In Silico Identification of Cholesterol Binding Motifs in the Chemokine Receptor CCR3

Abstract

CC motif chemokine receptor 3 (CCR3) is a Class A G protein-coupled receptor (GPCR) mainly responsible for the cellular trafficking of eosinophils. As such, it plays key roles in inflammatory conditions, such as asthma and arthritis, and the metastasis of many deadly forms of cancer. However, little is known about how CCR3 functionally interacts with its bilayer environment. Here, we investigate cholesterol binding sites in silico through Coarse-Grained Molecular Dynamics (MD) and Pylipid analysis using an extensively validated homology model based on the crystal structure of CCR5. These simulations identified several cholesterol binding sites containing Cholesterol Recognition/Interaction Amino Acid Consensus motif (CRAC) and its inversion CARC motifs in CCR3. One such site, a CARC site in TM1, in conjunction with aliphatic residues in TM7, emerged as a candidate for future investigation based on the cholesterol residency time within the binding pocket. This site forms the core of a cholesterol binding site previously observed in computational studies of CCR2 and CCR5. Most importantly, these cholesterol binding sites are conserved in other chemokine receptors and may provide clues to cholesterol regulation mechanisms in this subfamily of Class A GPCRs.

Allosteric Regulation of G-Protein-Coupled Receptors: From Diversity of Molecular Mechanisms to Multiple Allosteric Sites and Their Ligands

“…Among lipids, cholesterol is the most important allosteric regulator of GPCRs, and its effects on receptor activity are highly dependent on the content of cholesterol in the membrane, the type of receptor, and the nature of the orthosteric ligand [91,132,133]. A significant number of GPCRs contain consensus motifs for cholesterol binding (Cholesterol Recognition/Interaction Amino Acid Consensus motif, CRAC), which were first identified in β2-AR [134] and then found in other GPCRs, although often in modified form [91,135,136]. Along with cholesterol, other lipids are involved in the allosteric regulation of GPCRs, including phosphatidylinositol-4,5-bisphosphate, phosphoinositols [90] and phosphoserines [89].…”

LipIDens: Simulation assisted interpretation of lipid densities in cryo-EM structures of membrane proteins

“…2e). The methodological underpinnings of PyLipID are described extensively elsewhere 24 and have been applied to a number of recent examples [31][32][33] .…”

Mutational Insight into Allosteric Regulation of Kir Channel Activity

“…We investigate mutants of G137, L140, and F149 in TM2 that are involved in the main channel activation allosteric network. These functional data are paired with coarse grain molecular dynamics (CGMD) simulations in an activating, PG-rich environment using the Martini Forcefield. , MD experiments have been used to good effect to characterize large macromolecular complexes such as protein–protein interactions, − protein–lipid interactions, ,, and conformational dynamics of biomolecules. − These in silico experiments contextualize the effect of mutation on how PG interacts with KirBac1.1 via PyLipID analysis . It was found that loss of PG residency time on gating arginine residues as a function of mutation in silico was correlated with flux in vitro .…”

“…These functional data are paired with coarse grain molecular dynamics (CGMD) simulations in an activating, PG-rich environment using the Martini Forcefield. 33 , 34 MD experiments have been used to good effect to characterize large macromolecular complexes such as protein–protein interactions, 35 − 40 protein–lipid interactions, 19 , 20 , 41 and conformational dynamics of biomolecules. 42 − 46 These in silico experiments contextualize the effect of mutation on how PG interacts with KirBac1.1 via PyLipID analysis.…”