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 8 471.52 1.50 2 2 130 128 46.80 0.28 3 2 133 131 41.40 0.99 4 2 134 132 36.43 1.11 5 2 137 135 36.43 1.10 6 3 6 3 518.24 0.04 7 3 7 4 512.76 2.73 8 4 7 3 520.77 1.23 9 4 8 4 514.59 1.81 10 4 79 75 59.23 3.25 11 5 8 3 515.85 1.53 12 5 9 4 515.30 1.47 13 6 9 3 526.41 3.75 14 6 10 4 515.29 1.47 15 6 130 124 70.19 0.23 16 6 133 127 70.22 0.24 17 7 10 3 506.37 2.30 18 7 11 4 505.31 2.80 19 7 76 69 70.31 0.28 20 7 79 72 70.28 0.28 21 7 80 73 70.30 0.27 22 7 134 127 70.23 0.24 23 7 137 130 70.24 0.24 24 8 11 3 530.65 1.15 25 8 12 4 513.57 2.02 26 9 12 3 525.83 1.26 27 9 13 4 517.56 2.87 28 9 126 117 82.23 0.38 29 9 127 118 82.12 0.33 30 9 130 121 82.11 0.33 31 10 13 3 530.08 0.86 32 10 14 4 514.73 1.46 33 10 76 66 82.11 0.33 34 10 130 120 82.13 0.34 35 10 131 121 82.11 0.33 36 10 134 124 82.09 0.34 37 11 14 3 515.29 1.74 38 11 15 4 515.24 1.72 39 11 76 65 82.13 0.32 40 11 77 66 82.14 0.32 41 11 79 68 82.17 0.33 42 12 15 3 523.21 2.96 43 12 16 4 520.50 3.50 44 12 122 110 89.86 1.48 45 13 16 3 523.14 3.26 46 13 17 4 516.13 1.32 47 13 115 102 89.86 1.49 48 13 122 109 89.86 1.49 49 13 123 110 89.86 1.49 50 13 127 114 89.68 1.52 51 13 131 118 89.49 1.48 52 14 17 3 517.70 0.54 53 14 18 4 515.13 1.81 54 14 69 55 89.75 1.44 55 14 72 58 89.59 1.52 56 14 73 59 89.45 1.46 57 14 76 62 89.45 1.46 58 14 77 63 89.49 1.47 59 14 131 117 89.75 1.48 60 15 18 3 518.02 0.36 61 15 19 4 516.09 1.33 62 16 19 3 518.00 0.35 63 16 119 103 99.89 1.16 64 16 122 106 90.06 1.47 65 17 20 3 534.00 1.39 66 17 21 4 491.58 3.48 67 17 24 7 400.48 3.15 68 17 69 52 89.95 1.49 69 17 115 98 90.07 1.47 70 18 21 3 513.52 2.54 71 18 77 59 89.86 1.47 72 20 23 3 521.06 1.49 73 20 24 4 511.68 1.46 74 20 118 98 135.64 0.54 75 21 24 3 519.04 0.48 76 21 25 4 511.66 1.47 77 21 66 45 126.75 0.27 78 21 69 48 126.06 0.60 79 22 25 3 519.04 0.47 80 22 26 4 513.41 2.33 81 22 62 40 172.74 1.21 82 22 66 44 127.34 0.01 83 23 26 3 517.05 0.51 84 23 27 4 511.66 1.47 85 23 118 95 167.28 0.66 86 24 27 3 533.29 0.85 87 24 28 4 511.28 1.28 88 24 69 45 153.56 8.32 89 24 114 90 162.62 1.62 90 24 115 91 165.16 0.14 91 24 118 94 167.25 0.67 92 24 119 95 167.28 0.66 93 25 28 3 514.61 1.75 94 25 29 4 510.78 0.17 95 25 65 40 163.84 3.19 96 25 69 44 163.81 3.20 97 26 29 3 517.34 0.39 98 26 30 4 510.41 0.01 99 26 56 30 213.13 0.24 100 27 30 3 518.38 0.55 101 27 31 4 510.42 0.01 102 27 114 87 169.60 0.55 103 27 118 91 169.52 0.59 104 28 31 3 509.96 0.23 105 28 32 4 505.62 2.40 106 28 69 41 173.55 0.76 107 28 107 79 170.45 0.68 108 28 110 82 170.38 0.68 109 28 111 83 170.34 0.68 110 28 114 86 169.88 0.70 111 29 32 3 506.93 1.75 112 29 33 4 505.62 2.40 113 29 61 32 194.81 8.08 114 29 64 35 176.88 0.41 115 29 65 36 174.84 1.40 116 29 107 78 170.50 0.65 117 30 33 3 509.77 4.41 118 30 34 4 505.62 2.40 119 30 52 22 219.32 2.48 120 30 55 25 213.61 0.03 121 30 56 26 213.80 0.12 122 31 34 3 513.04 1.30 123 31 35 4 509.66 0.41 124 31 110 79 170.39 0.67 125 31 113 82 170.25 0.64 126 32 35 3 514.99 2.25 127 32 36 4 503.26 3.60 128 32 39 7 432.11 4.61 129 32 106 74 170.68 0.74 130 32 107 75 170.50 0.66 131 32 110 78 170.41 0.69 132 33 36 3 518.97 0.27 133 33 37 4 486.51 6.73 134 33 39 6 432.12 4.61 135 33 40 7 410.62 0.25 136 33 43 10 335.52 12.22 137 33 46 13 280.04 4.11 138 33 55 22 219.41 2.48 139 33 61 28 213.81 0.06 140 34 37 3 526.52 3.51 141 34 52 18 227.91 1.77 142 36 39 3 523.43 6.04 143 36 106 70 171.22 0.59 144 37 40 3 526.60 4.46 145 37 41 4 520.64 6.03 146 38 41 3 533.21 0.26 147 38 103 65 171.47 0.59 148 38 106 68 171.43 0.60 149 39 42 3 525.19 3.75 150 39 43 4 526.50 3.10 151 39 103 64 171.34 0.64 152 39 106 67 171.34 0.64 153 40 43 3 523.57 1.63 154 40 46 6 384.71 7.02 155 40 47 7 286.19 1.02 156 40 49 9 269.70 0.95 157 40 55 15 239.43 1.75 158 41 47 6 285.22 1.52 159 42 97 55 172.00 0.51 160 42 98 56 172.00 0.51 161 42 99 57 171.90 0.48 162 42 100 58 171.97 0.45 163 42 103 61 171.75 0.49 164 43 46 3 523.01 0.86 165 43 47 4 479.25 5.76 166 43 64 21 227.11 0.02 167 44 47 3 533.14 1.84 168 45 48 3 595.81 0.40 169 45 60 15 229.89 0.62 170 46 49 3 533.37 1.02 171 46 60 14 229.34 0.89 172 46 61 15 227.28 0.09 173 46 64 18 227.27 0.08 174 49 54 5 460.04 11.27 175 49 55 6 355.44 9.92 176 49 58 9 273.54 3.19 177 49 61 12 246.37 3.46 178 50 54 4 501.07 2.58 179 51 54 3 501.07 2.58 180 51 55 4 490.43 2.76 181 52 55 3 503.75 0.11 182 52 56 4 491.26 2.34 183 53 56 3 519.00 5.58 184 53 57 4 495.70 0.14 185 54 57 3 520.49 4.84 186 54 58 4 495.70 0.14 187 55 58 3 512.71 3.79 188 55 61 6 410.13 12.04 189 58 61 3 532.39 3.17 190 58 62 4 512.81 5.90 191 59 62 3 510.04 7.29 192 59 63 4 509.65 7.49 193 60 63 3 509.78 7.42 194 60 64 4 511.16 6.74 195 61 64 3 524.56 0.39 196 61 65 4 511.31 1.02 197 62 65 3 518.81 2.50 198 62 66 4 511.98 0.68 199 63 66 3 521.96 0.92 200 63 67 4 511.99 0.68 201 64 67 3 526.51 6.00 202 64 68 4 511.98 0.68 203 65 68 3 518.02 2.38 204 65 69 4 511.95 0.66 205 66 69 3 521.25 0.77 206 66 70 4 510.74 1.27 207 67 70 3 534.00 2.25 208 67 71 4 511.19 1.03 209 68 71 3 532.45 1.48 210 68 72 4 511.28 1.07 211 68 107 39 171.25 0.68 212 69 72 3 517.61 1.80 213 69 73 4 511.26 1.08 214 70 73 3 533.99 0.39 215 70 74 4 511.27 1.08 216 71 74 3 525.26 0.71 217 71 75 4 514.38 0.47 218 72 75 3 520.31 1.76 219 72 76 4 508.66 0.54 220 72 111 39 171.28 0.67 221 72 135 63 168.97 0.64 222 72 138 66 168.69 0.52 223 73 76 3 518.62 1.65 224 73 77 4 508.75 0.49 225 74 77 3 535.56 0.03 226 74 78 4 511.58 0.91 227 75 78 3 535.54 0.02 228 75 82 7 249.12 3.85 229 75 85 10 217.66 7.83 230 75 89 14 203.15 15.08 231 75 138 63 168.97 0.63 232 76 79 3 531.14 2.23 233 76 134 58 169.22 0.53 234 78 81 3 498.97 0.54 235 78 82 4 424.10 5.21 236 78 85 7 289.16 8.65 237 80 137 57 169.11 0.47 238 82 85 3 521.88 0.07 239 82 86 4 509.33 0.23 240 82 137 55 169.30 0.55 241 82 141 59 168.51 0.59 242 83 86 3 518.65 1.54 243 83 87 4 510.37 0.74 244 84 88 4 522.83 0.35 245 85 88 3 547.06 1.64 246 85 89 4 520.71 0.51 247 86 89 3 527.70 2.08 248 86 90 4 515.12 3.31 249 86 138 52 169.22 0.53 250 86 141 55 166.95 0.70 251 86 142 56 164.30 0.88 252 86 145 59 160.46 1.84 253 87 90 3 523.03 1.67 254 87 91 4 519.06 1.33 255 88 91 3 519.23 0.24 256 88 92 4 510.31 0.87 257 89 92 3 515.52 1.62 258 89 93 4 512.12 0.07 259 89 138 49 169.22 0.53 260 90 93 3 514.25 0.99 261 90 94 4 507.51 2.37 262 90 142 52 162.16 0.92 263 90 145 55 155.08 0.39 264 90 146 56 152.84 0.54 265 91 94 3 516.10 0.14 266 91 95 4 507.51 2.38 267 91 149 58 148.49 0.11 268 92 95 3 526.85 5.30 269 92 96 4 482.51 3.71 270 92 97 5 482.51 3.71 271 93 97 4 416.69 19.71 272 93 98 5 416.67 19.71 273 93 99 6 303.48 6.68 274 93 146 53 151.84 0.03 275 94 98 4 385.20 35.45 276 94 146 52 151.50 0.04 277 94 149 55 143.75 2.44 278 94 151 57 105.70 3.49 279 95 98 3 509.73 3.06 280 95 149 54 148.28 0.21 281 95 151 56 130.13 3.28 282 98 151 53 99.75 6.58 283 99 103 4 517.53 0.66 284 99 104 5 515.00 0.13 285 99 146 47 151.48 0.04 286 100 103 3 526.22 0.92 287 100 104 4 525.28 0.46 288 100 153 53 27.99 3.32 289 101 104 3 525.29 0.46 290 101 105 4 521.23 2.48 291 101 139 38 164.16 0.95 292 101 142 41 159.33 0.49 293 101 143 42 155.47 0.18 294 101 146 45 151.19 0.26 295 101 153 52 17.37 0.23 296 102 105 3 525.28 0.46 297 102 106 4 521.23 2.48 298 103 106 3 521.23 2.48 299 103 107 4 514.90 0.10 300 104 107 3 523.39 0.54 301 104 108 4 513.41 0.62 302 104 139 35 164.13 0.96 303 104 142 38 157.92 0.20 304 105 108 3 516.96 2.68 305 105 109 4 516.94 2.69 306 105 139 34 164.16 0.97 307 106 109 3 520.69 2.62 308 106 110 4 511.18 1.35 309 107 110 3 519.14 2.63 310 107 111 4 506.13 1.17 311 108 111 3 521.62 4.68 312 108 112 4 506.04 1.10 313 108 135 27 168.09 0.88 314 108 139 31 164.16 0.97 315 109 112 3 511.06 1.41 316 109 113 4 506.03 1.10 317 110 113 3 514.36 5.27 318 110 114 4 505.72 0.96 319 111 114 3 525.49 0.29 320 111 115 4 509.09 0.50 321 111 135 24 171.75 0.95 322 112 115 3 516.49 4.20 323 112 116 4 509.09 0.50 324 112 123 11 265.51 8.17 325 112 128 16 177.65 1.53 326 112 131 19 171.92 1.01 327 112 132 20 171.88 0.96 328 112 135 23 171.81 0.97 329 113 116 3 519.27 0.58 330 113 117 4 507.57 0.26 331 114 117 3 520.23 2.73 332 114 118 4 503.39 1.83 333 115 118 3 515.66 0.35 334 115 119 4 490.50 1.79 335 115 123 8 268.64 6.60 336 115 131 16 199.97 9.64 337 116 120 4 438.05 9.12 338 116 123 7 265.51 8.17 339 119 122 3 517.28 4.21 340 119 123 4 460.68 5.20 341 120 123 3 515.52 6.58 342 120 124 4 480.82 4.25 343 122 127 5 475.16 1.38 344 123 127 4 494.12 2.39 345 123 128 5 475.17 1.39 346 123 131 8 424.38 10.31 347 124 127 3 518.12 2.66 348 124 128 4 498.90 0.01 349 125 128 3 506.90 4.00 350 125 129 4 506.90 4.00 351 126 129 3 511.57 1.66 352 126 130 4 506.90 4.00 353 127 130 3 517.46 1.22 354 127 131 4 500.34 2.20 355 128 131 3 512.82 0.05 356 128 132 4 505.69 0.48 357 129 132 3 516.40 0.18 358 129 133 4 510.49 1.92 359 130 133 3 517.89 0.68 360 130 134 4 510.48 1.92 361 131 134 3 510.85 1.74 362 131 135 4 499.88 2.29 363 132 135 3 501.92 2.73 364 132 136 4 499.88 2.29 365 133 136 3 501.33 3.02 366 133 137 4 499.34 2.00 367 134 137 3 508.89 2.71 368 134 138 4 499.38 1.99 369 135 138 3 508.40 2.52 370 135 139 4 505.40 1.01 371 136 139 3 512.10 2.35 372 136 140 4 504.12 0.37 373 137 140 3 519.54 2.31 374 137 141 4 504.12 0.38 375 138 141 3 520.61 1.79 376 138 142 4 503.04 1.46 377 139 142 3 513.88 0.26 378 139 143 4 504.81 2.35 379 140 143 3 514.20 2.35 380 140 144 4 504.82 2.35 381 141 144 3 511.84 1.16 382 141 145 4 511.74 1.10 383 142 145 3 524.25 1.28 384 142 146 4 504.84 2.35 385 143 146 3 506.49 1.52 386 143 147 4 504.91 2.31 387 143 152 9 234.38 14.73 388 144 147 3 514.52 2.50 389 144 148 4 503.30 1.50 390 145 148 3 513.57 2.81 391 145 149 4 507.51 0.60 392 146 149 3 522.52 0.15 393 146 150 4 507.47 0.62 394 146 151 5 340.55 8.63 395 146 152 6 252.43 5.79 396 146 153 7 252.45 5.78 397 147 150 3 507.47 0.62 398 147 152 5 260.81 1.58