Difference between revisions of "Team:IIT Madras/Notebook"
Venkat1994 (Talk | contribs) |
|||
| Line 13: | Line 13: | ||
<ul> | <ul> | ||
<li>Inventory of all supplies is to be done.</li> | <li>Inventory of all supplies is to be done.</li> | ||
| − | <li>Alyteserin was chosen as the other | + | <li>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.</li> |
| + | <li>The pdb structure of Alyteserin-1a was generated in pymol, while introducing two mutations D4E and S23N in the pdb structure of Alyteserin-1c. | ||
| + | <li>The structural features of Alyteserin-1a was analyzed carefully to design a novel peptide which could interact with it.</li> | ||
| + | <li>Pymol and Pepstr, an online tool, were used to generate a large number of peptide pdb structures of size 10-18 amino acid.</li> | ||
| + | <li>A software, ZDOCK, was used to assess the docking parameters of Alyteserin-1a and novel peptide.</li> | ||
| + | <li>Best peforming peptide was chosen to test it's functionality in molecular dynamic simulation.</li> | ||
</ul> | </ul> | ||
| − | |||
| − | |||
| − | + | ||
| − | -> | + | <h3> June 1-7</h3> |
| + | <ul> | ||
| + | <li> MoleculGROMACS simulations started | ||
-> Made a catalog of all available materials | -> Made a catalog of all available materials | ||
-> Lacto Bacilus strains are available NZ9000 and MG1363 | -> Lacto Bacilus strains are available NZ9000 and MG1363 | ||
| Line 39: | Line 44: | ||
-------------------------------------------------------- | -------------------------------------------------------- | ||
| − | + | <!-- | |
Week 5 | Week 5 | ||
Revision as of 15:14, 12 September 2015
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 --------------------------------------------------------