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 5 502.38 2.69 2 2 130 128 40.44 0.34 3 2 133 131 34.48 0.29 4 2 134 132 30.62 0.02 5 2 137 135 30.62 0.01 6 3 6 3 517.00 3.73 7 3 7 4 515.61 1.60 8 4 7 3 522.43 1.02 9 4 8 4 515.64 1.58 10 4 79 75 58.94 1.17 11 5 8 3 516.44 1.97 12 5 9 4 516.42 1.97 13 6 9 3 523.27 3.95 14 6 10 4 516.42 1.97 15 6 130 124 73.69 0.59 16 6 133 127 73.69 0.59 17 7 10 3 515.66 1.58 18 7 11 4 510.21 1.14 19 7 76 69 73.69 0.60 20 7 79 72 73.69 0.60 21 7 80 73 73.75 0.57 22 7 134 127 73.70 0.59 23 7 137 130 73.70 0.59 24 8 11 3 521.28 1.23 25 8 12 4 512.90 2.03 26 8 79 71 81.79 0.10 27 9 12 3 522.08 2.01 28 9 13 4 513.19 1.93 29 9 126 117 83.51 0.43 30 9 127 118 83.44 0.46 31 9 130 121 83.33 0.41 32 10 13 3 528.91 1.07 33 10 14 4 513.19 1.93 34 10 76 66 83.57 0.40 35 10 130 120 83.50 0.43 36 10 131 121 83.39 0.44 37 10 134 124 83.16 0.48 38 11 14 3 514.80 2.73 39 11 15 4 513.19 1.93 40 11 76 65 83.60 0.40 41 11 77 66 83.60 0.40 42 11 79 68 83.59 0.40 43 12 15 3 523.19 3.86 44 12 16 4 516.25 0.40 45 12 122 110 86.98 1.01 46 13 16 3 515.22 3.96 47 13 17 4 506.19 1.27 48 13 115 102 86.80 0.95 49 13 119 106 87.06 0.99 50 13 122 109 86.98 1.01 51 13 123 110 86.98 1.01 52 13 131 118 86.45 0.80 53 14 17 3 507.60 0.67 54 14 18 4 506.10 1.42 55 14 69 55 133.80 24.46 56 14 72 58 86.67 0.91 57 14 73 59 86.13 0.63 58 14 76 62 86.13 0.63 59 14 77 63 86.63 0.88 60 14 131 117 86.78 0.96 61 15 18 3 516.16 2.10 62 15 19 4 521.48 1.28 63 16 19 3 531.46 0.98 64 16 119 103 90.70 0.70 65 16 122 106 87.20 1.04 66 17 20 3 527.48 1.02 67 17 21 4 499.11 2.10 68 17 24 7 326.99 11.35 69 17 69 52 188.85 1.98 70 17 115 98 90.69 0.70 71 18 77 59 86.96 0.97 72 20 23 3 525.99 2.58 73 20 24 4 511.94 2.75 74 20 118 98 142.32 0.84 75 21 24 3 525.99 2.58 76 21 25 4 517.53 0.04 77 21 66 45 201.02 3.56 78 21 69 48 199.28 2.80 79 22 25 3 519.22 0.81 80 22 26 4 519.21 0.80 81 22 62 40 204.71 1.85 82 22 66 44 201.29 3.43 83 23 26 3 519.25 0.80 84 23 27 4 515.12 1.27 85 23 118 95 165.78 0.65 86 24 27 3 518.79 2.43 87 24 28 4 512.92 2.36 88 24 69 45 204.58 1.90 89 24 118 94 165.78 0.65 90 24 119 95 165.80 0.64 91 25 28 3 520.61 0.26 92 25 29 4 516.09 1.99 93 25 65 40 204.61 1.89 94 25 69 44 204.58 1.90 95 26 29 3 526.54 0.56 96 26 30 4 516.09 1.99 97 26 56 30 220.66 1.71 98 26 62 36 205.68 1.99 99 27 30 3 522.51 1.56 100 27 31 4 519.68 0.20 101 27 114 87 167.18 1.00 102 27 118 91 167.00 0.97 103 28 31 3 520.13 0.38 104 28 32 4 519.69 0.20 105 28 69 41 205.04 1.71 106 28 107 79 168.18 0.73 107 28 110 82 168.00 0.72 108 28 111 83 167.97 0.72 109 28 114 86 167.21 1.01 110 29 32 3 523.92 1.93 111 29 33 4 519.61 0.23 112 29 43 14 284.59 3.52 113 29 61 32 220.19 1.88 114 29 64 35 206.80 1.77 115 29 65 36 206.52 1.62 116 29 68 39 206.46 1.65 117 29 107 78 168.17 0.73 118 30 33 3 527.14 0.32 119 30 34 4 519.50 0.18 120 30 52 22 222.86 2.35 121 30 55 25 222.61 2.25 122 30 56 26 222.72 2.31 123 30 61 31 220.66 1.71 124 31 34 3 527.15 0.32 125 31 35 4 517.83 1.02 126 31 110 79 168.00 0.73 127 31 113 82 167.70 0.80 128 31 114 83 167.65 0.78 129 32 35 3 522.75 1.88 130 32 36 4 499.45 3.60 131 32 39 7 388.56 20.12 132 32 106 74 168.22 0.73 133 32 107 75 168.19 0.74 134 32 110 78 168.01 0.73 135 33 36 3 519.54 0.31 136 33 37 4 483.48 2.10 137 33 39 6 366.77 5.95 138 33 40 7 328.84 0.60 139 33 43 10 313.37 6.48 140 33 55 22 222.99 2.39 141 33 61 28 222.71 2.29 142 34 37 3 518.22 0.35 143 34 52 18 223.00 2.39 144 34 55 21 223.33 2.23 145 36 39 3 534.50 2.73 146 36 106 70 168.36 0.73 147 36 109 73 168.37 0.80 148 37 40 3 531.83 4.06 149 38 41 3 528.01 1.55 150 38 103 65 169.05 0.66 151 38 106 68 168.90 0.72 152 39 42 3 533.08 0.98 153 39 43 4 533.08 0.98 154 39 103 64 168.69 0.75 155 39 106 67 168.64 0.74 156 40 43 3 533.08 0.98 157 40 46 6 314.62 1.54 158 40 47 7 272.02 0.15 159 40 49 9 264.68 1.13 160 42 97 55 169.25 0.60 161 42 98 56 169.24 0.60 162 42 99 57 169.22 0.63 163 42 103 61 169.12 0.66 164 43 46 3 527.91 0.16 165 43 47 4 491.53 7.19 166 43 64 21 223.87 1.92 167 44 47 3 527.91 0.16 168 45 48 3 565.19 1.15 169 45 60 15 224.25 2.02 170 46 49 3 531.38 2.56 171 46 60 14 231.38 1.54 172 46 61 15 224.25 2.02 173 46 64 18 224.24 2.02 174 49 54 5 461.51 1.02 175 49 55 6 411.55 23.96 176 49 58 9 288.33 2.38 177 49 61 12 265.39 1.61 178 50 54 4 511.61 2.40 179 51 54 3 528.70 6.06 180 51 55 4 509.07 3.67 181 52 55 3 516.49 0.04 182 52 56 4 511.61 2.40 183 53 56 3 516.66 1.04 184 53 57 4 502.80 0.52 185 54 57 3 522.50 1.40 186 54 58 4 497.74 2.02 187 55 58 3 522.50 1.40 188 55 61 6 438.43 9.18 189 58 61 3 519.31 3.38 190 58 62 4 509.44 1.56 191 59 62 3 519.66 3.20 192 59 63 4 519.31 3.38 193 60 63 3 519.79 3.14 194 60 64 4 519.31 3.38 195 61 64 3 522.93 4.71 196 61 65 4 506.01 0.18 197 62 65 3 514.38 3.91 198 62 66 4 506.17 0.11 199 63 66 3 517.36 2.43 200 63 67 4 506.19 0.12 201 64 67 3 517.99 2.10 202 64 68 4 506.16 0.12 203 65 68 3 519.54 2.14 204 65 69 4 509.22 1.66 205 66 69 3 516.88 0.81 206 66 70 4 509.19 1.68 207 67 70 3 524.86 1.96 208 67 71 4 512.69 0.06 209 68 71 3 520.79 3.98 210 68 72 4 515.67 1.43 211 69 72 3 515.67 1.43 212 69 73 4 510.96 0.81 213 70 73 3 514.26 2.44 214 70 74 4 508.16 0.60 215 71 74 3 526.75 1.86 216 71 75 4 513.84 2.23 217 72 75 3 514.25 2.44 218 72 76 4 513.84 2.24 219 72 111 39 168.32 0.83 220 72 135 63 166.20 0.70 221 73 76 3 508.75 4.79 222 73 77 4 508.38 4.96 223 74 77 3 515.85 3.21 224 74 78 4 513.89 2.21 225 75 78 3 523.10 0.58 226 75 82 7 258.22 3.44 227 75 85 10 209.94 20.86 228 75 86 11 223.85 13.90 229 75 89 14 195.06 13.43 230 75 138 63 166.07 0.77 231 76 79 3 524.25 0.01 232 76 134 58 166.33 0.73 233 78 81 3 517.97 3.14 234 78 82 4 417.12 3.19 235 78 85 7 366.69 28.70 236 80 83 3 678.71 2.48 237 80 137 57 166.38 0.73 238 82 85 3 523.75 3.33 239 82 86 4 517.31 0.96 240 82 137 55 166.39 0.73 241 82 141 59 165.81 0.64 242 83 86 3 528.63 0.18 243 83 87 4 521.85 3.21 244 84 87 3 534.94 0.13 245 84 88 4 532.77 0.05 246 85 88 3 553.88 1.45 247 85 89 4 517.34 0.95 248 86 89 3 527.21 1.47 249 86 90 4 516.32 1.27 250 86 138 52 166.00 0.68 251 86 141 55 164.70 0.14 252 86 142 56 162.32 0.48 253 87 90 3 527.53 2.58 254 87 91 4 508.90 2.41 255 87 145 58 161.17 0.25 256 88 91 3 527.17 2.76 257 88 92 4 513.77 0.03 258 89 92 3 522.64 2.71 259 89 93 4 512.42 0.70 260 89 138 49 166.03 0.66 261 89 142 53 162.31 0.49 262 90 93 3 514.15 0.15 263 90 94 4 498.75 5.65 264 90 142 52 162.03 0.59 265 90 145 55 155.55 0.65 266 90 146 56 151.91 1.17 267 90 149 59 138.51 1.89 268 91 94 3 517.23 1.39 269 91 95 4 493.75 3.16 270 91 149 58 143.32 1.82 271 92 96 4 482.34 8.87 272 92 97 5 451.31 24.37 273 93 97 4 388.00 7.29 274 93 98 5 317.29 4.31 275 93 99 6 277.57 4.15 276 93 146 53 150.02 0.92 277 94 98 4 311.97 1.62 278 94 146 52 149.88 0.85 279 94 149 55 134.52 0.11 280 94 151 57 74.48 5.67 281 98 151 53 97.83 5.23 282 99 103 4 514.41 1.75 283 99 104 5 503.71 0.53 284 99 146 47 149.85 0.83 285 99 151 52 97.83 5.23 286 100 103 3 526.36 2.93 287 100 104 4 514.73 1.59 288 100 151 51 76.67 5.36 289 100 153 53 17.50 0.04 290 101 104 3 515.29 1.31 291 101 105 4 514.41 1.75 292 101 142 41 161.32 0.30 293 101 143 42 156.94 0.32 294 101 146 45 149.87 0.84 295 101 153 52 17.21 0.17 296 102 105 3 519.51 3.42 297 102 106 4 514.39 1.75 298 103 106 3 515.28 1.30 299 103 107 4 514.26 1.81 300 104 107 3 521.20 1.65 301 104 108 4 518.42 0.73 302 104 139 35 161.91 0.29 303 104 142 38 161.28 0.29 304 105 108 3 520.73 1.88 305 105 109 4 518.43 0.73 306 105 139 34 163.24 0.95 307 106 109 3 528.38 1.95 308 106 110 4 513.78 1.58 309 107 110 3 525.93 3.17 310 107 111 4 495.29 1.51 311 108 111 3 521.65 5.30 312 108 112 4 505.57 3.02 313 108 135 27 165.93 0.58 314 108 139 31 161.99 0.32 315 109 112 3 526.61 0.02 316 109 113 4 506.10 2.76 317 110 113 3 526.61 0.02 318 110 114 4 506.00 2.81 319 111 114 3 526.61 0.02 320 111 115 4 508.12 3.47 321 111 135 24 165.93 0.58 322 112 115 3 516.03 0.48 323 112 116 4 503.12 6.94 324 112 123 11 262.62 2.42 325 112 128 16 166.27 0.70 326 112 131 19 166.12 0.64 327 112 132 20 165.99 0.58 328 112 135 23 165.94 0.59 329 113 116 3 523.65 4.28 330 113 117 4 503.12 6.93 331 114 117 3 523.65 4.28 332 114 118 4 514.60 0.22 333 115 118 3 519.46 2.65 334 115 119 4 496.38 8.87 335 115 123 8 272.00 0.02 336 115 131 16 195.74 15.44 337 116 120 4 459.05 9.80 338 116 123 7 271.18 0.39 339 117 120 3 536.82 2.21 340 119 122 3 520.00 1.23 341 119 123 4 420.62 16.14 342 120 123 3 506.40 2.34 343 122 127 5 492.74 3.90 344 123 127 4 492.75 3.90 345 123 128 5 470.38 7.30 346 123 131 8 434.95 5.51 347 124 127 3 512.34 2.88 348 124 128 4 492.81 3.87 349 125 128 3 514.30 3.40 350 125 129 4 504.57 8.26 351 126 129 3 508.49 4.80 352 126 130 4 494.56 3.25 353 127 130 3 504.76 2.78 354 127 131 4 497.97 1.60 355 128 131 3 505.17 2.20 356 128 132 4 498.01 1.59 357 129 132 3 505.90 2.56 358 129 133 4 498.01 1.59 359 130 133 3 500.99 0.11 360 130 134 4 504.12 2.64 361 131 134 3 510.87 0.72 362 131 135 4 500.03 0.59 363 132 135 3 521.40 2.52 364 132 136 4 506.85 2.73 365 133 136 3 515.17 0.60 366 133 137 4 506.95 2.67 367 134 137 3 520.09 0.54 368 134 138 4 509.25 3.56 369 135 138 3 510.43 0.94 370 135 139 4 507.20 2.54 371 136 139 3 507.80 2.24 372 136 140 4 502.15 0.57 373 137 140 3 507.79 2.24 374 137 141 4 507.19 2.54 375 138 141 3 516.68 2.90 376 138 142 4 507.17 2.55 377 139 142 3 516.99 0.61 378 139 143 4 511.75 0.26 379 140 143 3 511.75 0.26 380 140 144 4 511.75 0.26 381 141 144 3 515.33 1.62 382 141 145 4 506.11 2.57 383 142 145 3 506.11 2.64 384 142 146 4 500.67 0.26 385 143 146 3 510.09 0.65 386 143 147 4 512.44 5.34 387 144 147 3 518.25 2.44 388 144 148 4 512.85 5.14 389 145 148 3 507.76 2.60 390 145 149 4 505.18 1.71 391 146 149 3 507.36 2.80 392 146 150 4 505.18 1.71 393 146 151 5 434.30 7.40 394 146 153 7 261.00 5.54 395 147 150 3 501.92 0.35 396 147 151 4 482.14 1.19