Difference between revisions of "Part:BBa K5366020"
| (One intermediate revision by the same user not shown) | |||
| Line 3: | Line 3: | ||
<partinfo>BBa_K5366020 short</partinfo> | <partinfo>BBa_K5366020 short</partinfo> | ||
| − | Sequences of Thermotogales bacterium origin with tagatose-4- epimerase activity | + | Sequences of <i>Thermotogales bacterium</i> origin with tagatose-4- epimerase activity |
In the present study, an unknown functional protein from <i>Thermotogales bacterium</i>, exhibiting Tagatose-4-epimerase activity, was identified through gene mining and designated as HDM. | In the present study, an unknown functional protein from <i>Thermotogales bacterium</i>, exhibiting Tagatose-4-epimerase activity, was identified through gene mining and designated as HDM. | ||
| Line 14: | Line 14: | ||
</style> | </style> | ||
<p> | <p> | ||
| − | <img class="bild" src="https://static.igem.wiki/teams/5366/part/.png"><br> | + | <img class="bild" src="https://static.igem.wiki/teams/5366/part/binding-free-energy.png"><br> |
<i><b>Fig. 1 Binding free energy between the HDM sequence and fructose (using the final selected sequence as an example)<br><br></b></I> | <i><b>Fig. 1 Binding free energy between the HDM sequence and fructose (using the final selected sequence as an example)<br><br></b></I> | ||
<div class="unterschrift"><bFig. 1 Construction of pMTL-Pfba-Bs2 recombinant plasmid</b> | <div class="unterschrift"><bFig. 1 Construction of pMTL-Pfba-Bs2 recombinant plasmid</b> | ||
Latest revision as of 16:30, 30 September 2024
HDM
Sequences of Thermotogales bacterium origin with tagatose-4- epimerase activity
In the present study, an unknown functional protein from Thermotogales bacterium, exhibiting Tagatose-4-epimerase activity, was identified through gene mining and designated as HDM.
We calculated the binding free energy of the receptor-ligand complexes using the CHARMm-based energy function and an implicit solvent model. The binding energy between the receptor and ligand (ΔEBinding) is defined as EComplex = ELigand - EReceptor. To estimate these free energies, we minimized the ligand energy in the presence of the receptor using the steepest descent and conjugate gradient methods. The effective Born radii were computed using the Generalized Born Simple Switching (GBSW) implicit solvent model, replacing the costly molecular surface approximation with a smooth dielectric boundary combined with a van der Waals surface. Using this approach, we calculated the binding free energy between the HDM sequences and fructose(Fig. 1).
Fig. 1 Binding free energy between the HDM sequence and fructose (using the final selected sequence as an example)
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21INCOMPATIBLE WITH RFC[21]Illegal BglII site found at 363
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE WITH RFC[1000]