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 5 442.55 3.11 2 2 10 8 437.17 5.79 3 2 73 71 24.68 1.39 4 2 126 124 21.71 0.08 5 2 127 125 21.71 0.09 6 3 6 3 462.91 6.82 7 3 7 4 461.74 7.40 8 4 7 3 461.94 7.45 9 4 8 4 461.79 7.38 10 5 8 3 476.54 4.17 11 5 9 4 472.52 2.15 12 6 9 3 472.54 2.15 13 6 10 4 461.76 6.49 14 6 123 117 45.67 0.56 15 6 126 120 45.68 0.56 16 7 10 3 471.49 1.63 17 7 11 4 450.70 2.12 18 7 73 66 46.62 0.51 19 7 74 67 46.62 0.51 20 8 11 3 471.48 1.62 21 8 12 4 466.88 0.68 22 9 12 3 472.52 2.16 23 9 13 4 464.36 0.58 24 9 123 114 48.26 0.15 25 10 13 3 478.22 1.71 26 10 14 4 453.09 4.11 27 10 70 60 47.25 0.64 28 10 73 63 48.51 0.01 29 10 123 113 48.51 0.01 30 10 127 117 47.23 0.64 31 11 14 3 460.97 2.29 32 11 15 4 455.41 2.94 33 12 15 3 462.07 0.49 34 12 16 4 455.39 2.93 35 13 16 3 462.07 0.49 36 13 17 4 450.19 0.33 37 13 109 96 79.89 0.13 38 13 113 100 84.49 0.76 39 13 120 107 70.55 0.15 40 13 124 111 61.09 4.85 41 14 17 3 457.92 0.65 42 14 18 4 461.78 6.15 43 14 67 53 61.09 4.86 44 14 70 56 61.09 4.86 45 15 18 3 468.21 4.11 46 15 19 4 473.38 0.35 47 16 19 3 477.70 1.18 48 16 24 8 384.14 0.12 49 16 113 97 92.86 0.77 50 17 20 3 489.28 0.39 51 17 21 4 442.49 4.13 52 17 24 7 384.06 0.09 53 17 63 46 129.13 22.98 54 17 67 50 77.36 1.37 55 17 109 92 88.02 0.28 56 18 21 3 474.56 0.95 57 18 67 49 83.17 0.01 58 20 23 3 464.53 2.18 59 20 24 4 460.61 0.23 60 21 24 3 465.98 1.45 61 21 25 4 451.29 4.42 62 21 60 39 145.69 20.73 63 21 63 42 145.63 20.73 64 21 64 43 144.69 21.21 65 22 25 3 467.16 0.84 66 22 26 4 454.20 2.96 67 22 56 34 150.82 18.55 68 22 57 35 150.81 18.55 69 22 60 38 146.00 20.59 70 22 64 42 147.49 19.85 71 23 26 3 474.79 1.36 72 23 27 4 456.43 4.52 73 24 27 3 475.69 0.91 74 24 28 4 454.69 5.40 75 24 63 39 152.21 17.70 76 24 108 84 132.44 4.14 77 24 112 88 136.84 1.42 78 25 28 3 474.94 4.74 79 25 29 4 452.88 5.52 80 25 59 34 152.36 17.77 81 25 63 38 152.19 17.69 82 26 29 3 478.74 1.22 83 26 30 4 448.11 1.57 84 26 50 24 162.99 13.68 85 26 55 29 160.73 13.85 86 26 56 30 160.84 13.91 87 26 59 33 158.38 14.76 88 27 30 3 470.63 2.83 89 27 31 4 455.95 2.79 90 27 50 23 163.07 13.66 91 27 108 81 137.83 1.49 92 27 111 84 138.09 1.35 93 27 112 85 138.10 1.28 94 28 31 3 464.60 0.18 95 28 32 4 457.14 3.39 96 28 63 35 161.62 13.49 97 28 101 73 138.05 1.69 98 28 104 76 137.81 1.54 99 28 105 77 137.79 1.54 100 28 108 80 137.94 1.44 101 29 32 3 460.86 5.37 102 29 33 4 455.00 3.31 103 29 55 26 163.06 13.64 104 29 58 29 162.69 13.47 105 29 59 30 162.49 13.44 106 29 101 72 138.15 1.65 107 30 33 3 471.71 0.36 108 30 34 4 467.92 2.25 109 30 48 18 165.46 14.78 110 30 49 19 165.46 14.79 111 30 50 20 165.44 14.78 112 31 34 3 477.62 3.64 113 31 35 4 455.89 3.75 114 31 104 73 138.07 1.58 115 31 107 76 137.99 1.43 116 31 108 77 137.98 1.42 117 31 111 80 138.22 1.30 118 32 35 3 467.04 2.70 119 32 36 4 438.89 2.94 120 32 39 7 321.25 12.47 121 32 100 68 138.25 1.70 122 32 101 69 138.25 1.64 123 32 104 72 138.19 1.56 124 33 37 4 417.00 8.00 125 33 39 6 303.70 11.86 126 33 40 7 286.56 20.37 127 33 43 10 288.44 19.39 128 33 45 12 181.47 22.75 129 33 48 15 165.55 14.79 130 33 55 22 165.53 14.80 131 34 37 3 469.70 1.54 132 35 104 69 138.40 1.61 133 36 39 3 482.91 0.87 134 36 97 61 138.66 1.82 135 36 100 64 138.65 1.78 136 37 40 3 477.78 1.71 137 38 41 3 490.18 0.04 138 39 42 3 489.34 0.38 139 39 43 4 481.63 2.14 140 39 97 58 138.66 1.82 141 40 43 3 479.28 0.96 142 40 48 8 279.75 1.97 143 42 93 51 138.63 1.86 144 42 94 52 138.69 1.84 145 42 97 55 138.73 1.81 146 43 48 5 436.87 8.88 147 43 58 15 191.13 27.54 148 45 48 3 489.17 1.15 149 45 54 9 379.26 4.71 150 45 55 10 350.50 19.05 151 45 58 13 349.70 19.45 152 46 52 6 379.92 4.52 153 46 53 7 379.92 4.52 154 46 54 8 379.94 4.54 155 46 55 9 379.94 4.54 156 47 51 4 451.32 4.50 157 47 52 5 379.92 4.52 158 47 55 8 379.94 4.54 159 48 55 7 379.95 4.54 160 49 52 3 468.59 4.13 161 49 55 6 412.03 0.28 162 50 55 5 428.31 8.40 163 50 56 6 415.53 2.00 164 51 56 5 456.13 1.18 165 52 55 3 464.69 0.54 166 52 56 4 464.69 0.54 167 53 56 3 474.55 4.99 168 53 57 4 470.66 3.50 169 54 57 3 474.76 1.45 170 54 58 4 470.66 3.50 171 55 58 3 478.00 0.18 172 55 59 4 460.43 1.56 173 56 59 3 474.05 1.80 174 56 60 4 470.60 3.52 175 57 60 3 466.41 0.69 176 57 61 4 463.02 0.26 177 58 61 3 465.83 0.98 178 58 62 4 465.77 0.99 179 59 62 3 476.45 0.96 180 59 63 4 465.78 1.00 181 60 63 3 476.45 0.96 182 60 64 4 462.99 0.40 183 61 64 3 471.09 3.64 184 61 65 4 462.98 0.40 185 62 65 3 465.88 1.05 186 62 66 4 462.99 0.39 187 62 101 39 139.28 1.12 188 63 66 3 464.41 0.32 189 63 67 4 450.06 1.55 190 64 67 3 474.51 5.65 191 64 68 4 456.44 4.23 192 65 68 3 466.63 1.71 193 65 69 4 461.50 1.77 194 65 83 18 141.30 2.58 195 66 69 3 468.65 0.77 196 66 70 4 461.56 1.74 197 66 127 61 158.97 9.91 198 66 128 62 158.55 9.71 199 66 131 65 156.89 9.37 200 67 70 3 471.41 0.31 201 67 71 4 461.57 1.73 202 68 71 3 474.18 1.40 203 68 72 4 468.20 1.59 204 68 79 11 271.50 1.67 205 69 72 3 468.20 1.59 206 69 73 4 461.54 1.75 207 69 76 7 306.19 15.69 208 69 79 10 262.37 2.90 209 69 80 11 251.78 8.20 210 69 131 62 179.00 20.10 211 70 73 3 467.06 2.17 212 70 127 57 179.23 20.00 213 72 75 3 473.07 0.74 214 72 76 4 446.04 6.59 215 72 79 7 313.45 15.16 216 73 76 3 480.67 0.59 217 73 127 54 180.67 20.66 218 75 78 3 494.87 0.55 219 75 79 4 462.33 1.03 220 76 79 3 467.92 1.77 221 76 80 4 456.32 4.02 222 76 130 54 180.97 20.89 223 76 131 55 180.98 20.89 224 76 134 58 180.94 20.91 225 77 80 3 480.75 0.66 226 77 81 4 464.64 0.14 227 77 134 57 180.87 20.94 228 77 138 61 180.58 21.09 229 78 81 3 465.76 0.69 230 80 83 3 473.09 1.17 231 80 84 4 447.84 0.34 232 80 131 51 180.94 20.97 233 80 134 54 180.90 21.00 234 80 135 55 180.65 21.12 235 81 84 3 470.31 2.55 236 81 85 4 461.38 1.92 237 81 138 57 180.42 21.24 238 82 85 3 470.31 2.55 239 82 86 4 462.26 1.46 240 83 86 3 464.29 0.46 241 83 87 4 462.28 1.47 242 83 135 52 180.72 21.39 243 84 87 3 478.58 4.30 244 84 88 4 446.09 5.67 245 84 134 50 180.75 21.38 246 84 135 51 180.72 21.39 247 84 138 54 179.56 21.91 248 85 88 3 463.96 0.57 249 85 89 4 408.93 6.71 250 85 90 5 384.11 4.12 251 85 138 53 179.56 21.91 252 86 90 4 337.82 9.96 253 86 91 5 337.81 9.96 254 87 91 4 337.81 9.96 255 87 92 5 301.20 8.32 256 87 93 6 272.66 0.34 257 87 98 11 246.43 4.98 258 87 135 48 180.76 21.41 259 88 92 4 310.51 3.67 260 88 139 51 179.52 21.93 261 89 92 3 469.17 0.81 262 89 138 49 179.83 21.82 263 89 139 50 179.56 21.91 264 89 140 51 179.56 21.91 265 93 97 4 478.93 0.01 266 93 98 5 474.49 2.21 267 93 139 46 179.62 21.98 268 94 97 3 483.66 2.38 269 95 98 3 483.66 2.38 270 95 99 4 495.44 4.70 271 95 136 41 180.27 22.21 272 95 139 44 180.09 22.27 273 96 99 3 501.56 1.64 274 96 100 4 481.70 1.41 275 97 100 3 478.92 0.02 276 97 101 4 478.48 0.20 277 98 101 3 478.46 0.18 278 98 102 4 469.32 0.37 279 98 132 34 180.68 22.16 280 98 135 37 180.66 22.16 281 98 136 38 180.40 22.29 282 98 139 41 180.35 22.31 283 99 102 3 470.72 1.07 284 99 103 4 469.19 0.31 285 100 103 3 469.68 0.04 286 100 104 4 466.11 0.18 287 101 104 3 471.24 0.82 288 101 105 4 457.21 0.45 289 102 105 3 463.24 2.59 290 102 106 4 457.24 0.66 291 102 128 26 181.08 22.12 292 102 132 30 180.84 22.23 293 103 106 3 463.17 2.31 294 103 107 4 457.27 0.64 295 104 107 3 458.95 1.48 296 104 108 4 456.03 0.00 297 105 108 3 471.51 1.34 298 105 109 4 468.09 3.06 299 105 128 23 181.68 22.30 300 106 109 3 473.87 0.39 301 106 110 4 459.02 1.48 302 106 116 10 225.50 2.25 303 106 121 15 182.28 22.12 304 106 124 18 182.22 22.16 305 106 125 19 182.16 22.12 306 106 128 22 181.73 22.32 307 107 110 3 470.75 2.81 308 107 111 4 459.02 1.48 309 108 111 3 472.36 2.02 310 108 112 4 460.79 0.60 311 109 112 3 475.30 3.18 312 109 113 4 459.02 1.49 313 109 116 7 232.47 5.73 314 109 124 15 182.72 22.40 315 110 116 6 232.47 5.73 316 113 116 3 486.92 4.04 317 116 120 4 452.18 1.36 318 116 121 5 452.22 1.32 319 117 120 3 466.81 0.22 320 117 121 4 466.83 0.21 321 118 121 3 466.84 0.21 322 118 122 4 466.83 0.21 323 119 122 3 466.82 0.21 324 119 123 4 466.82 0.21 325 120 123 3 475.97 1.69 326 120 124 4 466.81 0.21 327 121 124 3 476.72 2.00 328 121 125 4 459.96 0.53 329 122 125 3 469.85 1.75 330 122 126 4 463.67 1.32 331 123 126 3 465.80 3.46 332 123 127 4 459.85 0.49 333 124 127 3 468.22 3.43 334 124 128 4 458.63 4.02 335 125 128 3 471.38 1.85 336 125 129 4 452.83 1.12 337 126 129 3 471.44 1.82 338 126 130 4 457.50 1.58 339 127 130 3 471.43 1.82 340 127 131 4 469.23 0.72 341 128 131 3 478.38 3.85 342 128 132 4 469.23 0.72 343 129 132 3 478.38 3.85 344 129 133 4 464.46 1.88 345 130 133 3 472.28 5.76 346 130 134 4 464.46 1.89 347 131 134 3 481.32 3.52 348 131 135 4 464.42 1.91 349 132 135 3 468.74 0.37 350 132 136 4 463.84 2.08 351 133 136 3 472.79 1.66 352 133 137 4 462.26 2.83 353 134 137 3 465.35 0.67 354 134 138 4 467.91 0.61 355 136 139 3 496.74 2.21