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 8 464.63 0.52 2 2 130 128 47.54 0.10 3 2 133 131 41.76 0.81 4 2 134 132 32.83 0.63 5 2 137 135 32.00 1.04 6 3 6 3 513.22 2.48 7 3 7 4 512.98 2.60 8 4 7 3 513.11 2.54 9 4 8 4 512.97 2.60 10 4 79 75 59.75 1.93 11 5 8 3 513.12 2.44 12 5 9 4 509.29 0.63 13 6 9 3 527.15 4.13 14 6 10 4 498.97 1.55 15 6 130 124 68.36 1.03 16 6 133 127 68.35 1.03 17 7 10 3 506.95 2.44 18 7 11 4 506.55 2.24 19 7 76 69 68.67 0.90 20 7 79 72 68.36 1.04 21 7 80 73 68.67 0.90 22 7 134 127 68.64 0.91 23 7 137 130 68.66 0.90 24 8 11 3 524.37 2.75 25 8 12 4 512.38 0.68 26 9 12 3 526.57 1.64 27 9 13 4 512.39 0.69 28 9 126 117 81.23 1.57 29 9 127 118 81.15 1.54 30 9 130 121 81.05 1.54 31 10 13 3 518.24 2.52 32 10 14 4 513.48 0.14 33 10 76 66 81.08 1.55 34 10 130 120 81.08 1.54 35 10 131 121 81.04 1.54 36 10 134 124 80.96 1.50 37 11 14 3 515.39 1.09 38 11 15 4 513.50 0.14 39 11 76 65 81.12 1.57 40 11 77 66 81.12 1.57 41 11 79 68 81.12 1.57 42 12 15 3 521.17 3.98 43 13 16 3 521.44 4.12 44 13 17 4 522.81 2.35 45 13 115 102 89.85 0.45 46 13 123 110 87.83 1.46 47 13 131 118 83.69 0.55 48 14 17 3 518.71 0.04 49 14 18 4 514.93 1.84 50 14 69 55 177.54 4.83 51 14 72 58 123.88 19.55 52 14 73 59 83.68 0.56 53 14 76 62 83.69 0.56 54 14 77 63 83.70 0.56 55 15 18 3 518.71 0.04 56 15 19 4 514.60 2.10 57 16 19 3 520.00 0.60 58 16 24 8 443.42 10.58 59 16 119 103 104.65 1.22 60 16 122 106 104.53 1.16 61 17 20 3 520.12 0.67 62 17 21 4 490.95 3.12 63 17 24 7 428.85 8.84 64 17 69 52 203.56 1.78 65 17 115 98 102.73 1.52 66 18 21 3 514.89 1.85 67 18 77 59 164.13 0.58 68 20 23 3 519.79 0.85 69 20 24 4 505.80 4.41 70 20 118 98 157.87 1.58 71 21 24 3 516.60 0.73 72 21 25 4 512.40 1.10 73 21 66 45 205.40 2.29 74 21 69 48 205.37 2.31 75 22 25 3 519.09 0.51 76 22 26 4 514.14 1.96 77 22 62 40 207.41 1.60 78 22 66 44 205.41 2.31 79 23 26 3 513.71 1.74 80 23 27 4 512.41 1.09 81 23 118 95 161.06 1.14 82 24 27 3 515.35 2.56 83 24 28 4 507.80 1.21 84 24 69 45 205.55 2.23 85 24 114 90 161.94 0.83 86 24 115 91 161.94 0.83 87 24 118 94 161.07 1.14 88 24 119 95 161.08 1.15 89 25 28 3 515.13 1.26 90 25 29 4 511.45 0.58 91 25 65 40 206.16 1.94 92 25 69 44 205.43 2.29 93 26 29 3 513.39 0.39 94 26 30 4 508.72 1.59 95 26 55 29 228.70 1.37 96 26 56 30 228.83 1.45 97 26 58 32 219.86 2.88 98 26 61 35 209.68 0.59 99 26 62 36 207.59 1.57 100 27 30 3 519.12 0.93 101 27 31 4 508.74 1.60 102 27 114 87 161.95 0.83 103 27 118 91 161.29 1.04 104 28 31 3 514.18 1.95 105 28 32 4 508.73 1.59 106 28 69 41 205.72 2.16 107 28 107 79 162.68 1.04 108 28 110 82 162.41 0.96 109 28 111 83 162.35 0.95 110 28 114 86 162.16 0.94 111 29 32 3 517.15 1.47 112 29 33 4 513.06 0.57 113 29 61 32 216.51 1.64 114 29 64 35 209.42 1.68 115 29 65 36 207.71 1.63 116 29 107 78 162.71 1.03 117 30 33 3 519.11 0.49 118 30 34 4 513.06 0.57 119 30 52 22 255.72 0.88 120 30 55 25 240.44 2.08 121 30 56 26 249.91 3.77 122 30 61 31 219.42 3.09 123 31 34 3 515.02 1.55 124 31 35 4 499.43 0.92 125 31 110 79 162.62 1.03 126 31 113 82 162.47 0.96 127 31 114 83 162.41 0.93 128 32 35 3 510.76 1.72 129 32 36 4 498.72 1.28 130 32 39 7 369.67 15.02 131 32 106 74 162.74 1.02 132 32 107 75 162.74 1.02 133 32 110 78 162.63 1.03 134 33 36 3 517.05 0.70 135 33 37 4 492.98 3.52 136 33 39 6 378.63 10.53 137 33 40 7 312.72 4.21 138 33 43 10 307.47 6.83 139 33 55 22 258.60 2.31 140 33 61 28 253.75 1.82 141 34 37 3 517.05 0.70 142 34 50 16 261.49 3.56 143 34 51 17 260.24 2.96 144 34 52 18 260.21 2.97 145 34 55 21 260.06 3.02 146 36 39 3 533.47 1.01 147 36 106 70 162.89 1.00 148 37 40 3 518.67 0.27 149 38 41 3 520.50 4.46 150 38 103 65 163.55 0.84 151 38 106 68 163.50 0.85 152 39 42 3 527.46 2.61 153 39 43 4 515.40 1.92 154 39 103 64 163.22 0.88 155 39 106 67 162.97 1.00 156 40 43 3 524.53 1.15 157 40 46 6 338.58 11.76 158 40 47 7 272.24 4.03 159 40 49 9 271.06 3.44 160 40 55 15 263.42 2.64 161 41 47 6 284.44 2.08 162 42 97 55 164.25 0.71 163 42 98 56 164.24 0.71 164 42 99 57 164.01 0.78 165 42 100 58 164.04 0.78 166 42 103 61 163.78 0.79 167 43 46 3 520.72 2.76 168 43 47 4 490.80 2.92 169 43 64 21 263.38 2.64 170 44 47 3 525.57 1.95 171 45 48 3 600.27 0.05 172 45 60 15 263.44 2.64 173 45 63 18 263.44 2.64 174 45 64 19 263.41 2.63 175 46 49 3 534.84 0.29 176 46 60 14 263.44 2.64 177 46 61 15 263.40 2.63 178 46 64 18 263.42 2.64 179 49 54 5 436.50 18.77 180 49 55 6 383.28 27.59 181 49 58 9 280.50 3.92 182 49 61 12 267.64 0.54 183 50 54 4 502.19 2.02 184 51 54 3 506.81 0.20 185 51 55 4 501.72 1.77 186 52 55 3 501.72 1.77 187 52 56 4 501.72 1.77 188 53 56 3 508.49 0.65 189 53 57 4 501.72 1.77 190 54 57 3 504.90 3.35 191 54 58 4 501.71 1.77 192 55 58 3 513.50 4.15 193 55 61 6 408.89 8.20 194 58 61 3 533.14 2.79 195 58 62 4 514.66 5.73 196 59 62 3 524.94 0.60 197 59 63 4 514.66 5.73 198 60 63 3 516.64 4.75 199 60 64 4 511.88 7.12 200 61 64 3 525.31 0.76 201 61 65 4 502.87 2.56 202 62 65 3 510.57 1.29 203 62 66 4 510.64 1.26 204 63 66 3 516.95 3.42 205 63 67 4 510.66 1.26 206 64 67 3 510.70 1.28 207 64 68 4 510.66 1.26 208 65 68 3 521.70 6.00 209 65 69 4 510.65 1.27 210 66 69 3 526.12 3.78 211 66 70 4 506.50 0.80 212 67 70 3 520.51 1.10 213 67 71 4 508.94 0.81 214 68 71 3 525.35 0.80 215 68 72 4 508.97 0.82 216 69 72 3 518.36 2.18 217 69 73 4 507.47 1.56 218 70 73 3 530.70 1.26 219 70 74 4 509.01 0.79 220 71 74 3 527.12 0.54 221 71 75 4 511.99 0.70 222 71 89 18 164.25 0.72 223 72 75 3 516.65 3.59 224 72 76 4 509.27 2.06 225 72 111 39 162.53 1.05 226 72 135 63 157.77 1.54 227 72 138 66 156.22 2.15 228 73 76 3 516.57 2.67 229 73 77 4 508.86 2.27 230 74 77 3 512.73 0.34 231 74 78 4 511.45 0.97 232 75 78 3 523.83 5.88 233 75 82 7 192.58 9.17 234 75 85 10 165.61 0.43 235 75 86 11 172.66 3.12 236 75 89 14 165.57 0.42 237 75 138 63 157.25 1.64 238 76 79 3 523.83 5.88 239 76 134 58 157.83 1.52 240 78 81 3 509.45 0.89 241 78 82 4 358.38 8.13 242 78 85 7 312.50 7.96 243 80 137 57 157.88 1.53 244 82 85 3 522.63 0.30 245 82 86 4 510.08 0.60 246 82 137 55 158.03 1.48 247 82 141 59 156.12 2.08 248 83 86 3 519.40 1.92 249 83 87 4 510.08 0.60 250 84 88 4 532.36 0.49 251 85 88 3 547.88 2.13 252 85 89 4 527.29 2.04 253 86 89 3 532.36 0.49 254 86 90 4 515.13 4.04 255 86 138 52 156.44 2.04 256 86 141 55 156.03 2.12 257 86 142 56 155.17 2.54 258 87 90 3 521.65 0.98 259 87 91 4 515.86 3.68 260 88 91 3 515.97 0.10 261 88 92 4 512.16 1.79 262 89 92 3 514.98 1.38 263 89 93 4 512.16 1.79 264 89 142 53 155.28 2.00 265 90 93 3 514.87 3.15 266 90 94 4 512.15 1.79 267 90 142 52 152.83 1.77 268 90 145 55 145.59 0.27 269 90 146 56 145.56 0.27 270 91 94 3 518.88 0.66 271 91 95 4 506.06 4.80 272 91 149 58 143.18 0.38 273 92 95 3 526.62 5.42 274 92 96 4 485.83 7.08 275 92 97 5 435.59 32.20 276 93 97 4 366.08 2.70 277 93 98 5 354.43 8.51 278 93 99 6 304.83 0.07 279 93 146 53 144.24 0.82 280 94 98 4 354.43 8.51 281 94 146 52 143.78 0.62 282 94 149 55 141.35 0.57 283 94 151 57 86.44 6.08 284 95 98 3 518.51 0.69 285 95 149 54 143.01 0.29 286 95 151 56 118.97 2.29 287 98 151 53 95.39 3.46 288 99 103 4 511.58 0.29 289 99 104 5 500.26 1.31 290 99 146 47 143.77 0.60 291 100 103 3 527.10 1.23 292 100 153 53 28.30 3.74 293 101 104 3 526.32 0.70 294 101 105 4 509.84 2.65 295 101 142 41 153.72 1.22 296 101 143 42 147.35 0.14 297 101 146 45 143.76 0.60 298 101 153 52 22.47 2.77 299 102 105 3 521.42 3.14 300 102 106 4 509.04 3.04 301 103 106 3 521.40 3.15 302 103 107 4 509.04 3.04 303 104 107 3 521.35 3.12 304 104 108 4 521.35 3.12 305 104 139 35 155.66 1.96 306 104 142 38 152.18 1.99 307 105 108 3 521.35 3.12 308 105 109 4 521.35 3.12 309 105 139 34 155.69 1.97 310 106 109 3 515.79 0.18 311 106 110 4 510.56 2.25 312 107 110 3 508.74 1.34 313 107 111 4 508.73 1.33 314 108 111 3 519.08 2.67 315 108 112 4 510.12 2.42 316 108 135 27 157.68 1.50 317 108 139 31 155.68 1.95 318 109 112 3 517.65 1.18 319 109 113 4 508.68 1.70 320 110 113 3 510.13 2.41 321 110 114 4 508.37 0.60 322 111 114 3 512.99 1.70 323 111 115 4 509.84 0.12 324 111 135 24 157.75 1.54 325 112 115 3 517.49 1.47 326 112 116 4 509.84 0.12 327 112 123 11 255.28 2.98 328 112 128 16 158.88 1.85 329 112 131 19 157.99 1.43 330 112 135 23 157.84 1.50 331 113 116 3 519.59 0.42 332 113 117 4 505.65 2.21 333 114 117 3 509.92 3.21 334 114 118 4 504.12 1.46 335 115 118 3 516.41 0.03 336 115 119 4 501.94 1.04 337 115 123 8 255.32 2.97 338 115 131 16 165.52 5.20 339 116 119 3 520.97 3.10 340 116 120 4 490.55 0.21 341 116 123 7 255.34 2.96 342 116 128 12 219.28 20.98 343 117 120 3 539.18 2.78 344 119 122 3 511.87 7.67 345 119 123 4 469.79 10.23 346 123 127 4 501.10 3.58 347 123 128 5 491.55 3.67 348 123 131 8 472.42 8.07 349 124 127 3 501.13 3.59 350 124 128 4 501.18 3.56 351 125 128 3 512.35 2.02 352 125 129 4 505.79 1.27 353 126 129 3 511.27 1.48 354 126 130 4 505.80 1.27 355 127 130 3 510.56 2.36 356 127 131 4 507.37 3.96 357 128 131 3 510.57 2.36 358 128 132 4 507.38 3.96 359 129 132 3 513.33 1.35 360 129 133 4 509.27 3.02 361 130 133 3 513.71 1.54 362 130 134 4 512.09 1.60 363 131 134 3 516.50 0.15 364 131 135 4 505.67 0.07 365 132 135 3 522.12 2.96 366 132 136 4 505.69 0.06 367 133 136 3 507.22 0.83 368 133 137 4 505.69 0.05 369 134 137 3 509.33 1.87 370 134 138 4 505.23 0.18 371 135 138 3 509.95 1.74 372 135 139 4 506.13 0.64 373 136 139 3 512.70 0.42 374 136 140 4 505.23 0.20 375 137 140 3 510.89 1.74 376 137 141 4 503.79 1.07 377 138 141 3 518.89 0.18 378 138 142 4 504.29 0.98 379 139 142 3 509.81 1.79 380 139 143 4 506.09 0.09 381 140 143 3 514.96 2.71 382 140 144 4 507.73 0.90 383 141 144 3 511.58 1.02 384 141 145 4 508.72 1.38 385 142 145 3 521.12 2.84 386 142 146 4 507.74 0.90 387 143 146 3 508.06 1.71 388 143 147 4 505.46 0.42 389 143 152 9 169.46 0.23 390 144 147 3 513.66 3.68 391 144 148 4 505.55 0.38 392 145 148 3 514.11 0.71 393 145 149 4 505.29 0.25 394 146 149 3 511.44 0.62 395 146 150 4 505.28 0.25 396 146 151 5 401.83 16.54 397 146 152 6 273.69 4.25 398 147 150 3 507.97 1.11 399 147 152 5 243.33 10.93