Team:IIT Madras/Notebook
May 18-24
- Cleaned fridge and transferred materials.
- Circuit finalised toggle switch/ mutual depressor switch using TAL repressor.
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
- MoleculGROMACS simulations started -> Made a catalog of all available materials -> Lacto Bacilus strains are available NZ9000 and MG1363 -> Simulations finished the proteins were found to interact favourably -> Heidelberg 2008 Auto Inducer 2 produced by LuxS sensed by LuxQ -> Reference:Quorum Sensing AI@ in campylobacter Orla Cloak, Barbara Solow doi:10.1128 Can we do the whole circuit using just Lux components??!! -------------------------------------------------------- Week 4 ->Circuit will be composed of purely Lux components. -> MD Simulations were done with ionic solution of protein complex. MD Simultions showed that naly interacts favorably with Alytesterin 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 and HFQ --------------------------------------------------------