Developing computational methods to determine the thermodynamics of lipid phase coexistence

NIH RePORTER · NIH · R21 · $220,200 · view on reporter.nih.gov ↗

Abstract

Project Description Recent years have brought a new appreciation for the role of phase separation in biology, and in particular phase coexistence in the lipid membranes that define the boundaries in and around our cells. Studying this phenomenon using molecular simulation methods remains challenging because of the time- and length-scales involved, and while coarse-grained simulations have reproduced the existence of phase coexistence, to date there are no methods for determining the thermodynamics governing the process. We will develop a new method that will fill this gap, built around the weighted ensemble simulation technique using a contact-based collective variable. We will implement and test a protocol for measuring the free energy to demix 3- component membranes, using coarse-grained simulation with the MARTINI force field as our test suite. In addition, we will implement and validate a new method to couple weighted ensemble with temperature replica exchange, as a way to further speed statistical convergence of the calculations. Finally, we will extend the method to handle the partitioning and aggregation of surface-bound peptides between coexisting phases, using the antifungal lipopeptide fengycin as a test case.

Key facts

NIH application ID
10042128
Project number
1R21GM138970-01
Recipient
UNIVERSITY OF ROCHESTER
Principal Investigator
Alan Grossfield
Activity code
R21
Funding institute
NIH
Fiscal year
2020
Award amount
$220,200
Award type
1
Project period
2020-07-01 → 2022-06-30