Difference between revisions of "Part:BBa K5366019"
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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 TET 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 TET and fructose (Fig. 1).
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  <div class="unterschrift"><bFig. 1 Construction of pMTL-Pfba-Bs2 recombinant plasmid</b>
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   Fig. 1 Free energy of binding between TET and fructose
 
   Fig. 1 Free energy of binding between TET and fructose
 
From Figure 1, the free energy of docking between TET and fructose is -6.5787.<!-- Add more about the biology of this part here
 
From Figure 1, the free energy of docking between TET and fructose is -6.5787.<!-- Add more about the biology of this part here

Revision as of 13:14, 27 September 2024


TET

Sequences from the source of Candidatus Aerophobetes bacterium with tagatose-4-epimerase activity

In the present study, an unknown functional protein from Candidatus Aerophobetes bacterium, exhibiting Tagatose-4-epimerase activity, was identified through gene mining and designated as TET.

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 TET and fructose (Fig. 1). 

 Fig. 1 Free energy of binding between TET and fructose

From Figure 1, the free energy of docking between TET and fructose is -6.5787. Sequence and Features


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal EcoRI site found at 25
    Illegal EcoRI site found at 160
    Illegal PstI site found at 64
    Illegal PstI site found at 709
    Illegal PstI site found at 1474
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal EcoRI site found at 25
    Illegal EcoRI site found at 160
    Illegal PstI site found at 64
    Illegal PstI site found at 709
    Illegal PstI site found at 1474
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal EcoRI site found at 25
    Illegal EcoRI site found at 160
    Illegal BglII site found at 629
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal EcoRI site found at 25
    Illegal EcoRI site found at 160
    Illegal PstI site found at 64
    Illegal PstI site found at 709
    Illegal PstI site found at 1474
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal EcoRI site found at 25
    Illegal EcoRI site found at 160
    Illegal PstI site found at 64
    Illegal PstI site found at 709
    Illegal PstI site found at 1474
    Illegal NgoMIV site found at 756
    Illegal AgeI site found at 313
  • 1000
    COMPATIBLE WITH RFC[1000]