101
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Structure-Based Biophysical Analysis of the Interaction of Rhodopsin with G Protein and Arrestin. Methods Enzymol 2015; 556:563-608. [DOI: 10.1016/bs.mie.2014.12.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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102
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Chattopadhyay A, Rao BD, Jafurulla M. Solubilization of G Protein-Coupled Receptors. Methods Enzymol 2015; 557:117-34. [DOI: 10.1016/bs.mie.2015.01.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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103
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Leman JK, Ulmschneider MB, Gray JJ. Computational modeling of membrane proteins. Proteins 2015; 83:1-24. [PMID: 25355688 PMCID: PMC4270820 DOI: 10.1002/prot.24703] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 10/01/2014] [Accepted: 10/18/2014] [Indexed: 02/06/2023]
Abstract
The determination of membrane protein (MP) structures has always trailed that of soluble proteins due to difficulties in their overexpression, reconstitution into membrane mimetics, and subsequent structure determination. The percentage of MP structures in the protein databank (PDB) has been at a constant 1-2% for the last decade. In contrast, over half of all drugs target MPs, only highlighting how little we understand about drug-specific effects in the human body. To reduce this gap, researchers have attempted to predict structural features of MPs even before the first structure was experimentally elucidated. In this review, we present current computational methods to predict MP structure, starting with secondary structure prediction, prediction of trans-membrane spans, and topology. Even though these methods generate reliable predictions, challenges such as predicting kinks or precise beginnings and ends of secondary structure elements are still waiting to be addressed. We describe recent developments in the prediction of 3D structures of both α-helical MPs as well as β-barrels using comparative modeling techniques, de novo methods, and molecular dynamics (MD) simulations. The increase of MP structures has (1) facilitated comparative modeling due to availability of more and better templates, and (2) improved the statistics for knowledge-based scoring functions. Moreover, de novo methods have benefited from the use of correlated mutations as restraints. Finally, we outline current advances that will likely shape the field in the forthcoming decade.
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Affiliation(s)
- Julia Koehler Leman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Martin B. Ulmschneider
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jeffrey J. Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
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104
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Karp JM, Erylimaz E, Cowburn D. Correlation of chemical shifts predicted by molecular dynamics simulations for partially disordered proteins. JOURNAL OF BIOMOLECULAR NMR 2015; 61:35-45. [PMID: 25416617 PMCID: PMC4715900 DOI: 10.1007/s10858-014-9879-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 11/17/2014] [Indexed: 06/04/2023]
Abstract
There has been a longstanding interest in being able to accurately predict NMR chemical shifts from structural data. Recent studies have focused on using molecular dynamics (MD) simulation data as input for improved prediction. Here we examine the accuracy of chemical shift prediction for intein systems, which have regions of intrinsic disorder. We find that using MD simulation data as input for chemical shift prediction does not consistently improve prediction accuracy over use of a static X-ray crystal structure. This appears to result from the complex conformational ensemble of the disordered protein segments. We show that using accelerated molecular dynamics (aMD) simulations improves chemical shift prediction, suggesting that methods which better sample the conformational ensemble like aMD are more appropriate tools for use in chemical shift prediction for proteins with disordered regions. Moreover, our study suggests that data accurately reflecting protein dynamics must be used as input for chemical shift prediction in order to correctly predict chemical shifts in systems with disorder.
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Affiliation(s)
- Jerome M. Karp
- Department of Biochemistry, Albert Einstein College of, Medicine of Yeshiva University, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Ertan Erylimaz
- Department of Biochemistry, Albert Einstein College of, Medicine of Yeshiva University, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - David Cowburn
- Department of Biochemistry, Albert Einstein College of, Medicine of Yeshiva University, 1300 Morris Park Avenue, Bronx, NY 10461, USA
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105
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Nussinov R, Tsai CJ, Liu J. Principles of allosteric interactions in cell signaling. J Am Chem Soc 2014; 136:17692-701. [PMID: 25474128 PMCID: PMC4291754 DOI: 10.1021/ja510028c] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Indexed: 02/07/2023]
Abstract
Linking cell signaling events to the fundamental physicochemical basis of the conformational behavior of single molecules and ultimately to cellular function is a key challenge facing the life sciences. Here we outline the emerging principles of allosteric interactions in cell signaling, with emphasis on the following points. (1) Allosteric efficacy is not a function of the chemical composition of the allosteric pocket but reflects the extent of the population shift between the inactive and active states. That is, the allosteric effect is determined by the extent of preferred binding, not by the overall binding affinity. (2) Coupling between the allosteric and active sites does not decide the allosteric effect; however, it does define the propagation pathways, the allosteric binding sites, and key on-path residues. (3) Atoms of allosteric effectors can act as "driver" or "anchor" and create attractive "pulling" or repulsive "pushing" interactions. Deciphering, quantifying, and integrating the multiple co-occurring events present daunting challenges to our scientific community.
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Affiliation(s)
- Ruth Nussinov
- Cancer
and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research,
National Cancer Institute, Frederick, Maryland 21702, United States
- Sackler
Institute of Molecular Medicine, Department of Human Genetics and
Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Chung-Jung Tsai
- Cancer
and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research,
National Cancer Institute, Frederick, Maryland 21702, United States
| | - Jin Liu
- Department
of Biophysics, University of Texas Southwestern
Medical Center, 5323
Harry Hines Boulevard, Dallas, Texas 75390, United
States
- Department
of Chemistry, Center for Drug Discovery, Design, and Delivery (CD4),
and Center for Scientific Computation, Southern
Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275, United
States
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106
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Shahane G, Parsania C, Sengupta D, Joshi M. Molecular insights into the dynamics of pharmacogenetically important N-terminal variants of the human β2-adrenergic receptor. PLoS Comput Biol 2014; 10:e1004006. [PMID: 25501358 PMCID: PMC4263363 DOI: 10.1371/journal.pcbi.1004006] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 10/28/2014] [Indexed: 12/27/2022] Open
Abstract
The human β2-adrenergic receptor (β2AR), a member of the G-protein coupled receptor (GPCR) family, is expressed in bronchial smooth muscle cells. Upon activation by agonists, β2AR causes bronchodilation and relief in asthma patients. The N-terminal polymorphism of β2AR at the 16th position, Arg16Gly, has warranted a lot of attention since it is linked to variations in response to albuterol (agonist) treatment. Although the β2AR is one of the well-studied GPCRs, the N-terminus which harbors this mutation, is absent in all available experimental structures. The goal of this work was to study the molecular level differences between the N-terminal variants using structural modeling and atomistic molecular dynamics simulations. Our simulations reveal that the N-terminal region of the Arg variant shows greater dynamics than the Gly variant, leading to differential placement. Further, the position and dynamics of the N-terminal region, further, affects the ligand binding-site accessibility. Interestingly, long-range effects are also seen at the ligand binding site, which is marginally larger in the Gly as compared to the Arg variant resulting in the preferential docking of albuterol to the Gly variant. This study thus reveals key differences between the variants providing a molecular framework towards understanding the variable drug response in asthma patients. The human β2-adrenergic receptor (β2AR) is an important member of the GPCR family and a mutation at the 16th position, Arg16Gly, is commonly found in the population. This variation in asthma patients is linked to differential (good/bad) response to the drug albuterol, an agonist of the β2AR. To date, the coordinates of the N-terminal residues harboring the 16th position mutation have not been resolved. In our study we sought to glean insights into the dynamics of the variants that could address the differential response to albuterol. We used knowledge from class A GPCRs to build the N-terminal region of β2AR variants in conjunction with the available structure of the inactive receptor. This was followed by atomistic simulations in triplicate totaling to a sampling of 6 µs. We observe that the N-terminal region of the Arg variant is more dynamic than the Gly variant. Amongst the various differences between the variants, we observe long-range effects at the binding site leading to preferential docking of albuterol to the Gly variant. Our work is a first step to unravel the molecular mechanism linking the Arg16Gly variation to the differential response to albuterol in asthma patients.
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Affiliation(s)
| | | | - Durba Sengupta
- CSIR-National Chemical Laboratory, Pune, India
- * E-mail: (DS); (MJ)
| | - Manali Joshi
- Bioinformatics Center, University of Pune, Pune, India
- * E-mail: (DS); (MJ)
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107
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Antibody Fragments Defining Biologically Relevant Conformations of Target Proteins. Antibodies (Basel) 2014. [DOI: 10.3390/antib3040289] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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108
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Schafer CT, Farrens DL. Conformational selection and equilibrium governs the ability of retinals to bind opsin. J Biol Chem 2014; 290:4304-18. [PMID: 25451936 DOI: 10.1074/jbc.m114.603134] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Despite extensive study, how retinal enters and exits the visual G protein-coupled receptor rhodopsin remains unclear. One clue may lie in two openings between transmembrane helix 1 (TM1) and TM7 and between TM5 and TM6 in the active receptor structure. Recently, retinal has been proposed to enter the inactive apoprotein opsin (ops) through these holes when the receptor transiently adopts the active opsin conformation (ops*). Here, we directly test this "transient activation" hypothesis using a fluorescence-based approach to measure rates of retinal binding to samples containing differing relative fractions of ops and ops*. In contrast to what the transient activation hypothesis model would predict, we found that binding for the inverse agonist, 11-cis-retinal (11CR), slowed when the sample contained more ops* (produced using M257Y, a constitutively activating mutation). Interestingly, the increased presence of ops* allowed for binding of the agonist, all-trans-retinal (ATR), whereas WT opsin showed no binding. Shifting the conformational equilibrium toward even more ops* using a G protein peptide mimic (either free in solution or fused to the receptor) accelerated the rate of ATR binding and slowed 11CR binding. An arrestin peptide mimic showed little effect on 11CR binding; however, it stabilized opsin · ATR complexes. The TM5/TM6 hole is apparently not involved in this conformational selection. Increasing its size by mutagenesis did not enable ATR binding but instead slowed 11CR binding, suggesting that it may play a role in trapping 11CR. In summary, our results indicate that conformational selection dictates stable retinal binding, which we propose involves ATR and 11CR binding to different states, the latter a previously unidentified, open-but-inactive conformation.
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Affiliation(s)
- Christopher T Schafer
- From the Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon 97239-3098
| | - David L Farrens
- From the Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon 97239-3098
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109
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Thompson GL, Canals M, Poole DP. Biological redundancy of endogenous GPCR ligands in the gut and the potential for endogenous functional selectivity. Front Pharmacol 2014; 5:262. [PMID: 25506328 PMCID: PMC4246669 DOI: 10.3389/fphar.2014.00262] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 11/12/2014] [Indexed: 01/27/2023] Open
Abstract
This review focuses on the existence and function of multiple endogenous agonists of the somatostatin and opioid receptors with an emphasis on their expression in the gastrointestinal tract. These agonists generally arise from the proteolytic cleavage of prepropeptides during peptide maturation or from degradation of peptides by extracellular or intracellular endopeptidases. In other examples, endogenous peptide agonists for the same G protein-coupled receptors can be products of distinct genes but contain high sequence homology. This apparent biological redundancy has recently been challenged by the realization that different ligands may engender distinct receptor conformations linked to different intracellular signaling profiles and, as such the existence of distinct ligands may underlie mechanisms to finely tune physiological responses. We propose that further characterization of signaling pathways activated by these endogenous ligands will provide invaluable insight into the mechanisms governing biased agonism. Moreover, these ligands may prove useful in the design of novel therapeutic tools to target distinct signaling pathways, thereby favoring desirable effects and limiting detrimental on-target effects. Finally we will discuss the limitations of this area of research and we will highlight the difficulties that need to be addressed when examining endogenous bias in tissues and in animals.
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Affiliation(s)
- Georgina L Thompson
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences Parkville, VIC, Australia
| | - Meritxell Canals
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences Parkville, VIC, Australia
| | - Daniel P Poole
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences Parkville, VIC, Australia ; Department of Anatomy and Neuroscience, The University of Melbourne Parkville, VIC, Australia
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110
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Prasanna X, Chattopadhyay A, Sengupta D. Cholesterol modulates the dimer interface of the β₂-adrenergic receptor via cholesterol occupancy sites. Biophys J 2014; 106:1290-300. [PMID: 24655504 DOI: 10.1016/j.bpj.2014.02.002] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 02/01/2014] [Accepted: 02/03/2014] [Indexed: 11/26/2022] Open
Abstract
The β2-adrenergic receptor is an important member of the G-protein-coupled receptor (GPCR) superfamily, whose stability and function are modulated by membrane cholesterol. The recent high-resolution crystal structure of the β2-adrenergic receptor revealed the presence of possible cholesterol-binding sites in the receptor. However, the functional relevance of cholesterol binding to the receptor remains unexplored. We used MARTINI coarse-grained molecular-dynamics simulations to explore dimerization of the β2-adrenergic receptor in lipid bilayers containing cholesterol. A novel (to our knowledge) aspect of our results is that receptor dimerization is modulated by membrane cholesterol. We show that cholesterol binds to transmembrane helix IV, and cholesterol occupancy at this site restricts its involvement at the dimer interface. With increasing cholesterol concentration, an increased presence of transmembrane helices I and II, but a reduced presence of transmembrane helix IV, is observed at the dimer interface. To our knowledge, this study is one of the first to explore the correlation between cholesterol occupancy and GPCR organization. Our results indicate that dimer plasticity is relevant not just as an organizational principle but also as a subtle regulatory principle for GPCR function. We believe these results constitute an important step toward designing better drugs for GPCR dimer targets.
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111
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Perez-Aguilar JM, Shan J, LeVine M, Khelashvili G, Weinstein H. A functional selectivity mechanism at the serotonin-2A GPCR involves ligand-dependent conformations of intracellular loop 2. J Am Chem Soc 2014; 136:16044-54. [PMID: 25314362 PMCID: PMC4235374 DOI: 10.1021/ja508394x] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Indexed: 01/16/2023]
Abstract
With recent progress in determination of G protein-coupled receptor (GPCR) structure with crystallography, a variety of other experimental approaches (e.g., NMR spectroscopy, fluorescent-based assays, mass spectrometry techniques) are also being used to characterize state-specific and ligand-specific conformational states. MD simulations offer a powerful complementary approach to elucidate the dynamic features associated with ligand-specific GPCR conformations. To shed light on the conformational elements and dynamics of the important aspect of GPCR functional selectivity, we carried out unbiased microsecond-length MD simulations of the human serotonin 2A receptor (5-HT(2A)R) in the absence of ligand and bound to four distinct serotonergic agonists. The 5-HT(2A)R is a suitable system to study the structural features involved in the ligand-dependent conformational heterogeneity of GPCRs because it is well-characterized experimentally and exhibits a strong agonist-specific phenotype in that some 5-HT(2A)R agonists induce LSD-like hallucinations, while others lack this psychoactive property entirely. Here we report evidence for structural and dynamic differences in 5-HT(2A)R interacting with such pharmacologically distinct ligands, hallucinogens, and nonhallucinogens obtained from all-atom MD simulations. Differential ligand binding contacts were identified for structurally similar hallucinogens and nonhallucinogens and found to correspond to different conformations in the intracellular loop 2 (ICL2). From the different ICL2 conformations, functional selective phenotypes are suggested through effects on dimerization and/or distinct direct interaction with effector proteins. The findings are presented in the context of currently proposed hallucinogenesis mechanisms, and ICL2 is proposed as a fine-tuning selective switch that can differentiates modes of 5-HT(2A)R activation.
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Affiliation(s)
- Jose Manuel Perez-Aguilar
- Department
of Physiology and Biophysics and The HRH Prince Alwaleed Bin Talal
Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, New York 10065, United States
| | - Jufang Shan
- Department
of Physiology and Biophysics and The HRH Prince Alwaleed Bin Talal
Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, New York 10065, United States
| | - Michael
V. LeVine
- Department
of Physiology and Biophysics and The HRH Prince Alwaleed Bin Talal
Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, New York 10065, United States
| | - George Khelashvili
- Department
of Physiology and Biophysics and The HRH Prince Alwaleed Bin Talal
Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, New York 10065, United States
| | - Harel Weinstein
- Department
of Physiology and Biophysics and The HRH Prince Alwaleed Bin Talal
Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, New York 10065, United States
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112
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Structure-bias relationships for fenoterol stereoisomers in six molecular and cellular assays at the β2-adrenoceptor. Naunyn Schmiedebergs Arch Pharmacol 2014; 388:51-65. [PMID: 25342094 DOI: 10.1007/s00210-014-1054-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 10/02/2014] [Indexed: 01/14/2023]
Abstract
Functional selectivity is well established as an underlying concept of ligand-specific signaling via G protein-coupled receptors (GPCRs). Functionally, selective drugs could show greater therapeutic efficacy and fewer adverse effects. Dual coupling of the β2-adrenoceptor (β2AR) triggers a signal transduction via Gsα and Giα proteins. Here, we examined 12 fenoterol stereoisomers in six molecular and cellular assays. Using β2AR-Gsα and β2AR-Giα fusion proteins, (R,S')- and (S,S')-isomers of 4'-methoxy-1-naphthyl-fenoterol were identified as biased ligands with preference for Gs. G protein-independent signaling via β-arrestin-2 was disfavored by these ligands. Isolated human neutrophils constituted an ex vivo model of β2AR signaling and demonstrated functional selectivity through the dissociation of cAMP accumulation and the inhibition of formyl peptide-stimulated production of reactive oxygen species. Ligand bias was calculated using an operational model of agonism and revealed that the fenoterol scaffold constitutes a promising lead structure for the development of Gs-biased β2AR agonists.
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113
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Schrage R, Seemann WK, Klöckner J, Dallanoce C, Racké K, Kostenis E, De Amici M, Holzgrabe U, Mohr K. Agonists with supraphysiological efficacy at the muscarinic M2 ACh receptor. Br J Pharmacol 2014; 169:357-70. [PMID: 23062057 DOI: 10.1111/bph.12003] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Revised: 09/18/2012] [Accepted: 09/19/2012] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND AND PURPOSE Artificial agonists may have higher efficacy for receptor activation than the physiological agonist. Until now, such 'superagonism' has rarely been reported for GPCRs. Iperoxo is an extremely potent muscarinic receptor agonist. We hypothesized that iperoxo is a 'superagonist'. EXPERIMENTAL APPROACH Signalling of iperoxo and newly synthesized structural analogues was compared with that of ACh at label-free M2 muscarinic receptors applying whole cell dynamic mass redistribution, measurement of G-protein activation, evaluation of cell surface agonist binding and computation of operational efficacies. KEY RESULTS In CHO-hM2 cells, iperoxo significantly exceeds ACh in Gi /Gs signalling competence. In the orthosteric loss-of-function mutant M2 -Y104(3.33) A, the maximum effect of iperoxo is hardly compromised in contrast to ACh. 'Superagonism' is preserved in the physiological cellular context of MRC-5 human lung fibroblasts. Structure-signalling relationships including iperoxo derivatives with either modified positively charged head group or altered tail suggest that 'superagonism' of iperoxo is mechanistically based on parallel activation of the receptor protein via two orthosteric interaction points. CONCLUSION AND IMPLICATIONS Supraphysiological agonist efficacy at muscarinic M2 ACh receptors is demonstrated for the first time. In addition, a possible underlying molecular mechanism of GPCR 'superagonism' is provided. We suggest that iperoxo-like orthosteric GPCR activation is a new avenue towards a novel class of receptor activators.
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Affiliation(s)
- R Schrage
- Pharmacology & Toxicology Section, Institute of Pharmacy, University of Bonn, Bonn, Germany
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114
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Abstract
G protein-coupled receptors (GPCRs) are the largest class of molecules involved in signal transduction across cell membranes and represent major targets in the development of novel drug candidates in all clinical areas. Although there have been some recent leads, structural information on GPCRs is relatively rare due to the difficulty associated with crystallization. A specific reason for this is the intrinsic flexibility displayed by GPCRs, which is necessary for their functional diversity. Since GPCRs are integral membrane proteins, interaction of membrane lipids with them constitutes an important area of research in GPCR biology. In particular, membrane cholesterol has been reported to have a modulatory role in the function of a number of GPCRs. The role of membrane cholesterol in GPCR function is discussed with specific example of the serotonin1A receptor. Recent results show that GPCRs are characterized with structural motifs that preferentially associate with cholesterol. An emerging and important concept is oligomerization of GPCRs and its role in GPCR function and signaling. The role of membrane cholesterol in GPCR oligomerization is highlighted. Future research in GPCR biology would offer novel insight in basic biology and provide new avenues for drug discovery.
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115
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Roth S, Bruggeman FJ. A conformation-equilibrium model captures ligand-ligand interactions and ligand-biased signalling by G-protein coupled receptors. FEBS J 2014; 281:4659-71. [DOI: 10.1111/febs.12970] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 07/07/2014] [Accepted: 08/11/2014] [Indexed: 12/31/2022]
Affiliation(s)
- Susanne Roth
- Systems Bioinformatics; VU University; Amsterdam The Netherlands
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116
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Córdova-Sintjago TC, Liu Y, Booth RG. Molecular interactions of agonist and inverse agonist ligands at serotonin 5-HT2CG protein-coupled receptors: computational ligand docking and molecular dynamics studies validated by experimental mutagenesis results. Mol Phys 2014. [DOI: 10.1080/00268976.2014.952695] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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117
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Hausrath AC. Model for coupled insertion and folding of membrane-spanning proteins. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 90:022707. [PMID: 25215758 DOI: 10.1103/physreve.90.022707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Indexed: 06/03/2023]
Abstract
Current understanding of the forces directing the folding of integral membrane proteins is very limited compared to the detailed picture available for water-soluble proteins. While mechanistic studies of the folding process in vitro have been conducted for only a small number of membrane proteins, the available evidence indicates that their folding process is thermodynamically driven like that of soluble proteins. In vivo, however, the majority of integral membrane proteins are installed in membranes by dedicated machinery, suggesting that the cellular systems may act to facilitate and regulate the spontaneous physical process of folding. Both the in vitro folding process and the in vivo pathway must navigate an energy landscape dominated by the energetically favorable burial of hydrophobic segments in the membrane interior and the opposition to folding due to the need for passage of polar segments across the membrane. This manuscript describes a simple, exactly solvable model which incorporates these essential features of membrane protein folding. The model is used to compare the folding time under conditions which depict both the in vitro and in vivo pathways. It is proposed that the cellular complexes responsible for insertion of membrane proteins act by lowering the energy barrier for passage of polar regions through the membrane, thereby allowing the chain to more rapidly achieve the folded state.
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Affiliation(s)
- Andrew C Hausrath
- Department of Chemistry and Biochemistry and Program in Applied Mathematics, University of Arizona, Tucson, Arizona 85721, USA
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118
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Thompson GL, Kelly E, Christopoulos A, Canals M. Novel GPCR paradigms at the μ-opioid receptor. Br J Pharmacol 2014; 172:287-96. [PMID: 24460711 DOI: 10.1111/bph.12600] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 01/12/2014] [Accepted: 01/19/2014] [Indexed: 01/14/2023] Open
Abstract
UNLABELLED Opioids, such as morphine, are the most clinically useful class of analgesic drugs for the treatment of acute and chronic pain. However, the use of opioids is greatly limited by the development of severe adverse side effects. Consequently, drug discovery efforts have been directed towards improving the therapeutic profile of opioid-based treatments. Opioid receptors are members of the family of GPCRs. As such, the recent GPCR paradigms of biased agonism and allosterism may provide novel avenues for more effective analgesics. Biased agonism (or functional selectivity) has been described for all the opioid receptor family members. Furthermore, the first allosteric modulators of opioid receptors have very recently been described. However, identification and quantification of biased agonism in a manner that is informative to medicinal chemists and drug discovery programmes still remains a challenge. In this review, we examine the progress, to date, towards identification and quantification of biased agonism and allosterism at the μ-opioid receptor in the context of its implications for the discovery of better and safer analgesics. LINKED ARTICLES This article is part of a themed section on Opioids: New Pathways to Functional Selectivity. To view the other articles in this section visit http://dx.doi.org/10.1111/bph.2015.172.issue-2.
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Affiliation(s)
- G L Thompson
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Vic., Australia
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119
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Litosch I. Regulation of phospholipase C-β(1) GTPase-activating protein (GAP) function and relationship to G(q) efficacy. IUBMB Life 2014; 65:936-40. [PMID: 24170560 DOI: 10.1002/iub.1218] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 09/30/2013] [Accepted: 09/30/2013] [Indexed: 11/08/2022]
Abstract
How cells regulate Gq efficacy (initiation and termination of Gq signaling) to effect response remains a central question in pharmacology and drug discovery. Phospholipase C-β1 (PLC-β1) is an effector and a GTPase activating protein (GAP) specific to Gαq. The physiological function of PLC-β1 GAP remains unclear and controversial. GAPs are generally thought to function in deactivation of Gq signaling. However, PLC-β1 GAP has also been shown to increase signaling efficiency through kinetic coupling with the ligand-activated GPCR. GPCRs function as guanine nucleotide exchange factors (GEF) on the G protein activation cycle. This article sets forth a new hypothesis that could unify these conflicting paradigms as it pertains to physiological signaling and native levels of protein. It is proposed that the physiological function of PLC-β1 GAP is context-dependent and regulated by phosphatidic acid (PA). PA stimulates PLC-β1 GAP activity. In the absence of ligand, PLC-β1 GAP does indeed deactivate Gq signaling, limiting leaky activation to set the threshold for stimulation to sharpen signal kinetics. However in the presence of activating ligand, the increase in levels of PA would stimulate PLC-β1 GAP to kinetically couple with GPCR GEF to increase signaling efficiency. We found that PA-increased Gq efficiency is dependent on signaling via the unique PLC-β1 PA binding domain.
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120
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Ahles A, Engelhardt S. Polymorphic Variants of Adrenoceptors: Pharmacology, Physiology, and Role in Disease. Pharmacol Rev 2014; 66:598-637. [DOI: 10.1124/pr.113.008219] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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121
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Novikov GV, Sivozhelezov VS, Shaitan KV. Influence of orthosteric ligand binding on the conformational dynamics of the β-2-adrenergic receptor via essential dynamics sampling simulation. Mol Biol 2014. [DOI: 10.1134/s0026893314030157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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122
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Unraveling structural mechanisms of allosteric drug action. Trends Pharmacol Sci 2014; 35:256-64. [PMID: 24742712 DOI: 10.1016/j.tips.2014.03.006] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 03/03/2014] [Accepted: 03/07/2014] [Indexed: 11/20/2022]
Abstract
Orthosteric drugs block the active site to obstruct function; allosteric drugs modify the population of the active state, to modulate function. Available data lead us to propose that allosteric drugs can constitute anchors and drivers. The anchor docks into an allosteric pocket. The conformation with which it interacts is unchanged during the transition between the inactive and active states. The anchor provides the foundation that allows the driver to exert a 'pull' and/or 'push' action that shifts the receptor population from the inactive to the active state. The presence or absence of driver atom in an allosteric drug can exert opposite agonism. We map a strategy for driver identification and expect the allosteric trigger concept to transform agonist/antagonist drug discovery.
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123
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Miao Y, Nichols SE, McCammon JA. Free energy landscape of G-protein coupled receptors, explored by accelerated molecular dynamics. Phys Chem Chem Phys 2014; 16:6398-406. [PMID: 24445284 PMCID: PMC3960983 DOI: 10.1039/c3cp53962h] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 01/14/2014] [Indexed: 11/21/2022]
Abstract
G-protein coupled receptors (GPCRs) mediate cellular responses to various hormones and neurotransmitters and are important targets for treating a wide spectrum of diseases. They are known to adopt multiple conformational states (e.g., inactive, intermediate and active) during their modulation of various cell signaling pathways. Here, the free energy landscape of GPCRs is explored using accelerated molecular dynamics (aMD) simulations as demonstrated on the M2 muscarinic receptor, a key GPCR that regulates human heart rate and contractile forces of cardiomyocytes. Free energy profiles of important structural motifs that undergo conformational transitions upon GPCR activation and allosteric signaling are analyzed in detail, including the Arg(3.50)-Glu(6.30) ionic lock, the Trp(6.48) toggle switch and the hydrogen interactions between Tyr(5.58)-Tyr(7.53).
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Affiliation(s)
- Yinglong Miao
- Howard Hughes Medical Institute , University of California at San Diego , La Jolla , CA 92093 , USA .
| | - Sara E. Nichols
- Department of Chemistry and Biochemistry , University of California at San Diego , La Jolla , CA 92093 , USA .
- Department of Pharmacology , University of California at San Diego , La Jolla , CA 92093 , USA
| | - J. Andrew McCammon
- Howard Hughes Medical Institute , University of California at San Diego , La Jolla , CA 92093 , USA .
- Department of Chemistry and Biochemistry , University of California at San Diego , La Jolla , CA 92093 , USA .
- Department of Pharmacology , University of California at San Diego , La Jolla , CA 92093 , USA
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124
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Wisler JW, Xiao K, Thomsen ARB, Lefkowitz RJ. Recent developments in biased agonism. Curr Opin Cell Biol 2014; 27:18-24. [PMID: 24680426 PMCID: PMC3971386 DOI: 10.1016/j.ceb.2013.10.008] [Citation(s) in RCA: 224] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 10/23/2013] [Accepted: 10/24/2013] [Indexed: 12/17/2022]
Abstract
The classic paradigm of G protein-coupled receptor (GPCR) activation was based on the understanding that agonist binding to a receptor induces or stabilizes a conformational change to an 'active' conformation. In the past decade, however, it has been appreciated that ligands can induce distinct 'active' receptor conformations with unique downstream functional signaling profiles. Building on the initial recognition of the existence of such 'biased ligands', recent years have witnessed significant developments in several areas of GPCR biology. These include increased understanding of structural and biophysical mechanisms underlying biased agonism, improvements in characterization and quantification of ligand efficacy, as well as clinical development of these novel ligands. Here we review recent major developments in these areas over the past several years.
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Affiliation(s)
- James W Wisler
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Kunhong Xiao
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Alex R B Thomsen
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Robert J Lefkowitz
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA; Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA; Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA.
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125
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Thaker TM, Sarwar M, Preininger AM, Hamm HE, Iverson TM. A transient interaction between the phosphate binding loop and switch I contributes to the allosteric network between receptor and nucleotide in Gαi1. J Biol Chem 2014; 289:11331-11341. [PMID: 24596087 DOI: 10.1074/jbc.m113.539064] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Receptor-mediated activation of the Gα subunit of heterotrimeric G proteins requires allosteric communication between the receptor binding site and the guanine nucleotide binding site, which are separated by >30 Å. Structural changes in the allosteric network connecting these sites are predicted to be transient in the wild-type Gα subunit, making studies of these connections challenging. In the current work, site-directed mutants that alter the energy barriers between the activation states are used as tools to better understand the transient features of allosteric signaling in the Gα subunit. The observed differences in relative receptor affinity for intact Gαi1 subunits versus C-terminal Gαi1 peptides harboring the K345L mutation are consistent with this mutation modulating the allosteric network in the protein subunit. Measurement of nucleotide exchange rates, affinity for metarhodopsin II, and thermostability suggest that the K345L Gαi1 variant has reduced stability in both the GDP-bound and nucleotide-free states as compared with wild type but similar stability in the GTPγS-bound state. High resolution x-ray crystal structures reveal conformational changes accompanying the destabilization of the GDP-bound state. Of these, the conformation for Switch I was stabilized by an ionic interaction with the phosphate binding loop. Further site-directed mutagenesis suggests that this interaction between Switch I and the phosphate binding loop is important for receptor-mediated nucleotide exchange in the wild-type Gαi1 subunit.
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Affiliation(s)
- Tarjani M Thaker
- Department of Biochemistry and Vanderbilt University Medical Center, Nashville, Tennessee 37232
| | - Maruf Sarwar
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee 37232
| | - Anita M Preininger
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee 37232
| | - Heidi E Hamm
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee 37232.
| | - T M Iverson
- Department of Biochemistry and Vanderbilt University Medical Center, Nashville, Tennessee 37232; Department of Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee 37232.
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126
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Manglik A, Kobilka B. The role of protein dynamics in GPCR function: insights from the β2AR and rhodopsin. Curr Opin Cell Biol 2014; 27:136-43. [PMID: 24534489 DOI: 10.1016/j.ceb.2014.01.008] [Citation(s) in RCA: 175] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2014] [Revised: 01/17/2014] [Accepted: 01/20/2014] [Indexed: 11/25/2022]
Abstract
G protein-coupled receptors (GPCRs) are versatile signaling proteins that mediate complex cellular responses to hormones and neurotransmitters. Recent advances in GPCR crystallography have provided inactive and active state structures for rhodopsin and the β2 adrenergic receptor (β2AR). Although these structures suggest a two-state 'on-off' mechanism of receptor activation, other biophysical studies and observed signaling versatility suggest that GPCRs are highly dynamic and exist in a multitude of functionally distinct conformations. To fully understand how GPCRs work, we must characterize these conformations and determine how ligands affect their energetics and rates of interconversion. This brief review will compare and contrast the dynamic properties of rhodopsin and β2AR that shed light on the role of structural dynamics in their distinct signaling behaviors.
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Affiliation(s)
- Aashish Manglik
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA
| | - Brian Kobilka
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA.
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127
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Ferguson SSG, Feldman RD. β-adrenoceptors as molecular targets in the treatment of hypertension. Can J Cardiol 2014; 30:S3-8. [PMID: 24685403 DOI: 10.1016/j.cjca.2014.01.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 01/31/2014] [Accepted: 01/31/2014] [Indexed: 01/14/2023] Open
Abstract
Regulation of sympathoadrenal activity has been a long-time target in the management of hypertension. Regulation of β-adrenoceptor (βAR) function has been the most therapeutically important of these targets. The development of effective antihypertensive treatments based on βAR antagonism paralleled the elucidation of the molecular basis of β-adrenergic effects by the family of βARs, which are members of the G-protein-coupled receptor (GPCR) superfamily. βARs serve as the extracellular face of the transmembrane signalling pathway that results in the consequent activation of heterotrimeric G-proteins and the activation of several other newly appreciated signalling molecules that include β-arrestins and GPCR kinases (GRKs). The aggregate effect of the activation of these signalling pathways mediates the response to βAR activation. Paradoxically, the hypertensive state is characterized by impaired βAR responsiveness. This defect is common to many other receptor systems linked to the stimulator G protein (Gs) and adenylyl cyclase activation. This impairment is principally mediated by receptor-G-protein uncoupling, which has been linked to increased expression and activity of GRK2.
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Affiliation(s)
- Stephen S G Ferguson
- J. Allyn Taylor Centre for Cell Biology, University of Western Ontario, London, Ontario, Canada; Department of Physiology and Pharmacology, University of Western Ontario, London, Ontario, Canada
| | - Ross D Feldman
- Department of Physiology and Pharmacology, University of Western Ontario, London, Ontario, Canada; Vascular Biology Research Group, Robarts Research Institute, University of Western Ontario, London, Ontario, Canada; Department of Medicine, University of Western Ontario, London, Ontario, Canada.
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128
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Miao Y, Nichols SE, McCammon JA. Mapping of allosteric druggable sites in activation-associated conformers of the M2 muscarinic receptor. Chem Biol Drug Des 2014; 83:237-46. [PMID: 24112716 PMCID: PMC4012891 DOI: 10.1111/cbdd.12233] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 09/15/2013] [Indexed: 11/29/2022]
Abstract
G-protein-coupled receptors (GPCRs) are key cellular signaling proteins and have been targeted by approximately 30-40% of marketed drugs for treating many human diseases including cancer and heart failure. Recently, we directly observed activation of the M2 muscarinic receptor through long-timescale accelerated molecular dynamics (aMD) simulation, which revealed distinct inactive, intermediate and active conformers of the receptor. Here, FTMAP is applied to search for 'hot spots' in these activation-associated conformers using a library of 16 organic probe molecules that represent fragments of potential drugs. Seven allosteric (non-orthosteric) binding sites are identified in the M2 receptor through the FTMAP analysis. These sites are distributed in the solvent-exposed extracellular and intracellular mouth regions, as well as the lipid-exposed pockets formed by the transmembrane α helices TM3-TM4, TM5-TM6 and TM7-TM1/TM2. They serve as promising target sites for designing novel allosteric modulators as receptor-selective drugs.
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Affiliation(s)
- Yinglong Miao
- Howard Hughes Medical Institute, University of California at San Diego, La Jolla, CA 92093
| | - Sara E. Nichols
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093
| | - J. Andrew McCammon
- Howard Hughes Medical Institute, University of California at San Diego, La Jolla, CA 92093
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093
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129
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Abstract
The question of how allostery works was posed almost 50 years ago. Since then it has been the focus of much effort. This is for two reasons: first, the intellectual curiosity of basic science and the desire to understand fundamental phenomena, and second, its vast practical importance. Allostery is at play in all processes in the living cell, and increasingly in drug discovery. Many models have been successfully formulated, and are able to describe allostery even in the absence of a detailed structural mechanism. However, conceptual schemes designed to qualitatively explain allosteric mechanisms usually lack a quantitative mathematical model, and are unable to link its thermodynamic and structural foundations. This hampers insight into oncogenic mutations in cancer progression and biased agonists' actions. Here, we describe how allostery works from three different standpoints: thermodynamics, free energy landscape of population shift, and structure; all with exactly the same allosteric descriptors. This results in a unified view which not only clarifies the elusive allosteric mechanism but also provides structural grasp of agonist-mediated signaling pathways, and guides allosteric drug discovery. Of note, the unified view reasons that allosteric coupling (or communication) does not determine the allosteric efficacy; however, a communication channel is what makes potential binding sites allosteric.
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Affiliation(s)
- Chung-Jung Tsai
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory, National Cancer Institute, Center for Cancer Research, Frederick, Maryland, United States of America
| | - Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory, National Cancer Institute, Center for Cancer Research, Frederick, Maryland, United States of America
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
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130
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Ferrie AM, Sun H, Zaytseva N, Fang Y. Divergent label-free cell phenotypic pharmacology of ligands at the overexpressed β₂-adrenergic receptors. Sci Rep 2014; 4:3828. [PMID: 24451999 PMCID: PMC3899747 DOI: 10.1038/srep03828] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 01/06/2014] [Indexed: 01/14/2023] Open
Abstract
We present subclone sensitive cell phenotypic pharmacology of ligands at the β2-adrenergic receptor (β2-AR) stably expressed in HEK-293 cells. The parental cell line was transfected with green fluorescent protein (GFP)-tagged β2-AR. Four stable subclones were established and used to profile a library of sixty-nine AR ligands. Dynamic mass redistribution (DMR) profiling resulted in a pharmacological activity map suggesting that HEK293 endogenously expresses functional Gi-coupled α2-AR and Gs-coupled β2-AR, and the label-free cell phenotypic activity of AR ligands are subclone dependent. Pathway deconvolution revealed that the DMR of epinephrine is originated mostly from the remodeling of actin microfilaments and adhesion complexes, to less extent from the microtubule networks and receptor trafficking, and certain agonists displayed different efficacy towards the cAMP-Epac pathway. We demonstrate that receptor signaling and ligand pharmacology is sensitive to the receptor expression level, and the organization of the receptor and its signaling circuitry.
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Affiliation(s)
- Ann M Ferrie
- 1] Biochemical Technologies, Science and Technology Division, Corning Incorporated, Corning, NY 14831, United States of America [2]
| | - Haiyan Sun
- 1] Biochemical Technologies, Science and Technology Division, Corning Incorporated, Corning, NY 14831, United States of America [2] [3]
| | - Natalya Zaytseva
- Biochemical Technologies, Science and Technology Division, Corning Incorporated, Corning, NY 14831, United States of America
| | - Ye Fang
- Biochemical Technologies, Science and Technology Division, Corning Incorporated, Corning, NY 14831, United States of America
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131
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Ernst OP, Lodowski DT, Elstner M, Hegemann P, Brown L, Kandori H. Microbial and animal rhodopsins: structures, functions, and molecular mechanisms. Chem Rev 2014; 114:126-63. [PMID: 24364740 PMCID: PMC3979449 DOI: 10.1021/cr4003769] [Citation(s) in RCA: 781] [Impact Index Per Article: 78.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Indexed: 12/31/2022]
Affiliation(s)
- Oliver P. Ernst
- Departments
of Biochemistry and Molecular Genetics, University of Toronto, 1 King’s College Circle, Medical Sciences Building, Toronto, Ontario M5S 1A8, Canada
| | - David T. Lodowski
- Center
for Proteomics and Bioinformatics, Case
Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Marcus Elstner
- Institute
for Physical Chemistry, Karlsruhe Institute
of Technology, Kaiserstrasse
12, 76131 Karlsruhe, Germany
| | - Peter Hegemann
- Institute
of Biology, Experimental Biophysics, Humboldt-Universität
zu Berlin, Invalidenstrasse
42, 10115 Berlin, Germany
| | - Leonid
S. Brown
- Department
of Physics and Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Hideki Kandori
- Department
of Frontier Materials, Nagoya Institute
of Technology, Showa-ku, Nagoya 466-8555, Japan
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132
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Flanagan CA. Receptor Conformation and Constitutive Activity in CCR5 Chemokine Receptor Function and HIV Infection. ADVANCES IN PHARMACOLOGY 2014; 70:215-63. [DOI: 10.1016/b978-0-12-417197-8.00008-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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133
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Johnston JM, Filizola M. Beyond standard molecular dynamics: investigating the molecular mechanisms of G protein-coupled receptors with enhanced molecular dynamics methods. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 796:95-125. [PMID: 24158803 PMCID: PMC4074508 DOI: 10.1007/978-94-007-7423-0_6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The majority of biological processes mediated by G Protein-Coupled Receptors (GPCRs) take place on timescales that are not conveniently accessible to standard molecular dynamics (MD) approaches, notwithstanding the current availability of specialized parallel computer architectures, and efficient simulation algorithms. Enhanced MD-based methods have started to assume an important role in the study of the rugged energy landscape of GPCRs by providing mechanistic details of complex receptor processes such as ligand recognition, activation, and oligomerization. We provide here an overview of these methods in their most recent application to the field.
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Affiliation(s)
- Jennifer M. Johnston
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Marta Filizola
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
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134
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Kleinau G, Biebermann H. Constitutive activities in the thyrotropin receptor: regulation and significance. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2014; 70:81-119. [PMID: 24931193 DOI: 10.1016/b978-0-12-417197-8.00003-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The thyroid-stimulating hormone receptor (TSHR, or thyrotropin receptor) is a family A G protein-coupled receptor. It not only binds thyroid-stimulating hormone (TSH, or thyrotropin) but also interacts with autoantibodies under pathological conditions. The TSHR and TSH are essential for thyroid growth and function and thus for all thyroid hormone-associated physiological superordinated processes, including metabolism and development of the central nervous system. In vitro studies have found that the TSHR permanently stimulates ligand-independent (constitutive) activation of Gs, which ultimately leads to intracellular cAMP accumulation. Furthermore, a vast variety of constitutively activating mutations of TSHR-at more than 50 different amino acid positions-have been reported to enhance basal signaling. These lead in vivo to a "gain-of-function" phenotype of nonautoimmune hyperthyroidism or toxic adenomas. Moreover, many naturally occurring inactivating mutations are known to cause a "loss-of-function" phenotype, resulting in resistance to thyroid hormone or hyperthyrotropinemia. Several of these mutations are also characterized by impaired basal signaling, and these are designated here as "constitutively inactivating mutations" (CIMs). More than 30 amino acid positions with CIMs have been identified so far. Moreover, the permanent TSHR signaling capacity can also be blocked by inverse agonistic antibodies or small drug-like molecules, which both have a potential for clinical usage. In this chapter, information on constitutive activity in the TSHR is described, including up- and downregulation, linked protein conformations, physiological and pathophysiological conditions, and related intracellular signaling.
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Affiliation(s)
- Gunnar Kleinau
- Institute of Experimental Pediatric Endocrinology, Charité-Universitätsmedizin Berlin, Berlin, Germany.
| | - Heike Biebermann
- Institute of Experimental Pediatric Endocrinology, Charité-Universitätsmedizin Berlin, Berlin, Germany
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135
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Affiliation(s)
- Xavier Deupi
- Department of Research with Neutrons and Muons and in the Department of Biology and Chemistry at the Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
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136
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Deupi X. Relevance of rhodopsin studies for GPCR activation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1837:674-82. [PMID: 24041646 DOI: 10.1016/j.bbabio.2013.09.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 09/02/2013] [Accepted: 09/05/2013] [Indexed: 10/26/2022]
Abstract
Rhodopsin, the dim-light photoreceptor present in the rod cells of the retina, is both a retinal-binding protein and a G protein-coupled receptor (GPCR). Due to this conjunction, it benefits from an arsenal of spectroscopy techniques that can be used for its characterization, while being a model system for the important family of Class A (also referred to as "rhodopsin-like") GPCRs. For instance, rhodopsin has been a crucial player in the field of GPCR structural biology. Until 2007, it was the only GPCR for which a high-resolution crystal structure was available, so all structure-activity analyses on GPCRs, from structure-based drug discovery to studies of structural changes upon activation, were based on rhodopsin. At present, about a third of currently available GPCR structures are still from rhodopsin. In this review, I show some examples of how these structures can still be used to gain insight into general aspects of GPCR activation. First, the analysis of the third intracellular loop in rhodopsin structures allows us to gain an understanding of the structural and dynamic properties of this region, which is absent (due to protein engineering or poor electron density) in most of the currently available GPCR structures. Second, a detailed analysis of the structure of the transmembrane domains in inactive, intermediate and active rhodopsin structures allows us to detect early conformational changes in the process of ligand-induced GPCR activation. Finally, the analysis of a conserved ligand-activated transmission switch in the transmembrane bundle of GPCRs in the context of the rhodopsin activation cycle, allows us to suggest that the structures of many of the currently available agonist-bound GPCRs may correspond to intermediate active states. While the focus in GPCR structural biology is inevitably moving away from rhodopsin, in other aspects rhodopsin is still at the forefront. For instance, the first studies of the structural basis of disease mutants in GPCRs, or the most detailed analysis of cellular GPCR signal transduction networks using a systems biology approach, have been carried out in rhodopsin. Finally, due again to its unique properties among GPCRs, rhodopsin will likely play an important role in the application of X-ray free electron laser crystallography to time-resolved structural biology in membrane proteins. Rhodopsin, thus, still remains relevant as a model system to study the molecular mechanisms of GPCR activation. This article is part of a Special Issue entitled: Retinal Proteins-You can teach an old dog new tricks.
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Affiliation(s)
- Xavier Deupi
- Condensed Matter Theory Group and Laboratory of Biomolecular Research, Paul Scherrer Institute, WHGA/106, CH-5232 Villigen PSI, Switzerland
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137
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Park JH, Morizumi T, Li Y, Hong JE, Pai EF, Hofmann KP, Choe HW, Ernst OP. Opsin, a structural model for olfactory receptors? Angew Chem Int Ed Engl 2013; 52:11021-4. [PMID: 24038729 DOI: 10.1002/anie.201302374] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 07/30/2013] [Indexed: 11/11/2022]
Abstract
Receptor-ligand interaction: Olfactory receptors (ORs) are G-protein-coupled receptors (GPCRs), which detect signaling molecules such as hormones and odorants. The structure of opsin, the GPCR employed in vision, with a detergent molecule bound deep in its orthosteric ligand-binding pocket provides a template for OR homology modeling, thus enabling investigation of the structural basis of the mechanism of odorant-receptor recognition.
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Affiliation(s)
- Jung Hee Park
- Division of Biotechnology, Advanced Institute of Environment and Bioscience, College of Environmental & Bioresources Sciences, Chonbuk National University, 570-752 Iksan (Republic of Korea).
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138
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Park JH, Morizumi T, Li Y, Hong JE, Pai EF, Hofmann KP, Choe HW, Ernst OP. Opsin, a Structural Model for Olfactory Receptors? Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201302374] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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139
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Tsukamoto H, Farrens DL. A constitutively activating mutation alters the dynamics and energetics of a key conformational change in a ligand-free G protein-coupled receptor. J Biol Chem 2013; 288:28207-16. [PMID: 23940032 DOI: 10.1074/jbc.m113.472464] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
G protein-coupled receptors (GPCRs) undergo dynamic transitions between active and inactive conformations. Usually, these conversions are triggered when the receptor detects an external signal, but some so-called constitutively activating mutations, or CAMs, induce a GPCR to bind and activate G proteins in the absence of external stimulation, in ways still not fully understood. Here, we investigated how a CAM alters the structure of a GPCR and the dynamics involved as the receptor transitions between different conformations. Our approach used site-directed fluorescence labeling (SDFL) spectroscopy to compare opsin, the ligand-free form of the GPCR rhodopsin, with opsin containing the CAM M257Y, focusing specifically on key movements that occur in the sixth transmembrane helix (TM6) during GPCR activation. The site-directed fluorescence labeling data indicate opsin is constrained to an inactive conformation both in detergent micelles and lipid membranes, but when it contains the M257Y CAM, opsin is more dynamic and can interact with a G protein mimetic. Further study of these receptors using tryptophan-induced quenching (TrIQ) methods indicates that in detergent, the CAM significantly increases the population of receptors in the active state, but not in lipids. Subsequent Arrhenius analysis of the TrIQ data suggests that, both in detergent and lipids, the CAM lowers the energy barrier for TM6 movement, a key transition required for conversion between the inactive and active conformations. Together, these data suggest that the lowered energy barrier is a primary effect of the CAM on the receptor dynamics and energetics.
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Affiliation(s)
- Hisao Tsukamoto
- From the Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon 97239-3098
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140
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Elgeti M, Rose AS, Bartl FJ, Hildebrand PW, Hofmann KP, Heck M. Precision vs flexibility in GPCR signaling. J Am Chem Soc 2013; 135:12305-12. [PMID: 23883288 DOI: 10.1021/ja405133k] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The G protein coupled receptor (GPCR) rhodopsin activates the heterotrimeric G protein transducin (Gt) to transmit the light signal into retinal rod cells. The rhodopsin activity is virtually zero in the dark and jumps by more than one billion fold after photon capture. Such perfect switching implies both high fidelity and speed of rhodopsin/Gt coupling. We employed Fourier transform infrared (FTIR) spectroscopy and supporting all-atom molecular dynamics (MD) simulations to study the conformational diversity of rhodopsin in membrane environment and extend the static picture provided by the available crystal structures. The FTIR results show how the equilibria of inactive and active protein states of the receptor (so-called metarhodopsin states) are regulated by the highly conserved E(D)RY and Yx7K(R) motives. The MD data identify an intrinsically unstructured cytoplasmic loop region connecting transmembrane helices 5 and 6 (CL3) and show how each protein state is split into conformational substates. The C-termini of the Gtγ- and Gtα-subunits (GαCT and GγCT), prepared as synthetic peptides, are likely to bind sequentially and at different sites of the active receptor. The peptides have different effects on the receptor conformation. While GγCT stabilizes the active states but preserves CL3 flexibility, GαCT selectively stabilizes a single conformational substate with largely helical CL3, as it is found in crystal structures. Based on these results we propose a mechanism for the fast and precise signal transfer from rhodopsin to Gt, which assumes a stepwise and mutual reduction of their conformational space. The mechanism relies on conserved amino acids and may therefore underlie GPCR/G protein coupling in general.
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Affiliation(s)
- Matthias Elgeti
- Institut für Medizinische Physik und Biophysik (CC2), Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
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141
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Seifert R. Functional selectivity of G-protein-coupled receptors: from recombinant systems to native human cells. Biochem Pharmacol 2013; 86:853-61. [PMID: 23933388 DOI: 10.1016/j.bcp.2013.07.029] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Revised: 07/25/2013] [Accepted: 07/25/2013] [Indexed: 10/26/2022]
Abstract
In the mid 1990s, it was assumed that a two-state model, postulating an inactive (R) state and an active (R*) state provides the molecular basis for GPCR activation. However, it became clear that this model could not accommodate many experimental observations. Accordingly, the two-state model was superseded by a multi-state model according to which any given ligand stabilizes a unique receptor conformation with distinct capabilities of activating down-stream G-proteins and β-arrestin. Much of this research was conducted with the β2-adrenoceptor in recombinant systems. At the molecular level, there is now no doubt anymore that ligand-specific receptor conformations, also referred to as functional selectivity, exist. This concept holds great potential for drug discovery in terms of developing drugs with higher selectivity for specific cells and/or cell functions and fewer side effects. A major challenge is the analysis for functional selectivity in native cells. Here, I discuss our current knowledge on functional selectivity of three representative GPCRs, the β2-adrenoceptor and the histamine H2- and H4-receptors, in recombinant systems and native human cells. Studies with human neutrophils and eosinophils support the concept of functional selectivity. A major strategy for the analysis of functional selectivity in native cells is to generate complete concentration/response curves with a large set of structurally diverse ligands for multiple parameters. Next, correlations of potencies and efficacies are analyzed, and deviations of the correlations from linearity are indicative for functional selectivity. Additionally, pharmacological inhibitors are used to dissect cell functions from each other.
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Affiliation(s)
- Roland Seifert
- Institute of Pharmacology, Medical School of Hannover, Carl-Neuberg-Str. 1, D-30625 Hannover, Germany.
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142
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Molecular modeling studies give hint for the existence of a symmetric hβ2R-Gαβγ-homodimer. J Mol Model 2013; 19:4443-57. [DOI: 10.1007/s00894-013-1923-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 06/16/2013] [Indexed: 01/13/2023]
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143
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Tikhonova IG, Selvam B, Ivetac A, Wereszczynski J, McCammon JA. Simulations of biased agonists in the β(2) adrenergic receptor with accelerated molecular dynamics. Biochemistry 2013; 52:5593-603. [PMID: 23879802 PMCID: PMC3763781 DOI: 10.1021/bi400499n] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The biased agonism of the G protein-coupled receptors (GPCRs), where in addition to a traditional G protein-signaling pathway a GPCR promotes intracellular signals though β-arrestin, is a novel paradigm in pharmacology. Biochemical and biophysical studies have suggested that a GPCR forms a distinct ensemble of conformations signaling through the G protein and β-arrestin. Here we report on the dynamics of the β2 adrenergic receptor bound to the β-arrestin and G protein-biased agonists and the empty receptor to further characterize the receptor conformational changes caused by biased agonists. We use conventional and accelerated molecular dynamics (aMD) simulations to explore the conformational transitions of the GPCR from the active state to the inactive state. We found that aMD simulations enable monitoring of the transition within the nanosecond time scale while capturing the known microscopic characteristics of the inactive states, such as the ionic lock, the inward position of F6.44, and water clusters. Distinct conformational states are shown to be stabilized by each biased agonist. In particular, in simulations of the receptor with the β-arrestin-biased agonist N-cyclopentylbutanepherine, we observe a different pattern of motions in helix 7 when compared to simulations with the G protein-biased agonist salbutamol that involves perturbations of the network of interactions within the NPxxY motif. Understanding the network of interactions induced by biased ligands and the subsequent receptor conformational shifts will lead to development of more efficient drugs.
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Affiliation(s)
- Irina G Tikhonova
- Molecular Therapeutics, School of Pharmacy, Medical Biology Centre, Queen's University, Belfast BT9 7BL, Northern Ireland, UK.
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144
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How ligands and signalling proteins affect G-protein-coupled receptors' conformational landscape. Biochem Soc Trans 2013; 41:144-7. [PMID: 23356274 DOI: 10.1042/bst20120267] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The dynamic character of GPCRs (G-protein-coupled receptors) is essential to their function. However, the details of how ligands and signalling proteins stabilize a receptor conformation to trigger the activation of a given signalling pathway remain largely unexplored. Multiple data, including recent results obtained with the purified ghrelin receptor, suggest a model where ligand efficacy and functional selectivity are directly related to different receptor conformations. Importantly, distinct effector proteins (G-proteins and arrestins) as well as ligands are likely to affect the conformational landscape of GPCRs in different manners, as we show with the isolated ghrelin receptor. Such modulation of the GPCR conformational landscape by pharmacologically distinct ligands and effector proteins has major implications for the design of new drugs that activate specific signalling pathways.
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145
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Changeux JP. The concept of allosteric interaction and its consequences for the chemistry of the brain. J Biol Chem 2013; 288:26969-26986. [PMID: 23878193 DOI: 10.1074/jbc.x113.503375] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Throughout this Reflections article, I have tried to follow up on the genesis in the 1960s and subsequent evolution of the concept of allosteric interaction and to examine its consequences within the past decades, essentially in the field of the neuroscience. The main conclusion is that allosteric mechanisms built on similar structural principles operate in bacterial regulatory enzymes, gene repressors (and the related nuclear receptors), rhodopsin, G-protein-coupled receptors, neurotransmitter receptors, ion channels, and so on from prokaryotes up to the human brain yet with important features of their own. Thus, future research on these basic cybernetic sensors is expected to develop in two major directions: at the elementary level, toward the atomic structure and molecular dynamics of the conformational changes involved in signal recognition and transduction, but also at a higher level of organization, the contribution of allosteric mechanisms to the modulation of brain functions.
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Affiliation(s)
- Jean-Pierre Changeux
- Collège de France, 75005 Paris and the Institut Pasteur, 75724 Paris Cedex 15, France.
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146
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Zocher M, Bippes CA, Zhang C, Müller DJ. Single-molecule force spectroscopy of G-protein-coupled receptors. Chem Soc Rev 2013; 42:7801-15. [PMID: 23799399 DOI: 10.1039/c3cs60085h] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The applicability of single-molecule force spectroscopy (SMFS) to characterize membrane proteins in vitro is developing rapidly and opening a wide range of fascinating possibilities to study how intra- and intermolecular interactions determine their structural stability and functional state. In particular, understanding how molecular interactions contribute to the functional state of G-protein-coupled receptors (GPCRs) is of importance because they mediate most of our physiological responses and act as therapeutic targets for a broad spectrum of diseases. In our review we focus on SMFS to characterize GPCRs embedded in their physiologically relevant membranes and exposed to physiologically relevant conditions. SMFS uses a molecularly sharp stylus to grasp the terminal end of a GPCR and to quickly unfold the receptor while recording interaction forces. The positional accuracy of SMFS localizes these interactions to structural segments of the GPCR whereas the sensitivity of SMFS enables their stabilizing interaction forces to be quantified. To further investigate the kinetic, energetic and mechanical properties of the structural segments, dynamic SMFS (DFS) probes their stability over a wide range of loading rates. These parameters provide insight into the energy landscape that provides information on the structural and functional properties of the GPCRs. Selected highlights exemplify the application of SMFS to characterize inter- and intramolecular interactions, which change the properties of GPCRs in relation to their functional state (e.g., ligand binding), diseased state (e.g., mutation), or lipid environment such as cholesterol.
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Affiliation(s)
- Michael Zocher
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland.
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147
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Kim TH, Chung KY, Manglik A, Hansen AL, Dror RO, Mildorf TJ, Shaw DE, Kobilka BK, Prosser RS. The role of ligands on the equilibria between functional states of a G protein-coupled receptor. J Am Chem Soc 2013; 135:9465-74. [PMID: 23721409 DOI: 10.1021/ja404305k] [Citation(s) in RCA: 137] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
G protein-coupled receptors exhibit a wide variety of signaling behaviors in response to different ligands. When a small label was incorporated on the cytosolic interface of transmembrane helix 6 (Cys-265), (19)F NMR spectra of the β2 adrenergic receptor (β2AR) reconstituted in maltose/neopentyl glycol detergent micelles revealed two distinct inactive states, an activation intermediate state en route to activation, and, in the presence of a G protein mimic, a predominant active state. Analysis of the spectra as a function of temperature revealed that for all ligands, the activation intermediate is entropically favored and enthalpically disfavored. β2AR enthalpy changes toward activation are notably lower than those observed with rhodopsin, a likely consequence of basal activity and the fact that the ionic lock and other interactions stabilizing the inactive state of β2AR are weaker. Positive entropy changes toward activation likely reflect greater mobility (configurational entropy) in the cytoplasmic domain, as confirmed through an order parameter analysis. Ligands greatly influence the overall changes in enthalpy and entropy of the system and the corresponding changes in population and amplitude of motion of given states, suggesting a complex landscape of states and substates.
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Affiliation(s)
- Tae Hun Kim
- Department of Chemistry, University of Toronto, UTM, 3359 Mississauga Road North, Mississauga, Ontario, Canada L5L 1C6
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148
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Maeda S, Schertler GFX. Production of GPCR and GPCR complexes for structure determination. Curr Opin Struct Biol 2013; 23:381-92. [PMID: 23707225 DOI: 10.1016/j.sbi.2013.04.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 04/11/2013] [Accepted: 04/11/2013] [Indexed: 01/12/2023]
Abstract
Since the first high-resolution structure of the beta 2 adrenergic receptor (b2AR) in 2007, we have seen a growing number of G-protein-coupled receptor (GPCR) structures coming to the repertory, providing a significant progress in our understanding of the structural basis of their function. This has been achieved by the interdisciplinary collaborative work between scientists with various expertise and the development of new methodologies as well as combining and optimizing existing techniques.
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Affiliation(s)
- Shoji Maeda
- Laboratory of Biomolecular Research, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
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149
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Kobilka B. The structural basis of G-protein-coupled receptor signaling (Nobel Lecture). Angew Chem Int Ed Engl 2013; 52:6380-8. [PMID: 23650120 DOI: 10.1002/anie.201302116] [Citation(s) in RCA: 137] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Indexed: 01/14/2023]
Affiliation(s)
- Brian Kobilka
- Stanford University School of Medicine, Department of Molecular and Cellular Physiology, 279 Campus Drive, Stanford, CA 94305, USA
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150
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Kobilka B. Die strukturelle Grundlage der Signaltransduktion mit G-Protein-gekoppelten Rezeptoren (Nobel-Aufsatz). Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201302116] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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