Molecular Dynamics Simulations of G-Protein Coupled Receptor Lipid Interactions

Abstract

Lipid molecules can bind selectively to specific sites on integral membrane proteins, modulating their structure, stability, and function. We have undertaken multiscale molecular dynamics simulations to investigate two distinct modes of lipid interaction with G-protein coupled receptors (GPCRs). Native mass spectrometry measurements suggest the presence of specific lipid binding sites on Neurotensin Receptor 1 (NTS1), in particular for phosphatidyl inositol phosphate (PIP) species. Coarse-grained molecular dynamics simulations of NTS1 embedded in a lipid bilayer indicate strong and specific interactions of PIP molecules with defined regions on the intracellular portion of NTS1. The predominant mode of PIP binding is via interaction with basic residues located within intracellular loop regions, inaccessible to other anionic lipid species such as phosphatidyl serine. In silico mutagenesis of key residues within these regions abrogates lipid binding. These simulation based predictions provide guidance for experimental mutagenesis of NTS1, toward structurally rationalising the proposed PIP binding sites. Molecular simulations have also been used to explore interactions of cholesterol with the extracellular domain of Smoothened (SMO), a Class F GPCR. The recent near full-length x-ray structure of SMO revealed the presence of a cholesterol molecule within a hydrophobic sterol binding groove on the extracellular cysteine rich domain (CRD). Atomistic simulations of SMO in a lipid bilayer suggest the cholesterol molecule exerts a marked effect on the structural stability of the CRD, as well as the potential for a degree of flexibility of extracellular domains of SMO relative to 7TM domain. Together these studies suggest how molecular simulations may be used in conjunction with experiment to guide the identification of lipid binding sites, and characterise the effects of lipid binding on GPCR structure and function.