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 This year's main project involved exploring finite size effects in self-assembly of lipid/peptide nanodiscs. As shown in paper (Jarin et al), we demonstrated that the "rule of 3" heuristic shown for one-component assembly holds well for our two-component ones. That is to say, it is necessary to generate at least 3 nanodiscs to confidently predict predict the size of the assembly. This information will be used in ongoing studies of HDL-like nanodiscs. Aim 2. Develop Simulation Methodology A revision of the CHARMM Drude polarizable force field was completed, earning a Ph.D. for graduate student Yalun Yu. A paper describing this work will be submitted in the fall of 2022. Aim 3. Simulate Complex Membranes We demonstrate a substantial ion effect in aggregation of PIP2 on membrane surfaces. Of particular note, the combination of calcium and potassium leads to greater clustering than either ion by itself (Paper 1). A combined experimental, simulation and theoretical study of how influenza fusion peptides aggregate and form pores in liposomes was completed and submitted for publication.