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 5 505.32 0.07 2 2 10 8 435.24 13.22 3 2 130 128 44.09 0.73 4 2 133 131 33.23 2.06 5 2 134 132 32.48 1.70 6 2 137 135 32.48 1.70 7 3 6 3 521.53 0.89 8 3 7 4 516.06 1.84 9 4 7 3 521.53 0.89 10 4 8 4 521.54 0.89 11 5 8 3 521.54 0.89 12 5 9 4 521.54 0.89 13 6 9 3 525.84 1.26 14 6 10 4 517.08 2.78 15 6 130 124 70.27 0.79 16 6 133 127 70.28 0.78 17 7 10 3 517.12 2.75 18 7 11 4 507.70 0.42 19 7 76 69 70.28 0.78 20 7 79 72 70.28 0.78 21 7 80 73 70.28 0.78 22 7 134 127 70.28 0.78 23 7 137 130 70.28 0.78 24 8 11 3 523.18 0.28 25 8 12 4 507.70 0.42 26 9 12 3 518.32 3.34 27 9 13 4 509.25 1.19 28 9 126 117 78.48 0.45 29 9 127 118 78.09 0.61 30 9 130 121 77.93 0.53 31 10 13 3 529.10 0.38 32 10 14 4 507.69 0.42 33 10 76 66 77.97 0.55 34 10 130 120 78.03 0.58 35 10 131 121 77.94 0.54 36 10 134 124 77.92 0.54 37 11 14 3 523.81 3.56 38 11 15 4 515.85 1.98 39 11 76 65 78.03 0.58 40 11 77 66 78.34 0.38 41 11 79 68 78.39 0.40 42 12 15 3 524.40 0.37 43 13 16 3 530.34 0.29 44 13 17 4 523.71 1.94 45 13 115 102 93.50 0.77 46 13 122 109 93.75 0.79 47 13 123 110 93.61 0.85 48 13 127 114 88.39 0.42 49 13 131 118 88.37 0.42 50 14 17 3 528.04 1.43 51 14 18 4 510.12 0.94 52 14 69 55 91.00 0.87 53 14 72 58 88.38 0.42 54 14 73 59 88.36 0.42 55 14 76 62 88.34 0.42 56 14 131 117 92.41 0.36 57 15 18 3 529.25 0.83 58 15 19 4 511.31 0.35 59 16 19 3 524.89 0.59 60 16 24 8 447.64 2.29 61 16 119 103 106.64 1.75 62 16 122 106 106.61 1.75 63 17 20 3 524.67 0.49 64 17 21 4 488.20 1.47 65 17 24 7 373.67 9.59 66 17 69 52 153.90 25.75 67 17 115 98 106.56 1.76 68 18 21 3 526.14 1.23 69 18 77 59 139.70 18.91 70 20 23 3 527.05 0.96 71 20 24 4 517.15 3.98 72 21 24 3 523.49 0.82 73 21 25 4 507.72 0.74 74 21 66 45 190.38 7.94 75 21 69 48 189.94 8.15 76 21 70 49 189.93 8.16 77 22 25 3 508.10 0.72 78 22 26 4 507.93 0.64 79 22 62 40 192.31 8.80 80 22 66 44 190.38 7.94 81 23 26 3 532.52 3.40 82 23 27 4 513.07 3.42 83 24 27 3 523.59 0.07 84 24 28 4 505.78 0.59 85 24 69 45 190.65 8.43 86 24 114 90 170.15 1.82 87 24 118 94 167.16 1.02 88 24 119 95 167.38 0.99 89 25 28 3 520.50 1.61 90 25 29 4 512.27 3.87 91 25 65 40 191.03 8.27 92 25 69 44 190.62 8.42 93 26 29 3 525.53 0.05 94 26 30 4 506.84 1.15 95 26 61 35 192.47 8.77 96 26 62 36 192.38 8.80 97 27 30 3 520.71 4.05 98 27 31 4 507.00 1.06 99 27 114 87 172.13 0.83 100 27 118 91 167.84 0.93 101 28 31 3 519.03 3.21 102 28 32 4 507.01 1.06 103 28 69 41 192.25 8.85 104 28 107 79 173.18 0.91 105 28 110 82 172.69 1.09 106 28 111 83 172.71 1.10 107 28 114 86 172.14 0.83 108 29 32 3 510.19 0.01 109 29 33 4 507.01 1.05 110 29 43 14 256.87 0.56 111 29 61 32 206.03 2.19 112 29 64 35 193.00 8.68 113 29 65 36 192.53 8.80 114 29 68 39 192.52 8.79 115 29 107 78 173.18 0.91 116 30 33 3 521.10 0.38 117 30 34 4 506.31 0.70 118 30 52 22 234.38 0.61 119 30 55 25 233.33 0.74 120 30 56 26 233.41 0.77 121 30 61 31 222.43 2.89 122 31 34 3 516.01 2.92 123 31 35 4 506.31 0.71 124 31 110 79 172.76 1.09 125 31 113 82 172.75 1.09 126 31 114 83 172.73 1.11 127 31 117 86 172.65 1.09 128 32 35 3 517.17 4.73 129 32 36 4 504.13 1.14 130 32 39 7 373.36 47.23 131 32 106 74 173.22 0.89 132 32 107 75 173.19 0.91 133 32 110 78 172.78 1.08 134 33 37 4 401.17 34.26 135 33 39 6 393.14 37.34 136 33 40 7 274.75 2.06 137 33 43 10 272.00 3.44 138 33 46 13 258.20 0.02 139 33 55 22 235.69 1.21 140 33 61 28 233.39 0.80 141 34 52 18 235.86 1.21 142 36 39 3 529.91 0.27 143 36 106 70 173.56 0.90 144 36 109 73 173.58 0.90 145 37 40 3 530.69 0.12 146 38 41 3 541.55 2.63 147 38 103 65 174.02 0.86 148 38 106 68 173.99 0.88 149 39 42 3 531.29 0.10 150 39 43 4 528.88 1.10 151 39 103 64 173.91 0.91 152 39 106 67 173.85 0.91 153 40 43 3 531.15 0.10 154 40 46 6 446.50 27.71 155 40 47 7 282.98 2.11 156 40 55 15 249.77 4.99 157 41 47 6 290.58 5.91 158 42 97 55 174.44 0.95 159 42 98 56 174.41 0.93 160 42 99 57 174.30 0.88 161 42 103 61 174.15 0.93 162 43 46 3 523.54 1.02 163 43 47 4 498.55 2.60 164 43 64 21 235.31 1.39 165 43 68 25 235.28 1.41 166 44 47 3 517.15 0.51 167 45 60 15 235.50 1.41 168 45 64 19 235.48 1.42 169 46 49 3 511.17 0.53 170 46 60 14 235.60 1.36 171 46 61 15 235.50 1.42 172 46 64 18 235.50 1.42 173 48 54 6 496.94 3.53 174 49 54 5 496.13 3.93 175 49 55 6 476.43 5.88 176 49 58 9 315.35 0.14 177 49 61 12 291.30 0.56 178 50 54 4 506.78 1.04 179 51 54 3 523.65 0.58 180 51 55 4 509.67 2.46 181 52 55 3 510.86 1.87 182 52 56 4 506.81 1.03 183 53 56 3 516.77 2.83 184 53 57 4 507.99 0.44 185 54 57 3 529.30 3.88 186 54 58 4 504.71 0.01 187 55 58 3 517.70 0.43 188 55 61 6 437.10 3.17 189 58 61 3 527.45 1.68 190 58 62 4 520.02 2.04 191 59 62 3 520.05 2.04 192 59 63 4 520.03 2.03 193 60 63 3 520.04 2.03 194 60 64 4 520.01 2.04 195 61 64 3 520.19 1.96 196 61 65 4 515.19 0.39 197 62 65 3 516.08 0.06 198 62 66 4 511.89 1.27 199 63 66 3 516.71 3.68 200 63 67 4 509.53 2.44 201 64 67 3 528.81 0.04 202 64 68 4 508.70 2.38 203 65 68 3 521.87 3.43 204 65 69 4 509.17 2.60 205 66 69 3 525.13 1.79 206 66 70 4 511.44 3.71 207 67 70 3 521.60 1.37 208 67 71 4 521.60 1.37 209 68 71 3 523.07 2.10 210 68 72 4 519.35 2.50 211 68 107 39 173.35 0.80 212 69 72 3 521.61 1.37 213 69 73 4 509.23 2.56 214 69 111 42 173.10 0.82 215 70 73 3 523.04 2.10 216 70 74 4 511.79 3.52 217 71 74 3 513.11 4.49 218 71 75 4 509.92 2.19 219 72 75 3 522.74 1.82 220 72 76 4 522.77 1.85 221 72 111 39 173.31 0.78 222 72 135 63 167.53 0.99 223 72 138 66 167.20 1.04 224 73 76 3 522.81 1.84 225 73 77 4 522.77 1.85 226 74 77 3 529.01 2.32 227 74 78 4 522.79 1.85 228 75 78 3 525.59 0.45 229 75 79 4 522.78 1.85 230 75 82 7 267.02 0.12 231 75 85 10 185.64 4.30 232 75 86 11 185.62 4.30 233 75 89 14 185.62 4.30 234 75 138 63 167.42 0.96 235 76 79 3 524.85 2.90 236 76 134 58 167.60 1.03 237 78 81 3 494.19 1.02 238 78 82 4 419.58 16.14 239 78 85 7 329.76 12.85 240 80 137 57 167.62 1.04 241 82 85 3 519.13 1.72 242 82 86 4 517.47 0.90 243 82 137 55 167.61 1.04 244 82 141 59 167.21 1.02 245 83 86 3 526.49 3.61 246 83 87 4 526.49 3.60 247 84 88 4 533.77 0.03 248 85 88 3 549.79 0.79 249 85 89 4 533.77 0.04 250 86 89 3 529.23 2.31 251 86 90 4 523.29 0.48 252 86 138 52 167.39 0.95 253 86 141 55 165.75 0.29 254 86 142 56 165.61 0.27 255 87 90 3 528.09 2.88 256 87 91 4 516.34 2.66 257 87 145 58 163.90 0.40 258 88 91 3 522.96 0.66 259 88 92 4 514.19 1.62 260 89 92 3 522.43 0.77 261 89 93 4 514.15 1.61 262 89 138 49 167.39 0.95 263 89 142 53 164.62 0.20 264 90 93 3 517.74 1.54 265 90 94 4 501.43 3.30 266 90 142 52 164.46 0.27 267 90 145 55 152.03 1.22 268 90 146 56 148.17 0.02 269 90 149 59 147.02 0.03 270 91 94 3 517.66 2.67 271 91 95 4 494.69 4.09 272 91 149 58 147.04 0.04 273 92 96 4 483.82 1.09 274 92 97 5 450.10 15.77 275 93 97 4 365.55 1.02 276 93 98 5 325.03 0.47 277 93 99 6 305.42 10.13 278 93 142 49 164.46 0.26 279 93 146 53 148.97 0.38 280 94 98 4 336.24 5.28 281 94 146 52 148.16 0.03 282 94 149 55 145.24 0.86 283 94 151 57 111.98 1.12 284 95 98 3 527.84 2.98 285 95 151 56 125.92 1.22 286 99 103 4 513.32 0.56 287 99 146 47 148.15 0.03 288 100 103 3 525.19 2.49 289 100 104 4 522.80 3.69 290 100 152 52 52.70 1.62 291 101 104 3 525.00 2.58 292 101 105 4 522.92 3.62 293 101 143 42 154.60 0.69 294 101 146 45 148.14 0.03 295 101 152 51 48.65 0.40 296 102 105 3 526.98 1.59 297 102 106 4 513.31 0.56 298 103 106 3 520.09 2.52 299 103 107 4 515.32 1.57 300 104 107 3 522.56 1.28 301 104 108 4 513.17 0.53 302 104 138 34 167.04 1.06 303 104 139 35 164.73 0.26 304 104 142 38 160.09 0.81 305 105 108 3 527.02 2.37 306 105 109 4 515.26 1.59 307 105 139 34 164.73 0.27 308 106 109 3 518.88 0.05 309 106 110 4 514.25 1.24 310 107 110 3 520.75 0.90 311 107 111 4 506.79 2.48 312 108 111 3 522.00 0.91 313 108 112 4 516.82 1.68 314 108 135 27 167.33 1.04 315 108 139 31 164.73 0.26 316 109 112 3 522.00 0.91 317 109 113 4 512.53 0.47 318 110 113 3 514.60 0.57 319 110 114 4 508.36 3.52 320 111 114 3 517.58 2.06 321 111 115 4 508.26 3.56 322 111 135 24 167.35 1.04 323 112 115 3 515.82 1.73 324 112 116 4 506.87 2.87 325 112 123 11 266.36 0.56 326 112 131 19 167.53 1.07 327 112 132 20 167.45 1.03 328 112 135 23 167.41 1.04 329 113 116 3 514.31 2.59 330 113 117 4 506.94 3.33 331 114 117 3 506.94 3.33 332 114 118 4 506.44 3.09 333 115 118 3 519.49 0.00 334 115 119 4 467.63 3.16 335 115 123 8 292.25 8.30 336 115 131 16 180.16 7.40 337 116 120 4 449.14 12.39 338 116 123 7 290.86 9.00 339 116 128 12 241.83 11.68 340 117 120 3 534.29 3.45 341 119 122 3 518.76 0.34 342 119 123 4 459.36 17.25 343 120 123 3 486.78 6.32 344 122 127 5 487.63 6.63 345 123 127 4 487.63 6.63 346 123 128 5 487.64 6.63 347 123 131 8 437.70 2.16 348 124 127 3 516.51 1.14 349 124 128 4 506.24 2.62 350 125 128 3 517.71 0.53 351 125 129 4 515.15 1.81 352 126 129 3 518.73 0.03 353 126 130 4 515.13 1.82 354 127 130 3 518.73 0.03 355 127 131 4 514.56 2.10 356 128 131 3 519.06 0.14 357 128 132 4 514.55 2.10 358 129 132 3 522.98 1.82 359 129 133 4 513.76 1.71 360 130 133 3 522.98 1.82 361 130 134 4 510.40 0.04 362 131 134 3 515.35 0.96 363 131 135 4 509.36 0.59 364 132 135 3 511.04 1.43 365 132 136 4 506.53 3.69 366 133 136 3 516.05 1.07 367 133 137 4 506.54 3.68 368 134 137 3 512.79 0.56 369 134 138 4 514.34 0.22 370 135 138 3 514.34 0.22 371 135 139 4 514.34 0.22 372 136 139 3 513.78 0.50 373 136 140 4 513.78 0.50 374 137 140 3 519.15 1.02 375 137 141 4 513.77 0.50 376 138 141 3 515.75 0.41 377 138 142 4 504.85 2.90 378 139 142 3 514.34 0.31 379 139 143 4 504.82 2.90 380 140 143 3 514.00 1.00 381 140 144 4 499.33 0.40 382 141 144 3 507.88 4.26 383 141 145 4 503.38 2.45 384 142 145 3 508.81 0.18 385 142 146 4 499.76 4.25 386 143 146 3 501.34 3.48 387 143 147 4 510.62 1.17 388 143 153 10 19.55 1.77 389 144 147 3 519.91 5.07 390 144 148 4 510.62 1.18 391 145 148 3 522.48 3.79 392 145 149 4 505.55 3.71 393 146 149 3 516.15 1.58 394 146 150 4 505.56 3.71 395 146 151 5 396.90 2.15 396 146 153 7 250.05 1.45 397 147 150 3 508.68 5.28 398 147 151 4 465.76 0.51 399 147 153 6 133.84 59.53