Difference between revisions of "Part:BBa K4347007:Design"

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<u>Residues to mutate</u>
 
<u>Residues to mutate</u>
  
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Since there is little literature about point mutations on Bst, point mutations made in Taq (Klentaq) were sought after. Three notable point mutations were found in the Klentaq thumb domain at positions K505A, K540A and K542A where each Lysine (K) residue was switched to an Arginine residue (R)[[Part:BBa_K4347007:Design#References|<sup>[1]</sup>]]. After superimposing and aligning the structures and sequences in Pymol, the corresponding positions in Bst were found:  
+
Since there is little literature about point mutations on Bst, point mutations made in Taq (Klentaq) were sought after. Three notable residues were found in the Klentaq thumb domain at positions K505, K540 and K542 where each residue hindered thermo stability to some degree.[[Part:BBa_K4347007:Design#References|<sup>[1]</sup>]]. After superimposing and aligning the structures and sequences in Pymol, the corresponding positions in Bst were found:  
  
 
*K505 in Klentaq = K549 in Bst
 
*K505 in Klentaq = K549 in Bst
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[[File:BBa K4347007 Q584.PNG|350px|center|thumb|YASARA position scan results for possible point mutations at residue Q584.]]
 
[[File:BBa K4347007 Q584.PNG|350px|center|thumb|YASARA position scan results for possible point mutations at residue Q584.]]
  
−
Further research was conducted to narrow down on the most optimal amino acid mutation for each position. It was found that hydrophobic interactions play a role in protien thermal stability[[Part:BBa_K4347007:Design#References|<sup>[3]</sup>]], thus substitutions of amino acids with hydrophobic side chains were made in accordance to the data obtained from the YASARA simulations:  
+
In accordance to the results obtained from YASARA, further research was conducted to narrow down on the most optimal amino acid mutation for each position. It was found that hydrophobic interactions play a role in protien thermal stability[[Part:BBa_K4347007:Design#References|<sup>[3]</sup>]], thus substitutions of amino acids with hydrophobic side chains were made in accordance to the data obtained from the YASARA simulations:  
 
*K549 --> W549 (-0.126 kcal/mol)
 
*K549 --> W549 (-0.126 kcal/mol)
 
*K582 --> L582 (-1.632 kcal/mol)
 
*K582 --> L582 (-1.632 kcal/mol)

Latest revision as of 20:59, 10 August 2022

Bst with point mutations for enhanced thermal stability codon optimized for E.coli


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal AgeI site found at 766
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

Sequence alignment

Since Bst is structurally homologous to Klentaq polymerase, we fetched the Bst (6MU6) and Klentaq (6QV4) FASTA sequences from the Protien Data Bank and ran a multiple sequence alignment using Seaview. A good amount of conservation between the amino acid sequences was found between the two polymerases.

Protien sequence alignment of Bst (6MU5) and Klentaq (6QV4) in Seaview.

Residues to mutate

Since there is little literature about point mutations on Bst, point mutations made in Taq (Klentaq) were sought after. Three notable residues were found in the Klentaq thumb domain at positions K505, K540 and K542 where each residue hindered thermo stability to some degree.[1]. After superimposing and aligning the structures and sequences in Pymol, the corresponding positions in Bst were found:

  • K505 in Klentaq = K549 in Bst
  • K540 in Klentaq = K582 in Bst
  • K542 in Klentaq = Q584 in Bst


To confirm if these residues in Bst were suitable to mutate, the amino acid stability was estimated using a protien simulation software YASARA. A position scan was ran for each residue to measure the change in free energy (Kcal/mol) if the other 19 amino acid residues were mutated into that position. A mutation is classified as stabilizing if the change in free energy is ≤-1 kcal/mol, it is classified as destabilizing if the change is ≥1 kcal/mol, and neutral if it falls between these values [2]. The changes in free energy for mutations at residues K549, K582 and K584 are shown below:

YASARA position scan results for possible point mutations at residue K549.
YASARA position scan results for possible point mutations at residue K582.
YASARA position scan results for possible point mutations at residue Q584.

In accordance to the results obtained from YASARA, further research was conducted to narrow down on the most optimal amino acid mutation for each position. It was found that hydrophobic interactions play a role in protien thermal stability[3], thus substitutions of amino acids with hydrophobic side chains were made in accordance to the data obtained from the YASARA simulations:

  • K549 --> W549 (-0.126 kcal/mol)
  • K582 --> L582 (-1.632 kcal/mol)
  • Q584 --> L584 (-2.039 kcal/mol)

To confirm if these point mutations were significant, the overall change in free energy was calculated and compared between the wildtype Bst and modified Bst. The overall change in free energy of wild-type Bst was calculated to be -150.13 kcal/mol, and the overall stability of the mutated Bst was calculated to be -151.81 kcal/mol, thus indicative of a more thermally stable protein.

Full Bst structure with point mutations (orange) in thumb domain.
Close up of point mutations in Bst polymerase thumb domain modelled in Pymol.

Design Considerations

Since the goal of these point mutations was to increase thermal stability and not necessarily improve polymerase function, residues in the polymerase active site and fingers domain were avoided. In an article by Raghunathan & Marx [4], it was found that only 25% of the mutations made in the fingers domain of Taq still resulted in a PCR active polymerase whereas over 70% and 60% of the mutations in the thumb and palm domains resulted in a PCR active polymerase. Due to the sequence similarity of Bst and Taq, these inactive mutations would likely have the same effect on Bst. It was further confirmed that residues 549, 582 and 584 in Bst were not involved with contacting the DNA strand and were not part of the polymerases active site[5].

Source

PDB: 6MU5: https://www.rcsb.org/structure/6mu5

References


1. Xi, L. (2009, December 23). WO2009155464A2 - mutated and chemically modified thermally stable DNA polymerases. Google Patents. Retrieved July 12, 2022, from https://patents.google.com/patent/WO2009155464A2/en

2. Frenz, B., Lewis, S. M., King, I., DiMaio, F., Park, H., & Song, Y. (2020). Prediction of protein mutational free energy: Benchmark and sampling improvements increase classification accuracy. Frontiers in Bioengineering and Biotechnology, 8. https://doi.org/10.3389/fbioe.2020.558247

3. Unsworth, L. D., van der Oost, J., & Koutsopoulos, S. (2007). Hyperthermophilic enzymes − stability, activity and implementation strategies for high temperature applications. FEBS Journal, 274(16), 4044–4056. https://doi.org/10.1111/j.1742-4658.2007.05954.x

4. Raghunathan, G., & Marx, A. (2019, January 24). Identification of thermus aquaticus DNA polymerase variants with increased mismatch discrimination and reverse transcriptase activity from a smart enzyme mutant library. Nature News. Retrieved July 12, 2022, from https://www.nature.com/articles/s41598-018-37233-y#Fig6

5. Chim, N., Jackson, L. N., Trinh, A. M., & Chaput, J. C. (2018). Crystal structures of DNA polymerase I capture novel intermediates in the DNA synthesis pathway. ELife, 7. https://doi.org/10.7554/elife.40444