title: Characterization of 3D Voronoi tessellation nearest neighbor lipid shells provides atomistic lipid disruption profile of protein containing lipid membranes.
abstract: Quantifying protein-induced lipid disruptions at the atomistic level is a challenging problem in membrane biophysics. Here we propose a novel 3D Voronoi tessellation nearest-atom-neighbor shell method to classify and characterize lipid domains into discrete concentric lipid shells surrounding membrane proteins in structurally heterogeneous lipid membranes. This method needs only the coordinates of the system and is independent of force fields and simulation conditions. As a proof-of-principle, we use this multiple lipid shell method to analyze the lipid disruption profiles of three simulated membrane systems: phosphatidylcholine, phosphatidylcholine/cholesterol, and beta-amyloid/phosphatidylcholine/cholesterol. We observed different atomic volume disruption mechanisms due to cholesterol and beta-amyloid. Additionally, several lipid fractional groups and lipid-interfacial water did not converge to their control values with increasing distance or shell order from the protein. This volume divergent behavior was confirmed by bilayer thickness and chain orientational order calculations. Our method can also be used to analyze high-resolution structural experimental data.
authors: Department of Physics, University of Texas at Austin, Austin, TX 78712, USA. Electronic address: sara.y.cheng@utexas.edu.
authors: Sara Y
authors: SY
authors: Cheng
authors: Department of Computer Science, Trinity University, San Antonio, TX 79212, USA.
authors: Hai V
authors: HV
authors: Duong
authors: Department of Computer Science, Trinity University, San Antonio, TX 79212, USA.
authors: Campbell
authors: C
authors: Compton
authors: Department of Chemical Engineering, Texas Tech University, Lubbock, TX 79409, USA.
authors: Mark W
authors: MW
authors: Vaughn
authors: Department of Mathematics, Trinity University, San Antonio, TX 78212, USA. Electronic address: hnguyen5@trinity.edu.
authors: Hoa
authors: H
authors: Nguyen
authors: Department of Physics and Astronomy, Trinity University, San Antonio, TX 78212, USA; Department of Physics, Texas Tech University, Lubbock, TX 79409, USA. Electronic address: biophysics.ttu@gmail.com.
authors: Kwan H
authors: KH
authors: Cheng
mesh_terms: D000595:Amino Acid Sequence; D016229:Amyloid beta-Peptides / Q000737:chemistry*; D008051:Lipid Bilayers; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D010743:Phospholipids / Q000737:chemistry*
chemical_list: D016229:Amyloid beta-Peptides; D008051:Lipid Bilayers; D010743:Phospholipids
keywords: Annular lipid; Cholesterol; Lipid domain; Lipid/protein interaction; Voro++
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