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 5 474.25 2.86 2 2 10 8 467.81 0.20 3 2 130 128 38.63 0.48 4 2 133 131 31.73 0.30 5 2 134 132 30.82 0.34 6 2 137 135 30.79 0.35 7 3 6 3 511.43 3.37 8 3 7 4 501.04 8.57 9 4 7 3 514.47 1.86 10 4 8 4 497.36 6.60 11 4 79 75 60.98 0.72 12 5 8 3 514.47 1.85 13 5 9 4 504.75 2.91 14 6 9 3 509.49 4.34 15 6 10 4 500.10 0.94 16 6 130 124 68.14 0.48 17 6 133 127 68.09 0.44 18 7 10 3 500.46 0.76 19 7 11 4 500.05 0.96 20 7 76 69 68.20 0.45 21 7 79 72 68.16 0.46 22 7 80 73 68.17 0.47 23 7 134 127 68.17 0.47 24 7 137 130 68.17 0.47 25 8 11 3 525.62 3.37 26 8 12 4 500.05 0.96 27 9 12 3 517.21 3.04 28 9 13 4 494.60 3.68 29 9 126 117 79.16 0.51 30 9 127 118 78.91 0.58 31 9 130 121 78.64 0.71 32 10 13 3 518.40 2.44 33 10 14 4 508.81 3.44 34 10 76 66 78.95 0.59 35 10 130 120 78.90 0.58 36 10 131 121 78.64 0.70 37 10 134 124 78.62 0.71 38 11 14 3 516.63 0.47 39 11 15 4 508.81 3.45 40 11 76 65 79.00 0.59 41 11 77 66 79.00 0.58 42 11 79 68 79.17 0.51 43 12 15 3 516.11 0.21 44 13 16 3 522.69 3.49 45 13 17 4 521.60 2.95 46 13 115 102 87.12 0.47 47 13 123 110 86.88 0.51 48 13 127 114 84.83 0.23 49 13 131 118 84.33 0.34 50 14 17 3 514.17 2.23 51 14 18 4 519.96 0.67 52 14 69 55 173.34 1.44 53 14 72 58 84.34 0.33 54 14 73 59 83.89 0.12 55 14 76 62 83.89 0.12 56 14 77 63 84.33 0.33 57 15 18 3 519.96 0.67 58 15 19 4 521.24 0.03 59 16 19 3 521.24 0.03 60 16 24 8 432.73 11.00 61 16 119 103 100.24 0.99 62 16 122 106 102.34 0.07 63 17 20 3 521.24 0.03 64 17 21 4 470.34 4.20 65 17 24 7 402.33 7.20 66 17 69 52 176.12 0.04 67 17 115 98 94.80 1.45 68 18 21 3 516.44 1.08 69 18 77 59 125.52 18.57 70 20 23 3 517.85 0.11 71 20 24 4 498.12 0.68 72 21 24 3 513.92 2.07 73 21 25 4 502.39 1.45 74 21 66 45 178.84 0.29 75 21 69 48 178.34 0.07 76 22 25 3 515.38 1.34 77 22 26 4 509.01 1.85 78 22 62 40 180.12 0.06 79 22 66 44 178.97 0.30 80 23 26 3 513.65 0.47 81 23 27 4 509.01 1.85 82 24 27 3 514.86 0.14 83 24 28 4 508.59 2.06 84 24 69 45 178.75 0.10 85 24 114 90 162.65 1.59 86 24 115 91 162.99 1.42 87 24 118 94 162.38 1.44 88 24 119 95 162.39 1.44 89 25 28 3 512.69 1.22 90 25 29 4 509.13 1.79 91 25 65 40 179.08 0.25 92 25 69 44 178.75 0.10 93 26 29 3 514.65 0.23 94 26 30 4 509.97 2.21 95 26 56 30 215.78 0.85 96 26 62 36 180.80 0.20 97 26 65 39 179.09 0.26 98 27 30 3 512.18 3.32 99 27 31 4 509.97 2.22 100 27 114 87 163.23 1.35 101 27 118 91 162.75 1.25 102 28 31 3 511.97 1.23 103 28 32 4 509.97 2.21 104 28 107 79 163.81 1.22 105 28 110 82 163.38 1.37 106 28 111 83 163.28 1.33 107 28 114 86 163.24 1.35 108 29 32 3 516.61 1.09 109 29 33 4 507.69 3.37 110 29 61 32 196.33 6.92 111 29 64 35 181.75 0.24 112 29 65 36 181.62 0.21 113 29 107 78 163.85 1.24 114 30 33 3 520.36 1.12 115 30 34 4 494.73 3.15 116 30 52 22 223.57 2.08 117 30 55 25 222.69 1.89 118 30 56 26 222.91 2.00 119 30 61 31 206.03 4.53 120 31 34 3 513.76 2.18 121 31 35 4 494.74 3.16 122 31 110 79 163.43 1.41 123 31 113 82 163.32 1.39 124 31 114 83 163.33 1.39 125 32 35 3 511.06 0.91 126 32 36 4 495.51 2.77 127 32 39 7 415.59 11.17 128 32 106 74 163.85 1.24 129 32 107 75 163.85 1.24 130 32 110 78 163.45 1.41 131 33 36 3 515.65 1.39 132 33 37 4 472.70 3.06 133 33 39 6 385.00 4.12 134 33 40 7 345.33 15.70 135 33 43 10 297.31 1.75 136 33 46 13 254.62 1.69 137 33 55 22 223.78 2.06 138 33 61 28 223.58 2.12 139 34 37 3 521.54 1.55 140 34 52 18 223.84 2.02 141 34 55 21 223.81 2.05 142 36 39 3 514.96 1.03 143 36 106 70 163.93 1.24 144 37 40 3 513.44 0.31 145 38 41 3 521.12 4.15 146 38 103 65 164.70 1.21 147 38 106 68 164.64 1.22 148 39 42 3 523.01 4.83 149 39 43 4 516.10 1.38 150 39 103 64 164.47 1.15 151 39 106 67 164.22 1.21 152 40 43 3 525.02 0.90 153 40 46 6 386.79 7.96 154 40 47 7 279.11 5.30 155 40 49 9 264.19 3.25 156 41 47 6 303.69 6.95 157 42 97 55 165.09 1.15 158 42 98 56 165.09 1.15 159 42 99 57 165.06 1.15 160 42 100 58 165.06 1.15 161 42 103 61 164.76 1.24 162 43 46 3 520.72 1.66 163 43 47 4 504.20 2.54 164 43 64 21 224.17 1.84 165 44 47 3 528.98 0.24 166 45 48 3 559.70 0.72 167 45 60 15 229.70 0.71 168 46 49 3 530.40 0.97 169 46 60 14 229.71 0.71 170 46 61 15 228.07 0.06 171 46 64 18 227.99 0.06 172 49 54 5 429.12 6.20 173 49 55 6 429.12 6.19 174 49 58 9 295.00 5.15 175 49 61 12 257.19 0.10 176 50 54 4 503.34 1.45 177 51 54 3 501.18 0.36 178 51 55 4 494.03 0.05 179 52 55 3 497.23 1.65 180 52 56 4 493.28 0.32 181 53 56 3 500.56 3.31 182 53 57 4 497.34 1.71 183 54 57 3 502.07 1.53 184 54 58 4 499.88 0.43 185 55 58 3 500.36 0.66 186 55 61 6 437.25 14.04 187 58 61 3 534.39 2.17 188 58 62 4 507.15 3.06 189 59 62 3 507.03 3.12 190 59 63 4 503.98 4.64 191 60 63 3 518.52 2.64 192 60 64 4 505.57 3.85 193 61 64 3 518.53 2.63 194 61 65 4 505.56 3.84 195 62 65 3 506.14 2.18 196 62 66 4 506.73 3.21 197 63 66 3 512.51 0.99 198 63 67 4 509.65 1.76 199 64 67 3 512.52 0.99 200 64 68 4 509.70 1.73 201 65 68 3 515.12 2.29 202 65 69 4 506.85 0.27 203 66 69 3 516.41 1.65 204 66 70 4 506.86 0.27 205 67 70 3 511.47 0.48 206 67 71 4 506.92 0.29 207 68 71 3 515.25 1.54 208 68 72 4 510.29 1.37 209 68 107 39 163.93 1.24 210 69 72 3 513.51 0.24 211 69 73 4 510.31 1.37 212 70 73 3 525.03 2.83 213 70 74 4 510.32 1.38 214 71 74 3 519.79 2.02 215 71 75 4 510.32 1.38 216 72 75 3 518.46 2.69 217 72 76 4 510.31 1.38 218 72 111 39 163.93 1.23 219 72 135 63 161.31 0.79 220 72 138 66 160.65 1.06 221 73 76 3 510.73 1.51 222 73 77 4 511.34 1.20 223 74 77 3 512.19 0.78 224 74 78 4 511.35 1.20 225 75 78 3 519.53 2.48 226 75 82 7 275.95 8.59 227 75 85 10 192.14 3.44 228 75 89 14 183.53 7.74 229 75 138 63 161.03 0.88 230 76 79 3 519.53 2.49 231 76 134 58 161.45 0.85 232 78 81 3 505.30 0.63 233 78 82 4 442.05 29.16 234 78 85 7 316.70 6.95 235 80 83 3 658.58 2.23 236 80 137 57 161.49 0.90 237 82 85 3 517.63 1.26 238 82 86 4 502.55 0.18 239 82 137 55 161.49 0.90 240 82 141 59 160.56 1.11 241 83 86 3 515.57 0.21 242 83 87 4 502.97 1.56 243 84 88 4 522.71 1.51 244 85 88 3 537.35 4.17 245 85 89 4 522.71 1.51 246 86 89 3 524.63 0.55 247 86 90 4 511.33 1.30 248 86 138 52 161.02 0.89 249 86 141 55 160.06 0.88 250 86 142 56 159.35 1.17 251 87 90 3 517.57 4.08 252 87 91 4 511.21 1.35 253 88 91 3 513.48 2.38 254 88 92 4 512.26 1.84 255 89 92 3 515.24 1.51 256 89 93 4 512.26 1.84 257 89 138 49 160.85 0.96 258 90 93 3 515.88 2.18 259 90 94 4 505.34 1.61 260 90 142 52 157.12 0.49 261 90 145 55 146.51 0.20 262 90 146 56 145.91 0.10 263 91 94 3 521.07 4.55 264 91 95 4 504.50 0.77 265 91 149 58 143.16 0.06 266 92 95 3 533.81 1.82 267 92 96 4 482.62 2.98 268 92 97 5 470.19 9.20 269 93 97 4 462.26 5.24 270 93 98 5 462.26 5.24 271 93 99 6 313.31 0.48 272 93 146 53 144.47 0.61 273 94 98 4 448.13 12.30 274 94 146 52 144.43 0.61 275 94 149 55 142.56 0.06 276 94 151 57 71.77 0.32 277 95 98 3 519.04 0.42 278 95 149 54 142.74 0.12 279 98 151 53 78.13 2.21 280 99 103 4 513.01 0.83 281 99 146 47 144.45 0.60 282 99 151 52 77.93 2.31 283 100 103 3 519.75 1.44 284 100 146 46 144.45 0.60 285 100 151 51 64.05 4.19 286 101 104 3 512.39 1.91 287 101 105 4 507.52 1.93 288 101 139 38 159.06 0.88 289 101 142 41 156.04 0.10 290 101 143 42 147.91 0.46 291 101 146 45 144.44 0.60 292 102 105 3 513.34 0.98 293 102 106 4 507.17 1.89 294 103 106 3 513.13 1.09 295 103 107 4 508.87 1.04 296 104 107 3 512.86 0.96 297 104 108 4 508.86 1.04 298 104 139 35 158.25 0.57 299 104 142 38 155.75 0.04 300 105 108 3 514.80 1.93 301 105 109 4 508.85 1.03 302 105 139 34 158.75 0.81 303 106 109 3 513.28 1.02 304 106 110 4 505.88 1.19 305 107 110 3 512.26 2.00 306 107 111 4 505.88 1.18 307 108 111 3 520.34 2.04 308 108 112 4 505.87 1.18 309 108 135 27 160.68 1.06 310 108 139 31 158.25 0.57 311 109 112 3 509.88 1.09 312 109 113 4 505.74 1.24 313 110 113 3 508.53 2.64 314 110 114 4 501.51 0.04 315 111 114 3 512.45 0.18 316 111 115 4 506.76 2.66 317 111 135 24 160.69 1.07 318 112 115 3 514.92 1.06 319 112 116 4 504.42 3.83 320 112 123 11 248.43 6.23 321 112 128 16 161.27 0.90 322 112 132 20 160.81 1.04 323 112 135 23 160.69 1.07 324 113 116 3 514.23 1.07 325 113 117 4 505.38 0.83 326 114 117 3 506.41 1.34 327 114 118 4 505.38 0.83 328 115 118 3 518.80 1.22 329 115 119 4 493.15 1.76 330 115 123 8 248.46 6.21 331 115 131 16 214.03 4.63 332 116 119 3 514.83 3.27 333 116 120 4 479.74 8.46 334 116 123 7 248.74 6.34 335 116 128 12 248.43 6.23 336 117 120 3 527.90 0.90 337 119 122 3 530.74 5.70 338 119 123 4 475.80 8.76 339 123 127 4 496.14 1.38 340 123 128 5 497.79 0.55 341 123 131 8 469.92 5.17 342 124 127 3 503.36 0.98 343 124 128 4 503.37 0.97 344 125 128 3 508.10 1.39 345 125 129 4 501.03 2.15 346 126 129 3 508.09 1.39 347 126 130 4 503.63 0.84 348 127 130 3 515.38 2.26 349 127 131 4 503.62 0.84 350 128 131 3 509.14 3.08 351 128 132 4 508.62 3.33 352 129 132 3 513.10 1.10 353 129 133 4 508.69 3.29 354 130 133 3 517.17 0.57 355 130 134 4 504.38 1.13 356 131 134 3 512.54 2.13 357 131 135 4 497.54 2.29 358 132 135 3 517.00 0.85 359 132 136 4 498.40 2.72 360 133 136 3 502.13 3.08 361 133 137 4 501.73 2.81 362 134 137 3 506.74 4.42 363 134 138 4 506.40 0.48 364 135 138 3 506.43 0.47 365 135 139 4 507.37 0.01 366 136 139 3 511.72 2.16 367 136 140 4 505.03 0.61 368 137 140 3 505.61 0.92 369 137 141 4 505.60 0.92 370 138 141 3 514.70 0.67 371 138 142 4 505.71 0.87 372 139 142 3 514.72 0.68 373 139 143 4 505.75 0.85 374 140 143 3 512.78 1.64 375 140 144 4 505.98 0.96 376 141 144 3 512.00 2.04 377 141 145 4 505.98 0.96 378 142 145 3 514.06 1.29 379 142 146 4 505.98 0.96 380 143 146 3 505.93 0.99 381 143 147 4 505.93 0.99 382 144 147 3 506.61 0.40 383 144 148 4 504.87 0.47 384 145 148 3 511.41 2.81 385 145 149 4 504.86 0.47 386 146 149 3 512.70 0.00 387 146 150 4 504.19 0.74 388 146 151 5 384.05 8.06 389 147 150 3 492.94 1.28