Comparative Molecular Dynamics Simulation Studies of Realistic Eukaryotic, Prokaryotic, and Archaeal Membranes

• Published in: Journal of chemical information and modeling Vol. 62; no. 4; pp. 1036 - 1051
• Main Authors: Pogozheva, Irina D, Armstrong, Grant A, Kong, Lingyang, Hartnagel, Timothy J, Carpino, Carly A, Gee, Stephen E, Picarello, Danielle M, Rubin, Amanda S, Lee, Jumin, Park, Soohyung, Lomize, Andrei L, Im, Wonpil
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 28-02-2022
• Subjects: Archaea - metabolism; Cell Membrane - metabolism; Cell membranes; Chain branching; Compressibility; Computational Biochemistry; Dynamic structural analysis; Eukaryota; Graphical user interface; Lipid Bilayers - chemistry; Lipids; Mechanical properties; Membranes; Molecular dynamics; Molecular Dynamics Simulation; Molecular interactions; Molecular structure; Penetration; Sterols; Thickness
• ISSN: 1549-9596; 1549-960X
• DOI: 10.1021/acs.jcim.1c01514

We present a comparative all-atom molecular dynamics simulation study of 18 biomembrane systems with lipid compositions corresponding to eukaryotic, bacterial, and archaebacterial membranes together with three single-component lipid bilayers. A total of 105 lipid types used in this study include diverse sterols and glycerol-based lipids with acyl chains of various lengths, unsaturation degrees, and branched or cyclic moieties. Our comparative analysis provides deeper insight into the influences of sterols and lipid unsaturation on the structural and mechanical properties of these biomembranes, including water permeation into the membrane hydrocarbon core. For sterol-containing membranes, sterol fraction is correlated with the membrane thickness, the area compressibility modulus, and lipid order but anticorrelated with the area per lipid and sterol tilt angles. Similarly, for all 18 biomembranes, lipid order is correlated with the membrane thickness and area compressibility modulus. Sterols and lipid unsaturation produce opposite effects on membrane thickness, but only sterols influence water permeation into the membrane. All membrane systems are accessible for public use in CHARMM-GUI Archive. They can be used as templates to expedite future modeling of realistic cell membranes with transmembrane and peripheral membrane proteins to study their structure, dynamics, molecular interactions, and function in a nativelike membrane environment.