ss-TEA: Entropy based identification of receptor specific ligand binding residues from a multiple sequence alignment of class A GPCRs
© Sanders et al; licensee BioMed Central Ltd. 2011
Received: 12 October 2010
Accepted: 10 August 2011
Published: 10 August 2011
G-protein coupled receptors (GPCRs) are involved in many different physiological processes and their function can be modulated by small molecules which bind in the transmembrane (TM) domain. Because of their structural and sequence conservation, the TM domains are often used in bioinformatics approaches to first create a multiple sequence alignment (MSA) and subsequently identify ligand binding positions. So far methods have been developed to predict the common ligand binding residue positions for class A GPCRs.
Here we present 1) ss-TEA, a method to identify specific ligand binding residue positions for any receptor, predicated on high quality sequence information. 2) The largest MSA of class A non olfactory GPCRs in the public domain consisting of 13324 sequences covering most of the species homologues of the human set of GPCRs. A set of ligand binding residue positions extracted from literature of 10 different receptors shows that our method has the best ligand binding residue prediction for 9 of these 10 receptors compared to another state-of-the-art method.
The combination of the large multi species alignment and the newly introduced residue selection method ss-TEA can be used to rapidly identify subfamily specific ligand binding residues. This approach can aid the design of site directed mutagenesis experiments, explain receptor function and improve modelling. The method is also available online via GPCRDB at http://www.gpcr.org/7tm/.
G-protein coupled receptors (GPCRs), also known as 7 transmembrane receptors, represent a large superfamily of proteins in the human genome and are responsible for the transduction of an endogenous signal into an intracellular message, which triggers a response in many different physiological pathways. The structural architecture and chemo-mechanical concept of G-protein coupled receptors can be seen as an evolutionarily success as witnessed by the large amount of family members and diversity of applications in biological processes .
Not surprisingly, an increasing number of these GPCRs is the subject of investigation as targets in drug discovery. Historical drug discovery approaches have identified GPCRs as a successful drug target, since 25-50% of the drugs currently on the market interact with a GPCR [1, 2].
Recently there has been a reclassification of receptors according to the GRAFS system which has the following groups: glutamate, rhodopsin, adhesion, frizzled/taste2, and secretin . From the structural and functional viewpoint the rhodopsin-like family, also known as the class A receptors, is the largest and best studied family .
Receptors from different families are very diverse [1, 5, 7], but can all be characterized by the presence of seven structurally conserved alpha helices, which span the cell membrane. Most GPCRs couple to a G-protein complex upon ligand binding, resulting in the dissociation of the alpha subunit from the beta and gamma subunit. The final signal depends on the alpha subunit of the G-protein (Gαi, Gαs, Gαq/11, Gα12/13) which is activated and is presumed to be receptor and ligand dependent [8–12]. The non olfactory Class A receptors recognize a large variety of ligands including photons , biogenic amines , nucleotides , peptides , proteins  and lipid-like substances [18–21]. Most ligands are believed to bind fully or partly within the transmembrane bundle and to trigger signaling through a conserved canonical switch . The assumption that similar molecules bind to similar receptors  and that small molecules bind within the upper part of the transmembrane helices, similar to 11-cis retinal in bovine rhodopsin, carazolol in the human beta adrenergic receptor 2, timolol in the turkey beta adrenergic receptor 1 and ZM-241385 in the human adenosine A2 receptor, gives rise to the application of pattern recognition analysis on multiple sequence alignments of those helices or parts thereof to identify ligand binding residues. It has also been shown that for some receptors which bind large proteins, like the luteinizing hormone receptor (LHR), low molecular weight (LMW) compounds can be designed which bind in between the TM-bundle and modify signaling [23, 24], suggesting that the same pattern detection techniques could be used for those receptors as well.
Structure based drug design strategies often rely on high resolution information derived from protein crystal structures. Elucidating GPCR structures at atomic resolution remains difficult and has only been successful for a small set of receptors so far (bovine rhodopsin , squid rhodopsin , human beta-2-adrenergic receptor , turkey beta-1-adrenergic receptor  and the human A2A adenosine receptor ). These structures have been extremely helpful for understanding the function and ligand binding properties of class A receptors and are a major step forward towards rational drug design in this class of receptors. However, understanding the differences in for example agonist and antagonist binding or extrapolating structural information on a small subset of GPCRs to evolutionary distant receptors remains problematic and perhaps may only be solved as more structures become available . As long as this information is limited there will be a need for comparative methods to explain the structural and functional differences between GPCRs.
With the recent genome sequencing efforts, more and more data becomes available to perform comparative modelling. Currently, data on 51 species is available in ensemble  (release 56) enabling the large scale comparison of sequences within and across species. Methods to mine sequence data and identify structurally and functionally important residues have been developed. For example, in 1996 Lichtarge introduced the evolutionary trace method to calculate the conservation of a residue in each trace of a phylogenetic tree . In 2004 Oliveira et al. introduced the entropy variability plot and showed that the location of the aligned residue positions in these plots correlate to structural characteristics . Based on a similar concept as the entropy variability plot Ye et al. introduced the two entropy analysis (TEA) in 2006 to identify structural and functional positions in the transmembrane region of class A GPCRs .
Here we present subfamily specific two entropy analysis (ss-TEA), the first method to identify the ligand binding residues on subfamily level. In contrast to the previously published methods ss-TEA is able to discriminate between subfamilies and able to identify the approximately five residues that are involved in ligand binding for each individual subfamily of the class A GPCRs. ss-TEA is predicated on high quality sequence information deduced from a multiple sequence alignment (MSA) which was generated by extracting species homologues of the class A non olfactory GPCR sequences with a method reported here. This new MSA is characterized by a more complete set of species orthologs which improves the subfamily definition and results of ss-TEA. Receptor specific sets of ligand binding residues, generated by ss-TEA, improve the understanding of receptor ligand interactions and the design of mutagenesis experiments, and guide the process of homology modelling.
Results & Discussion
Sequence retrieval & Alignment
Using a template set of 286 human GPCR sequences, a BLAST search was performed to retrieve non olfactory class A GPCR sequences. This resulted in 20111 sequences originating from 1941 species. An alignment of the transmembrane helices was obtained by gap free alignment of all retrieved sequences using HMM models of the TM domains. Subsequent removal of sequences with low HMM scores resulted in a MSA of 13324 class A GPCR sequences. 33 of the 1941 species contained over 100 class A non olfactory GPCR sequences and were deposited in a database and used for further analysis. The resulting multiple sequence alignment (MSA) comprises 6876 sequences of which 4816 sequences originate from Ensembl and 2060 from Swissprot and TrEMBL. For all aligned helices in the database, it can be shown that the overlap with the predicted helices in Swissprot is over 90% for 90% of the TM sequences and that almost no helices can be found which have less than 75% overlap (Additional file 1, Appendix 2). Due to the gap free alignment procedure of TM domains only those regions are subject to further analysis, loop regions will be omitted and anomalies in helix architecture, i.e. proline induced kinks will not be addressed.
It is impossible to conclude whether or not ligand binding residues are conserved in a subfamily based on solely phylogenetic distances. Important aspects to consider in subfamily selection are that the receptors in a subfamily must bind to relatively similar ligands ensuring evolutionary pressure on the conservation of the residue positions involved in ligand binding, and that evolutionary distances are large enough to observe different amino acid usage amongst residue positions which are not involved in maintaining the structural architecture of the GPCR, signal transduction or ligand binding. We have therefore chosen to calculate the entropy values of all subfamilies with at least 50 and at most 300 sequences.
Ligand binding residue prediction
Area under the semi logarithmic receiver operator curve (pROC AUC) of different rankings of residues for different targets
Reference set (Ballosteros & Weinstein numbering scheme)
Theoretically optimal (top-ranked)
3.32, 3.33, 5.42, 5.43, 5.46, 6.55, 7.35, 7.39
2.65, 3.28, 7.39, 7.40
3.28, 3.31, 4.64, 5.39
3.28, 3.32, 5.39, 5.42, 5.43, 7.35
2.61, 2.64, 2.65, 3.32, 5.39, 6.58
2.57, 2.61, 3.29, 3.32, 4.60, 5.43, 6.55
5.39, 6.55, 7.35
1.39, 2.60, 3.32, 7.39
3.29, 7.39, 6.55
22 res total
Three distinct receptors (ADRB2, CCR5 and GNRHR) which use different residue positions to bind ligands (see Figure 3) have been selected as an example to illustrate the advantage of the subfamily specific approach of ss-TEA.
However the comparison of individual receptors within a receptor family also reveals interesting differences in ligand binding behavior. This is illustrated by e.g. position 3.32, which is well conserved in about 50% of all subfamilies, including the aminergic receptors and a subset of the adenosine receptors. For the aminergic receptors it has been proposed that this aspartate is crucial for ligand binding due to its interaction with the positively charged nitrogen of the basic amines, a hypothesis which is confirmed by the crystal structures of ADRB2 and ADRB1. For other receptors this same position is thought to be important for ligand binding involving different amino acids. For example, AA2AR receptor has a conserved valine at position 3.32. Mutation of this valine to alanine or aspartate disrupts ligand binding and illustrates the importance of this conserved valine for this receptor . Position 3.32 ranks at position 45 in the AA1R subfamily, while it ranks at position 11 the AA2AR subfamily suggesting a less important function for the valine in the AA1R receptor, which is indeed confirmed by site directed mutagenesis .
Interestingly, receptors with endogenous ligands which completely or largely bind to the N-terminus and/or extracellular loops also demonstrate subfamily specific conservation of residues at the extracellular side of the transmembrane helices. It is remarkable, for example, that 8 of the top 10 ranked residues for the luteinizing hormone receptor are in fact pocket residues. Also noteworthy is that Asp2.64, known to interact with the endogenous ligand , is ranked 3rd.
We have introduced an alignment methodology to create a large multiple sequence alignment of the transmembrane domains of class A non olfactory GPCRs from multiple species. We also introduced a new method to identify ligand binding residues from a MSA, named ss-TEA, and demonstrated the advantage of this new method in combination with the new MSA for the selection of ligand binding residues. The results show the advantage of receptor specific residue selection compared to receptor class specific selection, as well as an improved residue selection for 9 of the 10 reference sets in comparison to the state-of-the-art method Multi-Relief. The large MSA including sequences of multiple species allows us to compare receptors with high sequence similarities and more identical ligand binding profiles which results in a better understanding of the characteristics of those receptors. If more sequence data becomes available for more species, larger alignments can be made, which could possibly even explain differences between close homologs. Our alignment in combination with the residue selection method described here can be used to quickly identify ligand binding residues. This can subsequently be used to design site directed mutagenesis experiments, explain receptor function and improve modelling. The ss-TEA predictions for class A GPCRs can be accessed via GPCRDB at http://www.gpcr.org/7tm/
The first step in our approach is to extract GPCR sequences for different species from available data sources. To obtain sequences we performed a BLAST  search with 286 manually curated query sequences from human class A non-olfactory GPCRs against Swissprot, Ensembl and TrEMBL. All query sequences were blasted against Swissprot 57.13 [41, 42], Translated EMBL (TrEMBL) 40.13 [42, 43] and Ensembl Protein 56 , using the BLOSUM62 scoring matrix, an expected cutoff of 10 and word size 3. Furthermore, a gap opening penalty of 11 and a gap extension penalty of 1 were used. Finally, we selected all sequences with an e-value < 0.01, subject length identity > 25%, alignment identity > 40% and a minimal query length of 20 amino acids.
Numbering Scheme and MSA boundaries
The aim of the Multiple sequence alignment (MSA) is to reflect a structural alignment and therefore the loop regions and termini of all receptors were omitted, since these are not structurally conserved. The positions included in our MSA according to the Ballosteros and Weinstein numbering scheme  are: 1.33-1.56 for TM1; 2.40-2.65 for TM2; 3.25-3.51 for TM3; 4.43-4.64 for TM4; 5.38-5.63 for TM5; 6.37-6.59 for TM6; and 7.34-7.56 for TM7. The pocket is defined by 28 residues which are directed towards the intramembrane cavity in the upper part of the transmembrane domains in the available crystal structures. The residues defined as pocket per transmembrane region are: 1.35, 1.39, 1.42, 1.46 for TM1; 2.57, 2.58, 2.61, 2.65 for TM2; 3.28, 3.29, 3.32, 3.33, 3.36 for TM3; 4.56 for TM4; 5.38, 5.39, 5.42, 5.43, 5.46 for TM5; 6.44, 6.48, 6.51, 6.52, 6.55 for TM6 and 7.35, 7.39, 7.43, 7.45 for TM7.
Incomplete sequencing of the genomes of many species causes bias towards certain receptor subfamilies. To prohibit such bias, all sequences of species with less than 100 amino acid sequences of GPCRs were removed from the MSA. All GPCR sequences of species of which at least 100 different sequences were obtained, were stored in a database and used in all analysis discussed below. To enable querying on a higher level than the individual sequences, a hierarchical tree of the phylogenetic distance matrix calculated from the alignment of all 7 TMs of all receptors was created, using the neighbor joining algorithm as implemented in clustalW  2.0.11 with a 100 fold bootstrap. The sequences which group together at a node in this tree, a so called subfamily, can be queried for their properties.
where j reflects the number of sequences selected in the branch. To validate the performance we finally ranked all residues according to the score with the minimum scoring residue at rank 1.
Site directed mutagenesis data is available for many GPCRs with different levels of detail depending on the research question. In this paper ten well studied and evolutionary diverse Class A GPCRs are used for which extensive site directed mutagenesis data exists as well as a binding model based on these data. For each of the receptors a reference set of residues crucial for ligand binding was compiled using the mutation data described in GPCRdb  and literature models of the binding mode. The choice of receptors from different branches of the sequence tree was made to emphasize the advantage of a method able to identify different ligand binding residues for different receptors and to show that the method does not have a bias towards certain subfamilies. The receptors in the reference set are; beta-2 adrenergic receptor (ADRB2) [27, 46]; Prostacyclin receptor (PI2R) ; C5a anaphylatoxin chemotactic receptor (C5AR) ; Cannabinoid receptor 2 (CNR2) [49, 50]; Gonadotropin-releasing hormone receptor (GNRHR) ; Vasopressin V1a receptor (V1AR) ; Free fatty acid receptor1 (FFAR1) ; C-C Chemokine receptor type 5 (CCR5) ; P2Y purinoceptor 11  and 13  (P2Y11, P2Y13). Residues that were not part of the pocket  were neglected as well as mutations which are debatable because of different effects using different ligands or because results were not consistent in different measurements. The final selection only includes residues with substantial effect on ligand binding. The A2A adenosine receptor was deliberately not used as a reference set in this study, since site directed mutagenesis data and the crystal structure suggest that there is no general, family conserved receptor binding pocket for the A2A adenosine receptor [29, 38].
Performance measure (Area Under the Log Curve)
Where n is the number of true ligand binding residues and β i is the false positive frequency corresponding to the point at which the i th true residue is found. β i is typically calculated as the fraction of false positives which is ranked higher than the i th true positive. The score of the pROC AUC corresponding to a random selection is 0.434 and is unbounded on the high side. A perfect ordering of ligand binding residues amongst 100 non ligand binding residues will for example score 2.0.
To illustrate the advantage of subfamily specific ranking over generic ranking we compiled a theoretically optimal generic ranking of ligand binding residues. This ranking is created by ordering the residues of ten different receptors according to the number of receptors which use these positions for ligand binding. The ranking of positions used by the same number of receptors is arbitrary, potentially altering the results, although it is expected to have only a minor effect. Because the theoretically compiled optimal ranking includes information about the location of the pocket we also included this information in the ss-TEA and Multi-Relief method and scored the 22 residues included in the theoretically compiled optimal ranking prior to all other residues. The rankings which include this information will be indicated in this paper as top ranked. As a benchmark we compared our top ranking to both the theoretically compiled optimal ranking and Multi-Relief + 3d contacts top ranking  (Additional file 1, Appendix 1). Briefly, Multi-Relief takes a multiple sequence alignment and predefined subfamily ontology as input, then iteratively selects 2 subfamilies and optimizes a weight vector able to optimally separate the sequences from both . The optimization of a single weight vector in the iterative process results in one vector able to discrimate between all provided classes. The weight of a residue in the Multi-Relief + 3d contacts method can be altered towards its local environment as obtained from recent crystal structures.
The authors thank Sander B. Nabuurs, Peter Groenen and Ross McGuire for critical reading the manuscript and Top Institute Pharma (project number D1-105) for funding.
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