Difference between revisions of "Part:BBa K5366018"
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In the present study, an unknown functional protein from <i>Chloroflexota bacterium</i>, exhibiting Tagatose-4-epimerase activity, was identified through gene mining and designated as MBC.
 
In the present study, an unknown functional protein from <i>Chloroflexota bacterium</i>, exhibiting Tagatose-4-epimerase activity, was identified through gene mining and designated as MBC.
 
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 MBC 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 MBC 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 MBC and fructose
 
   Fig. 1 Free energy of binding between MBC and fructose
 
From Figure 1, the free energy of docking between MBCand fructose is -0.25540.<!-- Add more about the biology of this part here
 
From Figure 1, the free energy of docking between MBCand fructose is -0.25540.<!-- Add more about the biology of this part here

Revision as of 13:12, 27 September 2024


MBC

Sequences of Chloroflexota bacterium origin with tagatose-4-epimerase activity

In the present study, an unknown functional protein from Chloroflexota bacterium, exhibiting Tagatose-4-epimerase activity, was identified through gene mining and designated as MBC. 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 MBC and fructose (Fig. 1). 

 Fig. 1 Free energy of binding between MBC and fructose

From Figure 1, the free energy of docking between MBCand fructose is -0.25540. Sequence and Features


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal PstI site found at 223
    Illegal PstI site found at 244
    Illegal PstI site found at 619
    Illegal PstI site found at 661
    Illegal PstI site found at 871
    Illegal PstI site found at 1429
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal PstI site found at 223
    Illegal PstI site found at 244
    Illegal PstI site found at 619
    Illegal PstI site found at 661
    Illegal PstI site found at 871
    Illegal PstI site found at 1429
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal PstI site found at 223
    Illegal PstI site found at 244
    Illegal PstI site found at 619
    Illegal PstI site found at 661
    Illegal PstI site found at 871
    Illegal PstI site found at 1429
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal PstI site found at 223
    Illegal PstI site found at 244
    Illegal PstI site found at 619
    Illegal PstI site found at 661
    Illegal PstI site found at 871
    Illegal PstI site found at 1429
    Illegal NgoMIV site found at 1078
    Illegal AgeI site found at 367
  • 1000
    COMPATIBLE WITH RFC[1000]