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 8 473.56 2.52 2 2 130 128 44.97 1.09 3 2 133 131 30.04 0.10 4 2 134 132 30.00 0.08 5 2 137 135 29.73 0.20 6 3 6 3 518.99 0.41 7 3 7 4 515.40 1.39 8 4 7 3 519.00 0.41 9 4 8 4 515.40 1.39 10 4 79 75 54.22 0.83 11 5 8 3 515.32 1.33 12 5 9 4 504.98 3.82 13 6 9 3 522.37 6.53 14 6 10 4 498.75 6.92 15 6 130 124 69.32 0.54 16 6 133 127 69.38 0.56 17 7 10 3 514.85 5.07 18 7 11 4 504.44 4.06 19 7 76 69 69.42 0.54 20 7 79 72 69.39 0.55 21 7 80 73 70.00 0.81 22 7 134 127 69.42 0.55 23 7 137 130 69.42 0.55 24 8 11 3 526.58 1.64 25 8 12 4 507.41 2.73 26 9 12 3 526.58 1.64 27 9 13 4 509.03 2.03 28 9 126 117 81.61 1.39 29 9 127 118 81.53 1.37 30 9 130 121 81.52 1.37 31 10 13 3 530.98 0.57 32 10 14 4 507.57 2.81 33 10 76 66 81.52 1.37 34 10 130 120 81.55 1.36 35 10 131 121 81.51 1.37 36 10 134 124 81.50 1.38 37 11 14 3 515.39 1.09 38 11 15 4 507.56 2.83 39 11 76 65 81.55 1.36 40 11 77 66 81.56 1.35 41 11 79 68 81.56 1.35 42 12 15 3 523.63 2.75 43 12 16 4 509.49 1.93 44 12 122 110 89.71 0.84 45 13 16 3 521.50 4.08 46 13 17 4 518.71 0.04 47 13 115 102 89.56 0.88 48 13 119 106 90.11 0.72 49 13 122 109 89.70 0.84 50 13 123 110 89.70 0.84 51 13 131 118 88.48 0.75 52 14 17 3 518.71 0.04 53 14 18 4 518.71 0.04 54 14 69 55 89.52 0.91 55 14 72 58 88.86 0.92 56 14 73 59 88.58 1.01 57 14 76 62 86.11 0.14 58 14 77 63 88.21 1.20 59 15 18 3 516.38 1.21 60 15 19 4 516.59 1.10 61 16 19 3 518.71 0.04 62 16 119 103 100.22 1.59 63 16 122 106 90.16 0.88 64 17 20 3 525.88 3.54 65 17 21 4 503.83 2.71 66 17 24 7 420.15 5.46 67 17 69 52 132.23 21.95 68 17 115 98 94.42 1.30 69 18 21 3 514.95 1.83 70 18 77 59 89.87 1.01 71 20 23 3 519.77 0.85 72 20 24 4 508.60 3.00 73 20 118 98 134.15 1.29 74 21 24 3 518.95 1.91 75 21 25 4 512.41 1.10 76 21 66 45 152.43 12.99 77 21 69 48 148.95 14.17 78 22 25 3 518.51 0.22 79 22 26 4 514.14 1.96 80 22 62 40 155.81 12.12 81 22 66 44 154.25 12.08 82 23 26 3 521.01 5.29 83 23 27 4 512.43 1.10 84 23 118 95 168.01 0.24 85 24 27 3 518.98 2.18 86 24 28 4 510.33 0.05 87 24 69 45 155.34 11.70 88 24 114 90 168.87 0.79 89 24 115 91 168.94 0.74 90 24 118 94 168.06 0.27 91 24 119 95 168.06 0.27 92 25 28 3 516.36 0.65 93 25 29 4 510.33 0.05 94 25 65 40 156.09 11.67 95 25 69 44 155.34 11.71 96 26 29 3 524.79 3.58 97 26 30 4 510.25 0.10 98 26 56 30 216.00 1.74 99 26 62 36 175.12 2.55 100 27 30 3 517.67 0.20 101 27 31 4 508.02 1.22 102 27 114 87 170.94 0.20 103 27 118 91 170.50 0.08 104 28 31 3 518.01 0.03 105 28 32 4 504.51 0.54 106 28 69 41 175.50 2.37 107 28 107 79 171.43 0.30 108 28 110 82 171.05 0.24 109 28 111 83 171.00 0.21 110 28 114 86 170.94 0.20 111 29 32 3 519.45 0.33 112 29 33 4 504.51 0.54 113 29 61 32 200.75 3.02 114 29 64 35 182.05 0.83 115 29 65 36 175.62 2.38 116 29 107 78 171.45 0.29 117 30 33 3 511.76 4.17 118 30 34 4 498.61 1.21 119 30 52 22 234.83 4.62 120 30 55 25 228.68 6.83 121 30 56 26 229.12 7.04 122 30 61 31 205.77 0.59 123 31 34 3 513.01 1.31 124 31 35 4 500.13 1.28 125 31 110 79 171.19 0.30 126 31 113 82 171.13 0.28 127 31 114 83 171.04 0.24 128 32 35 3 510.44 0.02 129 32 36 4 506.55 1.93 130 32 39 7 358.46 3.07 131 32 106 74 171.53 0.33 132 32 107 75 171.44 0.30 133 32 110 78 171.20 0.30 134 33 36 3 514.89 1.78 135 33 37 4 494.19 3.41 136 33 39 6 393.73 12.39 137 33 40 7 309.38 7.78 138 33 43 10 319.49 2.73 139 33 46 13 253.39 1.07 140 33 55 22 234.97 4.55 141 33 61 28 230.94 6.16 142 34 37 3 533.51 0.02 143 34 52 18 235.52 4.81 144 34 55 21 235.50 4.82 145 36 39 3 516.06 2.60 146 36 106 70 171.66 0.39 147 37 40 3 512.19 0.93 148 38 41 3 519.87 4.78 149 38 103 65 171.94 0.35 150 38 106 68 171.88 0.38 151 39 42 3 527.46 2.61 152 39 43 4 524.53 1.15 153 39 103 64 171.82 0.36 154 39 106 67 171.76 0.35 155 40 43 3 525.84 1.79 156 40 46 6 350.48 7.00 157 40 47 7 274.78 4.40 158 40 49 9 269.65 0.86 159 40 55 15 246.71 1.08 160 41 47 6 283.45 0.06 161 42 97 55 172.68 0.08 162 42 98 56 172.68 0.08 163 42 99 57 172.69 0.05 164 42 100 58 172.71 0.06 165 42 103 61 172.49 0.10 166 43 46 3 523.77 1.24 167 43 47 4 514.03 3.64 168 43 64 21 232.19 6.54 169 44 47 3 533.21 1.00 170 45 48 3 600.27 0.05 171 45 60 15 234.55 5.48 172 45 64 19 234.50 5.50 173 46 49 3 536.31 0.40 174 46 60 14 235.59 4.96 175 46 61 15 234.53 5.49 176 46 64 18 234.52 5.49 177 47 50 3 586.88 0.91 178 49 54 5 427.88 5.57 179 49 55 6 376.75 5.79 180 49 58 9 283.13 2.66 181 49 61 12 255.65 0.40 182 50 54 4 516.06 9.69 183 51 54 3 501.56 1.80 184 51 55 4 500.93 2.12 185 52 55 3 507.48 1.15 186 52 56 4 500.94 2.12 187 53 56 3 506.11 0.54 188 53 57 4 500.94 2.12 189 54 57 3 500.91 2.15 190 54 58 4 500.90 2.14 191 55 58 3 513.50 4.15 192 55 61 6 401.60 4.57 193 58 61 3 533.14 2.79 194 58 62 4 506.68 1.73 195 59 62 3 516.94 3.40 196 59 63 4 502.70 4.03 197 60 63 3 518.51 3.81 198 60 64 4 517.28 3.25 199 61 64 3 517.28 3.25 200 61 65 4 517.28 3.25 201 62 65 3 517.78 3.51 202 62 66 4 517.29 3.26 203 63 66 3 517.30 3.27 204 63 67 4 517.29 3.27 205 64 67 3 515.95 3.94 206 64 68 4 515.94 3.94 207 65 68 3 516.81 3.56 208 65 69 4 507.73 0.16 209 66 69 3 531.61 1.04 210 66 70 4 515.96 3.97 211 67 70 3 531.96 4.03 212 67 71 4 515.97 3.96 213 68 71 3 523.51 0.40 214 68 72 4 513.83 5.02 215 68 107 39 172.31 0.14 216 69 72 3 515.03 3.84 217 69 73 4 508.96 0.81 218 70 73 3 523.78 2.21 219 70 74 4 510.38 0.11 220 71 74 3 526.01 1.09 221 71 75 4 510.38 0.10 222 72 75 3 525.44 1.38 223 72 76 4 512.01 0.70 224 72 111 39 172.16 0.21 225 72 135 63 168.35 0.23 226 72 138 66 167.91 0.32 227 73 76 3 516.57 2.67 228 73 77 4 511.07 1.18 229 74 77 3 536.29 0.35 230 74 78 4 511.08 1.18 231 75 78 3 536.29 0.35 232 75 79 4 511.09 1.17 233 75 82 7 248.55 0.35 234 75 85 10 198.21 3.91 235 75 89 14 180.96 0.07 236 75 138 63 168.19 0.23 237 76 79 3 529.54 3.02 238 76 131 55 169.76 0.07 239 76 134 58 169.38 0.21 240 78 81 3 521.33 5.04 241 78 82 4 436.25 30.81 242 78 85 7 307.52 3.65 243 80 137 57 169.53 0.02 244 82 85 3 522.63 0.30 245 82 86 4 502.35 0.51 246 82 137 55 169.50 0.01 247 82 141 59 167.94 0.30 248 83 86 3 517.89 1.17 249 83 87 4 505.05 0.83 250 84 88 4 519.49 1.87 251 85 88 3 542.60 0.29 252 85 89 4 517.19 3.02 253 86 89 3 523.00 0.31 254 86 90 4 515.86 3.68 255 86 138 52 168.16 0.21 256 86 141 55 167.75 0.24 257 86 142 56 165.49 0.54 258 86 145 59 163.10 0.44 259 87 90 3 519.49 1.88 260 87 91 4 515.86 3.68 261 88 91 3 512.13 1.81 262 88 92 4 512.16 1.79 263 89 92 3 514.89 1.33 264 89 93 4 512.17 1.80 265 89 138 49 167.99 0.30 266 89 142 53 165.02 0.62 267 90 93 3 514.88 3.15 268 90 94 4 512.16 1.79 269 90 142 52 164.34 0.29 270 90 145 55 153.95 0.95 271 90 146 56 151.63 0.09 272 91 94 3 521.22 4.62 273 91 95 4 512.12 1.78 274 91 149 58 146.31 1.20 275 92 95 3 525.16 2.65 276 92 96 4 473.33 0.20 277 92 97 5 468.56 2.18 278 93 97 4 415.17 19.35 279 93 98 5 415.16 19.35 280 93 99 6 323.65 6.90 281 93 146 53 150.94 0.42 282 94 98 4 384.12 4.62 283 94 146 52 149.37 1.20 284 94 149 55 145.56 1.54 285 94 151 57 95.14 3.27 286 95 98 3 520.02 2.29 287 95 149 54 147.16 0.77 288 95 151 56 118.97 2.29 289 98 151 53 91.48 1.92 290 99 103 4 513.61 0.72 291 99 104 5 509.67 2.71 292 99 146 47 149.36 1.21 293 100 103 3 527.10 1.23 294 100 104 4 514.19 1.02 295 100 152 52 46.87 0.73 296 101 104 3 516.20 0.01 297 101 105 4 511.49 1.83 298 101 139 38 166.34 0.97 299 101 142 41 163.03 0.67 300 101 143 42 157.10 0.64 301 101 146 45 149.11 1.21 302 101 152 51 46.86 0.73 303 102 105 3 515.25 0.06 304 102 106 4 509.76 2.69 305 103 106 3 515.26 0.06 306 103 107 4 515.25 0.07 307 104 107 3 521.36 3.10 308 104 108 4 513.60 0.89 309 104 138 34 167.95 0.35 310 104 139 35 166.27 1.01 311 104 142 38 159.01 0.35 312 105 108 3 513.45 0.96 313 105 109 4 513.14 1.12 314 105 139 34 166.27 1.01 315 106 109 3 520.63 3.44 316 106 110 4 504.49 0.01 317 107 110 3 505.26 0.40 318 107 111 4 504.52 0.03 319 108 111 3 519.89 2.25 320 108 112 4 504.35 0.14 321 108 135 27 168.12 0.29 322 108 139 31 166.27 1.04 323 109 112 3 513.74 0.83 324 109 113 4 508.35 1.86 325 110 113 3 514.82 5.04 326 110 114 4 504.35 0.14 327 111 114 3 523.45 0.69 328 111 115 4 500.56 2.02 329 111 135 24 168.16 0.28 330 112 115 3 518.09 2.23 331 112 116 4 503.14 3.48 332 112 123 11 266.50 7.67 333 112 128 16 173.09 1.59 334 112 131 19 168.89 0.50 335 112 132 20 173.06 1.59 336 112 135 23 168.25 0.23 337 113 116 3 512.98 1.70 338 113 117 4 509.83 0.13 339 114 117 3 507.99 3.39 340 114 118 4 502.61 0.70 341 115 118 3 521.77 2.71 342 115 119 4 495.20 4.40 343 115 123 8 297.16 7.66 344 115 131 16 193.24 5.83 345 116 119 3 525.62 1.36 346 116 120 4 487.04 0.30 347 116 123 7 283.97 1.06 348 117 120 3 540.71 3.54 349 119 122 3 528.13 1.02 350 119 123 4 464.84 12.71 351 120 123 3 510.22 9.97 352 120 124 4 488.32 0.97 353 122 127 5 489.03 9.64 354 123 127 4 489.03 9.64 355 123 128 5 489.01 9.64 356 123 131 8 438.56 3.98 357 124 127 3 512.34 2.02 358 124 128 4 508.34 0.01 359 125 128 3 508.34 0.01 360 125 129 4 500.45 3.93 361 126 129 3 505.79 1.27 362 126 130 4 500.76 3.79 363 127 130 3 514.75 0.27 364 127 131 4 504.55 5.37 365 128 131 3 518.02 1.36 366 128 132 4 505.11 5.09 367 129 132 3 518.04 1.35 368 129 133 4 509.27 3.02 369 130 133 3 515.76 0.22 370 130 134 4 512.09 1.61 371 131 134 3 516.50 0.15 372 131 135 4 505.25 5.04 373 132 135 3 511.16 1.15 374 132 136 4 509.62 1.92 375 133 136 3 511.17 1.15 376 133 137 4 499.51 3.14 377 134 137 3 511.04 2.29 378 134 138 4 499.06 2.91 379 135 138 3 499.85 3.31 380 135 139 4 506.56 0.42 381 136 139 3 510.47 1.53 382 136 140 4 498.34 3.70 383 137 140 3 513.76 0.30 384 137 141 4 498.35 3.70 385 138 141 3 522.88 2.17 386 138 142 4 506.00 0.12 387 139 142 3 512.44 0.57 388 139 143 4 506.00 0.13 389 140 143 3 513.36 3.52 390 140 144 4 506.03 0.14 391 141 144 3 519.75 3.09 392 141 145 4 505.94 1.79 393 142 145 3 521.12 2.84 394 142 146 4 505.94 1.79 395 143 146 3 506.92 2.28 396 143 147 4 505.94 1.79 397 144 147 3 518.29 1.36 398 144 148 4 505.30 0.26 399 145 148 3 513.61 0.45 400 145 149 4 505.29 0.26 401 146 149 3 511.23 2.54 402 146 150 4 502.97 1.40 403 146 151 5 363.99 6.52 404 146 152 6 374.05 11.54 405 147 150 3 509.61 1.55