Understanding pH-dependent selectivity of alamethicin K18 channels by computer simulation

Area of Science:

• Biophysics
• Computational Biology
• Membrane Protein Channel Research

Background:

• Alamethicin K18, a modified alamethicin dimer, forms pH-dependent ion channels.
• Previous studies indicate maximum anion selectivity at pH 7 or lower, suggesting a fully charged channel state.
• The stability and selectivity of this highly charged channel in lipid bilayers remain incompletely understood.

Purpose of the Study:

• To investigate the structural stability and ion-binding properties of the octameric alamethicin K18 channel.
• To elucidate the role of lysine protonation and counterion interactions in channel behavior.
• To understand the factors contributing to the observed pH-dependent selectivity.

Main Methods:

• Performed 10 ns molecular dynamics simulations of the octameric alamethicin K18 bundle in a lipid bilayer.
• Simulations included varying lysine charge states (0, 4, or 8) and salt concentrations (0, 0.5 M, 1 M KCl).
• Utilized Poisson-Boltzmann calculations to model ion distribution near lysine residues.

Main Results:

• In the absence of salt, a fully charged channel deformed significantly, binding ~1.9 chloride ions.
• With increasing KCl concentration (0.5 M and 1 M), chloride ion binding increased (~2.9 and 4 ions, respectively), and channel structure stabilized.
• Poisson-Boltzmann calculations predicted 2-4 chloride ions near lysines, correlating with ionic strength and reduced apparent channel charge.

Conclusions:

• Membrane-bound alamethicin K18 channels are stabilized by counterions, which reduce the channel's apparent charge.
• The presence of counterions explains the experimentally observed decrease in anion selectivity with increasing salt concentrations.
• Engineering additional positive charges in narrower channel regions could enhance alamethicin K18 channel selectivity.