Mechanism of beta-purothionin antimicrobial peptide inhibition by metal ions: molecular dynamics simulation study |
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Authors: | Oard Svetlana Karki Bijaya |
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Institution: | LSU AgCenter Biotechnology Laboratory, Louisiana State University, 115 Wilson Building, LSU, Baton Rouge, LA, 70803, USA. soard@agctr.lsu.edu |
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Abstract: | Wheat beta-purothionin is a highly potent antimicrobial peptide which, however, is inactivated by metal ions. The key structural properties and mechanisms of inhibition of beta-purothionin were investigated for the first time using unconstrained molecular dynamics simulations in explicit water. A series of simulations were performed to determine effects of temperature and the metal ions. Analyses of the unconstrained simulations allowed the experimentally unavailable structural and dynamic details to be unambiguously examined. The global fold and the alpha1 helix of beta-purothionin are thermally stable and not affected by metal ions. In contrast, the alpha2 helix unfolds with shift of temperature from 300 K and in the presence of metal ions. The network of conserved residues including Arg30 and Lys5 is sensitive to environmental changes and triggers unfolding. Loop regions display high flexibility and elevated dynamics, but are affected by metal ions. Our study provides insights into the mechanism of metal ion-based inhibition. |
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Keywords: | ahRMSD RMSD for all heavy solute atoms bbRMSD RMSD for backbone heavy solute atoms MTS multiple-time-scale βPTH β-purothionin βPTH-300K the MD trajectory without metal ions at 300 K βPTH-K the MD trajectory in the presence of 100 mM K+ ions at 300 K βPTH-Mg the MD trajectory in the presence of 20 mM Mg2+ ions at 300 K |
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