Use of network model to explore dynamic and allosteric properties of three GPCR homodimers

Abstract

Recently, increasing experimental evidence has indicated that G-Protein Coupled Receptors (GPCRs) can form dimers, which are very possibly further potential functional units and new targets for drug development besides their monomeric units. However, knowledge about their structure and functional motion has been limited so far. Thus, we used an Elastic Network Model (ENM) and Protein Structure Network (PSN) to study three A GPCR homodimers (viz., CXCR4, κ-OR, β1AR) with two different interfaces based on their basic topologic structures. The low-frequency modes from ENM exhibit similarity to some extent, indicating similar functional motions shared by A GPCR dimers, such as asymmetric motion in the ECL2 and TM6 regions around the interface, which should contribute to the negative cooperation for ligand binding and asymmetric activation reported experimentally. The PSN results reveal that the dimerization can reduce the main informational flows from the extracellular to the intracellular domain and affect the contribution of TM regions to the allosteric paths. Some highly conserved residues were still observed to be hot residues in the meta-pathway, further confirming their conserved importance shared by A GPCR dimers; in particular for F6.44 and F6.48 residues and one non-conserved position X7.39. On the whole, dimerization plays a different role in influencing the dynamic motion of the protomer, dependent on the type of interface and contact area. Compared to the TM5–TM6 interface, TM1–TM2–H8 exhibits more a significant functional-role in influencing the dynamic behavior and allosteric paths.