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 4 508.29 1.25 2 2 7 5 487.46 9.88 3 2 10 8 473.46 2.88 4 2 130 128 37.45 0.28 5 2 133 131 30.03 0.21 6 2 134 132 29.39 0.45 7 2 137 135 29.39 0.45 8 3 6 3 514.48 1.85 9 3 7 4 508.31 1.23 10 4 7 3 508.42 1.28 11 4 8 4 508.29 1.24 12 5 8 3 524.84 3.42 13 5 9 4 508.29 1.24 14 6 9 3 499.91 5.42 15 6 10 4 497.15 6.88 16 6 130 124 62.27 4.19 17 6 133 127 62.27 4.19 18 7 10 3 497.90 6.50 19 7 11 4 510.35 0.29 20 7 76 69 64.95 2.88 21 7 79 72 64.95 2.88 22 7 80 73 64.95 2.88 23 7 134 127 62.29 4.20 24 7 137 130 62.30 4.20 25 8 11 3 523.62 2.37 26 8 12 4 514.57 1.52 27 9 12 3 538.78 5.21 28 9 13 4 514.58 1.53 29 9 126 117 81.03 1.03 30 9 127 118 81.00 1.02 31 9 130 121 80.91 1.04 32 10 13 3 528.29 1.75 33 10 14 4 514.51 1.56 34 10 76 66 80.90 1.04 35 10 130 120 81.00 1.02 36 10 131 121 80.89 1.05 37 10 134 124 80.88 1.05 38 11 14 3 514.59 1.53 39 11 15 4 514.66 1.49 40 11 76 65 80.97 1.05 41 11 77 66 80.96 1.06 42 11 79 68 80.99 1.07 43 12 15 3 528.74 1.43 44 12 16 4 529.56 1.02 45 13 16 3 530.64 0.48 46 13 17 4 517.96 0.33 47 13 115 102 93.13 0.20 48 13 123 110 93.11 0.20 49 13 127 114 92.43 0.01 50 13 131 118 89.47 1.43 51 14 17 3 525.12 3.25 52 14 18 4 513.92 1.69 53 14 69 55 147.46 27.39 54 14 72 58 89.66 1.42 55 14 73 59 89.45 1.44 56 14 76 62 89.45 1.44 57 14 77 63 89.46 1.44 58 14 131 117 92.47 0.01 59 15 18 3 516.91 0.20 60 15 19 4 513.84 1.73 61 16 19 3 524.98 3.83 62 16 24 8 427.06 13.97 63 16 115 99 103.60 0.43 64 16 119 103 103.70 0.42 65 16 122 106 103.73 0.42 66 16 123 107 103.69 0.41 67 17 20 3 530.99 3.61 68 17 21 4 483.35 0.01 69 17 24 7 380.67 9.21 70 17 69 52 154.69 25.16 71 17 115 98 103.62 0.44 72 18 21 3 514.83 1.23 73 18 77 59 137.50 16.57 74 20 23 3 515.85 1.11 75 20 24 4 500.05 9.01 76 21 24 3 515.79 1.14 77 21 25 4 500.06 9.01 78 21 66 45 165.13 20.70 79 21 69 48 162.81 21.86 80 21 70 49 162.34 22.09 81 22 25 3 513.50 2.28 82 22 26 4 500.06 9.01 83 22 62 40 168.55 19.23 84 22 66 44 165.28 20.66 85 23 27 4 512.65 0.78 86 23 118 95 165.61 0.24 87 24 27 3 526.50 4.25 88 24 28 4 508.23 1.45 89 24 69 45 168.37 19.08 90 24 114 90 161.58 1.11 91 24 115 91 165.81 0.60 92 24 118 94 165.66 0.26 93 24 119 95 165.74 0.21 94 25 28 3 519.91 0.96 95 25 29 4 508.34 1.40 96 25 65 40 187.85 9.44 97 25 69 44 187.75 9.39 98 26 29 3 524.27 3.08 99 26 30 4 506.72 0.59 100 26 56 30 218.91 2.65 101 26 62 36 191.85 7.79 102 26 65 39 188.16 9.43 103 27 30 3 517.34 0.39 104 27 31 4 495.92 4.81 105 27 114 87 167.00 0.03 106 27 118 91 166.93 0.00 107 28 31 3 517.30 0.36 108 28 32 4 506.46 5.78 109 28 69 41 188.44 9.44 110 28 107 79 168.52 0.30 111 28 110 82 168.25 0.35 112 28 111 83 168.27 0.36 113 28 114 86 167.99 0.46 114 29 32 3 508.31 4.86 115 29 33 4 506.32 5.84 116 29 46 17 241.18 1.58 117 29 61 32 210.67 1.00 118 29 64 35 205.61 1.04 119 29 65 36 192.39 7.64 120 29 68 39 188.63 9.51 121 29 107 78 168.56 0.29 122 30 33 3 507.18 0.85 123 30 34 4 506.66 1.11 124 30 52 22 219.91 2.92 125 30 55 25 219.25 2.67 126 30 56 26 219.37 2.71 127 30 61 31 219.03 2.73 128 31 34 3 512.27 1.69 129 31 35 4 504.44 2.23 130 31 110 79 168.31 0.38 131 31 113 82 168.17 0.41 132 31 114 83 168.02 0.48 133 32 35 3 521.71 1.71 134 32 36 4 504.43 2.23 135 32 39 7 398.62 2.09 136 32 106 74 168.64 0.29 137 32 107 75 168.63 0.29 138 32 110 78 168.31 0.39 139 33 36 3 518.70 0.13 140 33 37 4 487.19 6.38 141 33 39 6 417.98 7.59 142 33 40 7 314.93 10.56 143 33 43 10 293.95 2.85 144 33 46 13 244.90 3.25 145 33 55 22 220.52 3.20 146 33 61 28 219.81 2.94 147 34 37 3 525.83 3.86 148 34 55 21 220.37 3.10 149 36 39 3 516.58 3.89 150 36 106 70 169.00 0.46 151 37 40 3 525.19 3.75 152 38 41 3 528.21 3.70 153 38 103 65 169.72 0.53 154 38 106 68 169.61 0.49 155 39 42 3 530.75 0.67 156 39 103 64 169.58 0.51 157 39 106 67 169.19 0.38 158 40 43 3 527.29 1.07 159 40 46 6 339.02 12.72 160 40 47 7 258.95 2.78 161 40 49 9 258.94 2.79 162 42 98 56 170.05 0.51 163 42 99 57 169.99 0.54 164 42 100 58 170.05 0.51 165 42 103 61 169.69 0.49 166 43 46 3 523.02 0.86 167 43 47 4 513.28 4.01 168 43 64 21 220.71 3.19 169 44 47 3 533.14 1.84 170 45 48 3 590.10 3.26 171 46 49 3 535.85 0.21 172 46 60 14 225.32 0.91 173 46 61 15 220.97 3.08 174 46 64 18 220.97 3.06 175 47 50 3 586.13 1.28 176 49 54 5 491.79 4.99 177 49 55 6 496.11 2.79 178 49 58 9 329.38 2.08 179 49 61 12 284.70 1.89 180 50 54 4 515.36 10.04 181 50 55 5 498.67 1.69 182 51 54 3 503.59 0.77 183 51 55 4 498.68 1.70 184 52 55 3 508.88 0.84 185 52 56 4 498.69 1.70 186 53 56 3 512.61 2.16 187 53 57 4 498.68 1.70 188 54 57 3 503.41 4.09 189 54 58 4 498.66 1.72 190 55 58 3 512.71 3.79 191 55 61 6 400.20 11.07 192 58 61 3 514.64 5.71 193 58 62 4 501.97 0.62 194 59 62 3 516.19 3.77 195 59 63 4 506.30 1.53 196 60 63 3 519.33 2.21 197 60 64 4 510.03 0.34 198 61 64 3 518.92 2.44 199 61 65 4 516.63 3.58 200 62 65 3 516.63 3.58 201 62 66 4 516.64 3.58 202 63 66 3 520.44 1.69 203 63 67 4 516.58 3.62 204 64 67 3 516.63 3.60 205 64 68 4 516.57 3.62 206 65 68 3 528.81 2.48 207 65 69 4 508.33 0.41 208 66 69 3 528.82 2.48 209 66 70 4 508.24 0.45 210 67 70 3 524.86 0.51 211 67 71 4 516.49 3.68 212 68 71 3 525.01 0.58 213 68 72 4 511.61 1.20 214 68 107 39 168.78 0.18 215 69 72 3 518.85 2.42 216 69 73 4 511.55 1.23 217 69 111 42 168.50 0.24 218 70 73 3 529.96 1.62 219 70 74 4 512.88 0.56 220 71 74 3 517.79 3.02 221 71 75 4 512.61 0.43 222 71 89 18 170.41 0.61 223 72 75 3 511.26 1.11 224 72 76 4 505.54 3.96 225 72 111 39 168.71 0.14 226 72 135 63 166.06 0.09 227 72 138 66 165.90 0.06 228 73 76 3 511.61 0.94 229 73 77 4 522.67 6.47 230 74 77 3 535.56 0.03 231 74 78 4 522.68 6.47 232 75 78 3 535.56 0.03 233 75 79 4 522.71 6.46 234 75 82 7 258.36 5.00 235 75 85 10 207.02 17.28 236 75 86 11 207.01 17.28 237 75 89 14 207.01 17.28 238 75 138 63 165.93 0.05 239 76 79 3 535.56 0.03 240 76 134 58 166.22 0.07 241 78 81 3 521.79 4.81 242 78 82 4 463.61 23.09 243 78 85 7 331.36 14.26 244 80 137 57 166.31 0.01 245 82 85 3 520.38 0.83 246 82 86 4 488.62 6.63 247 82 137 55 166.34 0.01 248 82 141 59 165.94 0.04 249 83 86 3 509.38 0.24 250 83 87 4 498.17 1.86 251 84 88 4 523.29 4.28 252 85 88 3 531.61 0.12 253 86 89 3 518.23 1.75 254 86 90 4 503.94 0.42 255 86 138 52 165.95 0.08 256 86 141 55 165.30 0.24 257 86 142 56 164.50 0.55 258 86 145 59 154.62 0.35 259 87 90 3 520.62 4.20 260 87 91 4 508.69 2.78 261 88 91 3 515.61 1.70 262 88 92 4 511.42 1.42 263 89 92 3 513.25 0.51 264 89 93 4 511.42 1.42 265 90 93 3 514.12 2.77 266 90 94 4 511.42 1.43 267 90 142 52 162.43 0.09 268 90 145 55 152.49 0.26 269 90 146 56 152.48 0.26 270 91 94 3 511.43 1.43 271 91 95 4 511.37 1.40 272 91 149 58 150.75 0.40 273 92 96 4 427.89 6.87 274 92 97 5 430.45 5.58 275 93 97 4 388.65 10.54 276 93 98 5 305.01 0.52 277 93 99 6 294.60 0.07 278 93 146 53 152.23 0.14 279 94 98 4 304.66 0.69 280 94 146 52 152.19 0.15 281 94 149 55 146.09 1.26 282 94 151 57 77.11 2.17 283 95 98 3 517.16 0.66 284 95 149 54 150.92 0.29 285 98 151 53 86.44 0.09 286 99 103 4 512.97 1.15 287 99 104 5 507.89 3.64 288 99 146 47 152.18 0.15 289 99 151 52 72.52 4.48 290 100 103 3 526.88 0.59 291 100 104 4 515.45 0.39 292 100 146 46 152.11 0.17 293 100 151 51 69.25 6.11 294 100 152 52 56.01 2.62 295 101 104 3 525.50 0.29 296 101 105 4 510.80 2.23 297 101 139 38 164.59 0.58 298 101 142 41 157.13 0.54 299 101 143 42 154.02 0.03 300 101 146 45 151.24 0.23 301 101 152 51 54.67 3.21 302 102 105 3 515.73 2.48 303 102 106 4 514.56 0.34 304 103 106 3 518.56 1.68 305 103 107 4 514.50 0.31 306 104 107 3 518.52 1.82 307 104 108 4 512.39 0.74 308 104 138 34 165.21 0.29 309 104 139 35 164.12 0.66 310 104 142 38 156.02 0.72 311 104 146 42 151.69 0.04 312 105 108 3 516.41 2.75 313 105 109 4 512.39 0.74 314 105 139 34 164.47 0.53 315 106 109 3 510.49 1.70 316 106 110 4 508.09 2.11 317 107 110 3 509.36 1.47 318 107 111 4 508.09 2.10 319 108 111 3 518.35 3.02 320 108 112 4 510.25 1.02 321 108 135 27 165.56 0.18 322 108 139 31 164.12 0.66 323 109 112 3 519.92 5.53 324 109 113 4 503.29 0.26 325 110 113 3 508.20 1.93 326 110 114 4 500.75 0.99 327 111 114 3 516.92 2.06 328 111 115 4 500.75 0.99 329 111 135 24 165.72 0.14 330 112 115 3 522.97 0.96 331 112 116 4 502.98 0.14 332 112 123 11 264.99 8.43 333 112 128 16 170.03 2.04 334 112 132 20 165.77 0.14 335 112 135 23 165.72 0.12 336 113 116 3 522.75 2.75 337 113 117 4 501.12 2.31 338 114 117 3 518.62 0.70 339 114 118 4 499.07 3.33 340 115 119 4 481.52 1.46 341 115 123 8 269.00 6.44 342 115 131 16 197.60 15.84 343 116 119 3 510.65 3.37 344 116 120 4 453.67 1.35 345 116 123 7 272.69 4.58 346 116 128 12 254.66 3.27 347 117 120 3 525.90 0.10 348 119 122 3 524.29 2.48 349 119 123 4 480.20 4.56 350 123 127 4 505.27 1.52 351 123 128 5 500.48 3.91 352 123 131 8 464.13 14.28 353 124 127 3 520.25 2.69 354 124 128 4 507.59 0.36 355 125 128 3 514.23 0.33 356 125 129 4 505.29 1.52 357 126 129 3 507.59 0.36 358 126 130 4 505.29 1.52 359 127 130 3 506.65 2.58 360 127 131 4 499.17 3.08 361 128 131 3 509.81 2.73 362 128 132 4 504.20 1.23 363 129 132 3 514.82 0.24 364 129 133 4 514.81 0.24 365 130 133 3 532.76 5.15 366 130 134 4 515.00 0.15 367 131 134 3 532.76 5.15 368 131 135 4 508.74 3.28 369 132 135 3 515.99 3.23 370 132 136 4 508.87 2.29 371 133 136 3 507.48 1.02 372 133 137 4 504.87 0.29 373 134 137 3 507.06 2.44 374 134 138 4 498.02 0.98 375 135 138 3 505.35 0.05 376 135 139 4 508.06 1.90 377 136 139 3 514.58 1.35 378 136 140 4 500.26 2.00 379 137 140 3 514.50 0.81 380 137 141 4 508.06 1.90 381 138 141 3 523.16 2.02 382 138 142 4 505.85 0.80 383 139 142 3 514.18 0.41 384 139 143 4 503.05 1.64 385 140 143 3 513.17 2.86 386 140 144 4 503.05 1.64 387 141 144 3 504.72 0.81 388 141 145 4 503.24 1.54 389 142 145 3 507.94 1.77 390 142 146 4 502.96 1.41 391 143 146 3 512.06 0.29 392 143 147 4 504.83 2.35 393 144 147 3 515.50 2.00 394 144 148 4 506.46 1.54 395 145 148 3 511.24 0.85 396 145 149 4 507.26 1.13 397 146 149 3 519.19 1.82 398 146 150 4 502.24 1.78 399 146 151 5 400.25 16.55 400 146 152 6 400.26 16.55 401 147 150 3 485.06 3.81