The Effect of Force-Field Parameters on Cytochrome P450-Membrane Interactions: Structure and Dynamics

Ghulam Mustafa,Neil J Bruce,Prajwal P Nandekar,Rebecca C Wade,Goutam Mukherjee

doi:10.1038/s41598-020-64129-7

Abstract

The simulation of membrane proteins requires compatible protein and lipid force fields that reproduce the properties of both the protein and the lipid bilayer. Cytochrome P450 enzymes are bitopic membrane proteins with a transmembrane helical anchor and a large cytosolic globular domain that dips into the membrane. As such, they are representative and challenging examples of membrane proteins for simulations, displaying features of both peripheral and integral membrane proteins. We performed molecular dynamics simulations of three cytochrome P450 isoforms (2C9, 2C19 and 1A1) in a 2-oleoyl-1-palmitoyl-sn-glycerol-3-phosphocholine bilayer using two AMBER force field combinations: GAFF-LIPID with ff99SB for the protein, and LIPID14 with ff14SB for the protein. Comparison of the structural and dynamic properties of the proteins, the lipids and the protein-membrane interactions shows differing sensitivity of the cytochrome P450 isoforms to the choice of force field, with generally better agreement with experiment for the LIPID14 + ff14SB combination.

Highlights

Molecular dynamics (MD) simulation provides a powerful approach to obtain detailed insights into the structure and dynamics of complex biomolecular assemblies, such as protein-membrane systems
Atomic-detail MD simulations of up to about 200 ns duration were run after obtaining systems with converged arrangements of the proteins immersed in the bilayer from a set of independent coarse-grained simulations
While longer AA MD simulations might allow investigation of slow transitions in the Cytochrome P450 (CYP)-POPC systems, the AA MD simulations run were of sufficient length to examine protein-membrane interactions and to reveal differences in the systems simulated with the two AMBER ff combinations

Summary

Introduction

Molecular dynamics (MD) simulation provides a powerful approach to obtain detailed insights into the structure and dynamics of complex biomolecular assemblies, such as protein-membrane systems. CYP enzymes embody the key features of membrane proteins and thereby provide excellent systems for testing force fields (ff) for the simulation of membrane proteins. To provide a complete structural and dynamic picture, models of CYPs in membranes have been built and simulated and these studies have been conducted using a number of different force fields, see e.g. 9–15. Further analysis of the compatibility of the lipid ffs with protein ffs, which is crucial for studies of protein-membrane interactions, remains lacking We address this need by performing simulations of three CYP isoforms, CYP 2C9, CYP 2C19 and CYP 1A1, in a 2-oleoyl-1-palmitoyl-sn-glycerol-3-phosphocholine (POPC) membrane using two AMBER family ff combinations: GAFF-LIPID with AMBER ff99SB (GAFF-LIPID + ff99SB), and LIPID14 with AMBER ff14SB (LIPID14 + ff14SB). Dynamic and interaction properties of the simulated systems

Methods

Results

Conclusion