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 5 472.88 4.78 2 2 10 8 464.18 1.60 3 2 130 128 37.92 1.33 4 2 133 131 32.49 0.52 5 2 134 132 30.91 0.28 6 3 6 3 515.82 3.73 7 3 7 4 502.51 4.01 8 4 7 3 515.41 1.09 9 4 8 4 502.52 4.02 10 4 79 75 58.72 1.86 11 5 8 3 510.41 0.07 12 5 9 4 502.96 3.80 13 6 9 3 519.60 8.91 14 6 10 4 496.10 0.37 15 6 130 124 67.96 0.53 16 6 133 127 67.96 0.53 17 7 10 3 511.17 3.62 18 7 11 4 496.10 0.38 19 7 76 69 67.97 0.53 20 7 79 72 67.97 0.53 21 7 80 73 67.98 0.53 22 7 134 127 67.97 0.53 23 7 137 130 67.97 0.53 24 8 11 3 510.76 3.42 25 8 12 4 501.86 1.02 26 9 12 3 519.58 1.85 27 9 13 4 502.88 0.51 28 9 126 117 83.16 1.25 29 9 127 118 83.14 1.25 30 9 130 121 83.13 1.26 31 10 13 3 526.07 1.47 32 10 14 4 514.35 0.42 33 10 76 66 83.14 1.25 34 10 130 120 83.14 1.25 35 10 131 121 83.11 1.26 36 10 134 124 83.12 1.25 37 11 14 3 515.69 0.24 38 11 15 4 516.92 0.86 39 11 76 65 83.16 1.24 40 11 77 66 83.16 1.24 41 11 79 68 83.78 0.95 42 12 15 3 519.64 0.04 43 12 16 4 521.36 3.08 44 12 122 110 91.54 1.10 45 13 16 3 521.36 3.08 46 13 17 4 516.84 0.96 47 13 115 102 91.28 1.12 48 13 122 109 91.56 1.11 49 13 123 110 91.52 1.09 50 13 127 114 91.17 1.21 51 13 131 118 90.34 0.97 52 14 17 3 516.83 0.96 53 14 18 4 516.83 0.96 54 14 69 55 171.97 0.62 55 14 72 58 91.00 1.29 56 14 73 59 90.91 1.25 57 14 76 62 90.34 0.97 58 14 77 63 90.34 0.97 59 14 131 117 91.27 1.16 60 15 18 3 516.82 0.96 61 15 19 4 516.82 0.96 62 16 19 3 526.96 3.08 63 16 24 8 485.30 0.47 64 16 119 103 98.58 0.46 65 16 122 106 96.93 1.26 66 17 20 3 525.79 2.89 67 17 21 4 488.25 2.03 68 17 24 7 439.31 7.79 69 17 69 52 183.94 4.11 70 17 115 98 98.59 0.45 71 18 21 3 516.19 1.21 72 18 77 59 169.00 0.85 73 20 23 3 518.70 0.32 74 20 24 4 508.40 1.01 75 20 118 98 153.56 2.19 76 21 24 3 508.40 1.01 77 21 25 4 503.48 1.45 78 21 66 45 190.12 3.60 79 21 69 48 190.09 3.60 80 22 25 3 509.44 1.53 81 22 26 4 505.44 2.48 82 22 62 40 191.15 4.08 83 22 66 44 190.18 3.62 84 23 26 3 509.53 2.52 85 23 27 4 504.09 1.67 86 23 118 95 164.58 2.31 87 24 27 3 511.00 1.79 88 24 28 4 507.73 0.16 89 24 69 45 190.23 3.65 90 24 115 91 164.81 2.27 91 24 118 94 164.59 2.31 92 24 119 95 164.59 2.31 93 25 28 3 508.63 0.60 94 25 29 4 507.74 0.16 95 25 65 40 191.18 4.12 96 25 69 44 190.23 3.65 97 26 29 3 514.25 2.44 98 26 30 4 507.73 0.17 99 26 56 30 210.20 2.39 100 26 61 35 192.52 3.81 101 26 62 36 192.19 3.92 102 27 30 3 514.28 2.02 103 27 31 4 507.79 0.20 104 27 114 87 164.84 2.25 105 27 118 91 164.56 2.35 106 28 31 3 508.88 0.35 107 28 32 4 507.78 0.21 108 28 69 41 191.83 4.42 109 28 107 79 165.40 2.23 110 28 110 82 164.97 2.25 111 28 111 83 164.97 2.25 112 28 114 86 164.88 2.27 113 29 32 3 508.63 0.23 114 29 33 4 506.29 2.10 115 29 61 32 203.25 1.02 116 29 64 35 193.00 4.09 117 29 65 36 192.53 4.09 118 29 107 78 165.40 2.23 119 30 33 3 519.18 4.35 120 30 34 4 504.41 3.04 121 30 52 22 216.59 0.32 122 30 55 25 215.40 0.73 123 30 56 26 216.59 0.34 124 30 61 31 209.34 1.96 125 31 34 3 519.19 4.34 126 31 35 4 504.48 3.01 127 31 110 79 165.22 2.16 128 31 113 82 165.21 2.17 129 31 114 83 165.05 2.24 130 32 35 3 521.60 3.14 131 32 36 4 499.10 5.55 132 32 39 7 421.49 9.98 133 32 106 74 165.41 2.23 134 32 107 75 165.41 2.23 135 32 110 78 165.22 2.16 136 33 36 3 514.23 1.09 137 33 37 4 481.06 4.96 138 33 39 6 427.55 6.96 139 33 40 7 402.38 15.39 140 33 43 10 329.62 6.74 141 33 46 13 256.30 2.10 142 33 55 22 216.93 0.32 143 33 61 28 216.66 0.30 144 34 37 3 519.74 2.20 145 34 52 18 216.96 0.33 146 34 55 21 216.97 0.34 147 36 39 3 532.85 1.72 148 36 106 70 165.55 2.19 149 37 40 3 526.62 1.40 150 38 41 3 534.38 2.48 151 38 103 65 166.14 2.17 152 38 106 68 166.00 2.21 153 39 42 3 526.62 1.40 154 39 43 4 526.62 1.40 155 39 103 64 166.01 2.21 156 39 106 67 165.96 2.19 157 40 43 3 521.53 1.15 158 40 46 6 383.17 9.54 159 40 55 15 228.67 1.10 160 42 98 56 166.54 2.35 161 42 99 57 166.51 2.35 162 42 100 58 166.59 2.33 163 42 103 61 166.38 2.29 164 43 46 3 523.49 1.21 165 43 47 4 518.99 1.04 166 43 64 21 217.06 0.31 167 44 47 3 533.15 1.53 168 45 48 3 615.87 4.65 169 45 60 15 219.99 1.06 170 46 49 3 530.01 0.04 171 46 60 14 220.86 0.62 172 46 61 15 219.99 1.05 173 46 64 18 219.97 1.06 174 47 50 3 607.38 2.36 175 48 54 6 481.48 1.78 176 48 60 12 256.57 2.54 177 49 54 5 481.24 1.68 178 49 55 6 448.24 14.76 179 49 58 9 288.50 2.54 180 49 61 12 260.64 1.81 181 50 54 4 487.91 1.89 182 51 54 3 506.09 0.48 183 51 55 4 497.64 3.75 184 52 55 3 505.31 0.72 185 52 56 4 499.63 1.03 186 53 56 3 513.82 3.54 187 53 57 4 499.62 1.03 188 54 57 3 513.26 2.96 189 54 58 4 496.49 0.54 190 55 58 3 500.38 1.41 191 55 61 6 387.76 9.74 192 58 61 3 509.35 1.07 193 58 62 4 505.72 0.74 194 59 62 3 509.92 1.59 195 59 63 4 505.73 0.73 196 60 63 3 509.92 1.59 197 60 64 4 505.70 0.74 198 61 64 3 519.53 2.06 199 61 65 4 505.69 0.74 200 62 65 3 522.50 0.58 201 62 66 4 505.68 0.75 202 63 66 3 516.50 1.21 203 63 67 4 505.66 0.74 204 64 67 3 505.75 0.80 205 64 68 4 505.73 0.80 206 65 68 3 505.73 0.81 207 65 69 4 503.57 1.91 208 66 69 3 517.58 2.48 209 66 70 4 503.59 1.92 210 67 70 3 514.23 4.16 211 67 71 4 503.79 1.83 212 68 71 3 525.74 1.59 213 68 72 4 503.81 1.84 214 68 107 39 165.35 2.21 215 69 72 3 509.20 2.40 216 69 73 4 503.81 1.85 217 70 73 3 516.77 0.03 218 70 74 4 505.79 0.87 219 71 74 3 516.77 0.03 220 71 75 4 505.81 0.88 221 71 89 18 166.75 2.23 222 72 75 3 514.13 1.35 223 72 76 4 503.82 1.88 224 72 111 39 165.05 2.21 225 72 135 63 161.26 1.35 226 72 138 66 159.26 1.14 227 73 76 3 511.09 0.18 228 73 77 4 509.15 0.79 229 74 77 3 518.88 2.82 230 74 78 4 517.62 3.45 231 75 78 3 520.53 2.00 232 75 82 7 275.01 14.95 233 75 85 10 225.31 0.49 234 75 86 11 225.31 0.49 235 75 89 14 225.29 0.50 236 75 138 63 159.36 1.19 237 76 79 3 520.53 1.99 238 76 131 55 162.05 1.53 239 76 134 58 161.63 1.45 240 78 81 3 492.68 9.29 241 78 82 4 400.17 9.51 242 78 84 6 400.19 9.50 243 78 85 7 301.05 1.93 244 80 137 57 161.41 1.42 245 82 85 3 510.91 2.27 246 82 86 4 495.91 5.94 247 82 137 55 161.42 1.42 248 82 141 59 159.30 1.21 249 83 86 3 507.07 0.35 250 83 87 4 504.45 1.66 251 84 88 4 523.17 1.23 252 85 88 3 547.07 0.11 253 86 89 3 534.62 4.50 254 86 90 4 514.41 0.56 255 86 138 52 160.13 1.08 256 86 141 55 158.87 1.19 257 86 142 56 158.15 1.50 258 86 145 59 153.41 2.27 259 87 90 3 521.11 0.21 260 87 91 4 509.94 1.68 261 88 91 3 523.19 3.51 262 88 92 4 506.45 0.06 263 89 92 3 521.00 4.61 264 89 93 4 509.17 1.29 265 89 138 49 160.19 1.04 266 90 93 3 521.00 4.61 267 90 94 4 504.50 0.91 268 90 142 52 155.97 1.12 269 90 145 55 147.28 0.68 270 90 146 56 146.83 0.86 271 91 94 3 511.37 0.18 272 91 95 4 504.45 0.90 273 91 149 58 142.38 0.02 274 92 95 3 508.30 2.82 275 92 96 4 476.73 8.35 276 92 97 5 466.02 3.00 277 93 97 4 422.43 24.78 278 93 98 5 422.41 24.79 279 93 99 6 332.09 13.24 280 93 146 53 145.49 0.20 281 94 98 4 395.31 11.23 282 94 146 52 144.13 0.48 283 94 149 55 142.16 0.10 284 94 151 57 55.56 0.01 285 95 98 3 523.14 3.65 286 95 149 54 142.59 0.09 287 98 151 53 71.26 0.07 288 99 103 4 514.91 2.00 289 99 104 5 512.01 0.54 290 99 146 47 143.09 0.04 291 99 151 52 66.33 2.53 292 100 103 3 524.03 0.33 293 100 104 4 519.29 0.19 294 100 153 53 15.29 1.10 295 101 104 3 521.10 0.71 296 101 105 4 512.03 0.53 297 101 142 41 153.43 0.67 298 101 143 42 147.68 0.59 299 101 146 45 143.10 0.01 300 102 105 3 523.92 0.70 301 102 106 4 512.03 0.52 302 103 106 3 506.99 2.00 303 103 107 4 505.94 2.52 304 104 107 3 516.78 4.44 305 104 108 4 500.67 1.18 306 104 139 35 157.48 1.31 307 104 142 38 152.87 0.55 308 105 108 3 514.34 5.66 309 105 109 4 505.63 1.30 310 105 139 34 157.49 1.31 311 106 109 3 527.14 1.21 312 106 110 4 511.51 1.64 313 107 110 3 511.57 1.61 314 107 111 4 510.61 2.10 315 108 111 3 513.91 0.92 316 108 112 4 511.51 1.64 317 108 135 27 161.16 1.29 318 108 139 31 157.38 1.25 319 109 112 3 519.89 2.07 320 109 113 4 505.02 1.59 321 110 113 3 515.03 4.51 322 110 114 4 499.63 1.99 323 111 114 3 519.44 2.31 324 111 115 4 507.60 1.99 325 111 135 24 161.17 1.28 326 112 115 3 518.62 2.73 327 112 116 4 507.63 2.00 328 112 123 11 234.91 5.53 329 112 128 16 162.05 1.57 330 112 131 19 161.97 1.55 331 112 132 20 161.78 1.47 332 112 135 23 161.25 1.31 333 113 116 3 508.41 2.38 334 113 117 4 507.65 2.00 335 114 117 3 512.16 0.27 336 114 118 4 507.63 1.99 337 115 118 3 512.16 0.26 338 115 119 4 491.37 1.18 339 115 123 8 253.34 3.68 340 115 131 16 190.90 16.02 341 116 120 4 468.17 2.19 342 116 123 7 235.75 5.24 343 116 128 12 234.90 5.54 344 117 120 3 527.26 2.69 345 119 122 3 511.37 0.46 346 119 123 4 422.18 20.57 347 120 123 3 504.12 4.08 348 122 127 5 477.10 2.03 349 123 127 4 477.10 2.03 350 123 128 5 476.99 2.08 351 123 131 8 423.47 16.69 352 124 127 3 505.61 1.79 353 124 128 4 501.96 3.62 354 125 128 3 501.97 3.62 355 125 129 4 501.97 3.62 356 126 129 3 508.73 0.24 357 126 130 4 502.37 3.42 358 127 130 3 514.35 2.77 359 127 131 4 494.59 0.70 360 128 131 3 509.81 0.29 361 128 132 4 494.59 0.71 362 129 132 3 512.12 0.86 363 129 133 4 504.96 4.44 364 130 133 3 508.54 2.65 365 130 134 4 504.98 4.43 366 131 134 3 512.36 0.74 367 131 135 4 508.62 2.61 368 132 135 3 520.00 1.06 369 132 136 4 508.69 2.58 370 133 136 3 509.43 2.21 371 133 137 4 498.86 2.37 372 134 137 3 518.00 2.07 373 134 138 4 498.33 2.66 374 135 138 3 499.48 2.09 375 135 139 4 499.48 2.09 376 136 139 3 499.48 2.09 377 136 140 4 499.46 2.08 378 137 140 3 506.56 1.45 379 137 141 4 497.23 3.21 380 138 141 3 517.91 2.27 381 138 142 4 507.69 7.38 382 139 142 3 517.91 2.27 383 139 143 4 501.25 2.27 384 140 143 3 515.91 3.27 385 140 144 4 507.17 0.69 386 141 144 3 511.24 2.71 387 141 145 4 507.20 0.67 388 142 145 3 507.48 0.58 389 142 146 4 507.26 0.64 390 143 146 3 508.94 0.20 391 143 147 4 507.26 0.64 392 144 147 3 509.03 0.26 393 144 148 4 509.01 0.26 394 145 148 3 508.62 0.46 395 145 149 4 508.62 0.46 396 146 149 3 520.65 1.18 397 146 150 4 501.05 2.42 398 146 151 5 337.56 9.09 399 146 152 6 334.98 9.99 400 147 150 3 503.13 0.49