Biomod/2013/Harvard/results: Difference between revisions

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==Raw Data==
==Raw Data==


Raw data can be found [[https://db.tt/lzft2Jpp|at this link]].
Raw data can be found [https://db.tt/lzft2Jpp |at this link].
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Revision as of 13:40, 26 October 2013

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Results

Input

One round of directed evolution produced one library member with improved affinity to δ-toxin. Variant H3 of BlaCaM saw a marked increase in δ-toxin activity over the negative control (no peptide) (Figure 1). While the improved activity is not nearly as high as the m13 activity, this variant appears to have begun mutating in the correct direction to improve binding. For variant H3, activity with both m13 and δ-toxin has increased, suggesting that any improvements to δ-toxin binding are not specific to δ-toxin. This evolution of "promiscuity," where a protein expands the number of targets it can bind to, is seen as a crucial intermediate step in directed evolution of novel protein targets (Bloom JD, Arnold FH. 2009. PNAS. 106 (Supplement 1) 9995-10000).

Figure1: Library Member H3 displayed an improvement in δ-toxin activity above the negative control

Sequencing of variant H3 revealed 4 mutations to the calmodulin region of the encoding gene. One of these mutations, F19L, altered the large hydrophobic residue phenylalanine to a smaller, still hydrophobic leucine. Residue 19 sits directly in the peptide binding area of calmodulin, indicating that this mutation, and this specific residue, could be very important for determining calmodulin binding specificity.

Residue 19, F (yellow), on CaM mutated to L (green). CaM is shown bound to m13. PDB ID: 2BBM

While random directed evolution will eventually produce positive results, knowledge of important regions or residues for peptide binding in CaM can greatly narrow the mutation space that must be explored to develop improvements. Identifying key residues like residue 19 will help direct further evolution and accelerate the process developing binding to δ-toxin. Through directed evolution, we improved the binding of BlaCaM to δ-toxin and identified a possible key residue for peptide specificity and affinity.

Output

Cysteine Mutations

GLucCaM contains ten cysteine residues. Since our protein could not be deactivated with calcium, we considered the possibility of disulfide bonds forming across the protein, preventing conformation changes. Unfortunately, we do not know the specific amino acids responsible for the disulfide bonds, so we selected a reasonable set of four cysteine residues highlighted in yellow below. The light blue indicates the two halves of GLuc, the red indicates calmodulin, and the green regions indicates the two linkers.

We mutated out various combinations of the four cysteine residues to alanine, but these mutated GLucCaM showed no activity. This suggests that these cysteine residues are essential to the structure of GLucCaM.

Linker Variations

Another possibility we explored was varying the linker length and rigidity relative to the GLucCaM linkers. The original GLucCam structure has amino acid strands GGGGT and GGGS as the first and second linker sequences. We explored the following linker variations:

Short-rigid: GPG GPG

Long-rigid: APAPAP APAPAP

Short-flexible: GGGGSGGGGS GGGGSGGGGS

All linker variations showed a decrease in luminescence level, but they all exhibited significant decrease in activity when exposed to high concentration of calcium. Unfortunately, the protein switch does not respond to increased levels of M13, but this is a promising start for continued modification to the output domain.

Raw Data

Raw data can be found |at this link.

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