Functional characterization of G-protein-coupled receptors: a bioinformatics approach

Abstract

Complex molecular and cellular mechanisms regulate G protein-coupled receptors (GPCRs). It is suggested that proteins intrinsically disordered regions (IDRs) are to play a role in GPCR's intra and extracellular regions plasticity, due to their potential for post-translational modification and interaction with other proteins. These regions are defined as lacking a stable three-dimensional (3D) structure. They are rich in hydrophilic and charged, amino acids and are capable to assume different conformations which allow them to interact with multiple partners. In this study we analyzed 75 GPCR involved in synaptic transmission using computational tools for sequence-based prediction of IDRs within a protein. We also evaluated putative ligand-binding motifs using receptor sequences. The disorder analysis indicated that neurotransmitter GPCRs have a significant amount of disorder in their N-terminus, third intracellular loop (3IL) and C-terminus. About 31%, 39% and 53% of human GPCR involved in synaptic transmission are disordered in these regions. Thirty-three percent of receptors show at least one predicted PEST motif, this being statistically greater than the estimate for the rest of human GPCRs. About 90% of the receptors had at least one putative site for dimerization in their 3IL or C-terminus. ELM instances sampled in these domains were 14-3-3, SH3, SH2 and PDZ motifs. In conclusion, the increased flexibility observed in GPCRs, added to the enrichment of linear motifs, PEST and heteromerization sites, may be critical for the nervous system's functional plasticity.

Keywords: GPCR; disordered proteins; linear motifs; noncovalent interactions; pest motifs.

Figure 1

RONN disorder prediction plot analyses. (a) Percentage of proteins in the dataset analyzed in this study considering the consecutive residues predicted to be disordered in N-terminal tail, third intracellular loop and C-terminal tail (b) Percentage of disordered residues per analyzed domain in each GPCR family plotted by box plots.

Figure 2

Graphic representation of disorder values for each amino acid (generated from RONN predictor), position of putative binding sites estimated from ELM, and PEST motifs estimated from epestfind. The graphics represent the receptors with highest disorder indexes for 3IL(a) and C-terminal tail (b).

Figure 3

Percentage of putative basic and acidic epitopes identified in the C-terminal tail and third intracellular loop of receptors from the same family.