An evolutionary perspective on chemokine receptor family

Chemokine Receptors (CR) are class-A G-protein coupled Receptors (GPCR). They are implicated in cell signalling, communication and sensory reception. They play an important role in inflammation responses, haemostasis, cancer metastasis and many other regulatory pathways. They are classified into CCR, CXCR based on their specific binding to two major (CC, CXC) classes of chemokine ligands. Atypical Chemokine Receptors (ACKR) is a special category for the members which fail to transduce the signal to G-Proteins. ACKR lacks the DRY motif in II intercellular loop connecting TM helix 3-4. This motif is responsible for interaction with G-Proteins. One such member is Duffy Antigen/Chemokine Receptor (DARC). It further contradicts the ACKR family as it binds to both types of chemokine ligands- CXC types and CC types non specifically. Therefore, it is often ascribed as a scavenger receptor and is designated as ACKR1. Most interestingly, DARC also plays a major role in the host entry mechanism of Plasmodium vivax , the second most endemic strain of malaria. Previously, the evolution of CRs had been analysed with a concentrated approach containing either a few species or couple of CR in focus. We generated a comprehensive CR phylogeny using all possible NCBI-nr homologs thus depicting the macro as well as micro-evolution in the CR family, including ACKR. This study represents the CR members in a new perspective by filling in the gaps present in previous phylogenetic approaches on CR. According to some major observations, CXCR1 & CXCR2 cluster together sharing the same clade owing to a high level of similarity amongst them and also binds to the same set of ligands. While, some members of CCR5 clusters in the monophyletic clade of CCR2 with both sharing most of their ligands. These could encourage to merge the taxonomic classification of these. Mapping of the taxonomic information on ACKR1 indicates that the protein sequences are highly restricted to mammals and the clade distribution follows the tree of life topology.  Except for the clades of CCR4, CCR8 and CXCR4 most of the sequences are represented by mammals with rodents being the majority.  A striking observation is the occurrence of viral CR in the CCR8 clade. This could potentially hint towards the viral mimicry of mammalian chemokine ligands. Since the dataset also include proteins from genomic experiments, this phylogeny can assist in resolving their classification. We employ the findings from this phylogenetic study in template selection for structural modelling of DARC. The resulting structure of double-dimer interaction model is mapped for crucial interacting residues, conserved cysteines, conserved TM regions and is embedded in a lipid bilayer mimicking the real erythrocyte membrane composition. The molecular dynamics study of this model along with mapping of annotations, like disulphide bonds, accessibility and local structural adaptation (using a specific structural alphabet; protein blocks ) would provide crucial insights into the mechanism and may help to establish DARC as a drug-able target.