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 5 494.17 0.01 2 2 10 8 481.55 5.77 3 2 130 128 39.16 0.11 4 2 133 131 32.29 1.24 5 2 134 132 30.57 0.40 6 2 137 135 30.56 0.41 7 3 6 3 511.93 2.71 8 3 7 4 501.35 1.41 9 4 7 3 515.42 0.96 10 4 8 4 508.40 2.12 11 4 79 75 51.05 1.51 12 5 8 3 515.34 1.01 13 5 9 4 512.72 0.04 14 6 9 3 526.81 0.83 15 6 10 4 512.75 0.03 16 6 130 124 65.64 0.97 17 6 133 127 65.60 0.99 18 7 10 3 525.92 0.39 19 7 11 4 509.76 1.47 20 7 76 69 65.67 0.99 21 7 79 72 65.62 1.01 22 7 80 73 65.69 0.99 23 7 134 127 65.61 1.00 24 7 137 130 65.66 0.98 25 8 11 3 520.00 1.36 26 8 12 4 507.53 2.58 27 8 79 71 72.18 0.06 28 9 12 3 508.44 2.12 29 9 13 4 508.38 2.14 30 9 126 117 75.97 0.48 31 9 127 118 74.96 0.85 32 9 130 121 74.86 0.81 33 10 13 3 509.76 1.37 34 10 14 4 518.42 3.63 35 10 130 120 74.88 0.82 36 10 131 121 74.40 0.58 37 10 134 124 74.35 0.58 38 11 14 3 518.43 3.62 39 11 15 4 518.42 3.63 40 11 76 65 74.87 0.81 41 11 77 66 74.97 0.77 42 11 79 68 74.86 0.82 43 12 15 3 523.62 1.04 44 13 16 3 528.18 2.94 45 13 17 4 520.78 2.60 46 13 115 102 85.49 3.35 47 13 123 110 78.64 0.07 48 13 131 118 77.19 0.76 49 14 17 3 514.25 1.64 50 14 18 4 513.69 1.92 51 14 69 55 133.69 27.45 52 14 72 58 77.52 0.58 53 14 73 59 77.19 0.75 54 14 76 62 77.19 0.73 55 14 77 63 77.19 0.75 56 15 18 3 526.17 0.10 57 15 19 4 513.70 1.92 58 16 19 3 537.70 0.72 59 16 24 8 442.57 8.15 60 16 119 103 109.48 1.93 61 16 122 106 106.63 0.55 62 17 20 3 537.70 0.72 63 17 21 4 493.38 3.35 64 17 24 7 391.68 9.96 65 17 69 52 206.16 2.42 66 17 115 98 106.63 0.56 67 18 21 3 519.87 3.27 68 18 77 59 137.75 16.70 69 20 23 3 530.17 1.79 70 20 24 4 506.79 4.87 71 21 24 3 511.22 2.71 72 21 25 4 506.80 4.88 73 21 66 45 206.62 2.56 74 21 69 48 206.50 2.54 75 21 70 49 206.57 2.56 76 22 25 3 516.55 1.26 77 22 26 4 506.80 4.88 78 22 62 40 207.42 2.65 79 22 66 44 206.81 2.49 80 23 26 3 519.00 1.17 81 23 27 4 513.06 1.84 82 23 118 95 167.30 0.45 83 24 27 3 518.90 1.22 84 24 28 4 511.26 0.93 85 24 69 45 206.83 2.46 86 24 118 94 167.30 0.45 87 24 119 95 167.81 0.20 88 25 28 3 517.35 2.35 89 25 29 4 513.78 0.27 90 25 65 40 207.31 2.71 91 25 69 44 206.84 2.47 92 26 29 3 519.26 1.40 93 26 30 4 502.86 5.21 94 26 56 30 218.69 0.79 95 26 61 35 207.84 2.65 96 26 62 36 207.66 2.68 97 27 30 3 517.67 2.19 98 27 31 4 511.95 0.67 99 27 114 87 169.22 0.26 100 27 118 91 168.55 0.02 101 28 31 3 517.50 2.10 102 28 32 4 511.97 0.67 103 28 69 41 207.44 2.68 104 28 107 79 169.75 0.07 105 28 110 82 169.38 0.20 106 28 111 83 169.40 0.19 107 28 114 86 169.22 0.26 108 29 32 3 527.17 0.35 109 29 33 4 518.56 3.96 110 29 61 32 212.01 0.95 111 29 64 35 211.47 0.78 112 29 65 36 211.46 0.78 113 29 107 78 169.78 0.08 114 30 33 3 523.00 1.74 115 30 34 4 518.55 3.97 116 30 52 22 221.74 2.01 117 30 55 25 221.61 2.03 118 30 56 26 221.63 2.04 119 30 61 31 214.02 1.80 120 31 34 3 525.57 0.47 121 31 35 4 511.95 0.69 122 31 110 79 169.38 0.21 123 31 113 82 169.25 0.26 124 31 114 83 169.25 0.27 125 32 35 3 525.56 0.47 126 32 36 4 508.62 0.97 127 32 39 7 361.89 6.12 128 32 106 74 169.85 0.08 129 32 107 75 169.81 0.09 130 33 36 3 522.75 1.88 131 33 37 4 478.50 8.15 132 33 39 6 364.71 4.71 133 33 40 7 312.32 0.57 134 33 43 10 314.21 0.35 135 33 55 22 222.98 2.56 136 33 61 28 221.62 1.97 137 34 37 3 522.73 0.12 138 34 52 18 223.36 2.73 139 34 55 21 225.36 1.38 140 36 39 3 529.75 2.49 141 36 106 70 169.94 0.12 142 37 40 3 533.42 4.33 143 38 41 3 535.60 3.23 144 38 103 65 170.55 0.10 145 38 106 68 170.49 0.10 146 39 42 3 533.97 4.05 147 39 43 4 517.99 1.14 148 39 103 64 170.33 0.09 149 39 106 67 170.40 0.12 150 40 43 3 526.52 0.91 151 40 46 6 367.93 9.43 152 40 47 7 267.04 10.10 153 40 49 9 271.54 7.84 154 40 50 10 248.03 0.58 155 40 55 15 247.27 0.34 156 41 47 6 289.97 2.41 157 42 97 55 170.94 0.17 158 42 98 56 170.93 0.17 159 42 99 57 170.79 0.15 160 42 100 58 170.94 0.18 161 42 103 61 170.63 0.08 162 43 46 3 522.28 1.50 163 43 47 4 479.19 18.27 164 43 64 21 231.91 1.27 165 44 47 3 531.49 3.10 166 45 48 3 613.09 5.05 167 46 49 3 532.17 1.35 168 46 60 14 242.25 2.10 169 46 61 15 239.33 3.54 170 46 64 18 237.88 4.17 171 47 50 3 544.06 1.81 172 48 54 6 488.19 4.58 173 49 54 5 488.13 4.60 174 49 55 6 467.64 12.32 175 49 58 9 393.23 20.48 176 49 61 12 274.15 0.92 177 50 54 4 508.02 1.34 178 50 55 5 501.16 1.90 179 51 54 3 526.35 2.18 180 51 55 4 511.65 0.47 181 52 55 3 517.29 2.35 182 52 56 4 511.97 0.31 183 53 56 3 517.29 2.35 184 53 57 4 517.29 2.35 185 54 57 3 516.23 1.81 186 54 58 4 516.23 1.82 187 55 58 3 530.17 3.13 188 55 61 6 486.92 4.70 189 58 61 3 527.96 1.86 190 58 62 4 521.42 3.10 191 59 62 3 521.42 3.10 192 59 63 4 521.42 3.10 193 60 63 3 527.74 0.07 194 60 64 4 521.42 3.10 195 61 64 3 527.74 0.07 196 61 65 4 505.67 1.64 197 62 65 3 518.61 4.50 198 62 66 4 509.12 0.08 199 63 66 3 514.57 2.64 200 63 67 4 510.24 0.64 201 64 67 3 520.48 0.33 202 64 68 4 511.10 0.24 203 65 68 3 518.86 0.50 204 65 69 4 511.59 0.49 205 66 69 3 520.50 0.32 206 66 70 4 514.23 1.82 207 67 70 3 519.17 0.64 208 67 71 4 514.23 1.82 209 68 71 3 519.17 0.63 210 68 72 4 514.21 1.83 211 68 107 39 170.03 0.01 212 69 72 3 514.21 1.83 213 69 73 4 510.31 0.10 214 69 111 42 169.87 0.03 215 70 73 3 511.24 0.55 216 70 74 4 517.42 3.46 217 71 74 3 521.56 1.39 218 71 75 4 521.54 1.39 219 72 75 3 528.73 2.20 220 72 76 4 521.54 1.39 221 72 111 39 170.02 0.02 222 72 135 63 167.91 0.04 223 72 138 66 166.15 0.01 224 73 76 3 530.95 1.09 225 73 77 4 521.55 1.39 226 74 77 3 534.33 3.22 227 74 78 4 517.45 0.66 228 75 78 3 525.58 0.58 229 75 82 7 287.63 6.28 230 75 85 10 171.40 0.16 231 75 89 14 171.38 0.15 232 75 138 63 166.81 0.17 233 76 79 3 531.40 0.25 234 76 134 58 167.96 0.01 235 78 81 3 493.40 0.19 236 78 82 4 420.27 10.19 237 78 85 7 358.68 9.31 238 80 137 57 168.06 0.01 239 82 85 3 531.84 1.80 240 82 86 4 504.84 2.41 241 82 137 55 168.13 0.04 242 82 141 59 166.15 0.01 243 83 86 3 528.79 3.33 244 83 87 4 496.94 0.83 245 84 88 4 517.71 0.12 246 85 88 3 545.04 1.17 247 85 89 4 517.10 0.18 248 86 89 3 536.20 3.25 249 86 90 4 506.96 1.73 250 86 138 52 167.22 0.05 251 86 141 55 165.38 0.34 252 86 142 56 165.09 0.27 253 86 145 59 158.79 1.22 254 87 90 3 519.72 1.49 255 87 91 4 508.05 1.19 256 87 145 58 154.40 0.21 257 87 148 61 154.23 0.28 258 88 91 3 522.14 0.28 259 88 92 4 497.83 2.84 260 89 92 3 526.01 2.21 261 89 93 4 497.82 2.85 262 90 93 3 519.91 0.64 263 90 94 4 498.45 3.96 264 90 142 52 164.77 0.12 265 90 145 55 154.24 0.29 266 90 146 56 154.22 0.28 267 91 94 3 516.47 0.12 268 91 95 4 488.42 3.67 269 91 149 58 149.41 0.35 270 92 96 4 470.11 2.34 271 92 97 5 454.69 10.04 272 93 97 4 426.14 24.32 273 93 98 5 317.14 2.32 274 93 99 6 313.89 3.92 275 93 146 53 154.22 0.29 276 94 98 4 316.25 2.77 277 94 146 52 154.09 0.35 278 94 149 55 143.38 0.51 279 94 151 57 71.56 1.47 280 95 98 3 525.56 4.75 281 95 149 54 149.18 0.35 282 98 151 53 74.41 0.32 283 99 103 4 501.38 4.80 284 99 104 5 501.74 0.59 285 99 146 47 154.09 0.35 286 99 151 52 71.37 1.55 287 100 103 3 524.34 2.88 288 100 146 46 151.06 0.36 289 100 151 51 70.97 1.61 290 100 153 53 15.53 2.17 291 101 104 3 509.12 0.93 292 101 105 4 505.77 2.60 293 101 139 38 165.28 0.35 294 101 142 41 160.16 0.52 295 101 143 42 154.22 0.29 296 101 146 45 149.62 0.30 297 102 105 3 504.65 0.29 298 102 106 4 505.63 0.17 299 103 106 3 512.02 0.07 300 103 107 4 505.65 0.17 301 104 107 3 525.35 2.70 302 104 108 4 505.65 0.17 303 104 139 35 164.88 0.17 304 104 142 38 157.09 1.02 305 105 108 3 517.96 0.99 306 105 109 4 510.63 2.67 307 105 139 34 164.88 0.17 308 106 109 3 515.62 0.17 309 106 110 4 510.63 2.67 310 107 110 3 510.56 2.71 311 107 111 4 510.56 2.71 312 108 111 3 519.73 4.29 313 108 112 4 513.55 1.21 314 108 135 27 167.47 0.10 315 108 139 31 164.87 0.18 316 109 112 3 517.89 0.96 317 109 113 4 510.12 2.79 318 110 113 3 525.25 4.66 319 110 114 4 510.11 2.79 320 111 114 3 528.04 3.26 321 111 115 4 510.10 2.79 322 111 135 24 167.53 0.12 323 112 115 3 521.07 0.33 324 112 116 4 509.03 2.94 325 112 123 11 264.48 0.14 326 112 128 16 168.19 0.02 327 112 131 19 168.01 0.01 328 112 132 20 167.92 0.03 329 112 135 23 167.89 0.04 330 113 116 3 522.86 0.25 331 113 117 4 512.44 4.64 332 114 117 3 512.44 4.64 333 114 118 4 512.42 4.63 334 115 118 3 527.91 2.16 335 115 119 4 512.41 4.63 336 115 123 8 264.76 0.01 337 115 131 16 216.87 16.89 338 116 119 3 526.96 2.64 339 116 120 4 466.41 2.56 340 116 123 7 270.44 0.58 341 116 128 12 261.50 1.34 342 117 120 3 531.67 2.52 343 119 122 3 505.40 3.16 344 119 123 4 482.44 6.52 345 123 127 4 504.58 0.10 346 123 128 5 496.07 4.35 347 123 131 8 468.48 9.44 348 124 127 3 510.32 2.77 349 124 128 4 504.56 0.12 350 125 128 3 504.61 0.11 351 125 129 4 504.57 0.12 352 126 129 3 514.77 4.97 353 126 130 4 505.01 0.09 354 127 130 3 518.37 3.18 355 127 131 4 504.50 0.08 356 128 131 3 512.88 4.11 357 128 132 4 504.78 0.06 358 129 132 3 513.24 4.29 359 129 133 4 504.69 0.10 360 130 133 3 523.01 3.35 361 130 134 4 510.58 2.85 362 131 134 3 510.40 2.95 363 131 135 4 504.29 0.39 364 132 135 3 513.05 1.62 365 132 136 4 509.31 2.85 366 133 136 3 516.65 6.07 367 133 137 4 509.34 2.87 368 134 137 3 520.62 5.71 369 134 138 4 509.38 2.85 370 135 138 3 518.86 6.59 371 135 139 4 509.44 2.83 372 136 139 3 509.45 2.83 373 136 140 4 509.42 2.82 374 137 140 3 511.33 1.83 375 137 141 4 509.38 2.80 376 138 141 3 517.92 1.47 377 138 142 4 509.38 2.80 378 139 142 3 517.91 1.47 379 139 143 4 497.78 2.98 380 140 143 3 494.49 1.32 381 140 144 4 494.04 1.09 382 141 144 3 508.25 1.84 383 141 145 4 508.25 1.84 384 142 145 3 511.41 0.26 385 142 146 4 507.36 2.29 386 143 146 3 503.92 0.96 387 143 147 4 498.86 1.37 388 144 147 3 520.73 0.06 389 144 148 4 508.47 2.85 390 145 148 3 517.54 1.69 391 145 149 4 507.89 3.14 392 146 149 3 509.60 2.29 393 146 150 4 507.88 3.13 394 146 151 5 376.76 8.96 395 147 150 3 494.57 3.48