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 5 450.50 5.05 2 2 74 72 29.53 0.53 3 2 128 126 22.43 0.14 4 2 129 127 22.38 0.17 5 3 6 3 468.17 2.00 6 3 7 4 463.26 5.82 7 4 7 3 470.69 2.11 8 4 8 4 468.07 3.42 9 5 8 3 484.14 2.54 10 5 9 4 476.98 1.03 11 6 9 3 479.31 0.13 12 6 10 4 476.98 1.03 13 6 125 119 47.46 0.58 14 6 128 122 47.44 0.58 15 7 10 3 489.97 3.55 16 7 11 4 472.20 3.21 17 7 74 67 47.54 0.63 18 7 75 68 47.98 0.42 19 8 11 3 479.55 0.46 20 8 12 4 472.09 3.16 21 9 12 3 480.54 0.96 22 9 13 4 471.44 3.46 23 9 125 116 62.77 0.28 24 10 13 3 476.86 0.76 25 10 14 4 471.00 3.25 26 10 71 61 63.08 0.31 27 10 74 64 63.09 0.31 28 10 125 115 62.84 0.26 29 10 126 116 62.77 0.27 30 10 129 119 62.77 0.28 31 11 14 3 476.56 0.59 32 11 15 4 469.18 4.16 33 11 71 60 63.02 0.35 34 11 74 63 62.86 0.26 35 12 15 3 476.56 0.59 36 12 16 4 469.19 4.16 37 13 16 3 472.70 2.92 38 13 17 4 469.18 4.16 39 13 117 104 75.30 0.58 40 13 122 109 64.17 0.17 41 13 126 113 64.11 0.15 42 14 17 3 475.31 1.60 43 14 18 4 456.55 1.85 44 14 21 7 393.93 2.29 45 14 64 50 64.14 0.16 46 14 67 53 64.11 0.15 47 14 68 54 64.11 0.15 48 14 71 57 64.11 0.15 49 16 19 3 538.62 2.79 50 16 117 101 89.61 0.73 51 17 20 3 500.36 1.14 52 17 24 7 390.69 0.35 53 17 110 93 92.64 0.81 54 17 114 97 94.50 1.57 55 18 21 3 480.22 4.11 56 20 23 3 491.00 0.52 57 20 24 4 460.03 1.92 58 20 114 94 117.96 0.10 59 21 24 3 466.42 5.11 60 21 25 4 469.50 2.03 61 21 64 43 105.40 0.82 62 22 25 3 490.98 0.53 63 22 26 4 475.14 0.78 64 22 61 39 111.84 0.76 65 23 26 3 480.54 0.78 66 23 27 4 475.13 0.78 67 23 113 90 140.32 0.40 68 24 27 3 485.39 1.98 69 24 28 4 475.13 0.80 70 24 64 40 124.26 0.35 71 24 109 85 129.10 2.74 72 24 110 86 128.78 2.58 73 24 113 89 141.53 0.03 74 24 114 90 141.81 0.17 75 25 28 3 484.04 0.95 76 25 29 4 472.79 1.96 77 25 60 35 124.30 0.34 78 25 64 39 124.26 0.35 79 26 29 3 481.28 0.43 80 26 30 4 473.54 1.58 81 26 56 30 141.35 0.34 82 26 57 31 139.78 0.83 83 26 60 34 129.62 0.50 84 27 30 3 475.41 2.50 85 27 31 4 474.54 1.07 86 27 109 82 142.47 0.07 87 27 113 86 142.65 0.10 88 28 31 3 476.54 1.94 89 28 32 4 473.18 3.75 90 28 102 74 142.43 0.06 91 28 105 77 142.50 0.02 92 28 106 78 142.43 0.06 93 28 109 81 142.59 0.12 94 29 32 3 479.06 0.82 95 29 33 4 472.62 4.04 96 29 56 27 143.25 0.21 97 29 59 30 142.88 0.04 98 29 60 31 142.67 0.10 99 29 63 34 142.65 0.09 100 29 102 73 142.64 0.09 101 30 33 3 481.76 0.53 102 30 34 4 472.62 4.03 103 30 51 21 143.46 0.24 104 30 56 26 143.30 0.21 105 31 34 3 472.63 4.03 106 31 35 4 461.54 0.81 107 31 105 74 143.31 0.21 108 31 108 77 143.38 0.18 109 31 109 78 143.35 0.20 110 32 36 4 402.38 15.36 111 32 39 7 320.00 7.29 112 32 43 11 297.71 3.85 113 32 101 69 143.32 0.23 114 32 102 70 143.30 0.21 115 32 105 73 143.34 0.22 116 33 37 4 405.22 14.98 117 33 39 6 320.00 7.28 118 33 40 7 273.07 10.17 119 33 43 10 260.73 4.00 120 33 49 16 144.04 0.35 121 33 51 18 144.01 0.34 122 33 56 23 143.98 0.34 123 34 37 3 489.85 6.45 124 34 51 17 143.99 0.35 125 36 39 3 496.76 3.07 126 36 101 65 143.63 0.38 127 36 104 68 143.72 0.35 128 36 105 69 143.72 0.34 129 37 40 3 498.56 3.98 130 38 41 3 510.03 0.08 131 38 98 60 143.72 0.38 132 38 101 63 143.79 0.36 133 39 42 3 506.15 0.18 134 39 43 4 495.57 4.62 135 39 98 59 143.70 0.39 136 39 101 62 143.77 0.38 137 40 43 3 488.44 1.05 138 40 44 4 480.73 1.51 139 40 49 9 244.60 5.55 140 41 44 3 484.06 1.14 141 42 45 3 578.36 1.60 142 42 94 52 143.45 0.26 143 42 95 53 143.63 0.29 144 42 98 56 143.79 0.36 145 43 46 3 496.66 0.03 146 43 49 6 264.09 2.58 147 46 49 3 496.99 0.01 148 46 55 9 257.17 0.71 149 46 56 10 268.96 2.73 150 46 59 13 257.17 0.71 151 47 55 8 275.73 0.56 152 48 53 5 350.25 37.80 153 48 54 6 353.69 36.08 154 49 56 7 350.24 37.80 155 50 53 3 479.31 0.85 156 50 56 6 435.53 4.83 157 51 56 5 440.18 6.92 158 52 57 5 469.26 1.20 159 53 56 3 486.27 2.75 160 53 57 4 471.47 0.11 161 54 57 3 492.64 0.44 162 54 58 4 471.66 0.01 163 55 58 3 486.64 0.74 164 55 59 4 469.34 0.96 165 56 59 3 489.94 0.91 166 56 60 4 467.19 2.23 167 57 60 3 486.63 0.74 168 57 61 4 474.26 1.30 169 58 61 3 486.62 0.74 170 58 62 4 476.64 0.12 171 59 62 3 481.00 2.06 172 59 63 4 474.38 1.25 173 60 63 3 481.00 2.06 174 60 64 4 473.83 0.94 175 61 64 3 478.61 1.11 176 61 65 4 474.10 1.06 177 62 65 3 478.57 1.10 178 62 66 4 474.09 1.06 179 63 66 3 472.92 0.46 180 63 67 4 471.92 0.03 181 63 102 39 172.27 0.45 182 64 67 3 471.93 0.04 183 64 68 4 471.93 0.04 184 65 68 3 479.35 2.75 185 65 69 4 469.27 1.36 186 66 69 3 486.46 2.62 187 66 70 4 471.56 0.95 188 66 84 18 160.47 6.28 189 67 70 3 480.17 0.39 190 67 71 4 476.42 1.49 191 67 129 62 208.02 1.66 192 67 130 63 189.79 2.18 193 67 133 66 172.84 0.19 194 68 71 3 477.28 1.92 195 68 72 4 476.44 1.50 196 69 72 3 482.17 0.53 197 69 73 4 461.29 4.70 198 69 80 11 230.51 3.30 199 69 81 12 204.38 16.36 200 70 73 3 465.67 6.88 201 70 74 4 454.36 8.16 202 70 77 7 297.66 4.71 203 70 81 11 204.39 16.36 204 70 129 59 214.00 1.12 205 70 133 63 193.56 4.33 206 71 74 3 468.00 2.04 207 71 129 58 214.16 1.21 208 73 76 3 496.26 0.58 209 73 77 4 472.10 0.69 210 73 80 7 287.76 6.82 211 74 77 3 503.57 4.42 212 74 129 55 216.58 2.39 213 76 79 3 482.89 2.45 214 76 80 4 459.55 4.10 215 77 80 3 469.68 6.98 216 77 81 4 449.70 0.83 217 77 129 52 220.16 1.01 218 77 132 55 219.83 0.85 219 77 133 56 219.84 0.86 220 77 136 59 219.74 0.85 221 78 82 4 452.66 0.89 222 78 136 58 219.75 0.85 223 78 139 61 219.74 0.85 224 79 82 3 485.60 1.28 225 81 84 3 469.91 2.75 226 81 85 4 469.47 2.96 227 81 133 52 221.69 1.34 228 81 136 55 221.59 1.35 229 82 85 3 477.38 0.98 230 82 86 4 462.78 6.30 231 82 139 57 221.59 1.35 232 82 140 58 221.57 1.34 233 83 86 3 481.72 5.58 234 83 87 4 464.80 1.09 235 84 87 3 481.72 5.57 236 84 88 4 464.19 1.40 237 84 137 53 222.31 1.67 238 85 88 3 485.11 3.88 239 85 89 4 450.17 2.01 240 85 90 5 447.99 3.10 241 85 136 51 222.44 1.63 242 85 137 52 222.31 1.67 243 85 139 54 222.29 1.67 244 85 140 55 222.00 1.56 245 86 90 4 430.87 10.29 246 86 91 5 430.86 10.29 247 86 140 54 222.16 1.63 248 87 91 4 376.50 16.89 249 87 92 5 376.50 16.89 250 88 92 4 376.44 16.87 251 88 93 5 337.30 0.10 252 88 94 6 310.19 0.73 253 88 99 11 265.55 0.55 254 89 93 4 326.27 5.61 255 89 137 48 222.71 1.52 256 89 140 51 222.31 1.68 257 89 141 52 222.03 1.55 258 90 93 3 478.25 7.94 259 90 140 50 222.30 1.68 260 93 141 48 222.47 1.58 261 94 98 4 482.29 3.41 262 94 99 5 473.29 1.26 263 94 141 47 222.70 1.52 264 95 98 3 492.11 0.55 265 95 141 46 222.73 1.52 266 96 99 3 488.34 0.39 267 96 141 45 222.80 1.51 268 97 100 3 496.47 1.76 269 97 101 4 478.37 3.67 270 98 101 3 478.03 2.44 271 98 102 4 484.90 3.03 272 99 102 3 485.23 2.87 273 99 103 4 482.00 4.48 274 99 134 35 223.28 1.49 275 99 137 38 223.28 1.49 276 99 141 42 223.25 1.49 277 100 103 3 484.91 3.03 278 100 104 4 482.00 4.49 279 101 104 3 484.91 3.03 280 101 105 4 481.99 4.49 281 102 105 3 469.70 1.75 282 102 106 4 469.62 1.71 283 103 106 3 476.97 2.30 284 103 107 4 469.65 1.72 285 103 130 27 224.07 1.89 286 104 107 3 483.38 2.66 287 104 108 4 465.14 3.97 288 105 108 3 479.40 4.65 289 105 109 4 470.50 0.20 290 106 109 3 481.22 3.76 291 106 110 4 470.49 0.20 292 106 130 24 225.22 1.79 293 107 110 3 485.92 1.42 294 107 111 4 470.37 0.13 295 107 118 11 264.51 7.33 296 107 123 16 226.73 2.49 297 107 126 19 225.86 2.08 298 107 127 20 225.83 2.08 299 107 130 23 225.80 2.06 300 108 111 3 479.42 4.67 301 108 112 4 470.14 0.24 302 109 112 3 470.88 2.14 303 109 113 4 466.44 2.07 304 110 113 3 471.25 1.96 305 110 114 4 464.38 1.06 306 110 118 8 264.86 7.18 307 110 126 16 226.99 2.43 308 111 114 3 476.47 3.08 309 111 115 4 435.00 5.91 310 111 118 7 272.98 3.10 311 114 117 3 483.08 0.29 312 114 118 4 442.97 9.70 313 115 118 3 475.26 0.01 314 116 119 3 515.02 3.61 315 117 122 5 467.18 0.18 316 118 122 4 467.18 0.18 317 118 123 5 463.19 1.80 318 118 126 8 442.36 2.09 319 119 122 3 470.75 1.97 320 119 123 4 470.76 1.98 321 120 123 3 472.61 1.05 322 120 124 4 470.76 1.98 323 121 124 3 484.24 0.85 324 121 125 4 476.38 4.79 325 122 125 3 486.43 0.24 326 122 126 4 473.47 4.30 327 123 126 3 478.31 1.89 328 123 127 4 470.58 2.85 329 124 127 3 483.00 0.47 330 124 128 4 478.73 2.62 331 125 128 3 480.13 1.93 332 125 129 4 476.87 3.54 333 126 129 3 478.09 2.94 334 126 130 4 476.88 3.54 335 127 130 3 476.88 3.55 336 127 131 4 476.87 3.54 337 128 131 3 476.79 3.58 338 128 132 4 476.75 3.57 339 129 132 3 473.10 0.45 340 129 133 4 466.84 1.33 341 130 133 3 470.38 0.44 342 130 134 4 468.13 2.00 343 131 134 3 471.66 1.38 344 131 135 4 468.12 2.02 345 132 135 3 479.66 3.75 346 132 136 4 468.12 2.02 347 133 136 3 479.84 3.66 348 133 137 4 479.49 3.66 349 134 137 3 488.70 0.78 350 134 138 4 479.50 3.66 351 135 138 3 474.37 0.06 352 135 139 4 468.23 2.16 353 136 139 3 477.33 0.86 354 138 141 3 486.44 1.47