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 10 8 466.41 0.59 2 2 130 128 45.30 0.93 3 2 133 131 32.94 0.58 4 2 134 132 32.46 0.75 5 2 137 135 31.59 1.12 6 3 6 3 513.65 2.76 7 3 7 4 509.40 0.58 8 4 7 3 517.88 2.68 9 4 8 4 509.40 0.58 10 4 79 75 57.48 0.46 11 5 8 3 518.22 2.43 12 5 9 4 509.41 0.58 13 6 9 3 526.55 4.19 14 6 10 4 505.01 1.61 15 6 130 124 67.06 1.34 16 6 133 127 67.07 1.33 17 7 10 3 515.19 2.74 18 7 11 4 506.56 2.39 19 7 76 69 70.35 0.30 20 7 79 72 70.33 0.29 21 7 80 73 70.34 0.29 22 7 134 127 67.09 1.34 23 7 137 130 67.09 1.34 24 8 11 3 524.12 2.62 25 8 12 4 506.25 2.14 26 9 12 3 526.33 1.52 27 9 13 4 514.11 1.79 28 9 126 117 82.31 0.80 29 9 127 118 82.20 0.78 30 9 130 121 82.12 0.82 31 10 13 3 525.01 1.99 32 10 14 4 515.20 1.25 33 10 76 66 82.20 0.78 34 10 130 120 82.20 0.78 35 10 131 121 82.11 0.82 36 10 134 124 82.06 0.80 37 11 14 3 515.21 1.25 38 11 15 4 515.20 1.25 39 11 76 65 82.23 0.77 40 11 77 66 82.24 0.77 41 11 79 68 82.24 0.77 42 12 15 3 523.38 2.88 43 12 16 4 516.12 0.78 44 12 122 110 90.39 1.16 45 13 16 3 521.19 4.24 46 13 17 4 515.66 1.48 47 13 115 102 90.11 1.40 48 13 119 106 90.59 1.22 49 13 122 109 90.43 1.18 50 13 123 110 89.95 1.25 51 13 131 118 85.32 0.04 52 14 17 3 518.12 0.25 53 14 18 4 518.46 0.09 54 14 69 55 90.05 1.11 55 14 72 58 88.89 1.41 56 14 73 59 88.51 1.60 57 14 76 62 87.97 1.33 58 14 77 63 88.34 1.14 59 15 18 3 518.00 0.15 60 15 19 4 516.34 0.98 61 16 19 3 518.46 0.08 62 16 119 103 98.22 1.99 63 16 122 106 95.17 3.52 64 17 20 3 534.50 1.64 65 17 21 4 509.97 0.35 66 17 24 7 421.53 6.88 67 17 69 52 98.07 2.57 68 17 115 98 90.58 1.22 69 18 21 3 514.94 1.83 70 18 77 59 90.22 1.16 71 20 23 3 517.81 1.58 72 20 24 4 512.21 1.20 73 20 118 98 132.28 0.62 74 21 24 3 518.29 1.35 75 21 25 4 513.96 2.06 76 21 66 45 152.56 12.79 77 21 69 48 151.81 12.94 78 22 25 3 518.84 0.39 79 22 26 4 513.96 2.05 80 22 62 40 174.50 2.10 81 22 66 44 152.78 12.69 82 23 26 3 524.31 3.64 83 23 27 4 514.00 2.08 84 23 118 95 167.63 0.42 85 24 27 3 521.85 4.87 86 24 28 4 514.00 2.07 87 24 69 45 174.27 2.01 88 24 114 90 162.91 1.78 89 24 115 91 162.91 1.77 90 24 118 94 167.65 0.42 91 24 119 95 169.02 1.10 92 25 28 3 522.63 4.48 93 25 29 4 515.12 1.51 94 25 65 40 174.34 2.02 95 25 69 44 174.27 2.00 96 26 29 3 525.08 3.18 97 26 30 4 514.76 1.68 98 26 55 29 226.59 4.12 99 26 56 30 226.28 3.96 100 27 30 3 519.29 0.59 101 27 31 4 508.47 1.47 102 27 114 87 171.06 0.86 103 27 118 91 170.81 0.93 104 28 31 3 510.46 0.48 105 28 32 4 507.42 2.00 106 28 69 41 179.21 0.12 107 28 107 79 171.45 0.92 108 28 110 82 171.34 0.96 109 28 111 83 171.33 0.96 110 28 114 86 171.09 0.86 111 29 32 3 519.20 0.20 112 29 33 4 512.81 0.70 113 29 61 32 211.94 3.27 114 29 64 35 199.83 2.31 115 29 65 36 180.62 0.58 116 29 107 78 171.48 0.93 117 30 33 3 519.20 0.20 118 30 34 4 516.89 1.35 119 30 52 22 232.50 2.38 120 30 55 25 232.16 2.35 121 30 56 26 232.16 2.35 122 30 61 31 212.38 3.12 123 31 34 3 516.94 1.33 124 31 35 4 494.91 2.55 125 31 110 79 171.35 0.95 126 31 113 82 171.14 0.90 127 31 114 83 171.06 0.85 128 32 35 3 514.86 1.71 129 32 36 4 493.53 3.23 130 32 39 7 433.65 11.21 131 32 106 74 171.56 0.92 132 32 107 75 171.55 0.93 133 32 110 78 171.35 0.95 134 33 36 3 519.47 0.52 135 33 37 4 491.33 4.31 136 33 39 6 451.73 5.12 137 33 40 7 365.39 0.43 138 33 43 10 342.74 4.29 139 33 46 13 269.37 0.74 140 33 55 22 232.66 2.30 141 33 61 28 232.42 2.37 142 34 37 3 525.74 3.91 143 34 52 18 232.66 2.30 144 34 55 21 232.66 2.30 145 36 39 3 526.16 4.68 146 36 106 70 171.62 0.92 147 37 40 3 527.10 4.21 148 37 41 4 514.97 1.95 149 38 41 3 533.70 0.51 150 38 103 65 172.11 0.96 151 38 106 68 172.10 0.96 152 39 42 3 524.85 3.92 153 39 43 4 521.88 5.40 154 39 103 64 171.96 0.94 155 39 106 67 171.94 0.94 156 40 43 3 524.06 1.38 157 40 46 6 380.83 9.45 158 40 47 7 282.13 1.89 159 40 49 9 262.46 4.21 160 40 55 15 246.43 1.27 161 41 47 6 299.77 12.26 162 42 97 55 172.37 0.96 163 42 98 56 172.35 0.96 164 42 99 57 172.33 0.97 165 42 100 58 172.35 0.96 166 42 103 61 172.15 0.96 167 43 46 3 519.40 3.17 168 43 47 4 494.04 9.51 169 43 64 21 233.75 2.97 170 44 47 3 527.60 0.93 171 45 48 3 597.45 1.22 172 45 60 15 234.21 3.12 173 45 64 19 233.99 3.07 174 46 49 3 533.87 0.77 175 46 60 14 234.06 3.06 176 46 61 15 234.05 3.05 177 46 64 18 234.00 3.06 178 49 54 5 482.01 0.42 179 49 55 6 389.66 1.54 180 49 58 9 269.17 0.80 181 49 61 12 260.47 3.06 182 50 54 4 491.71 0.41 183 51 54 3 499.08 1.42 184 51 55 4 495.72 2.40 185 52 55 3 501.74 2.81 186 52 56 4 488.20 1.36 187 53 56 3 524.04 3.56 188 53 57 4 496.45 0.97 189 54 57 3 502.93 3.94 190 54 58 4 494.96 0.23 191 55 58 3 513.21 4.04 192 55 61 6 434.59 9.78 193 58 61 3 532.89 2.92 194 58 62 4 512.55 6.53 195 59 62 3 516.69 3.52 196 59 63 4 501.49 0.99 197 60 63 3 524.71 0.46 198 60 64 4 512.56 6.54 199 61 64 3 525.06 0.64 200 61 65 4 501.68 0.97 201 62 65 3 514.91 4.44 202 62 66 4 508.49 2.43 203 63 66 3 522.46 0.67 204 63 67 4 511.81 0.76 205 64 67 3 511.82 0.76 206 64 68 4 511.83 0.76 207 65 68 3 522.01 5.84 208 65 69 4 511.81 0.74 209 66 69 3 525.88 3.91 210 66 70 4 508.26 2.48 211 67 70 3 534.50 2.50 212 67 71 4 508.76 0.73 213 68 71 3 525.85 1.81 214 68 72 4 506.77 1.74 215 68 107 39 171.70 0.94 216 69 72 3 518.11 2.06 217 69 73 4 511.84 0.80 218 70 73 3 530.45 1.38 219 70 74 4 511.85 0.80 220 71 74 3 525.76 0.96 221 71 75 4 511.86 0.81 222 72 75 3 520.08 1.88 223 72 76 4 508.65 2.41 224 72 111 39 171.68 0.96 225 72 135 63 170.11 1.03 226 72 138 66 168.72 0.75 227 73 76 3 516.32 2.79 228 73 77 4 512.10 0.68 229 74 77 3 524.98 5.76 230 74 78 4 512.10 0.68 231 75 78 3 536.04 0.23 232 75 82 7 253.97 2.60 233 75 85 10 204.49 14.41 234 75 86 11 178.39 1.35 235 75 89 14 193.25 0.55 236 75 138 63 168.96 0.69 237 76 79 3 524.82 5.38 238 76 131 55 170.98 0.91 239 76 134 58 170.56 0.95 240 78 81 3 511.24 1.79 241 78 82 4 424.20 5.65 242 78 85 7 279.70 3.93 243 80 137 57 170.69 0.93 244 82 85 3 520.88 0.58 245 82 86 4 503.92 2.48 246 82 137 55 170.75 0.94 247 82 141 59 168.70 0.83 248 83 86 3 517.64 1.04 249 83 87 4 509.88 0.51 250 84 88 4 523.33 0.10 251 85 88 3 543.15 0.23 252 85 89 4 521.21 0.76 253 86 89 3 526.27 3.29 254 86 90 4 516.34 1.68 255 86 138 52 169.50 0.45 256 86 141 55 167.96 0.70 257 86 142 56 165.60 1.20 258 86 145 59 160.12 1.02 259 87 90 3 523.53 1.92 260 87 91 4 515.83 0.29 261 88 91 3 521.21 0.76 262 88 92 4 512.01 1.62 263 89 92 3 517.48 2.62 264 89 93 4 512.01 1.62 265 89 138 49 169.03 0.70 266 89 142 53 164.60 0.70 267 90 93 3 515.71 3.52 268 90 94 4 511.92 1.66 269 90 142 52 163.58 0.68 270 90 145 55 155.38 0.23 271 90 146 56 153.34 0.79 272 91 94 3 518.71 0.74 273 91 95 4 511.87 1.65 274 91 149 58 149.18 0.04 275 92 95 3 526.34 5.56 276 92 96 4 466.28 2.69 277 92 97 5 439.75 10.56 278 93 97 4 432.17 12.26 279 93 98 5 420.51 18.07 280 93 99 6 302.41 3.50 281 93 146 53 151.57 0.10 282 94 98 4 420.51 18.07 283 94 146 52 151.47 0.06 284 94 149 55 145.44 1.58 285 94 151 57 85.21 1.46 286 95 98 3 515.53 0.16 287 95 149 54 148.94 0.12 288 95 151 56 118.73 2.42 289 98 151 53 94.61 3.73 290 99 103 4 513.40 0.87 291 99 104 5 509.66 2.81 292 99 146 47 151.46 0.06 293 100 103 3 525.85 1.60 294 100 104 4 513.94 1.14 295 100 153 53 22.32 2.60 296 101 104 3 526.07 0.57 297 101 105 4 510.43 2.43 298 101 139 38 166.31 1.53 299 101 142 41 162.50 0.12 300 101 143 42 156.94 0.56 301 101 146 45 151.26 0.14 302 101 153 52 22.23 2.64 303 102 105 3 526.07 0.57 304 102 106 4 509.68 2.79 305 103 106 3 521.23 2.98 306 103 107 4 515.07 0.10 307 104 107 3 523.70 0.39 308 104 108 4 514.95 0.04 309 104 139 35 165.94 1.36 310 104 142 38 160.37 0.98 311 104 146 42 151.46 0.06 312 105 108 3 513.30 1.18 313 105 109 4 512.91 0.98 314 105 139 34 165.95 1.36 315 106 109 3 521.19 2.88 316 106 110 4 507.00 0.72 317 107 110 3 511.67 1.61 318 107 111 4 507.00 0.72 319 108 111 3 518.83 2.79 320 108 112 4 507.90 2.09 321 108 135 27 168.79 0.73 322 108 139 31 165.94 1.37 323 109 112 3 517.40 1.30 324 109 113 4 507.90 2.09 325 110 113 3 508.75 2.52 326 110 114 4 505.09 2.50 327 111 114 3 519.00 0.71 328 111 115 4 509.59 0.25 329 111 135 24 168.93 0.70 330 112 115 3 514.76 2.83 331 112 116 4 508.69 0.20 332 112 123 11 262.06 6.00 333 112 128 16 173.53 0.56 334 112 131 19 170.06 1.06 335 112 132 20 170.03 1.06 336 112 135 23 169.13 0.75 337 113 116 3 519.34 0.55 338 113 117 4 506.53 1.27 339 114 117 3 517.89 4.40 340 114 118 4 503.15 0.43 341 115 118 3 511.53 2.42 342 115 119 4 496.11 3.09 343 115 123 8 269.10 2.48 344 115 131 16 225.16 11.83 345 116 120 4 439.16 3.12 346 116 123 7 269.10 2.48 347 119 122 3 507.39 5.42 348 119 123 4 469.72 9.21 349 120 123 3 509.95 9.86 350 120 124 4 474.50 6.83 351 122 127 5 479.88 9.51 352 123 127 4 479.88 9.51 353 123 128 5 481.93 1.46 354 123 131 8 451.03 13.99 355 124 127 3 507.39 4.25 356 124 128 4 493.52 2.69 357 125 128 3 510.59 2.65 358 125 129 4 504.03 0.63 359 126 129 3 506.58 0.64 360 126 130 4 504.03 0.63 361 127 130 3 504.04 0.63 362 127 131 4 502.12 1.58 363 128 131 3 509.13 1.89 364 128 132 4 497.68 0.64 365 129 132 3 518.14 1.05 366 129 133 4 510.99 2.17 367 130 133 3 516.25 0.28 368 130 134 4 504.70 0.98 369 131 134 3 516.25 0.28 370 131 135 4 505.98 0.34 371 132 135 3 511.19 2.26 372 132 136 4 505.43 0.07 373 133 136 3 507.19 0.58 374 133 137 4 505.43 0.07 375 134 137 3 509.07 1.75 376 134 138 4 504.97 0.30 377 135 138 3 505.95 0.01 378 135 139 4 505.88 0.76 379 136 139 3 512.60 2.60 380 136 140 4 505.87 0.77 381 137 140 3 510.63 1.62 382 137 141 4 505.17 0.40 383 138 141 3 522.62 2.29 384 138 142 4 505.18 0.40 385 139 142 3 509.31 2.03 386 139 143 4 505.33 0.47 387 140 143 3 514.71 2.60 388 140 144 4 507.49 1.02 389 141 144 3 514.71 2.59 390 141 145 4 507.49 1.02 391 142 145 3 512.24 1.35 392 142 146 4 505.88 0.22 393 143 146 3 505.88 0.22 394 143 147 4 505.88 0.22 395 143 152 9 191.37 6.78 396 144 147 3 513.41 3.54 397 144 148 4 504.01 1.16 398 145 148 3 513.86 0.58 399 145 149 4 502.75 1.52 400 146 149 3 513.35 0.33 401 146 150 4 497.65 1.02 402 146 151 5 340.53 2.91 403 146 152 6 254.05 5.32 404 147 150 3 500.04 4.83 405 147 152 5 255.11 4.79