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 6 91 85 233.88 1.04 2 6 92 86 233.91 1.03 3 6 93 87 233.94 1.03 4 7 29 22 337.17 0.10 5 7 42 35 310.61 10.55 6 7 90 83 233.94 1.02 7 7 91 84 233.91 1.02 8 8 42 34 328.97 2.22 9 8 43 35 336.88 0.75 10 8 44 36 337.07 0.66 11 8 45 37 337.11 0.65 12 8 91 83 233.97 1.02 13 9 91 82 233.98 1.02 14 9 95 86 233.97 1.02 15 9 97 88 233.91 1.02 16 9 98 89 233.87 1.03 17 9 99 90 233.87 1.04 18 10 42 32 337.31 0.69 19 10 43 33 337.24 0.68 20 10 99 89 233.87 1.03 21 11 41 30 337.39 0.72 22 11 42 31 337.31 0.69 23 11 43 32 337.31 0.69 24 11 98 87 233.96 1.02 25 11 99 88 233.91 1.03 26 11 100 89 233.88 1.03 27 11 101 90 233.88 1.03 28 12 40 28 337.87 0.66 29 12 41 29 337.63 0.77 30 12 43 31 337.46 0.68 31 12 49 37 337.21 0.58 32 12 52 40 337.19 0.58 33 12 53 41 337.06 0.59 34 12 56 44 337.12 0.61 35 12 101 89 233.88 1.03 36 12 103 91 233.87 1.04 37 13 38 25 338.34 0.54 38 13 39 26 338.31 0.55 39 13 40 27 337.88 0.66 40 13 100 87 233.95 1.02 41 13 101 88 233.91 1.02 42 13 102 89 233.87 1.03 43 13 103 90 233.87 1.03 44 13 138 125 55.44 0.29 45 13 141 128 54.43 0.38 46 14 38 24 338.39 0.55 47 14 39 25 338.29 0.56 48 14 53 39 337.20 0.58 49 14 57 43 337.17 0.58 50 14 72 58 233.96 1.03 51 14 103 89 233.88 1.03 52 14 105 91 233.84 1.02 53 15 38 23 338.44 0.53 54 15 103 88 233.92 1.02 55 15 104 89 233.87 1.03 56 15 105 90 233.87 1.03 57 15 141 126 54.91 0.15 58 15 142 127 52.62 0.50 59 15 146 131 39.86 0.98 60 16 24 8 342.25 0.89 61 16 25 9 342.17 0.85 62 16 39 23 339.33 0.09 63 16 57 41 337.24 0.58 64 16 61 45 336.51 0.57 65 16 105 89 233.87 1.03 66 16 107 91 233.83 1.03 67 16 123 107 134.80 0.20 68 17 23 6 349.47 2.12 69 17 24 7 342.25 0.89 70 17 105 88 233.92 1.03 71 17 106 89 233.87 1.03 72 17 107 90 233.85 1.02 73 17 123 106 134.80 0.20 74 17 146 129 41.91 0.04 75 18 21 3 484.24 1.86 76 18 22 4 414.31 3.06 77 18 23 5 380.67 13.46 78 18 107 89 233.86 1.02 79 18 109 91 210.31 2.16 80 18 110 92 169.35 0.10 81 18 123 105 134.89 0.22 82 19 22 3 468.74 2.02 83 19 106 87 233.94 1.02 84 19 107 88 233.91 1.02 85 19 108 89 233.87 1.03 86 20 108 88 233.91 1.02 87 20 109 89 233.87 1.03 88 20 110 90 233.86 1.02 89 21 110 89 233.78 1.04 90 22 146 124 52.30 0.60 91 23 110 87 221.61 1.09 92 23 123 100 134.88 0.16 93 23 124 101 133.88 0.10 94 23 125 102 129.19 1.21 95 24 122 98 135.03 0.21 96 24 123 99 134.59 0.24 97 24 124 100 132.99 0.14 98 24 126 102 101.25 0.91 99 24 129 105 78.44 0.74 100 24 142 118 55.26 0.19 101 24 146 122 48.48 2.46 102 25 38 13 342.63 0.04 103 25 61 36 334.50 0.45 104 25 113 88 141.72 1.00 105 25 121 96 135.06 0.21 106 25 122 97 134.97 0.20 107 25 123 98 134.68 0.29 108 26 36 10 343.05 0.14 109 26 37 11 342.78 0.10 110 26 38 12 342.65 0.04 111 26 121 95 135.03 0.21 112 26 122 96 134.93 0.20 113 26 124 98 133.85 0.11 114 26 129 103 60.09 2.34 115 26 132 106 58.16 1.39 116 26 133 107 56.84 0.72 117 26 142 116 55.41 0.28 118 27 36 9 343.11 0.15 119 27 37 10 342.93 0.10 120 27 39 12 342.87 0.08 121 27 61 34 333.89 0.74 122 27 113 86 141.72 1.00 123 27 115 88 141.43 0.96 124 27 118 91 141.22 0.97 125 27 120 93 136.08 0.07 126 27 121 94 134.96 0.18 127 28 33 5 391.30 8.02 128 28 35 7 344.41 0.47 129 28 36 8 343.13 0.15 130 28 118 90 141.27 0.99 131 28 119 91 141.12 1.02 132 28 120 92 139.43 0.39 133 29 32 3 460.74 1.15 134 29 33 4 394.64 6.36 135 29 35 6 344.46 0.49 136 29 37 8 343.18 0.15 137 29 118 89 141.28 0.98 138 29 119 90 141.27 0.99 139 30 117 87 141.41 1.01 140 30 119 89 141.27 0.99 141 31 87 56 228.84 1.69 142 32 35 3 466.92 1.33 143 32 86 54 229.05 1.61 144 32 134 102 58.13 1.41 145 33 119 86 141.21 1.00 146 34 134 100 56.82 0.74 147 35 84 49 217.60 4.37 148 35 87 52 229.01 1.63 149 35 133 98 56.81 0.72 150 35 134 99 56.75 0.72 151 35 135 100 56.73 0.72 152 36 120 84 141.08 1.03 153 36 121 85 135.12 0.17 154 36 122 86 135.00 0.19 155 36 132 96 56.81 0.72 156 36 133 97 56.66 0.65 157 37 40 3 575.00 0.06 158 37 118 81 141.21 0.99 159 37 138 101 55.47 0.28 160 38 138 100 55.45 0.29 161 39 56 17 337.19 0.57 162 39 57 18 337.10 0.58 163 39 60 21 325.86 0.86 164 39 61 22 325.86 0.86 165 40 56 16 337.19 0.58 166 40 60 20 325.86 0.86 167 41 56 15 337.14 0.54 168 42 55 13 345.76 0.44 169 43 47 4 463.92 0.20 170 43 48 5 428.66 2.70 171 43 49 6 394.11 3.19 172 43 52 9 347.35 1.24 173 44 47 3 482.57 0.68 174 44 55 11 394.12 3.19 175 47 51 4 462.37 0.70 176 47 52 5 460.11 1.87 177 47 55 8 443.49 0.71 178 48 51 3 477.79 1.42 179 48 52 4 464.00 0.06 180 49 52 3 476.68 1.97 181 49 53 4 461.69 1.11 182 49 103 54 233.90 1.02 183 50 53 3 471.32 0.72 184 50 54 4 463.11 1.81 185 50 72 22 234.06 1.06 186 50 103 53 233.91 1.02 187 51 54 3 467.61 3.12 188 51 55 4 463.59 2.06 189 52 55 3 470.28 1.26 190 52 56 4 470.19 1.22 191 53 56 3 470.28 1.25 192 53 57 4 470.23 1.24 193 53 72 19 234.05 1.06 194 53 103 50 233.90 1.02 195 54 57 3 478.28 5.25 196 54 58 4 470.23 1.24 197 54 65 11 355.39 2.46 198 54 66 12 360.18 4.86 199 54 72 18 234.06 1.06 200 55 58 3 470.48 1.36 201 55 59 4 470.21 1.24 202 56 59 3 470.95 0.86 203 56 60 4 470.18 1.26 204 57 61 4 449.02 4.11 205 57 62 5 436.84 1.59 206 57 63 6 392.67 4.50 207 57 65 8 375.50 0.37 208 57 105 48 233.85 1.02 209 58 62 4 403.31 0.01 210 58 63 5 381.95 0.86 211 58 64 6 381.93 0.86 212 59 116 57 141.31 0.99 213 59 117 58 141.30 0.99 214 60 115 55 141.34 0.99 215 60 116 56 141.30 0.99 216 60 117 57 141.22 1.01 217 60 118 58 141.19 1.01 218 61 113 52 141.52 0.99 219 61 114 53 141.43 1.00 220 61 115 54 141.34 0.99 221 62 114 52 141.53 0.99 222 62 116 54 141.37 0.97 223 63 68 5 452.91 2.19 224 63 70 7 414.94 3.45 225 63 107 44 233.80 1.04 226 63 111 48 148.56 2.07 227 63 113 50 141.59 1.01 228 64 67 3 470.20 0.19 229 64 68 4 463.94 3.31 230 65 68 3 476.11 2.76 231 65 69 4 452.92 2.19 232 65 70 5 414.91 3.46 233 65 72 7 386.35 1.04 234 65 105 40 233.91 1.02 235 66 69 3 469.39 0.70 236 68 111 43 233.28 0.84 237 70 105 35 233.94 1.02 238 70 107 37 233.90 1.02 239 70 108 38 233.87 1.01 240 71 105 34 233.94 1.02 241 72 103 31 234.03 1.00 242 72 105 33 233.89 1.02 243 73 103 30 234.03 1.00 244 73 104 31 233.97 0.99 245 74 103 29 234.05 0.99 246 75 102 27 234.08 1.00 247 75 103 28 234.06 0.99 248 75 104 29 234.05 0.99 249 75 145 70 42.02 0.11 250 77 101 24 234.38 0.97 251 77 102 25 234.30 0.96 252 77 144 67 48.54 0.07 253 77 145 68 44.38 0.38 254 78 99 21 235.05 1.19 255 78 100 22 234.42 0.97 256 78 101 23 234.40 0.96 257 79 99 20 235.06 1.19 258 79 100 21 234.52 1.01 259 79 102 23 234.43 0.97 260 79 136 57 55.62 0.26 261 79 137 58 55.43 0.32 262 80 97 17 235.66 1.25 263 80 98 18 235.14 1.21 264 80 99 19 235.07 1.19 265 80 136 56 55.61 0.26 266 81 97 16 235.68 1.25 267 81 98 17 235.62 1.25 268 81 100 19 235.46 1.32 269 81 136 55 55.51 0.30 270 81 137 56 55.38 0.34 271 82 96 14 235.83 1.26 272 82 97 15 235.72 1.25 273 83 87 4 474.29 0.24 274 83 88 5 449.30 4.83 275 83 91 8 389.18 0.61 276 83 95 12 235.94 1.25 277 83 96 13 235.87 1.24 278 83 97 14 235.83 1.26 279 83 98 15 235.78 1.25 280 84 87 3 481.88 1.88 281 84 88 4 475.41 0.55 282 84 134 50 55.58 0.25 283 84 135 51 55.52 0.27 284 85 88 3 493.26 0.99 285 86 89 3 523.38 0.43 286 86 134 48 55.65 0.25 287 87 90 3 495.28 3.83 288 87 91 4 491.22 1.79 289 88 91 3 488.38 3.21 290 88 95 7 368.87 6.83 291 88 96 8 296.82 29.19 292 91 95 4 410.67 1.10 293 92 95 3 478.79 0.34 294 100 137 37 55.45 0.30 295 102 137 35 55.55 0.25 296 102 140 38 55.37 0.26 297 102 141 39 52.51 0.43 298 102 144 42 46.36 0.48 299 102 145 43 41.86 0.01 300 107 111 4 501.41 0.85 301 107 123 16 135.00 0.22 302 110 123 13 135.00 0.22 303 111 123 12 135.14 0.18 304 112 121 9 141.14 0.96 305 113 121 8 139.79 1.20 306 113 123 10 136.52 0.83 307 115 118 3 488.92 2.54 308 115 119 4 488.92 2.54 309 115 120 5 456.05 2.84 310 115 121 6 384.94 7.99 311 124 128 4 463.90 3.95 312 124 129 5 456.46 4.44 313 124 132 8 428.13 2.21 314 125 128 3 468.50 1.65 315 125 129 4 464.43 3.68 316 126 129 3 470.04 0.88 317 126 130 4 464.43 3.68 318 126 142 16 55.48 0.25 319 126 146 20 50.75 1.31 320 126 147 21 40.17 0.83 321 127 130 3 471.28 1.50 322 127 131 4 468.05 0.13 323 127 147 20 41.02 1.13 324 128 131 3 472.15 1.92 325 128 132 4 468.05 0.13 326 129 132 3 473.71 2.70 327 129 133 4 472.15 1.92 328 129 142 13 55.38 0.30 329 130 133 3 477.68 2.91 330 130 139 9 55.63 0.33 331 130 142 12 55.38 0.30 332 130 143 13 55.05 0.37 333 133 138 5 433.48 8.82 334 133 139 6 400.68 6.60 335 135 138 3 471.72 1.57 336 135 139 4 461.23 1.09 337 136 139 3 467.82 2.21 338 136 140 4 460.65 0.81 339 137 140 3 469.41 1.62 340 137 141 4 459.93 1.75 341 138 141 3 471.87 0.70 342 138 142 4 459.36 1.45 343 139 142 3 480.49 2.17 344 139 143 4 461.41 1.62 345 140 143 3 475.03 4.90 346 140 144 4 459.29 1.44 347 141 144 3 474.36 4.56 348 141 145 4 454.50 0.67 349 142 146 4 443.41 4.87 350 142 147 5 436.11 8.52 351 143 147 4 432.19 0.74 352 143 148 5 414.05 8.30 353 144 148 4 414.01 8.31