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 5 491.95 4.38 2 2 10 8 487.54 6.39 3 2 130 128 52.56 1.48 4 2 133 131 28.94 2.94 5 2 134 132 28.87 2.98 6 2 137 135 28.61 2.85 7 3 6 3 519.80 0.02 8 3 7 4 513.06 3.35 9 4 7 3 518.21 0.78 10 4 8 4 513.06 3.35 11 5 8 3 524.64 1.86 12 5 9 4 518.21 0.78 13 6 9 3 522.52 2.94 14 6 10 4 515.81 2.09 15 6 130 124 69.67 1.40 16 6 133 127 69.67 1.40 17 7 10 3 527.35 0.52 18 7 11 4 515.90 2.07 19 7 76 69 69.70 1.41 20 7 79 72 69.68 1.39 21 7 80 73 69.68 1.39 22 7 134 127 69.68 1.40 23 7 137 130 69.68 1.40 24 8 11 3 525.02 0.65 25 8 12 4 515.91 2.07 26 9 12 3 519.04 3.64 27 9 13 4 515.91 2.08 28 9 126 117 83.63 1.27 29 9 127 118 80.17 1.73 30 9 130 121 80.09 1.69 31 10 13 3 523.75 0.02 32 10 14 4 515.88 2.06 33 10 76 66 80.08 1.70 34 10 130 120 80.10 1.69 35 10 131 121 79.96 1.64 36 10 134 124 79.96 1.64 37 11 14 3 519.57 0.12 38 11 15 4 519.57 0.12 39 11 76 65 80.09 1.68 40 11 77 66 81.65 0.90 41 12 15 3 521.50 1.08 42 13 16 3 527.35 1.78 43 13 17 4 521.79 0.99 44 13 115 102 91.56 0.85 45 13 123 110 92.11 1.12 46 13 127 114 88.69 0.57 47 13 131 118 88.64 0.56 48 14 17 3 525.12 2.90 49 14 18 4 513.78 2.77 50 14 69 55 189.31 0.98 51 14 72 58 88.66 0.56 52 14 73 59 88.64 0.56 53 14 76 62 88.48 0.48 54 14 131 117 88.69 0.57 55 15 18 3 513.89 2.82 56 15 19 4 514.91 2.15 57 16 19 3 523.16 1.28 58 16 24 8 448.62 2.53 59 16 119 103 108.73 0.48 60 17 20 3 526.26 0.22 61 17 21 4 470.06 13.52 62 17 24 7 411.76 4.71 63 17 69 52 208.16 1.46 64 17 115 98 108.64 0.51 65 18 21 3 524.01 0.94 66 18 77 59 181.13 0.76 67 20 23 3 534.90 1.97 68 20 24 4 519.58 0.23 69 21 24 3 522.64 0.40 70 21 25 4 511.00 0.73 71 21 66 45 211.91 3.08 72 21 69 48 211.86 3.10 73 21 70 49 211.81 3.12 74 22 25 3 519.86 0.10 75 22 26 4 519.86 0.10 76 22 62 40 213.58 2.46 77 22 66 44 211.91 3.09 78 23 26 3 529.54 4.88 79 23 27 4 520.34 0.14 80 23 62 39 213.66 2.42 81 24 27 3 523.41 1.67 82 24 28 4 520.35 0.14 83 24 69 45 211.88 3.11 84 24 114 90 165.78 0.41 85 24 115 91 165.78 0.40 86 24 118 94 164.75 0.03 87 24 119 95 164.66 0.08 88 25 28 3 522.19 0.78 89 25 29 4 520.31 0.15 90 25 65 40 213.12 2.65 91 25 69 44 211.90 3.11 92 26 29 3 533.60 2.40 93 26 30 4 514.90 2.86 94 26 56 30 228.46 2.40 95 26 61 35 213.77 2.43 96 26 62 36 213.72 2.41 97 26 65 39 213.56 2.47 98 27 30 3 524.72 2.04 99 27 31 4 520.32 0.15 100 27 114 87 165.81 0.42 101 27 118 91 164.78 0.01 102 28 31 3 523.89 0.78 103 28 32 4 515.56 2.29 104 28 69 41 213.55 2.45 105 28 107 79 166.71 0.36 106 28 110 82 166.19 0.28 107 28 111 83 166.16 0.27 108 28 114 86 165.81 0.41 109 29 32 3 521.61 1.43 110 29 33 4 505.79 1.70 111 29 61 32 214.13 2.30 112 29 64 35 214.02 2.31 113 29 65 36 213.97 2.29 114 29 107 78 166.71 0.37 115 30 33 3 521.61 1.43 116 30 34 4 507.40 0.88 117 30 52 22 231.61 2.38 118 30 55 25 230.68 2.03 119 30 56 26 230.69 2.02 120 30 61 31 215.65 2.95 121 31 34 3 521.61 1.43 122 31 35 4 505.74 1.71 123 31 110 79 166.38 0.38 124 31 113 82 166.03 0.53 125 31 114 83 166.10 0.41 126 32 35 3 521.31 2.23 127 32 36 4 498.52 0.03 128 32 39 7 363.52 12.84 129 32 106 74 166.78 0.36 130 32 107 75 166.75 0.37 131 32 110 78 166.53 0.45 132 33 36 3 520.28 2.75 133 33 37 4 472.84 3.39 134 33 39 6 380.68 4.25 135 33 40 7 297.51 3.16 136 33 43 10 295.49 2.14 137 33 46 13 267.36 2.73 138 33 55 22 232.00 2.32 139 33 61 28 231.74 2.41 140 34 52 18 231.99 2.33 141 34 55 21 232.00 2.32 142 36 39 3 536.95 1.94 143 36 106 70 167.34 0.50 144 36 109 73 167.33 0.51 145 37 40 3 536.15 2.33 146 38 41 3 528.50 1.50 147 38 103 65 167.87 0.51 148 38 106 68 167.79 0.53 149 39 42 3 530.15 0.39 150 39 43 4 530.15 0.39 151 39 103 64 167.66 0.51 152 39 106 67 167.49 0.52 153 40 43 3 530.15 0.39 154 40 46 6 365.19 10.53 155 40 47 7 297.99 3.36 156 40 55 15 251.18 4.25 157 41 47 6 411.35 10.13 158 42 97 55 168.25 0.42 159 42 98 56 168.24 0.43 160 42 99 57 168.13 0.48 161 42 100 58 168.15 0.47 162 42 103 61 168.02 0.46 163 43 46 3 523.83 0.94 164 43 47 4 518.89 2.87 165 43 64 21 232.95 2.94 166 44 47 3 547.71 0.41 167 45 48 3 635.18 0.21 168 45 60 15 233.35 2.80 169 46 49 3 533.94 1.49 170 46 60 14 237.84 5.04 171 46 61 15 233.34 2.80 172 46 64 18 237.83 5.04 173 48 54 6 493.09 2.81 174 49 54 5 451.87 0.42 175 49 55 6 381.86 2.23 176 49 58 9 320.82 2.83 177 49 61 12 293.04 11.03 178 50 54 4 523.48 7.30 179 51 54 3 530.29 3.90 180 51 55 4 523.48 7.30 181 52 55 3 526.35 5.88 182 52 56 4 523.48 7.30 183 53 56 3 526.48 5.80 184 53 57 4 523.48 7.30 185 54 57 3 519.91 3.85 186 54 58 4 509.62 3.41 187 55 58 3 510.56 2.94 188 55 61 6 452.12 7.69 189 58 61 3 517.03 0.56 190 58 62 4 517.03 0.55 191 59 62 3 517.03 0.56 192 59 63 4 517.02 0.56 193 60 63 3 517.03 0.56 194 60 64 4 517.01 0.56 195 61 64 3 523.73 3.73 196 61 65 4 513.15 1.38 197 62 65 3 511.38 0.38 198 62 66 4 509.91 0.28 199 63 66 3 513.71 2.18 200 63 67 4 508.44 1.01 201 64 67 3 519.55 4.67 202 64 68 4 508.31 0.95 203 65 68 3 517.84 5.63 204 65 69 4 509.65 1.60 205 66 69 3 525.61 1.75 206 66 70 4 513.68 4.51 207 67 70 3 516.92 6.08 208 67 71 4 523.52 0.41 209 68 71 3 523.60 0.37 210 68 72 4 518.64 2.85 211 68 107 39 166.67 0.38 212 69 72 3 523.52 0.41 213 69 73 4 509.50 1.73 214 69 111 42 166.13 0.24 215 70 73 3 519.70 1.81 216 70 74 4 509.50 1.73 217 71 74 3 512.17 3.06 218 71 75 4 514.88 2.77 219 72 75 3 514.89 2.77 220 72 76 4 514.91 2.79 221 72 111 39 166.24 0.18 222 72 135 63 162.46 0.38 223 72 138 66 158.79 0.05 224 73 76 3 522.66 2.50 225 73 77 4 515.01 2.74 226 74 77 3 526.51 0.58 227 74 78 4 523.03 2.32 228 75 78 3 528.48 1.56 229 75 79 4 523.03 2.32 230 75 82 7 260.22 4.44 231 75 85 10 198.80 15.20 232 75 86 11 204.09 17.84 233 75 89 14 169.27 0.43 234 75 138 63 160.92 0.17 235 76 79 3 522.83 2.43 236 76 131 55 162.69 0.40 237 76 134 58 162.52 0.35 238 78 81 3 511.12 1.93 239 78 82 4 408.45 20.46 240 78 85 7 309.03 8.33 241 80 137 57 162.56 0.44 242 82 85 3 525.64 1.54 243 82 86 4 510.23 4.50 244 82 137 55 162.63 0.41 245 82 141 59 160.25 0.75 246 83 86 3 524.00 2.37 247 83 87 4 510.62 3.61 248 84 88 4 531.27 1.28 249 85 88 3 549.02 1.18 250 86 89 3 526.49 1.11 251 86 90 4 516.49 3.89 252 86 138 52 162.35 0.51 253 86 141 55 158.44 0.04 254 86 142 56 158.37 0.07 255 86 145 59 157.22 0.07 256 87 90 3 525.22 1.74 257 87 91 4 505.38 1.67 258 87 145 58 154.37 1.50 259 88 91 3 519.96 2.16 260 88 92 4 511.03 1.81 261 89 92 3 531.78 3.91 262 89 93 4 511.03 1.81 263 89 138 49 162.34 0.52 264 89 142 53 158.33 0.07 265 90 93 3 520.56 2.94 266 90 94 4 500.99 3.21 267 90 142 52 158.19 0.12 268 90 145 55 147.90 0.38 269 90 146 56 143.44 0.65 270 91 94 3 519.38 3.53 271 91 95 4 505.15 1.14 272 91 149 58 140.91 0.06 273 92 95 3 531.11 2.33 274 92 96 4 475.52 3.06 275 92 97 5 466.83 1.28 276 93 97 4 424.59 19.80 277 93 98 5 424.57 19.80 278 93 99 6 291.89 0.06 279 93 142 49 158.15 0.10 280 93 146 53 143.44 0.66 281 94 146 52 143.41 0.65 282 94 149 55 135.80 0.84 283 94 151 57 105.12 4.48 284 95 98 3 524.88 1.47 285 95 151 56 123.11 0.69 286 99 103 4 525.58 2.29 287 99 104 5 514.53 2.25 288 99 146 47 143.43 0.65 289 100 103 3 530.88 4.95 290 100 104 4 525.58 2.29 291 101 104 3 525.58 2.29 292 101 105 4 525.58 2.29 293 101 143 42 151.47 0.55 294 101 146 45 143.44 0.67 295 101 153 52 25.61 3.25 296 102 105 3 523.98 3.10 297 102 106 4 522.10 4.04 298 103 106 3 519.59 2.78 299 103 107 4 519.58 2.77 300 104 107 3 519.93 2.61 301 104 108 4 514.49 2.25 302 104 139 35 158.53 0.15 303 104 142 38 155.25 1.25 304 105 108 3 525.45 0.15 305 105 109 4 513.32 1.71 306 105 139 34 158.55 0.16 307 106 109 3 517.51 0.48 308 106 110 4 517.50 0.48 309 107 110 3 517.50 0.48 310 107 111 4 516.64 0.05 311 108 111 3 525.17 0.68 312 108 112 4 514.08 0.05 313 108 135 27 162.44 0.39 314 108 139 31 158.55 0.16 315 109 112 3 528.11 2.15 316 109 113 4 513.83 0.18 317 110 113 3 513.56 0.04 318 110 114 4 513.52 6.63 319 111 114 3 522.17 2.31 320 111 115 4 513.53 6.62 321 111 135 24 162.47 0.36 322 112 115 3 519.91 3.44 323 112 116 4 513.53 6.63 324 112 123 11 266.08 1.10 325 112 131 19 162.61 0.37 326 112 132 20 162.58 0.36 327 112 135 23 162.47 0.36 328 113 116 3 522.17 2.31 329 113 117 4 513.54 6.63 330 114 117 3 522.17 2.31 331 114 118 4 513.52 6.63 332 115 118 3 523.15 1.82 333 115 119 4 515.50 1.02 334 115 123 8 297.51 1.54 335 115 131 16 168.87 3.50 336 116 119 3 521.90 1.54 337 116 120 4 502.25 5.61 338 116 123 7 283.18 2.86 339 116 128 12 228.24 19.65 340 117 120 3 539.14 1.02 341 119 122 3 515.48 1.02 342 119 123 4 485.28 4.29 343 120 123 3 520.59 0.11 344 122 127 5 488.94 6.00 345 123 127 4 488.94 6.00 346 123 128 5 488.88 6.02 347 123 131 8 451.06 6.49 348 124 127 3 528.57 3.46 349 124 128 4 513.13 2.82 350 125 128 3 520.59 0.53 351 125 129 4 513.14 2.82 352 126 129 3 532.08 6.65 353 126 130 4 513.53 2.63 354 127 130 3 520.21 0.71 355 127 131 4 513.52 2.62 356 128 131 3 515.98 1.40 357 128 132 4 513.50 2.62 358 129 132 3 519.98 3.32 359 129 133 4 512.13 2.59 360 130 133 3 519.98 3.32 361 130 134 4 508.75 0.90 362 131 134 3 509.19 0.68 363 131 135 4 508.75 0.89 364 132 135 3 517.04 0.89 365 132 136 4 509.19 0.65 366 133 136 3 513.29 2.46 367 133 137 4 509.20 0.66 368 134 137 3 509.79 0.95 369 134 138 4 507.61 1.45 370 135 138 3 511.32 1.72 371 135 139 4 501.56 1.57 372 136 139 3 522.24 3.73 373 136 140 4 509.69 2.54 374 137 140 3 523.13 3.28 375 137 141 4 503.97 5.40 376 138 141 3 524.60 4.01 377 138 142 4 495.86 1.34 378 139 142 3 523.65 4.48 379 139 143 4 505.67 6.25 380 140 143 3 516.34 0.93 381 140 144 4 505.68 6.25 382 141 144 3 511.17 3.51 383 141 145 4 501.72 8.23 384 142 145 3 528.72 2.33 385 142 146 4 510.00 0.86 386 143 146 3 524.14 6.21 387 143 147 4 516.16 3.94 388 143 153 10 21.89 4.69 389 144 147 3 516.91 3.57 390 144 148 4 519.47 2.29 391 145 148 3 513.32 0.80 392 145 149 4 513.31 0.80 393 146 149 3 515.53 1.90 394 146 150 4 515.52 1.90 395 146 151 5 404.91 2.65 396 146 152 6 381.99 8.80 397 146 153 7 249.34 2.04 398 147 150 3 517.36 0.98 399 147 151 4 469.47 2.38 400 147 153 6 259.12 2.54