Theoretical mimicry of biomembranes

Abstract 

The study of membrane proteins requires a proper consideration of the specific environment provided by the biomembrane. The compositional complexity of this environment poses great challenges to all experimental and theoretical approaches. In this article a rather simple theoretical concept is discussed for its ability to mimic the biomembrane. The biomembrane is approximated by three mimicry solvents forming individual continuum layers of characteristic physical properties. Several specific structural problems are studied with a focus on the biological significance of such an approach. Our results support the general perception that the biomembrane is crucial for correct positioning and embedding of its constituents. The described model provides a semi-quantitative tool of potential interest to many problems in structural membrane biology.

Abbreviations: PH, polar headgroup domain of the biomembrane, HC, hydrophobic core domain of the biomembrane, AQ, aqueous domains above and below the biomembrane, PCM, polarizable continuum method, BEM, boundary element method, PDBTM, database for membrane proteins, 2CPS, 1JDM, 2HAC, pdb codes of 3 membrane proteins, TM, transmembrane domain, MP, membrane protein, NMR, nuclear magnetic resonance, AMBER, a molecular mechanics program and force field, MD, molecular dynamics, rmsd, root mean square deviation

Keywords: Biomembrane, Membranous environment, Mimicry solvent, Polarizable continuum method