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 5 445.06 6.09 2 2 73 71 27.48 1.02 3 2 76 74 26.62 0.80 4 2 127 125 23.45 0.12 5 2 128 126 23.40 0.10 6 2 131 129 23.40 0.10 7 3 6 3 462.28 2.02 8 3 7 4 461.80 2.25 9 4 7 3 469.04 4.04 10 4 8 4 468.68 1.20 11 5 8 3 475.75 2.33 12 5 9 4 465.40 2.84 13 6 9 3 479.67 0.41 14 6 10 4 469.03 4.91 15 6 124 118 46.96 0.26 16 6 127 121 46.95 0.26 17 7 10 3 484.39 1.29 18 7 11 4 470.11 0.48 19 7 73 66 47.19 0.34 20 7 74 67 48.19 0.10 21 8 11 3 477.62 0.68 22 8 12 4 470.12 0.47 23 9 12 3 473.87 2.35 24 9 13 4 470.09 0.46 25 9 120 111 66.65 0.88 26 9 121 112 66.22 0.96 27 9 124 115 66.14 0.96 28 10 13 3 479.53 5.17 29 10 14 4 463.64 2.77 30 10 70 60 66.19 0.96 31 10 124 114 66.35 1.02 32 10 125 115 66.17 0.96 33 10 128 118 66.16 0.97 34 11 14 3 477.47 0.55 35 11 15 4 458.73 0.30 36 11 70 59 66.36 1.02 37 11 71 60 66.36 1.03 38 11 73 62 66.36 1.03 39 12 15 3 479.39 2.52 40 12 16 4 480.38 2.24 41 13 16 3 484.88 0.01 42 13 17 4 480.38 2.25 43 13 113 100 77.69 0.73 44 13 121 108 66.84 0.97 45 13 125 112 66.80 0.98 46 14 17 3 480.39 2.24 47 14 18 4 480.39 2.24 48 14 21 7 374.75 9.14 49 14 63 49 75.78 0.34 50 14 66 52 66.78 0.97 51 14 67 53 66.75 0.96 52 14 70 56 66.74 0.96 53 14 109 95 77.67 0.73 54 15 18 3 482.91 0.98 55 16 113 97 78.25 0.58 56 16 116 100 78.18 0.59 57 17 20 3 487.78 0.25 58 17 21 4 438.00 8.20 59 17 24 7 368.43 10.60 60 17 109 92 77.95 0.64 61 17 113 96 87.11 4.94 62 18 21 3 491.12 2.38 63 20 23 3 481.06 1.95 64 20 24 4 444.70 5.67 65 21 24 3 474.76 0.92 66 21 25 4 447.75 7.19 67 21 63 42 94.20 1.42 68 22 25 3 456.59 2.77 69 22 26 4 458.99 1.57 70 22 59 37 101.28 1.86 71 22 60 38 94.47 1.54 72 22 63 41 97.42 0.06 73 23 26 3 488.83 1.15 74 23 27 4 462.93 2.27 75 24 27 3 467.39 0.04 76 24 28 4 468.03 0.27 77 24 108 84 120.64 1.01 78 24 109 85 128.91 0.94 79 24 112 88 133.82 1.32 80 24 113 89 133.88 1.28 81 25 28 3 476.66 4.02 82 25 29 4 468.04 0.28 83 25 59 34 118.70 1.85 84 25 105 80 120.23 1.22 85 26 29 3 487.46 1.38 86 26 30 4 468.06 0.29 87 26 55 29 126.12 1.16 88 26 56 30 124.91 0.98 89 26 59 33 118.80 1.88 90 27 30 3 476.68 4.02 91 27 31 4 468.10 0.25 92 27 108 81 134.94 1.05 93 27 112 85 136.25 0.56 94 28 31 3 474.26 0.03 95 28 32 4 471.44 1.38 96 28 101 73 134.10 1.37 97 28 104 76 134.16 1.37 98 28 105 77 134.13 1.37 99 28 108 80 135.91 0.68 100 29 32 3 471.79 1.21 101 29 33 4 471.45 1.38 102 29 58 29 135.04 1.04 103 29 59 30 134.21 1.44 104 29 62 33 134.20 1.41 105 29 101 72 134.23 1.42 106 30 33 3 481.03 1.52 107 30 34 4 468.43 0.14 108 30 50 20 136.55 0.43 109 31 34 3 480.00 1.01 110 31 35 4 468.42 0.14 111 31 104 73 136.24 0.47 112 31 107 76 136.38 0.48 113 31 108 77 136.39 0.48 114 31 111 80 136.55 0.48 115 32 35 3 487.42 1.87 116 32 36 4 437.91 3.23 117 32 39 7 278.21 4.61 118 32 100 68 136.21 0.48 119 32 101 69 136.18 0.48 120 32 104 72 136.30 0.49 121 33 37 4 351.08 2.46 122 33 39 6 278.21 4.61 123 33 40 7 262.06 3.82 124 33 43 10 270.90 8.21 125 33 48 15 136.80 0.49 126 33 55 22 136.74 0.47 127 36 39 3 498.03 2.61 128 36 100 64 136.22 0.46 129 36 103 67 136.49 0.48 130 36 104 68 136.53 0.47 131 37 40 3 480.81 3.13 132 38 41 3 495.37 4.15 133 39 42 3 495.05 0.71 134 39 43 4 490.23 2.10 135 39 97 58 136.23 0.46 136 39 100 61 136.47 0.48 137 40 43 3 486.31 1.39 138 40 44 4 483.20 1.41 139 40 48 8 197.64 28.69 140 41 44 3 498.44 0.72 141 42 45 3 637.01 0.20 142 42 92 50 136.10 0.29 143 42 93 51 136.06 0.32 144 42 94 52 136.28 0.42 145 42 97 55 136.47 0.48 146 43 46 3 477.33 1.47 147 43 48 5 436.06 11.13 148 43 58 15 136.80 0.47 149 45 54 9 139.19 0.97 150 46 54 8 139.17 0.97 151 46 58 12 139.16 0.97 152 47 52 5 202.58 30.66 153 47 54 7 139.21 0.97 154 47 55 8 139.22 0.96 155 48 55 7 139.23 0.96 156 49 52 3 481.51 1.21 157 51 56 5 449.31 2.22 158 52 55 3 471.02 1.44 159 52 56 4 466.49 6.32 160 53 56 3 480.38 0.62 161 53 57 4 466.49 6.32 162 54 57 3 472.84 4.75 163 54 58 4 458.03 1.47 164 55 58 3 481.98 0.19 165 55 59 4 464.39 1.41 166 56 59 3 476.50 2.52 167 56 60 4 469.33 1.06 168 57 60 3 488.36 2.99 169 57 61 4 482.89 5.72 170 58 61 3 487.85 3.25 171 58 62 4 482.89 5.72 172 59 62 3 488.94 2.70 173 59 63 4 466.96 0.12 174 60 63 3 475.70 2.93 175 60 64 4 461.50 0.34 176 61 64 3 471.49 5.04 177 61 65 4 471.62 4.98 178 62 65 3 466.81 1.06 179 62 66 4 463.17 0.75 180 63 66 3 482.09 3.04 181 63 67 4 461.91 0.12 182 64 67 3 476.92 1.56 183 64 68 4 475.72 1.31 184 65 68 3 482.35 2.91 185 65 69 4 475.72 1.31 186 65 80 15 155.91 2.81 187 65 83 18 153.34 2.04 188 66 69 3 482.18 3.07 189 66 70 4 470.70 4.73 190 66 105 39 192.97 11.15 191 66 128 62 209.22 3.06 192 66 129 63 192.61 11.34 193 66 132 66 164.66 0.88 194 67 70 3 480.70 3.81 195 67 71 4 478.21 0.99 196 68 71 3 478.22 0.99 197 68 72 4 478.21 0.99 198 68 79 11 168.88 0.61 199 68 80 12 168.87 0.61 200 69 72 3 477.42 1.39 201 69 73 4 466.56 6.80 202 69 76 7 266.29 5.04 203 69 80 11 168.88 0.62 204 69 128 59 225.62 2.64 205 69 132 63 209.02 3.12 206 70 73 3 455.66 2.02 207 70 128 58 228.33 3.98 208 72 75 3 484.76 2.43 209 72 76 4 448.44 3.58 210 72 79 7 292.34 9.39 211 73 76 3 482.94 2.54 212 73 128 55 242.66 0.69 213 75 78 3 486.62 0.47 214 75 79 4 468.18 6.25 215 76 79 3 475.49 2.61 216 76 80 4 453.37 1.15 217 76 128 52 247.97 1.58 218 76 131 55 245.62 0.73 219 76 132 56 242.75 0.70 220 76 135 59 242.70 0.70 221 77 80 3 481.12 0.11 222 77 81 4 445.73 2.08 223 77 135 58 242.71 0.70 224 78 81 3 469.64 0.94 225 80 83 3 494.81 3.11 226 80 84 4 453.95 1.86 227 80 132 52 248.28 1.69 228 80 135 55 248.16 1.67 229 80 136 56 248.14 1.66 230 81 84 3 475.62 0.64 231 81 85 4 454.01 1.83 232 81 139 58 248.14 1.66 233 82 85 3 471.68 3.08 234 82 86 4 454.62 1.70 235 83 86 3 460.62 1.30 236 83 87 4 454.61 1.70 237 83 136 53 248.33 1.67 238 84 87 3 473.29 7.62 239 84 88 4 453.88 1.70 240 84 135 51 248.37 1.68 241 84 136 52 248.29 1.66 242 84 139 55 248.28 1.66 243 85 88 3 469.01 5.49 244 85 89 4 453.88 1.71 245 85 90 5 453.88 1.71 246 85 139 54 248.28 1.65 247 86 89 3 491.25 4.21 248 86 90 4 450.25 0.10 249 86 91 5 450.15 0.06 250 87 91 4 445.22 2.40 251 87 92 5 442.01 0.81 252 87 98 11 271.22 7.44 253 87 136 49 248.43 1.69 254 87 140 53 248.28 1.65 255 88 92 4 441.97 0.78 256 88 139 51 248.36 1.69 257 88 140 52 248.27 1.66 258 89 92 3 481.44 0.84 259 89 139 50 248.41 1.69 260 93 97 4 489.02 0.69 261 93 98 5 485.50 2.45 262 93 140 47 248.50 1.71 263 94 97 3 500.98 2.71 264 94 98 4 490.98 1.66 265 95 98 3 495.02 2.31 266 95 99 4 489.04 0.69 267 95 137 42 249.20 1.69 268 95 140 45 248.86 1.75 269 96 99 3 497.59 1.02 270 96 100 4 489.03 0.70 271 97 100 3 484.41 2.98 272 97 101 4 478.76 0.17 273 98 101 3 480.06 0.82 274 98 102 4 471.75 0.89 275 98 133 35 249.83 1.58 276 98 136 38 249.81 1.59 277 98 137 39 249.80 1.59 278 98 140 42 249.80 1.59 279 99 102 3 474.50 0.49 280 99 103 4 471.75 0.89 281 99 133 34 249.97 1.56 282 100 103 3 467.79 1.08 283 100 104 4 467.04 1.46 284 101 104 3 467.04 1.46 285 101 105 4 466.93 1.51 286 102 105 3 477.11 0.73 287 102 106 4 460.98 4.44 288 102 129 27 250.00 1.58 289 102 133 31 250.00 1.58 290 103 106 3 475.56 1.51 291 103 107 4 453.57 0.69 292 104 107 3 453.57 0.69 293 104 108 4 453.57 0.69 294 105 108 3 467.81 1.94 295 105 109 4 460.51 1.74 296 105 129 24 251.18 1.51 297 106 109 3 473.35 0.84 298 106 110 4 460.50 1.73 299 106 117 11 251.96 1.48 300 106 122 16 251.77 1.47 301 106 125 19 251.50 1.36 302 106 126 20 251.49 1.36 303 106 129 23 251.44 1.38 304 107 110 3 473.40 0.81 305 107 111 4 460.50 1.73 306 108 111 3 465.36 0.69 307 108 112 4 460.52 1.74 308 109 112 3 468.04 2.02 309 109 113 4 458.12 2.91 310 109 125 16 251.78 1.47 311 110 117 7 252.20 1.29 312 113 116 3 473.20 3.21 313 113 117 4 404.66 12.88 314 114 117 3 442.46 5.06 315 116 121 5 424.56 4.12 316 117 121 4 434.79 9.22 317 117 122 5 424.51 4.11 318 117 125 8 423.56 3.69 319 118 121 3 462.87 4.94 320 118 122 4 444.55 14.10 321 119 122 3 475.95 5.19 322 119 123 4 457.13 7.83 323 120 123 3 469.25 1.78 324 120 124 4 469.18 1.81 325 121 124 3 469.27 1.79 326 121 125 4 461.14 5.83 327 122 125 3 472.66 1.01 328 122 126 4 469.16 1.80 329 123 126 3 477.10 5.11 330 123 127 4 462.19 1.79 331 124 127 3 470.73 1.96 332 124 128 4 464.07 2.73 333 125 128 3 466.75 1.40 334 125 129 4 447.77 2.83 335 126 129 3 472.80 0.83 336 126 130 4 447.75 2.82 337 127 130 3 470.94 0.69 338 127 131 4 447.58 2.74 339 128 131 3 461.59 3.98 340 128 132 4 458.54 7.81 341 129 132 3 465.14 4.50 342 129 133 4 458.55 7.81 343 130 133 3 476.42 1.13 344 130 134 4 468.84 2.66 345 131 134 3 476.43 1.13 346 131 135 4 476.42 1.13 347 132 135 3 476.43 1.13 348 132 136 4 464.26 7.21 349 133 136 3 475.86 1.42 350 133 137 4 476.51 1.09 351 134 137 3 484.85 5.26 352 134 138 4 460.10 7.12 353 135 138 3 473.07 0.62 354 136 140 4 500.25 1.28 355 137 140 3 481.24 0.88