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 5 498.81 2.37 2 2 10 8 482.24 5.42 3 2 130 128 42.16 0.16 4 2 133 131 35.53 0.01 5 2 134 132 35.19 0.02 6 2 137 135 35.14 0.03 7 3 6 3 515.56 5.26 8 3 7 4 519.78 1.97 9 4 7 3 520.16 2.16 10 4 8 4 519.78 1.97 11 4 79 75 57.73 0.55 12 5 8 3 519.79 1.97 13 5 9 4 519.78 1.97 14 6 9 3 525.22 0.75 15 6 10 4 514.13 4.78 16 6 130 124 70.95 2.36 17 6 133 127 70.98 2.38 18 7 10 3 508.54 1.98 19 7 11 4 508.53 1.98 20 7 76 69 71.00 2.39 21 7 79 72 70.99 2.38 22 7 80 73 71.00 2.38 23 7 134 127 71.00 2.39 24 7 137 130 71.00 2.38 25 8 11 3 523.18 0.28 26 8 12 4 506.70 1.01 27 9 12 3 524.36 0.86 28 9 13 4 523.06 0.34 29 9 126 117 80.95 1.06 30 9 127 118 80.80 1.12 31 9 130 121 80.71 1.14 32 10 13 3 526.84 2.10 33 10 14 4 517.62 2.38 34 10 76 66 80.83 1.09 35 10 130 120 80.89 1.08 36 10 131 121 80.70 1.16 37 10 134 124 80.67 1.14 38 11 14 3 523.06 0.35 39 11 15 4 517.62 2.38 40 11 76 65 80.96 1.06 41 11 77 66 80.95 1.05 42 11 79 68 80.97 1.06 43 12 15 3 520.94 2.73 44 12 16 4 518.91 1.73 45 12 122 110 94.23 0.78 46 13 16 3 519.01 1.66 47 13 17 4 517.33 2.50 48 13 115 102 94.20 0.77 49 13 119 106 94.73 0.94 50 13 122 109 94.23 0.77 51 13 123 110 94.23 0.78 52 13 131 118 93.92 0.78 53 14 17 3 513.98 0.82 54 14 18 4 511.01 2.38 55 14 69 55 136.91 20.67 56 14 72 58 94.03 0.74 57 14 73 59 93.92 0.78 58 14 76 62 93.92 0.78 59 14 131 117 94.08 0.74 60 15 18 3 524.06 2.71 61 15 19 4 522.63 3.43 62 16 19 3 529.21 0.14 63 16 24 8 469.32 3.52 64 16 119 103 97.92 1.25 65 16 122 106 97.82 1.28 66 17 20 3 529.53 0.01 67 17 21 4 488.49 1.11 68 17 24 7 401.84 23.93 69 17 69 52 191.28 3.93 70 17 115 98 97.86 1.21 71 18 77 59 96.66 1.81 72 20 23 3 522.04 2.30 73 20 24 4 518.21 0.38 74 21 24 3 523.74 1.46 75 21 25 4 516.13 0.67 76 21 66 45 193.99 3.86 77 21 69 48 193.78 3.80 78 22 25 3 523.74 1.46 79 22 26 4 519.23 0.79 80 22 62 40 195.69 3.08 81 22 66 44 194.01 3.86 82 23 26 3 520.09 0.36 83 23 27 4 515.12 1.26 84 23 118 95 167.97 0.44 85 24 27 3 516.54 1.30 86 24 28 4 512.88 0.14 87 24 69 45 194.09 3.89 88 24 118 94 168.27 0.29 89 24 119 95 167.97 0.45 90 25 28 3 515.27 0.68 91 25 29 4 517.47 1.29 92 25 65 40 195.03 3.38 93 25 69 44 194.36 3.71 94 26 29 3 525.09 0.17 95 26 30 4 517.47 1.29 96 26 56 30 220.78 0.29 97 26 62 36 196.29 3.06 98 27 30 3 523.79 1.81 99 27 31 4 517.52 1.32 100 27 114 87 170.22 0.13 101 27 118 91 169.59 0.23 102 28 31 3 517.88 1.50 103 28 32 4 517.38 1.35 104 28 69 41 196.15 2.98 105 28 107 79 170.50 0.23 106 28 110 82 170.38 0.18 107 28 111 83 170.31 0.14 108 28 114 86 170.23 0.13 109 29 32 3 521.72 0.78 110 29 33 4 513.15 0.75 111 29 43 14 270.38 3.46 112 29 61 32 214.59 2.40 113 29 64 35 197.02 2.78 114 29 65 36 196.56 2.90 115 29 68 39 196.54 2.89 116 29 107 78 170.51 0.23 117 30 33 3 524.89 0.81 118 30 34 4 521.58 0.85 119 30 52 22 237.87 1.50 120 30 55 25 236.69 0.97 121 30 56 26 236.74 0.96 122 31 34 3 521.71 0.79 123 31 35 4 506.74 0.48 124 31 110 79 170.38 0.18 125 31 113 82 170.35 0.20 126 31 114 83 170.34 0.18 127 32 35 3 521.09 2.71 128 32 36 4 500.03 2.92 129 32 39 7 328.52 6.91 130 32 106 74 170.54 0.24 131 32 107 75 170.54 0.24 132 32 110 78 170.38 0.18 133 33 37 4 473.49 2.77 134 33 39 6 327.45 7.44 135 33 40 7 316.83 6.73 136 33 43 10 301.31 1.12 137 33 55 22 238.38 1.40 138 33 61 28 237.88 1.52 139 34 37 3 515.10 1.91 140 34 51 17 240.61 2.43 141 34 52 18 238.49 1.38 142 34 55 21 238.49 1.38 143 36 39 3 535.25 2.35 144 36 106 70 170.78 0.21 145 36 109 73 170.78 0.21 146 37 40 3 535.16 2.40 147 38 41 3 525.76 0.42 148 38 103 65 171.40 0.12 149 38 106 68 171.22 0.09 150 39 42 3 535.60 0.29 151 39 43 4 530.82 2.10 152 39 103 64 171.16 0.11 153 39 106 67 171.11 0.10 154 40 43 3 530.82 2.10 155 40 46 6 321.72 4.50 156 40 47 7 280.27 3.62 157 40 49 9 280.25 3.62 158 40 55 15 245.54 0.33 159 41 47 6 308.44 0.97 160 42 97 55 171.85 0.16 161 42 98 56 171.84 0.17 162 42 99 57 171.78 0.18 163 42 100 58 171.84 0.17 164 42 103 61 171.70 0.21 165 43 46 3 525.66 0.96 166 43 47 4 478.34 5.75 167 43 64 21 242.19 1.78 168 44 47 3 533.40 2.91 169 45 48 3 597.66 0.90 170 45 60 15 242.69 1.70 171 45 64 19 242.66 1.71 172 46 49 3 535.96 4.15 173 46 60 14 242.69 1.71 174 46 61 15 242.66 1.71 175 46 64 18 242.63 1.70 176 49 54 5 468.91 4.42 177 49 55 6 383.84 1.79 178 49 58 9 299.34 3.12 179 49 61 12 263.31 0.39 180 50 54 4 504.81 1.46 181 51 54 3 523.42 3.50 182 51 55 4 509.17 3.62 183 52 55 3 515.01 0.70 184 52 56 4 504.84 1.46 185 53 56 3 517.01 1.38 186 53 57 4 504.36 1.14 187 54 57 3 510.92 2.15 188 54 58 4 504.35 1.14 189 55 58 3 521.51 1.89 190 55 61 6 459.73 3.74 191 58 61 3 521.69 0.07 192 58 62 4 513.28 0.36 193 59 62 3 517.05 2.25 194 59 63 4 517.05 2.25 195 60 63 3 517.06 2.25 196 60 64 4 517.05 2.25 197 61 64 3 513.56 4.00 198 61 65 4 508.97 2.58 199 62 65 3 513.56 4.00 200 62 66 4 508.97 2.58 201 63 66 3 511.63 3.04 202 63 67 4 505.41 4.37 203 64 67 3 511.56 1.28 204 64 68 4 511.24 1.45 205 65 68 3 514.16 2.58 206 65 69 4 511.15 1.41 207 66 69 3 518.64 0.33 208 66 70 4 501.04 3.48 209 67 70 3 522.61 0.83 210 67 71 4 510.41 1.20 211 68 71 3 518.54 2.87 212 68 72 4 513.36 0.27 213 68 107 39 170.71 0.26 214 69 72 3 518.54 2.87 215 69 73 4 508.77 2.56 216 70 73 3 512.83 1.75 217 70 74 4 511.63 1.13 218 71 74 3 525.28 2.60 219 71 75 4 511.64 1.14 220 72 75 3 514.74 2.68 221 72 76 4 511.59 1.11 222 72 111 39 170.66 0.26 223 72 135 63 168.79 0.35 224 73 76 3 514.78 2.66 225 73 77 4 511.58 1.12 226 74 77 3 518.12 2.18 227 74 78 4 511.64 1.09 228 75 78 3 520.85 0.55 229 75 79 4 516.80 3.71 230 75 82 7 264.62 4.24 231 75 85 10 227.81 9.09 232 75 86 11 207.24 1.19 233 75 89 14 207.11 1.25 234 75 138 63 168.47 0.20 235 76 79 3 522.00 1.12 236 76 131 55 169.37 0.19 237 76 134 58 168.90 0.39 238 78 81 3 515.73 4.26 239 78 82 4 410.90 12.19 240 78 85 7 369.89 3.96 241 80 83 3 654.79 0.90 242 80 137 57 169.01 0.31 243 82 85 3 521.88 1.33 244 82 86 4 521.88 1.33 245 82 137 55 169.06 0.34 246 82 141 59 168.25 0.18 247 83 86 3 528.60 2.03 248 83 87 4 526.40 0.93 249 84 87 3 538.22 1.78 250 84 88 4 531.69 0.50 251 85 88 3 559.17 1.20 252 85 89 4 528.62 2.04 253 86 89 3 527.34 1.39 254 86 90 4 513.22 1.98 255 86 138 52 168.67 0.26 256 86 141 55 167.92 0.12 257 86 142 56 167.43 0.12 258 87 90 3 524.98 1.70 259 87 91 4 511.52 1.15 260 87 145 58 161.89 0.70 261 88 91 3 516.21 0.47 262 88 92 4 511.52 1.16 263 89 92 3 519.42 2.08 264 89 93 4 511.89 0.96 265 89 138 49 168.69 0.26 266 89 142 53 167.36 0.14 267 90 93 3 518.69 2.43 268 90 94 4 498.76 5.62 269 90 142 52 167.00 0.04 270 90 145 55 154.61 1.12 271 90 146 56 149.53 0.02 272 90 149 59 138.19 0.97 273 91 94 3 518.03 1.43 274 91 95 4 488.88 5.17 275 91 149 58 142.34 0.89 276 92 96 4 420.35 6.00 277 92 97 5 361.23 1.31 278 93 97 4 317.02 2.21 279 93 98 5 315.43 3.00 280 93 99 6 286.97 11.22 281 93 146 53 148.28 0.32 282 94 98 4 363.44 26.99 283 94 146 52 148.12 0.29 284 94 149 55 132.09 1.11 285 94 151 57 72.87 5.05 286 98 151 53 75.53 3.77 287 99 103 4 498.38 0.95 288 99 104 5 498.36 0.95 289 99 146 47 148.09 0.28 290 99 151 52 75.48 3.75 291 100 103 3 514.20 1.86 292 100 104 4 512.49 2.73 293 100 151 51 74.45 4.25 294 100 153 53 15.55 0.90 295 101 104 3 512.50 2.73 296 101 105 4 509.12 4.42 297 101 139 38 167.75 0.01 298 101 142 41 165.63 0.71 299 101 143 42 159.50 0.29 300 101 146 45 148.24 0.35 301 101 153 52 15.55 0.90 302 102 105 3 514.38 1.79 303 102 106 4 509.12 4.42 304 103 106 3 513.06 2.44 305 103 107 4 517.64 0.14 306 104 107 3 517.62 0.14 307 104 108 4 516.16 0.38 308 104 138 34 168.18 0.10 309 104 139 35 167.72 0.01 310 104 142 38 163.62 0.03 311 105 108 3 517.14 0.11 312 105 109 4 523.83 4.21 313 105 139 34 167.74 0.01 314 106 109 3 526.36 2.96 315 106 110 4 523.83 4.22 316 107 110 3 526.57 2.85 317 107 111 4 514.92 8.67 318 108 111 3 521.17 5.54 319 108 112 4 518.04 7.11 320 108 135 27 168.50 0.26 321 108 139 31 167.73 0.01 322 109 112 3 518.07 2.00 323 109 113 4 508.95 2.56 324 110 113 3 524.36 1.15 325 110 114 4 510.62 1.74 326 111 114 3 524.36 1.15 327 111 115 4 512.36 0.90 328 111 135 24 168.58 0.29 329 112 115 3 521.39 5.41 330 112 116 4 505.09 4.53 331 112 123 11 224.08 8.48 332 112 128 16 168.88 0.34 333 112 131 19 168.77 0.37 334 112 132 20 168.73 0.35 335 112 135 23 168.59 0.30 336 113 116 3 521.40 5.41 337 113 117 4 512.36 0.91 338 114 117 3 524.89 3.67 339 114 118 4 512.35 0.91 340 115 118 3 521.79 0.65 341 115 119 4 490.69 4.91 342 115 123 8 260.65 3.35 343 115 131 16 168.87 0.33 344 116 120 4 490.56 4.98 345 116 123 7 260.57 2.11 346 117 120 3 543.15 0.42 347 119 122 3 518.90 0.68 348 119 123 4 432.78 9.88 349 120 123 3 488.61 8.98 350 122 127 5 433.07 9.59 351 123 127 4 491.19 5.49 352 123 128 5 447.84 2.19 353 123 131 8 426.65 10.74 354 124 127 3 510.09 4.00 355 124 128 4 498.46 1.85 356 125 128 3 518.07 1.51 357 125 129 4 514.39 3.35 358 126 129 3 513.03 2.53 359 126 130 4 505.07 1.46 360 127 130 3 521.39 5.91 361 127 131 4 508.70 0.43 362 128 131 3 521.39 5.91 363 128 132 4 504.73 1.55 364 129 132 3 522.12 5.54 365 129 133 4 504.68 1.58 366 130 133 3 508.63 0.40 367 130 134 4 508.62 0.39 368 131 134 3 508.87 0.27 369 131 135 4 505.17 1.32 370 132 135 3 509.54 1.17 371 132 136 4 498.48 2.08 372 133 136 3 509.97 0.96 373 133 137 4 499.66 1.50 374 134 137 3 517.86 0.58 375 134 138 4 507.37 2.27 376 135 138 3 510.23 0.83 377 135 139 4 507.37 2.26 378 136 139 3 503.15 0.08 379 136 140 4 499.75 1.54 380 137 140 3 505.72 1.21 381 137 141 4 505.20 1.19 382 138 141 3 524.77 3.41 383 138 142 4 509.41 0.91 384 139 142 3 514.74 1.74 385 139 143 4 509.42 0.92 386 140 143 3 512.28 0.51 387 140 144 4 511.26 0.01 388 141 144 3 514.76 1.74 389 141 145 4 511.26 0.01 390 142 145 3 511.34 0.03 391 142 146 4 511.25 0.01 392 143 146 3 511.33 0.03 393 143 147 4 503.63 0.34 394 144 147 3 516.01 1.31 395 144 148 4 510.23 4.20 396 145 148 3 505.14 1.66 397 145 149 4 494.90 3.46 398 146 149 3 507.05 2.61 399 146 150 4 494.87 3.48 400 146 151 5 391.24 12.99 401 146 153 7 222.84 22.14 402 147 150 3 506.07 2.12