Difference between revisions of "Part:BBa K3381002:Design"

 
 
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<partinfo>BBa_K3381002 short</partinfo>
 
<partinfo>BBa_K3381002 short</partinfo>
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===Design Notes===
 
===Design Notes===
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The periplasmic localization tags were determined by the SignalP-5.0 Server and removed. The sequences were then codon optimized for *E. coli*, removing all cut sites for RFc 25 and NdeI/BamHI (required for cloning into pET 11a). Lastly, the prefix and suffix for RFc 25 were appended.
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The periplasmic localization tags were determined by the SignalP-5.0 Server and removed. The sequences were then codon optimized for E. coli, removing all cut sites for RFc 25 and NdeI/BamHI (required for cloning into pET 11a). Lastly, the prefix and suffix for RFc 25 were appended.
  
  
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Methylosinus trichosporium O3B, sequence found through GenBank https://www.ncbi.nlm.nih.gov/protein/ATQ66671
 
Methylosinus trichosporium O3B, sequence found through GenBank https://www.ncbi.nlm.nih.gov/protein/ATQ66671
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===References===
 
===References===
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Lawton, T. J., Kenney, G. E., Hurley, J. D., & Rosenzweig, A. C. (2016). The CopC Family: Structural and Bioinformatic Insights into a Diverse Group of Periplasmic Copper Binding Proteins. Biochemistry, 55(15), 2278-2290. doi:10.1021/acs.biochem.6b00175.s003
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Vanommeslaeghe, K. Hatcher, E. Acharya, C. Kundu, S. Zhong, S. Shim, J. E. Darian, E. Guvench, O. Lopes, P. Vorobyov, I. and MacKerell, Jr. A.D. "CHARMM General Force Field (CGenFF): A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields," Journal of Computational Chemistry 31: 671-90, 2010, PMC2888302

Latest revision as of 01:29, 24 October 2020

Mst-CopC (copper-binding)


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

The periplasmic localization tags were determined by the SignalP-5.0 Server and removed. The sequences were then codon optimized for E. coli, removing all cut sites for RFc 25 and NdeI/BamHI (required for cloning into pET 11a). Lastly, the prefix and suffix for RFc 25 were appended.


Source

Methylosinus trichosporium O3B, sequence found through GenBank https://www.ncbi.nlm.nih.gov/protein/ATQ66671


References

Lawton, T. J., Kenney, G. E., Hurley, J. D., & Rosenzweig, A. C. (2016). The CopC Family: Structural and Bioinformatic Insights into a Diverse Group of Periplasmic Copper Binding Proteins. Biochemistry, 55(15), 2278-2290. doi:10.1021/acs.biochem.6b00175.s003


Vanommeslaeghe, K. Hatcher, E. Acharya, C. Kundu, S. Zhong, S. Shim, J. E. Darian, E. Guvench, O. Lopes, P. Vorobyov, I. and MacKerell, Jr. A.D. "CHARMM General Force Field (CGenFF): A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields," Journal of Computational Chemistry 31: 671-90, 2010, PMC2888302