Difference between revisions of "Part:BBa K5366017"

Revision as of 15:43, 30 September 2024

AJC7

Pseudothermotoga hypogea DSM-derived sequences with tagatose-4-epimerase activity

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 (ΔE_Binding) is defined as E_Complex = E_Ligand - E_Receptor. 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 AJC7 sequences and fructose(Fig. 1).

Fig. 1 Free energy of binding between AJC7 and fructose

From Figure 1, the free energy of docking between AJC7 and fructose is -9.9971kcal/mol.

Sequence and Features

Assembly Compatibility:

10
COMPATIBLE WITH RFC[10]
12
COMPATIBLE WITH RFC[12]
21
INCOMPATIBLE WITH RFC[21]
Illegal BglII site found at 501
23
COMPATIBLE WITH RFC[23]
25
INCOMPATIBLE WITH RFC[25]
Illegal AgeI site found at 1003
1000
COMPATIBLE WITH RFC[1000]

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 <partinfo>BBa_K5366017 short</partinfo>
-<i>Pseudothermotoga</i> <i>hypogea</i> <i>DSM</i>-derived sequences with tagatose-4-epimerase activity
+<i>Pseudothermotoga</i> <i>hypogea</i> DSM-derived sequences with tagatose-4-epimerase activity
-In the present study, an unknown functional protein from <i>Pseudothermotoga</i> <i>hypogea</i> <i>DSM</i>, exhibiting Tagatose-4-epimerase activity, was identified through gene mining and designated as AJC7.
+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 (ΔE<sub>Binding</sub>) is defined as E<sub>Complex</sub> = E<sub>Ligand</sub> - E<sub>Receptor</sub>. 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.
-The binding free energy of the receptor-ligand complex was calculated using a CHARMm-based energy functional along with implicit solvent methods. These free energies were estimated by minimizing the ligand energy in the presence of the receptor, employing both the steepest descent and conjugate gradient methods. Instead of utilizing the more costly molecular surface approximation, the effective Born radius was calculated using the Generalized Born Simple Switching (GBSW) implicit solvent model. This model features smooth dielectric boundaries that incorporate van der Waals surfaces. Using this approach, we calculated the free energy of binding between AJC7 and fructose (Fig. 1).
+Using this approach, we calculated the binding free energy between the AJC7 sequences and fructose(Fig. 1).
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    <img class="bild" src="https://static.igem.wiki/teams/5366/part/.png"><br>
    <i><b>Fig. 1 Free energy of binding between AJC7 and fructose<br><br></b></I>
-   <div class="unterschrift"><bFig. 1 Construction of pMTL-Pfba-Bs2 recombinant plasmid</b>
+   <div class="unterschrift"><bFig.1 Binding self-energy between selected sequences and fructose</b>
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-From Figure 1, the free energy of docking between AJC7 and fructose is -9.9971.
+From Figure 1, the free energy of docking between AJC7 and fructose is -9.9971kcal/mol.
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