Sept 17
- First meeting of Team:IIT_Madras for iGEM 2015.
- Ideation begins.
May 18-24
May 25-31
- Inventory of all supplies is to be done.
- Alyteserin-1a was chosen to test our model as the structural feature, mechanism of action and other relevent details of anit-microbial peptide Alyteserin-1c, which has two mutations (D4E, N23S), were available in the literature.
- The pdb structure of Alyteserin-1a was generated in pymol, while introducing two mutations D4E and S23N in the pdb structure of Alyteserin-1c.
- The structural features of Alyteserin-1a was analyzed carefully to design a novel peptide which could interact with it.
- Pymol and Pepstr, an online tool, were used to generate a large number of peptide pdb structures of size 10-18 amino acid.
- A software, ZDOCK, was used to assess the docking parameters of Alyteserin-1a and novel peptide.
- Best peforming peptide was chosen to test it's functionality in molecular dynamic simulation.
June 1-7
- Molecul Dynamic Simulation started.
- Made a catalog of all available materials.
- Lacto Bacilus strains, NZ9000 and MG1363, were collected from Prof. KBR's lab.
- MD Simulations finished the proteins were found to interact favourably.
June 8-14
- Started working on the design of genetic circuit.
- One more MD Simulation was performed with the ionic solution of protein complex. MD Simultions showed that naly
interacts favorably with Alyteserin forming a cavity of hydrophobic residues.
- Sender is finalised to be E.Coli DH5Alpha with LuxP-PFS gene.
- Receiver is L.lactis NZ9000/MG1316 with LUXPQOU coupled with Lux R through sRNA's qrr1-5, HFQ and sigma54 gene.
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