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Getting the structure of Alyteserin-1a

Alyteserin-1a is a modified antimicrobial peptide which was made by introducing two mutations (D4E & N23S) in Alyteserin-1c peptide. The structure for Alyteserin-1a is not available therefore we obtained the pdb structure for Alyteserin-1c (pdb id : 2L5R) and created the given mutations in pymol. We carefully analyzed the structural feature of Alyteserin-1a peptide to come up with another peptide which could interact with it. We seem to find an interesting pattern which was a hydrophobic groove on one side of the peptide. We targeted this region to neutralize the anit-microbial peptide.

Predicting the structure of Naly

In our project, a key step was to neutralize the antimicrobial peptide, Alyteserin-1a, so that we can create a stress free environment. For this, we designed a novel peptide of smaller length, which can interact favorably with Alyteserin-1a. We used following step to get the best possible peptide :

• We used pepstr, an online tool, which takes amino-acid sequence as input and gives us possible structures, in pdb form, of the protein.
• After getting several possible structures, we used another online tool, ZDOCK, which docks two molecules and give a score, which tells us about that how favorably peptides are interacting.
• We screened few peptides from above process and proceeded for MD simulations.

Molecular Dynamics Simulation

We performed molecular dynamics simulation experiments to confirm that Naly is able to interact with Alyteserin-1a antimicrobial peptide, hence it can neutralize it's activity to kill the pathogemic bacteria. Following are the steps that we followed in this experiment :

• 1. Convert both the pdb files to .gro files using pdb2gmx tool.
• 2.