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 5 474.66 2.87 2 2 10 8 450.63 6.85 3 2 130 128 36.98 0.66 4 2 133 131 31.32 0.32 5 2 134 132 30.21 0.06 6 2 137 135 29.98 0.05 7 3 6 3 514.95 1.61 8 3 7 4 507.25 5.47 9 4 7 3 513.81 2.53 10 4 8 4 503.75 3.41 11 4 79 75 55.04 1.25 12 5 8 3 513.66 2.27 13 5 9 4 513.65 2.26 14 6 9 3 527.05 4.43 15 6 10 4 499.90 1.04 16 6 130 124 62.20 1.50 17 6 133 127 62.29 1.55 18 7 10 3 505.56 1.79 19 7 11 4 499.90 1.04 20 7 76 69 65.28 0.06 21 7 79 72 65.28 0.06 22 7 80 73 67.75 1.28 23 7 134 127 62.32 1.55 24 7 137 130 62.31 1.54 25 8 11 3 524.61 2.87 26 8 12 4 505.78 3.98 27 9 12 3 516.21 3.54 28 9 13 4 511.00 1.37 29 9 126 117 81.86 1.45 30 9 127 118 81.86 1.45 31 9 130 121 81.84 1.46 32 10 13 3 517.69 2.13 33 10 14 4 513.73 0.01 34 10 76 66 81.84 1.46 35 10 130 120 81.86 1.46 36 10 131 121 81.84 1.46 37 10 134 124 81.71 1.45 38 11 14 3 515.64 0.96 39 11 15 4 513.74 0.02 40 11 76 65 81.84 1.44 41 11 77 66 81.85 1.44 42 11 79 68 81.86 1.45 43 12 15 3 523.88 2.63 44 12 16 4 521.69 3.99 45 13 16 3 524.14 2.76 46 13 17 4 524.48 2.60 47 13 115 102 89.36 0.69 48 13 123 110 89.42 0.71 49 13 127 114 86.44 0.17 50 13 131 118 86.34 0.12 51 14 17 3 523.40 2.06 52 14 18 4 516.01 1.30 53 14 69 55 137.55 24.83 54 14 72 58 86.58 0.05 55 14 73 59 86.33 0.12 56 14 76 62 86.28 0.15 57 14 77 63 88.59 1.01 58 14 131 117 86.70 0.10 59 15 18 3 523.40 2.06 60 15 19 4 520.25 0.48 61 16 19 3 521.47 0.12 62 16 24 8 446.81 3.40 63 16 119 103 104.23 1.02 64 16 122 106 104.37 0.95 65 17 20 3 520.25 0.48 66 17 21 4 483.66 0.48 67 17 24 7 413.97 8.62 68 17 69 52 144.42 24.40 69 17 115 98 99.00 3.61 70 18 21 3 509.05 0.10 71 18 77 59 90.40 0.47 72 20 23 3 506.86 3.89 73 20 24 4 494.97 1.60 74 21 24 3 509.80 2.90 75 21 25 4 497.49 0.36 76 21 66 45 158.32 18.74 77 21 69 48 157.07 19.36 78 21 70 49 157.06 19.34 79 22 25 3 512.67 0.97 80 22 26 4 508.01 1.35 81 22 62 40 164.91 16.48 82 22 66 44 161.31 17.34 83 23 26 3 513.87 0.38 84 23 27 4 508.01 1.35 85 23 62 39 171.60 13.12 86 24 27 3 513.87 0.37 87 24 28 4 508.03 1.35 88 24 69 45 163.94 15.94 89 24 114 90 152.41 3.48 90 24 115 91 152.31 3.52 91 24 118 94 154.65 2.76 92 24 119 95 154.69 2.74 93 25 28 3 515.38 1.13 94 25 29 4 509.00 1.74 95 25 65 40 163.94 15.93 96 25 69 44 163.94 15.93 97 26 29 3 515.51 0.67 98 26 30 4 508.47 2.01 99 26 55 29 188.72 19.02 100 26 56 30 188.75 19.04 101 26 58 32 188.19 18.81 102 26 61 35 173.96 12.44 103 26 62 36 173.46 12.20 104 27 30 3 519.38 1.05 105 27 31 4 509.01 1.74 106 27 56 29 188.78 19.04 107 27 114 87 155.85 3.23 108 28 31 3 509.02 1.74 109 28 32 4 507.95 2.27 110 28 107 79 156.16 3.51 111 28 110 82 156.15 3.42 112 28 111 83 156.12 3.40 113 28 114 86 155.95 3.18 114 29 32 3 507.93 2.25 115 29 33 4 506.95 2.73 116 29 61 32 185.41 17.39 117 29 64 35 174.66 12.08 118 29 65 36 173.29 11.51 119 29 107 78 156.31 3.46 120 30 33 3 514.47 3.06 121 30 34 4 506.81 2.80 122 30 52 22 189.59 19.05 123 30 55 25 189.43 19.02 124 30 56 26 189.53 19.07 125 30 61 31 188.20 18.80 126 31 34 3 515.26 1.42 127 31 35 4 494.85 3.31 128 31 110 79 156.31 3.35 129 31 113 82 156.72 3.12 130 31 114 83 156.71 3.11 131 32 35 3 523.18 6.14 132 32 36 4 489.61 0.70 133 32 39 7 423.12 9.16 134 32 106 74 156.34 3.46 135 32 107 75 156.41 3.42 136 32 110 78 156.56 3.21 137 33 36 3 514.67 1.89 138 33 37 4 492.31 3.60 139 33 39 6 423.44 7.25 140 33 40 7 337.09 12.56 141 33 43 10 337.11 12.55 142 33 46 13 210.33 28.78 143 33 55 22 189.75 19.07 144 33 61 28 189.65 19.08 145 34 37 3 520.54 1.05 146 34 52 18 189.76 19.07 147 34 55 21 189.90 19.04 148 36 39 3 523.42 6.03 149 36 106 70 156.77 3.42 150 37 40 3 512.51 0.84 151 38 41 3 520.13 4.65 152 38 103 65 157.00 3.54 153 38 106 68 157.28 3.37 154 39 42 3 522.95 4.87 155 39 43 4 527.49 2.60 156 39 103 64 156.81 3.58 157 39 106 67 157.25 3.37 158 40 43 3 524.57 1.13 159 40 46 6 357.04 29.38 160 40 47 7 281.43 1.06 161 40 49 9 267.54 5.46 162 41 47 6 284.53 2.59 163 42 97 55 157.09 3.70 164 42 98 56 157.09 3.69 165 42 99 57 157.08 3.68 166 42 100 58 157.35 3.55 167 42 103 61 157.34 3.37 168 43 46 3 522.02 2.35 169 43 47 4 510.16 1.45 170 43 64 21 190.34 18.86 171 44 47 3 527.98 0.74 172 45 48 3 587.00 2.00 173 45 60 15 190.59 18.97 174 45 64 19 190.56 18.96 175 46 49 3 527.95 0.76 176 46 60 14 190.61 18.96 177 46 61 15 190.56 18.98 178 46 64 18 190.57 18.96 179 49 54 5 428.57 17.86 180 49 55 6 357.50 6.34 181 49 58 9 286.87 2.49 182 49 61 12 232.27 28.11 183 50 54 4 502.07 2.08 184 51 54 3 498.31 0.05 185 51 55 4 496.16 0.90 186 52 55 3 499.36 0.70 187 52 56 4 496.17 0.89 188 53 56 3 508.74 0.78 189 53 57 4 499.35 0.70 190 54 57 3 504.12 1.68 191 54 58 4 499.35 0.70 192 55 58 3 513.70 4.29 193 55 61 6 411.92 1.88 194 58 61 3 533.39 2.67 195 58 62 4 499.62 0.70 196 59 62 3 508.95 3.97 197 59 63 4 498.00 0.12 198 60 63 3 517.53 3.13 199 60 64 4 504.53 3.37 200 61 64 3 517.53 3.13 201 61 65 4 504.05 2.93 202 62 65 3 512.47 1.68 203 62 66 4 511.53 0.82 204 63 66 3 512.87 0.14 205 63 67 4 511.53 0.82 206 64 67 3 510.86 1.16 207 64 68 4 510.90 1.18 208 65 68 3 514.95 2.38 209 65 69 4 511.73 0.76 210 66 69 3 521.32 0.81 211 66 70 4 508.75 0.73 212 67 70 3 514.27 2.02 213 67 71 4 508.75 0.73 214 68 71 3 523.49 0.14 215 68 72 4 506.75 1.73 216 68 107 39 165.81 1.28 217 69 72 3 514.23 2.05 218 69 73 4 506.36 1.89 219 69 111 42 166.01 1.49 220 70 73 3 524.03 2.33 221 70 74 4 511.78 0.82 222 71 74 3 526.26 1.22 223 71 75 4 511.78 0.83 224 72 75 3 520.58 1.63 225 72 76 4 512.58 0.42 226 72 111 39 166.20 1.49 227 72 135 63 165.36 2.18 228 72 138 66 165.16 2.27 229 73 76 3 509.62 1.06 230 73 77 4 509.57 1.08 231 74 77 3 512.57 0.42 232 74 78 4 510.34 0.70 233 75 78 3 531.00 3.25 234 75 82 7 210.18 20.12 235 75 85 10 171.97 1.01 236 75 86 11 201.61 15.84 237 75 89 14 167.53 1.21 238 75 138 63 165.44 2.27 239 76 79 3 523.65 5.96 240 76 131 55 179.18 8.85 241 76 134 58 178.24 8.53 242 78 81 3 509.16 1.30 243 78 82 4 409.20 8.24 244 78 85 7 303.04 12.94 245 80 83 3 619.98 1.34 246 80 137 57 182.15 10.44 247 82 85 3 523.83 2.84 248 82 86 4 505.18 3.31 249 82 137 55 211.71 25.23 250 82 141 59 210.88 25.09 251 83 86 3 514.67 0.24 252 83 87 4 509.78 1.01 253 84 88 4 523.83 0.15 254 85 88 3 540.15 1.74 255 85 89 4 521.71 1.01 256 86 89 3 528.69 2.58 257 86 90 4 516.57 3.58 258 86 138 52 213.66 26.37 259 86 141 55 213.26 26.51 260 86 142 56 212.96 26.66 261 87 90 3 523.83 0.15 262 87 91 4 516.12 3.80 263 87 145 58 211.05 27.62 264 88 91 3 516.22 0.03 265 88 92 4 512.41 1.92 266 89 92 3 516.47 2.12 267 89 93 4 512.41 1.92 268 89 138 49 213.66 26.38 269 90 93 3 513.41 2.41 270 90 94 4 512.41 1.92 271 90 142 52 212.34 27.02 272 90 145 55 209.37 28.50 273 90 146 56 209.36 28.50 274 91 94 3 520.20 3.98 275 91 95 4 505.75 0.59 276 91 149 58 208.83 28.66 277 92 95 3 524.01 2.08 278 92 96 4 435.81 11.54 279 92 97 5 428.05 7.79 280 93 97 4 419.53 3.53 281 93 98 5 419.51 3.52 282 93 99 6 289.98 3.35 283 93 146 53 209.38 28.51 284 94 98 4 381.48 22.54 285 94 146 52 209.36 28.52 286 94 149 55 207.41 29.40 287 94 151 57 168.50 48.68 288 95 98 3 512.38 1.92 289 98 151 53 174.32 45.89 290 99 103 4 508.34 1.75 291 99 104 5 508.35 1.75 292 99 146 47 209.88 28.78 293 99 151 52 168.62 48.75 294 100 103 3 521.72 0.46 295 100 104 4 514.44 0.89 296 100 146 46 209.75 28.84 297 100 151 51 164.18 50.99 298 100 153 53 93.75 40.70 299 101 104 3 515.67 0.28 300 101 105 4 508.38 1.75 301 101 139 38 213.76 27.07 302 101 142 41 211.83 28.00 303 101 143 42 211.10 28.34 304 101 146 45 209.75 28.87 305 102 105 3 513.25 0.86 306 102 106 4 508.41 1.74 307 103 106 3 517.91 3.01 308 103 107 4 508.50 1.70 309 104 107 3 525.83 1.12 310 104 108 4 508.34 1.61 311 104 139 35 213.72 27.12 312 104 142 38 211.27 28.34 313 104 146 42 209.95 28.95 314 105 108 3 519.81 4.13 315 105 109 4 508.32 1.60 316 105 139 34 213.83 27.10 317 106 109 3 518.10 4.92 318 106 110 4 507.41 0.42 319 107 110 3 510.78 1.26 320 107 111 4 506.62 0.81 321 108 111 3 522.62 4.18 322 108 112 4 508.94 1.56 323 108 135 27 214.53 26.78 324 108 139 31 213.84 27.11 325 109 112 3 516.64 1.68 326 109 113 4 503.43 0.07 327 110 113 3 507.79 2.14 328 110 114 4 503.44 0.05 329 111 114 3 508.17 2.32 330 111 115 4 503.54 0.04 331 111 131 20 215.18 26.98 332 111 135 24 215.04 27.03 333 112 115 3 506.78 1.65 334 112 116 4 503.55 0.03 335 112 123 11 263.35 3.98 336 112 128 16 215.31 27.04 337 112 135 23 215.05 27.03 338 113 116 3 520.27 0.07 339 113 117 4 503.56 0.03 340 114 117 3 509.93 3.21 341 114 118 4 499.69 1.90 342 115 118 3 515.45 0.46 343 115 119 4 496.37 1.91 344 115 123 8 265.13 4.87 345 115 131 16 215.34 27.05 346 116 119 3 513.83 2.77 347 116 120 4 475.66 12.26 348 116 123 7 288.66 6.88 349 116 128 12 256.74 7.28 350 117 120 3 527.48 0.69 351 119 122 3 503.06 3.87 352 119 123 4 486.42 6.57 353 123 127 4 491.79 3.55 354 123 128 5 490.39 2.85 355 123 131 8 446.16 5.32 356 124 127 3 510.95 2.96 357 124 128 4 499.09 3.12 358 125 128 3 511.28 2.80 359 125 129 4 501.75 1.79 360 126 129 3 510.06 2.33 361 126 130 4 502.68 1.37 362 127 130 3 514.38 2.76 363 127 131 4 502.63 1.35 364 128 131 3 507.62 3.83 365 128 132 4 498.17 0.88 366 129 132 3 512.10 1.60 367 129 133 4 500.07 1.83 368 130 133 3 510.29 3.26 369 130 134 4 502.17 3.60 370 131 134 3 511.21 2.75 371 131 135 4 500.25 2.56 372 132 135 3 515.08 0.82 373 132 136 4 505.47 0.05 374 133 136 3 511.41 1.02 375 133 137 4 505.48 0.05 376 134 137 3 513.50 0.03 377 134 138 4 505.48 0.05 378 135 138 3 505.93 0.18 379 135 139 4 506.84 0.29 380 136 139 3 510.72 1.66 381 136 140 4 505.90 0.18 382 137 140 3 517.06 1.09 383 137 141 4 506.09 0.08 384 138 141 3 516.64 1.30 385 138 142 4 506.10 0.07 386 139 142 3 509.81 1.78 387 139 143 4 503.79 0.91 388 140 143 3 511.16 2.62 389 140 144 4 503.98 0.94 390 141 144 3 511.01 1.55 391 141 145 4 504.22 1.04 392 142 145 3 513.71 1.11 393 142 146 4 504.01 0.95 394 143 146 3 505.56 0.33 395 143 147 4 504.00 0.95 396 144 147 3 505.56 0.33 397 144 148 4 504.00 0.95 398 145 148 3 513.94 3.63 399 145 149 4 497.69 1.54 400 146 149 3 513.85 0.58 401 146 150 4 496.12 2.87 402 146 151 5 456.55 10.47 403 147 150 3 510.90 0.10