CHARMM GUI Membrane Builder for oxidized phospholipid membrane modeling and simulation

Turner P Brown; Dane E Santa; Brett A Berger; Lingyang Kong; Nathan J Wittenberg; Wonpil Im

doi:10.1016/j.sbi.2024.102813

CHARMM GUI Membrane Builder for oxidized phospholipid membrane modeling and simulation

Curr Opin Struct Biol. 2024 Apr 9:86:102813. doi: 10.1016/j.sbi.2024.102813. Online ahead of print.

Authors

Turner P Brown¹, Dane E Santa², Brett A Berger², Lingyang Kong³, Nathan J Wittenberg⁴, Wonpil Im⁵

Affiliations

¹ Department of Bioengineering, Lehigh University, Bethlehem, PA 18015, USA.
² Department of Chemistry, Lehigh University, Bethlehem, PA 18015, USA.
³ Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA.
⁴ Department of Chemistry, Lehigh University, Bethlehem, PA 18015, USA. Electronic address: njw@lehigh.edu.
⁵ Department of Bioengineering, Lehigh University, Bethlehem, PA 18015, USA; Department of Chemistry, Lehigh University, Bethlehem, PA 18015, USA; Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA. Electronic address: wonpil@lehigh.edu.

PMID: 38598982
DOI: 10.1016/j.sbi.2024.102813

Abstract

Oxidative stress leads to the production of oxidized phospholipids (oxPLs) that modulate the biophysical properties of phospholipid monolayers and bilayers. As many immune cells are responsible for surveilling cells and tissues for the presence of oxPLs, oxPL-dependent mechanisms have been suggested as targets for treating chronic kidney disease, atherosclerosis, diabetes, and cancer metastasis. This review details recent experimental and computational studies that characterize oxPLs' behaviors in various monolayers and bilayers. These studies investigate how the tail length and polar functional groups of OxPLs impact membrane properties, how oxidized membranes can be stabilized, and how membrane integrity is generally affected by oxidized lipids. In addition, for oxPL-containing membrane modeling and simulation, CHARMM-GUI Membrane Builder has been extended to support a variety of oxPLs, accelerating the simulation system building process for these biologically relevant lipid bilayers.

Keywords: Membrane; Molecular dynamics simulation; Molecular modeling; Oxidized phospholipid.

Publication types

Review