Analysis of Asymmetry of Membrane Proteins by Evolutionary Trace

Abstract

The investigation of membrane proteins has revealed the difference in amino acid composition between the cytoplasmic and the extracellular segments. Von Heijine showed that positively charged residues are relatively abundant in the cytoplasmic segments, and the tendency in the amino acid composition is called ‘positive inside rule’ [6]. Nakashima and Nishikawa reported that alanine and arginine residues tend to be more prevalent in the cytoplasmic segment, while threonine and cysteine residues are preferentially located in the extracellular segment [4]. That is, there is asymmetry between the extracellular region and the cytosolic region in membrane proteins. Recently, the tertiary structures of two proteins belonging to the aquaporin family, transmembrane water-conduction channel (PDB code 1J4N) and glycerol-conducting channels (PDB code 1LDF), have been determined. The structures of two eubacterial ClC chloride channels have been also determined (PDB codes 1KPL and 1KPK). The difference in sequence and structure, suggests that the two membrane protein families have derived from different evolutionary origins. However, the two protein families share a common structural pattern. Both of them have a two-fold internal duplication in the primary structure. In addition, the X-ray crystallographic studies revealed that the two repetitive units are arranged in the anti-parallel manner in each tertiary structure. That is, the orientation of the N-terminal domain is opposite to that of the C-terminal domain against the membrane. Considering the asymmetric features of membrane proteins, it is expected that the N-terminal and the C-terminal domains in the same membrane protein have been subjected to different structural and/or functional pressures due to the opposite orientation. We applied several different methods of evolutionary trace (ET) to the multiple alignments of the repetitive units, in order to extract novel asymmetric features of the membrane proteins.