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 5 498.38 0.93 2 2 10 8 489.77 4.54 3 2 130 128 51.38 1.31 4 2 133 131 28.47 2.44 5 2 134 132 28.59 2.37 6 2 137 135 28.59 2.37 7 3 6 3 522.19 1.22 8 3 7 4 519.05 0.35 9 4 7 3 522.19 1.22 10 4 8 4 519.07 0.35 11 5 8 3 525.30 2.94 12 5 9 4 522.29 1.27 13 6 9 3 526.60 0.88 14 6 10 4 515.11 1.71 15 6 130 124 71.98 0.25 16 6 133 127 71.97 0.25 17 7 10 3 518.27 3.27 18 7 11 4 515.12 1.71 19 7 76 69 72.01 0.26 20 7 79 72 72.02 0.27 21 7 80 73 72.06 0.26 22 7 134 127 72.00 0.26 23 7 137 130 72.04 0.27 24 8 11 3 524.28 0.28 25 8 12 4 515.14 1.70 26 9 12 3 515.16 1.70 27 9 13 4 515.15 1.70 28 9 126 117 81.84 0.32 29 9 127 118 80.40 0.07 30 9 130 121 80.36 0.07 31 10 13 3 521.00 0.65 32 10 14 4 515.92 2.08 33 10 76 66 77.98 1.13 34 10 130 120 80.39 0.07 35 10 131 121 77.96 1.12 36 10 134 124 77.86 1.17 37 11 14 3 519.95 0.07 38 11 15 4 515.93 2.08 39 11 76 65 78.03 1.11 40 11 77 66 78.21 1.01 41 12 15 3 521.88 0.89 42 13 16 3 526.60 2.16 43 13 17 4 517.10 2.59 44 13 115 102 88.56 2.29 45 13 123 110 87.60 2.77 46 13 127 114 84.80 1.40 47 13 131 118 84.67 1.43 48 14 17 3 524.75 3.08 49 14 18 4 508.20 1.85 50 14 69 55 192.99 6.04 51 14 72 58 132.78 22.62 52 14 73 59 84.69 1.43 53 14 76 62 84.69 1.43 54 14 131 117 84.77 1.39 55 15 18 3 515.26 1.67 56 15 19 4 515.26 1.67 57 16 19 3 522.41 0.91 58 16 24 8 460.44 7.85 59 16 119 103 107.95 0.16 60 17 20 3 525.51 0.15 61 17 21 4 492.74 2.87 62 17 24 7 460.42 7.86 63 17 69 52 209.72 2.08 64 17 115 98 104.92 1.35 65 18 21 3 508.82 0.90 66 18 77 59 174.51 1.85 67 20 23 3 534.15 2.34 68 20 24 4 515.66 2.73 69 21 24 3 521.89 0.02 70 21 25 4 514.26 2.02 71 21 66 45 212.19 2.17 72 21 69 48 211.03 1.86 73 21 70 49 209.98 2.20 74 22 25 3 519.17 0.43 75 22 26 4 514.25 2.02 76 22 62 40 213.68 1.60 77 22 66 44 212.19 2.17 78 23 26 3 529.21 5.05 79 23 27 4 514.64 2.23 80 23 62 39 213.87 1.66 81 24 27 3 523.21 2.05 82 24 28 4 519.52 0.20 83 24 69 45 212.95 1.78 84 24 114 90 167.36 1.17 85 24 115 91 167.35 1.17 86 24 118 94 166.24 1.61 87 24 119 95 166.22 1.61 88 25 28 3 519.52 0.20 89 25 29 4 519.52 0.20 90 25 65 40 213.08 1.73 91 25 69 44 212.96 1.79 92 26 29 3 532.85 2.02 93 26 30 4 519.57 0.22 94 26 56 30 230.05 0.29 95 26 61 35 213.88 1.65 96 26 62 36 213.88 1.65 97 26 65 39 213.61 1.69 98 27 30 3 523.97 2.42 99 27 31 4 519.33 3.06 100 27 114 87 167.55 1.26 101 27 118 91 166.77 1.36 102 28 31 3 523.14 1.16 103 28 32 4 517.19 1.41 104 28 69 41 213.49 1.63 105 28 107 79 168.25 1.10 106 28 110 82 167.84 1.28 107 28 111 83 167.74 1.28 108 28 114 86 167.59 1.26 109 29 32 3 520.72 0.82 110 29 33 4 517.17 1.41 111 29 61 32 213.97 1.65 112 29 64 35 213.93 1.65 113 29 65 36 213.81 1.62 114 29 107 78 168.33 1.10 115 30 33 3 518.62 0.69 116 30 34 4 503.78 1.32 117 30 52 22 234.11 0.36 118 30 55 25 234.02 0.35 119 30 56 26 234.05 0.37 120 30 61 31 214.67 1.33 121 31 34 3 520.26 1.04 122 31 35 4 509.65 1.62 123 31 110 79 168.21 1.11 124 31 113 82 168.16 1.12 125 31 114 83 168.10 1.09 126 32 35 3 520.52 1.88 127 32 36 4 504.12 1.14 128 32 39 7 436.88 3.23 129 32 106 74 168.37 1.08 130 32 107 75 168.36 1.09 131 32 110 78 168.22 1.11 132 33 36 3 519.53 2.37 133 33 37 4 459.78 5.13 134 33 39 6 369.44 30.50 135 33 40 7 275.31 1.93 136 33 43 10 275.29 1.93 137 33 46 13 264.75 3.22 138 33 55 22 234.35 0.34 139 33 61 28 234.13 0.36 140 34 52 18 234.25 0.40 141 34 55 21 234.38 0.33 142 36 39 3 534.35 2.48 143 36 106 70 168.72 0.99 144 36 109 73 168.71 0.96 145 37 40 3 535.40 1.96 146 38 41 3 535.40 1.96 147 38 103 65 169.23 1.11 148 38 106 68 169.09 1.07 149 39 42 3 541.52 1.26 150 39 103 64 169.01 1.05 151 39 106 67 169.00 1.06 152 40 43 3 529.49 0.81 153 40 46 6 304.31 1.40 154 40 49 9 266.63 1.81 155 40 55 15 242.06 1.53 156 41 47 6 333.94 28.57 157 42 97 55 169.58 0.99 158 42 98 56 169.58 0.99 159 42 99 57 169.50 1.01 160 42 100 58 169.54 1.02 161 42 103 61 169.39 1.03 162 43 46 3 527.99 0.42 163 43 47 4 526.97 0.94 164 44 47 3 555.15 0.12 165 45 48 3 608.76 1.79 166 45 60 15 236.32 1.31 167 45 64 19 236.31 1.31 168 46 49 3 537.28 0.94 169 46 60 14 236.33 1.32 170 46 61 15 236.32 1.31 171 46 64 18 236.31 1.32 172 47 50 3 590.08 1.42 173 48 54 6 501.44 2.23 174 49 54 5 493.43 1.77 175 49 55 6 460.31 18.32 176 49 58 9 318.20 1.37 177 49 61 12 288.04 2.19 178 50 54 4 524.32 6.14 179 51 54 3 525.60 5.50 180 51 55 4 523.98 6.31 181 52 55 3 525.60 5.50 182 52 56 4 523.99 6.30 183 53 56 3 529.01 3.79 184 53 57 4 523.98 6.30 185 54 57 3 519.12 3.50 186 54 58 4 509.58 0.00 187 55 58 3 520.60 2.76 188 55 61 6 478.78 5.78 189 58 61 3 526.05 2.38 190 58 62 4 516.28 0.18 191 59 62 3 525.83 2.27 192 59 63 4 516.31 0.17 193 60 63 3 516.46 0.10 194 60 64 4 516.27 0.17 195 61 64 3 522.98 3.35 196 61 65 4 511.32 2.32 197 62 65 3 522.83 3.44 198 62 66 4 511.32 2.32 199 63 66 3 516.26 0.15 200 63 67 4 512.33 1.81 201 64 67 3 521.37 3.10 202 64 68 4 521.34 3.15 203 65 68 3 521.41 3.12 204 65 69 4 517.72 4.96 205 66 69 3 524.91 1.40 206 66 70 4 516.09 5.78 207 67 70 3 526.00 0.83 208 67 71 4 526.00 0.83 209 68 71 3 526.02 0.84 210 68 72 4 517.88 3.23 211 68 107 39 168.25 1.10 212 69 72 3 517.89 3.23 213 69 73 4 508.30 1.55 214 69 111 42 167.66 1.27 215 70 73 3 525.43 1.05 216 70 74 4 510.08 2.25 217 71 74 3 511.19 2.79 218 71 75 4 510.10 2.25 219 71 89 18 170.00 0.76 220 72 75 3 528.44 4.76 221 72 76 4 519.04 0.05 222 72 111 39 167.72 1.29 223 72 135 63 157.82 0.04 224 72 138 66 156.24 0.13 225 73 76 3 522.66 1.76 226 73 77 4 524.61 2.77 227 74 77 3 524.65 2.75 228 74 78 4 524.64 2.75 229 75 78 3 527.75 1.20 230 75 79 4 522.66 1.76 231 75 82 7 256.10 4.53 232 75 85 10 170.36 0.70 233 75 86 11 170.34 0.70 234 75 89 14 170.34 0.70 235 75 138 63 156.88 0.20 236 76 79 3 527.25 1.45 237 76 134 58 157.87 0.05 238 78 81 3 513.86 2.58 239 78 82 4 335.60 5.18 240 78 85 7 302.82 5.17 241 80 137 57 157.89 0.04 242 82 85 3 516.67 2.94 243 82 86 4 511.14 4.07 244 82 137 55 157.90 0.04 245 82 141 59 156.85 0.20 246 83 86 3 524.44 2.58 247 83 87 4 513.21 3.03 248 84 88 4 531.71 1.06 249 85 88 3 556.57 2.60 250 85 89 4 530.54 1.65 251 86 89 3 525.75 0.74 252 86 90 4 524.59 1.29 253 86 138 52 157.30 0.17 254 86 141 55 154.51 0.92 255 86 142 56 153.58 0.62 256 87 90 3 524.47 1.36 257 87 91 4 512.60 0.79 258 87 145 58 147.45 1.21 259 88 91 3 516.74 3.61 260 88 92 4 507.60 0.18 261 89 92 3 531.03 3.53 262 89 93 4 506.92 0.52 263 89 138 49 157.72 0.03 264 89 142 53 153.51 0.66 265 90 93 3 516.85 1.37 266 90 94 4 506.88 0.52 267 90 142 52 151.69 0.18 268 90 145 55 146.34 1.04 269 90 146 56 146.27 1.03 270 91 94 3 522.26 1.34 271 91 95 4 506.86 0.52 272 91 149 58 140.05 0.11 273 92 95 3 521.35 1.80 274 92 96 4 475.88 9.53 275 92 97 5 463.72 8.78 276 93 97 4 407.25 12.67 277 93 98 5 402.98 10.54 278 93 99 6 303.32 7.38 279 93 142 49 151.78 0.17 280 93 146 53 142.44 0.91 281 94 146 52 142.43 0.91 282 94 149 55 137.47 1.18 283 94 151 57 117.21 1.51 284 95 98 3 530.17 1.94 285 95 149 54 141.62 0.83 286 95 151 56 127.63 0.35 287 99 103 4 519.25 0.40 288 99 104 5 513.43 2.51 289 99 146 47 142.74 0.74 290 100 103 3 530.80 4.99 291 100 104 4 525.10 2.54 292 101 104 3 525.11 2.53 293 101 105 4 524.82 2.68 294 101 143 42 148.91 0.36 295 101 146 45 142.32 0.85 296 101 153 52 26.62 2.71 297 102 105 3 525.10 2.54 298 102 106 4 522.59 1.27 299 103 106 3 520.71 2.21 300 103 107 4 518.83 3.15 301 104 107 3 527.21 1.04 302 104 108 4 515.54 1.51 303 104 139 35 155.02 0.72 304 104 142 38 149.72 0.74 305 105 108 3 524.70 0.21 306 105 109 4 516.87 0.85 307 105 139 34 155.05 0.71 308 106 109 3 516.88 0.84 309 106 110 4 516.88 0.84 310 107 110 3 516.88 0.84 311 107 111 4 516.88 0.84 312 108 111 3 527.73 4.58 313 108 112 4 516.70 1.61 314 108 135 27 157.62 0.06 315 108 139 31 155.02 0.72 316 109 112 3 527.36 1.77 317 109 113 4 514.32 0.43 318 110 113 3 516.00 0.48 319 110 114 4 513.33 5.98 320 111 114 3 521.12 2.08 321 111 115 4 518.83 3.23 322 111 135 24 157.71 0.10 323 112 115 3 524.56 0.37 324 112 116 4 513.34 5.98 325 112 123 11 286.35 7.52 326 112 131 19 157.84 0.04 327 112 132 20 157.81 0.04 328 112 135 23 157.81 0.04 329 113 116 3 521.71 1.80 330 113 117 4 513.35 5.98 331 114 117 3 528.96 1.82 332 114 118 4 513.36 5.98 333 115 118 3 528.76 1.73 334 115 119 4 503.31 0.97 335 115 123 8 289.63 5.88 336 115 131 16 157.85 0.04 337 116 119 3 522.36 1.44 338 116 120 4 472.85 13.95 339 116 123 7 289.63 5.88 340 116 128 12 238.03 9.71 341 117 120 3 533.21 3.99 342 119 122 3 518.74 0.61 343 119 123 4 464.63 14.61 344 120 123 3 519.84 0.27 345 122 127 5 492.13 4.22 346 123 127 4 492.13 4.22 347 123 128 5 492.07 4.25 348 123 131 8 450.20 6.29 349 124 127 3 530.63 2.43 350 124 128 4 511.36 2.94 351 125 128 3 519.96 3.34 352 125 129 4 511.97 2.65 353 126 129 3 515.42 1.68 354 126 130 4 515.43 1.68 355 127 130 3 525.10 2.89 356 127 131 4 515.42 1.68 357 128 131 3 520.46 0.83 358 128 132 4 512.12 3.33 359 129 132 3 524.37 1.12 360 129 133 4 512.12 3.33 361 130 133 3 520.58 0.89 362 130 134 4 510.11 3.62 363 131 134 3 512.57 3.12 364 131 135 4 502.12 8.36 365 132 135 3 516.30 1.27 366 132 136 4 510.42 4.21 367 133 136 3 512.62 3.11 368 133 137 4 510.43 4.21 369 134 137 3 512.39 3.23 370 134 138 4 512.40 3.22 371 135 138 3 514.20 7.00 372 135 139 4 501.73 2.12 373 136 139 3 514.49 6.86 374 136 140 4 495.92 2.15 375 137 140 3 522.38 2.91 376 137 141 4 494.64 1.46 377 138 141 3 523.85 3.64 378 138 142 4 502.01 2.23 379 139 142 3 524.64 3.23 380 139 143 4 502.01 2.23 381 140 143 3 512.32 2.93 382 140 144 4 503.31 1.57 383 141 144 3 512.32 2.93 384 141 145 4 510.98 1.35 385 142 145 3 527.98 2.71 386 142 146 4 510.98 1.35 387 143 146 3 525.13 5.72 388 143 147 4 515.41 3.56 389 143 153 10 20.62 4.75 390 144 147 3 520.94 0.81 391 144 148 4 510.34 6.11 392 145 148 3 522.42 4.38 393 145 149 4 516.49 1.42 394 146 149 3 516.61 1.36 395 146 150 4 514.77 2.27 396 146 151 5 416.50 3.42 397 146 152 6 415.83 3.08 398 146 153 7 255.47 6.17 399 147 150 3 510.15 0.80 400 147 151 4 466.54 2.58 401 147 153 6 305.02 15.90