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 7 5 499.11 3.00 2 2 10 8 492.42 0.24 3 2 130 128 42.58 0.36 4 2 133 131 35.57 0.01 5 2 134 132 33.24 1.16 6 2 137 135 33.13 1.22 7 3 6 3 521.91 1.28 8 3 7 4 519.00 2.35 9 4 7 3 520.16 2.16 10 4 8 4 519.00 2.35 11 4 79 75 57.72 0.55 12 5 8 3 520.62 1.58 13 5 9 4 519.00 2.34 14 6 9 3 525.17 0.75 15 6 10 4 513.41 0.46 16 6 130 124 67.05 2.77 17 6 133 127 67.05 2.77 18 7 10 3 513.41 0.46 19 7 11 4 512.49 0.01 20 7 76 69 67.10 2.79 21 7 79 72 67.10 2.79 22 7 80 73 67.10 2.79 23 7 134 127 67.09 2.79 24 7 137 130 67.09 2.79 25 8 11 3 520.22 2.94 26 8 12 4 509.26 1.60 27 9 12 3 523.62 1.24 28 9 13 4 515.50 3.39 29 9 126 117 81.19 0.88 30 9 127 118 80.62 1.10 31 9 130 121 80.61 1.11 32 10 13 3 528.04 1.50 33 10 14 4 512.54 1.61 34 10 76 66 80.80 1.08 35 10 130 120 80.64 1.09 36 10 131 121 80.61 1.11 37 10 134 124 80.60 1.10 38 11 14 3 515.82 3.25 39 11 15 4 512.54 1.61 40 11 76 65 80.85 1.09 41 11 77 66 80.86 1.10 42 11 79 68 80.89 1.08 43 12 15 3 520.94 2.73 44 12 16 4 519.01 1.66 45 12 122 110 84.48 0.13 46 13 16 3 521.07 2.69 47 13 17 4 514.75 3.79 48 13 115 102 84.34 0.06 49 13 119 106 88.25 1.93 50 13 122 109 84.46 0.12 51 13 123 110 84.45 0.12 52 13 131 118 83.80 0.10 53 14 17 3 513.36 0.52 54 14 18 4 510.94 2.33 55 14 69 55 131.24 23.55 56 14 72 58 83.94 0.12 57 14 73 59 83.78 0.10 58 14 76 62 83.78 0.10 59 14 131 117 84.21 0.01 60 15 18 3 526.24 1.64 61 15 19 4 513.58 1.09 62 16 19 3 522.64 3.43 63 16 24 8 485.06 3.71 64 16 119 103 99.25 3.56 65 16 122 106 93.83 0.86 66 17 20 3 529.53 0.01 67 17 21 4 494.06 0.64 68 17 24 7 422.34 18.12 69 17 69 52 135.31 21.54 70 17 115 98 93.91 0.83 71 18 77 59 88.23 1.94 72 20 23 3 523.12 1.76 73 20 24 4 518.21 0.38 74 21 24 3 522.05 2.29 75 21 25 4 516.12 0.67 76 21 66 45 153.66 13.63 77 21 69 48 151.91 14.42 78 22 25 3 521.61 1.32 79 22 26 4 519.52 2.36 80 22 62 40 177.02 2.65 81 22 66 44 154.81 13.06 82 23 26 3 521.80 1.23 83 23 27 4 519.50 2.37 84 23 118 95 167.98 0.45 85 24 27 3 521.70 1.27 86 24 28 4 512.93 0.12 87 24 69 45 160.47 11.50 88 24 118 94 167.98 0.45 89 24 119 95 169.28 0.20 90 25 28 3 519.60 3.46 91 25 29 4 517.47 1.29 92 25 65 40 160.49 11.50 93 25 69 44 160.47 11.50 94 26 29 3 521.66 0.75 95 26 30 4 517.47 1.29 96 26 56 30 213.06 0.25 97 26 62 36 180.15 3.43 98 27 30 3 523.80 1.82 99 27 31 4 517.37 1.34 100 27 114 87 170.47 0.10 101 27 118 91 170.28 0.18 102 28 31 3 523.80 1.82 103 28 32 4 517.37 1.35 104 28 69 41 178.69 2.71 105 28 107 79 171.05 0.28 106 28 110 82 170.90 0.27 107 28 111 83 170.88 0.27 108 28 114 86 170.48 0.10 109 29 32 3 524.91 0.81 110 29 33 4 510.99 1.83 111 29 43 14 269.86 3.54 112 29 61 32 203.69 2.71 113 29 64 35 183.46 1.80 114 29 65 36 180.12 3.40 115 29 68 39 180.12 3.40 116 29 107 78 171.06 0.28 117 30 33 3 530.89 2.19 118 30 34 4 513.78 3.04 119 30 52 22 239.06 0.90 120 30 55 25 238.25 1.26 121 30 56 26 238.28 1.25 122 31 34 3 523.29 1.71 123 31 35 4 509.22 5.33 124 31 110 79 170.94 0.24 125 31 113 82 170.68 0.16 126 31 114 83 170.83 0.24 127 32 35 3 521.09 2.70 128 32 36 4 486.69 3.77 129 32 39 7 345.64 1.65 130 32 106 74 171.18 0.33 131 32 107 75 171.08 0.29 132 32 110 78 170.94 0.24 133 33 37 4 414.47 13.43 134 33 39 6 348.90 0.02 135 33 40 7 301.29 1.15 136 33 43 10 293.93 4.84 137 33 55 22 239.24 0.88 138 33 61 28 239.17 0.84 139 34 37 3 517.93 0.96 140 34 51 17 240.21 1.29 141 34 52 18 240.19 1.31 142 34 55 21 240.19 1.28 143 36 39 3 532.72 3.62 144 36 106 70 171.54 0.32 145 36 109 73 171.55 0.31 146 37 40 3 533.28 3.33 147 38 41 3 525.76 0.42 148 38 103 65 171.78 0.32 149 38 106 68 171.63 0.32 150 39 42 3 536.24 0.04 151 39 43 4 530.82 2.10 152 39 103 64 171.62 0.34 153 39 106 67 171.59 0.33 154 40 43 3 531.46 2.43 155 40 46 6 386.29 23.18 156 40 47 7 293.35 8.56 157 40 49 9 293.31 8.54 158 40 55 15 241.83 0.91 159 41 47 6 299.03 5.73 160 42 97 55 172.02 0.29 161 42 98 56 172.02 0.29 162 42 99 57 172.00 0.28 163 42 100 58 172.02 0.29 164 42 103 61 171.82 0.33 165 43 46 3 528.42 0.42 166 43 47 4 463.68 18.84 167 43 64 21 241.13 0.99 168 44 47 3 533.40 2.91 169 45 48 3 597.66 0.90 170 45 60 15 241.45 1.08 171 45 64 19 241.21 0.98 172 46 49 3 535.96 4.15 173 46 60 14 241.46 1.08 174 46 61 15 241.38 1.11 175 46 64 18 241.16 1.00 176 49 54 5 467.31 5.44 177 49 55 6 416.56 14.56 178 49 58 9 286.08 3.50 179 49 61 12 261.97 0.20 180 50 54 4 505.05 1.33 181 51 54 3 522.57 3.93 182 51 55 4 509.41 3.50 183 52 55 3 512.98 1.72 184 52 56 4 503.99 0.79 185 53 56 3 514.41 0.08 186 53 57 4 500.61 0.91 187 54 57 3 510.38 2.41 188 54 58 4 500.60 0.91 189 55 58 3 520.25 2.52 190 55 61 6 433.59 4.51 191 58 61 3 514.97 3.29 192 58 62 4 499.51 0.99 193 59 62 3 506.30 0.66 194 59 63 4 499.55 0.97 195 60 63 3 517.06 2.25 196 60 64 4 513.74 3.91 197 61 64 3 513.76 3.92 198 61 65 4 513.75 3.91 199 62 65 3 513.75 3.91 200 62 66 4 513.76 3.91 201 63 66 3 513.76 3.91 202 63 67 4 511.83 2.94 203 64 67 3 511.83 2.94 204 64 68 4 503.76 1.09 205 65 68 3 515.56 1.88 206 65 69 4 503.69 1.06 207 66 69 3 517.29 1.01 208 66 70 4 506.94 0.56 209 67 70 3 522.61 0.83 210 67 71 4 510.44 1.19 211 68 71 3 518.54 2.87 212 68 72 4 513.42 0.30 213 68 107 39 171.50 0.37 214 69 72 3 518.54 2.87 215 69 73 4 511.67 1.18 216 70 73 3 512.81 1.76 217 70 74 4 512.00 1.32 218 71 74 3 525.29 2.60 219 71 75 4 511.69 1.04 220 72 75 3 514.86 2.62 221 72 76 4 511.69 1.04 222 72 111 39 171.49 0.37 223 72 135 63 169.83 0.21 224 73 76 3 514.85 2.62 225 73 77 4 511.69 1.04 226 74 77 3 518.81 0.39 227 74 78 4 513.78 0.01 228 75 78 3 520.85 0.55 229 75 79 4 519.01 2.61 230 75 82 7 234.47 15.30 231 75 85 10 222.40 14.87 232 75 86 11 194.87 1.10 233 75 89 14 194.87 1.10 234 75 138 63 168.97 0.04 235 76 79 3 522.00 1.12 236 76 131 55 170.24 0.30 237 76 134 58 169.88 0.22 238 78 81 3 515.72 4.27 239 78 82 4 402.62 14.27 240 78 85 7 443.44 10.67 241 80 83 3 667.98 3.85 242 80 137 57 170.09 0.33 243 82 85 3 521.86 1.29 244 82 86 4 521.83 1.30 245 82 137 55 170.03 0.32 246 82 141 59 168.45 0.34 247 83 86 3 526.40 0.94 248 83 87 4 528.59 2.06 249 84 87 3 534.47 0.10 250 84 88 4 531.70 0.50 251 85 88 3 559.17 1.20 252 85 89 4 523.24 0.63 253 86 89 3 523.21 0.61 254 86 90 4 509.84 0.34 255 86 138 52 169.71 0.27 256 86 141 55 167.42 0.17 257 86 142 56 166.59 0.58 258 87 90 3 524.98 1.70 259 87 91 4 509.84 0.34 260 87 145 58 163.73 0.24 261 88 91 3 515.48 0.83 262 88 92 4 510.24 0.14 263 89 92 3 519.42 2.08 264 89 93 4 500.62 2.95 265 89 138 49 169.66 0.24 266 89 142 53 166.35 0.59 267 90 93 3 518.71 2.43 268 90 94 4 490.20 2.75 269 90 142 52 166.10 0.71 270 90 145 55 155.55 0.65 271 90 146 56 154.08 1.38 272 90 149 59 141.99 0.17 273 91 94 3 521.21 1.19 274 91 95 4 482.55 6.57 275 91 149 58 141.28 5.71 276 92 96 4 448.48 6.73 277 92 97 5 403.98 12.70 278 93 97 4 362.79 7.90 279 93 98 5 317.20 2.11 280 93 99 6 317.15 2.13 281 93 146 53 151.87 0.74 282 94 98 4 317.20 2.10 283 94 146 52 151.86 0.74 284 94 149 55 138.34 1.96 285 94 151 57 71.53 5.76 286 95 98 3 520.56 0.85 287 98 151 53 75.89 4.09 288 99 103 4 498.38 0.96 289 99 104 5 495.48 2.39 290 99 146 47 151.85 0.74 291 99 151 52 75.48 4.29 292 100 103 3 522.82 2.45 293 100 104 4 512.48 2.72 294 100 151 51 73.54 5.28 295 100 153 53 15.50 0.89 296 101 104 3 519.39 0.73 297 101 105 4 509.12 4.40 298 101 139 38 167.00 0.39 299 101 142 41 165.39 0.73 300 101 143 42 160.97 0.37 301 101 146 45 151.81 0.74 302 101 153 52 15.49 0.89 303 102 105 3 513.06 2.44 304 102 106 4 509.10 4.40 305 103 106 3 514.37 1.78 306 103 107 4 516.65 0.62 307 104 107 3 517.62 0.14 308 104 108 4 516.18 0.39 309 104 139 35 166.57 0.59 310 104 142 38 163.87 0.32 311 104 146 42 151.82 0.74 312 105 108 3 516.19 0.38 313 105 109 4 516.19 0.38 314 105 139 34 166.59 0.60 315 106 109 3 526.36 2.96 316 106 110 4 516.18 0.38 317 107 110 3 523.83 4.21 318 107 111 4 514.74 0.33 319 108 111 3 519.41 6.42 320 108 112 4 510.61 1.75 321 108 135 27 169.62 0.30 322 108 139 31 166.59 0.59 323 109 112 3 518.09 1.99 324 109 113 4 505.78 4.16 325 110 113 3 524.36 1.15 326 110 114 4 512.34 0.89 327 111 114 3 524.36 1.15 328 111 115 4 512.34 0.88 329 111 135 24 169.70 0.28 330 112 115 3 525.25 3.48 331 112 116 4 505.89 2.34 332 112 123 11 236.70 14.09 333 112 128 16 169.93 0.24 334 112 131 19 169.76 0.26 335 112 132 20 169.72 0.28 336 112 135 23 169.71 0.27 337 113 116 3 521.40 5.41 338 113 117 4 513.78 1.60 339 114 117 3 524.89 3.67 340 114 118 4 505.91 2.34 341 115 118 3 521.67 0.71 342 115 119 4 503.31 1.42 343 115 123 8 260.64 2.10 344 115 131 16 198.75 4.15 345 116 120 4 490.56 4.98 346 116 123 7 260.66 2.10 347 116 128 12 201.25 3.62 348 117 120 3 547.25 1.64 349 119 122 3 520.25 0.00 350 119 123 4 441.15 19.60 351 120 123 3 504.14 1.21 352 122 127 5 466.18 7.04 353 123 127 4 471.55 4.36 354 123 128 5 468.04 6.13 355 123 131 8 452.00 0.12 356 124 127 3 511.59 4.75 357 124 128 4 483.24 0.18 358 125 128 3 518.07 1.51 359 125 129 4 507.94 6.58 360 126 129 3 513.03 2.53 361 126 130 4 505.67 1.16 362 127 130 3 509.15 0.58 363 127 131 4 508.63 0.48 364 128 131 3 508.62 0.48 365 128 132 4 508.62 0.48 366 129 132 3 509.97 1.16 367 129 133 4 499.38 4.13 368 130 133 3 508.54 0.44 369 130 134 4 505.34 1.16 370 131 134 3 508.62 0.40 371 131 135 4 505.43 1.21 372 132 135 3 519.15 3.65 373 132 136 4 505.43 1.21 374 133 136 3 507.46 2.21 375 133 137 4 505.42 1.21 376 134 137 3 515.34 0.69 377 134 138 4 507.42 2.23 378 135 138 3 510.22 0.83 379 135 139 4 507.41 2.23 380 136 139 3 505.54 1.11 381 136 140 4 505.32 1.22 382 137 140 3 505.72 1.21 383 137 141 4 505.30 1.23 384 138 141 3 524.77 3.41 385 138 142 4 509.48 0.88 386 139 142 3 509.66 0.80 387 139 143 4 509.41 0.92 388 140 143 3 509.49 0.88 389 140 144 4 511.26 0.01 390 141 144 3 514.93 1.82 391 141 145 4 509.41 0.91 392 142 145 3 511.33 0.03 393 142 146 4 503.44 0.43 394 143 146 3 506.93 2.18 395 143 147 4 510.60 4.01 396 144 147 3 515.01 1.81 397 144 148 4 514.76 1.93 398 145 148 3 505.51 1.48 399 145 149 4 494.99 4.67 400 146 149 3 506.19 3.04 401 146 150 4 490.37 2.40 402 146 151 5 391.11 12.92 403 146 153 7 249.46 0.57 404 147 150 3 503.04 3.95