Transbilayer pores formed by β-barrels: molecular modeling of pore structures and properties

Journal article

Transmembrane β-barrels, first observed in bacterial porins, are possible models for a number of membrane channels. Restrained molecular dynamics simulations based on idealized Cαβ templates have been used to generate models of such β-barrels. Model β-barrels have been analyzed in terms of their conformational, energetic, and pore properties. Model β-barrels formed by N = 4, 8, 12 and 16 anti-parallel Ala₁₀ strands have been developed. For each N, β-barrels with shear numbers S = N to 2N have been modeled. In all β-barrel models the constituent β-strands adopt a pronounced right-handed twist. Interstrand interactions are of approximately equal stability for all models with N ≥ 8, whereas such interactions are weaker for the N = 4 β-barrels. In N = 4 β-barrels the pore is too narrow (minimum radius approximately 0.6 Å) to allow ion permeation. For N ≥ 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 β-barrel models are compared with experimental values for porins and for K⁺ channels.

Authors: Sansom, M; Kerr, I

• Publication status: Published
• Peer review status: Peer reviewed
• Publisher: Elsevier
• Journal: Biophysical Journal
• Volume: 69
• Issue: 4
• Pages: 1334-1343
• Publication date: 1995-10-01
• Edition: Publisher's version
• DOI: 10.1016/S0006-3495(95)80000-7
• ISSN: 0006-3495
• Language: English