Difference between revisions of "Part:BBa K5366017"
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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 AGC7 and fructose (Fig. 1). | 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 AGC7 and fructose (Fig. 1). | ||
https://static.igem.wiki/teams/5366/part/1-free-energy-of-binding.png | https://static.igem.wiki/teams/5366/part/1-free-energy-of-binding.png | ||
| − | + | Fig. 1 Free energy of binding between AJC7 and fructose | |
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 -9.9971. | ||
Revision as of 12:05, 27 September 2024
AJC7
Pseudothermotoga<i> <i>hypogea<i> <i>DSM<i>-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 AGC7.
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 AGC7 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 -9.9971.
Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21INCOMPATIBLE WITH RFC[21]Illegal BglII site found at 501
- 23COMPATIBLE WITH RFC[23]
- 25INCOMPATIBLE WITH RFC[25]Illegal AgeI site found at 1003
- 1000COMPATIBLE WITH RFC[1000]