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 5 449.35 1.92 2 2 74 72 28.05 0.20 3 2 77 75 24.40 0.33 4 2 128 126 23.46 0.29 5 2 129 127 23.27 0.28 6 3 6 3 466.43 1.12 7 3 7 4 471.78 1.53 8 4 7 3 482.80 3.21 9 4 8 4 471.78 1.53 10 5 8 3 480.28 2.72 11 5 9 4 473.56 2.42 12 6 9 3 483.06 2.23 13 6 10 4 477.34 0.64 14 6 125 119 47.77 0.43 15 6 128 122 47.52 0.54 16 7 10 3 491.41 2.83 17 7 11 4 475.49 1.56 18 7 74 67 48.80 0.04 19 7 75 68 48.84 0.04 20 8 11 3 484.42 2.90 21 8 12 4 475.49 1.56 22 9 12 3 483.85 2.62 23 9 13 4 478.67 0.14 24 9 125 116 62.05 0.29 25 10 13 3 480.14 0.89 26 10 14 4 474.12 2.12 27 10 71 61 61.98 0.32 28 10 74 64 61.98 0.33 29 10 125 115 62.05 0.29 30 10 126 116 62.01 0.27 31 10 129 119 61.94 0.31 32 11 14 3 480.13 0.89 33 11 15 4 480.12 0.88 34 11 71 60 62.30 0.30 35 11 74 63 62.32 0.30 36 12 15 3 480.13 0.89 37 12 16 4 479.69 1.09 38 13 16 3 480.22 0.84 39 13 17 4 479.68 1.10 40 13 117 104 73.95 0.98 41 13 122 109 63.29 0.10 42 13 126 113 62.42 0.33 43 14 17 3 479.68 1.10 44 14 18 4 473.03 2.21 45 14 21 7 385.19 2.40 46 14 67 53 62.41 0.34 47 14 68 54 62.43 0.34 48 14 71 57 62.41 0.34 49 16 19 3 529.01 2.01 50 16 117 101 84.40 3.29 51 17 20 3 501.45 1.03 52 17 24 7 411.50 12.20 53 17 110 93 89.18 0.92 54 17 114 97 95.78 0.01 55 18 21 3 486.52 0.96 56 19 114 95 119.53 0.88 57 20 23 3 489.24 1.40 58 20 24 4 475.96 5.26 59 20 114 94 119.53 0.88 60 21 24 3 481.55 2.46 61 21 25 4 475.96 5.26 62 21 64 43 105.14 0.69 63 22 25 3 489.28 1.38 64 22 26 4 475.97 5.26 65 22 61 39 112.41 1.02 66 23 26 3 487.41 0.45 67 23 27 4 475.73 5.40 68 23 113 90 139.94 0.89 69 24 27 3 487.39 2.98 70 24 28 4 475.03 5.74 71 24 64 40 122.25 0.39 72 24 109 85 131.24 0.69 73 24 110 86 128.18 2.22 74 24 113 89 140.16 0.99 75 24 114 90 139.97 0.88 76 25 28 3 482.73 1.89 77 25 29 4 481.75 2.38 78 25 60 35 122.58 0.48 79 25 64 39 122.51 0.52 80 26 29 3 483.25 1.42 81 26 30 4 472.42 3.20 82 26 56 30 142.21 0.38 83 26 57 31 139.54 1.33 84 26 60 34 131.82 0.43 85 27 30 3 479.62 0.40 86 27 31 4 477.95 0.43 87 27 109 82 142.31 0.39 88 27 112 85 142.85 0.42 89 27 113 86 143.57 0.04 90 28 31 3 479.62 0.40 91 28 32 4 477.94 0.43 92 28 102 74 142.16 0.37 93 28 105 77 142.20 0.35 94 28 106 78 142.16 0.36 95 28 109 81 142.35 0.39 96 29 32 3 479.19 0.19 97 29 33 4 477.94 0.43 98 29 43 14 143.38 0.70 99 29 56 27 142.85 0.43 100 29 59 30 142.68 0.51 101 29 60 31 142.34 0.35 102 29 63 34 142.28 0.38 103 29 102 73 142.33 0.40 104 30 33 3 480.31 1.26 105 30 34 4 477.01 0.09 106 30 51 21 143.75 0.07 107 30 56 26 143.59 0.06 108 31 34 3 483.06 3.08 109 31 35 4 472.42 2.18 110 31 105 74 142.53 0.31 111 31 108 77 143.68 0.01 112 31 109 78 143.64 0.03 113 32 36 4 451.49 5.94 114 32 39 7 301.07 0.50 115 32 43 11 223.48 39.27 116 32 101 69 142.55 0.32 117 32 102 70 142.54 0.32 118 32 105 73 143.53 0.03 119 33 37 4 412.29 13.67 120 33 39 6 224.96 38.56 121 33 40 7 223.43 39.26 122 33 43 10 223.43 39.26 123 33 49 16 144.25 0.12 124 33 56 23 144.20 0.14 125 34 37 3 488.46 5.40 126 34 51 17 144.26 0.15 127 36 39 3 497.95 0.73 128 36 101 65 142.58 0.33 129 36 104 68 144.11 0.12 130 36 105 69 144.11 0.12 131 37 40 3 496.81 3.10 132 38 41 3 511.93 0.79 133 38 98 60 143.00 0.52 134 38 101 63 144.12 0.13 135 39 42 3 506.03 1.50 136 39 43 4 501.90 1.46 137 39 98 59 142.99 0.53 138 39 101 62 144.11 0.12 139 40 43 3 498.15 2.58 140 40 44 4 486.68 3.16 141 41 44 3 482.31 0.26 142 42 45 3 576.61 2.48 143 42 94 52 142.94 0.52 144 42 95 53 143.87 0.08 145 42 98 56 144.03 0.12 146 43 46 3 494.92 0.90 147 43 49 6 144.53 0.09 148 43 59 16 144.28 0.15 149 46 49 3 505.64 2.28 150 46 55 9 144.69 0.05 151 46 56 10 144.71 0.06 152 46 59 13 144.65 0.07 153 47 55 8 144.97 0.18 154 48 53 5 262.62 40.80 155 49 53 4 453.61 8.72 156 50 53 3 480.81 0.10 157 50 56 6 404.54 17.30 158 53 56 3 484.52 1.88 159 53 57 4 472.50 0.26 160 54 57 3 485.39 2.31 161 54 58 4 478.31 3.17 162 55 58 3 490.03 0.87 163 55 59 4 478.30 3.17 164 56 59 3 491.57 0.10 165 56 60 4 472.73 0.44 166 57 60 3 484.89 0.13 167 57 61 4 472.74 0.44 168 58 61 3 484.34 0.40 169 58 62 4 472.76 0.42 170 59 62 3 484.87 0.13 171 59 63 4 477.19 1.79 172 60 63 3 485.93 0.40 173 60 64 4 477.30 1.84 174 61 64 3 486.24 0.24 175 61 65 4 476.85 2.06 176 62 65 3 477.26 1.86 177 62 66 4 476.85 2.06 178 63 66 3 477.50 1.74 179 63 67 4 475.66 2.66 180 63 102 39 179.35 1.27 181 64 67 3 473.82 1.05 182 64 68 4 473.68 1.14 183 64 106 42 180.32 1.49 184 65 68 3 474.00 0.98 185 65 69 4 473.64 1.15 186 66 69 3 483.60 2.30 187 66 70 4 473.65 1.15 188 66 84 18 179.87 1.58 189 67 70 3 483.99 3.19 190 67 71 4 473.63 1.15 191 67 106 39 211.12 0.62 192 67 129 62 211.39 0.48 193 67 130 63 191.84 0.20 194 67 133 66 180.27 1.53 195 68 71 3 482.79 2.58 196 68 72 4 474.67 0.61 197 69 72 3 480.42 1.41 198 69 73 4 475.53 1.04 199 69 81 12 180.12 1.61 200 69 83 14 180.31 1.53 201 70 73 3 461.01 6.61 202 70 74 4 457.31 4.93 203 70 77 7 256.22 23.75 204 70 81 11 180.13 1.62 205 70 129 59 246.13 7.50 206 70 133 63 187.64 1.77 207 71 74 3 475.56 1.03 208 71 129 58 262.31 1.06 209 73 76 3 492.98 1.06 210 73 77 4 470.36 1.56 211 73 80 7 254.74 20.34 212 74 77 3 485.56 4.42 213 74 129 55 276.39 4.24 214 76 79 3 495.46 3.83 215 76 80 4 462.33 1.35 216 77 80 3 475.92 0.27 217 77 81 4 465.75 3.07 218 77 129 52 288.39 0.09 219 77 132 55 286.46 0.28 220 77 133 56 279.28 3.31 221 77 136 59 276.48 4.24 222 78 81 3 505.92 3.23 223 78 82 4 475.09 0.17 224 78 136 58 276.50 4.24 225 78 139 61 276.44 4.26 226 79 82 3 485.41 0.04 227 80 83 3 581.95 0.71 228 81 84 3 493.13 0.01 229 81 85 4 465.11 1.23 230 81 133 52 289.26 0.01 231 81 136 55 289.12 0.00 232 81 137 56 289.12 0.00 233 82 85 3 486.50 3.19 234 82 86 4 465.11 1.23 235 82 139 57 289.17 0.05 236 82 140 58 288.89 0.06 237 83 86 3 486.62 3.25 238 83 87 4 471.38 4.37 239 84 87 3 493.81 0.48 240 84 88 4 465.10 1.23 241 84 137 53 289.58 0.09 242 85 88 3 473.67 0.24 243 85 89 4 465.01 1.20 244 85 90 5 452.63 4.99 245 85 136 51 289.58 0.08 246 85 137 52 289.58 0.09 247 85 139 54 289.53 0.09 248 85 140 55 289.41 0.06 249 86 90 4 418.32 5.33 250 86 91 5 418.32 5.33 251 86 140 54 289.48 0.09 252 87 91 4 391.91 3.87 253 87 92 5 391.88 3.86 254 88 92 4 391.88 3.86 255 88 93 5 391.87 3.86 256 88 94 6 346.69 18.68 257 88 99 11 293.20 0.16 258 89 93 4 391.87 3.87 259 89 137 48 289.68 0.09 260 89 138 49 289.62 0.09 261 89 140 51 289.53 0.10 262 89 141 52 289.43 0.05 263 90 93 3 477.64 0.93 264 90 140 50 289.56 0.09 265 93 141 48 289.63 0.10 266 94 98 4 480.55 4.29 267 94 99 5 474.96 4.05 268 94 141 47 289.72 0.10 269 95 98 3 488.34 0.41 270 96 99 3 497.78 1.86 271 96 100 4 488.35 0.41 272 96 141 45 289.88 0.10 273 97 100 3 488.34 0.41 274 97 101 4 481.47 3.83 275 98 101 3 485.36 1.88 276 98 102 4 478.38 2.29 277 99 102 3 488.29 0.41 278 99 103 4 480.33 3.57 279 99 134 35 290.05 0.12 280 99 137 38 290.05 0.12 281 99 141 42 290.03 0.12 282 100 103 3 485.09 1.20 283 100 104 4 483.17 2.16 284 101 104 3 485.09 1.20 285 101 105 4 484.54 1.47 286 102 105 3 484.54 1.46 287 102 106 4 473.70 3.96 288 103 106 3 482.23 3.23 289 103 107 4 473.70 3.96 290 103 130 27 290.30 0.10 291 103 134 31 290.26 0.11 292 104 107 3 481.63 3.54 293 104 108 4 474.09 3.75 294 105 108 3 484.83 1.93 295 105 109 4 474.08 3.75 296 106 109 3 484.86 1.95 297 106 110 4 477.45 5.65 298 106 130 24 290.59 0.17 299 107 110 3 484.86 1.95 300 107 111 4 477.47 5.63 301 107 118 11 292.08 0.49 302 107 123 16 290.88 0.03 303 107 126 19 290.85 0.04 304 107 127 20 290.83 0.05 305 107 130 23 290.69 0.13 306 108 111 3 483.21 2.77 307 108 112 4 470.69 2.23 308 109 112 3 477.44 1.14 309 109 113 4 471.22 1.98 310 110 113 3 477.44 1.14 311 110 114 4 466.88 0.19 312 110 118 8 292.24 0.42 313 110 126 16 291.68 0.30 314 111 115 4 437.61 8.60 315 111 118 7 292.26 0.43 316 112 115 3 505.17 0.96 317 114 117 3 491.55 1.39 318 114 118 4 450.55 11.65 319 116 119 3 535.33 1.24 320 117 122 5 468.14 0.56 321 118 122 4 468.14 0.56 322 118 123 5 465.12 2.04 323 118 126 8 450.69 1.82 324 119 122 3 485.96 5.63 325 119 123 4 471.66 2.31 326 120 123 3 474.58 3.77 327 120 124 4 471.82 2.34 328 121 124 3 485.78 0.09 329 121 125 4 484.68 0.64 330 122 125 3 485.78 0.09 331 122 126 4 482.75 0.33 332 123 126 3 482.76 0.33 333 123 127 4 474.62 3.73 334 124 127 3 484.23 0.41 335 124 128 4 478.45 2.48 336 125 128 3 476.98 1.75 337 125 129 4 475.01 2.73 338 126 129 3 475.03 2.73 339 126 130 4 475.01 2.71 340 127 130 3 475.25 2.58 341 127 131 4 475.02 2.70 342 128 131 3 481.57 0.58 343 128 132 4 475.02 2.69 344 129 132 3 472.48 1.42 345 129 133 4 465.13 2.25 346 130 133 3 471.94 1.16 347 130 134 4 465.12 2.25 348 131 134 3 471.09 1.67 349 131 135 4 462.23 0.83 350 132 135 3 477.94 2.85 351 132 136 4 465.83 3.16 352 133 136 3 482.19 4.83 353 133 137 4 478.09 2.78 354 134 137 3 486.95 1.65 355 134 138 4 477.92 2.69 356 135 138 3 478.10 2.78 357 135 139 4 472.29 0.12 358 136 139 3 479.62 2.01 359 138 141 3 486.87 1.26