Molecular dynamics studies of purothionins
| | Fig. 1. Superposition of the average MD structure 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 structure of β1PTH (red) with crystal structures of βPTH (gray) and α-hordothionin (blue). |
| | | Fig. 3. Superposition of the average MD structure of β1PTH in the absence of metal ions (blue) with MD structures in the presence of Mg ions (purple) or K ions (yellow). |
|
We use molecular dynamics (MD) methods to determine the structure and dynamics of antimicrobial peptides, purothionins. Our interests are in elucidating properties and mechanisms of metal-ion-based inhibition of purothionins. These valuable peptides, produced in wheat seeds, demonstrate properties important in the development of new antimicrobial agents. Unconstrained, explicit solvent MD simulations were used to elucidate structural and dynamic properties of two purothionins. We focused on accuracy of MD computations to adequately represent the experimental model and to make reliable predictions of peptide properties. Because accuracy of MD calculations depends on a number of simulation parameters, special care was taken to determine an optimal set of parameters for the model system, insuring accurate computation of electrostatic and van der Waals interactions. The relatively small size of βPTH and use of the massively parallel computer cluster allowed us to achieve the nanosecond timescale without compromising computational accuracy. Our computational model, in fact, produced results comparable with the experimentally observed data. We performed MD simulations of βPTH and β1PTH under different temperatures and in the presence of mono- and divalent metal cations. Calculated MD trajectories at different environmental conditions shed light on new details of βPTH properties and the mechanism of metal ion inhibition of βPTH membrane permeabilization activity.
In βPTH, the global Γ fold and the α1 helix are resistant to changes of temperature and presence of metal ions unlike the α2 helix (S. Oard and B. Karki, 20061). Addition of K+ and Mg2+ in the concentrations inhibiting antimicrobial activity induces large conformational changes by altering the hydrophobic region between the α-helices and in the α2 helix (Fig. 1). Mg2+ ions cause larger structural and dynamic changes than K+ ions. Unfolding of the α2 is triggered by altering a hydrogen bonding network Asp42-Lys5-Arg30-Asn27. The Arg30 side chain becomes destabilized causing conformational perturbations in the Arg30 and Asn27 backbone atoms that trigger unfolding of the α2 helix.
β1PTH, which structure is similar to that of βPTH (Fig. 2) is more resistant to the presence of metal ions (S. Oard, B. Karki, and F. Enright, 2007 2). Mg 2+ ions have no significant effect on β1PTH. K+ ions induce perturbations in the α2 helix in β1PTH and significantly alter the peptide dynamics, although less than in βPTH (Fig. 3). Movie 1 (see below) illustrates dynamics of β1PTH in an absence of metal ions, and movies 2 and 3 demonstrate effects of Mg 2+ and K+ ions on β1PTH dynamics, respectively. The key characteristics, which are important for resistance to metal ions, include the stabilized α2 helix and elevated stability in the loop regions to compensate interactions of the positively charged peptide with cations. Substitution of Gln at position 27 to Gly largely contributes to stabilization of the α2 helix in the presence of divalent ions.
|
| Last Updated: 1/26/2010 9:21:50 AM |
|
Please click a number to rate this article:
|
Have a question or comment about the information on this page?
Click here to contact us. |
|
|
|