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 2 129 127 30.44 0.15 2 3 7 4 476.43 0.69 3 3 8 5 440.28 6.53 4 3 75 72 31.69 0.88 5 3 78 75 30.25 0.16 6 3 129 126 30.57 0.14 7 3 130 127 30.38 0.18 8 3 133 130 30.26 0.17 9 4 7 3 485.84 0.57 10 4 8 4 476.44 0.69 11 5 8 3 489.78 2.39 12 5 9 4 481.41 1.80 13 6 9 3 497.61 1.53 14 6 10 4 476.43 0.69 15 6 122 116 69.20 0.33 16 6 125 119 62.23 1.75 17 6 126 120 55.45 0.29 18 7 10 3 488.82 1.99 19 7 11 4 476.73 0.84 20 7 126 119 55.41 0.28 21 7 129 122 55.44 0.29 22 8 11 3 491.93 3.54 23 8 12 4 477.86 1.42 24 8 75 67 55.43 0.30 25 8 76 68 55.45 0.29 26 9 12 3 479.75 2.37 27 9 13 4 477.86 1.43 28 10 13 3 484.91 0.21 29 10 14 4 479.59 2.30 30 10 122 112 72.64 0.25 31 10 123 113 70.97 0.49 32 10 126 116 70.94 0.49 33 11 14 3 484.15 1.79 34 11 15 4 467.89 4.65 35 11 72 61 70.93 0.49 36 11 75 64 70.94 0.49 37 11 126 115 70.96 0.48 38 11 127 116 70.94 0.49 39 11 130 119 70.84 0.45 40 12 15 3 482.52 0.97 41 12 16 4 487.51 1.68 42 12 72 60 70.94 0.49 43 12 75 63 70.98 0.48 44 13 16 3 487.59 1.65 45 13 17 4 481.26 4.80 46 14 17 3 488.41 1.79 47 14 18 4 481.35 4.77 48 14 118 104 87.42 0.47 49 14 119 105 82.12 0.04 50 14 123 109 75.44 1.61 51 14 127 113 72.57 0.21 52 15 18 3 487.56 1.67 53 15 19 4 461.22 1.64 54 15 22 7 423.12 2.08 55 15 65 50 82.48 0.17 56 15 68 53 75.84 1.92 57 15 69 54 72.50 0.24 58 15 72 57 72.48 0.26 59 17 20 3 530.27 4.00 60 17 115 98 99.73 0.37 61 17 118 101 97.54 0.69 62 18 21 3 493.70 2.31 63 18 22 4 481.87 5.09 64 18 25 7 428.40 9.12 65 18 111 93 97.57 0.70 66 18 115 97 99.73 0.37 67 19 22 3 486.78 2.63 68 20 115 95 125.65 0.36 69 21 24 3 489.13 1.15 70 21 25 4 471.83 1.42 71 21 114 93 125.65 0.36 72 21 115 94 125.67 0.35 73 22 25 3 488.93 4.47 74 22 26 4 472.50 1.76 75 22 65 43 105.69 0.35 76 23 26 3 498.09 2.60 77 23 27 4 479.00 3.63 78 23 62 39 112.78 1.26 79 24 27 3 490.53 0.66 80 24 28 4 486.59 0.17 81 24 114 90 147.41 0.11 82 25 28 3 490.52 0.66 83 25 29 4 486.58 0.17 84 25 65 40 125.56 0.32 85 25 107 82 125.68 0.35 86 25 110 85 137.81 0.01 87 25 111 86 135.82 1.64 88 25 114 89 147.49 0.08 89 25 115 90 147.49 0.08 90 26 29 3 498.16 4.48 91 26 30 4 480.55 3.19 92 26 61 35 125.67 0.35 93 26 65 39 125.56 0.32 94 27 30 3 489.12 1.44 95 27 31 4 481.02 2.94 96 27 57 30 148.18 0.15 97 27 58 31 147.88 0.29 98 27 61 34 136.72 1.06 99 28 31 3 488.70 1.57 100 28 32 4 475.39 0.12 101 28 110 82 148.48 0.01 102 28 113 85 148.74 0.08 103 29 32 3 482.74 1.92 104 29 33 4 475.39 0.12 105 29 103 74 148.42 0.01 106 29 106 77 148.44 0.01 107 29 107 78 148.41 0.01 108 29 110 81 148.53 0.01 109 30 33 3 477.34 1.09 110 30 34 4 475.17 0.01 111 30 44 14 214.02 31.09 112 30 47 17 150.80 0.40 113 30 57 27 149.53 0.32 114 30 60 30 148.97 0.16 115 30 61 31 148.65 0.04 116 30 64 34 148.58 0.00 117 30 103 73 148.50 0.03 118 31 34 3 484.98 0.95 119 31 35 4 479.12 1.98 120 31 52 21 149.76 0.29 121 31 57 26 149.54 0.32 122 32 35 3 487.29 0.21 123 32 36 4 468.93 3.16 124 32 106 74 149.65 0.30 125 32 110 78 149.97 0.16 126 32 113 81 150.03 0.15 127 33 36 3 497.19 4.28 128 33 37 4 475.20 0.01 129 33 40 7 332.80 13.59 130 33 44 11 331.92 14.02 131 33 102 69 149.66 0.32 132 33 103 70 149.62 0.30 133 33 106 73 149.68 0.31 134 34 37 3 502.66 1.54 135 34 38 4 458.98 2.52 136 34 40 6 332.80 13.59 137 34 41 7 256.00 51.98 138 34 44 10 225.20 36.58 139 34 50 16 150.71 0.42 140 34 57 23 150.62 0.42 141 35 38 3 495.05 6.75 142 37 40 3 501.42 0.80 143 37 102 65 149.83 0.39 144 37 105 68 150.40 0.35 145 37 106 69 150.50 0.40 146 38 41 3 490.15 0.60 147 39 42 3 505.82 2.96 148 39 102 63 150.50 0.42 149 40 43 3 517.14 1.15 150 40 44 4 496.06 0.58 151 40 99 59 150.12 0.55 152 40 102 62 150.49 0.43 153 41 44 3 493.10 2.64 154 41 45 4 490.40 3.41 155 41 50 9 150.84 0.43 156 43 46 3 604.34 2.21 157 43 94 51 150.10 0.58 158 43 95 52 150.10 0.59 159 43 96 53 150.31 0.54 160 43 99 56 150.53 0.45 161 44 47 3 505.19 1.64 162 44 50 6 220.66 34.45 163 44 60 16 150.68 0.43 164 45 50 5 452.43 1.91 165 47 50 3 519.04 2.10 166 47 56 9 151.24 0.30 167 47 57 10 151.28 0.29 168 47 60 13 151.24 0.30 169 48 56 8 151.29 0.29 170 49 54 5 311.96 8.04 171 50 57 7 219.03 27.11 172 51 54 3 488.00 0.23 173 51 57 6 428.06 8.46 174 53 57 4 466.86 0.64 175 53 58 5 461.61 0.70 176 54 57 3 495.99 3.26 177 54 58 4 470.98 2.70 178 55 58 3 496.00 3.27 179 55 59 4 471.19 4.12 180 56 59 3 490.98 5.77 181 56 60 4 471.19 4.12 182 57 60 3 493.29 1.81 183 57 61 4 481.98 1.25 184 58 61 3 490.07 3.43 185 58 62 4 488.23 4.35 186 59 62 3 493.29 1.82 187 59 63 4 482.03 1.23 188 60 63 3 482.12 1.28 189 60 64 4 482.02 1.23 190 61 64 3 499.29 2.45 191 61 65 4 481.17 0.81 192 62 65 3 499.29 2.45 193 62 66 4 482.98 0.10 194 63 66 3 496.41 3.89 195 63 67 4 488.18 2.26 196 64 67 3 488.18 2.26 197 64 68 4 488.18 2.26 198 64 103 39 176.91 2.23 199 65 68 3 483.41 0.12 200 65 69 4 481.16 1.00 201 65 107 42 193.59 5.80 202 66 69 3 483.50 0.17 203 66 70 4 478.92 2.37 204 67 70 3 485.03 0.29 205 67 71 4 480.03 0.44 206 67 85 18 176.90 2.21 207 68 71 3 493.18 5.02 208 68 72 4 480.02 0.45 209 68 107 39 209.57 5.32 210 68 130 62 217.07 8.00 211 68 131 63 202.19 1.70 212 69 72 3 484.09 2.50 213 69 73 4 484.07 2.50 214 70 73 3 484.07 2.50 215 70 74 4 484.07 2.50 216 70 81 11 240.29 23.18 217 70 82 12 234.20 26.22 218 70 85 15 234.18 26.21 219 71 74 3 484.06 2.50 220 71 75 4 468.92 0.58 221 71 78 7 287.51 0.16 222 71 82 11 234.16 26.25 223 71 130 59 234.78 6.64 224 71 134 63 201.79 1.79 225 72 75 3 480.75 0.83 226 72 130 58 246.50 0.79 227 74 77 3 494.28 3.09 228 74 78 4 423.03 7.37 229 74 81 7 277.45 4.57 230 75 78 3 487.03 0.54 231 75 130 55 269.81 4.57 232 77 80 3 499.29 1.54 233 77 81 4 482.99 0.79 234 78 81 3 485.95 0.69 235 78 82 4 482.18 1.20 236 78 130 52 273.50 5.08 237 78 133 55 272.18 5.32 238 78 134 56 272.18 5.32 239 78 137 59 270.46 4.48 240 79 82 3 503.23 0.01 241 79 83 4 476.03 4.27 242 79 137 58 270.49 4.48 243 79 140 61 270.49 4.48 244 80 83 3 486.02 0.04 245 82 85 3 482.98 0.28 246 82 86 4 472.83 4.79 247 82 134 52 273.51 5.09 248 82 137 55 273.10 5.18 249 82 138 56 273.16 5.17 250 83 86 3 489.63 3.53 251 83 87 4 473.96 4.30 252 83 141 58 273.10 5.18 253 84 87 3 479.28 1.57 254 84 88 4 472.24 3.45 255 85 88 3 480.43 3.33 256 85 89 4 476.45 1.34 257 85 138 53 273.48 5.11 258 86 89 3 491.30 2.11 259 86 90 4 463.38 0.04 260 86 137 51 273.63 5.17 261 86 138 52 273.48 5.11 262 86 140 54 273.47 5.11 263 86 141 55 273.37 5.13 264 87 90 3 492.81 1.36 265 87 91 4 465.83 1.27 266 87 141 54 273.25 5.15 267 88 91 3 501.31 1.23 268 88 92 4 424.99 8.81 269 88 93 5 424.98 8.81 270 89 93 4 405.19 11.62 271 89 94 5 386.55 2.48 272 89 95 6 306.02 7.91 273 89 100 11 279.45 6.07 274 89 142 53 273.39 5.15 275 90 94 4 386.22 2.65 276 90 141 51 273.62 5.20 277 90 142 52 273.25 5.15 278 91 94 3 486.42 5.01 279 91 141 50 273.64 5.20 280 94 142 48 273.69 5.21 281 95 99 4 483.30 0.15 282 95 100 5 473.43 5.04 283 95 142 47 273.85 5.17 284 96 99 3 499.91 2.05 285 97 100 3 494.38 1.46 286 97 139 42 274.06 5.17 287 97 142 45 273.95 5.12 288 98 101 3 502.20 0.60 289 98 102 4 491.19 0.81 290 99 102 3 490.62 1.09 291 99 103 4 487.64 2.58 292 100 103 3 492.84 0.01 293 100 104 4 487.64 2.58 294 100 135 35 274.31 5.22 295 100 138 38 274.32 5.22 296 100 139 39 274.31 5.21 297 100 142 42 274.29 5.20 298 101 104 3 491.20 0.81 299 101 105 4 487.63 2.58 300 102 105 3 487.66 2.58 301 102 106 4 486.00 4.50 302 103 106 3 486.00 4.50 303 103 107 4 486.00 4.50 304 104 107 3 486.50 4.25 305 104 108 4 484.09 5.45 306 104 131 27 274.51 5.20 307 105 108 3 488.95 3.02 308 105 109 4 478.09 2.45 309 106 109 3 478.09 2.45 310 106 110 4 478.08 2.45 311 107 110 3 482.06 4.45 312 107 111 4 474.18 0.52 313 107 131 24 275.10 5.00 314 108 111 3 489.86 2.29 315 108 112 4 474.17 0.52 316 108 119 11 276.78 4.98 317 108 124 16 275.50 5.00 318 108 127 19 275.42 4.99 319 108 128 20 275.21 5.02 320 108 131 23 275.24 5.00 321 109 112 3 489.86 2.29 322 109 113 4 471.52 0.78 323 110 113 3 474.09 0.55 324 110 114 4 471.47 0.76 325 111 114 3 477.30 1.23 326 111 115 4 463.68 2.23 327 111 119 8 280.97 5.67 328 111 127 16 275.74 4.95 329 112 116 4 406.98 1.83 330 112 119 7 280.97 5.67 331 113 116 3 497.07 1.44 332 115 118 3 497.23 1.37 333 115 119 4 462.95 1.43 334 116 119 3 486.84 0.56 335 117 120 3 521.62 0.59 336 118 123 5 467.41 1.32 337 119 123 4 467.41 1.32 338 119 124 5 467.16 1.55 339 119 127 8 453.15 8.04 340 120 123 3 481.01 5.28 341 120 124 4 467.51 1.38 342 121 124 3 481.20 5.17 343 121 125 4 467.65 1.79 344 122 125 3 500.56 0.43 345 122 126 4 477.19 3.11 346 123 126 3 500.57 0.43 347 123 127 4 479.94 1.74 348 124 127 3 494.79 0.29 349 124 128 4 474.04 4.68 350 125 128 3 494.78 0.29 351 125 129 4 474.44 4.47 352 126 129 3 494.78 0.29 353 126 130 4 472.44 3.48 354 127 130 3 472.44 3.48 355 127 131 4 472.89 3.70 356 128 131 3 478.54 3.00 357 128 132 4 474.93 2.69 358 129 132 3 481.33 0.50 359 129 133 4 474.94 2.69 360 130 133 3 483.85 0.77 361 130 134 4 481.32 0.50 362 131 134 3 481.32 0.51 363 131 135 4 481.30 0.51 364 132 135 3 481.29 0.52 365 132 136 4 481.29 0.51 366 133 136 3 488.26 2.98 367 133 137 4 480.18 1.06 368 134 137 3 482.52 0.11 369 134 138 4 464.85 6.62 370 135 138 3 477.69 0.20 371 135 139 4 464.82 6.61 372 136 139 3 480.94 6.22 373 136 140 4 464.09 6.24 374 137 140 3 480.32 1.50 375 138 142 4 501.14 2.44 376 139 142 3 497.90 0.81