in silico

Predicting structure of a neutralising protein

To achieve our goal of achieving an antimicrobial free environment, it was necessary to inactivate the antimicrobial peptide Alyteserin. When a protein interacts with another protein, its structure is altered. This prevents the protein from performing from it's usual function. This was what we set out to do-design a small peptide that would interact with Alyteserin favourably under specified conditions. We also tried to simulate the interaction between the two peptides using GROMACS, and the results will be discussed later on on this page. First let's analyse the structure of Alyteserin-1a and Naly.

Structural Features of Alyteserin and Naly

Fig1:Structural features of Alyteserin-1a, aa sequence GLKDIFKAGLGSLVKGIAAHVAN and Naly, aa sequecne IAGYAEEILEHVIAE

Interactions

Fig2:Interacting amino acids of both peptides in the final complex structure.

Analyzing MD Simulation Results

Fig3:Distance between both the peptides over time in MD simulations.

Fig4:Total energy of the system in vaccum over time in MD simulations.

Fig5:Radius of gyration of Alyteserin-1a, antimicrobial peptide, over time in MD simulations.

Fig6:Radius of gyration of Naly, neutralizing antimicrobial peptide, over time in MD simulations.

Results oobtained from MD simlations are given above. Fig1 highlights the residues which were proposed to interact with each other in peptide complex. Fig2 gives the final structure of peptide complex, which clearly show a hydrophobic moeity in the peptide complex and supports the fact that the peptides are interacting favorably. Both the peptides come closser to each other to interact quickly and then make a relatively complex structure (Fig3). The peptide complex in vaccum becomes more stable over time (Fig4). The 3D structure of Alyteserin-1a is being changed and it becomes more globular, creating a cavity inside (Fig5) while there is reltively no effect on the 3D structure of Naly (Fig6).