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 5 501.09 2.06 2 2 130 128 39.74 0.69 3 2 133 131 35.19 0.24 4 2 134 132 33.84 0.34 5 2 137 135 31.90 0.63 6 3 6 3 526.68 0.29 7 3 7 4 520.16 2.16 8 4 7 3 520.19 2.15 9 4 8 4 514.19 0.83 10 4 79 75 57.72 0.55 11 5 8 3 514.19 0.83 12 5 9 4 514.19 0.83 13 6 9 3 526.37 1.31 14 6 10 4 514.17 0.84 15 6 130 124 69.12 1.67 16 6 133 127 69.11 1.66 17 7 10 3 526.32 1.29 18 7 11 4 514.50 4.62 19 7 76 69 69.16 1.67 20 7 79 72 69.16 1.67 21 7 80 73 69.17 1.67 22 7 134 127 69.16 1.67 23 7 137 130 69.16 1.67 24 8 11 3 519.32 3.39 25 8 12 4 510.63 0.96 26 8 79 71 76.91 0.67 27 9 12 3 519.33 3.39 28 9 13 4 524.06 0.89 29 9 126 117 78.55 0.10 30 9 127 118 77.48 0.47 31 9 130 121 77.45 0.47 32 10 13 3 526.83 2.10 33 10 14 4 512.54 1.61 34 10 76 66 77.59 0.53 35 10 130 120 77.53 0.49 36 10 131 121 77.45 0.48 37 10 134 124 77.44 0.48 38 11 14 3 515.83 3.25 39 11 15 4 512.54 1.61 40 11 76 65 77.73 0.52 41 11 77 66 77.74 0.53 42 12 15 3 520.94 2.73 43 12 16 4 514.85 0.30 44 12 122 110 87.67 2.56 45 13 16 3 517.04 0.80 46 13 17 4 505.96 0.67 47 13 115 102 87.72 2.52 48 13 119 106 87.92 2.46 49 13 122 109 87.67 2.56 50 13 123 110 87.05 2.88 51 13 131 118 85.75 3.03 52 14 17 3 504.62 0.01 53 14 18 4 504.54 0.04 54 14 69 55 129.69 24.27 55 14 72 58 129.67 24.27 56 14 73 59 86.03 3.15 57 14 76 62 86.05 3.16 58 14 131 117 86.88 2.91 59 15 18 3 518.50 5.21 60 16 19 3 529.21 0.14 61 16 119 103 97.75 1.26 62 16 122 106 93.66 0.79 63 17 20 3 529.52 0.01 64 17 21 4 488.79 0.81 65 17 24 7 339.14 1.24 66 17 69 52 181.67 1.64 67 17 115 98 96.89 1.69 68 17 119 102 107.29 2.69 69 18 77 59 88.33 2.56 70 20 23 3 519.78 3.43 71 20 24 4 510.61 3.43 72 20 118 98 154.55 0.64 73 21 24 3 523.74 1.45 74 21 25 4 512.28 4.26 75 21 66 45 186.27 2.67 76 21 69 48 186.17 2.69 77 22 25 3 519.16 0.83 78 22 26 4 519.16 0.83 79 22 62 40 189.68 3.58 80 22 66 44 186.28 2.68 81 23 26 3 521.79 1.22 82 23 27 4 518.87 0.60 83 23 118 95 161.37 0.39 84 24 27 3 523.67 1.43 85 24 28 4 511.50 1.64 86 24 69 45 186.44 2.75 87 24 115 91 161.78 0.24 88 24 118 94 161.37 0.39 89 24 119 95 161.36 0.41 90 25 28 3 523.32 1.60 91 25 29 4 517.49 1.30 92 25 65 40 188.81 3.77 93 25 69 44 186.44 2.74 94 26 29 3 526.00 0.29 95 26 30 4 517.49 1.30 96 26 56 30 219.07 1.43 97 26 62 36 190.30 3.31 98 27 30 3 524.16 1.64 99 27 31 4 517.42 1.31 100 27 114 87 161.80 0.24 101 27 118 91 161.42 0.42 102 28 31 3 526.99 0.23 103 28 32 4 517.47 1.29 104 28 69 41 189.83 3.58 105 28 107 79 162.66 0.14 106 28 110 82 162.53 0.14 107 28 111 83 162.47 0.17 108 28 114 86 161.81 0.23 109 29 32 3 524.91 0.81 110 29 33 4 512.31 1.21 111 29 43 14 282.06 2.58 112 29 61 32 197.75 4.57 113 29 65 36 189.91 3.56 114 29 68 39 189.90 3.56 115 29 107 78 162.68 0.13 116 30 33 3 524.90 0.81 117 30 34 4 521.59 0.85 118 30 52 22 220.47 1.19 119 30 55 25 220.42 1.20 120 30 56 26 220.43 1.21 121 31 34 3 524.90 0.81 122 31 35 4 521.58 0.85 123 31 110 79 162.54 0.14 124 31 113 82 162.49 0.12 125 31 114 83 162.49 0.12 126 32 35 3 522.88 1.80 127 32 36 4 502.37 1.19 128 32 39 7 385.03 1.47 129 32 106 74 162.74 0.13 130 32 107 75 162.72 0.12 131 32 110 78 162.55 0.13 132 33 36 3 517.35 0.79 133 33 37 4 477.88 8.18 134 33 39 6 365.47 8.31 135 33 40 7 327.09 0.99 136 33 43 10 324.28 0.37 137 33 55 22 232.27 3.06 138 33 61 28 228.29 4.75 139 34 37 3 523.52 2.31 140 34 52 18 233.28 2.58 141 36 39 3 532.72 3.62 142 36 106 70 163.17 0.22 143 36 109 73 163.13 0.23 144 37 40 3 532.29 2.84 145 38 41 3 525.76 0.42 146 38 103 65 163.43 0.15 147 39 42 3 535.60 0.29 148 39 43 4 530.82 2.10 149 39 103 64 163.24 0.21 150 39 106 67 163.19 0.22 151 40 43 3 531.46 2.43 152 40 46 6 330.57 0.07 153 40 47 7 276.10 0.30 154 40 49 9 266.38 3.54 155 40 55 15 240.24 2.59 156 42 97 55 164.18 0.27 157 42 98 56 164.18 0.28 158 42 99 57 164.00 0.34 159 42 100 58 164.12 0.30 160 42 103 61 163.88 0.33 161 43 46 3 528.42 0.42 162 43 47 4 459.91 16.96 163 43 64 21 235.62 2.81 164 44 47 3 529.79 1.10 165 45 48 3 597.66 0.90 166 45 60 15 235.84 2.78 167 45 64 19 235.81 2.77 168 46 49 3 535.25 4.50 169 46 60 14 235.84 2.79 170 46 61 15 235.83 2.79 171 46 64 18 235.80 2.79 172 49 54 5 450.08 8.70 173 49 55 6 380.08 23.21 174 49 58 9 292.25 0.42 175 49 61 12 280.29 2.94 176 50 54 4 500.31 1.03 177 51 54 3 523.41 3.51 178 51 55 4 515.01 0.69 179 52 55 3 515.02 0.69 180 52 56 4 503.70 0.67 181 53 56 3 514.41 0.08 182 53 57 4 503.70 0.67 183 54 57 3 514.89 0.16 184 54 58 4 503.68 0.68 185 55 58 3 526.35 3.25 186 55 61 6 428.57 8.89 187 58 61 3 521.69 0.07 188 58 62 4 516.23 1.83 189 59 62 3 517.41 2.07 190 59 63 4 513.28 0.36 191 60 63 3 518.53 1.51 192 60 64 4 517.06 2.25 193 61 64 3 523.24 2.30 194 61 65 4 513.74 3.91 195 62 65 3 516.87 2.35 196 62 66 4 514.94 1.39 197 63 66 3 517.04 2.27 198 63 67 4 511.84 2.94 199 64 67 3 514.94 1.38 200 64 68 4 510.07 2.02 201 65 68 3 519.00 0.15 202 65 69 4 510.08 2.02 203 66 69 3 515.64 0.18 204 66 70 4 509.97 1.96 205 67 70 3 522.62 0.84 206 67 71 4 513.41 0.30 207 68 71 3 521.49 1.41 208 68 72 4 518.56 2.87 209 69 72 3 518.56 2.87 210 69 73 4 516.83 3.73 211 70 73 3 518.23 4.42 212 70 74 4 516.83 3.73 213 71 74 3 527.38 1.55 214 71 75 4 514.74 2.69 215 72 75 3 519.99 0.06 216 72 76 4 514.72 2.69 217 72 111 39 162.58 0.16 218 73 76 3 517.16 1.48 219 73 77 4 509.61 2.10 220 74 77 3 518.35 2.06 221 74 78 4 513.79 0.01 222 75 78 3 520.85 0.55 223 75 82 7 247.62 8.72 224 75 85 10 224.49 7.45 225 75 86 11 224.49 7.46 226 75 89 14 227.73 9.08 227 75 138 63 158.62 0.02 228 76 79 3 522.00 1.12 229 76 134 58 159.51 0.03 230 78 81 3 515.73 4.26 231 78 82 4 423.92 23.50 232 78 85 7 365.49 18.66 233 80 83 3 676.46 1.35 234 80 137 57 159.31 0.09 235 82 85 3 528.23 1.84 236 82 86 4 521.88 1.33 237 82 137 55 159.56 0.06 238 82 141 59 158.19 0.26 239 83 86 3 528.84 1.93 240 83 87 4 528.62 2.04 241 84 87 3 539.15 1.96 242 84 88 4 532.69 0.99 243 85 88 3 559.17 1.20 244 85 89 4 528.60 2.05 245 86 89 3 528.57 2.06 246 86 90 4 516.35 0.41 247 86 138 52 159.11 0.22 248 86 141 55 158.10 0.28 249 86 142 56 157.03 0.11 250 87 90 3 523.75 2.31 251 87 91 4 517.33 0.90 252 87 145 58 154.76 0.10 253 88 91 3 516.21 0.47 254 88 92 4 509.44 3.02 255 89 92 3 523.42 0.07 256 89 93 4 506.11 1.44 257 89 138 49 159.30 0.14 258 90 93 3 520.44 1.56 259 90 94 4 500.25 3.13 260 90 142 52 155.62 0.04 261 90 145 55 152.38 0.17 262 90 146 56 150.30 0.28 263 90 149 59 138.15 2.06 264 91 94 3 521.78 0.89 265 91 95 4 491.14 2.07 266 91 149 58 140.56 0.86 267 92 96 4 467.12 7.19 268 92 97 5 415.64 18.55 269 93 97 4 380.01 25.70 270 93 98 5 344.31 11.45 271 93 99 6 304.18 8.62 272 93 146 53 149.59 0.34 273 94 98 4 340.99 9.79 274 94 146 52 149.49 0.39 275 94 151 57 74.74 4.22 276 98 151 53 81.05 1.48 277 99 103 4 501.45 0.58 278 99 104 5 501.44 0.59 279 99 146 47 149.40 0.41 280 99 151 52 75.81 4.04 281 100 103 3 524.11 1.80 282 100 104 4 516.28 0.48 283 100 151 51 75.45 4.28 284 100 153 53 15.71 0.94 285 101 104 3 519.06 0.91 286 101 105 4 511.68 2.64 287 101 142 41 155.73 0.23 288 101 143 42 153.66 0.21 289 101 146 45 148.00 0.46 290 101 153 52 15.69 0.94 291 102 105 3 520.84 2.75 292 102 106 4 512.58 2.19 293 103 106 3 517.62 0.14 294 103 107 4 513.91 1.53 295 104 107 3 518.94 0.53 296 104 108 4 516.19 0.39 297 104 139 35 156.28 0.28 298 104 142 38 154.21 0.21 299 105 108 3 519.13 0.42 300 105 109 4 523.84 4.21 301 105 139 34 156.28 0.28 302 106 109 3 523.84 4.21 303 106 110 4 516.17 0.38 304 107 110 3 523.84 4.21 305 107 111 4 514.75 0.34 306 108 111 3 523.84 4.21 307 108 112 4 512.47 0.82 308 108 135 27 159.53 0.07 309 108 139 31 156.43 0.34 310 109 112 3 524.36 1.15 311 109 113 4 512.41 0.87 312 110 113 3 524.36 1.15 313 110 114 4 512.43 0.86 314 111 114 3 524.36 1.15 315 111 115 4 512.46 0.88 316 111 135 24 159.58 0.06 317 112 115 3 513.87 1.56 318 112 116 4 512.46 0.87 319 112 123 11 277.42 3.01 320 112 128 16 159.88 0.17 321 112 131 19 159.84 0.15 322 112 132 20 159.81 0.14 323 112 135 23 159.63 0.07 324 113 116 3 521.48 5.37 325 113 117 4 512.46 0.87 326 114 117 3 524.89 3.67 327 114 118 4 506.82 1.90 328 115 118 3 521.67 0.71 329 115 119 4 490.46 5.02 330 115 123 8 284.54 0.55 331 115 131 16 184.28 12.07 332 116 120 4 466.59 16.96 333 116 123 7 295.19 11.89 334 117 120 3 537.37 2.48 335 119 122 3 517.76 0.10 336 119 123 4 441.26 3.86 337 120 123 3 497.98 4.30 338 122 127 5 442.25 6.78 339 123 127 4 452.30 1.76 340 123 128 5 438.45 8.69 341 123 131 8 428.31 9.06 342 124 127 3 511.59 4.75 343 124 128 4 484.55 4.96 344 125 128 3 515.00 3.04 345 125 129 4 507.90 6.59 346 126 129 3 513.03 2.53 347 126 130 4 508.17 0.17 348 127 130 3 508.70 0.43 349 127 131 4 502.25 3.66 350 128 131 3 521.39 5.91 351 128 132 4 498.16 1.60 352 129 132 3 522.74 5.24 353 129 133 4 498.19 1.63 354 130 133 3 508.54 0.45 355 130 134 4 504.55 1.54 356 131 134 3 508.62 0.41 357 131 135 4 498.03 1.72 358 132 135 3 509.54 1.17 359 132 136 4 498.17 1.92 360 133 136 3 512.92 0.52 361 133 137 4 499.29 1.36 362 134 137 3 515.32 0.68 363 134 138 4 506.96 2.46 364 135 138 3 510.22 0.83 365 135 139 4 507.01 2.43 366 136 139 3 512.64 2.24 367 136 140 4 509.70 0.77 368 137 140 3 509.71 0.77 369 137 141 4 509.71 0.78 370 138 141 3 523.00 3.62 371 138 142 4 509.50 0.88 372 139 142 3 511.25 0.01 373 139 143 4 509.49 0.86 374 140 143 3 512.30 0.49 375 140 144 4 511.25 0.03 376 141 144 3 514.94 1.81 377 141 145 4 500.75 5.28 378 142 145 3 511.35 0.01 379 142 146 4 497.25 3.52 380 143 146 3 511.33 0.03 381 143 147 4 510.60 4.01 382 144 147 3 516.01 1.31 383 144 148 4 510.60 4.01 384 145 148 3 509.69 0.61 385 145 149 4 498.85 2.62 386 146 149 3 509.70 0.62 387 146 150 4 498.85 2.62 388 146 151 5 427.86 6.91 389 146 153 7 263.40 1.93 390 147 150 3 507.51 1.71 391 147 151 4 478.48 3.48