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 5 455.28 1.10 2 2 73 71 25.84 0.60 3 2 127 125 27.86 1.11 4 2 128 126 24.21 0.70 5 3 6 3 469.36 1.69 6 3 7 4 469.37 1.69 7 4 7 3 476.11 0.76 8 4 8 4 469.37 1.69 9 5 8 3 472.49 2.25 10 5 9 4 469.36 1.69 11 6 9 3 473.69 1.02 12 6 10 4 471.81 2.00 13 6 124 118 49.75 0.34 14 6 127 121 48.83 0.80 15 7 10 3 476.92 4.55 16 7 11 4 471.81 2.00 17 7 73 66 49.77 0.32 18 7 74 67 50.15 0.14 19 8 11 3 474.33 0.74 20 8 12 4 471.81 2.00 21 9 12 3 481.06 0.34 22 9 13 4 472.75 1.53 23 9 121 112 57.48 3.00 24 9 124 115 57.17 3.15 25 10 13 3 481.20 0.40 26 10 14 4 470.76 2.50 27 10 70 60 57.16 3.15 28 10 124 114 57.19 3.15 29 10 125 115 57.17 3.14 30 10 128 118 57.16 3.14 31 11 14 3 484.30 1.15 32 11 15 4 466.75 0.42 33 11 70 59 57.45 3.00 34 11 73 62 57.45 3.00 35 12 15 3 478.34 1.83 36 12 16 4 474.39 0.15 37 13 16 3 475.72 0.51 38 13 17 4 474.38 0.16 39 13 121 108 57.87 2.93 40 13 125 112 57.80 2.90 41 14 17 3 475.73 0.51 42 14 18 4 474.37 0.17 43 14 21 7 397.94 4.84 44 14 63 49 69.11 2.31 45 14 66 52 57.67 2.98 46 14 67 53 57.68 2.98 47 14 70 56 57.68 2.98 48 14 109 95 80.03 1.19 49 15 18 3 475.19 0.48 50 16 113 97 81.31 0.71 51 16 116 100 80.20 1.16 52 17 20 3 479.18 1.77 53 17 21 4 450.32 0.51 54 17 24 7 380.72 2.08 55 17 109 92 81.29 0.70 56 17 113 96 81.31 0.71 57 18 21 3 488.06 1.18 58 20 23 3 493.79 2.60 59 20 24 4 462.39 0.43 60 21 24 3 482.09 3.25 61 21 25 4 463.01 0.74 62 21 63 42 105.89 1.25 63 22 25 3 473.06 2.73 64 22 26 4 466.46 0.57 65 22 60 38 107.83 0.33 66 22 63 41 105.98 1.26 67 23 26 3 470.85 2.38 68 23 27 4 462.42 0.42 69 23 56 33 119.91 0.72 70 24 27 3 470.85 2.38 71 24 28 4 466.01 1.40 72 24 108 84 127.81 0.18 73 24 109 85 128.07 0.04 74 24 112 88 132.22 1.19 75 24 113 89 132.37 1.26 76 25 28 3 480.94 1.52 77 25 29 4 473.86 0.88 78 25 59 34 119.61 0.60 79 25 63 38 119.09 0.82 80 26 29 3 480.94 1.52 81 26 30 4 472.39 0.07 82 26 55 29 127.88 0.04 83 26 56 30 126.62 1.22 84 26 59 33 122.31 0.18 85 27 30 3 475.91 1.70 86 27 31 4 472.45 0.03 87 27 108 81 132.59 1.18 88 27 112 85 132.97 1.25 89 28 31 3 472.46 0.03 90 28 32 4 472.47 0.03 91 28 101 73 132.41 1.25 92 28 104 76 132.41 1.25 93 28 105 77 132.40 1.26 94 28 108 80 132.68 1.14 95 29 32 3 479.42 2.08 96 29 33 4 470.35 1.03 97 29 55 26 132.89 1.19 98 29 58 29 132.88 1.19 99 29 59 30 132.71 1.10 100 29 101 72 132.49 1.23 101 30 33 3 476.28 0.50 102 30 34 4 469.77 1.32 103 30 50 20 133.80 1.50 104 31 34 3 480.35 1.80 105 31 35 4 470.06 1.48 106 31 104 73 133.49 1.44 107 31 107 76 133.55 1.42 108 31 108 77 133.52 1.44 109 32 35 3 479.70 2.12 110 32 36 4 466.09 3.46 111 32 39 7 352.27 2.77 112 32 100 68 133.50 1.44 113 32 101 69 133.45 1.46 114 32 104 72 133.51 1.44 115 33 37 4 446.41 2.88 116 33 39 6 352.27 2.78 117 33 40 7 272.88 1.24 118 33 43 10 278.36 3.98 119 33 48 15 133.90 1.48 120 33 55 22 133.79 1.49 121 34 37 3 475.72 1.22 122 36 39 3 488.72 4.67 123 36 100 64 133.58 1.48 124 36 103 67 133.75 1.47 125 36 104 68 133.76 1.48 126 37 40 3 478.85 0.98 127 38 41 3 482.69 2.91 128 39 42 3 502.31 4.16 129 39 97 58 133.54 1.48 130 39 100 61 133.75 1.48 131 40 43 3 490.00 1.53 132 40 48 8 244.28 1.64 133 41 44 3 493.40 3.62 134 42 93 51 133.51 1.48 135 42 94 52 133.76 1.47 136 42 97 55 133.78 1.47 137 43 46 3 474.63 1.00 138 43 48 5 414.36 2.64 139 43 58 15 185.93 24.50 140 45 54 9 246.66 0.87 141 46 54 8 246.63 0.88 142 46 58 12 246.50 0.84 143 47 52 5 275.23 9.91 144 47 54 7 246.68 0.88 145 47 55 8 246.69 0.89 146 48 52 4 371.94 27.19 147 48 55 7 248.58 1.87 148 49 52 3 463.18 0.93 149 52 55 3 472.86 0.06 150 52 56 4 480.29 7.67 151 53 56 3 484.07 5.78 152 53 57 4 468.88 1.93 153 54 57 3 480.34 7.65 154 54 58 4 465.81 0.09 155 55 58 3 488.74 3.45 156 55 59 4 465.78 0.10 157 56 59 3 469.95 1.97 158 56 60 4 467.59 0.73 159 57 60 3 475.47 1.37 160 57 61 4 473.53 0.40 161 58 61 3 474.86 1.06 162 58 62 4 473.53 0.40 163 59 62 3 476.49 2.58 164 59 63 4 468.50 2.92 165 60 63 3 480.68 0.49 166 60 64 4 464.44 0.90 167 61 64 3 469.50 1.02 168 61 65 4 468.87 1.33 169 62 65 3 469.11 1.46 170 62 66 4 476.64 2.55 171 62 101 39 172.08 2.43 172 63 66 3 476.64 2.55 173 63 67 4 476.64 2.55 174 64 67 3 478.12 1.81 175 64 68 4 476.63 2.56 176 65 68 3 482.20 0.23 177 65 69 4 476.37 2.69 178 65 83 18 169.05 3.53 179 66 69 3 482.19 0.23 180 66 70 4 475.60 2.31 181 66 105 39 188.72 5.42 182 66 128 62 190.51 4.73 183 66 129 63 181.08 1.45 184 66 132 66 180.28 1.71 185 67 70 3 482.19 0.24 186 67 71 4 478.11 1.80 187 68 71 3 480.28 2.88 188 68 72 4 476.61 1.05 189 68 79 11 247.82 2.96 190 69 72 3 477.12 1.31 191 69 73 4 464.09 0.63 192 69 76 7 293.56 9.36 193 69 80 11 209.33 16.28 194 69 128 59 191.58 4.28 195 69 132 63 181.40 1.54 196 70 73 3 476.61 1.05 197 70 128 58 207.90 5.64 198 72 75 3 467.93 1.79 199 72 76 4 387.42 10.84 200 72 79 7 291.02 2.50 201 73 76 3 487.51 1.71 202 73 128 55 220.80 3.39 203 75 78 3 490.88 2.60 204 75 79 4 476.44 2.73 205 76 79 3 478.76 1.57 206 76 80 4 467.84 1.49 207 76 128 52 223.29 3.52 208 76 131 55 222.90 3.33 209 76 132 56 222.15 3.05 210 76 135 59 222.21 3.00 211 77 80 3 481.39 0.54 212 77 81 4 467.84 1.48 213 77 135 58 222.22 2.99 214 77 140 63 185.68 1.45 215 78 81 3 486.92 1.15 216 80 83 3 473.40 1.26 217 80 84 4 467.66 1.61 218 80 132 52 224.25 3.06 219 80 135 55 224.14 3.00 220 80 136 56 224.15 3.00 221 81 84 3 467.66 1.61 222 81 85 4 467.66 1.61 223 81 140 59 221.85 3.06 224 81 141 60 184.65 1.14 225 82 85 3 477.68 1.73 226 82 86 4 477.67 1.73 227 83 86 3 472.67 0.90 228 83 87 4 472.55 0.84 229 83 136 53 224.41 3.01 230 84 87 3 486.67 2.75 231 84 88 4 459.58 2.33 232 84 89 5 459.55 2.31 233 84 135 51 224.40 3.02 234 84 136 52 224.41 3.02 235 84 138 54 224.38 3.02 236 84 140 56 224.11 3.06 237 85 89 4 459.34 2.40 238 85 90 5 431.00 16.56 239 86 90 4 398.69 0.42 240 86 91 5 398.68 0.42 241 87 91 4 398.69 0.42 242 87 92 5 398.65 0.43 243 87 93 6 348.78 24.45 244 87 98 11 284.31 5.08 245 87 136 49 224.46 3.00 246 88 92 4 398.64 0.43 247 88 136 48 224.52 3.03 248 88 137 49 224.47 3.01 249 88 138 50 224.47 3.00 250 88 139 51 224.44 3.01 251 89 92 3 491.34 0.72 252 89 139 50 224.46 3.02 253 93 97 4 486.50 0.25 254 93 98 5 476.04 2.73 255 94 97 3 489.62 1.81 256 95 98 3 486.91 0.45 257 95 99 4 486.50 0.25 258 95 137 42 225.08 3.11 259 96 99 3 486.50 0.25 260 96 100 4 483.75 1.12 261 97 100 3 482.30 1.85 262 97 101 4 474.00 1.68 263 98 101 3 482.17 1.90 264 98 102 4 473.38 1.39 265 98 133 35 225.45 3.17 266 98 136 38 225.45 3.17 267 98 137 39 225.45 3.17 268 99 102 3 477.49 0.66 269 99 103 4 473.31 1.43 270 100 103 3 479.93 1.91 271 100 104 4 464.66 2.90 272 101 104 3 479.94 1.91 273 101 105 4 464.20 3.12 274 102 105 3 477.92 1.67 275 102 106 4 477.17 0.67 276 102 129 27 225.82 3.18 277 102 133 31 225.74 3.23 278 103 106 3 486.47 2.59 279 103 107 4 478.56 1.37 280 104 107 3 486.31 2.50 281 104 108 4 478.56 1.38 282 105 108 3 486.31 2.50 283 105 109 4 480.67 0.32 284 105 129 24 226.71 3.22 285 106 109 3 486.31 2.50 286 106 110 4 476.99 1.54 287 106 117 11 286.44 5.13 288 106 122 16 227.31 3.35 289 106 125 19 227.16 3.35 290 106 126 20 227.12 3.38 291 106 129 23 226.91 3.27 292 107 110 3 479.75 0.18 293 107 111 4 477.00 1.54 294 108 111 3 479.75 0.17 295 108 112 4 476.97 1.55 296 109 112 3 479.73 0.17 297 109 113 4 450.10 14.98 298 109 117 8 286.99 5.40 299 109 125 16 228.00 3.35 300 110 114 4 412.34 4.20 301 110 117 7 286.44 5.13 302 111 114 3 505.65 1.76 303 113 116 3 484.64 0.08 304 113 117 4 467.01 3.39 305 114 117 3 477.54 3.63 306 115 118 3 511.08 2.15 307 116 121 5 436.41 1.47 308 117 122 5 422.55 5.46 309 117 125 8 410.18 5.76 310 118 121 3 467.11 1.60 311 118 122 4 445.38 5.83 312 119 122 3 473.54 4.82 313 119 123 4 451.22 4.92 314 120 123 3 484.21 7.83 315 120 124 4 471.27 4.01 316 121 124 3 474.72 2.29 317 121 125 4 471.27 4.01 318 122 125 3 476.66 3.26 319 122 126 4 468.61 0.14 320 123 126 3 479.12 4.26 321 123 127 4 471.54 1.59 322 124 127 3 481.18 3.23 323 124 128 4 469.90 8.53 324 125 128 3 477.19 4.88 325 125 129 4 475.22 5.87 326 126 129 3 485.85 0.56 327 126 130 4 477.19 4.88 328 127 130 3 485.85 0.56 329 127 131 4 475.21 5.87 330 128 131 3 479.16 2.65 331 128 132 4 468.67 2.60 332 129 132 3 472.81 0.54 333 129 133 4 466.87 3.52 334 130 133 3 478.03 2.06 335 130 134 4 466.88 3.52 336 131 134 3 480.77 3.43 337 131 135 4 476.63 1.35 338 132 135 3 478.04 2.06 339 132 136 4 476.63 1.36 340 133 136 3 481.94 0.96 341 133 137 4 469.01 0.97 342 134 137 3 481.95 0.96 343 134 138 4 469.01 0.97 344 135 138 3 478.98 0.24 345 135 140 5 454.55 0.46