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 5 488.95 10.64 2 2 10 8 475.79 4.05 3 2 130 128 46.33 0.51 4 2 133 131 34.26 0.32 5 2 134 132 26.33 1.85 6 3 6 3 504.47 3.05 7 3 7 4 508.29 1.25 8 4 7 3 518.49 2.38 9 4 8 4 508.30 1.25 10 4 79 75 55.66 0.38 11 5 8 3 515.31 1.34 12 5 9 4 511.03 0.12 13 6 9 3 530.50 3.71 14 6 10 4 511.01 0.12 15 6 130 124 62.73 0.21 16 7 10 3 515.97 0.82 17 7 11 4 506.32 2.17 18 7 76 69 69.31 2.30 19 7 79 72 62.77 0.24 20 7 80 73 68.58 2.67 21 7 134 127 62.80 0.21 22 7 137 130 62.82 0.21 23 8 11 3 521.81 5.28 24 8 12 4 494.37 3.81 25 9 12 3 512.42 0.65 26 9 13 4 511.74 0.99 27 9 126 117 82.80 1.99 28 9 127 118 82.70 1.96 29 9 130 121 82.70 1.96 30 10 13 3 522.35 3.33 31 10 14 4 508.83 3.44 32 10 130 120 82.70 1.96 33 10 131 121 82.68 1.97 34 10 134 124 82.61 1.94 35 11 14 3 518.90 0.67 36 11 15 4 508.80 3.45 37 11 76 65 82.77 1.99 38 11 77 66 82.73 1.98 39 11 79 68 82.78 2.00 40 12 15 3 517.17 0.73 41 12 16 4 508.87 3.42 42 12 122 110 91.63 0.55 43 13 16 3 522.69 3.49 44 13 17 4 514.21 2.21 45 13 115 102 91.61 0.55 46 13 122 109 91.64 0.54 47 13 123 110 91.61 0.55 48 13 127 114 91.31 0.51 49 13 131 118 90.04 0.28 50 14 17 3 511.82 3.40 51 14 18 4 507.81 5.41 52 14 69 55 91.06 0.72 53 14 72 58 90.63 0.57 54 14 73 59 88.65 0.22 55 14 76 62 89.72 0.32 56 14 77 63 90.86 0.71 57 14 115 101 91.73 0.54 58 14 131 117 91.16 0.60 59 15 18 3 510.51 5.39 60 15 19 4 515.83 2.73 61 16 19 3 517.84 1.73 62 16 119 103 92.50 0.83 63 16 122 106 92.45 0.82 64 17 20 3 520.76 0.75 65 17 21 4 503.85 2.71 66 17 24 7 424.30 3.50 67 17 115 98 92.48 0.83 68 18 21 3 518.01 0.30 69 18 77 59 92.28 0.86 70 20 23 3 545.66 2.75 71 20 24 4 510.80 2.40 72 20 118 98 132.52 0.47 73 21 24 3 523.65 3.01 74 21 25 4 507.44 3.62 75 21 66 45 151.72 13.48 76 21 69 48 149.70 14.21 77 22 25 3 507.44 3.62 78 22 26 4 513.69 0.48 79 22 62 40 156.10 12.83 80 22 66 44 151.76 13.49 81 23 26 3 513.70 0.48 82 23 27 4 515.40 1.34 83 24 27 3 526.50 2.54 84 24 28 4 516.60 0.74 85 24 69 45 156.44 11.80 86 24 114 90 161.49 1.05 87 24 118 94 161.82 1.22 88 24 119 95 161.82 1.22 89 25 28 3 531.98 0.14 90 25 29 4 516.62 0.76 91 25 65 40 164.09 8.02 92 25 69 44 156.43 11.81 93 26 29 3 531.98 0.14 94 26 30 4 516.27 0.94 95 26 56 30 214.43 0.18 96 26 61 35 176.34 4.26 97 26 62 36 176.27 4.30 98 27 30 3 518.48 0.17 99 27 31 4 516.27 0.93 100 27 114 87 164.16 1.55 101 27 118 91 163.89 1.64 102 28 31 3 516.28 0.93 103 28 32 4 516.27 0.93 104 28 69 41 174.94 3.64 105 28 107 79 164.46 1.54 106 28 110 82 164.34 1.58 107 28 111 83 164.31 1.59 108 28 114 86 164.16 1.55 109 29 32 3 516.27 0.93 110 29 33 4 516.27 0.93 111 29 61 32 199.00 1.79 112 29 64 35 193.33 3.29 113 29 65 36 175.96 4.05 114 30 33 3 516.27 0.93 115 30 34 4 512.46 0.98 116 30 52 22 225.94 3.39 117 30 55 25 225.78 3.31 118 30 56 26 225.82 3.33 119 30 61 31 217.68 2.93 120 31 34 3 508.66 0.93 121 31 35 4 504.55 2.96 122 31 110 79 164.35 1.58 123 31 113 82 164.31 1.57 124 32 35 3 513.88 2.21 125 32 36 4 494.19 2.88 126 32 39 7 309.69 2.15 127 32 106 74 164.50 1.56 128 32 107 75 164.51 1.55 129 32 110 78 164.34 1.58 130 33 37 4 463.78 10.93 131 33 39 6 354.50 7.21 132 33 40 7 332.26 18.34 133 33 43 10 277.32 3.30 134 33 46 13 252.18 1.63 135 33 55 22 226.16 3.41 136 33 61 28 225.82 3.37 137 34 37 3 515.67 1.39 138 34 52 18 226.15 3.40 139 34 55 21 226.16 3.41 140 36 39 3 513.46 0.29 141 36 106 70 164.62 1.51 142 37 40 3 513.44 0.31 143 37 41 4 513.33 0.37 144 38 41 3 521.12 4.15 145 38 103 65 165.15 1.36 146 38 106 68 165.03 1.41 147 39 42 3 522.75 4.96 148 39 103 64 164.87 1.45 149 39 106 67 164.78 1.50 150 40 43 3 511.88 1.18 151 40 46 6 337.10 16.88 152 40 47 7 274.13 3.16 153 40 49 9 274.12 3.16 154 41 47 6 295.75 4.07 155 42 97 55 165.54 1.33 156 42 98 56 165.53 1.34 157 42 99 57 165.46 1.35 158 42 100 58 165.50 1.35 159 42 103 61 165.35 1.33 160 43 46 3 521.97 3.39 161 43 47 4 508.36 3.58 162 43 64 21 229.02 3.70 163 44 47 3 537.51 1.66 164 45 48 3 588.00 2.50 165 45 60 15 229.40 3.87 166 45 63 18 229.40 3.86 167 45 64 19 229.36 3.85 168 46 49 3 528.95 0.26 169 46 60 14 229.40 3.87 170 46 61 15 229.25 3.80 171 46 64 18 229.31 3.83 172 49 54 5 388.27 9.04 173 49 55 6 337.16 3.46 174 49 58 9 256.42 0.42 175 50 54 4 503.07 1.58 176 51 54 3 508.63 4.09 177 51 55 4 500.25 0.14 178 52 55 3 500.94 0.48 179 52 56 4 500.25 0.14 180 53 56 3 515.14 0.89 181 53 57 4 500.26 0.14 182 54 57 3 523.99 2.29 183 54 58 4 497.68 1.14 184 55 61 6 399.80 22.46 185 58 61 3 534.39 2.17 186 59 62 3 518.19 2.77 187 59 63 4 508.88 1.88 188 60 63 3 521.35 1.22 189 60 64 4 499.10 3.01 190 61 64 3 514.21 4.79 191 61 65 4 498.70 0.24 192 62 65 3 504.97 2.87 193 62 66 4 506.88 3.13 194 63 66 3 513.87 0.35 195 63 67 4 499.42 0.60 196 64 67 3 513.15 0.01 197 64 68 4 513.14 0.01 198 65 68 3 516.72 1.72 199 65 69 4 513.20 0.03 200 66 69 3 513.27 0.00 201 66 70 4 510.22 1.46 202 67 70 3 530.41 6.04 203 67 71 4 513.26 0.00 204 68 71 3 524.49 0.36 205 68 72 4 513.25 0.01 206 69 72 3 527.19 1.76 207 69 73 4 510.32 1.38 208 70 73 3 519.21 5.74 209 70 74 4 510.40 1.33 210 71 74 3 528.37 1.16 211 71 75 4 510.39 1.33 212 72 75 3 513.46 0.14 213 72 76 4 503.82 1.88 214 72 111 39 164.76 1.53 215 72 135 63 163.28 1.67 216 72 138 66 163.08 1.75 217 73 76 3 511.23 1.25 218 73 77 4 503.98 1.72 219 74 78 4 492.79 3.46 220 74 85 11 210.17 11.38 221 75 78 3 512.26 0.54 222 75 82 7 246.72 0.65 223 75 85 10 200.26 16.33 224 75 86 11 200.27 16.34 225 75 89 14 200.24 16.32 226 75 138 63 163.30 1.66 227 76 79 3 498.73 0.42 228 76 131 55 163.89 1.67 229 76 134 58 163.50 1.56 230 78 81 3 512.74 2.54 231 78 82 4 399.19 19.66 232 78 85 7 303.52 6.67 233 82 85 3 519.02 1.51 234 82 86 4 508.40 2.69 235 82 137 55 163.69 1.62 236 82 138 56 163.52 1.61 237 82 141 59 162.63 1.36 238 83 86 3 515.58 0.23 239 83 87 4 511.54 2.25 240 84 88 4 529.70 3.08 241 85 88 3 546.28 0.29 242 86 89 3 533.60 1.12 243 86 90 4 506.03 3.91 244 86 138 52 163.16 1.70 245 86 141 55 160.22 0.82 246 86 142 56 160.16 0.81 247 87 90 3 522.71 1.51 248 87 91 4 512.23 1.86 249 87 145 58 155.66 0.12 250 88 91 3 517.22 0.53 251 88 92 4 513.41 2.42 252 89 92 3 518.16 0.05 253 89 93 4 491.36 7.37 254 89 138 49 162.15 1.14 255 89 142 53 160.05 0.85 256 90 93 3 514.32 2.87 257 90 94 4 513.41 2.42 258 90 142 52 158.83 0.24 259 90 145 55 152.68 0.61 260 90 146 56 147.43 0.90 261 91 94 3 519.03 0.41 262 91 95 4 507.32 0.62 263 91 149 58 141.56 0.85 264 92 95 3 501.81 2.14 265 92 96 4 460.36 7.37 266 92 97 5 460.36 7.37 267 93 97 4 446.66 14.21 268 93 98 5 446.65 14.21 269 93 99 6 326.47 7.03 270 93 104 11 296.89 0.89 271 93 146 53 147.43 0.90 272 94 98 4 377.69 18.01 273 94 146 52 145.71 0.20 274 94 149 55 136.79 2.21 275 94 151 57 78.53 4.03 276 95 98 3 513.38 2.42 277 95 149 54 141.30 0.36 278 95 151 56 120.22 1.67 279 98 151 53 92.73 1.29 280 99 103 4 513.00 0.83 281 99 104 5 500.82 3.19 282 99 146 47 145.63 0.23 283 100 103 3 519.65 2.50 284 100 104 4 513.00 0.83 285 100 153 53 28.84 0.53 286 101 104 3 514.23 1.45 287 101 105 4 511.09 1.94 288 101 139 38 160.43 0.76 289 101 142 41 157.28 0.52 290 101 143 42 154.59 0.03 291 101 146 45 145.85 0.12 292 101 152 51 32.00 0.54 293 102 105 3 511.10 1.94 294 102 106 4 511.08 1.95 295 103 106 3 516.42 0.72 296 103 107 4 509.01 0.95 297 104 107 3 516.42 0.73 298 104 108 4 508.76 1.07 299 104 142 38 156.88 0.53 300 105 108 3 514.40 1.73 301 105 109 4 514.38 1.75 302 105 139 34 160.56 0.82 303 106 109 3 512.48 2.69 304 106 110 4 500.20 3.21 305 107 110 3 510.05 0.74 306 107 111 4 501.62 2.48 307 108 111 3 520.34 2.04 308 108 112 4 515.57 4.43 309 108 135 27 162.00 1.27 310 108 139 31 160.56 0.83 311 109 112 3 521.35 1.78 312 109 113 4 513.85 5.29 313 110 113 3 513.89 5.26 314 110 114 4 513.85 5.29 315 111 114 3 518.24 3.09 316 111 115 4 504.06 0.18 317 111 135 24 162.05 1.33 318 112 115 3 509.24 1.42 319 112 116 4 504.06 0.18 320 112 123 11 266.83 7.50 321 112 128 16 190.40 5.58 322 112 131 19 162.61 1.41 323 112 132 20 162.50 1.35 324 112 135 23 162.30 1.30 325 114 117 3 506.90 1.59 326 114 118 4 506.90 1.59 327 115 118 3 508.38 0.85 328 115 119 4 492.56 2.08 329 115 123 8 268.60 6.62 330 115 131 16 192.75 4.41 331 116 119 3 515.72 2.83 332 116 120 4 492.56 2.07 333 116 123 7 272.53 4.66 334 117 120 3 556.27 2.38 335 119 122 3 534.12 4.00 336 119 123 4 476.45 2.69 337 120 123 3 517.52 7.58 338 120 124 4 476.45 2.69 339 122 127 5 473.28 4.45 340 123 127 4 489.48 3.65 341 123 128 5 489.23 3.56 342 123 131 8 444.64 7.02 343 124 127 3 516.23 1.32 344 124 128 4 505.66 1.30 345 125 128 3 509.57 0.65 346 125 129 4 505.67 1.31 347 126 129 3 509.58 0.64 348 126 130 4 505.68 1.31 349 127 130 3 518.31 0.80 350 127 131 4 505.60 1.34 351 128 131 3 516.00 0.36 352 128 132 4 510.51 2.39 353 129 132 3 516.81 0.76 354 129 133 4 516.81 0.76 355 130 133 3 515.89 1.21 356 130 134 4 510.87 1.29 357 131 134 3 517.75 0.48 358 131 135 4 509.63 1.93 359 132 135 3 517.00 0.85 360 132 136 4 509.62 1.92 361 133 136 3 509.62 1.92 362 133 137 4 509.62 1.92 363 134 137 3 504.77 0.52 364 134 138 4 504.77 0.52 365 135 138 3 504.77 0.52 366 135 139 4 500.60 2.61 367 136 139 3 523.34 1.03 368 136 140 4 501.04 2.40 369 137 140 3 505.31 0.27 370 137 141 4 501.04 2.40 371 138 141 3 524.12 1.54 372 138 142 4 500.11 1.93 373 139 142 3 505.30 0.28 374 139 143 4 497.26 3.35 375 140 143 3 512.78 1.64 376 140 144 4 504.93 0.48 377 141 144 3 515.40 3.75 378 141 145 4 511.99 2.04 379 142 145 3 514.72 1.61 380 142 146 4 505.42 0.28 381 143 146 3 509.94 0.77 382 143 147 4 505.43 0.29 383 143 152 9 236.28 15.70 384 144 147 3 507.12 1.21 385 144 148 4 505.36 0.33 386 145 148 3 505.06 0.48 387 145 149 4 504.96 0.52 388 146 149 3 516.28 0.36 389 146 150 4 493.19 1.81 390 146 151 5 387.92 15.70 391 146 152 6 263.86 28.03 392 147 150 3 492.24 2.32 393 147 152 5 282.68 18.62