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The density-threshold affinity: Calculating lipid binding affinities from unbiased coarse-grained molecular dynamics

Jesse W Sandberg¹, Ezry Santiago-McRae¹, Jahmal Ennis¹

¹Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, United States.

Methods in Enzymology

|July 18, 2024

Summary

This study introduces a new method, "density threshold affinity," to calculate lipid-protein binding affinities using coarse-grained molecular dynamics simulations. This approach simplifies affinity calculations for membrane proteins, which are crucial for understanding their function.

Keywords:

Coarse-grained molecular dynamics Free energy calculations Ion channels Lipid binding affinity Lipid-protein interactions Receptors

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Published on: November 1, 2018

Area of Science:

Biochemistry
Computational Biology
Structural Biology

Background:

Membrane proteins
are influenced by their surrounding lipid environment.
Specific lipid-protein interactions are increasingly recognized but difficult to quantify.
Experimental determination of binding affinities for membrane protein-lipid systems is challenging.

Purpose of the Study:

To present a novel computational protocol for determining lipid-protein binding affinities.
To enable quantitative analysis of lipid interactions with membrane proteins.
To provide a method for comparing affinities across different sites, lipids, or force fields.

Main Methods:

Utilizing coarse-grained molecular dynamics (CG-MD) simulations.
Applying the "density threshold affinity" method to quantify lipid binding.
Analyzing localized lipid densities around membrane proteins.

Main Results:

The density threshold affinity method provides a robust way to extract binding affinities.
It overcomes limitations in distinguishing bound vs. bulk lipids.
The method offers bead-level resolution, suitable for shared binding sites and avoiding reference state ambiguities.

Conclusions:

Coarse-grained molecular dynamics simulations coupled with the density threshold affinity method offer a powerful approach to study membrane protein-lipid interactions.
This protocol facilitates comparative analysis of binding affinities in complex membrane environments.
The method enhances our understanding of how lipids modulate membrane protein structure and function.