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 5 488.33 2.80 2 2 10 8 469.44 2.89 3 2 130 128 34.47 0.81 4 2 133 131 30.30 1.01 5 2 134 132 26.20 1.05 6 2 137 135 26.19 1.05 7 3 6 3 513.10 1.70 8 3 7 4 495.98 0.94 9 4 7 3 503.09 3.31 10 4 8 4 496.91 0.48 11 5 8 3 509.18 0.27 12 5 9 4 497.14 0.35 13 6 9 3 497.55 0.54 14 6 10 4 498.25 0.06 15 6 130 124 62.85 0.22 16 6 133 127 62.85 0.22 17 7 10 3 500.07 0.73 18 7 11 4 498.27 0.06 19 7 76 69 62.88 0.23 20 7 79 72 62.87 0.23 21 7 80 73 63.47 0.07 22 7 134 127 62.87 0.22 23 7 137 130 62.88 0.22 24 8 11 3 511.61 4.21 25 8 12 4 500.44 1.14 26 9 12 3 503.56 0.18 27 9 13 4 500.68 1.27 28 9 126 117 76.33 0.55 29 9 127 118 76.14 0.51 30 9 130 121 76.09 0.52 31 10 13 3 515.11 2.29 32 10 14 4 510.98 2.54 33 10 76 66 76.14 0.51 34 10 130 120 76.18 0.49 35 10 131 121 76.09 0.52 36 10 134 124 76.09 0.52 37 11 14 3 516.75 1.20 38 11 15 4 515.22 0.43 39 11 76 65 76.20 0.48 40 11 77 66 76.20 0.48 41 11 79 68 76.20 0.49 42 12 15 3 521.22 2.73 43 12 16 4 516.92 1.27 44 13 16 3 522.24 1.39 45 13 17 4 516.91 1.27 46 13 115 102 85.27 0.09 47 13 123 110 83.74 0.68 48 13 127 114 83.15 0.41 49 13 131 118 83.11 0.40 50 14 17 3 516.90 1.28 51 14 18 4 516.90 1.29 52 14 21 7 482.45 2.76 53 14 69 55 83.50 0.58 54 14 72 58 83.13 0.40 55 14 73 59 83.04 0.39 56 14 76 62 83.02 0.39 57 14 77 63 83.03 0.39 58 14 131 117 83.14 0.40 59 15 18 3 516.90 1.29 60 15 19 4 516.90 1.29 61 16 19 3 517.78 0.85 62 16 24 8 449.78 3.80 63 16 119 103 101.64 0.93 64 16 122 106 101.48 0.86 65 17 20 3 521.51 1.01 66 17 21 4 491.91 3.40 67 17 24 7 383.97 1.47 68 17 69 52 144.03 25.93 69 17 115 98 97.80 0.96 70 18 77 59 89.84 1.17 71 20 23 3 511.09 3.90 72 20 24 4 498.80 2.35 73 21 24 3 515.42 3.63 74 21 25 4 498.81 2.35 75 21 66 45 154.14 21.07 76 21 69 48 153.61 21.23 77 21 70 49 153.61 21.23 78 22 25 3 500.92 1.68 79 22 26 4 498.25 2.63 80 22 62 40 163.51 17.23 81 22 66 44 157.06 19.62 82 23 26 3 509.73 1.51 83 23 27 4 502.92 0.29 84 24 27 3 511.51 2.25 85 24 28 4 501.32 0.52 86 24 69 45 163.27 16.52 87 24 114 90 149.16 5.47 88 24 115 91 149.22 5.48 89 24 118 94 152.25 3.60 90 24 119 95 152.72 3.38 91 25 28 3 511.51 2.25 92 25 29 4 501.32 0.51 93 25 65 40 164.13 16.68 94 25 69 44 163.26 16.52 95 26 29 3 509.70 1.26 96 26 30 4 509.37 3.52 97 26 56 30 187.46 19.41 98 26 61 35 171.03 13.76 99 26 62 36 171.81 13.38 100 26 65 39 170.84 13.76 101 27 30 3 509.68 3.37 102 27 31 4 509.35 3.52 103 27 114 87 153.12 3.55 104 27 118 91 153.88 2.81 105 28 31 3 511.54 2.44 106 28 32 4 504.64 5.88 107 28 107 79 153.10 4.01 108 28 110 82 153.47 3.75 109 28 111 83 153.30 3.66 110 28 114 86 154.09 3.06 111 29 32 3 509.44 3.48 112 29 33 4 509.43 3.48 113 29 61 32 173.72 12.49 114 29 64 35 173.65 12.51 115 29 65 36 172.67 12.85 116 29 107 78 153.56 3.79 117 30 33 3 509.42 3.48 118 30 34 4 493.60 11.38 119 30 52 22 190.12 20.32 120 30 55 25 189.88 20.27 121 30 56 26 189.88 20.27 122 30 61 31 187.53 19.38 123 31 34 3 519.25 1.44 124 31 35 4 509.24 3.55 125 31 110 79 154.85 3.06 126 31 113 82 154.84 3.00 127 31 114 83 154.60 2.88 128 32 35 3 519.25 1.45 129 32 36 4 509.24 3.54 130 32 39 7 350.56 7.29 131 32 106 74 155.00 3.16 132 32 107 75 154.94 3.11 133 32 110 78 154.89 3.04 134 33 36 3 509.25 3.54 135 33 37 4 485.06 8.54 136 33 39 6 345.10 4.57 137 33 40 7 235.80 27.98 138 33 43 10 235.80 27.98 139 33 46 13 197.62 24.05 140 33 55 22 190.16 20.32 141 33 61 28 190.06 20.35 142 34 37 3 521.15 4.51 143 34 52 18 190.19 20.34 144 34 55 21 190.18 20.34 145 36 39 3 528.81 0.42 146 36 106 70 155.09 3.13 147 37 40 3 527.27 1.20 148 38 41 3 523.60 3.04 149 38 103 65 156.31 3.72 150 38 106 68 155.31 3.11 151 39 42 3 528.34 0.41 152 39 43 4 514.82 1.36 153 39 103 64 155.09 3.17 154 39 106 67 155.27 3.10 155 40 43 3 519.20 0.78 156 40 46 6 266.77 38.41 157 40 47 7 200.38 25.30 158 40 49 9 200.42 25.28 159 40 55 15 193.31 21.73 160 42 97 55 156.38 3.77 161 42 98 56 156.39 3.75 162 42 99 57 156.35 3.74 163 42 100 58 156.43 3.71 164 42 103 61 156.41 3.65 165 43 46 3 513.99 4.37 166 43 47 4 492.24 3.62 167 43 64 21 192.96 21.73 168 44 47 3 523.68 2.50 169 45 48 3 558.38 2.13 170 45 60 15 193.38 21.70 171 45 64 19 193.24 21.70 172 46 49 3 527.77 3.64 173 46 60 14 193.32 21.66 174 46 61 15 193.31 21.66 175 46 64 18 193.29 21.66 176 47 50 3 571.25 0.43 177 49 54 5 427.77 17.16 178 49 55 6 445.42 8.21 179 49 58 9 221.67 25.56 180 49 61 12 199.09 24.52 181 50 54 4 484.74 1.83 182 51 54 3 514.88 0.80 183 51 55 4 486.90 0.74 184 52 55 3 496.97 4.28 185 52 56 4 486.95 0.75 186 53 56 3 519.66 4.13 187 53 57 4 493.84 2.69 188 54 57 3 514.71 1.66 189 54 58 4 493.84 2.69 190 55 58 3 504.45 0.72 191 55 61 6 404.31 18.00 192 58 61 3 521.57 6.04 193 58 62 4 502.99 2.66 194 59 62 3 510.62 0.34 195 59 63 4 503.33 2.83 196 60 63 3 510.62 0.34 197 60 64 4 506.25 1.85 198 61 64 3 510.63 0.34 199 61 65 4 506.25 1.85 200 62 65 3 505.78 1.61 201 62 66 4 508.31 0.35 202 63 66 3 514.51 3.45 203 63 67 4 508.98 0.69 204 64 67 3 514.51 3.45 205 64 68 4 503.30 2.86 206 65 68 3 514.51 3.45 207 65 69 4 501.91 0.95 208 66 69 3 521.00 0.97 209 66 70 4 503.68 1.84 210 67 70 3 517.08 2.94 211 67 71 4 509.30 0.96 212 68 71 3 522.40 2.74 213 68 72 4 509.30 0.96 214 68 107 39 157.62 1.85 215 69 72 3 516.23 2.51 216 69 73 4 502.75 4.23 217 70 73 3 513.23 0.29 218 70 74 4 510.02 1.31 219 71 74 3 513.02 1.04 220 71 75 4 510.01 1.31 221 71 89 18 160.24 1.91 222 72 75 3 511.80 0.43 223 72 76 4 507.97 1.16 224 72 111 39 158.97 1.18 225 72 135 63 157.64 0.48 226 72 138 66 156.64 0.01 227 73 76 3 513.50 1.61 228 73 77 4 505.95 0.19 229 74 77 3 507.88 1.14 230 74 78 4 505.98 0.18 231 75 78 3 510.13 1.04 232 75 82 7 208.97 26.04 233 75 85 10 160.75 1.94 234 75 86 11 160.74 1.94 235 75 89 14 160.75 1.94 236 75 138 63 157.82 0.35 237 76 79 3 508.40 0.41 238 76 131 55 192.65 16.71 239 76 134 58 175.73 8.37 240 78 81 3 504.60 0.05 241 78 82 4 354.32 8.65 242 78 85 7 308.19 5.84 243 80 137 57 201.56 21.22 244 82 85 3 513.85 0.45 245 82 86 4 495.55 5.81 246 82 137 55 234.86 37.85 247 82 141 59 230.44 36.91 248 83 86 3 506.32 0.42 249 83 87 4 495.56 5.81 250 83 145 62 232.34 38.37 251 84 88 4 514.19 0.58 252 85 88 3 542.25 1.56 253 85 89 4 514.19 0.58 254 86 89 3 514.98 0.97 255 86 90 4 508.60 2.22 256 86 138 52 236.16 39.05 257 86 141 55 235.02 39.62 258 86 142 56 234.87 39.61 259 86 145 59 234.38 39.85 260 87 90 3 514.19 0.58 261 87 91 4 508.60 2.21 262 87 145 58 233.88 40.19 263 88 91 3 507.50 2.77 264 88 92 4 506.98 3.02 265 89 92 3 509.71 1.65 266 89 93 4 498.75 1.10 267 90 93 3 507.59 1.09 268 90 94 4 499.68 0.63 269 90 142 52 234.78 39.76 270 90 145 55 233.27 40.51 271 90 146 56 231.78 41.23 272 91 94 3 507.73 1.18 273 91 95 4 485.50 5.84 274 91 149 58 229.55 42.34 275 92 95 3 515.62 2.77 276 92 96 4 468.01 3.25 277 92 97 5 459.24 1.14 278 93 97 4 406.70 19.59 279 93 98 5 398.98 23.45 280 93 99 6 310.79 7.24 281 93 146 53 231.84 41.27 282 94 98 4 356.35 2.14 283 94 146 52 231.84 41.27 284 94 149 55 225.06 44.62 285 94 151 57 184.06 64.47 286 95 98 3 514.84 0.18 287 95 149 54 229.59 42.37 288 98 151 53 189.16 62.44 289 99 103 4 499.23 1.10 290 99 104 5 498.68 0.83 291 99 146 47 232.03 41.42 292 99 151 52 189.16 62.44 293 100 103 3 519.25 0.98 294 100 104 4 511.44 1.86 295 100 146 46 231.99 41.45 296 100 151 51 184.44 64.80 297 100 152 52 178.31 67.64 298 101 104 3 508.77 3.01 299 101 105 4 506.22 2.39 300 101 139 38 235.71 40.01 301 101 142 41 235.22 39.89 302 101 143 42 233.56 40.66 303 101 146 45 231.37 41.77 304 102 105 3 507.78 1.60 305 102 106 4 505.66 2.67 306 103 106 3 506.80 2.10 307 103 107 4 506.79 2.09 308 104 107 3 510.62 0.19 309 104 108 4 504.37 0.88 310 104 139 35 235.72 40.02 311 104 142 38 234.34 40.69 312 104 146 42 231.71 41.94 313 105 108 3 512.99 1.01 314 105 109 4 512.99 1.01 315 105 139 34 235.74 40.03 316 106 109 3 522.62 1.80 317 106 110 4 512.98 1.01 318 107 110 3 513.39 0.80 319 107 111 4 499.75 1.84 320 108 111 3 522.62 1.80 321 108 112 4 502.07 3.00 322 108 135 27 237.26 39.38 323 108 139 31 235.75 40.04 324 109 112 3 512.55 1.16 325 109 113 4 500.83 2.40 326 110 113 3 514.42 0.22 327 110 114 4 498.63 3.50 328 111 114 3 515.32 0.03 329 111 115 4 504.04 0.79 330 111 135 24 237.65 39.54 331 112 115 3 523.59 4.08 332 112 116 4 508.22 2.88 333 112 123 11 287.99 15.21 334 112 128 16 237.97 39.46 335 112 131 19 237.96 39.47 336 112 132 20 237.74 39.51 337 112 135 23 237.69 39.55 338 113 116 3 522.93 4.41 339 113 117 4 505.72 4.12 340 114 117 3 505.72 4.12 341 114 118 4 498.63 0.58 342 115 118 3 514.66 0.33 343 115 119 4 498.62 0.58 344 115 123 8 288.70 14.86 345 115 131 16 285.86 15.56 346 116 119 3 508.64 2.85 347 116 120 4 484.59 6.42 348 116 123 7 289.08 14.66 349 116 128 12 287.92 15.23 350 117 120 3 516.18 0.41 351 119 122 3 493.49 5.12 352 119 123 4 482.00 0.63 353 123 127 4 495.25 3.50 354 123 128 5 495.19 3.49 355 123 131 8 449.47 1.08 356 124 127 3 502.50 1.23 357 124 128 4 501.14 0.56 358 125 128 3 511.69 4.92 359 125 129 4 502.03 0.10 360 126 129 3 517.53 2.00 361 126 130 4 506.81 2.48 362 127 130 3 520.14 0.69 363 127 131 4 502.51 0.15 364 128 131 3 509.18 3.48 365 128 132 4 499.92 1.45 366 129 132 3 511.44 2.35 367 129 133 4 503.13 3.09 368 130 133 3 508.03 0.65 369 130 134 4 503.13 3.09 370 131 134 3 503.15 3.09 371 131 135 4 503.12 3.09 372 132 135 3 520.50 3.04 373 132 136 4 503.11 3.10 374 133 136 3 519.48 2.54 375 133 137 4 499.44 4.90 376 134 137 3 516.59 1.14 377 134 138 4 500.44 1.29 378 135 138 3 517.10 4.32 379 135 139 4 500.47 1.28 380 136 139 3 514.38 5.67 381 136 140 4 506.50 1.74 382 137 140 3 517.72 2.94 383 137 141 4 495.55 1.18 384 138 141 3 517.46 3.06 385 138 142 4 502.45 4.44 386 139 142 3 512.46 0.74 387 139 143 4 507.67 4.80 388 140 143 3 509.08 4.12 389 140 144 4 507.69 4.82 390 141 144 3 516.51 0.71 391 141 145 4 507.69 4.82 392 142 145 3 516.51 0.71 393 142 146 4 503.74 6.79 394 143 146 3 512.16 2.58 395 143 147 4 503.69 6.82 396 144 147 3 500.70 3.15 397 144 148 4 494.92 0.27 398 145 148 3 511.09 1.45 399 145 149 4 502.38 4.00 400 146 149 3 514.42 1.62 401 146 150 4 490.83 0.79 402 146 151 5 392.36 9.99 403 147 150 3 511.75 5.97