Conformation and orientation of branched acyl chains responsible for the physical stability of diphytanoylphosphatidylcholine

Hiroshi Tsuchikawa, Takuya Ono, Masaki Yamagami, Yuichi Umegawa, Wataru Shinoda*, and Michio Murata*

Diphytanoylphosphatidylcholine (DPhPC) is a synthetic phospholipid in which two methyl-branched acyl chains are introduced into the glycerol moiety, mimicking phospholipids of eukaryote and eubacteria origins. The lipid bilayers of DPhPC reproduce the outstanding physical properties of methyl-branched lipids that occur in archaea membranes. DPhPC is commonly used as the base lipid in biophysical experiments, particularly for recording ion-channel currents. However, the dynamics of lipid molecules that induces their useful physical properties is still unclear. In this study we examined the conformation and orientation of the methyl-branched acyl chain of DPhPC in membrane using 2H NMR measurements of the synthetic lipid with a high stereochemical purity and molecular dynamics (MD) simulations. Deuterium-labeled 3’,3’-CD3,D-DPhPC (2) and 7’,7’-CD3,D-DPhPC (3) showed the characteristic quadrupole splitting width in the 2H NMR spectra, which corresponded to the bent orientation reported for the archaeal lipid PGP-Me (Yamagami et al. Biochemistry 2019, 58, 3869-3879). However, MD simulations, which reproduced the 2H NMR results well, unveiled the unknown features of DPhPC in membrane; DPhPC has chain-specific average orientation, where two bent orientations with upward and downward methyl groups occur at the C3 and C7 positions of the sn-1 and sn-2 chains of DPhPC, respectively. These MD and NMR results reveal that these two bent orientations defines the average orientation of DPhPC for the shallow part of the acyl chains, which is considered to be an important factor in the stability of DPhPC membranes.