Coding

Part:BBa_K3945003

Designed by: Ramin Kahidi   Group: iGEM21_Calgary   (2021-10-20)
Revision as of 03:41, 22 October 2021 by ArshiaMostoufi (Talk | contribs) (→‎Design)

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Genetic Algorithm Mutated Lanmodulin (GA LanM)


Usage and Biology

Lanmodulin is recently a novel lanthanide binding protein from Methylobacterium extorquens that displays more than 100-million fold selectivity for rare earth elements [1]. Such affinity and selectivity have not been observed in any previously studied macromolecule. In addition, lanmodulin is extremely robust, capable of withstanding temperatures as high as 95 °C and pH levels as low as 2.5 [2]. Thus, allowing it to be the perfect molecular tool for us in an efficient rare earth recovery system.

We have mutated the lanmodulin sequence using a Genetic algorithm to improve the binding capacity of lanmodulin's fourth binding pocket.

Design

A genetic algorithm was used to generate large populations of sequences and perform in silico natural selection to obtain a viable binding pocket to replace the unviable fourth pocket present in the wildtype lanmodulin. The proteins were selected in accordance to their fitness value. The fitness function selected for this case was the weighted sum of wildtype homology, charge proximity, and Efhe’s score. The generated sequence exhibited the highest fitness value of the >25000 generated mutants. This mutant poses an improvement on the wildtype protein as it has a higher likelihood of binding an additional lanthanide in its otherwise unable fourth pocket.

Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BamHI site found at 111
    Illegal BamHI site found at 186
    Illegal BamHI site found at 264
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]

References

1. JA C, ER F, JA M, JV H, TN L. Lanmodulin: A Highly Selective Lanthanide-Binding Protein from a Lanthanide-Utilizing Bacterium. Journal of the American Chemical Society. 2018 [accessed 2021 Sep 17];140(44):15056–15061. https://pubmed.ncbi.nlm.nih.gov/30351021/. doi:10.1021/JACS.8B09842

2. GJ D, JA M, DM P, DW R, JA C, Y J. Selective and Efficient Biomacromolecular Extraction of Rare-Earth Elements using Lanmodulin. Inorganic chemistry. 2020 [accessed 2021 Sep 17];59(17):11855–11867. https://pubmed.ncbi.nlm.nih.gov/32686425/. doi:10.1021/ACS.INORGCHEM.0C01303

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