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 6 4 481.70 6.38 2 2 7 5 475.32 3.20 3 2 10 8 473.28 2.35 4 2 130 128 41.80 0.78 5 2 133 131 31.04 0.40 6 2 134 132 30.59 0.21 7 2 137 135 30.57 0.21 8 3 6 3 513.96 2.10 9 3 7 4 490.13 3.84 10 4 7 3 498.88 5.44 11 4 8 4 491.24 3.29 12 4 79 75 55.79 1.62 13 5 8 3 499.13 5.56 14 5 9 4 497.88 0.27 15 6 9 3 527.79 4.81 16 6 10 4 499.90 1.04 17 6 130 124 64.57 2.18 18 6 133 127 64.62 2.19 19 7 10 3 503.72 3.00 20 7 11 4 499.86 1.06 21 7 76 69 64.75 2.14 22 7 79 72 64.68 2.17 23 7 80 73 64.69 2.18 24 7 134 127 64.63 2.20 25 7 137 130 64.69 2.18 26 8 11 3 525.37 3.25 27 8 12 4 490.78 5.60 28 9 12 3 514.00 4.64 29 9 13 4 490.81 5.60 30 9 126 117 78.03 0.47 31 9 127 118 77.86 0.55 32 9 130 121 77.75 0.52 33 10 13 3 518.15 2.57 34 10 14 4 508.58 3.31 35 10 76 66 77.77 0.49 36 10 130 120 77.79 0.53 37 10 131 121 77.78 0.52 38 10 134 124 77.75 0.52 39 11 14 3 516.38 0.59 40 11 15 4 508.57 3.31 41 11 76 65 77.81 0.51 42 11 77 66 77.81 0.51 43 11 79 68 77.82 0.51 44 12 15 3 515.86 0.33 45 13 16 3 522.44 3.62 46 13 17 4 521.35 3.08 47 13 115 102 82.89 1.06 48 13 123 110 82.08 1.47 49 13 127 114 81.98 1.51 50 13 131 118 80.75 0.90 51 14 17 3 519.71 0.54 52 14 18 4 512.63 3.00 53 14 69 55 82.00 1.50 54 14 72 58 80.81 0.91 55 14 73 59 80.78 0.90 56 14 76 62 80.78 0.90 57 14 77 63 80.78 0.90 58 15 18 3 519.71 0.55 59 15 19 4 518.66 1.06 60 16 19 3 523.67 1.45 61 16 24 8 434.14 10.45 62 16 119 103 103.58 0.69 63 16 122 106 103.58 0.69 64 17 20 3 521.12 0.17 65 17 21 4 502.07 1.22 66 17 24 7 429.44 12.79 67 17 69 52 89.70 1.00 68 17 115 98 95.73 1.95 69 18 21 3 519.70 0.54 70 18 77 59 89.55 1.01 71 20 23 3 518.24 0.09 72 20 24 4 506.79 3.91 73 21 24 3 508.87 4.60 74 21 25 4 495.67 1.66 75 21 66 45 149.72 14.04 76 22 25 3 513.68 2.19 77 22 26 4 506.79 3.90 78 22 62 40 153.72 12.94 79 22 66 44 152.69 12.62 80 23 26 3 513.40 0.59 81 23 27 4 513.40 0.59 82 23 118 95 163.63 0.42 83 24 27 3 517.55 1.46 84 24 28 4 511.32 0.45 85 24 69 45 153.38 12.16 86 24 115 91 163.29 0.56 87 24 118 94 164.74 0.12 88 24 119 95 164.73 0.12 89 25 28 3 521.09 3.23 90 25 29 4 513.22 0.50 91 25 65 40 153.47 12.21 92 25 69 44 153.36 12.17 93 26 29 3 522.71 4.24 94 26 30 4 511.87 1.16 95 26 55 29 214.47 1.26 96 26 56 30 211.76 2.62 97 26 58 32 209.72 1.61 98 26 62 36 180.06 0.07 99 27 30 3 516.25 1.03 100 27 31 4 500.28 0.92 101 27 114 87 165.48 0.13 102 27 118 91 165.21 0.23 103 28 31 3 509.70 2.08 104 28 32 4 500.93 1.24 105 28 107 79 165.97 0.20 106 28 110 82 165.78 0.15 107 28 111 83 165.77 0.14 108 28 114 86 165.49 0.13 109 29 32 3 515.99 1.06 110 29 33 4 500.92 1.25 111 29 61 32 205.37 2.76 112 29 64 35 203.43 1.79 113 29 65 36 185.29 2.54 114 29 107 78 166.00 0.19 115 30 34 4 490.70 0.62 116 30 52 22 215.33 1.11 117 30 55 25 215.08 1.04 118 30 56 26 215.12 1.02 119 30 61 31 209.12 1.32 120 31 34 3 520.10 0.99 121 31 35 4 500.06 5.21 122 31 110 79 165.78 0.15 123 31 113 82 165.75 0.14 124 31 114 83 165.63 0.10 125 32 35 3 505.50 2.48 126 32 36 4 490.82 0.56 127 32 39 7 351.81 6.12 128 32 106 74 166.09 0.16 129 32 107 75 166.00 0.19 130 33 36 3 515.39 1.53 131 33 37 4 473.82 7.92 132 33 39 6 370.51 3.23 133 33 40 7 298.56 2.35 134 33 43 10 297.84 2.71 135 33 46 13 257.87 7.73 136 33 55 22 215.84 1.16 137 33 61 28 215.44 0.99 138 34 37 3 515.42 1.51 139 34 55 21 215.85 1.16 140 36 39 3 514.46 0.20 141 36 106 70 166.13 0.16 142 37 40 3 513.19 0.43 143 38 41 3 520.88 4.28 144 38 103 65 167.24 0.66 145 38 106 68 166.41 0.26 146 39 42 3 522.53 5.08 147 39 103 64 166.34 0.26 148 39 106 67 166.34 0.26 149 40 43 3 521.52 1.14 150 40 46 6 347.25 27.53 151 40 47 7 249.26 3.17 152 40 49 9 258.16 7.61 153 42 97 55 167.81 0.47 154 42 98 56 167.81 0.47 155 42 99 57 167.71 0.43 156 42 100 58 167.72 0.43 157 42 103 61 167.28 0.63 158 43 46 3 513.31 0.13 159 43 47 4 500.95 3.91 160 43 64 21 219.30 0.48 161 44 47 3 526.85 1.30 162 45 48 3 564.54 1.95 163 45 60 15 221.19 1.30 164 45 64 19 220.97 1.21 165 46 49 3 535.84 0.21 166 46 60 14 221.19 1.30 167 46 61 15 220.99 1.22 168 46 64 18 220.97 1.21 169 47 50 3 609.04 1.53 170 49 54 5 476.16 2.52 171 49 55 6 401.56 14.14 172 49 58 9 320.18 7.70 173 49 61 12 265.63 0.72 174 50 54 4 502.81 1.71 175 51 54 3 499.19 0.39 176 51 55 4 502.32 1.44 177 52 55 3 504.17 1.85 178 52 56 4 502.86 1.20 179 53 56 3 515.18 1.70 180 53 57 4 502.85 1.19 181 54 57 3 504.17 1.85 182 54 58 4 502.85 1.19 183 55 58 3 515.83 3.98 184 55 61 6 434.61 7.62 185 58 61 3 534.14 2.29 186 58 62 4 506.57 2.78 187 59 62 3 506.57 2.78 188 59 63 4 505.03 3.56 189 60 63 3 505.02 3.56 190 60 64 4 490.80 3.56 191 61 64 3 514.76 4.51 192 61 65 4 498.60 0.38 193 62 65 3 517.81 3.56 194 62 66 4 498.83 0.47 195 63 66 3 511.65 0.48 196 63 67 4 498.83 0.47 197 64 67 3 504.43 2.33 198 64 68 4 498.82 0.47 199 65 69 4 495.83 1.97 200 66 70 4 502.30 1.29 201 67 70 3 516.27 3.12 202 67 71 4 502.31 1.29 203 68 71 3 508.66 0.68 204 68 72 4 502.31 1.29 205 69 72 3 518.12 2.78 206 69 73 4 503.50 1.89 207 70 73 3 509.99 1.28 208 70 74 4 509.99 1.29 209 71 74 3 519.54 2.15 210 71 75 4 517.25 2.33 211 72 75 3 520.33 1.75 212 72 76 4 510.48 1.46 213 72 135 63 165.16 0.19 214 72 138 66 165.00 0.18 215 73 76 3 517.66 2.12 216 73 77 4 510.59 1.43 217 74 77 3 519.30 2.60 218 74 78 4 513.75 0.17 219 75 78 3 524.84 5.37 220 75 79 4 513.75 0.17 221 75 82 7 243.90 4.48 222 75 85 10 236.25 4.42 223 75 86 11 236.23 4.42 224 75 89 14 236.22 4.42 225 75 138 63 165.06 0.20 226 76 79 3 524.85 5.37 227 76 131 55 165.56 0.20 228 76 134 58 165.38 0.12 229 78 81 3 508.74 1.20 230 78 82 4 447.56 0.86 231 78 85 7 376.86 1.84 232 80 137 57 165.46 0.15 233 82 85 3 511.69 0.55 234 82 86 4 506.25 0.11 235 82 137 55 165.53 0.18 236 82 141 59 165.03 0.25 237 83 86 3 515.33 0.10 238 83 87 4 506.36 0.10 239 83 88 5 509.92 1.44 240 84 87 3 522.65 1.48 241 84 88 4 522.46 1.39 242 85 88 3 533.36 0.99 243 85 89 4 520.19 2.52 244 86 89 3 520.19 2.52 245 86 90 4 510.63 1.06 246 86 138 52 164.96 0.17 247 86 141 55 163.68 0.57 248 86 142 56 161.06 0.41 249 87 90 3 516.87 4.18 250 87 91 4 516.86 4.18 251 87 145 58 154.63 0.60 252 88 92 4 509.53 0.48 253 89 92 3 515.98 1.88 254 89 93 4 507.05 0.76 255 89 138 49 164.90 0.20 256 90 93 3 521.98 0.60 257 90 94 4 505.63 1.47 258 90 142 52 158.89 1.03 259 90 145 55 151.86 0.12 260 90 146 56 151.69 0.05 261 91 94 3 514.34 1.67 262 91 95 4 490.87 0.47 263 91 149 58 147.81 0.70 264 92 96 4 478.95 1.95 265 92 97 5 394.97 9.15 266 93 97 4 337.43 16.46 267 93 98 5 325.83 22.23 268 93 99 6 287.61 5.19 269 93 146 53 150.09 0.74 270 94 98 4 325.82 22.23 271 94 146 52 149.88 0.82 272 94 149 55 146.57 1.03 273 94 151 57 65.24 2.37 274 95 98 3 503.29 2.62 275 95 149 54 148.22 0.24 276 98 151 53 80.64 0.95 277 99 103 4 508.93 2.62 278 99 146 47 149.85 0.80 279 99 151 52 76.94 2.80 280 100 103 3 517.19 0.49 281 100 104 4 508.94 2.61 282 100 146 46 149.85 0.80 283 100 151 51 62.82 3.58 284 101 104 3 513.10 1.76 285 101 105 4 502.61 0.57 286 101 139 38 162.37 0.20 287 101 142 41 157.02 0.48 288 101 143 42 153.18 0.55 289 101 146 45 148.25 0.75 290 102 105 3 502.61 0.57 291 102 106 4 506.46 2.48 292 103 106 3 525.54 0.06 293 103 107 4 508.76 1.33 294 104 107 3 527.62 0.98 295 104 108 4 520.50 4.54 296 104 138 34 162.94 0.34 297 104 139 35 160.94 0.40 298 104 142 38 154.94 0.45 299 104 146 42 149.85 0.80 300 105 108 3 527.62 0.98 301 105 109 4 527.61 0.98 302 105 139 34 160.94 0.39 303 106 109 3 525.74 1.84 304 106 110 4 509.73 0.83 305 107 110 3 513.65 1.06 306 107 111 4 513.50 1.13 307 108 111 3 520.08 2.16 308 108 112 4 506.88 2.60 309 108 135 27 163.28 0.46 310 108 139 31 160.85 0.29 311 109 112 3 509.63 1.22 312 109 113 4 506.88 2.60 313 110 113 3 506.88 2.59 314 110 114 4 498.54 1.58 315 111 114 3 509.44 1.69 316 111 115 4 499.29 1.96 317 111 135 24 163.28 0.46 318 112 115 3 509.25 1.16 319 112 116 4 499.29 1.96 320 112 123 11 259.90 0.67 321 112 128 16 164.90 0.09 322 112 131 19 164.75 0.14 323 112 132 20 163.83 0.51 324 112 135 23 163.38 0.42 325 113 116 3 514.41 0.98 326 113 117 4 505.12 0.96 327 114 117 3 513.97 1.19 328 114 118 4 505.12 0.96 329 115 118 3 513.98 1.19 330 115 119 4 502.93 0.54 331 115 123 8 280.50 10.96 332 115 131 16 220.23 1.28 333 116 119 3 512.44 4.21 334 116 120 4 475.09 2.37 335 116 123 7 280.50 10.96 336 116 128 12 256.28 2.48 337 117 120 3 522.39 3.40 338 119 122 3 533.87 3.88 339 119 123 4 475.97 8.72 340 123 127 4 501.45 3.40 341 123 128 5 487.39 2.77 342 123 131 8 463.73 4.19 343 124 127 3 515.59 1.39 344 124 128 4 496.77 1.06 345 125 128 3 507.85 1.26 346 125 129 4 500.00 2.66 347 126 129 3 506.75 0.75 348 126 130 4 503.88 0.73 349 127 130 3 515.13 2.39 350 127 131 4 503.86 0.72 351 128 131 3 512.15 3.88 352 128 132 4 505.27 0.01 353 129 132 3 513.22 1.41 354 129 133 4 500.82 2.21 355 130 133 3 515.62 1.09 356 130 134 4 500.11 2.57 357 131 134 3 515.81 1.20 358 131 135 4 500.18 2.53 359 132 135 3 512.32 2.94 360 132 136 4 500.92 2.26 361 133 136 3 506.62 0.58 362 133 137 4 504.45 0.49 363 134 137 3 504.53 0.18 364 134 138 4 500.04 2.06 365 135 138 3 509.01 2.21 366 135 139 4 505.78 0.81 367 136 139 3 511.47 2.03 368 136 140 4 504.17 0.34 369 137 140 3 520.27 1.95 370 137 141 4 504.18 0.34 371 138 141 3 516.95 1.79 372 138 142 4 504.49 0.18 373 139 142 3 517.48 4.87 374 139 143 4 504.46 0.17 375 140 143 3 506.81 1.34 376 140 144 4 505.03 0.42 377 141 144 3 507.00 1.26 378 141 145 4 505.10 0.38 379 142 145 3 505.32 0.49 380 142 146 4 505.08 0.37 381 143 146 3 506.36 0.03 382 143 147 4 505.09 0.36 383 144 147 3 506.12 0.14 384 144 148 4 505.11 0.36 385 145 148 3 509.01 1.59 386 145 149 4 509.01 1.60 387 146 149 3 519.37 1.43 388 146 150 4 500.35 5.93 389 146 151 5 399.72 22.20 390 147 150 3 512.46 0.12