1
|
Yaduvanshi S, Kumar V. Fungal alkaloid malbrancheamide reorients the lipid binding domain of GRK5. J Biomol Struct Dyn 2024:1-12. [PMID: 38661007 DOI: 10.1080/07391102.2024.2333987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 03/16/2024] [Indexed: 04/26/2024]
Abstract
G protein-coupled receptors (GPCRs) are the largest group of receptors involved in various types of signaling. GPCR signaling is regulated via receptor phosphorylation by G protein-coupled receptor kinases 5 (GRK5). Calmodulin (CaM), a universal Ca2+ sensor, inhibits receptor phosphorylation by binding to GRK5. However, the inhibitor malbrancheamide (MBC), which binds at CaM C-lobe, allows for receptor phosphorylation. To understand the phosphorylation mechanism by GRK5, we carried out a MD simulation of the CaM/GRK5 complex in the presence and absence of the MBC inhibitor. The lipid binding domain (LBD) of GRK5 adopted different positions in the presence and absence of inhibitor. Furthermore, the inhibitor MBC restricted the movement of the N-lobe tether (NLT) loop, probably blocking the autophosphorylation of GRK5.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Shivani Yaduvanshi
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University, Noida, Uttar Pradesh, India
| | - Veerendra Kumar
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University, Noida, Uttar Pradesh, India
| |
Collapse
|
2
|
Amisaki T. Multilevel superposition for deciphering the conformational variability of protein ensembles. Brief Bioinform 2024; 25:bbae137. [PMID: 38557679 PMCID: PMC10983786 DOI: 10.1093/bib/bbae137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 02/14/2024] [Accepted: 03/10/2024] [Indexed: 04/04/2024] Open
Abstract
The dynamics and variability of protein conformations are directly linked to their functions. Many comparative studies of X-ray protein structures have been conducted to elucidate the relevant conformational changes, dynamics and heterogeneity. The rapid increase in the number of experimentally determined structures has made comparison an effective tool for investigating protein structures. For example, it is now possible to compare structural ensembles formed by enzyme species, variants or the type of ligands bound to them. In this study, the author developed a multilevel model for estimating two covariance matrices that represent inter- and intra-ensemble variability in the Cartesian coordinate space. Principal component analysis using the two estimated covariance matrices identified the inter-/intra-enzyme variabilities, which seemed to be important for the enzyme functions, with the illustrative examples of cytochrome P450 family 2 enzymes and class A $\beta$-lactamases. In P450, in which each enzyme has its own active site of a distinct size, an active-site motion shared universally between the enzymes was captured as the first principal mode of the intra-enzyme covariance matrix. In this case, the method was useful for understanding the conformational variability after adjusting for the differences between enzyme sizes. The developed method is advantageous in small ensemble-size problems and hence promising for use in comparative studies on experimentally determined structures where ensemble sizes are smaller than those generated, for example, by molecular dynamics simulations.
Collapse
Affiliation(s)
- Takashi Amisaki
- Department of Biological Regulation, Faculty of Medicine, Tottori University, Yonago, Tottori 683-8503, Japan
| |
Collapse
|
3
|
Miller WE, O'Connor CM. CMV-encoded GPCRs in infection, disease, and pathogenesis. Adv Virus Res 2024; 118:1-75. [PMID: 38461029 DOI: 10.1016/bs.aivir.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2024]
Abstract
G protein coupled receptors (GPCRs) are seven-transmembrane domain proteins that modulate cellular processes in response to external stimuli. These receptors represent the largest family of membrane proteins, and in mammals, their signaling regulates important physiological functions, such as vision, taste, and olfaction. Many organisms, including yeast, slime molds, and viruses encode GPCRs. Cytomegaloviruses (CMVs) are large, betaherpesviruses, that encode viral GPCRs (vGPCRs). Human CMV (HCMV) encodes four vGPCRs, including UL33, UL78, US27, and US28. Each of these vGPCRs, as well as their rodent and primate orthologues, have been investigated for their contributions to viral infection and disease. Herein, we discuss how the CMV vGPCRs function during lytic and latent infection, as well as our understanding of how they impact viral pathogenesis.
Collapse
Affiliation(s)
- William E Miller
- Department of Molecular and Cellular Bioscience, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Christine M O'Connor
- Infection Biology, Sheikha Fatima bint Mubarak Global Center for Pathogen and Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States; Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland Clinic, Cleveland, OH, United States; Case Comprehensive Cancer Center, Cleveland, OH, United States.
| |
Collapse
|
4
|
Chen Q, Tesmer JJG. G protein-coupled receptor interactions with arrestins and GPCR kinases: the unresolved issue of signal bias. J Biol Chem 2022; 298:102279. [PMID: 35863432 PMCID: PMC9418498 DOI: 10.1016/j.jbc.2022.102279] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 07/05/2022] [Accepted: 07/08/2022] [Indexed: 12/25/2022] Open
Abstract
G protein–coupled receptor (GPCR) kinases (GRKs) and arrestins interact with agonist-bound GPCRs to promote receptor desensitization and downregulation. They also trigger signaling cascades distinct from those of heterotrimeric G proteins. Biased agonists for GPCRs that favor either heterotrimeric G protein or GRK/arrestin signaling are of profound pharmacological interest because they could usher in a new generation of drugs with greatly reduced side effects. One mechanism by which biased agonism might occur is by stabilizing receptor conformations that preferentially bind to GRKs and/or arrestins. In this review, we explore this idea by comparing structures of GPCRs bound to heterotrimeric G proteins with those of the same GPCRs in complex with arrestins and GRKs. The arrestin and GRK complexes all exhibit high conformational heterogeneity, which is likely a consequence of their unusual ability to adapt and bind to hundreds of different GPCRs. This dynamic behavior, along with the experimental tactics required to stabilize GPCR complexes for biophysical analysis, confounds these comparisons, but some possible molecular mechanisms of bias are beginning to emerge. We also examine if and how the recent structures advance our understanding of how arrestins parse the “phosphorylation barcodes” installed in the intracellular loops and tails of GPCRs by GRKs. In the future, structural analyses of arrestins in complex with intact receptors that have well-defined native phosphorylation barcodes, such as those installed by the two nonvisual subfamilies of GRKs, will be particularly illuminating.
Collapse
Affiliation(s)
- Qiuyan Chen
- Departments of Biological Sciences and of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - John J G Tesmer
- Departments of Biological Sciences and of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA.
| |
Collapse
|
5
|
Structures of rhodopsin in complex with G-protein-coupled receptor kinase 1. Nature 2021; 595:600-605. [PMID: 34262173 PMCID: PMC8607881 DOI: 10.1038/s41586-021-03721-x] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 06/11/2021] [Indexed: 02/06/2023]
Abstract
G-protein-coupled receptor (GPCR) kinases (GRKs) selectively phosphorylate activated GPCRs, thereby priming them for desensitization1. Although it is unclear how GRKs recognize these receptors2-4, a conserved region at the GRK N terminus is essential for this process5-8. Here we report a series of cryo-electron microscopy single-particle reconstructions of light-activated rhodopsin (Rho*) bound to rhodopsin kinase (GRK1), wherein the N terminus of GRK1 forms a helix that docks into the open cytoplasmic cleft of Rho*. The helix also packs against the GRK1 kinase domain and stabilizes it in an active configuration. The complex is further stabilized by electrostatic interactions between basic residues that are conserved in most GPCRs and acidic residues that are conserved in GRKs. We did not observe any density for the regulator of G-protein signalling homology domain of GRK1 or the C terminus of rhodopsin. Crosslinking with mass spectrometry analysis confirmed these results and revealed dynamic behaviour in receptor-bound GRK1 that would allow the phosphorylation of multiple sites in the receptor tail. We have identified GRK1 residues whose mutation augments kinase activity and crosslinking with Rho*, as well as residues that are involved in activation by acidic phospholipids. From these data, we present a general model for how a small family of protein kinases can recognize and be activated by hundreds of different GPCRs.
Collapse
|
6
|
The Open Question of How GPCRs Interact with GPCR Kinases (GRKs). Biomolecules 2021; 11:biom11030447. [PMID: 33802765 PMCID: PMC8002388 DOI: 10.3390/biom11030447] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/13/2021] [Accepted: 03/15/2021] [Indexed: 01/14/2023] Open
Abstract
G protein-coupled receptors (GPCRs), which regulate a vast number of eukaryotic processes, are desensitized by various mechanisms but, most importantly, by the GPCR kinases (GRKs). Ever since GRKs were first identified, investigators have sought to determine which structural features of GRKs are used to select for the agonist-bound states of GPCRs and how this binding event in turn enhances GRK catalytic activity. Despite a wealth of molecular information from high-resolution crystal structures of GRKs, the mechanisms driving activation have remained elusive, in part because the GRK N-terminus and active site tether region, previously proposed to serve as a receptor docking site and to be key to kinase domain closure, are often disordered or adopt inconsistent conformations. However, two recent studies have implicated other regions of GRKs as being involved in direct interactions with active GPCRs. Atomic resolution structures of GPCR–GRK complexes would help refine these models but are, so far, lacking. Here, we assess three distinct models for how GRKs recognize activated GPCRs, discuss limitations in the approaches used to generate them, and then experimentally test a hypothetical GPCR interaction site in GRK2 suggested by the two newest models.
Collapse
|
7
|
Sulon SM, Benovic JL. Targeting G protein-coupled receptor kinases (GRKs) to G protein-coupled receptors. ACTA ACUST UNITED AC 2021; 16:56-65. [PMID: 33718657 DOI: 10.1016/j.coemr.2020.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
G protein-coupled receptors (GPCRs) interact with three protein families following agonist binding: heterotrimeric G proteins, G protein-coupled receptor kinases (GRKs) and arrestins. GRK-mediated phosphorylation of GPCRs promotes arrestin binding to uncouple the receptor from G protein, a process called desensitization, and for many GPCRs, arrestin binding also promotes receptor endocytosis and intracellular signaling. Thus, GRKs play a central role in modulating GPCR signaling and localization. Here we review recent advances in this field which include additional insight into how GRKs target GPCRs and bias signaling, and the development of specific inhibitors to dissect GRK function in model systems.
Collapse
Affiliation(s)
- Sarah M Sulon
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Jeffrey L Benovic
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| |
Collapse
|
8
|
Stabilization of the Hinge Region of Human E-selectin Enhances Binding Affinity to Ligands Under Force. Cell Mol Bioeng 2021; 14:65-74. [PMID: 33633813 PMCID: PMC7878631 DOI: 10.1007/s12195-021-00666-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 01/04/2021] [Indexed: 12/30/2022] Open
Abstract
Introduction E-selectin is a member of the selectin family of cell adhesion molecules expressed on the plasma membrane of inflamed endothelium and facilitates initial leukocyte tethering and subsequent cell rolling during the early stages of the inflammatory response via binding to glycoproteins expressing sialyl LewisX and sialyl LewisA (sLeX/A). Existing crystal structures of the extracellular lectin/EGF-like domain of E-selectin complexed with sLeX have revealed that E-selectin can exist in two conformation states, a low affinity (bent) conformation, and a high affinity (extended) conformation. The differentiating characteristic of the two conformations is the interdomain angle between the lectin and the EGF-like domain. Methods Using molecular dynamics (MD) simulations we observed that in the absence of tensile force E-selectin undergoes spontaneous switching between the two conformational states at equilibrium. A single amino acid substitution at residue 2 (serine to tyrosine) on the lectin domain favors the extended conformation. Results Steered molecular dynamics (SMD) simulations of E-selectin and PSGL-1 in conjunction with experimental cell adhesion assays show a longer binding lifetime of E-selectin (S2Y) to PSGL-1 compared to wildtype protein. Conclusions The findings in this study advance our understanding into how the structural makeup of E-selectin allosterically influences its adhesive dynamics.
Collapse
|
9
|
Komolov KE, Sulon SM, Bhardwaj A, van Keulen SC, Duc NM, Laurinavichyute DK, Lou HJ, Turk BE, Chung KY, Dror RO, Benovic JL. Structure of a GRK5-Calmodulin Complex Reveals Molecular Mechanism of GRK Activation and Substrate Targeting. Mol Cell 2020; 81:323-339.e11. [PMID: 33321095 DOI: 10.1016/j.molcel.2020.11.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 09/15/2020] [Accepted: 11/12/2020] [Indexed: 10/22/2022]
Abstract
The phosphorylation of G protein-coupled receptors (GPCRs) by GPCR kinases (GRKs) facilitates arrestin binding and receptor desensitization. Although this process can be regulated by Ca2+-binding proteins such as calmodulin (CaM) and recoverin, the molecular mechanisms are poorly understood. Here, we report structural, computational, and biochemical analysis of a CaM complex with GRK5, revealing how CaM shapes GRK5 response to calcium. The CaM N and C domains bind independently to two helical regions at the GRK5 N and C termini to inhibit GPCR phosphorylation, though only the C domain interaction disrupts GRK5 membrane association, thereby facilitating cytoplasmic translocation. The CaM N domain strongly activates GRK5 via ordering of the amphipathic αN-helix of GRK5 and allosteric disruption of kinase-RH domain interaction for phosphorylation of cytoplasmic GRK5 substrates. These results provide a framework for understanding how two functional effects, GRK5 activation and localization, can cooperate under control of CaM for selective substrate targeting by GRK5.
Collapse
Affiliation(s)
- Konstantin E Komolov
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Sarah M Sulon
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Anshul Bhardwaj
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Siri C van Keulen
- Department of Computer Science, Department of Molecular and Cellular Physiology, Department of Structural Biology, and Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Nguyen Minh Duc
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, South Korea; Division of Precision Medicine, Research Institute, National Cancer Center, Goyang, South Korea
| | - Daniela K Laurinavichyute
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Hua Jane Lou
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Benjamin E Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Ka Young Chung
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, South Korea
| | - Ron O Dror
- Department of Computer Science, Department of Molecular and Cellular Physiology, Department of Structural Biology, and Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA; Biophysics Program, Stanford University, Stanford, CA 94305, USA
| | - Jeffrey L Benovic
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA.
| |
Collapse
|
10
|
Yao XQ, Hamelberg D. Detecting Functional Dynamics in Proteins with Comparative Perturbed-Ensembles Analysis. Acc Chem Res 2019; 52:3455-3464. [PMID: 31793290 DOI: 10.1021/acs.accounts.9b00485] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Recent advances have made all-atom molecular dynamics (MD) a powerful tool to sample the conformational energy landscape. There are still however three major challenges in the application of MD to biological systems: accuracy of force field, time scale, and the analysis of simulation trajectories. Significant progress in addressing the first two challenges has been made and extensively reviewed previously. This Account focuses on strategies of analyzing simulation data of biomolecules that also covers ways to properly design simulations and validate simulation results. In particular, we examine an approach named comparative perturbed-ensembles analysis, which we developed to efficiently detect dynamics in protein MD simulations that can be linked to biological functions. In our recent studies, we implemented this approach to understand allosteric regulations in several disease-associated human proteins. The central task of a comparative perturbed-ensembles analysis is to compare two or more conformational ensembles of a system generated by MD simulations under distinct perturbation conditions. Perturbations can be different sequence variations, ligand-binding conditions, and other physical/chemical modifications of the system. Each simulation is long enough (e.g., microsecond-long) to ensure sufficient sampling of the local substate. Then, sophisticated bioinformatic and statistical tools are applied to extract function-related information from the simulation data, including principal component analysis, residue-residue contact analysis, difference contact network analysis (dCNA) based on the graph theory, and statistical analysis of side-chain conformations. Computational findings are further validated with experimental data. By comparing distinct conformational ensembles, functional micro- to millisecond dynamics can be inferred. In contrast, such a time scale is difficult to reach in a single simulation; even when reached for a single condition of a system, it is elusive as to what dynamical motions are related to functions without, for example, comparing free and substrate-bound proteins at the minimum. We illustrate our approach with three examples. First, we discuss using the approach to identify allosteric pathways in cyclophilin A (CypA), a member of a ubiquitous class of peptidyl-prolyl cis-trans isomerase enzymes. By comparing side-chain torsion-angle distributions of CypA in wild-type and mutant forms, we identified three pathways: two are consistent with recent nuclear magnetic resonance experiments, whereas the third is a novel pathway. Second, we show how the approach enables a dynamical-evolution analysis of the human cyclophilin family. In the analysis, both conserved and divergent conformational dynamics across three cyclophilin isoforms (CypA, CypD, and CypE) were summarized. The conserved dynamics led to the discovery of allosteric networks resembling those found in CypA. A residue wise determinant underlying the unique dynamics in CypD was also detected and validated with additional mutational MD simulations. In the third example, we applied the approach to elucidate a peptide sequence-dependent allosteric mechanism in human Pin 1, a phosphorylation-dependent peptidyl-prolyl isomerase. We finally present our outlook of future directions. Especially, we envisage how the approach could help open a new avenue in drug discovery.
Collapse
Affiliation(s)
- Xin-Qiu Yao
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Donald Hamelberg
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302-3965, United States
| |
Collapse
|
11
|
Rowlands RA, Cato MC, Waldschmidt HV, Bouley RA, Chen Q, Avramova L, Larsen SD, Tesmer JJG, White AD. Structure-Based Design of Selective, Covalent G Protein-Coupled Receptor Kinase 5 Inhibitors. ACS Med Chem Lett 2019; 10:1628-1634. [PMID: 31857838 DOI: 10.1021/acsmedchemlett.9b00365] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 11/12/2019] [Indexed: 12/12/2022] Open
Abstract
The ability of G protein-coupled receptor (GPCR) kinases (GRKs) to regulate desensitization of GPCRs has made GRK2 and GRK5 attractive targets for treating heart failure and other diseases such as cancer. Although advances have been made toward developing inhibitors that are selective for GRK2, there have been far fewer reports of GRK5 selective compounds. Herein, we describe the development of GRK5 subfamily selective inhibitors, 5 and 16d that covalently interact with a nonconserved cysteine (Cys474) unique to this subfamily. Compounds 5 and 16d feature a highly amenable pyrrolopyrimidine scaffold that affords high nanomolar to low micromolar activity that can be easily modified with Michael acceptors with various reactivities and geometries. Our work thereby establishes a new pathway toward further development of subfamily selective GRK inhibitors and establishes Cys474 as a new and useful covalent handle in GRK5 drug discovery.
Collapse
Affiliation(s)
- Rachel A. Rowlands
- University of Michigan, Vahlteich Medicinal Chemistry Core, College of Pharmacy, 428 Church Street, Ann Arbor, Michigan 48109, United States
| | - M. Claire Cato
- University of Michigan, Life Sciences Institute, Departments of Pharmacology and Biological Chemistry, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States
| | - Helen V. Waldschmidt
- University of Michigan, Vahlteich Medicinal Chemistry Core, College of Pharmacy, 428 Church Street, Ann Arbor, Michigan 48109, United States
| | - Renee A. Bouley
- University of Michigan, Life Sciences Institute, Departments of Pharmacology and Biological Chemistry, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States
| | - Qiuyan Chen
- Purdue University, Departments of Biological Sciences and Medicinal Chemistry and Molecular Pharmacology, 915 W State Street, West Lafayette, Indiana 47907, United States
| | - Larisa Avramova
- Purdue University, Departments of Biological Sciences and Medicinal Chemistry and Molecular Pharmacology, 915 W State Street, West Lafayette, Indiana 47907, United States
| | - Scott D. Larsen
- University of Michigan, Vahlteich Medicinal Chemistry Core, College of Pharmacy, 428 Church Street, Ann Arbor, Michigan 48109, United States
| | - John J. G. Tesmer
- Purdue University, Departments of Biological Sciences and Medicinal Chemistry and Molecular Pharmacology, 915 W State Street, West Lafayette, Indiana 47907, United States
| | - Andrew D. White
- University of Michigan, Vahlteich Medicinal Chemistry Core, College of Pharmacy, 428 Church Street, Ann Arbor, Michigan 48109, United States
| |
Collapse
|
12
|
Beyett TS, Chen Q, Labudde EJ, Krampen J, Sharma PV, Tesmer JJG. Characterization of a hyperphosphorylated variant of G protein-coupled receptor kinase 5 expressed in E. coli. Protein Expr Purif 2019; 168:105547. [PMID: 31786308 DOI: 10.1016/j.pep.2019.105547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 11/21/2019] [Accepted: 11/25/2019] [Indexed: 11/27/2022]
Abstract
G protein-coupled receptors (GPCRs) are the largest family of cell-surface receptors in humans and regulate numerous physiological processes through the activation of heterotrimeric G proteins. GPCR kinases (GRKs) selectively phosphorylate active GPCRs, which promotes arrestin binding, receptor internalization, and initiation of alternative signaling pathways. GRK5 is a representative member of one of three GRK subfamilies that does not need post-translational lipidation or other binding partners to exhibit full activity against GPCRs, rendering it a useful tool for biophysical studies directed at characterizing GRK function. However, recombinant expression of GRK5 has thus far been limited to insect and mammalian systems. Here, we describe the expression of functional GRK5 in E. coli and its purification and biochemical characterization. Bacterially expressed GRK5 is hyperphosphorylated, primarily in regions known to be flexible from prior crystal structures, which slightly decreases its catalytic activity toward receptor substrates. Mutation of a single phosphorylation site, Thr10, restores kinetic parameters to those of GRK5 purified from insect cells. Consequently, bacterial expression will allow for production of GRK5 at a reduced cost and faster pace and would facilitate production of isotopically labeled kinase for NMR studies or for the incorporation of unnatural amino acids.
Collapse
Affiliation(s)
- Tyler S Beyett
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA; Life Sciences Institute, University of Michigan, USA
| | - Qiuyan Chen
- Departments of Biological Sciences and of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | | | - Joseph Krampen
- Departments of Biological Sciences and of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | | | - John J G Tesmer
- Departments of Biological Sciences and of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA.
| |
Collapse
|
13
|
Keretsu S, Bhujbal SP, Joo Cho S. Computational study of paroxetine-like inhibitors reveals new molecular insight to inhibit GRK2 with selectivity over ROCK1. Sci Rep 2019; 9:13053. [PMID: 31506468 PMCID: PMC6736929 DOI: 10.1038/s41598-019-48949-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 07/19/2019] [Indexed: 01/08/2023] Open
Abstract
The G-protein coupled receptor kinase 2 (GRK2) regulates the desensitization of beta-adrenergic receptors (β-AR), and its overexpression has been implicated in heart failure. Hence, the inhibition of GRK2 is considered to be an important drug target for the treatment of heart failure. Due to the high sequence similarity of GRK2 with the A, G, and C family (AGC family) of kinases, the inhibition of GRK2 also leads to the inhibition of AGC kinases such as Rho-associated coiled-coil kinase 1 (ROCK1). Therefore, unraveling the mechanisms to selectively inhibit GRK2 poses an important challenge. We have performed molecular docking, three dimensional quantitative structure activity relationship (3D-QSAR), molecular dynamics (MD) simulation, and free energy calculations techniques on a series of 53 paroxetine-like compounds to understand the structural properties desirable for enhancing the inhibitory activity for GRK2 with selectivity over ROCK1. The formation of stable hydrogen bond interactions with the residues Phe202 and Lys220 of GRK2 seems to be important for selective inhibition of GRK2. Electropositive substituents at the piperidine ring and electronegative substituents near the amide linker between the benzene ring and pyrazole ring showed a higher inhibitory preference for GRK2 over ROCK1. This study may be used in designing more potent and selective GRK2 inhibitors for therapeutic intervention of heart failure.
Collapse
Affiliation(s)
- Seketoulie Keretsu
- Department of Biomedical Sciences, College of Medicine, Chosun University, Gwangju, 501-759, Republic of Korea
| | - Swapnil P Bhujbal
- Department of Biomedical Sciences, College of Medicine, Chosun University, Gwangju, 501-759, Republic of Korea
| | - Seung Joo Cho
- Department of Biomedical Sciences, College of Medicine, Chosun University, Gwangju, 501-759, Republic of Korea. .,Department of Cellular Molecular Medicine, College of Medicine, Chosun University, Gwangju, 501-759, Republic of Korea.
| |
Collapse
|
14
|
Mahmod Al-Qattan MN, Mordi MN. Molecular Basis of Modulating Adenosine Receptors Activities. Curr Pharm Des 2019; 25:817-831. [DOI: 10.2174/1381612825666190304122624] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 02/26/2019] [Indexed: 01/04/2023]
Abstract
Modulating cellular processes through extracellular chemical stimuli is medicinally an attractive approach to control disease conditions. GPCRs are the most important group of transmembranal receptors that produce different patterns of activations using intracellular mediators (such as G-proteins and Beta-arrestins). Adenosine receptors (ARs) belong to GPCR class and are divided into A1AR, A2AAR, A2BAR and A3AR. ARs control different physiological activities thus considered valuable target to control neural, heart, inflammatory and other metabolic disorders. Targeting ARs using small molecules essentially works by binding orthosteric and/or allosteric sites of the receptors. Although targeting orthosteric site is considered typical to modulate receptor activity, allosteric sites provide better subtype selectivity, saturable modulation of activity and variable activation patterns. Each receptor exists in dynamical equilibrium between conformational ensembles. The equilibrium is affected by receptor interaction with other molecules. Changing the population of conformational ensembles of the receptor is the method by which orthosteric, allosteric and other cellular components control receptor signaling. Herein, the interactions of ARs with orthosteric, allosteric ligands as well as intracellular mediators are described. A quinary interaction model for the receptor is proposed and energy wells for major conformational ensembles are retrieved.
Collapse
Affiliation(s)
| | - Mohd Nizam Mordi
- Centre For Drug Research, Universiti Sains Malaysia, 11800 Gelugor, Penang, Malaysia
| |
Collapse
|
15
|
Abstract
G protein-coupled receptors (GPCRs), which mediate processes as diverse as olfaction and maintenance of metabolic homeostasis, have become the single most effective class of therapeutic drug targets. As a result, understanding the molecular basis for their activity is of paramount importance. Recent technological advances have made GPCR structural biology increasingly tractable, offering views of these receptors in unprecedented atomic detail. Structural and biophysical data have shown that GPCRs function as complex allosteric machines, communicating ligand-binding events through conformational change. Changes in receptor conformation lead to activation of effector proteins, such as G proteins and arrestins, which are themselves conformational switches. Here, we review how structural biology has illuminated the agonist-induced cascade of conformational changes that culminate in a cellular response to GPCR activation.
Collapse
Affiliation(s)
- Sarah C Erlandson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA;
| | - Conor McMahon
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA;
| | - Andrew C Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA;
| |
Collapse
|
16
|
Pack TF, Orlen MI, Ray C, Peterson SM, Caron MG. The dopamine D2 receptor can directly recruit and activate GRK2 without G protein activation. J Biol Chem 2018; 293:6161-6171. [PMID: 29487132 DOI: 10.1074/jbc.ra117.001300] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 02/13/2018] [Indexed: 01/11/2023] Open
Abstract
The dopamine D2 receptor (D2R) is a G protein-coupled receptor (GPCR) that is critical for many central nervous system functions. The D2R carries out these functions by signaling through two transducers: G proteins and β-arrestins (βarrs). Selectively engaging either the G protein or βarr pathway may be a way to improve drugs targeting GPCRs. The current model of GPCR signal transduction posits a chain of events where G protein activation ultimately leads to βarr recruitment. GPCR kinases (GRKs), which are regulated by G proteins and whose kinase action facilitates βarr recruitment, bridge these pathways. Therefore, βarr recruitment appears to be intimately tied to G protein activation via GRKs. Here we sought to understand how GRK2 action at the D2R would be disrupted when G protein activation is eliminated and the effect of this on βarr recruitment. We used two recently developed biased D2R mutants that can preferentially interact either with G proteins or βarrs as well as a βarr-biased D2R ligand, UNC9994. With these functionally selective tools, we investigated the mechanism whereby the βarr-preferring D2R achieves βarr pathway activation in the complete absence of G protein activation. We describe how direct, G protein-independent recruitment of GRK2 drives interactions at the βarr-preferring D2R and also contributes to βarr recruitment at the WT D2R. Additionally, we found an additive interaction between the βarr-preferring D2R mutant and UNC9994. These results reveal that the D2R can directly recruit GRK2 without G protein activation and that this mechanism may have relevance to achieving βarr-biased signaling.
Collapse
Affiliation(s)
- Thomas F Pack
- From the Departments of Pharmacology and Cancer Biology.,Cell Biology
| | | | | | | | - Marc G Caron
- Cell Biology, .,Neurobiology, and.,Medicine, Duke University Medical Center, Duke University School of Medicine, Durham, North Carolina 27710
| |
Collapse
|
17
|
Bouley R, Waldschmidt HV, Cato MC, Cannavo A, Song J, Cheung JY, Yao XQ, Koch WJ, Larsen SD, Tesmer JJG. Structural Determinants Influencing the Potency and Selectivity of Indazole-Paroxetine Hybrid G Protein-Coupled Receptor Kinase 2 Inhibitors. Mol Pharmacol 2017; 92:707-717. [PMID: 29070696 DOI: 10.1124/mol.117.110130] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 10/11/2017] [Indexed: 11/22/2022] Open
Abstract
G protein-coupled receptor kinases (GRKs) phosphorylate activated receptors to promote arrestin binding, decoupling from heterotrimeric G proteins, and internalization. GRK2 and GRK5 are overexpressed in the failing heart and thus have become therapeutic targets. Previously, we discovered two classes of GRK2-selective inhibitors, one stemming from GSK180736A, a Rho-associated coiled-coil containing kinase 1 (ROCK1) inhibitor, the other from paroxetine, a selective serotonin-reuptake inhibitor. These two classes of compounds bind to the GRK2 active site in a similar configuration but contain different hinge-binding "warheads": indazole and benzodioxole, respectively. We surmised from our prior studies that an indazole would be the stronger hinge binder and would impart increased potency when substituted for benzodioxole in paroxetine derivatives. To test this hypothesis, we synthesized a series of hybrid compounds that allowed us to compare the effects of inhibitors that differ only in the identity of the warhead. The indazole-paroxetine analogs were indeed more potent than their respective benzodioxole derivatives but lost selectivity. To investigate how these two warheads dictate selectivity, we determined the crystal structures of three of the indazole hybrid compounds (CCG224061, CCG257284, and CCG258748) in complex with GRK2-Gβγ Comparison of these structures with those of analogous benzodioxole-containing complexes confirmed that the indazole-paroxetine hybrids form stronger interactions with the hinge of the kinase but also stabilize a distinct conformation of the kinase domain of GRK2 compared with previous complexes with paroxetine analogs. This conformation is analogous to one that can be assumed by GRK5, at least partially explaining the loss in selectivity.
Collapse
Affiliation(s)
- Renee Bouley
- Life Sciences Institute (R.B., H.V.W., M.C.C., J.J.G.T.), Departments of Medicinal Chemistry (H.V.W., S.D.L., J.J.G.T.), Pharmacology (R.B., J.J.G.T.), Biological Chemistry (M.C.C., J.J.G.T.), and Vahlteich Medicinal Chemistry Core, College of Pharmacy (H.V.W., S.D.L.), University of Michigan, Ann Arbor, Michigan; Department of Chemistry, Georgia State University, Atlanta, Georgia (X.-Q.Y.); Center for Translational Medicine, Temple University, Philadelphia, Pennsylvania (A.C., J.S., J.Y.C, W.J.K.); and Department of Biological Sciences, Purdue University, West Lafayette Indiana (J.J.G.T.)
| | - Helen V Waldschmidt
- Life Sciences Institute (R.B., H.V.W., M.C.C., J.J.G.T.), Departments of Medicinal Chemistry (H.V.W., S.D.L., J.J.G.T.), Pharmacology (R.B., J.J.G.T.), Biological Chemistry (M.C.C., J.J.G.T.), and Vahlteich Medicinal Chemistry Core, College of Pharmacy (H.V.W., S.D.L.), University of Michigan, Ann Arbor, Michigan; Department of Chemistry, Georgia State University, Atlanta, Georgia (X.-Q.Y.); Center for Translational Medicine, Temple University, Philadelphia, Pennsylvania (A.C., J.S., J.Y.C, W.J.K.); and Department of Biological Sciences, Purdue University, West Lafayette Indiana (J.J.G.T.)
| | - M Claire Cato
- Life Sciences Institute (R.B., H.V.W., M.C.C., J.J.G.T.), Departments of Medicinal Chemistry (H.V.W., S.D.L., J.J.G.T.), Pharmacology (R.B., J.J.G.T.), Biological Chemistry (M.C.C., J.J.G.T.), and Vahlteich Medicinal Chemistry Core, College of Pharmacy (H.V.W., S.D.L.), University of Michigan, Ann Arbor, Michigan; Department of Chemistry, Georgia State University, Atlanta, Georgia (X.-Q.Y.); Center for Translational Medicine, Temple University, Philadelphia, Pennsylvania (A.C., J.S., J.Y.C, W.J.K.); and Department of Biological Sciences, Purdue University, West Lafayette Indiana (J.J.G.T.)
| | - Alessandro Cannavo
- Life Sciences Institute (R.B., H.V.W., M.C.C., J.J.G.T.), Departments of Medicinal Chemistry (H.V.W., S.D.L., J.J.G.T.), Pharmacology (R.B., J.J.G.T.), Biological Chemistry (M.C.C., J.J.G.T.), and Vahlteich Medicinal Chemistry Core, College of Pharmacy (H.V.W., S.D.L.), University of Michigan, Ann Arbor, Michigan; Department of Chemistry, Georgia State University, Atlanta, Georgia (X.-Q.Y.); Center for Translational Medicine, Temple University, Philadelphia, Pennsylvania (A.C., J.S., J.Y.C, W.J.K.); and Department of Biological Sciences, Purdue University, West Lafayette Indiana (J.J.G.T.)
| | - Jianliang Song
- Life Sciences Institute (R.B., H.V.W., M.C.C., J.J.G.T.), Departments of Medicinal Chemistry (H.V.W., S.D.L., J.J.G.T.), Pharmacology (R.B., J.J.G.T.), Biological Chemistry (M.C.C., J.J.G.T.), and Vahlteich Medicinal Chemistry Core, College of Pharmacy (H.V.W., S.D.L.), University of Michigan, Ann Arbor, Michigan; Department of Chemistry, Georgia State University, Atlanta, Georgia (X.-Q.Y.); Center for Translational Medicine, Temple University, Philadelphia, Pennsylvania (A.C., J.S., J.Y.C, W.J.K.); and Department of Biological Sciences, Purdue University, West Lafayette Indiana (J.J.G.T.)
| | - Joseph Y Cheung
- Life Sciences Institute (R.B., H.V.W., M.C.C., J.J.G.T.), Departments of Medicinal Chemistry (H.V.W., S.D.L., J.J.G.T.), Pharmacology (R.B., J.J.G.T.), Biological Chemistry (M.C.C., J.J.G.T.), and Vahlteich Medicinal Chemistry Core, College of Pharmacy (H.V.W., S.D.L.), University of Michigan, Ann Arbor, Michigan; Department of Chemistry, Georgia State University, Atlanta, Georgia (X.-Q.Y.); Center for Translational Medicine, Temple University, Philadelphia, Pennsylvania (A.C., J.S., J.Y.C, W.J.K.); and Department of Biological Sciences, Purdue University, West Lafayette Indiana (J.J.G.T.)
| | - Xin-Qiu Yao
- Life Sciences Institute (R.B., H.V.W., M.C.C., J.J.G.T.), Departments of Medicinal Chemistry (H.V.W., S.D.L., J.J.G.T.), Pharmacology (R.B., J.J.G.T.), Biological Chemistry (M.C.C., J.J.G.T.), and Vahlteich Medicinal Chemistry Core, College of Pharmacy (H.V.W., S.D.L.), University of Michigan, Ann Arbor, Michigan; Department of Chemistry, Georgia State University, Atlanta, Georgia (X.-Q.Y.); Center for Translational Medicine, Temple University, Philadelphia, Pennsylvania (A.C., J.S., J.Y.C, W.J.K.); and Department of Biological Sciences, Purdue University, West Lafayette Indiana (J.J.G.T.)
| | - Walter J Koch
- Life Sciences Institute (R.B., H.V.W., M.C.C., J.J.G.T.), Departments of Medicinal Chemistry (H.V.W., S.D.L., J.J.G.T.), Pharmacology (R.B., J.J.G.T.), Biological Chemistry (M.C.C., J.J.G.T.), and Vahlteich Medicinal Chemistry Core, College of Pharmacy (H.V.W., S.D.L.), University of Michigan, Ann Arbor, Michigan; Department of Chemistry, Georgia State University, Atlanta, Georgia (X.-Q.Y.); Center for Translational Medicine, Temple University, Philadelphia, Pennsylvania (A.C., J.S., J.Y.C, W.J.K.); and Department of Biological Sciences, Purdue University, West Lafayette Indiana (J.J.G.T.)
| | - Scott D Larsen
- Life Sciences Institute (R.B., H.V.W., M.C.C., J.J.G.T.), Departments of Medicinal Chemistry (H.V.W., S.D.L., J.J.G.T.), Pharmacology (R.B., J.J.G.T.), Biological Chemistry (M.C.C., J.J.G.T.), and Vahlteich Medicinal Chemistry Core, College of Pharmacy (H.V.W., S.D.L.), University of Michigan, Ann Arbor, Michigan; Department of Chemistry, Georgia State University, Atlanta, Georgia (X.-Q.Y.); Center for Translational Medicine, Temple University, Philadelphia, Pennsylvania (A.C., J.S., J.Y.C, W.J.K.); and Department of Biological Sciences, Purdue University, West Lafayette Indiana (J.J.G.T.)
| | - John J G Tesmer
- Life Sciences Institute (R.B., H.V.W., M.C.C., J.J.G.T.), Departments of Medicinal Chemistry (H.V.W., S.D.L., J.J.G.T.), Pharmacology (R.B., J.J.G.T.), Biological Chemistry (M.C.C., J.J.G.T.), and Vahlteich Medicinal Chemistry Core, College of Pharmacy (H.V.W., S.D.L.), University of Michigan, Ann Arbor, Michigan; Department of Chemistry, Georgia State University, Atlanta, Georgia (X.-Q.Y.); Center for Translational Medicine, Temple University, Philadelphia, Pennsylvania (A.C., J.S., J.Y.C, W.J.K.); and Department of Biological Sciences, Purdue University, West Lafayette Indiana (J.J.G.T.)
| |
Collapse
|