Transbilayer pores formed by beta-barrels: molecular modeling of pore structures and properties.
Transmembrane beta-barrels, first observed in bacterial porins, are possible models for a number of membrane channels. Restrained molecular dynamics simulations based on idealized C alpha beta templates have been used to generate models of such beta-barrels. Model beta-barrels have been analyzed in terms of their conformational, energetic, and pore properties. Model beta-barrels formed by N = 4, 8, 12 and 16 anti-parallel Ala10 strands have been developed. For each N, beta-barrels with shear numbers S = N to 2N have been modeled. In all beta-barrel models the constituent beta-strands adopt a pronounced right-handed twist. Interstrand interactions are of approximately equal stability for all models with N > or = 8, whereas such interactions are weaker for the N = 4 beta-barrels. In N = 4 beta-barrels the pore is too narrow (minimum radius approximately 0.6 A) to allow ion permeation. For N > or = 8, the pore radius depends on both N and S; for a given value of N an increase in S from N to 2N is predicted to result in an approximately threefold increase in pore conductance. Calculated maximal conductances for the beta-barrel models are compared with experimental values for porins and for K+ channels.
Sansom
M S
MS
Laboratory of Molecular Biophysics, University of Oxford, United Kingdom.
Kerr
I D
ID
D000409:Alanine; D008051:Lipid Bilayers / Q000737:chemistry*; D008433:Mathematics; D008565:Membrane Proteins / Q000737:chemistry*; D008958:Models, Molecular; D008962:Models, Theoretical; D008968:Molecular Conformation; D018272:Porins / Q000737:chemistry; D015221:Potassium Channels / Q000737:chemistry; D017433:Protein Structure, Secondary; D013314:Stress, Mechanical
D008051:Lipid Bilayers; D008565:Membrane Proteins; D018272:Porins; D015221:Potassium Channels; D000409:Alanine