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 6 4 493.48 4.39 2 2 7 5 480.12 0.82 3 2 130 128 36.95 1.31 4 2 133 131 30.59 0.26 5 2 134 132 30.54 0.23 6 2 137 135 30.53 0.23 7 3 6 3 514.44 1.87 8 3 7 4 504.09 0.85 9 4 7 3 504.09 0.85 10 4 8 4 504.09 0.85 11 5 8 3 516.01 0.99 12 5 9 4 502.10 0.15 13 6 9 3 524.34 6.54 14 6 10 4 502.12 0.17 15 6 130 124 60.23 3.17 16 6 133 127 60.26 3.19 17 7 10 3 509.51 0.87 18 7 11 4 502.12 0.17 19 7 76 69 60.40 3.25 20 7 79 72 60.40 3.25 21 7 80 73 65.83 0.54 22 7 134 127 60.38 3.24 23 7 137 130 60.38 3.25 24 8 11 3 516.82 7.52 25 8 12 4 482.82 0.61 26 9 12 3 527.57 2.14 27 9 13 4 494.23 5.25 28 9 126 117 79.47 0.64 29 9 127 118 77.50 0.35 30 9 130 121 77.34 0.31 31 10 14 4 510.47 0.29 32 10 76 66 77.34 0.30 33 10 130 120 77.35 0.30 34 10 131 121 77.34 0.30 35 10 134 124 77.34 0.31 36 11 14 3 516.39 0.59 37 11 15 4 512.56 1.32 38 11 77 66 77.39 0.30 39 11 79 68 77.41 0.30 40 12 15 3 512.57 1.32 41 12 16 4 512.79 1.21 42 13 16 3 522.44 3.62 43 13 17 4 514.60 0.30 44 13 115 102 96.01 0.10 45 13 123 110 93.31 1.24 46 13 127 114 88.80 0.30 47 13 131 118 88.15 0.01 48 14 17 3 519.70 0.55 49 14 18 4 515.58 2.60 50 14 69 55 145.84 28.20 51 14 72 58 88.62 0.21 52 14 73 59 88.36 0.11 53 14 76 62 88.36 0.11 54 14 77 63 88.36 0.11 55 15 18 3 519.14 0.83 56 15 19 4 517.38 1.71 57 16 19 3 519.58 0.61 58 16 24 8 439.62 7.69 59 16 115 99 104.43 0.85 60 16 119 103 105.61 0.42 61 16 122 106 105.61 0.42 62 17 20 3 521.12 0.17 63 17 21 4 479.44 3.71 64 17 24 7 426.59 14.20 65 17 69 52 154.63 24.29 66 17 115 98 104.50 0.82 67 18 21 3 513.08 0.57 68 18 77 59 141.04 17.52 69 20 23 3 512.49 1.07 70 20 24 4 502.39 6.10 71 21 24 3 515.31 1.54 72 21 25 4 511.31 0.45 73 21 66 45 187.60 9.46 74 21 69 48 164.07 21.22 75 21 70 49 164.05 21.21 76 22 25 3 515.31 1.54 77 22 26 4 515.14 1.46 78 22 62 40 188.47 9.07 79 22 66 44 187.62 9.47 80 23 26 3 526.84 2.37 81 23 27 4 515.14 1.46 82 24 27 3 528.46 1.56 83 24 28 4 508.77 1.73 84 24 69 45 188.00 9.27 85 24 114 90 160.91 3.71 86 24 118 94 165.85 0.43 87 24 119 95 166.20 0.61 88 25 28 3 511.20 0.45 89 25 29 4 508.28 1.91 90 25 65 40 188.02 9.27 91 25 69 44 188.01 9.27 92 26 29 3 525.96 4.00 93 26 30 4 500.63 1.91 94 26 56 30 224.19 3.60 95 26 62 36 188.67 9.15 96 27 30 3 500.93 1.25 97 27 31 4 500.12 1.65 98 27 114 87 167.72 0.34 99 27 118 91 167.43 0.25 100 28 31 3 527.25 2.58 101 28 32 4 500.93 1.26 102 28 69 41 193.64 6.51 103 28 107 79 168.27 0.21 104 28 110 82 168.18 0.20 105 28 111 83 168.16 0.20 106 28 114 86 167.72 0.33 107 29 32 3 520.44 0.83 108 29 33 4 506.20 1.39 109 29 61 32 208.56 1.69 110 29 64 35 206.09 0.49 111 29 65 36 193.84 6.55 112 29 68 39 193.75 6.54 113 30 33 3 513.27 4.42 114 30 34 4 506.59 2.90 115 30 52 22 225.58 3.45 116 30 55 25 225.34 3.34 117 30 56 26 225.37 3.35 118 30 61 31 210.27 0.84 119 31 34 3 514.29 3.90 120 31 35 4 496.55 2.12 121 31 110 79 168.22 0.20 122 31 113 82 167.95 0.21 123 31 114 83 167.72 0.33 124 32 35 3 510.57 0.91 125 32 36 4 492.62 0.15 126 32 39 7 459.07 8.61 127 32 106 74 168.60 0.28 128 32 107 75 168.47 0.25 129 32 110 78 168.22 0.20 130 33 36 3 515.67 1.39 131 33 37 4 482.00 3.69 132 33 39 6 430.69 5.38 133 33 40 7 399.32 16.91 134 33 43 10 334.28 12.00 135 33 46 13 248.55 0.19 136 33 55 22 225.94 3.56 137 33 61 28 225.71 3.58 138 34 37 3 522.98 5.29 139 34 52 18 226.03 3.55 140 34 55 21 226.51 3.83 141 36 39 3 528.42 2.14 142 36 106 70 168.90 0.17 143 37 40 3 537.68 1.03 144 37 41 4 526.94 2.88 145 38 41 3 536.41 0.41 146 38 103 65 169.13 0.18 147 38 106 68 169.05 0.21 148 39 42 3 530.47 1.10 149 39 43 4 525.31 2.06 150 39 103 64 168.97 0.20 151 39 106 67 168.96 0.20 152 40 43 3 519.43 5.00 153 40 46 6 340.78 11.85 154 40 47 7 270.99 1.49 155 40 49 9 269.23 0.66 156 40 55 15 234.99 1.42 157 42 97 55 169.31 0.10 158 42 98 56 169.31 0.10 159 42 99 57 169.27 0.12 160 42 100 58 169.30 0.12 161 42 103 61 169.16 0.17 162 43 46 3 520.49 0.41 163 43 47 4 492.78 3.18 164 43 64 21 228.32 3.80 165 44 47 3 530.21 1.07 166 45 48 3 600.03 0.04 167 45 60 15 229.14 3.98 168 46 49 3 528.70 0.38 169 46 60 14 231.18 2.96 170 46 61 15 229.13 3.98 171 46 64 18 229.12 3.98 172 49 54 5 399.65 5.25 173 49 55 6 403.03 6.86 174 49 58 9 277.68 2.88 175 49 61 12 248.29 4.24 176 50 54 4 502.78 1.73 177 51 54 3 499.19 0.39 178 51 55 4 486.60 1.92 179 52 55 3 497.20 3.38 180 52 56 4 494.42 2.00 181 53 56 3 503.59 1.80 182 53 57 4 486.60 1.92 183 54 57 3 501.06 2.03 184 54 58 4 495.57 2.58 185 55 58 3 505.62 0.24 186 55 61 6 411.44 10.95 187 58 61 3 534.14 2.29 188 58 62 4 501.58 0.82 189 59 62 3 507.53 2.31 190 59 63 4 507.98 2.39 191 60 63 3 518.22 2.72 192 60 64 4 518.28 2.75 193 61 64 3 518.28 2.76 194 61 65 4 513.04 0.14 195 62 65 3 518.27 2.76 196 62 66 4 518.27 2.76 197 63 66 3 522.18 0.81 198 63 67 4 513.09 0.17 199 64 67 3 509.55 1.96 200 64 68 4 509.54 1.95 201 65 68 3 511.75 0.85 202 65 69 4 513.04 0.21 203 66 69 3 517.86 0.93 204 66 70 4 511.73 0.85 205 67 70 3 519.08 2.81 206 67 71 4 511.65 0.81 207 68 71 3 528.97 2.12 208 68 72 4 511.65 0.81 209 68 107 39 168.77 0.23 210 69 72 3 508.00 2.35 211 69 73 4 503.45 4.54 212 69 111 42 168.38 0.23 213 70 73 3 527.04 1.57 214 70 74 4 518.25 2.83 215 71 74 3 519.58 2.16 216 71 75 4 518.25 2.83 217 71 89 18 169.67 0.12 218 72 75 3 518.25 2.83 219 72 76 4 518.57 2.67 220 72 111 39 168.76 0.21 221 72 135 63 166.56 0.30 222 72 138 66 165.05 0.23 223 73 76 3 524.43 5.58 224 73 77 4 518.58 2.67 225 74 77 3 537.31 0.84 226 74 78 4 524.42 5.58 227 75 78 3 524.44 5.58 228 75 82 7 251.36 2.72 229 75 85 10 227.98 8.54 230 75 86 11 207.50 18.79 231 75 89 14 207.50 18.78 232 75 138 63 165.85 0.12 233 76 79 3 530.56 2.52 234 76 134 58 166.72 0.29 235 78 81 3 503.78 1.95 236 78 82 4 424.86 29.37 237 78 85 7 317.87 16.76 238 80 137 57 166.84 0.24 239 82 85 3 517.71 2.16 240 82 86 4 511.13 1.13 241 82 137 55 166.84 0.24 242 82 141 59 164.73 0.41 243 83 86 3 516.83 0.63 244 83 87 4 511.14 1.14 245 84 88 4 533.36 0.99 246 85 88 3 544.75 0.23 247 85 89 4 520.48 2.37 248 86 89 3 533.36 0.99 249 86 90 4 510.93 1.21 250 86 138 52 165.04 0.25 251 86 141 55 162.57 0.15 252 86 142 56 162.28 0.24 253 86 145 59 153.99 0.92 254 87 90 3 512.78 0.28 255 87 91 4 514.99 1.38 256 88 91 3 515.01 1.38 257 88 92 4 513.16 2.29 258 89 92 3 514.99 1.38 259 89 93 4 513.16 2.29 260 90 93 3 514.08 2.74 261 90 94 4 513.16 2.29 262 90 142 52 160.41 1.06 263 90 145 55 148.56 0.34 264 90 146 56 147.90 0.67 265 91 94 3 513.12 2.27 266 91 95 4 482.01 4.88 267 91 149 58 141.82 0.47 268 92 96 4 422.89 11.12 269 92 97 5 417.64 13.74 270 93 97 4 315.75 1.57 271 93 98 5 313.06 0.23 272 93 99 6 294.14 2.01 273 93 146 53 147.89 0.67 274 94 98 4 302.58 0.35 275 94 146 52 147.88 0.67 276 94 149 55 131.62 1.26 277 94 151 57 82.52 2.05 278 95 98 3 524.79 2.46 279 98 151 53 82.95 1.89 280 99 103 4 512.39 1.28 281 99 146 47 147.10 0.34 282 99 151 52 82.61 2.00 283 100 103 3 519.45 0.64 284 100 104 4 514.63 0.24 285 100 151 51 82.51 2.04 286 100 152 52 55.81 2.60 287 101 104 3 521.55 1.69 288 101 105 4 512.48 1.32 289 101 139 38 162.71 0.07 290 101 142 41 156.35 0.30 291 101 143 42 153.09 0.49 292 101 146 45 145.92 0.38 293 101 152 51 55.61 2.58 294 102 105 3 512.49 1.32 295 102 106 4 510.74 2.19 296 103 106 3 516.25 0.57 297 103 107 4 516.25 0.57 298 104 107 3 522.34 3.62 299 104 108 4 516.24 0.57 300 104 138 34 163.69 0.04 301 104 139 35 162.69 0.06 302 104 142 38 155.17 0.29 303 105 108 3 514.15 1.61 304 105 109 4 514.14 1.61 305 105 139 34 162.69 0.07 306 106 109 3 522.44 2.54 307 106 110 4 506.53 4.62 308 107 110 3 506.53 4.62 309 107 111 4 506.53 4.62 310 108 111 3 521.61 1.40 311 108 112 4 509.17 1.45 312 108 135 27 164.96 0.06 313 108 139 31 162.68 0.07 314 109 112 3 523.38 3.79 315 109 113 4 509.17 1.45 316 110 113 3 517.74 1.97 317 110 114 4 501.50 2.38 318 111 114 3 506.91 0.33 319 111 115 4 504.93 0.66 320 111 131 20 166.71 0.38 321 111 135 24 165.18 0.14 322 112 115 3 526.39 0.93 323 112 116 4 507.04 0.32 324 112 123 11 256.42 2.37 325 112 128 16 169.01 0.78 326 112 131 19 166.70 0.38 327 112 132 20 166.67 0.37 328 112 135 23 165.51 0.01 329 113 116 3 519.91 4.17 330 113 117 4 506.93 0.37 331 114 117 3 519.91 4.17 332 114 118 4 503.42 0.11 333 115 119 4 486.83 0.39 334 115 123 8 259.88 0.65 335 115 131 16 232.59 4.91 336 116 119 3 501.99 1.41 337 116 120 4 445.21 4.83 338 116 123 7 262.12 1.77 339 116 128 12 256.55 2.31 340 117 120 3 527.65 0.77 341 119 122 3 527.65 0.77 342 119 123 4 481.36 5.73 343 123 127 4 497.25 5.53 344 123 128 5 483.86 1.16 345 123 131 8 427.41 10.68 346 124 127 3 513.34 2.52 347 124 128 4 509.35 0.52 348 125 128 3 512.83 1.23 349 125 129 4 509.35 0.52 350 126 129 3 509.35 0.52 351 126 130 4 509.35 0.52 352 127 130 3 509.36 0.52 353 127 131 4 507.85 1.27 354 128 131 3 507.85 1.28 355 128 132 4 508.52 0.94 356 129 132 3 523.64 0.44 357 129 133 4 512.84 1.23 358 130 133 3 517.50 0.35 359 130 134 4 510.27 2.52 360 131 135 4 496.25 0.07 361 132 135 3 513.04 1.08 362 132 136 4 501.04 2.20 363 133 136 3 501.04 2.20 364 133 137 4 501.04 2.21 365 134 137 3 500.96 2.25 366 134 138 4 500.96 2.25 367 135 138 3 506.16 0.35 368 135 139 4 507.55 0.07 369 136 139 3 514.10 3.34 370 136 140 4 506.23 0.73 371 137 140 3 515.83 0.14 372 137 141 4 507.60 0.08 373 138 141 3 523.74 1.74 374 138 142 4 507.60 0.08 375 139 142 3 523.74 1.74 376 139 143 4 507.60 0.07 377 140 143 3 515.95 3.22 378 140 144 4 506.17 0.21 379 141 144 3 507.05 0.21 380 141 145 4 506.18 0.21 381 142 145 3 509.06 1.22 382 142 146 4 500.97 2.42 383 143 146 3 509.05 1.22 384 143 147 4 505.05 0.38 385 144 147 3 519.59 1.71 386 144 148 4 506.35 0.28 387 145 148 3 511.16 2.68 388 145 149 4 507.16 0.68 389 146 149 3 511.55 2.38 390 146 150 4 503.15 0.50 391 146 151 5 451.89 12.71 392 146 152 6 457.66 9.82 393 147 150 3 507.43 2.64