Insights from the analysis of conserved motifs and permitted amino acid exchanges in the human, the fly and the worm GPCR clusters

Abstract

G-protein coupled receptors (GPCRs) belong to biologically important and functionally diverse and largest super family of membrane proteins. GPCRs retain a characteristic membrane topology of seven alpha helices with three intracellular, three extracellular loops and flanking N' and C' terminal residues. Subtle differences do exist in the helix boundaries (TM-domain), loop lengths, sequence features such as conserved motifs, and substituting amino acid patterns and their physiochemical properties amongst these sequences (clusters) at intra-genomic and inter-genomic level (please re-phrase into 2 statements for clarity). In the current study, we employ prediction of helix boundaries and scores derived from amino acid substitution exchange matrices to identify the conserved amino acid residues (motifs) as consensus in aligned set of homologous GPCR sequences. Co-clustered GPCRs from human and other genomes, organized as 32 clusters, were employed to study the amino acid conservation patterns and species-specific or cluster-specific motifs. Critical analysis on sequence composition and properties provide clues to connect functional relevance within and across genome for vast practical applications such as design of mutations and understanding of disease-causing genetic abnormalities.

GPCRs from fusarium graminearum detection, modeling and virtual screening - the search for new routes to control head blight disease

“…Moreover, it appears clearly from recent studies that the accuracy of the model greatly depends on the phylogenetic tree proximity of the template and the target [47]. Consequently, when considering (i) the remarks above, (ii) the conservation of the 7TM bundles in all GPCRs and the observed deformation of its helices [48], and (iii) the sequence conservation of several motifs [49] we decided to start our homology modeling phase using both phylogenetic data (for selecting the most suitable template) and helix predictions information (to align the TM helices sequences between the template and the target). Next the loops connecting the TM helices were added to the models obtained this way, considering also the constraint of the possible disulfide bridges [50, 51].…”

TM-MOTIF: an alignment viewer to annotate predicted transmembrane helices and conserved motifs in aligned set of sequences

“…Cross-genome GPCR/OR cluster alignments were taken as an input (test set) to our in-house MOTIFS program [5] to identify residue conservation and substitutions in each position of the alignment. Here, conservation simply refers to an average of all possible pairwise sequences and the score is consulted from a normalized AA exchange matrix.…”

“…Once conserved amino acid patterns were recorded, the substituting AA residues were also identified and the properties for the AAS (like hydrophobic (@), aromatic (*), polar positive (+), polar negative (­) and polar uncharged ($)) were denoted by symbolic representation. The significant observation on preserved motifs and AAS in the helices and loop regions of the cross-genome GPCR cluster dataset was published recently [5] and the same principle was implemented in the package.…”

“…The motifs discovered by the in-house program [5], was mapped on predicted membrane topology (refer Step2 in Methodology) of multiple sequence alignment (MSA) both for the in-built cluster alignment and user-submitted query. The predicted seven TM helices are displayed in seven varying colors such as Violet (V), Indigo (I), Blue (B), Green (G), yellow (Y), Orange (O) and Red (R) colors namely “VIBGYOR coloring scheme” along with the identified motifs, in self highlighting darker shades of VIBGYOR coloring scheme.…”

“…As discussed in our recent publication [5], the package is very handy to document not only the conserved motifs, but also permitted amino acid exchanges within GPCR families at varying level of conservation at cross- genome level.…”