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 5 496.82 1.85 2 2 10 8 480.05 3.68 3 2 130 128 39.94 0.52 4 2 133 131 36.02 0.69 5 2 134 132 34.46 0.28 6 2 137 135 32.70 0.45 7 3 6 3 508.11 3.48 8 3 7 4 507.71 3.48 9 4 7 3 517.07 0.72 10 4 8 4 507.71 3.48 11 5 8 3 515.69 0.51 12 5 9 4 501.99 0.57 13 6 9 3 518.32 0.11 14 6 10 4 502.00 0.56 15 6 130 124 67.04 1.92 16 6 133 127 67.05 1.92 17 7 10 3 518.62 1.50 18 7 11 4 513.01 1.31 19 7 76 69 67.06 1.93 20 7 79 72 67.06 1.93 21 7 80 73 67.06 1.93 22 7 134 127 67.06 1.92 23 7 137 130 67.06 1.92 24 8 11 3 520.11 1.01 25 8 12 4 515.79 0.02 26 9 12 3 516.97 0.56 27 9 13 4 515.87 0.01 28 9 126 117 80.14 0.99 29 9 127 118 80.09 0.98 30 9 130 121 80.09 0.98 31 10 13 3 524.12 1.33 32 10 14 4 515.88 0.01 33 10 76 66 80.03 0.97 34 10 130 120 80.09 0.98 35 10 131 121 80.06 0.97 36 10 134 124 80.03 0.97 37 11 14 3 520.11 2.12 38 11 15 4 515.88 0.01 39 11 76 65 80.06 0.97 40 11 77 66 80.06 0.97 41 11 79 68 80.06 0.97 42 12 15 3 527.72 2.65 43 13 16 3 522.43 0.00 44 13 17 4 519.06 1.68 45 13 115 102 94.79 0.58 46 13 119 106 96.20 0.70 47 13 122 109 95.89 0.57 48 13 123 110 95.20 0.42 49 13 131 118 94.66 0.62 50 14 17 3 515.96 0.13 51 14 18 4 515.95 0.14 52 14 69 55 95.25 0.42 53 14 72 58 94.79 0.59 54 14 73 59 94.72 0.62 55 14 76 62 94.68 0.64 56 14 77 63 94.72 0.62 57 14 131 117 94.87 0.56 58 15 18 3 520.48 3.92 59 16 19 3 533.59 0.10 60 16 24 8 428.27 3.08 61 16 119 103 100.13 0.35 62 16 122 106 98.95 0.23 63 17 20 3 528.10 0.10 64 17 21 4 486.62 0.64 65 17 24 7 391.39 15.35 66 17 69 52 98.59 0.07 67 17 115 98 98.95 0.23 68 18 21 3 525.14 1.58 69 18 77 59 98.41 0.27 70 20 23 3 519.23 1.73 71 20 24 4 503.77 0.18 72 21 24 3 519.11 1.67 73 21 25 4 509.90 3.24 74 21 66 45 130.22 2.12 75 21 69 48 123.52 0.72 76 21 70 49 123.51 0.73 77 22 25 3 519.41 1.52 78 22 26 4 519.36 1.49 79 22 62 40 137.25 0.35 80 22 66 44 130.22 2.12 81 23 26 3 521.76 0.32 82 23 27 4 519.38 1.50 83 23 62 39 140.50 0.38 84 24 27 3 519.39 1.50 85 24 28 4 519.38 1.50 86 24 69 45 137.56 0.21 87 24 118 94 154.65 0.53 88 24 119 95 154.73 0.49 89 25 28 3 521.72 2.71 90 25 29 4 514.35 4.02 91 25 65 40 137.60 0.21 92 25 69 44 137.58 0.20 93 26 29 3 524.38 0.07 94 26 30 4 514.34 4.01 95 26 61 35 153.88 0.54 96 26 62 36 153.09 0.14 97 26 65 39 149.90 1.43 98 27 30 3 528.14 1.82 99 27 31 4 510.34 2.93 100 27 114 87 157.20 0.09 101 27 118 91 157.91 0.40 102 28 31 3 519.96 2.26 103 28 32 4 509.95 2.74 104 28 69 41 154.63 0.53 105 28 107 79 154.63 0.53 106 28 110 82 154.64 0.53 107 28 111 83 154.70 0.56 108 28 114 86 157.24 0.10 109 29 32 3 520.42 2.48 110 29 33 4 509.99 2.76 111 29 61 32 158.18 0.42 112 29 64 35 158.03 0.49 113 29 65 36 157.62 0.29 114 29 107 78 156.41 0.30 115 30 33 3 525.54 0.07 116 30 34 4 509.97 2.77 117 30 52 22 158.70 0.34 118 30 55 25 158.50 0.34 119 30 56 26 158.57 0.38 120 30 61 31 158.30 0.36 121 31 34 3 527.29 0.48 122 31 35 4 514.42 5.86 123 31 110 79 157.97 0.35 124 31 113 82 158.14 0.29 125 31 114 83 158.15 0.29 126 31 117 86 158.43 0.29 127 32 35 3 525.88 0.23 128 32 36 4 513.78 6.19 129 32 39 7 397.10 1.19 130 32 106 74 157.97 0.35 131 32 107 75 157.97 0.35 132 32 110 78 158.03 0.34 133 33 36 3 525.40 0.47 134 33 37 4 490.20 0.38 135 33 39 6 412.11 8.68 136 33 40 7 326.28 0.34 137 33 43 10 303.50 1.82 138 33 46 13 226.33 29.07 139 33 55 22 158.71 0.33 140 33 61 28 158.67 0.35 141 34 37 3 526.79 0.72 142 34 52 18 158.83 0.34 143 36 39 3 534.49 3.25 144 36 106 70 158.02 0.33 145 37 40 3 530.73 1.38 146 38 41 3 535.79 1.16 147 38 103 65 158.06 0.33 148 38 106 68 158.23 0.30 149 39 42 3 540.17 1.04 150 39 43 4 531.35 1.06 151 39 103 64 158.00 0.34 152 39 106 67 158.19 0.29 153 40 43 3 551.06 4.41 154 40 46 6 420.70 14.74 155 40 47 7 220.03 25.80 156 40 49 9 217.22 24.41 157 40 55 15 160.27 0.26 158 41 47 6 347.95 21.63 159 42 97 55 158.06 0.32 160 42 98 56 158.07 0.31 161 42 99 57 158.06 0.30 162 42 103 61 158.22 0.29 163 43 46 3 535.77 2.83 164 43 47 4 463.75 1.48 165 43 64 21 158.97 0.39 166 44 47 3 535.20 3.12 167 45 48 3 625.31 3.85 168 45 60 15 160.12 0.28 169 45 64 19 160.11 0.28 170 46 49 3 532.00 0.61 171 46 60 14 160.12 0.28 172 46 61 15 160.06 0.29 173 46 64 18 160.09 0.27 174 49 54 5 438.93 14.05 175 49 55 6 362.98 1.57 176 49 58 9 301.87 5.59 177 50 54 4 513.66 4.59 178 51 54 3 513.66 4.58 179 51 55 4 513.66 4.58 180 52 55 3 514.42 4.20 181 52 56 4 499.92 2.30 182 53 56 3 519.49 7.46 183 53 57 4 499.94 2.31 184 54 57 3 519.49 7.46 185 54 58 4 504.14 0.21 186 55 58 3 521.32 6.55 187 55 61 6 464.43 0.77 188 58 61 3 517.14 1.37 189 58 62 4 510.53 1.94 190 59 62 3 524.35 4.97 191 59 63 4 510.12 2.14 192 60 63 3 517.92 1.76 193 60 64 4 513.38 0.50 194 61 64 3 527.77 1.25 195 61 65 4 510.49 0.95 196 62 65 3 514.60 1.10 197 62 66 4 519.15 3.39 198 63 66 3 523.67 1.14 199 63 67 4 519.16 3.39 200 64 67 3 533.75 3.91 201 64 68 4 519.13 3.40 202 65 68 3 523.57 1.20 203 65 69 4 519.12 3.39 204 66 69 3 530.46 2.60 205 66 70 4 509.10 1.62 206 67 70 3 530.45 2.59 207 67 71 4 521.65 2.09 208 68 71 3 525.86 0.00 209 68 72 4 521.67 2.08 210 68 107 39 161.16 0.54 211 69 72 3 521.67 2.08 212 69 73 4 511.71 2.90 213 69 111 42 162.09 0.54 214 70 73 3 523.36 1.93 215 70 74 4 512.12 0.01 216 71 74 3 519.43 0.04 217 71 75 4 518.93 3.74 218 72 75 3 518.97 3.73 219 72 76 4 515.21 1.55 220 72 111 39 186.69 4.50 221 72 135 63 169.44 3.94 222 73 76 3 525.07 3.38 223 73 77 4 512.42 2.94 224 74 77 3 525.11 3.36 225 74 78 4 515.50 4.46 226 75 78 3 528.34 1.74 227 75 82 7 216.06 27.41 228 75 85 10 168.77 4.21 229 75 89 14 169.25 4.02 230 75 138 63 169.44 3.94 231 76 79 3 534.94 1.66 232 76 131 55 218.62 11.27 233 76 134 58 189.31 5.25 234 78 81 3 509.72 4.30 235 78 82 4 385.13 24.38 236 78 85 7 321.09 12.79 237 80 137 57 247.21 1.36 238 82 85 3 524.58 0.10 239 82 86 4 505.28 0.60 240 82 137 55 259.41 3.87 241 82 141 59 256.48 2.46 242 83 86 3 530.39 0.52 243 83 87 4 512.82 3.17 244 83 145 62 256.50 2.48 245 84 88 4 530.39 0.52 246 85 88 3 552.96 0.84 247 85 89 4 525.35 3.04 248 86 89 3 528.11 0.62 249 86 90 4 521.19 2.58 250 86 138 52 260.29 4.06 251 86 141 55 260.25 4.05 252 86 142 56 260.25 4.05 253 86 145 59 260.25 4.05 254 87 90 3 523.07 1.90 255 87 91 4 517.60 0.80 256 87 145 58 260.25 4.05 257 88 91 3 522.01 2.43 258 88 92 4 517.99 1.04 259 89 92 3 524.09 1.15 260 89 93 4 510.62 0.62 261 89 138 49 260.48 4.04 262 89 142 53 260.34 4.07 263 90 93 3 528.72 4.73 264 90 94 4 510.60 0.61 265 90 142 52 260.33 4.07 266 90 145 55 260.28 4.07 267 90 146 56 260.27 4.06 268 90 149 59 259.40 3.96 269 91 94 3 523.71 3.35 270 91 95 4 510.39 0.70 271 91 149 58 259.40 3.96 272 92 95 3 526.31 3.13 273 92 96 4 472.85 7.11 274 92 97 5 452.55 3.01 275 93 97 4 416.09 6.38 276 93 98 5 363.81 19.75 277 93 99 6 352.67 25.31 278 93 142 49 260.48 4.04 279 93 146 53 260.36 4.07 280 94 98 4 367.34 17.98 281 94 146 52 260.32 4.08 282 94 149 55 259.56 3.88 283 94 151 57 257.04 3.75 284 95 98 3 523.56 2.06 285 98 151 53 257.92 3.44 286 99 103 4 506.51 0.59 287 99 104 5 496.14 5.78 288 99 146 47 260.86 3.90 289 99 151 52 257.83 3.38 290 100 103 3 524.75 4.08 291 100 104 4 506.54 0.59 292 100 151 51 257.72 3.44 293 100 153 53 217.47 12.39 294 101 104 3 514.49 4.58 295 101 105 4 514.50 4.58 296 101 143 42 260.88 3.91 297 101 146 45 261.01 3.83 298 101 153 52 208.68 8.07 299 102 105 3 518.15 2.76 300 102 106 4 514.50 4.59 301 103 106 3 514.50 4.59 302 103 107 4 514.49 4.59 303 104 107 3 515.12 4.28 304 104 108 4 505.47 9.11 305 104 139 35 261.49 3.89 306 104 142 38 261.42 3.93 307 104 146 42 261.37 3.94 308 105 108 3 511.03 0.88 309 105 109 4 506.72 5.24 310 105 139 34 261.57 3.88 311 106 109 3 514.99 1.10 312 106 110 4 506.72 5.24 313 107 110 3 506.73 5.23 314 107 111 4 514.97 1.12 315 108 111 3 518.24 2.75 316 108 112 4 518.24 2.75 317 108 135 27 261.95 3.85 318 108 139 31 261.79 3.85 319 109 112 3 518.24 2.75 320 109 113 4 518.24 2.75 321 110 113 3 518.69 2.97 322 110 114 4 523.90 0.08 323 111 114 3 533.16 1.27 324 111 115 4 523.90 0.08 325 111 135 24 262.31 3.90 326 112 115 3 523.90 0.08 327 112 116 4 515.50 4.28 328 112 123 11 265.22 4.49 329 112 131 19 262.51 3.95 330 112 132 20 262.40 3.90 331 112 135 23 262.38 3.91 332 113 116 3 521.37 1.34 333 113 117 4 515.50 4.28 334 114 117 3 531.78 0.55 335 114 118 4 498.21 0.67 336 115 118 3 535.33 1.23 337 115 119 4 481.93 0.10 338 115 123 8 284.30 3.34 339 115 131 16 264.52 4.29 340 116 120 4 445.44 6.73 341 116 123 7 284.30 3.34 342 116 128 12 264.71 4.27 343 117 120 3 539.80 0.73 344 119 122 3 515.06 2.13 345 119 123 4 432.25 19.11 346 120 123 3 476.91 1.05 347 123 127 4 482.61 0.77 348 123 128 5 482.61 0.77 349 123 131 8 417.31 0.40 350 124 127 3 513.28 3.00 351 124 128 4 508.56 0.66 352 125 128 3 513.48 3.10 353 125 129 4 508.57 0.66 354 126 129 3 518.22 1.79 355 126 130 4 512.26 1.19 356 127 130 3 509.87 3.09 357 127 131 4 506.01 1.93 358 128 131 3 524.29 3.42 359 128 132 4 509.81 3.83 360 129 132 3 517.84 0.18 361 129 133 4 510.41 6.42 362 130 133 3 520.73 1.26 363 130 134 4 509.43 6.91 364 131 134 3 520.72 1.26 365 131 135 4 509.08 1.34 366 132 135 3 524.32 0.54 367 132 136 4 503.72 4.04 368 133 136 3 517.71 2.83 369 133 137 4 503.69 4.06 370 134 137 3 514.88 1.53 371 134 138 4 512.47 0.32 372 135 138 3 513.01 0.06 373 135 139 4 512.46 0.33 374 136 139 3 513.29 0.18 375 136 140 4 513.01 0.05 376 137 140 3 511.09 0.92 377 137 141 4 495.85 8.54 378 138 141 3 511.06 0.93 379 138 142 4 495.87 8.53 380 139 142 3 504.18 3.37 381 139 143 4 487.19 3.54 382 140 143 3 514.76 0.99 383 140 144 4 496.05 7.98 384 141 144 3 518.16 3.08 385 141 145 4 514.83 1.42 386 142 145 3 527.12 1.40 387 142 146 4 507.25 1.89 388 143 146 3 527.12 1.40 389 143 147 4 507.30 1.86 390 144 147 3 526.59 1.66 391 144 148 4 514.49 1.59 392 145 148 3 522.60 0.33 393 145 149 4 507.28 1.85 394 146 149 3 501.98 3.60 395 146 150 4 499.17 2.20 396 146 151 5 365.11 11.47 397 146 153 7 257.51 8.20 398 147 150 3 499.16 2.19