82 220 72 76 4 495.25 1.85 221 72 134 62 189.72 0.36 222 73 76 3 500.81 0.93 223 73 77 4 491.79 0.01 224 74 77 3 493.59 0.89 225 74 78 4 493.58 0.89 226 74 84 10 223.97 17.42 227 74 141 67 188.30 0.44 228 75 78 3 503.41 2.25 229 75 79 4 503.31 2.28 230 75 137 62 189.68 0.37 231 76 79 3 508.88 0.50 232 76 80 4 503.31 2.29 233 77 80 3 504.36 1.76 234 77 81 4 480.22 4.58 235 77 82 5 480.22 4.58 236 77 83 6 366.27 1.23 237 77 84 7 314.00 12.17 238 77 85 8 279.72 4.98 239 78 82 4 405.31 5.13 240 78 83 5 346.89 9.30 241 78 84 6 346.89 9.30 242 78 136 58 236.14 2.01 243 78 137 59 210.52 9.87 244 78 140 62 201.41 5.35 245 84 90 6 497.43 2.86 246 84 140 56 248.98 0.24 247 84 141 57 248.98 0.24 248 84 144 60 248.96 0.25 249 85 90 5 497.43 2.86 250 86 90 4 497.43 2.86 251 86 91 5 497.38 2.85 252 86 144 58 249.34 0.35 253 86 147 61 249.28 0.39 254 86 148 62 249.28 0.39 255 87 90 3 523.49 0.71 256 87 91 4 510.15 3.86 257 88 91 3 513.32 2.27 258 88 92 4 502.79 0.18 259 89 92 3 512.69 2.59 260 89 93 4 502.78 0.18 261 90 93 3 498.92 1.17 262 90 94 4 501.69 0.21 263 90 141 51 250.36 0.58 264 90 144 54 250.14 0.65 265 90 148 58 250.00 0.65 266 91 94 3 501.88 0.12 267 91 95 4 501.87 0.12 268 91 148 57 250.00 0.65 269 92 95 3 514.54 0.12 270 92 96 4 496.76 2.44 271 93 96 3 501.88 0.12 272 93 97 4 501.66 0.22 273 93 145 52 250.37 0.59 274 94 97 3 512.38 2.23 275 94 98 4 502.05 0.68 276 94 145 51 250.37 0.59 277 94 148 54 250.07 0.62 278 94 149 55 250.02 0.65 279 95 98 3 502.06 0.68 280 95 99 4 502.07 0.68 281 95 152 57 249.78 0.69 282 96 99 3 503.36 1.31 283 96 100 4 502.08 0.68 284 97 100 3 502.11 0.67 285 97 101 4 502.07 0.69 286 97 102 5 451.45 7.79 287 97 145 48 250.55 0.60 288 97 149 52 250.39 0.60 289 98 101 3 502.10 0.67 290 98 149 51 250.44 0.58 291 98 152 54 250.05 0.60 292 98 153 55 250.03 0.61 293 102 106 4 514.49 0.32 294 102 107 5 514.38 0.36 295 102 149 47 250.71 0.55 296 103 106 3 518.92 2.53 297 103 107 4 518.92 2.53 298 103 149 46 250.77 0.57 299 104 107 3 527.49 0.52 300 104 108 4 527.95 0.78 301 104 146 42 251.03 0.55 302 104 149 45 251.02 0.56 303 105 108 3 537.18 0.61 304 106 109 3 521.67 3.92 305 106 110 4 511.52 1.09 306 107 110 3 516.12 3.43 307 107 111 4 503.93 1.27 308 107 138 31 253.46 0.34 309 107 142 35 251.47 0.47 310 107 145 38 251.47 0.47 311 107 146 39 251.43 0.48 312 107 149 42 251.45 0.47 313 108 111 3 509.09 0.09 314 108 112 4 506.30 1.31 315 109 112 3 524.38 0.93 316 109 113 4 502.14 0.55 317 110 113 3 511.10 0.91 318 110 114 4 500.71 0.34 319 110 138 28 253.81 0.39 320 111 114 3 518.96 9.36 321 111 115 4 518.96 9.36 322 111 135 24 253.84 0.26 323 111 138 27 253.62 0.36 324 111 139 28 253.62 0.36 325 112 115 3 518.96 9.36 326 112 116 4 500.65 0.21 327 113 116 3 525.27 6.21 328 113 117 4 492.41 3.90 329 114 117 3 502.70 1.50 330 114 118 4 502.70 1.50 331 114 134 20 254.41 0.27 332 114 138 24 254.24 0.32 333 115 118 3 511.06 5.67 334 115 119 4 502.72 1.49 335 115 131 16 254.44 0.26 336 115 134 19 254.42 0.27 337 115 135 20 254.31 0.32 338 116 119 3 506.44 0.36 339 116 120 4 500.13 0.19 340 117 120 3 511.54 2.91 341 117 121 4 500.95 0.60 342 118 121 3 500.96 0.60 343 118 122 4 500.13 0.18 344 118 130 12 254.75 0.20 345 118 134 16 254.57 0.18 346 119 122 3 514.87 0.91 347 119 123 4 500.06 0.20 348 119 126 7 266.67 5.91 349 120 123 3 508.94 1.21 350 122 125 3 507.08 3.74 351 122 126 4 474.47 0.16 352 122 130 8 294.93 0.89 353 123 126 3 523.13 1.22 354 126 130 4 490.94 3.82 355 126 131 5 486.56 6.07 356 127 130 3 510.94 5.54 357 127 131 4 491.14 3.81 358 128 131 3 508.16 3.95 359 128 132 4 491.16 3.81 360 129 132 3 508.81 3.63 361 129 133 4 501.27 0.14 362 130 133 3 507.30 2.88 363 130 134 4 507.30 2.88 364 131 134 3 513.44 3.69 365 131 135 4 498.31 7.37 366 132 135 3 505.55 3.75 367 132 136 4 498.31 7.36 368 133 136 3 501.28 0.67 369 133 137 4 493.34 2.85 370 134 137 3 500.41 6.37 371 134 138 4 493.36 2.84 372 135 138 3 510.74 5.23 373 135 139 4 501.69 5.08 374 136 139 3 507.14 3.43 375 136 140 4 501.69 5.08 376 137 140 3 516.31 2.44 377 137 141 4 501.70 5.08 378 138 141 3 514.00 1.08 379 138 142 4 500.58 0.56 380 139 142 3 509.96 1.58 381 139 143 4 500.58 0.56 382 140 143 3 500.91 0.40 383 140 144 4 500.58 0.56 384 141 144 3 500.58 0.56 385 141 145 4 499.24 3.33 386 142 145 3 499.25 3.33 387 142 146 4 499.24 3.33 388 143 146 3 518.49 3.34 389 143 147 4 500.56 2.68 390 144 147 3 508.87 1.47 391 144 148 4 500.56 2.68 392 145 148 3 512.12 0.16 393 145 149 4 498.20 6.92 394 146 149 3 512.69 0.32 395 146 150 4 498.56 6.75 396 147 150 3 514.73 0.70 397 147 151 4 512.69 0.32 398 148 151 3 512.70 0.32 399 148 152 4 512.69 0.32 400 149 152 3 509.01 2.16 401 149 153 4 489.19 2.06 402 150 153 3 491.10 3.51