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 19 27 8 455.89 13.75 2 19 96 77 27.61 0.46 3 19 153 134 21.80 0.23 4 19 154 135 21.80 0.22 5 19 157 138 21.80 0.22 6 20 23 3 510.56 1.40 7 20 24 4 510.25 1.26 8 21 24 3 524.44 2.48 9 21 25 4 514.97 1.03 10 22 25 3 517.05 2.07 11 22 26 4 510.34 1.28 12 23 26 3 520.38 4.51 13 23 27 4 515.11 1.10 14 23 149 126 51.80 1.32 15 23 150 127 51.74 1.31 16 24 27 3 524.62 2.39 17 24 28 4 523.34 3.00 18 24 96 72 51.77 1.30 19 24 97 73 51.80 1.30 20 25 28 3 523.97 2.70 21 25 29 4 515.09 1.12 22 26 29 3 524.37 2.66 23 26 30 4 515.46 0.94 24 26 147 121 75.45 0.98 25 26 150 124 75.42 0.99 26 27 30 3 516.32 1.17 27 27 31 4 508.62 1.99 28 27 93 66 75.44 0.99 29 27 96 69 75.47 0.99 30 27 150 123 75.45 0.98 31 27 151 124 75.43 0.99 32 27 154 127 75.42 0.99 33 28 31 3 518.86 3.13 34 28 32 4 515.09 1.25 35 28 93 65 75.51 0.96 36 28 94 66 75.53 0.96 37 28 97 69 75.59 0.96 38 29 32 3 521.42 3.91 39 29 33 4 515.14 1.28 40 30 33 3 533.59 2.17 41 30 34 4 516.52 1.98 42 30 135 105 89.22 0.03 43 30 139 109 89.70 0.20 44 30 143 113 89.22 0.03 45 30 147 117 89.11 0.02 46 30 151 121 89.05 0.02 47 31 34 3 520.89 4.17 48 31 35 4 514.70 1.41 49 31 86 55 127.84 19.32 50 31 89 58 127.67 19.29 51 31 90 59 89.08 0.06 52 31 93 62 89.04 0.01 53 31 94 63 89.10 0.04 54 31 151 120 89.09 0.04 55 32 35 3 533.58 2.18 56 32 36 4 511.09 1.94 57 33 36 3 529.95 0.38 58 33 139 106 91.48 0.57 59 33 142 109 91.47 0.57 60 34 37 3 534.96 1.66 61 34 38 4 507.10 0.02 62 34 41 7 400.80 1.77 63 34 86 52 129.06 18.93 64 34 135 101 91.26 0.63 65 34 139 105 91.53 0.58 66 35 38 3 507.10 0.01 67 35 86 51 129.06 18.93 68 35 87 52 129.02 18.90 69 35 90 55 128.12 18.46 70 37 40 3 527.90 0.24 71 37 41 4 513.33 0.55 72 38 41 3 525.81 0.13 73 38 42 4 513.33 0.55 74 38 86 48 137.47 22.11 75 39 42 3 525.81 0.14 76 39 43 4 522.03 0.01 77 40 43 3 523.81 0.87 78 40 44 4 511.35 2.14 79 41 44 3 520.26 0.89 80 41 45 4 512.19 1.72 81 41 86 45 152.87 15.78 82 41 139 98 144.81 4.02 83 42 45 3 518.89 1.56 84 42 46 4 512.19 1.72 85 42 82 40 154.80 14.83 86 42 86 44 152.87 15.78 87 43 46 3 530.87 0.52 88 43 47 4 513.82 0.74 89 43 73 30 165.89 11.33 90 43 78 35 161.73 12.85 91 43 79 36 160.41 12.18 92 43 82 39 157.44 13.65 93 44 47 3 530.87 0.52 94 44 48 4 513.80 0.75 95 45 48 3 528.96 0.39 96 45 49 4 508.75 6.30 97 45 127 82 146.62 4.85 98 45 130 85 146.62 4.83 99 45 131 86 146.49 4.79 100 45 134 89 146.29 4.66 101 46 49 3 516.56 2.40 102 46 50 4 512.01 4.67 103 46 78 32 167.06 10.52 104 46 81 35 166.50 10.46 105 46 82 36 165.94 10.44 106 46 127 81 146.69 4.88 107 47 50 3 525.53 2.08 108 47 51 4 512.02 4.67 109 47 69 22 189.22 21.46 110 47 72 25 170.46 12.20 111 47 73 26 170.47 12.19 112 47 78 31 167.31 10.63 113 48 51 3 524.72 1.68 114 48 52 4 499.80 4.55 115 48 130 82 151.17 2.56 116 48 133 85 151.09 2.52 117 48 134 86 150.83 2.39 118 48 137 89 151.10 2.50 119 49 52 3 529.47 2.05 120 49 53 4 496.92 5.99 121 49 56 7 463.76 4.51 122 49 123 74 151.43 2.71 123 49 126 77 151.30 2.63 124 49 127 78 151.25 2.60 125 49 130 81 151.18 2.56 126 50 53 3 522.31 2.89 127 50 54 4 493.98 4.65 128 50 56 6 425.61 14.56 129 50 57 7 367.98 16.03 130 50 60 10 359.29 11.68 131 50 63 13 195.56 22.09 132 50 72 22 189.38 21.44 133 50 78 28 172.97 13.25 134 51 54 3 529.34 0.61 135 51 69 18 189.47 21.34 136 51 72 21 189.52 21.36 137 53 56 3 530.46 0.06 138 53 126 73 151.50 2.67 139 53 130 77 151.48 2.62 140 54 57 3 527.46 1.43 141 55 58 3 536.78 3.24 142 55 123 68 152.03 2.92 143 56 59 3 549.82 0.83 144 56 60 4 533.47 1.56 145 56 123 67 151.75 2.79 146 57 60 3 533.12 1.73 147 57 63 6 363.30 29.09 148 57 64 7 209.87 29.28 149 57 66 9 290.86 11.23 150 57 67 10 290.86 11.23 151 57 72 15 194.03 22.68 152 58 64 6 292.73 10.30 153 59 117 58 152.55 3.19 154 59 118 59 152.54 3.17 155 59 119 60 152.52 3.16 156 59 120 61 152.54 3.16 157 59 123 64 152.54 3.14 158 60 63 3 527.43 1.54 159 60 64 4 487.00 0.02 160 60 77 17 190.65 21.11 161 60 81 21 189.60 21.45 162 61 64 3 536.82 0.48 163 61 77 16 190.73 21.08 164 62 66 4 523.82 1.52 165 62 77 15 190.73 21.08 166 63 66 3 508.87 1.66 167 63 77 14 190.86 21.14 168 63 78 15 190.69 21.06 169 66 71 5 491.14 7.53 170 66 72 6 466.65 6.25 171 67 72 5 509.01 3.86 172 68 71 3 519.77 1.51 173 68 72 4 514.47 1.14 174 69 72 3 514.48 1.13 175 69 73 4 514.47 1.14 176 70 73 3 514.48 1.14 177 70 74 4 514.47 1.14 178 71 74 3 514.47 1.12 179 71 75 4 509.00 3.86 180 72 75 3 513.25 1.65 181 72 78 6 415.63 0.80 182 73 79 6 487.74 1.64 183 74 79 5 491.86 3.27 184 75 78 3 511.81 1.43 185 75 79 4 499.64 2.60 186 76 79 3 514.64 0.34 187 76 80 4 506.63 1.38 188 77 80 3 513.75 2.19 189 77 81 4 508.48 0.45 190 78 81 3 517.03 0.55 191 78 82 4 508.67 0.45 192 79 82 3 516.07 3.29 193 79 83 4 508.68 0.45 194 80 83 3 511.60 1.91 195 80 84 4 508.68 0.45 196 81 84 3 511.60 1.91 197 81 85 4 508.67 0.45 198 82 85 3 516.24 0.57 199 82 86 4 508.64 0.45 200 83 86 3 521.08 2.56 201 83 87 4 508.62 0.44 202 84 87 3 512.23 2.29 203 84 88 4 507.56 0.84 204 85 88 3 523.19 1.51 205 85 89 4 509.38 0.12 206 86 89 3 515.15 3.00 207 86 90 4 509.37 0.14 208 87 90 3 509.84 0.38 209 87 91 4 515.86 3.39 210 88 91 3 515.86 3.40 211 88 92 4 515.86 3.40 212 88 105 17 153.96 3.25 213 88 109 21 153.40 3.11 214 89 92 3 515.92 3.37 215 89 93 4 512.67 4.99 216 89 131 42 154.68 1.07 217 89 158 69 150.83 1.59 218 90 93 3 521.36 0.65 219 90 94 4 505.69 1.49 220 91 94 3 528.35 3.07 221 91 95 4 506.15 1.26 222 91 101 10 216.80 24.12 223 91 105 14 190.43 18.63 224 92 95 3 532.32 1.08 225 92 96 4 509.09 0.21 226 92 102 10 190.09 18.80 227 92 105 13 187.72 19.98 228 92 106 14 187.72 19.99 229 92 154 62 174.70 9.84 230 93 96 3 532.32 1.08 231 93 154 61 174.71 9.84 232 94 97 3 611.22 0.71 233 95 98 3 521.50 0.60 234 95 101 6 358.13 24.80 235 95 102 7 337.27 20.14 236 96 102 6 404.85 10.65 237 96 154 58 197.85 21.14 238 96 157 61 197.81 21.16 239 98 101 3 521.82 0.92 240 98 102 4 512.50 2.41 241 99 102 3 512.11 2.60 242 99 103 4 508.41 4.45 243 100 103 3 522.30 6.14 244 100 104 4 503.90 2.20 245 101 104 3 515.62 2.88 246 101 105 4 506.50 0.90 247 102 105 3 525.70 4.44 248 102 106 4 513.03 4.17 249 102 157 55 219.12 32.09 250 103 106 3 522.00 0.30 251 103 107 4 515.59 2.90 252 103 161 58 216.94 33.17 253 104 107 3 530.90 3.71 254 104 108 4 515.94 2.72 255 105 108 3 530.79 3.66 256 105 109 4 510.98 0.24 257 106 109 3 517.41 2.98 258 106 110 4 504.69 2.90 259 106 157 51 220.27 32.98 260 106 158 52 220.13 33.05 261 106 161 55 218.24 33.96 262 106 162 56 217.96 34.10 263 107 110 3 510.97 0.24 264 107 111 4 506.16 2.17 265 107 165 58 213.11 36.41 266 108 111 3 521.53 0.06 267 108 112 4 512.09 4.83 268 109 112 3 521.72 0.03 269 109 113 4 512.10 4.83 270 109 124 15 246.28 20.70 271 110 113 3 529.12 2.40 272 110 114 4 505.25 2.52 273 110 162 52 213.40 36.41 274 110 165 55 213.21 36.47 275 110 166 56 213.11 36.52 276 111 114 3 513.76 1.74 277 111 115 4 503.55 3.35 278 111 165 54 213.24 36.48 279 111 169 58 211.67 37.09 280 112 115 3 524.25 3.75 281 112 116 4 498.87 1.46 282 112 117 5 472.81 5.22 283 113 117 4 414.99 9.51 284 113 118 5 380.23 7.88 285 113 119 6 347.63 7.17 286 113 124 11 271.50 8.71 287 113 166 53 212.72 36.75 288 114 118 4 363.15 0.59 289 114 166 52 212.71 36.76 290 114 171 57 172.96 55.72 291 115 118 3 501.62 2.35 292 115 169 54 211.59 37.29 293 118 171 53 182.28 51.93 294 119 123 4 516.37 4.92 295 119 166 47 212.88 36.84 296 120 123 3 540.41 5.25 297 120 171 51 174.68 55.66 298 121 124 3 528.62 1.26 299 121 159 38 220.06 33.44 300 121 166 45 212.84 36.88 301 121 171 50 173.75 56.13 302 122 125 3 524.11 1.04 303 122 126 4 514.00 4.01 304 122 159 37 220.09 33.45 305 123 126 3 524.61 1.28 306 123 127 4 514.00 4.01 307 124 127 3 514.01 4.01 308 124 128 4 514.00 4.01 309 124 159 35 220.03 33.48 310 124 162 38 213.70 36.62 311 124 166 42 213.06 36.93 312 125 128 3 514.02 4.01 313 125 129 4 515.22 3.41 314 125 155 30 220.46 33.36 315 125 159 34 220.06 33.50 316 126 129 3 517.34 1.79 317 126 130 4 509.05 1.40 318 127 130 3 523.49 1.29 319 127 131 4 512.59 0.37 320 128 131 3 516.38 1.52 321 128 132 4 512.59 0.38 322 128 155 27 220.37 33.34 323 129 132 3 512.61 0.37 324 129 133 4 512.58 0.38 325 129 155 26 220.47 33.38 326 130 133 3 512.58 0.39 327 130 134 4 512.58 0.38 328 131 134 3 518.61 2.00 329 131 135 4 510.88 0.38 330 131 151 20 220.97 33.53 331 132 135 3 508.82 0.68 332 132 136 4 508.79 0.67 333 132 143 11 277.97 6.52 334 132 151 19 220.75 33.43 335 132 155 23 220.50 33.41 336 133 136 3 516.08 2.15 337 133 137 4 508.79 0.67 338 134 137 3 510.96 0.41 339 134 138 4 508.78 0.66 340 135 138 3 518.25 1.07 341 135 139 4 478.30 8.62 342 135 143 8 283.25 3.91 343 135 151 16 252.89 17.67 344 136 140 4 380.36 12.27 345 136 143 7 278.08 6.58 346 139 142 3 501.22 2.69 347 139 143 4 500.25 3.18 348 140 143 3 501.21 2.69 349 143 147 4 495.87 0.09 350 143 148 5 495.81 0.11 351 143 151 8 452.67 2.24 352 144 147 3 502.73 2.05 353 144 148 4 502.29 2.27 354 145 148 3 506.98 0.07 355 145 149 4 510.62 7.42 356 146 149 3 524.77 0.35 357 146 150 4 510.62 7.42 358 147 150 3 516.14 4.67 359 147 151 4 500.05 2.16 360 148 151 3 516.15 4.66 361 148 152 4 509.10 2.21 362 149 152 3 512.40 0.57 363 149 153 4 511.57 0.98 364 150 153 3 511.57 0.98 365 150 154 4 511.57 0.98 366 151 154 3 512.15 1.27 367 151 155 4 511.56 0.98 368 152 155 3 511.07 1.22 369 152 156 4 511.07 1.22 370 153 156 3 518.78 2.54 371 153 157 4 496.72 0.66 372 154 157 3 518.78 2.53 373 154 158 4 499.81 2.40 374 155 158 3 509.85 1.94 375 155 159 4 519.76 3.30 376 156 159 3 522.09 2.14 377 156 160 4 508.90 2.14 378 157 160 3 526.87 0.25 379 157 161 4 508.90 2.14 380 158 161 3 520.47 3.46 381 158 162 4 510.43 1.37 382 159 162 3 521.21 0.93 383 159 163 4 510.43 1.37 384 160 163 3 516.25 1.55 385 160 164 4 502.37 2.66 386 161 164 3 516.22 1.56 387 161 165 4 523.60 1.79 388 162 165 3 526.67 0.26 389 162 166 4 519.14 4.01 390 163 166 3 523.61 1.79 391 163 167 4 526.74 0.21 392 164 167 3 532.09 2.46 393 164 168 4 526.73 0.21 394 165 168 3 524.96 0.95 395 165 169 4 524.96 0.96 396 166 169 3 526.47 0.20 397 166 170 4 518.25 4.30 398 166 171 5 464.66 0.80 399 167 170 3 524.95 0.96