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 8 473.48 2.88 2 2 130 128 47.29 0.02 3 2 133 131 31.66 5.81 4 2 134 132 26.92 3.45 5 2 137 135 26.85 3.48 6 3 6 3 514.46 1.86 7 3 7 4 514.46 1.86 8 4 7 3 517.58 2.83 9 4 8 4 515.07 1.56 10 4 79 75 54.63 0.95 11 5 8 3 515.78 1.21 12 5 9 4 515.09 1.55 13 6 9 3 526.90 4.01 14 6 10 4 507.25 2.37 15 6 130 124 71.31 0.78 16 6 133 127 71.30 0.78 17 7 10 3 515.96 2.35 18 7 11 4 507.24 2.37 19 7 76 69 71.31 0.78 20 7 79 72 71.30 0.78 21 7 80 73 71.32 0.78 22 7 134 127 71.31 0.78 23 7 137 130 71.32 0.78 24 8 11 3 531.15 0.90 25 8 12 4 514.75 1.43 26 9 12 3 526.34 1.51 27 9 13 4 518.00 2.66 28 9 126 117 82.28 0.79 29 9 127 118 82.20 0.79 30 9 130 121 82.20 0.78 31 10 13 3 529.17 0.09 32 10 14 4 515.17 1.24 33 10 76 66 82.23 0.77 34 10 130 120 82.20 0.78 35 10 131 121 82.11 0.82 36 10 134 124 82.11 0.82 37 11 14 3 515.19 1.23 38 11 15 4 515.68 1.49 39 11 76 65 82.23 0.77 40 11 77 66 82.24 0.77 41 11 79 68 82.23 0.77 42 12 15 3 523.38 2.88 43 12 16 4 520.11 3.70 44 12 122 110 89.31 1.81 45 13 16 3 523.64 3.01 46 13 17 4 518.51 0.11 47 13 115 102 89.25 1.84 48 13 122 109 89.32 1.81 49 13 123 110 89.31 1.81 50 13 127 114 89.11 1.80 51 13 131 118 88.84 1.72 52 14 17 3 518.51 0.11 53 14 18 4 518.51 0.11 54 14 69 55 88.97 1.73 55 14 72 58 88.90 1.72 56 14 73 59 88.89 1.72 57 14 76 62 88.89 1.72 58 14 77 63 88.89 1.72 59 15 18 3 522.90 2.30 60 15 19 4 519.75 0.73 61 16 19 3 519.75 0.73 62 16 119 103 94.08 4.07 63 16 122 106 89.74 1.63 64 17 20 3 534.50 1.64 65 17 21 4 506.72 1.27 66 17 24 7 430.32 11.62 67 17 69 52 89.43 1.76 68 17 115 98 89.47 1.77 69 18 21 3 514.68 1.71 70 18 77 59 89.44 1.76 71 20 23 3 531.07 0.54 72 20 24 4 505.57 4.54 73 20 118 98 134.30 1.22 74 21 24 3 521.54 1.74 75 21 25 4 505.57 4.54 76 21 66 45 174.20 1.96 77 21 69 48 173.87 2.04 78 22 25 3 517.13 1.24 79 22 26 4 512.19 1.23 80 22 62 40 174.51 2.10 81 22 66 44 174.28 1.99 82 23 26 3 512.28 1.17 83 23 27 4 512.18 1.23 84 23 118 95 165.97 0.42 85 24 27 3 521.85 4.87 86 24 28 4 511.79 1.03 87 24 69 45 174.25 2.03 88 24 114 90 166.14 0.57 89 24 115 91 167.78 0.26 90 24 118 94 165.98 0.42 91 24 119 95 166.08 0.39 92 25 28 3 521.46 4.67 93 25 29 4 512.99 0.44 94 25 65 40 174.31 2.00 95 25 69 44 174.18 2.06 96 26 29 3 524.19 3.31 97 26 30 4 510.93 0.24 98 26 56 30 206.01 2.95 99 26 62 36 175.03 2.15 100 27 30 3 518.88 0.80 101 27 31 4 506.76 2.32 102 27 114 87 168.63 0.68 103 27 118 91 168.44 0.76 104 28 31 3 512.81 0.70 105 28 32 4 506.20 2.61 106 28 69 41 174.85 2.06 107 28 107 79 169.41 0.78 108 28 110 82 169.16 0.86 109 28 111 83 169.15 0.87 110 28 114 86 168.78 0.74 111 29 32 3 515.11 1.84 112 29 33 4 512.81 0.69 113 29 61 32 179.70 0.12 114 29 65 36 174.93 2.06 115 29 107 78 169.44 0.78 116 30 33 3 519.20 0.20 117 30 34 4 506.74 2.34 118 30 52 22 223.31 4.13 119 30 55 25 223.03 4.27 120 30 56 26 223.03 4.26 121 31 34 3 519.19 0.20 122 31 35 4 508.48 0.99 123 31 110 79 169.16 0.86 124 31 113 82 168.90 0.82 125 32 35 3 514.89 1.70 126 32 36 4 498.73 5.88 127 32 39 7 354.82 4.91 128 32 106 74 169.47 0.78 129 32 107 75 169.45 0.78 130 32 110 78 169.17 0.86 131 33 36 3 519.47 0.52 132 33 37 4 483.41 8.28 133 33 39 6 423.00 0.42 134 33 40 7 287.32 0.50 135 33 43 10 296.41 2.10 136 33 46 13 262.60 2.60 137 33 55 22 223.37 4.15 138 33 61 28 223.22 4.13 139 34 37 3 521.73 5.91 140 34 52 18 223.34 4.14 141 36 39 3 526.14 4.67 142 36 106 70 169.72 0.90 143 37 40 3 523.02 6.25 144 38 41 3 533.70 0.51 145 38 103 65 170.38 1.03 146 38 106 68 170.29 1.06 147 39 42 3 527.21 2.73 148 39 43 4 521.51 5.58 149 39 103 64 169.91 0.90 150 39 106 67 169.84 0.92 151 40 43 3 524.28 1.27 152 40 46 6 335.98 5.16 153 40 49 9 253.24 2.10 154 40 55 15 247.09 0.96 155 41 47 6 295.86 9.20 156 42 97 55 170.95 0.95 157 42 98 56 170.94 0.95 158 42 99 57 170.74 0.99 159 42 100 58 170.85 0.99 160 42 103 61 170.66 0.96 161 43 46 3 520.47 2.64 162 43 47 4 491.98 3.58 163 44 47 3 527.60 0.93 164 45 48 3 596.31 0.65 165 45 60 15 234.36 0.24 166 45 64 19 224.94 4.45 167 46 49 3 530.90 0.72 168 46 60 14 228.30 2.79 169 46 61 15 225.03 4.39 170 46 64 18 224.93 4.45 171 49 54 5 421.50 15.00 172 49 55 6 385.30 15.73 173 49 58 9 280.96 0.92 174 49 61 12 255.65 0.70 175 50 54 4 501.84 2.19 176 51 54 3 501.85 2.19 177 51 55 4 498.73 0.89 178 52 55 3 500.73 1.62 179 52 56 4 491.09 2.94 180 53 56 3 520.99 5.08 181 53 57 4 498.87 0.95 182 54 57 3 510.91 0.05 183 54 58 4 498.87 0.94 184 55 58 3 519.96 7.42 185 55 61 6 441.01 12.82 186 58 61 3 532.89 2.92 187 58 62 4 506.74 1.76 188 59 62 3 524.68 0.47 189 59 63 4 514.43 5.59 190 60 63 3 524.71 0.46 191 60 64 4 514.44 5.59 192 61 64 3 525.06 0.64 193 61 65 4 504.23 3.02 194 62 65 3 519.32 2.25 195 62 66 4 517.72 3.05 196 63 66 3 526.35 2.61 197 63 67 4 517.72 3.04 198 64 67 3 513.07 0.71 199 64 68 4 512.42 0.39 200 65 68 3 528.74 2.48 201 65 69 4 512.45 0.41 202 66 69 3 519.46 0.12 203 66 70 4 512.47 0.42 204 67 70 3 534.50 2.50 205 67 71 4 511.25 1.02 206 68 71 3 528.59 0.45 207 68 72 4 511.70 0.81 208 68 107 39 169.70 0.91 209 69 72 3 518.11 2.06 210 69 73 4 511.70 0.81 211 70 73 3 534.48 0.64 212 70 74 4 514.87 0.72 213 71 74 3 525.77 0.96 214 71 75 4 520.09 1.88 215 71 89 18 170.60 0.93 216 72 75 3 520.08 1.88 217 72 76 4 508.60 2.44 218 72 111 39 169.60 0.88 219 72 135 63 167.55 1.18 220 72 138 66 167.33 1.27 221 73 76 3 516.33 2.79 222 73 77 4 512.11 0.69 223 74 77 3 530.50 3.00 224 74 78 4 512.51 0.48 225 75 78 3 536.04 0.23 226 75 82 7 248.44 0.15 227 75 85 10 234.94 6.54 228 75 89 14 219.12 1.36 229 75 138 63 167.34 1.27 230 76 79 3 524.81 5.39 231 76 134 58 167.91 1.05 232 78 81 3 492.98 5.08 233 78 82 4 371.74 20.58 234 78 85 7 310.95 1.93 235 80 137 57 167.96 1.06 236 82 85 3 522.38 0.18 237 82 86 4 503.58 0.38 238 82 137 55 167.97 1.06 239 82 141 59 167.33 1.20 240 83 86 3 521.48 0.63 241 83 87 4 505.05 1.09 242 84 88 4 523.33 0.10 243 85 88 3 543.15 0.23 244 85 89 4 521.21 0.76 245 86 89 3 528.19 2.33 246 86 90 4 517.49 2.62 247 86 138 52 167.34 1.18 248 86 141 55 166.22 1.06 249 86 142 56 162.88 0.00 250 86 145 59 160.58 0.91 251 87 90 3 525.45 0.96 252 87 91 4 519.56 1.58 253 88 91 3 517.47 1.11 254 88 92 4 512.64 0.20 255 89 92 3 514.66 1.20 256 89 93 4 512.61 0.18 257 89 138 49 167.34 1.18 258 89 142 53 162.40 0.07 259 90 93 3 514.73 1.26 260 90 94 4 512.07 2.58 261 90 142 52 162.28 0.06 262 90 145 55 156.88 0.53 263 90 146 56 153.66 0.62 264 91 94 3 518.62 0.62 265 91 95 4 504.76 1.07 266 91 149 58 150.34 0.74 267 92 95 3 527.35 5.05 268 92 96 4 482.25 3.60 269 92 97 5 469.63 0.92 270 93 97 4 466.31 3.97 271 93 98 5 407.50 25.43 272 93 99 6 323.44 7.01 273 93 146 53 151.88 0.26 274 94 98 4 421.33 18.52 275 94 146 52 151.87 0.25 276 94 149 55 145.46 1.57 277 94 151 57 79.14 1.60 278 95 98 3 518.26 0.82 279 95 149 54 150.04 0.58 280 95 151 56 118.74 2.41 281 98 151 53 107.84 2.88 282 99 103 4 517.62 2.86 283 99 104 5 507.83 1.99 284 99 146 47 151.87 0.26 285 100 103 3 527.38 0.84 286 100 104 4 521.72 2.75 287 100 146 46 151.44 0.39 288 100 153 53 29.81 3.62 289 101 104 3 521.72 2.75 290 101 105 4 519.78 1.78 291 101 139 38 163.31 0.06 292 101 142 41 162.33 0.04 293 101 143 42 157.44 0.81 294 101 146 45 151.06 0.58 295 101 152 51 36.38 0.35 296 101 153 52 29.05 3.46 297 102 105 3 521.09 3.06 298 102 106 4 519.15 2.09 299 103 106 3 519.54 3.83 300 103 107 4 508.88 1.50 301 104 107 3 523.45 0.07 302 104 108 4 508.99 1.55 303 104 139 35 162.97 0.06 304 104 142 38 161.88 0.26 305 105 108 3 517.71 2.80 306 105 109 4 515.76 4.95 307 105 139 34 162.97 0.06 308 106 109 3 519.51 3.71 309 106 110 4 508.60 1.36 310 107 110 3 508.81 1.63 311 107 111 4 506.62 2.35 312 108 111 3 518.83 2.79 313 108 112 4 507.00 2.54 314 108 135 27 165.40 0.24 315 108 139 31 164.46 0.70 316 109 112 3 513.82 0.49 317 109 113 4 506.99 2.54 318 110 113 3 514.88 4.76 319 110 114 4 501.92 0.82 320 111 114 3 523.75 1.66 321 111 115 4 497.91 1.40 322 111 135 24 165.44 0.26 323 112 115 3 522.38 0.97 324 112 116 4 505.39 2.34 325 112 123 11 273.97 0.05 326 112 128 16 210.38 4.50 327 112 131 19 183.30 9.04 328 112 132 20 166.81 0.94 329 112 135 23 165.79 0.43 330 113 116 3 519.77 0.33 331 113 117 4 505.40 2.34 332 114 117 3 508.62 3.08 333 114 118 4 506.19 1.95 334 115 118 3 522.10 2.88 335 115 119 4 504.95 1.33 336 115 123 8 283.64 0.91 337 115 131 16 210.91 4.70 338 116 119 3 521.76 2.71 339 116 120 4 493.62 0.79 340 116 123 7 275.02 0.58 341 117 120 3 542.45 1.87 342 119 122 3 521.08 4.29 343 119 123 4 470.77 9.75 344 120 123 3 512.15 8.76 345 120 124 4 470.77 9.75 346 122 127 5 486.74 1.53 347 123 127 4 491.29 3.80 348 123 128 5 491.75 0.97 349 123 131 8 462.40 8.31 350 124 127 3 509.12 3.38 351 124 128 4 496.30 1.29 352 125 128 3 509.12 3.38 353 125 129 4 499.51 2.89 354 126 129 3 506.58 0.64 355 126 130 4 499.55 2.88 356 127 130 3 505.50 1.37 357 127 131 4 499.55 2.88 358 128 131 3 510.31 2.48 359 128 132 4 498.76 2.48 360 129 132 3 514.50 0.39 361 129 133 4 515.28 0.01 362 130 133 3 514.57 0.57 363 130 134 4 510.99 2.16 364 131 134 3 516.25 0.28 365 131 135 4 505.98 0.35 366 132 135 3 511.19 2.26 367 132 136 4 500.64 2.33 368 133 136 3 500.66 2.33 369 133 137 4 500.64 2.33 370 134 137 3 510.40 2.46 371 134 138 4 505.40 0.05 372 135 138 3 509.70 1.86 373 135 139 4 505.88 0.76 374 136 139 3 512.60 2.60 375 136 140 4 504.13 1.64 376 137 140 3 519.02 2.58 377 137 141 4 504.62 1.41 378 138 141 3 512.50 3.38 379 138 142 4 504.62 1.41 380 139 142 3 509.31 2.03 381 139 143 4 504.28 1.58 382 140 143 3 514.70 2.60 383 140 144 4 507.46 1.02 384 141 144 3 512.56 1.53 385 141 145 4 511.43 1.76 386 142 145 3 512.23 1.36 387 142 146 4 505.88 0.22 388 143 146 3 505.88 0.21 389 143 147 4 510.17 1.93 390 143 152 9 241.37 11.73 391 144 147 3 515.02 2.75 392 144 148 4 511.79 1.13 393 145 148 3 518.18 1.01 394 145 149 4 511.79 1.13 395 146 149 3 519.01 1.60 396 146 150 4 510.17 1.94 397 146 151 5 381.49 8.28 398 146 152 6 261.00 1.97 399 146 153 7 261.04 1.99 400 147 150 3 516.00 0.09 401 147 152 5 261.00 1.97