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Designing antimicrobial peptides to develop biobased products
| | Fig. 1. Superposition of the average MD structures of βPTH in the absence of metal ions (blue) with MD structures in the presence of Mg ions (purple) or K ions (yellow) with the βPTH crystal structure shown in gray. |
| | | Fig. 2. Superposition of the average MD structures of the β1PTH (red), β1PTH-Var-K (cyan), and β1PTH-var-P (green)in the presence of Mg ions with β1PTH in absence of metal ions (blue). |
| | | Fig. 3. Superposition of the average MD structures of the β1PTH-MP variant in absence of metal ions (blue) and in the presence of K ions (yellow) and Mg ions (purple). |
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Wheat β-purothionin (βPTH) is a promising antimicrobial peptide that could be used as antimicrobial agent in many fields such as the animal and food sciences, the pharmaceutical, and cosmetic industries (S. Oard et al., 20041). βPTH has strong inhibitory activity to a broad range of bacteria and fungi. It is thermally and proteolytically stable, and emergence of resistant microbial strains is highly unlikely due to the mechanism of microbial inhibition. However, βPTH is inactivated by metal ions. Modification of βPTH to improve resistance to metal ions would lead to the development of a new powerful antimicrobial agent with broad application.
Using computational tools based on molecular dynamics (MD) simulations combined with homology alignment analysis, we designed βPTH variants with increased resistance to both mono- and divalent metal ions. MD simulations are indispensable tools for evaluating structural and dynamic properties of biological macromolecules which cannot be studied by currently available experimental methods. Advances in computer science and improvements in accuracy of force fields have allowed reproducible experimental results in MD simulations. We performed several series of MD simulations of two purothionins, βPTH (S Oard and B Karki, 20062) and β1PTH at different temperatures and in the presence of K+ and Mg+2 ions that allowed identification of key amino acid residues responsible for inhibition of βPTH by metal ions. Figure 1 illustrates the effects of metal ions on the structure of βPTH. Use of homology alignment data for thionin family members and the results of MD simulations, allowed for the selection of potential mutations for improving peptide stability in the presence of metal ions. The predicted purothionin variants were tested with in silico mutagenesis. This strategy allowed us to design two βPTH variants with increased resistance to both mono- and divalent metal ions. New antimicrobial peptides are predicted to have structures similar to that of the wild type peptide but are dynamically different. Importantly, the selected βPTH variants show considerable increase in resistance to the presence of metal ions added at physiological concentrations. Figures 2 and 3 demonstrate effects of mutations on resistance of the peptide to the presence of K+ and Mg2+ ions. The next step is to experimentally verify computationally predicted properties of the promising βPTH variants.
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| Posted on: 12/8/2006 1:25:49 PM |
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