Preferential Location of Amino Acids Across the Membrane in α-Helices and β-Barrel Membrane Protein Structures

Abstract

Membrane proteins perform important physiological functions since they act as sensors for extra-cellular stimuli and gates for transport and communication. However, the basic forces and principles that drive membrane protein folding and assembly remain elusive. The key to the thermodynamic stability of membrane proteins is the complex physiochemical environment of the lipid bilayer. At the most basic level the hydrophobic core of the bilayer has been used to develop hydrophobicity scales that can identify putative transmembrane helices in membrane proteins. Recent refinements have utilized the realization that different amino acid types have strong preferences for particular insertion depths along the membrane normal, allowing a more detailed prediction and differentiation of buried, interfacial, and loop segments.However, prediction of beta-barrel membrane protein segments has so far resisted this analysis. This was primarily due to a lack of sufficient high resolution structures. Here we extend a method previously developed and successfully applied to alpha-helical membrane proteins to beta-barrels. We report the distribution of amino acids along the membrane normal for beta-barrels and compare the differences to alpha-helical proteins. For both protein types membrane interfaces are dominated by small residues such as glycine, alanine, and serine. Charged residues displayed non-symmetric distributions with charged residues generally preferring the intracellular interface. This effect was more prominent for Arg and Lys resulting in a direct confirmation of the positive inside rule. Even though there are many similarities the overall distributions are remarkably different between alpha and beta proteins, with beta-barrels displaying a much narrower hydrophobic core. We confirm that hydrophobic residues are the main driving force behind membrane protein insertion, while polar, charged and aromatic residues were found to be important for the correct orientation of the helix inside the membrane.