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 8 478.75 1.89 2 2 130 128 40.68 0.55 3 2 133 131 32.14 0.73 4 2 134 132 30.81 0.28 5 2 137 135 30.34 0.05 6 3 6 3 514.62 0.90 7 3 7 4 504.40 4.20 8 4 7 3 515.62 1.41 9 4 8 4 511.67 0.56 10 4 79 75 50.01 1.81 11 5 8 3 511.68 0.57 12 5 9 4 511.68 0.57 13 6 9 3 518.20 2.42 14 6 10 4 511.67 0.56 15 6 130 124 57.70 1.91 16 6 133 127 57.70 1.91 17 7 10 3 517.70 2.66 18 7 11 4 511.46 0.46 19 7 76 69 58.95 2.52 20 7 79 72 58.52 2.31 21 7 80 73 61.59 1.25 22 7 134 127 58.98 2.54 23 7 137 130 58.99 2.55 24 8 11 3 517.49 2.56 25 8 12 4 511.43 0.46 26 9 12 3 517.84 2.39 27 9 13 4 511.79 0.64 28 9 126 117 80.32 2.25 29 9 127 118 77.50 3.56 30 9 130 121 77.42 3.52 31 10 13 3 527.22 3.27 32 10 14 4 511.38 0.84 33 10 76 66 77.52 3.56 34 10 130 120 77.52 3.56 35 10 131 121 77.41 3.51 36 10 134 124 77.34 3.54 37 11 14 3 507.93 2.71 38 11 15 4 507.99 2.75 39 11 76 65 77.56 3.56 40 11 77 66 77.57 3.56 41 11 79 68 77.56 3.56 42 12 15 3 516.41 1.46 43 12 16 4 517.34 1.01 44 12 122 110 87.91 0.46 45 13 16 3 524.62 1.44 46 13 17 4 517.34 1.01 47 13 115 102 87.17 0.69 48 13 119 106 88.05 0.52 49 13 122 109 87.92 0.46 50 13 123 110 87.91 0.46 51 13 131 118 86.68 0.84 52 14 17 3 517.34 1.01 53 14 18 4 519.33 0.01 54 14 69 55 87.17 0.69 55 14 72 58 86.67 0.86 56 14 73 59 84.66 1.86 57 14 76 62 84.65 1.86 58 14 77 63 85.16 1.61 59 14 131 117 87.17 0.69 60 15 18 3 520.40 0.53 61 15 19 4 519.33 0.01 62 16 19 3 527.10 2.83 63 16 119 103 95.59 2.48 64 16 122 106 88.96 0.01 65 17 20 3 533.13 0.09 66 17 21 4 502.51 2.81 67 17 24 7 406.60 17.96 68 17 69 52 132.50 21.82 69 17 115 98 88.72 0.12 70 18 21 3 517.78 4.02 71 18 77 59 95.64 3.68 72 20 23 3 522.61 0.73 73 20 24 4 514.44 1.81 74 20 118 98 134.52 0.51 75 21 24 3 528.38 2.17 76 21 25 4 514.44 1.81 77 21 66 45 175.40 2.02 78 21 69 48 174.61 1.66 79 22 25 3 521.08 1.49 80 22 26 4 514.45 1.81 81 22 62 40 176.42 2.08 82 22 66 44 175.51 1.99 83 23 26 3 522.76 4.81 84 23 27 4 513.89 0.38 85 23 118 95 167.43 0.97 86 24 27 3 519.24 2.30 87 24 28 4 513.87 0.38 88 24 69 45 175.71 2.00 89 24 114 90 165.24 0.12 90 24 118 94 167.49 0.95 91 24 119 95 167.44 0.97 92 25 28 3 522.83 0.51 93 25 29 4 508.27 1.36 94 25 65 40 175.90 1.92 95 25 69 44 175.88 1.92 96 26 29 3 523.30 4.57 97 26 30 4 508.75 1.12 98 26 56 30 205.19 2.44 99 26 61 35 177.70 2.13 100 26 62 36 176.81 2.00 101 27 30 3 532.42 5.68 102 27 31 4 507.99 1.46 103 27 56 29 205.47 2.35 104 27 114 87 170.04 0.82 105 27 118 91 169.83 0.88 106 28 31 3 531.42 6.18 107 28 32 4 508.69 1.09 108 28 69 41 177.22 2.27 109 28 107 79 171.05 0.79 110 28 110 82 170.56 0.68 111 28 111 83 170.54 0.68 112 28 114 86 170.06 0.83 113 29 32 3 507.31 0.09 114 29 33 4 506.45 0.03 115 29 61 32 196.91 1.43 116 29 64 35 177.55 2.12 117 29 65 36 177.25 2.27 118 29 107 78 171.09 0.77 119 30 33 3 519.42 4.06 120 30 34 4 505.42 0.49 121 30 52 22 207.55 1.50 122 30 55 25 205.64 2.44 123 30 56 26 205.66 2.44 124 31 34 3 519.62 0.67 125 31 35 4 498.70 3.85 126 31 110 79 170.58 0.68 127 31 113 82 170.38 0.75 128 31 114 83 170.33 0.76 129 32 35 3 528.16 2.14 130 32 36 4 498.68 3.83 131 32 39 7 393.80 1.11 132 32 106 74 171.18 0.72 133 32 107 75 171.10 0.77 134 32 110 78 170.58 0.68 135 33 36 3 527.27 3.14 136 33 37 4 466.40 4.86 137 33 39 6 393.80 1.11 138 33 40 7 317.95 9.79 139 33 43 10 317.98 9.79 140 33 55 22 207.84 1.65 141 33 61 28 206.27 2.18 142 34 37 3 527.03 3.26 143 36 39 3 536.78 2.05 144 36 106 70 171.25 0.71 145 36 109 73 171.25 0.71 146 37 40 3 526.99 2.85 147 38 41 3 528.06 2.31 148 38 103 65 171.84 0.83 149 38 106 68 171.72 0.79 150 39 42 3 538.05 2.96 151 39 43 4 531.35 6.32 152 39 103 64 171.59 0.74 153 39 106 67 171.48 0.74 154 40 43 3 531.35 6.32 155 40 46 6 453.49 5.91 156 40 47 7 300.19 1.57 157 40 55 15 245.46 1.69 158 41 47 6 395.01 23.34 159 42 97 55 172.31 0.86 160 42 98 56 172.32 0.86 161 42 99 57 172.20 0.90 162 42 103 61 171.88 0.80 163 43 46 3 522.97 3.24 164 43 47 4 514.96 0.35 165 43 64 21 208.87 1.07 166 44 47 3 536.48 1.15 167 45 48 3 559.21 0.15 168 45 60 15 227.79 1.86 169 46 49 3 536.94 1.09 170 46 60 14 227.77 1.85 171 46 61 15 223.44 3.93 172 46 64 18 227.64 1.86 173 47 50 3 580.01 0.49 174 49 54 5 472.56 0.81 175 49 55 6 395.35 6.61 176 49 58 9 289.53 3.68 177 49 61 12 269.07 6.03 178 50 54 4 511.70 5.58 179 51 54 3 513.85 4.50 180 51 55 4 504.64 2.05 181 52 55 3 520.38 1.24 182 52 56 4 511.69 5.58 183 53 56 3 515.02 3.92 184 53 57 4 505.34 2.29 185 54 57 3 506.66 2.95 186 54 58 4 505.34 2.29 187 55 58 3 514.08 2.08 188 55 61 6 425.48 10.05 189 58 61 3 530.45 5.94 190 58 62 4 507.28 2.00 191 59 62 3 510.11 0.58 192 59 63 4 499.65 1.83 193 60 63 3 514.09 3.06 194 60 64 4 507.28 1.99 195 61 64 3 522.00 0.90 196 61 65 4 514.76 1.76 197 62 65 3 524.61 2.21 198 62 66 4 514.77 1.76 199 63 66 3 523.78 2.62 200 63 67 4 510.90 3.81 201 64 67 3 520.61 1.04 202 64 68 4 510.38 4.08 203 65 68 3 512.17 2.13 204 65 69 4 497.65 2.27 205 66 69 3 522.22 6.84 206 66 70 4 505.32 1.60 207 67 70 3 511.48 0.56 208 67 71 4 510.56 1.02 209 68 71 3 523.86 0.47 210 68 72 4 518.84 2.54 211 68 107 39 171.21 0.74 212 69 72 3 518.84 2.54 213 69 73 4 518.84 2.54 214 70 73 3 518.85 2.54 215 70 74 4 518.84 2.54 216 71 74 3 524.25 0.16 217 71 75 4 518.84 2.54 218 71 89 18 190.34 9.86 219 72 75 3 517.46 3.20 220 72 76 4 517.46 3.20 221 72 111 39 171.21 0.71 222 72 135 63 168.69 0.95 223 73 76 3 512.26 0.60 224 73 77 4 514.40 4.78 225 74 77 3 524.35 0.20 226 74 78 4 514.41 4.78 227 75 78 3 527.22 4.18 228 75 82 7 244.25 1.61 229 75 85 10 205.78 10.40 230 75 86 11 203.40 11.03 231 75 89 14 205.34 10.05 232 75 138 63 167.89 0.95 233 76 79 3 527.33 4.12 234 76 131 55 169.47 0.86 235 76 134 58 169.05 0.79 236 78 81 3 497.72 4.42 237 78 82 4 383.69 15.19 238 78 85 7 291.50 6.71 239 80 137 57 169.15 0.93 240 82 85 3 507.36 0.76 241 82 86 4 493.86 3.95 242 82 137 55 169.05 0.97 243 82 141 59 167.47 0.98 244 83 86 3 506.56 1.34 245 83 87 4 507.09 2.38 246 83 145 62 163.19 0.44 247 84 88 4 534.67 1.66 248 85 88 3 556.71 3.37 249 86 89 3 518.48 1.87 250 86 90 4 503.49 0.17 251 86 138 52 167.72 0.89 252 86 141 55 165.27 0.53 253 86 142 56 164.81 0.73 254 87 90 3 507.68 0.40 255 87 91 4 509.69 3.27 256 87 145 58 156.66 0.01 257 88 91 3 514.25 1.01 258 88 92 4 514.26 1.02 259 89 92 3 522.90 1.03 260 89 93 4 512.43 1.93 261 89 138 49 167.72 0.89 262 89 142 53 163.69 0.50 263 90 93 3 516.52 2.16 264 90 94 4 512.42 1.93 265 90 142 52 163.28 0.48 266 90 145 55 155.43 0.21 267 90 146 56 149.34 0.97 268 90 149 59 144.75 0.70 269 91 94 3 521.50 0.32 270 91 95 4 512.38 1.91 271 91 149 58 144.22 0.97 272 92 95 3 514.08 1.06 273 92 96 4 490.82 12.68 274 92 97 5 462.39 1.54 275 93 97 4 438.80 10.14 276 93 98 5 355.10 6.54 277 93 99 6 306.16 2.43 278 93 146 53 147.55 0.07 279 93 151 58 113.47 0.40 280 94 98 4 426.67 16.21 281 94 146 52 147.27 0.06 282 94 149 55 145.88 0.13 283 94 151 57 108.09 2.07 284 95 98 3 539.98 0.84 285 95 149 54 145.87 0.14 286 98 151 53 108.09 2.08 287 99 103 4 508.83 3.00 288 99 104 5 501.29 0.76 289 99 146 47 147.59 0.06 290 99 151 52 113.25 0.51 291 100 103 3 527.40 1.24 292 100 104 4 514.68 0.11 293 100 151 51 112.25 0.01 294 100 153 53 13.35 1.96 295 101 104 3 514.68 0.11 296 101 105 4 515.62 0.36 297 101 139 38 165.91 0.99 298 101 142 41 163.22 0.42 299 101 143 42 156.65 0.02 300 101 146 45 147.49 0.10 301 101 153 52 13.36 1.95 302 102 105 3 522.49 3.78 303 102 106 4 515.62 0.36 304 103 106 3 510.13 2.95 305 103 107 4 509.56 2.67 306 104 107 3 509.41 3.31 307 104 108 4 507.12 2.91 308 104 138 34 167.00 1.35 309 104 139 35 164.91 0.66 310 104 142 38 159.66 1.28 311 105 108 3 509.16 2.19 312 105 109 4 507.16 2.91 313 105 139 34 165.07 0.58 314 106 109 3 508.88 2.04 315 106 110 4 508.88 2.05 316 107 110 3 508.88 2.04 317 107 111 4 508.79 2.10 318 108 111 3 520.35 2.27 319 108 112 4 508.75 2.06 320 108 135 27 168.20 0.84 321 108 139 31 164.91 0.66 322 109 112 3 526.37 5.28 323 109 113 4 508.77 2.06 324 110 113 3 509.82 2.58 325 110 114 4 507.42 1.35 326 111 114 3 524.85 2.42 327 111 115 4 507.43 1.35 328 111 135 24 168.59 0.85 329 112 115 3 514.64 4.95 330 112 116 4 507.41 1.33 331 112 123 11 264.75 1.79 332 112 131 19 173.56 1.28 333 112 132 20 168.68 0.89 334 112 135 23 168.72 0.92 335 113 116 3 516.14 4.20 336 113 117 4 506.93 1.09 337 114 117 3 506.93 1.09 338 114 118 4 506.92 1.09 339 115 118 3 512.31 3.83 340 115 119 4 498.94 2.39 341 115 123 8 298.33 8.20 342 115 131 16 230.66 3.12 343 116 120 4 443.07 0.71 344 116 123 7 276.58 2.65 345 116 128 12 264.42 6.39 346 117 120 3 532.17 0.68 347 119 122 3 509.53 5.62 348 119 123 4 490.39 2.94 349 120 123 3 502.23 2.98 350 120 124 4 490.38 2.94 351 122 127 5 462.69 6.09 352 123 127 4 462.67 6.08 353 123 128 5 458.09 3.75 354 123 131 8 438.51 5.32 355 124 127 3 521.83 1.91 356 124 128 4 508.59 0.14 357 125 128 3 517.19 0.96 358 125 129 4 508.60 0.14 359 126 129 3 515.00 0.14 360 126 130 4 512.09 1.60 361 127 130 3 516.78 0.35 362 127 131 4 514.79 2.96 363 128 131 3 517.73 1.51 364 128 132 4 509.81 5.46 365 129 132 3 514.24 3.25 366 129 133 4 511.24 4.75 367 130 133 3 512.77 4.62 368 130 134 4 511.23 4.75 369 131 134 3 516.06 0.33 370 131 135 4 509.31 3.04 371 132 135 3 508.57 3.42 372 132 136 4 508.55 3.43 373 133 136 3 507.46 3.98 374 133 137 4 498.39 1.61 375 134 137 3 521.79 2.17 376 134 138 4 501.32 0.15 377 135 138 3 507.51 2.21 378 135 139 4 500.98 0.33 379 136 139 3 522.40 3.14 380 136 140 4 500.99 0.33 381 137 140 3 515.25 0.19 382 137 141 4 500.97 0.32 383 138 141 3 520.80 0.78 384 138 142 4 501.69 0.71 385 139 142 3 518.99 1.68 386 139 143 4 508.76 3.39 387 140 143 3 518.23 0.49 388 140 144 4 521.55 2.19 389 141 144 3 522.60 1.67 390 141 145 4 521.54 2.19 391 142 145 3 521.57 2.18 392 142 146 4 521.52 2.20 393 143 146 3 521.53 2.19 394 143 147 4 521.53 2.19 395 144 147 3 519.72 1.25 396 144 148 4 506.04 5.54 397 145 148 3 515.58 0.30 398 145 149 4 504.96 5.00 399 146 149 3 518.99 2.00 400 146 150 4 504.94 5.00 401 146 151 5 376.11 11.65 402 147 150 3 497.84 3.66 403 147 151 4 465.41 6.00 404 147 152 5 376.12 11.66