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Coevolution Underlies GPCR-G Protein Selectivity and Functionality

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Coevolution Underlies GPCR-G Protein Selectivity and Functionality www.nature.com/scientificreports OPEN Coevolution underlies GPCR‑G protein selectivity and functionality Min Jae Seo1, Joongyu Heo2, Kyunghui Kim2, Ka Young Chung4 & Wookyung Yu1,3* G protein‑coupled receptors (GPCRs) regulate diverse physiological events, which makes them as the major targets for many approved drugs. G proteins are downstream molecules that receive signals from GPCRs and trigger cell responses. The GPCR‑G protein selectivity mechanism on how they properly and timely interact is still unclear. Here, we analyzed model GPCRs (i.e. HTR, DAR) and Gα proteins with a coevolutionary tool, statistical coupling analysis. The results suggested that 5‑hydroxytryptamine receptors and dopamine receptors have common conserved and coevolved residues. The Gα protein also have conserved and coevolved residues. These coevolved residues were implicated in the molecular functions of the analyzed proteins. We also found specifc coevolving pairs related to the selectivity between GPCR and G protein were identifed. We propose that these results would contribute to better understandings of not only the functional residues of GPCRs and Gα proteins but also GPCR‑G protein selectivity mechanisms. G protein-coupled receptors (GPCRs) are one of the most important signal transduction systems to transmit extracellular signals (e.g., light, odorants, and hormones) into cells. GPCRs regulate critical physiological func- tions including sense recognition, neural transmission, and hormonal responses 1. Since they play important roles in human physiology and pathology 2, GPCRs have been extensively studied over the past decades. However, a number of questions regarding GPCR systems still remain to be addressed, and moreover new phenomena have been identifed day by day in recent years. Current active research into GPCRs would help to understand the fundamentals of cell signaling and would be useful for GPCR-targeted drug developments2–4. Much of the recent progress in GPCRs has been achieved afer the crystal structure of β2-adrenergic recep- 5, 6 tor (β2AR) has been revealed . GPCRs share common structural features with seven-transmembrane (TM) helices (Fig. 1a). Upon ligand-binding, the seven TM helices undergo conformational changes, which promote the interaction of the receptor with downstream signaling molecules in cells 7. Te canonical downstream sign- aling molecules for GPCRs are heterotrimeric G proteins. G proteins consist of three subunits: Gα, Gβ, and Gγ (Fig. 1a). Te Gα subunit consists of a Ras-like domain and α-helical domain’, and the nucleotide-binding pocket is located between these two domains (Fig. 1b). Te Ras-like domain directly interacts with the receptor (Fig. 1b) and transduces signals to other efectors 8. In the basal state, the Gα subunit is occupied by GDP and forms a heterotrimer with the Gβγ subunits. Active GPCRs act as guanine nucleotide exchange factors (GEFs) by releasing GDP from G proteins. Under physiological conditions, GTP is quickly inserted into the Gα subunit, which then dissociates from the receptor and Gβγ subunit. G proteins are sub-categorized depending on the Gα subunit. In human, there are 16 Gα subunit genes, which are classifed into four subtype families (G s, Gi/o, Gq/11, and G12/13) (Fig. 1c). Each subtype family of G proteins interacts with diferent downstream efector molecules to induce distinct cell responses9. In human, approxi- mately 1000 ligands and 800 GPCRs have been identifed (Fig. 1c). Terefore, one G protein subtype interacts with more than one receptor. Moreover, many receptors can couple to not only one G protein subtype but also more than one G protein subtypes (Fig. 1d). In recent years there has been an increased research interest in explaining how GPCRs and G proteins rec- ognize each other in a timely manner 10, 11. However, complicated interaction patterns exacerbate to solve the selectivity problem (Fig. 1d). To determine the GPCR-G protein coupling selectivity, Flock et al. recently used an evolutionary approach 10. Tey used the concepts of paralogue and orthologue conservation. If some positions in Gα protein have pronounced conservation of orthologue and paralogue, they are defned as the conserved group concerning their major function. Positions with a highly conserved orthologue and low paralogue con- servation are defned as ‘selectivity barcode’. Te authors identifed the selectivity barcode positions critical for 1Department of Brain and Cognitive Sciences, DGIST, 333 Techno jungang-daero, Daegu 42988, Republic of Korea. 2Department of Undergraduate Studies, DGIST, 333 Techno jungang-daero, Daegu 42988, Republic of Korea. 3Core Protein Resources Center, DGIST, 333 Techno jungang-daero, Daegu 42988, Republic of Korea. 4School of Pharmacy, Sungkyunkwan University, 2066 Seoburo, Jangan-gu, Suwon 16419, Republic of Korea. *email: [email protected] Scientifc Reports | (2021) 11:7858 | https://doi.org/10.1038/s41598-021-87251-6 1 Vol.:(0123456789) www.nature.com/scientificreports/ Figure 1. Structure and selectivity of GPCR and G protein. (a) Structure of GPCR-G protein complex. Tis structure is obtained from GPCRdb (modeling structure of 5HT2B-Gq complex). (b) Structure of G protein alpha subunit. It is consisted of Ras-like domain and α-helical domain (AHD). Please note that AHD is displaced in the GPCR-G protein complex structure in (a). (c) Approximate number of currently identifed ligands, GPCRs and Gα families. (d) Diverse mechanism of GPCR-G protein activation. One GPCR can activate diferent G proteins, and one G protein can be activated by diverse GPCRs. GPCR-G protein selectivity, which are available at GPCRdb (https:// GPCRdb. org). Tis concept explaining selectivity determinants is innovative and persuasive. However, it is difcult to defne the key components of selectivity determinants because (as discussed later in the paper) approximately 30–40% of amino acids are defned as selectivity barcodes (Supplementary Fig. S5a). Flock et al.10 mainly focused on GPCR-G protein interface regions, hence they could not fully explain the efects on selective binding of other residues outside the GPCR-G protein interface. Here, we adopted another approach, sequence coevolution, to understand the GPCR-G protein coupling system. Sequence coevolution is used to predict protein contacts, folding network, allosteric network, functional sites, and other features12. It is similar to the evolutionary approach but difers in that it can coincidentally observe pairs of amino acids. Among the various coevolutionary approaches, statistical coupling analysis (SCA) defnes functional clusters, also termed sectors. Sectors consist of highly coevolved residues13. We applied SCA to explain the selectivity and functionality of the GPCR-G protein coupling system. Results To analyze the GPCR-G protein coupling system from a coevolutionary perspective, we applied the SCA which is one of the biophysical and bioinformatic tools. Originally, SCA was developed to measure the energetic coupling between residues in a protein14. It can now defne functional coevolutionary units13, 15. Tis method measures conservation at position i and covariance between pairs of positions i and j in a protein multiple sequence alignment (Fig. 2a,b). Afer cleaning noise and clustering highly coevolving residues together from a pairwise coevolution matrix, a sector matrix is generated (Fig. 2c). Generally, a protein family with high sequence identity is a good target for SCA analysis. Terefore, Gα proteins are good candidates for SCA analysis. However, SCA has practical problems for analyzing GPCR families. GPCRs have numerous subfamilies, but they share very low sequence identity, even in the same subfamilies. Te extremely low sequence identities make it difcult to interpret SCA results. We seek to choose GPCR subfamilies with relatively well-defned coupling G proteins and selected two subfamilies of Class A GPCRs as model receptors: 5-hydroxytryptamine (5-HT) receptors (HTRs) and dopamine receptors (DARs) (Supplementary Fig. S1). Scientifc Reports | (2021) 11:7858 | https://doi.org/10.1038/s41598-021-87251-6 2 Vol:.(1234567890) www.nature.com/scientificreports/ Figure 2. Overview of statistical coupling analysis (SCA). (a) Multiple sequence alignment is provided by GPCRdb (GPCRdb.org). (b) Calculation of Kullback–Leibler divergence for site-specifc conservation and covariation between pairwise position. (c) Pairwise coevolution matrix is generated from (b). Ten, through the noise cleaning and clustering process, sectors are defned. GPCRs have coevolved sectors and a common conserved sector. We used multiple sequence alignments from GPCRdb because they provide well-labeled alignments using the Generic-GPCRdb number- ing system by each receptor16. Tis labeling system makes comparisons much easier among the results of each receptor. We selected HTRs and DARs as model systems, as discussed above. Applying SCA and sector refne- ment algorithms to HTRs, we defned three sectors that were designated HTR-Red, HTR-Blue, and HTR-Yellow (Fig. 3a,b, Supplementary Table S1). Four DAR sectors were defned: DAR-Red, DAR-Blue, DAR-Orange1, and DAR-Orange2 (Fig. 3c,d, Supplementary Table S2). Te total number of residues in the HTR and DAR sectors were 132 and 145, respectively. To characterize the conservation of each sector, we examined the Kullback–Leibler divergence (KLD) of each sector (Fig. 3e,f) using the Mann–Whitney test. Higher KLD values meant more conservation. Te HTR-Blue and DAR-Blue sectors consisted of more conserved residues
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