Limits...
Structure-Based Sequence Alignment of the Transmembrane Domains of All Human GPCRs: Phylogenetic, Structural and Functional Implications.

Cvicek V, Goddard WA, Abrol R - PLoS Comput. Biol. (2016)

Bottom Line: The resulting superfamily-wide GpcR Sequence-Structure (GRoSS) alignment of the TM domains for all human GPCR sequences is sufficient to generate a phylogenetic tree that correctly distinguishes all different GPCR classes, suggesting that the class-level differences in the GPCR superfamily are encoded at least partly in the TM domains.Furthermore, this alignment identifies structurally and functionally important residues in all human GPCRs.These residues can be used to make testable hypotheses about the structural basis of receptor function and about the molecular basis of disease-associated single nucleotide polymorphisms.

View Article: PubMed Central - PubMed

Affiliation: Materials and Process Simulation Center, California Institute of Technology, Pasadena, California, United States of America.

ABSTRACT
The understanding of G-protein coupled receptors (GPCRs) is undergoing a revolution due to increased information about their signaling and the experimental determination of structures for more than 25 receptors. The availability of at least one receptor structure for each of the GPCR classes, well separated in sequence space, enables an integrated superfamily-wide analysis to identify signatures involving the role of conserved residues, conserved contacts, and downstream signaling in the context of receptor structures. In this study, we align the transmembrane (TM) domains of all experimental GPCR structures to maximize the conserved inter-helical contacts. The resulting superfamily-wide GpcR Sequence-Structure (GRoSS) alignment of the TM domains for all human GPCR sequences is sufficient to generate a phylogenetic tree that correctly distinguishes all different GPCR classes, suggesting that the class-level differences in the GPCR superfamily are encoded at least partly in the TM domains. The inter-helical contacts conserved across all GPCR classes describe the evolutionarily conserved GPCR structural fold. The corresponding structural alignment of the inactive and active conformations, available for a few GPCRs, identifies activation hot-spot residues in the TM domains that get rewired upon activation. Many GPCR mutations, known to alter receptor signaling and cause disease, are located at these conserved contact and activation hot-spot residue positions. The GRoSS alignment places the chemosensory receptor subfamilies for bitter taste (TAS2R) and pheromones (Vomeronasal, VN1R) in the rhodopsin family, known to contain the chemosensory olfactory receptor subfamily. The GRoSS alignment also enables the quantification of the structural variability in the TM regions of experimental structures, useful for homology modeling and structure prediction of receptors. Furthermore, this alignment identifies structurally and functionally important residues in all human GPCRs. These residues can be used to make testable hypotheses about the structural basis of receptor function and about the molecular basis of disease-associated single nucleotide polymorphisms.

Show MeSH

Related in: MedlinePlus

Testing the robustness of the alignment of the Taste2 receptors with the other groups.The table shows similarity between TMs averaged over all pairs of sequences formed from the two groups (red denotes high similarity, blue low similarity). For most TMs the optimal choices agree with the optimal alignment to Aα (full table in S6 Fig) only TM6 shows a second possible alignment at offset +4. The same table but using the GPCRtm substitution matrix instead of BLOSUM62 is in S8 Fig. Again, both matrices result in the same alignment.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4814114&req=5

pcbi.1004805.g004: Testing the robustness of the alignment of the Taste2 receptors with the other groups.The table shows similarity between TMs averaged over all pairs of sequences formed from the two groups (red denotes high similarity, blue low similarity). For most TMs the optimal choices agree with the optimal alignment to Aα (full table in S6 Fig) only TM6 shows a second possible alignment at offset +4. The same table but using the GPCRtm substitution matrix instead of BLOSUM62 is in S8 Fig. Again, both matrices result in the same alignment.

Mentions: We performed a similar analysis for the Taste2 receptors, for which adjustments were necessary. The profile alignment of Taste2 with Aα has some gaps, but it is still the best alignment (i.e., it has the fewest gaps) compared to aligning to classes other than class A. TM3 has two gaps in the alignment: a gap of length 4 in the middle of TM3, and a gap of length 5 at the DRY motive. As the first iteration we kept the alignment fixed on residue 3.50, then we computed the similarity to other groups for ±5 residue shifts. The shift by +3 residues gives better similarity and so it was kept. See Fig 4 for the computed similarities after the shift has been made. All class A subclasses favor this new choice, as the highest similarity has offset 0. Class B would favor shift by 2 residues, but the similarity is less than 30%.


Structure-Based Sequence Alignment of the Transmembrane Domains of All Human GPCRs: Phylogenetic, Structural and Functional Implications.

Cvicek V, Goddard WA, Abrol R - PLoS Comput. Biol. (2016)

Testing the robustness of the alignment of the Taste2 receptors with the other groups.The table shows similarity between TMs averaged over all pairs of sequences formed from the two groups (red denotes high similarity, blue low similarity). For most TMs the optimal choices agree with the optimal alignment to Aα (full table in S6 Fig) only TM6 shows a second possible alignment at offset +4. The same table but using the GPCRtm substitution matrix instead of BLOSUM62 is in S8 Fig. Again, both matrices result in the same alignment.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4814114&req=5

pcbi.1004805.g004: Testing the robustness of the alignment of the Taste2 receptors with the other groups.The table shows similarity between TMs averaged over all pairs of sequences formed from the two groups (red denotes high similarity, blue low similarity). For most TMs the optimal choices agree with the optimal alignment to Aα (full table in S6 Fig) only TM6 shows a second possible alignment at offset +4. The same table but using the GPCRtm substitution matrix instead of BLOSUM62 is in S8 Fig. Again, both matrices result in the same alignment.
Mentions: We performed a similar analysis for the Taste2 receptors, for which adjustments were necessary. The profile alignment of Taste2 with Aα has some gaps, but it is still the best alignment (i.e., it has the fewest gaps) compared to aligning to classes other than class A. TM3 has two gaps in the alignment: a gap of length 4 in the middle of TM3, and a gap of length 5 at the DRY motive. As the first iteration we kept the alignment fixed on residue 3.50, then we computed the similarity to other groups for ±5 residue shifts. The shift by +3 residues gives better similarity and so it was kept. See Fig 4 for the computed similarities after the shift has been made. All class A subclasses favor this new choice, as the highest similarity has offset 0. Class B would favor shift by 2 residues, but the similarity is less than 30%.

Bottom Line: The resulting superfamily-wide GpcR Sequence-Structure (GRoSS) alignment of the TM domains for all human GPCR sequences is sufficient to generate a phylogenetic tree that correctly distinguishes all different GPCR classes, suggesting that the class-level differences in the GPCR superfamily are encoded at least partly in the TM domains.Furthermore, this alignment identifies structurally and functionally important residues in all human GPCRs.These residues can be used to make testable hypotheses about the structural basis of receptor function and about the molecular basis of disease-associated single nucleotide polymorphisms.

View Article: PubMed Central - PubMed

Affiliation: Materials and Process Simulation Center, California Institute of Technology, Pasadena, California, United States of America.

ABSTRACT
The understanding of G-protein coupled receptors (GPCRs) is undergoing a revolution due to increased information about their signaling and the experimental determination of structures for more than 25 receptors. The availability of at least one receptor structure for each of the GPCR classes, well separated in sequence space, enables an integrated superfamily-wide analysis to identify signatures involving the role of conserved residues, conserved contacts, and downstream signaling in the context of receptor structures. In this study, we align the transmembrane (TM) domains of all experimental GPCR structures to maximize the conserved inter-helical contacts. The resulting superfamily-wide GpcR Sequence-Structure (GRoSS) alignment of the TM domains for all human GPCR sequences is sufficient to generate a phylogenetic tree that correctly distinguishes all different GPCR classes, suggesting that the class-level differences in the GPCR superfamily are encoded at least partly in the TM domains. The inter-helical contacts conserved across all GPCR classes describe the evolutionarily conserved GPCR structural fold. The corresponding structural alignment of the inactive and active conformations, available for a few GPCRs, identifies activation hot-spot residues in the TM domains that get rewired upon activation. Many GPCR mutations, known to alter receptor signaling and cause disease, are located at these conserved contact and activation hot-spot residue positions. The GRoSS alignment places the chemosensory receptor subfamilies for bitter taste (TAS2R) and pheromones (Vomeronasal, VN1R) in the rhodopsin family, known to contain the chemosensory olfactory receptor subfamily. The GRoSS alignment also enables the quantification of the structural variability in the TM regions of experimental structures, useful for homology modeling and structure prediction of receptors. Furthermore, this alignment identifies structurally and functionally important residues in all human GPCRs. These residues can be used to make testable hypotheses about the structural basis of receptor function and about the molecular basis of disease-associated single nucleotide polymorphisms.

Show MeSH
Related in: MedlinePlus