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 8 472.26 1.88 2 2 130 128 47.45 0.14 3 2 133 131 37.88 2.75 4 2 134 132 31.83 0.99 5 2 137 135 31.83 0.99 6 3 6 3 512.98 2.60 7 3 7 4 513.44 2.37 8 4 7 3 515.97 3.64 9 4 8 4 512.99 2.59 10 4 79 75 57.64 2.46 11 5 8 3 513.44 2.37 12 5 9 4 513.42 2.38 13 6 9 3 526.80 4.31 14 6 10 4 505.23 1.72 15 6 130 124 66.97 1.05 16 6 133 127 67.00 1.05 17 7 10 3 506.91 2.46 18 7 11 4 505.23 1.72 19 7 76 69 67.02 1.05 20 7 79 72 67.01 1.05 21 7 80 73 70.27 0.57 22 7 134 127 67.02 1.05 23 7 137 130 67.02 1.05 24 8 11 3 526.58 1.64 25 8 12 4 495.61 6.53 26 9 12 3 526.58 1.64 27 9 13 4 518.07 2.62 28 9 126 117 81.81 1.42 29 9 127 118 81.75 1.40 30 9 130 121 81.67 1.42 31 10 13 3 527.64 0.68 32 10 14 4 515.42 1.11 33 10 76 66 81.71 1.44 34 10 130 120 81.77 1.40 35 10 131 121 81.73 1.39 36 10 134 124 81.66 1.42 37 11 14 3 515.94 1.36 38 11 15 4 515.41 1.10 39 11 76 65 81.77 1.41 40 11 77 66 81.80 1.42 41 11 79 68 81.81 1.41 42 12 15 3 519.81 0.84 43 12 16 4 515.94 1.36 44 12 122 110 90.02 1.00 45 13 16 3 523.89 2.89 46 13 17 4 515.91 1.35 47 13 115 102 89.84 0.99 48 13 119 106 90.59 0.99 49 13 122 109 90.31 0.87 50 13 123 110 89.98 0.99 51 13 131 118 88.80 0.92 52 14 17 3 518.38 0.12 53 14 18 4 518.71 0.04 54 14 69 55 89.90 1.02 55 14 72 58 89.15 1.28 56 14 73 59 88.60 1.01 57 14 76 62 88.21 1.20 58 14 77 63 88.59 1.02 59 15 18 3 516.91 0.95 60 15 19 4 519.99 0.59 61 16 19 3 518.02 0.39 62 16 119 103 95.45 3.39 63 16 122 106 95.42 3.39 64 17 20 3 525.29 1.93 65 17 21 4 491.03 3.08 66 17 24 7 416.75 10.27 67 17 69 52 188.58 3.17 68 17 115 98 90.62 0.99 69 18 21 3 513.48 2.57 70 18 77 59 126.84 19.25 71 20 23 3 525.67 3.49 72 20 24 4 511.12 1.74 73 20 118 98 159.50 0.77 74 21 24 3 519.77 0.85 75 21 25 4 512.40 1.09 76 21 66 45 204.03 1.63 77 21 69 48 203.70 1.51 78 22 25 3 519.09 0.51 79 22 26 4 512.41 1.09 80 22 62 40 205.53 2.36 81 22 66 44 204.21 1.71 82 23 26 3 518.64 0.73 83 23 27 4 512.03 0.91 84 23 118 95 164.47 0.83 85 24 27 3 522.88 4.35 86 24 28 4 512.03 0.91 87 24 69 45 205.09 2.16 88 24 114 90 165.27 0.70 89 24 115 91 165.13 0.73 90 24 118 94 164.46 0.83 91 24 119 95 164.47 0.83 92 25 28 3 516.16 0.56 93 25 29 4 513.24 0.31 94 25 65 40 205.34 2.12 95 25 69 44 205.10 2.16 96 26 29 3 524.61 3.67 97 26 30 4 511.20 0.39 98 26 61 35 206.03 2.30 99 26 62 36 205.94 2.29 100 26 65 39 205.65 2.19 101 27 30 3 519.13 0.93 102 27 31 4 508.75 1.61 103 27 114 87 165.48 0.67 104 27 118 91 164.71 0.80 105 28 31 3 508.80 2.69 106 28 32 4 504.76 3.61 107 28 69 41 205.71 2.16 108 28 107 79 166.19 0.65 109 28 110 82 166.06 0.70 110 28 111 83 165.66 0.68 111 28 114 86 165.49 0.67 112 29 32 3 515.04 1.53 113 29 33 4 504.70 3.59 114 29 61 32 206.61 2.17 115 29 64 35 206.18 2.23 116 29 65 36 205.85 2.15 117 29 68 39 205.94 2.20 118 29 107 78 166.21 0.66 119 30 33 3 519.11 0.49 120 30 34 4 494.32 1.04 121 30 52 22 229.70 1.33 122 30 55 25 229.31 1.43 123 30 56 26 229.60 1.28 124 30 61 31 206.91 2.29 125 31 34 3 519.11 0.49 126 31 35 4 503.44 3.52 127 31 110 79 166.18 0.65 128 31 113 82 166.09 0.64 129 31 114 83 166.01 0.60 130 32 35 3 509.45 0.52 131 32 36 4 498.23 6.12 132 32 39 7 354.18 8.16 133 32 106 74 166.26 0.62 134 32 107 75 166.24 0.65 135 32 110 78 166.19 0.65 136 33 37 4 459.81 2.38 137 33 39 6 354.18 8.16 138 33 40 7 333.75 14.20 139 33 43 10 293.44 0.19 140 33 46 13 263.33 2.25 141 33 55 22 233.86 0.57 142 33 61 28 229.47 1.20 143 34 37 3 515.62 1.44 144 34 52 18 233.95 0.53 145 36 39 3 515.67 1.41 146 36 106 70 166.39 0.65 147 37 40 3 525.94 3.37 148 37 41 4 512.23 0.92 149 38 41 3 525.94 3.38 150 38 103 65 166.66 0.61 151 38 106 68 166.60 0.63 152 39 42 3 527.46 2.61 153 39 43 4 525.94 3.37 154 39 103 64 166.56 0.62 155 39 106 67 166.47 0.66 156 40 43 3 522.91 1.96 157 40 46 6 408.00 3.90 158 40 47 7 282.94 2.46 159 40 49 9 267.31 5.36 160 40 55 15 250.50 3.00 161 41 47 6 285.78 1.05 162 42 97 55 167.16 0.50 163 42 98 56 167.14 0.49 164 42 99 57 166.97 0.55 165 42 100 58 167.07 0.53 166 42 103 61 166.72 0.66 167 43 46 3 520.72 2.76 168 43 47 4 491.65 3.16 169 43 64 21 238.82 0.53 170 44 47 3 533.89 2.22 171 45 48 3 596.75 0.88 172 45 60 15 239.15 0.51 173 45 64 19 239.02 0.47 174 46 49 3 534.84 0.29 175 46 60 14 239.15 0.51 176 46 61 15 239.12 0.49 177 46 64 18 238.91 0.52 178 47 50 3 620.02 1.95 179 49 54 5 427.89 5.58 180 49 55 6 398.32 5.50 181 49 58 9 283.33 2.51 182 49 61 12 255.55 0.40 183 50 54 4 498.81 3.71 184 51 54 3 509.87 4.67 185 51 55 4 502.79 1.14 186 52 55 3 504.51 0.28 187 52 56 4 495.82 4.62 188 53 56 3 508.49 0.65 189 53 57 4 501.74 1.67 190 54 57 3 505.10 0.01 191 54 58 4 500.25 2.40 192 55 58 3 513.46 4.17 193 55 61 6 420.36 15.21 194 58 61 3 533.14 2.79 195 58 62 4 514.66 5.73 196 59 62 3 514.50 5.82 197 59 63 4 502.80 4.02 198 60 63 3 524.96 0.58 199 60 64 4 502.88 3.98 200 61 64 3 517.31 3.24 201 61 65 4 504.25 3.28 202 62 65 3 514.28 1.93 203 62 66 4 511.99 0.58 204 63 66 3 518.07 1.78 205 63 67 4 511.99 0.58 206 64 67 3 512.72 0.89 207 64 68 4 510.12 1.52 208 65 68 3 526.06 3.81 209 65 69 4 510.20 1.55 210 66 69 3 528.06 2.81 211 66 70 4 510.66 1.32 212 67 70 3 522.62 0.04 213 67 71 4 511.51 0.90 214 68 71 3 520.52 1.10 215 68 72 4 511.53 0.89 216 68 107 39 166.19 0.65 217 69 72 3 519.66 1.53 218 69 73 4 509.06 0.74 219 70 73 3 530.70 1.26 220 70 74 4 509.06 0.74 221 71 74 3 526.01 1.09 222 71 75 4 512.01 0.72 223 72 75 3 526.01 1.09 224 72 76 4 512.35 0.56 225 72 111 39 165.66 0.68 226 72 135 63 160.69 1.07 227 72 138 66 158.56 0.98 228 73 76 3 516.57 2.67 229 73 77 4 512.35 0.56 230 74 77 3 530.75 3.12 231 74 78 4 512.35 0.56 232 75 78 3 536.29 0.35 233 75 82 7 245.13 2.06 234 75 85 10 167.24 0.62 235 75 89 14 167.23 0.62 236 75 138 63 158.62 0.96 237 76 79 3 523.83 5.88 238 76 131 55 162.09 0.96 239 76 134 58 160.83 1.06 240 78 81 3 509.46 0.90 241 78 82 4 331.56 27.20 242 78 85 7 285.16 2.02 243 80 137 57 160.77 1.09 244 82 85 3 521.12 0.45 245 82 86 4 505.03 0.83 246 82 137 55 160.76 1.08 247 82 141 59 159.25 1.33 248 83 86 3 512.05 0.74 249 83 87 4 510.10 1.71 250 84 88 4 521.46 0.89 251 85 88 3 544.45 0.42 252 85 89 4 521.46 0.89 253 86 89 3 526.52 3.42 254 86 90 4 515.53 2.08 255 86 138 52 160.13 0.90 256 86 141 55 156.24 2.02 257 86 142 56 156.02 1.94 258 86 145 59 153.71 2.23 259 87 90 3 521.66 0.98 260 87 91 4 510.06 0.66 261 88 91 3 516.08 0.16 262 88 92 4 511.10 1.18 263 89 92 3 514.98 1.38 264 89 93 4 511.06 1.20 265 89 138 49 160.14 0.90 266 89 142 53 155.75 1.82 267 90 93 3 513.17 2.28 268 90 94 4 507.35 0.61 269 90 142 52 155.31 1.88 270 90 145 55 152.02 1.70 271 90 146 56 144.60 0.75 272 91 94 3 520.25 0.03 273 91 95 4 506.13 1.22 274 91 149 58 141.60 0.42 275 92 95 3 526.56 5.45 276 92 96 4 468.11 11.64 277 92 97 5 430.76 19.73 278 93 97 4 400.07 7.84 279 93 98 5 400.05 7.83 280 93 99 6 295.67 0.24 281 93 146 53 144.48 0.70 282 94 98 4 362.24 11.06 283 94 146 52 143.03 0.10 284 94 149 55 140.25 0.01 285 94 151 57 93.61 2.50 286 95 98 3 517.79 1.04 287 95 149 54 141.36 0.54 288 95 151 56 118.92 2.26 289 98 151 53 106.34 3.88 290 99 103 4 511.80 0.18 291 99 104 5 507.86 1.77 292 99 146 47 142.30 0.47 293 100 103 3 527.10 1.23 294 100 104 4 514.19 1.02 295 100 153 53 24.50 2.79 296 101 104 3 510.40 2.91 297 101 105 4 509.76 2.60 298 101 142 41 155.25 1.85 299 101 143 42 146.94 1.24 300 101 146 45 142.30 0.48 301 101 153 52 23.48 2.27 302 102 105 3 521.34 3.19 303 102 106 4 510.03 2.47 304 103 106 3 512.15 0.33 305 103 107 4 513.16 1.10 306 104 107 3 523.94 0.26 307 104 108 4 508.04 1.48 308 104 139 35 155.93 1.94 309 104 142 38 155.01 1.78 310 105 108 3 513.58 1.29 311 105 109 4 520.51 2.57 312 105 139 34 156.91 1.47 313 106 109 3 512.50 0.64 314 106 110 4 512.42 0.71 315 107 110 3 512.42 0.71 316 107 111 4 512.42 0.72 317 108 111 3 519.86 2.27 318 108 112 4 511.04 1.42 319 108 135 27 160.38 0.92 320 108 139 31 155.99 1.94 321 109 112 3 519.85 2.27 322 109 113 4 510.50 1.69 323 110 113 3 513.80 0.00 324 110 114 4 503.77 1.69 325 111 114 3 526.23 0.67 326 111 115 4 504.55 1.28 327 111 135 24 160.39 0.92 328 112 115 3 515.00 2.71 329 112 116 4 505.64 2.22 330 112 123 11 262.58 0.69 331 112 128 16 161.70 1.15 332 112 131 19 161.54 1.17 333 112 132 20 161.50 1.16 334 112 135 23 160.74 1.08 335 113 116 3 514.15 1.11 336 113 117 4 506.54 1.77 337 114 117 3 508.88 2.94 338 114 118 4 509.35 0.36 339 115 118 3 522.36 3.00 340 115 119 4 506.52 1.78 341 115 123 8 295.19 7.13 342 115 131 16 161.58 1.19 343 116 119 3 527.95 0.20 344 116 120 4 496.62 3.16 345 116 123 7 307.12 16.38 346 117 120 3 542.70 1.75 347 119 122 3 519.62 5.27 348 119 123 4 490.37 0.23 349 120 123 3 512.67 8.75 350 120 124 4 494.25 2.17 351 122 127 5 478.31 2.96 352 123 127 4 491.55 3.67 353 123 128 5 481.30 1.45 354 123 131 8 414.69 15.91 355 124 127 3 512.32 2.03 356 124 128 4 495.68 4.83 357 125 128 3 510.85 2.76 358 125 129 4 499.60 4.35 359 126 129 3 508.33 0.01 360 126 130 4 503.88 2.21 361 127 130 3 504.41 1.96 362 127 131 4 503.88 2.21 363 128 131 3 506.45 1.59 364 128 132 4 509.26 3.00 365 129 132 3 511.85 1.73 366 129 133 4 509.28 3.00 367 130 133 3 515.55 0.13 368 130 134 4 512.08 1.60 369 131 134 3 515.74 0.24 370 131 135 4 504.17 0.70 371 132 135 3 511.42 2.39 372 132 136 4 504.16 0.70 373 133 136 3 507.22 0.83 374 133 137 4 505.19 0.18 375 134 137 3 505.20 0.17 376 134 138 4 505.20 0.17 377 135 138 3 509.15 2.15 378 135 139 4 506.13 0.64 379 136 139 3 512.85 2.72 380 136 140 4 506.12 0.65 381 137 140 3 505.40 1.02 382 137 141 4 504.50 1.47 383 138 141 3 518.89 0.18 384 138 142 4 504.95 1.25 385 139 142 3 513.47 0.05 386 139 143 4 504.41 0.96 387 140 143 3 513.36 3.52 388 140 144 4 505.20 1.34 389 141 144 3 512.00 2.05 390 141 145 4 511.68 1.89 391 142 145 3 521.12 2.83 392 142 146 4 504.42 0.95 393 143 146 3 507.19 1.15 394 143 147 4 504.35 0.98 395 143 152 9 213.74 4.59 396 144 147 3 513.62 3.70 397 144 148 4 508.22 0.99 398 145 148 3 511.10 2.21 399 145 149 4 508.16 1.02 400 146 149 3 508.44 0.89 401 146 150 4 508.22 0.99 402 146 151 5 353.80 20.89 403 146 152 6 236.47 14.41 404 147 150 3 508.22 0.99 405 147 152 5 261.17 2.00