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 5 495.34 1.21 2 2 10 8 454.87 1.11 3 2 130 128 35.99 0.73 4 2 133 131 25.04 0.20 5 2 134 132 21.62 1.49 6 2 137 135 21.62 1.49 7 3 6 3 505.99 3.81 8 3 7 4 505.71 3.95 9 4 7 3 527.26 0.81 10 4 8 4 513.25 0.18 11 4 79 75 48.06 2.21 12 5 8 3 519.27 3.19 13 5 9 4 513.25 0.18 14 6 9 3 519.27 3.19 15 6 10 4 509.56 1.67 16 6 130 124 57.76 0.56 17 6 133 127 57.76 0.55 18 7 10 3 512.26 1.38 19 7 11 4 501.99 1.98 20 7 79 72 57.76 0.55 21 7 80 73 58.06 0.70 22 7 134 127 57.77 0.55 23 7 137 130 57.77 0.55 24 8 11 3 517.30 1.62 25 8 12 4 501.99 1.98 26 9 12 3 519.26 0.65 27 9 13 4 515.35 1.31 28 9 126 117 76.81 2.21 29 9 127 118 76.77 2.19 30 9 130 121 76.70 2.20 31 10 13 3 521.26 1.58 32 10 14 4 515.31 1.33 33 10 76 66 76.78 2.18 34 10 130 120 76.77 2.19 35 10 131 121 76.74 2.19 36 10 134 124 76.70 2.20 37 11 14 3 515.28 1.34 38 11 15 4 515.40 1.28 39 11 76 65 76.80 2.18 40 11 77 66 76.84 2.19 41 11 79 68 76.80 2.17 42 12 15 3 519.27 0.65 43 12 16 4 517.74 1.42 44 12 122 110 94.47 0.51 45 13 16 3 513.89 0.51 46 13 17 4 513.88 0.52 47 13 119 106 94.68 0.48 48 13 122 109 94.50 0.51 49 13 123 110 94.38 0.55 50 13 131 118 82.80 0.47 51 14 17 3 513.88 0.52 52 14 18 4 513.87 0.52 53 14 69 55 94.11 0.66 54 14 72 58 87.64 0.89 55 14 73 59 82.58 0.62 56 14 76 62 82.57 0.62 57 14 77 63 82.58 0.62 58 15 18 3 513.80 0.56 59 15 19 4 512.24 0.23 60 16 19 3 511.85 0.03 61 16 24 8 414.40 1.90 62 16 119 103 98.17 0.06 63 16 122 106 98.17 0.06 64 17 20 3 520.07 4.08 65 17 21 4 487.69 2.91 66 17 24 7 411.69 0.55 67 17 69 52 98.10 0.06 68 17 115 98 98.16 0.06 69 18 21 3 502.20 3.12 70 18 77 59 96.69 0.61 71 20 23 3 513.94 0.13 72 20 24 4 505.50 4.34 73 20 118 98 134.14 0.29 74 21 24 3 518.00 1.88 75 21 25 4 511.23 1.49 76 21 66 45 119.70 0.61 77 21 69 48 112.96 0.12 78 22 25 3 511.24 1.49 79 22 26 4 511.23 1.49 80 22 62 40 133.63 0.54 81 22 66 44 127.11 0.38 82 23 26 3 513.07 0.57 83 23 27 4 502.02 3.10 84 23 118 95 149.34 0.18 85 24 27 3 514.91 0.46 86 24 28 4 506.56 3.68 87 24 69 45 134.60 0.55 88 24 114 90 147.25 0.27 89 24 115 91 147.62 0.28 90 24 118 94 149.40 0.15 91 24 119 95 149.98 0.35 92 25 28 3 516.41 0.61 93 25 29 4 512.05 0.97 94 25 65 40 134.91 0.40 95 25 69 44 134.88 0.42 96 26 29 3 519.10 4.48 97 26 30 4 512.00 0.95 98 26 56 30 150.99 0.18 99 26 62 36 149.44 0.36 100 27 30 3 512.70 1.25 101 27 31 4 512.10 0.93 102 27 114 87 150.29 0.20 103 27 118 91 150.49 0.24 104 28 31 3 521.39 3.22 105 28 32 4 512.62 1.17 106 28 69 41 150.25 0.23 107 28 107 79 150.19 0.21 108 28 110 82 150.20 0.21 109 28 111 83 150.19 0.20 110 28 114 86 150.32 0.21 111 29 32 3 515.95 1.16 112 29 33 4 512.11 0.91 113 29 61 32 150.90 0.13 114 29 64 35 150.66 0.14 115 29 65 36 150.58 0.10 116 29 107 78 150.31 0.21 117 30 33 3 515.95 1.16 118 30 34 4 501.94 4.15 119 30 52 22 151.68 0.23 120 30 55 25 151.51 0.21 121 30 56 26 151.53 0.21 122 31 34 3 513.68 0.02 123 31 35 4 496.29 1.33 124 31 110 79 150.61 0.10 125 31 113 82 150.66 0.14 126 32 35 3 519.78 2.43 127 32 36 4 477.53 3.92 128 32 39 7 259.27 36.69 129 32 106 74 150.62 0.10 130 32 107 75 150.62 0.10 131 32 110 78 150.63 0.12 132 33 37 4 354.09 9.08 133 33 39 6 328.68 1.99 134 33 40 7 174.47 5.59 135 33 43 10 171.56 4.26 136 33 46 13 151.72 0.23 137 33 55 22 151.71 0.23 138 34 52 18 151.77 0.24 139 36 39 3 528.64 0.28 140 36 106 70 150.78 0.06 141 37 40 3 511.99 1.57 142 38 41 3 526.47 0.92 143 38 103 65 150.78 0.03 144 38 106 68 150.94 0.07 145 39 42 3 521.69 2.02 146 39 43 4 519.27 2.69 147 39 103 64 150.71 0.06 148 39 106 67 150.90 0.06 149 40 43 3 514.34 0.21 150 40 46 6 332.00 1.53 151 40 47 7 161.02 4.53 152 40 55 15 152.44 0.35 153 41 47 6 180.41 5.17 154 42 97 55 150.58 0.04 155 42 98 56 150.64 0.07 156 42 99 57 150.63 0.07 157 42 103 61 150.94 0.06 158 43 46 3 506.92 1.94 159 43 47 4 442.05 8.21 160 43 64 21 151.90 0.24 161 44 47 3 524.74 3.44 162 45 60 15 152.28 0.32 163 46 49 3 515.80 0.83 164 46 60 14 152.22 0.35 165 46 61 15 152.19 0.35 166 46 64 18 152.19 0.35 167 49 54 5 437.63 17.95 168 49 55 6 329.20 0.01 169 49 58 9 158.59 0.12 170 49 61 12 153.52 0.71 171 50 54 4 491.03 0.28 172 51 54 3 509.10 5.00 173 51 55 4 500.40 4.41 174 52 55 3 511.48 1.13 175 52 56 4 505.73 1.74 176 53 56 3 507.93 0.65 177 53 57 4 507.92 0.65 178 54 57 3 510.32 1.84 179 54 58 4 489.87 0.83 180 55 58 3 514.21 1.78 181 55 61 6 406.19 15.58 182 58 61 3 507.94 0.99 183 58 62 4 505.07 2.27 184 59 62 3 507.00 1.46 185 59 63 4 500.79 0.12 186 60 63 3 504.25 1.02 187 60 64 4 502.63 1.05 188 61 64 3 513.02 5.29 189 61 65 4 505.43 0.35 190 62 65 3 507.31 0.59 191 62 66 4 508.15 0.99 192 63 66 3 518.02 2.33 193 63 67 4 508.16 0.99 194 64 67 3 509.77 1.80 195 64 68 4 504.69 0.75 196 65 68 3 508.15 0.98 197 65 69 4 504.68 0.76 198 66 69 3 512.24 1.06 199 66 70 4 497.60 2.77 200 67 70 3 515.17 2.54 201 67 71 4 508.14 0.98 202 68 71 3 518.81 0.72 203 68 72 4 510.40 0.15 204 69 72 3 510.38 0.15 205 69 73 4 500.81 4.62 206 70 73 3 513.38 2.00 207 70 74 4 509.72 0.17 208 71 74 3 509.72 0.17 209 71 75 4 509.72 0.17 210 72 75 3 522.66 1.20 211 72 76 4 509.71 0.17 212 72 111 39 154.74 1.44 213 72 135 63 154.62 1.50 214 73 76 3 523.31 0.89 215 73 77 4 511.81 1.22 216 74 77 3 527.96 1.44 217 74 78 4 517.27 1.51 218 75 78 3 521.28 3.52 219 75 82 7 161.14 1.51 220 75 85 10 156.13 0.98 221 75 86 11 154.62 1.54 222 75 138 63 159.10 0.01 223 76 79 3 534.60 3.17 224 76 134 58 168.37 1.61 225 78 81 3 497.60 1.17 226 78 82 4 337.18 9.94 227 78 85 7 275.74 20.34 228 80 137 57 256.89 1.89 229 82 85 3 518.36 1.43 230 82 86 4 495.01 0.04 231 82 137 55 313.02 1.11 232 82 141 59 293.52 4.34 233 83 86 3 512.85 1.32 234 83 87 4 509.61 2.53 235 84 87 3 528.42 0.84 236 84 88 4 525.94 2.10 237 85 88 3 536.13 0.07 238 86 89 3 525.92 2.09 239 86 90 4 512.82 2.34 240 86 138 52 314.61 0.96 241 86 141 55 314.51 0.95 242 86 142 56 314.48 0.94 243 86 145 59 314.42 0.95 244 87 90 3 519.11 0.78 245 87 91 4 516.74 0.40 246 87 145 58 314.43 0.96 247 88 91 3 519.12 0.79 248 88 92 4 516.75 0.40 249 89 92 3 544.48 4.82 250 89 93 4 512.53 2.50 251 89 138 49 314.78 0.94 252 89 142 53 314.73 0.93 253 90 93 3 519.12 0.79 254 90 94 4 501.51 2.96 255 90 142 52 314.73 0.93 256 90 145 55 314.67 0.92 257 90 146 56 314.46 0.94 258 90 149 59 314.37 0.98 259 91 94 3 510.42 1.86 260 91 95 4 494.53 2.52 261 91 145 54 314.69 0.93 262 91 149 58 314.28 1.01 263 92 95 3 506.47 0.11 264 92 96 4 436.13 2.43 265 92 97 5 436.13 2.43 266 93 97 4 367.05 3.93 267 93 98 5 350.58 4.11 268 93 99 6 318.85 0.04 269 93 146 53 314.73 0.94 270 94 98 4 350.58 4.11 271 94 146 52 314.72 0.94 272 94 149 55 314.38 0.98 273 94 151 57 313.57 1.16 274 95 98 3 527.02 3.15 275 95 149 54 314.41 0.98 276 98 151 53 314.27 0.94 277 99 103 4 497.79 3.33 278 99 104 5 497.79 3.33 279 99 146 47 314.82 0.94 280 99 151 52 314.35 0.98 281 100 103 3 507.36 8.11 282 100 104 4 500.30 2.10 283 100 151 51 314.30 0.95 284 100 152 52 313.98 0.86 285 101 104 3 512.45 3.98 286 101 105 4 500.29 2.10 287 101 139 38 315.17 0.95 288 101 142 41 315.07 0.97 289 101 143 42 314.99 0.94 290 101 146 45 315.01 0.95 291 101 152 51 313.33 0.70 292 102 105 3 501.19 2.54 293 102 106 4 500.28 2.08 294 103 106 3 509.25 2.41 295 103 107 4 509.20 2.44 296 104 107 3 515.39 0.66 297 104 108 4 509.18 2.44 298 104 139 35 315.23 0.93 299 104 142 38 315.23 0.94 300 105 108 3 515.39 0.66 301 105 109 4 503.86 5.11 302 105 139 34 315.36 0.93 303 106 109 3 518.38 0.84 304 106 110 4 508.31 2.89 305 107 110 3 512.07 4.00 306 107 111 4 497.29 2.61 307 108 111 3 521.73 0.83 308 108 112 4 507.30 6.42 309 108 135 27 315.64 1.05 310 108 139 31 315.61 1.05 311 109 112 3 520.00 1.70 312 109 113 4 507.31 6.41 313 110 113 3 507.91 6.12 314 110 114 4 507.31 6.41 315 111 114 3 515.88 5.49 316 111 115 4 501.17 0.51 317 111 135 24 316.25 0.98 318 112 115 3 504.65 0.13 319 112 116 4 496.38 4.00 320 112 123 11 317.29 0.92 321 112 128 16 316.60 0.85 322 112 131 19 316.44 0.95 323 112 132 20 316.39 0.95 324 112 135 23 316.33 0.95 325 113 116 3 503.15 0.62 326 113 117 4 494.79 4.37 327 114 117 3 503.92 2.21 328 114 118 4 493.04 4.53 329 115 118 3 517.80 0.84 330 115 119 4 486.28 1.17 331 115 123 8 319.17 0.02 332 115 131 16 316.75 0.86 333 116 119 3 524.79 2.66 334 116 120 4 475.19 0.54 335 116 123 7 328.80 4.80 336 117 120 3 530.39 5.15 337 119 122 3 503.86 0.98 338 119 123 4 432.30 20.03 339 120 123 3 468.34 7.13 340 122 127 5 459.67 12.52 341 123 127 4 459.68 12.52 342 123 128 5 457.46 13.64 343 123 131 8 428.73 22.53 344 124 127 3 487.34 2.31 345 124 128 4 466.25 9.26 346 125 128 3 496.78 0.93 347 125 129 4 483.12 0.82 348 126 129 3 496.05 0.56 349 126 130 4 491.55 2.79 350 127 130 3 494.41 4.22 351 127 131 4 494.30 4.17 352 128 131 3 511.24 2.88 353 128 132 4 494.31 4.17 354 129 132 3 512.02 0.76 355 129 133 4 499.75 6.89 356 130 133 3 521.92 4.20 357 130 134 4 506.59 1.96 358 131 134 3 514.78 0.63 359 131 135 4 496.06 5.42 360 132 135 3 508.72 0.90 361 132 136 4 496.07 5.43 362 133 136 3 507.45 0.26 363 133 137 4 504.07 1.44 364 134 137 3 507.97 0.51 365 134 138 4 504.06 1.43 366 135 138 3 504.07 1.43 367 135 139 4 502.24 2.32 368 136 139 3 509.23 1.18 369 136 140 4 499.44 0.92 370 137 140 3 494.69 7.87 371 137 141 4 490.13 5.59 372 138 141 3 508.94 1.14 373 138 142 4 491.25 5.25 374 139 142 3 500.29 9.62 375 139 143 4 501.43 0.21 376 140 143 3 510.59 4.46 377 140 144 4 505.20 1.65 378 140 147 7 501.48 0.21 379 141 144 3 522.20 5.01 380 141 145 4 505.25 1.63 381 142 145 3 512.06 0.06 382 142 146 4 510.22 0.86 383 143 146 3 510.22 0.85 384 143 147 4 510.22 0.85 385 143 152 9 318.80 1.71 386 144 147 3 517.87 2.52 387 144 148 4 510.20 0.86 388 145 148 3 510.75 1.04 389 145 149 4 505.20 1.64 390 146 149 3 511.01 0.91 391 146 150 4 504.70 1.88 392 146 151 5 434.56 14.88 393 146 152 6 319.57 1.45 394 147 150 3 503.60 2.43 395 147 151 4 483.94 7.41 396 147 152 5 327.43 5.32