Computer Simulations of Membranes and Biopolymers

National Heart, Lung, And Blood Institute

Investigators

Linked publications & trials

Abstract

This overall project focuses on the study of membranes, proteins and carbohydrates by molecular dynamics computer simulation. Progress is reported under each Aim listed above Aim 1. Understand Model Membranes Permeability is an essential property of cell membranes, and computer simulations lend invaluable insight to this process. Paper 1 focused on methods for determining permeability from unbiased simulations, and Paper 4 evaluated permeabilities and partition coefficients of assorted drug molecules in membranes. Aim 2. Develop Simulation Methodology The CHARMM 36 (C36) lipid force field (FF) published by the lab in 2010 is by far the most widely used FF in the simulation field, with over 2800 citations at the time of this entry (Google Scholar, 8/4/2021). This years accomplishment, reported in Papers 2 and 3, involved adding long range Lennard-Jones terms to C36 using a semi-automated optimization procedure. Aim 3. Simulate Complex Membranes Paper 5 reported simulations of Archaeal membranes, in particular the locations of menaquinone and menaquinol, and how these lipid modulate the permeability. A combined experimental, simulation and theoretical study of how influenza fusion peptides form pores in liposomes was completed and submitted for publication.