1
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Nguyen KDQ, Vigers M, Sefah E, Seppälä S, Hoover JP, Schonenbach NS, Mertz B, O'Malley MA, Han S. Homo-oligomerization of the human adenosine A 2A receptor is driven by the intrinsically disordered C-terminus. eLife 2021; 10:e66662. [PMID: 34269678 PMCID: PMC8328514 DOI: 10.7554/elife.66662] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 07/15/2021] [Indexed: 11/27/2022] Open
Abstract
G protein-coupled receptors (GPCRs) have long been shown to exist as oligomers with functional properties distinct from those of the monomeric counterparts, but the driving factors of oligomerization remain relatively unexplored. Herein, we focus on the human adenosine A2A receptor (A2AR), a model GPCR that forms oligomers both in vitro and in vivo. Combining experimental and computational approaches, we discover that the intrinsically disordered C-terminus of A2AR drives receptor homo-oligomerization. The formation of A2AR oligomers declines progressively with the shortening of the C-terminus. Multiple interaction types are responsible for A2AR oligomerization, including disulfide linkages, hydrogen bonds, electrostatic interactions, and hydrophobic interactions. These interactions are enhanced by depletion interactions, giving rise to a tunable network of bonds that allow A2AR oligomers to adopt multiple interfaces. This study uncovers the disordered C-terminus as a prominent driving factor for the oligomerization of a GPCR, offering important insight into the effect of C-terminus modification on receptor oligomerization of A2AR and other GPCRs reconstituted in vitro for biophysical studies.
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Affiliation(s)
- Khanh Dinh Quoc Nguyen
- Department of Chemistry and Biochemistry, University of California, Santa BarbaraSanta BarbaraUnited States
| | - Michael Vigers
- Department of Chemical Engineering, University of California, Santa BarbaraSanta BarbaraUnited States
| | - Eric Sefah
- C. Eugene Bennett Department of Chemistry, West Virginia UniversityMorgantownUnited States
| | - Susanna Seppälä
- Department of Chemical Engineering, University of California, Santa BarbaraSanta BarbaraUnited States
| | - Jennifer Paige Hoover
- Department of Chemistry and Biochemistry, University of California, Santa BarbaraSanta BarbaraUnited States
| | - Nicole Star Schonenbach
- Department of Chemical Engineering, University of California, Santa BarbaraSanta BarbaraUnited States
| | - Blake Mertz
- C. Eugene Bennett Department of Chemistry, West Virginia UniversityMorgantownUnited States
| | - Michelle Ann O'Malley
- Department of Chemical Engineering, University of California, Santa BarbaraSanta BarbaraUnited States
| | - Songi Han
- Department of Chemistry and Biochemistry, University of California, Santa BarbaraSanta BarbaraUnited States
- Department of Chemical Engineering, University of California, Santa BarbaraSanta BarbaraUnited States
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2
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Singh G, Inoue A, Gutkind JS, Russell RB, Raimondi F. PRECOG: PREdicting COupling probabilities of G-protein coupled receptors. Nucleic Acids Res 2020; 47:W395-W401. [PMID: 31143927 PMCID: PMC6602504 DOI: 10.1093/nar/gkz392] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Revised: 04/13/2019] [Accepted: 05/01/2019] [Indexed: 01/08/2023] Open
Abstract
G-protein coupled receptors (GPCRs) control multiple physiological states by transducing a multitude of extracellular stimuli into the cell via coupling to intra-cellular heterotrimeric G-proteins. Deciphering which G-proteins couple to each of the hundreds of GPCRs present in a typical eukaryotic organism is therefore critical to understand signalling. Here, we present PRECOG (precog.russelllab.org): a web-server for predicting GPCR coupling, which allows users to: (i) predict coupling probabilities for GPCRs to individual G-proteins instead of subfamilies; (ii) visually inspect the protein sequence and structural features that are responsible for a particular coupling; (iii) suggest mutations to rationally design artificial GPCRs with new coupling properties based on predetermined coupling features.
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Affiliation(s)
- Gurdeep Singh
- CellNetworks, Bioquant, Heidelberg University, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany.,Biochemie Zentrum Heidelberg (BZH), Heidelberg University, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - J Silvio Gutkind
- Department of Pharmacology and Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Robert B Russell
- CellNetworks, Bioquant, Heidelberg University, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany.,Biochemie Zentrum Heidelberg (BZH), Heidelberg University, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Francesco Raimondi
- CellNetworks, Bioquant, Heidelberg University, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany.,Biochemie Zentrum Heidelberg (BZH), Heidelberg University, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
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3
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Integrated structural modeling and super-resolution imaging resolve GPCR oligomers. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2019; 169:151-179. [PMID: 31952685 DOI: 10.1016/bs.pmbts.2019.11.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Formation of G protein-coupled receptors (GPCRs) dimers and higher order oligomers represents a key mechanism in pleiotropic signaling, yet how individual protomers function within oligomers remains poorly understood. For the Class A/rhodopsin subfamily of glycoprotein hormone receptors (GpHRs), di/oligomerization has been demonstrated to play a significant role in regulating its signaling activity at a cellular and physiological level and even pathophysiologically. Here we will describe and discuss the developments in our understanding of GPCR oligomerization, in both health and disease, from the study of this unique and complex subfamily of GPCRs with light on the luteinizing hormone receptor (LHR). Focus will be put on the results of an approach relying on the combination of atomistic modeling by protein-protein docking with super-resolution imaging. The latter could resolve single LHR molecules to ~8nm resolution in functional asymmetric dimers and oligomers, using dual-color photoactivatable dyes and localization microscopy (PD-PALM). Structural modeling of functionally asymmetric LHR trimers and tetramers strongly aligned with PD-PALM-imaged spatial arrangements, identifying multiple possible helix interfaces mediating inter-protomer associations. Diverse spatial and structural assemblies mediating GPCR oligomerization may acutely fine-tune the cellular signaling profile.
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4
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Fukutani Y, Tamaki R, Inoue R, Koshizawa T, Sakashita S, Ikegami K, Ohsawa I, Matsunami H, Yohda M. The N-terminal region of RTP1S plays important roles in dimer formation and odorant receptor-trafficking. J Biol Chem 2019; 294:14661-14673. [PMID: 31395660 PMCID: PMC6779431 DOI: 10.1074/jbc.ra118.007110] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 07/30/2019] [Indexed: 12/31/2022] Open
Abstract
Receptor-transporting protein 1S (RTP1S) is an accessory protein that mediates the transport of mammalian odorant receptors (ORs) into the plasma membrane. Although most ORs fail to localize to the cell surface when expressed alone in nonolfactory cells, functional expression of ORs is achieved with the coexpression of RTP1S. However, the mechanism for RTP1S-mediated OR trafficking remains unclear. In this study, we attempted to reveal the mode of action and critical residues of RTP1S in OR trafficking. Experiments using N-terminal truncation and Ala substitution mutants of RTP1S demonstrated that four N-terminal amino acids have essential roles in OR trafficking. Additionally, using recombinant proteins and split luciferase assays in mammalian cells, we provided evidence for the dimer formation of RTP1S. Furthermore, we determined that the 2nd Cys residue is required for the efficient dimerization of RTP1S. Altogether, these findings provide insights into the mechanism for plasma membrane transport of ORs by RTP1S.
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Affiliation(s)
- Yosuke Fukutani
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan.,Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710
| | - Ryohei Tamaki
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Ryosuke Inoue
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Tomoyo Koshizawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Shuto Sakashita
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Kentaro Ikegami
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Ikuroh Ohsawa
- Biological Process of Aging, Tokyo Metropolitan Institute of Gerontology, Tokyo 173-0015, Japan
| | - Hiroaki Matsunami
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710.,Department of Neurobiology, Duke Institute for Brain Sciences, Duke University Medical Center, Durham, North Carolina 27705.,Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Masafumi Yohda
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan .,Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
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5
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Al-Shar'i NA, Al-Balas QA. Molecular Dynamics Simulations of Adenosine Receptors: Advances, Applications and Trends. Curr Pharm Des 2019; 25:783-816. [DOI: 10.2174/1381612825666190304123414] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 02/26/2019] [Indexed: 01/09/2023]
Abstract
:
Adenosine receptors (ARs) are transmembrane proteins that belong to the G protein-coupled receptors
(GPCRs) superfamily and mediate the biological functions of adenosine. To date, four AR subtypes are known,
namely A1, A2A, A2B and A3 that exhibit different signaling pathways, tissue localization, and mechanisms of
activation. Moreover, the widespread ARs and their implication in numerous physiological and pathophysiological
conditions had made them pivotal therapeutic targets for developing clinically effective agents.
:
The crystallographic success in identifying the 3D crystal structures of A2A and A1 ARs has dramatically enriched
our understanding of their structural and functional properties such as ligand binding and signal transduction.
This, in turn, has provided a structural basis for a larger contribution of computational methods, particularly molecular
dynamics (MD) simulations, toward further investigation of their molecular properties and designing
bioactive ligands with therapeutic potential. MD simulation has been proved to be an invaluable tool in investigating
ARs and providing answers to some critical questions. For example, MD has been applied in studying ARs
in terms of ligand-receptor interactions, molecular recognition, allosteric modulations, dimerization, and mechanisms
of activation, collectively aiding in the design of subtype selective ligands.
:
In this review, we focused on the advances and different applications of MD simulations utilized to study the
structural and functional aspects of ARs that can foster the structure-based design of drug candidates. In addition,
relevant literature was briefly discussed which establishes a starting point for future advances in the field of drug
discovery to this pivotal group of drug targets.
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Affiliation(s)
- Nizar A. Al-Shar'i
- Department of Medicinal Chemistry and Pharmacognosy, Faculty of Pharmacy, Jordan University of Science and Technology, P.O. Box 3030, Irbid 22110, Jordan
| | - Qosay A. Al-Balas
- Department of Medicinal Chemistry and Pharmacognosy, Faculty of Pharmacy, Jordan University of Science and Technology, P.O. Box 3030, Irbid 22110, Jordan
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6
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Townsend-Nicholson A, Altwaijry N, Potterton A, Morao I, Heifetz A. Computational prediction of GPCR oligomerization. Curr Opin Struct Biol 2019; 55:178-184. [PMID: 31170578 DOI: 10.1016/j.sbi.2019.04.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 04/16/2019] [Accepted: 04/17/2019] [Indexed: 01/08/2023]
Abstract
There has been a recent and prolific expansion in the number of GPCR crystal structures being solved: in both active and inactive forms and in complex with ligand, with G protein and with each other. Despite this, there is relatively little experimental information about the precise configuration of GPCR oligomers during these different biologically relevant states. While it may be possible to identify the experimental conditions necessary to crystallize a GPCR preferentially in a specific structural conformation, computational approaches afford a potentially more tractable means of describing the probability of formation of receptor dimers and higher order oligomers. Ensemble-based computational methods based on structurally determined dimers, coupled with a computational workflow that uses quantum mechanical methods to analyze the chemical nature of the molecular interactions at a GPCR dimer interface, will generate the reproducible and accurate predictions needed to predict previously unidentified GPCR dimers and to inform future advances in our ability to understand and begin to precisely manipulate GPCR oligomers in biological systems. It may also provide information needed to achieve an increase in the number of experimentally determined oligomeric GPCR structures.
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Affiliation(s)
- Andrea Townsend-Nicholson
- Institute of Structural & Molecular Biology, Research Department of Structural & Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom.
| | - Nojood Altwaijry
- Institute of Structural & Molecular Biology, Research Department of Structural & Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - Andrew Potterton
- Institute of Structural & Molecular Biology, Research Department of Structural & Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom; Evotec (UK) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Inaki Morao
- Evotec (UK) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Alexander Heifetz
- Evotec (UK) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
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7
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Ottensmeyer PF, Witzler M, Schulze M, Tobiasch E. Small Molecules Enhance Scaffold-Based Bone Grafts via Purinergic Receptor Signaling in Stem Cells. Int J Mol Sci 2018; 19:E3601. [PMID: 30441872 PMCID: PMC6274752 DOI: 10.3390/ijms19113601] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 11/08/2018] [Accepted: 11/09/2018] [Indexed: 12/15/2022] Open
Abstract
The need for bone grafts is high, due to age-related diseases, such as tumor resections, but also accidents, risky sports, and military conflicts. The gold standard for bone grafting is the use of autografts from the iliac crest, but the limited amount of accessible material demands new sources of bone replacement. The use of mesenchymal stem cells or their descendant cells, namely osteoblast, the bone-building cells and endothelial cells for angiogenesis, combined with artificial scaffolds, is a new approach. Mesenchymal stem cells (MSCs) can be obtained from the patient themselves, or from donors, as they barely cause an immune response in the recipient. However, MSCs never fully differentiate in vitro which might lead to unwanted effects in vivo. Interestingly, purinergic receptors can positively influence the differentiation of both osteoblasts and endothelial cells, using specific artificial ligands. An overview is given on purinergic receptor signaling in the most-needed cell types involved in bone metabolism-namely osteoblasts, osteoclasts, and endothelial cells. Furthermore, different types of scaffolds and their production methods will be elucidated. Finally, recent patents on scaffold materials, as wells as purinergic receptor-influencing molecules which might impact bone grafting, are discussed.
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Affiliation(s)
- Patrick Frank Ottensmeyer
- Department of Natural Sciences, Bonn-Rhine-Sieg University of Applied Sciences, D-53359 Rheinbach, Germany.
| | - Markus Witzler
- Department of Natural Sciences, Bonn-Rhine-Sieg University of Applied Sciences, D-53359 Rheinbach, Germany.
| | - Margit Schulze
- Department of Natural Sciences, Bonn-Rhine-Sieg University of Applied Sciences, D-53359 Rheinbach, Germany.
| | - Edda Tobiasch
- Department of Natural Sciences, Bonn-Rhine-Sieg University of Applied Sciences, D-53359 Rheinbach, Germany.
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8
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Role of Extracellular Loops and Membrane Lipids for Ligand Recognition in the Neuronal Adenosine Receptor Type 2A: An Enhanced Sampling Simulation Study. Molecules 2018; 23:molecules23102616. [PMID: 30322034 PMCID: PMC6222423 DOI: 10.3390/molecules23102616] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 10/09/2018] [Accepted: 10/10/2018] [Indexed: 01/12/2023] Open
Abstract
Human G-protein coupled receptors (GPCRs) are important targets for pharmaceutical intervention against neurological diseases. Here, we use molecular simulation to investigate the key step in ligand recognition governed by the extracellular domains in the neuronal adenosine receptor type 2A (hA2AR), a target for neuroprotective compounds. The ligand is the high-affinity antagonist (4-(2-(7-amino-2-(furan-2-yl)-[1,2,4]triazolo[1,5-a][1,3,5]triazin-5-ylamino)ethyl)phenol), embedded in a neuronal membrane mimic environment. Free energy calculations, based on well-tempered metadynamics, reproduce the experimentally measured binding affinity. The results are consistent with the available mutagenesis studies. The calculations identify a vestibular binding site, where lipids molecules can actively participate to stabilize ligand binding. Bioinformatic analyses suggest that such vestibular binding site and, in particular, the second extracellular loop, might drive the ligand toward the orthosteric binding pocket, possibly by allosteric modulation. Taken together, these findings point to a fundamental role of the interaction between extracellular loops and membrane lipids for ligands’ molecular recognition and ligand design in hA2AR.
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9
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Durdagi S, Erol I, Salmas RE, Aksoydan B, Kantarcioglu I. Oligomerization and cooperativity in GPCRs from the perspective of the angiotensin AT1 and dopamine D2 receptors. Neurosci Lett 2018; 700:30-37. [PMID: 29684528 DOI: 10.1016/j.neulet.2018.04.028] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 04/13/2018] [Accepted: 04/16/2018] [Indexed: 12/22/2022]
Abstract
G Protein-Coupled Receptors (GPCRs) can form homo- and heterodimers or constitute higher oligomeric clusters with other heptahelical GPCRs. In this article, multiscale molecular modeling approaches as well as experimental techniques which are used to study oligomerization of GPCRs are reviewed. In particular, the effect of dimerization/oligomerization to the ligand binding affinity of individual protomers and also on the efficacy of the oligomer are discussed by including diverse examples from the literature. In addition, possible allosteric effects that may emerge upon interaction of GPCRs with membrane components, like cholesterol, is also discussed. Investigation of these above-mentioned interactions may greatly contribute to the candidate molecule screening studies and development of novel therapeutics with fewer adverse effects.
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Affiliation(s)
- Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey; Neuroscience Program, Graduate School of Health Sciences, Bahcesehir University, Istanbul, Turkey.
| | - Ismail Erol
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey; Department of Chemistry, Gebze Technical University, Kocaeli, Turkey
| | - Ramin Ekhteiari Salmas
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey
| | - Busecan Aksoydan
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey; Neuroscience Program, Graduate School of Health Sciences, Bahcesehir University, Istanbul, Turkey
| | - Isik Kantarcioglu
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey; Bioengineering Program, Graduate School of Natural and Applied Sciences, Bahcesehir University, Istanbul, Turkey
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10
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Guidolin D, Marcoli M, Tortorella C, Maura G, Agnati LF. G protein-coupled receptor-receptor interactions give integrative dynamics to intercellular communication. Rev Neurosci 2018; 29:703-726. [DOI: 10.1515/revneuro-2017-0087] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 01/01/2018] [Indexed: 01/14/2023]
Abstract
Abstract
The proposal of receptor-receptor interactions (RRIs) in the early 1980s broadened the view on the role of G protein-coupled receptors (GPCR) in the dynamics of the intercellular communication. RRIs, indeed, allow GPCR to operate not only as monomers but also as receptor complexes, in which the integration of the incoming signals depends on the number, spatial arrangement, and order of activation of the protomers forming the complex. The main biochemical mechanisms controlling the functional interplay of GPCR in the receptor complexes are direct allosteric interactions between protomer domains. The formation of these macromolecular assemblies has several physiologic implications in terms of the modulation of the signaling pathways and interaction with other membrane proteins. It also impacts on the emerging field of connectomics, as it contributes to set and tune the synaptic strength. Furthermore, recent evidence suggests that the transfer of GPCR and GPCR complexes between cells via the exosome pathway could enable the target cells to recognize/decode transmitters and/or modulators for which they did not express the pertinent receptors. Thus, this process may also open the possibility of a new type of redeployment of neural circuits. The fundamental aspects of GPCR complex formation and function are the focus of the present review article.
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Affiliation(s)
- Diego Guidolin
- Department of Neuroscience , University of Padova, via Gabelli 65 , I-35121 Padova , Italy
| | - Manuela Marcoli
- Department of Pharmacy and Center of Excellence for Biomedical Research , University of Genova , I-16126 Genova , Italy
| | - Cinzia Tortorella
- Department of Neuroscience , University of Padova, via Gabelli 65 , I-35121 Padova , Italy
| | - Guido Maura
- Department of Pharmacy and Center of Excellence for Biomedical Research , University of Genova , I-16126 Genova , Italy
| | - Luigi F. Agnati
- Department of Biomedical Sciences , University of Modena and Reggio Emilia , I-41121 Modena , Italy
- Department of Neuroscience , Karolinska Institutet , S-17177 Stockholm , Sweden
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11
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Marino KA, Filizola M. Investigating Small-Molecule Ligand Binding to G Protein-Coupled Receptors with Biased or Unbiased Molecular Dynamics Simulations. Methods Mol Biol 2018; 1705:351-364. [PMID: 29188572 DOI: 10.1007/978-1-4939-7465-8_17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
An increasing number of G protein-coupled receptor (GPCR) crystal structures provide important-albeit static-pictures of how small molecules or peptides interact with their receptors. These high-resolution structures represent a tremendous opportunity to apply molecular dynamics (MD) simulations to capture atomic-level dynamical information that is not easy to obtain experimentally. Understanding ligand binding and unbinding processes, as well as the related responses of the receptor, is crucial to the design of better drugs targeting GPCRs. Here, we discuss possible ways to study the dynamics involved in the binding of small molecules to GPCRs, using long timescale MD simulations or metadynamics-based approaches.
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Affiliation(s)
- Kristen A Marino
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1677, New York, NY, 10029, USA
| | - Marta Filizola
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1677, New York, NY, 10029, USA.
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12
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Fanelli F, Felline A. Uncovering GPCR and G Protein Function by Protein Structure Network Analysis. COMPUTATIONAL TOOLS FOR CHEMICAL BIOLOGY 2017. [DOI: 10.1039/9781788010139-00198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Protein structure network (PSN) analysis is one of the graph theory-based approaches currently used for investigating structural communication in biomolecular systems. Information on the system's dynamics can be provided by atomistic molecular dynamics (MD) simulations or coarse grained elastic network models paired with normal mode analysis (ENM-NMA). This chapter reports on selected applications of PSN analysis to uncover the structural communication in G protein coupled receptors (GPCRs) and G proteins. Strategies to highlight changes in structural communication caused by mutations, ligand and protein binding are described. Conserved amino acids, sites of misfolding mutations, or ligands acting as functional switches tend to behave as hubs in the native structure networks. Densely linked regions in the protein structure graphs could be identified as playing central roles in protein stability and function. Changes in the communication pathway fingerprints depending on the bound ligand or following amino acid mutation could be highlighted as well. A bridge between misfolding and misrouting could be established in rhodopsin mutants linked to inherited blindness. The analysis of native network perturbations by misfolding mutations served to infer key structural elements of protein responsiveness to small chaperones with implications for drug discovery.
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Affiliation(s)
- Francesca Fanelli
- Department of Life Sciences University of Modena and Reggio Emilia Italy
- Center for Neuroscience and Neurotechnology University of Modena and Reggio Emilia Italy
| | - Angelo Felline
- Department of Life Sciences University of Modena and Reggio Emilia Italy
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13
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Dissecting intrinsic and ligand-induced structural communication in the β3 headpiece of integrins. Biochim Biophys Acta Gen Subj 2017; 1861:2367-2381. [DOI: 10.1016/j.bbagen.2017.05.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 05/20/2017] [Accepted: 05/22/2017] [Indexed: 12/15/2022]
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14
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Bartuzi D, Kaczor AA, Matosiuk D. Signaling within Allosteric Machines: Signal Transmission Pathways Inside G Protein-Coupled Receptors. Molecules 2017; 22:molecules22071188. [PMID: 28714871 PMCID: PMC6152049 DOI: 10.3390/molecules22071188] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 07/04/2017] [Accepted: 07/10/2017] [Indexed: 11/16/2022] Open
Abstract
In recent years, our understanding of function of G protein-coupled receptors (GPCRs) has changed from a picture of simple signal relays, transmitting only a particular signal to a particular G protein heterotrimer, to versatile machines, capable of various responses to different stimuli and being modulated by various factors. Some recent reports provide not only the data on ligands/modulators and resultant signals induced by them, but also deeper insights into exact pathways of signal migration and mechanisms of signal transmission through receptor structure. Combination of these computational and experimental data sheds more light on underlying mechanisms of signal transmission and signaling bias in GPCRs. In this review we focus on available clues on allosteric pathways responsible for complex signal processing within GPCRs structures, with particular emphasis on linking compatible in silico- and in vitro-derived data on the most probable allosteric connections.
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Affiliation(s)
- Damian Bartuzi
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Lab, Medical University of Lublin, 4A Chodźki Str., Lublin PL20093, Poland.
| | - Agnieszka A Kaczor
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Lab, Medical University of Lublin, 4A Chodźki Str., Lublin PL20093, Poland.
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1, P.O. Box 1627, Kuopio FI-70211, Finland.
| | - Dariusz Matosiuk
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Lab, Medical University of Lublin, 4A Chodźki Str., Lublin PL20093, Poland.
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15
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Oliveira PAD, Dalton JAR, López-Cano M, Ricarte A, Morató X, Matheus FC, Cunha AS, Müller CE, Takahashi RN, Fernández-Dueñas V, Giraldo J, Prediger RD, Ciruela F. Angiotensin II type 1/adenosine A 2A receptor oligomers: a novel target for tardive dyskinesia. Sci Rep 2017; 7:1857. [PMID: 28500295 PMCID: PMC5431979 DOI: 10.1038/s41598-017-02037-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 04/06/2017] [Indexed: 01/28/2023] Open
Abstract
Tardive dyskinesia (TD) is a serious motor side effect that may appear after long-term treatment with neuroleptics and mostly mediated by dopamine D2 receptors (D2Rs). Striatal D2R functioning may be finely regulated by either adenosine A2A receptor (A2AR) or angiotensin receptor type 1 (AT1R) through putative receptor heteromers. Here, we examined whether A2AR and AT1R may oligomerize in the striatum to synergistically modulate dopaminergic transmission. First, by using bioluminescence resonance energy transfer, we demonstrated a physical AT1R-A2AR interaction in cultured cells. Interestingly, by protein-protein docking and molecular dynamics simulations, we described that a stable heterotetrameric interaction may exist between AT1R and A2AR bound to antagonists (i.e. losartan and istradefylline, respectively). Accordingly, we subsequently ascertained the existence of AT1R/A2AR heteromers in the striatum by proximity ligation in situ assay. Finally, we took advantage of a TD animal model, namely the reserpine-induced vacuous chewing movement (VCM), to evaluate a novel multimodal pharmacological TD treatment approach based on targeting the AT1R/A2AR complex. Thus, reserpinized mice were co-treated with sub-effective losartan and istradefylline doses, which prompted a synergistic reduction in VCM. Overall, our results demonstrated the existence of striatal AT1R/A2AR oligomers with potential usefulness for the therapeutic management of TD.
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Affiliation(s)
- Paulo A de Oliveira
- Departamento de Farmacologia, Universidade Federal de Santa Catarina, Trindade, 88049-900, Florianópolis, SC, Brazil
| | - James A R Dalton
- Institut de Neurociències and Unitat de Bioestadística, Universitat Autònoma de Barcelona, Network Biomedical Research Center on Mental Health (CIBERSAM), Bellaterra, Spain
| | - Marc López-Cano
- Unitat de Farmacologia, Departament de Patologia i Terapèutica Experimental, Facultat de Medicina, IDIBELL-Universitat de Barcelona, L'Hospitalet de Llobregat, Spain.,Institut de Neurociències, Universitat de Barcelona, Barcelona, Spain
| | - Adrià Ricarte
- Institut de Neurociències and Unitat de Bioestadística, Universitat Autònoma de Barcelona, Network Biomedical Research Center on Mental Health (CIBERSAM), Bellaterra, Spain
| | - Xavier Morató
- Unitat de Farmacologia, Departament de Patologia i Terapèutica Experimental, Facultat de Medicina, IDIBELL-Universitat de Barcelona, L'Hospitalet de Llobregat, Spain.,Institut de Neurociències, Universitat de Barcelona, Barcelona, Spain
| | - Filipe C Matheus
- Departamento de Farmacologia, Universidade Federal de Santa Catarina, Trindade, 88049-900, Florianópolis, SC, Brazil
| | - Andréia S Cunha
- Departamento de Farmacologia, Universidade Federal de Santa Catarina, Trindade, 88049-900, Florianópolis, SC, Brazil
| | - Christa E Müller
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, Bonn, Germany
| | - Reinaldo N Takahashi
- Departamento de Farmacologia, Universidade Federal de Santa Catarina, Trindade, 88049-900, Florianópolis, SC, Brazil
| | - Víctor Fernández-Dueñas
- Unitat de Farmacologia, Departament de Patologia i Terapèutica Experimental, Facultat de Medicina, IDIBELL-Universitat de Barcelona, L'Hospitalet de Llobregat, Spain.,Institut de Neurociències, Universitat de Barcelona, Barcelona, Spain
| | - Jesús Giraldo
- Institut de Neurociències and Unitat de Bioestadística, Universitat Autònoma de Barcelona, Network Biomedical Research Center on Mental Health (CIBERSAM), Bellaterra, Spain.
| | - Rui D Prediger
- Departamento de Farmacologia, Universidade Federal de Santa Catarina, Trindade, 88049-900, Florianópolis, SC, Brazil. .,Programa de Pós-graduação em Neurociências, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Trindade, 88049-900, Florianópolis, SC, Brazil.
| | - Francisco Ciruela
- Unitat de Farmacologia, Departament de Patologia i Terapèutica Experimental, Facultat de Medicina, IDIBELL-Universitat de Barcelona, L'Hospitalet de Llobregat, Spain. .,Institut de Neurociències, Universitat de Barcelona, Barcelona, Spain.
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16
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Altwaijry NA, Baron M, Wright DW, Coveney PV, Townsend-Nicholson A. An Ensemble-Based Protocol for the Computational Prediction of Helix-Helix Interactions in G Protein-Coupled Receptors using Coarse-Grained Molecular Dynamics. J Chem Theory Comput 2017; 13:2254-2270. [PMID: 28383913 PMCID: PMC5557214 DOI: 10.1021/acs.jctc.6b01246] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
![]()
The
accurate identification of the specific points of interaction
between G protein-coupled receptor (GPCR) oligomers is essential for
the design of receptor ligands targeting oligomeric receptor targets.
A coarse-grained molecular dynamics computer simulation approach would
provide a compelling means of identifying these specific protein–protein
interactions and could be applied both for known oligomers of interest
and as a high-throughput screen to identify novel oligomeric targets.
However, to be effective, this in silico modeling must provide accurate,
precise, and reproducible information. This has been achieved recently
in numerous biological systems using an ensemble-based all-atom molecular
dynamics approach. In this study, we describe an equivalent methodology
for ensemble-based coarse-grained simulations. We report the performance
of this method when applied to four different GPCRs known to oligomerize
using error analysis to determine the ensemble size and individual
replica simulation time required. Our measurements of distance between
residues shown to be involved in oligomerization of the fifth transmembrane
domain from the adenosine A2A receptor are in very good
agreement with the existing biophysical data and provide information
about the nature of the contact interface that cannot be determined
experimentally. Calculations of distance between rhodopsin, CXCR4,
and β1AR transmembrane domains reported to form contact
points in homodimers correlate well with the corresponding measurements
obtained from experimental structural data, providing an ability to predict
contact interfaces computationally. Interestingly, error analysis
enables identification of noninteracting regions. Our results confirm
that GPCR interactions can be reliably predicted using this novel
methodology.
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Affiliation(s)
- Nojood A Altwaijry
- Institute of Structural and Molecular Biology, Research Department of Structural and Molecular Biology, Division of Biosciences, University College London , London, WC1E 6BT, United Kingdom.,King Saud University , Riyadh, Kingdom of Saudi Arabia
| | - Michael Baron
- Institute of Structural and Molecular Biology, Research Department of Structural and Molecular Biology, Division of Biosciences, University College London , London, WC1E 6BT, United Kingdom
| | - David W Wright
- Centre for Computational Science, Department of Chemistry, University College London , London WC1H 0AJ, United Kingdom
| | - Peter V Coveney
- Centre for Computational Science, Department of Chemistry, University College London , London WC1H 0AJ, United Kingdom
| | - Andrea Townsend-Nicholson
- Institute of Structural and Molecular Biology, Research Department of Structural and Molecular Biology, Division of Biosciences, University College London , London, WC1E 6BT, United Kingdom
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17
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Farran B. An update on the physiological and therapeutic relevance of GPCR oligomers. Pharmacol Res 2017; 117:303-327. [PMID: 28087443 DOI: 10.1016/j.phrs.2017.01.008] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 01/06/2017] [Accepted: 01/09/2017] [Indexed: 01/17/2023]
Abstract
The traditional view on GPCRs held that they function as single monomeric units composed of identical subunits. This notion was overturned by the discovery that GPCRs can form homo- and hetero-oligomers, some of which are obligatory, and can further assemble into receptor mosaics consisting of three or more protomers. Oligomerisation exerts significant impacts on receptor function and physiology, offering a platform for the diversification of receptor signalling, pharmacology, regulation, crosstalk, internalization and trafficking. Given their involvement in the modulation of crucial physiological processes, heteromers could constitute important therapeutic targets for a wide range of diseases, including schizophrenia, Parkinson's disease, substance abuse or obesity. This review aims at depicting the current developments in GPCR oligomerisation research, documenting various class A, B and C GPCR heteromers detected in vitro and in vivo using biochemical and biophysical approaches, as well as recently identified higher-order oligomeric complexes. It explores the current understanding of dimerization dynamics and the possible interaction interfaces that drive oligomerisation. Most importantly, it provides an inventory of the wide range of physiological processes and pathophysiological conditions to which GPCR oligomers contribute, surveying some of the oligomers that constitute potential drug targets. Finally, it delineates the efforts to develop novel classes of ligands that specifically target and tether to receptor oligomers instead of a single monomeric entity, thus ameliorating their ability to modulate GPCR function.
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Affiliation(s)
- Batoul Farran
- Department of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, United Kingdom.
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18
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Schonenbach NS, Rieth MD, Han S, O'Malley MA. Adenosine A2a receptors form distinct oligomers in protein detergent complexes. FEBS Lett 2016; 590:3295-306. [PMID: 27543907 DOI: 10.1002/1873-3468.12367] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Revised: 08/10/2016] [Accepted: 08/15/2016] [Indexed: 12/12/2022]
Abstract
The human adenosine A2a receptor (A2aR) tunes its function by forming homo-oligomers and hetero-oligomers with other G protein-coupled receptors, but the biophysical characterization of these oligomeric species is limited. Here, we show that upon reconstitution into an optimized mixed micelle system, and purification via an antagonist affinity column, full-length A2aR exists as a distribution of oligomers. We isolated the dimer population from the other oligomers via size exclusion chromatography and showed that it is stable upon dilution, thus supporting the hypotheses that the A2aR dimer has a defined structure and function. This study presents a crucial enabling step to a detailed biophysical characterization of A2aR homodimers.
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Affiliation(s)
- Nicole S Schonenbach
- Department of Chemical Engineering, University of California Santa Barbara, CA, USA
| | - Monica D Rieth
- Department of Chemical Engineering, University of California Santa Barbara, CA, USA
| | - Songi Han
- Department of Chemical Engineering, University of California Santa Barbara, CA, USA.,Department of Chemistry and Biochemistry, University of California Santa Barbara, CA, USA
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California Santa Barbara, CA, USA.
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19
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Structure network analysis to gain insights into GPCR function. Biochem Soc Trans 2016; 44:613-8. [DOI: 10.1042/bst20150283] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Indexed: 11/17/2022]
Abstract
G protein coupled receptors (GPCRs) are allosteric proteins whose functioning fundamentals are the communication between the two poles of the helix bundle. Protein structure network (PSN) analysis is one of the graph theory-based approaches currently used to investigate the structural communication in biomolecular systems. Information on system's dynamics can be provided by atomistic molecular dynamics (MD) simulations or coarse grained elastic network models paired with normal mode analysis (ENM–NMA). The present review article describes the application of PSN analysis to uncover the structural communication in G protein coupled receptors (GPCRs). Strategies to highlight changes in structural communication upon misfolding, dimerization and activation are described. Focus is put on the ENM–NMA-based strategy applied to the crystallographic structures of rhodopsin in its inactive (dark) and signalling active (meta II (MII)) states, highlighting changes in structure network and centrality of the retinal chromophore in differentiating the inactive and active states of the receptor.
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20
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Parravicini C, Daniele S, Palazzolo L, Trincavelli ML, Martini C, Zaratin P, Primi R, Coppolino G, Gianazza E, Abbracchio MP, Eberini I. A promiscuous recognition mechanism between GPR17 and SDF-1: Molecular insights. Cell Signal 2016; 28:631-42. [PMID: 26971834 DOI: 10.1016/j.cellsig.2016.03.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 02/29/2016] [Accepted: 03/06/2016] [Indexed: 01/19/2023]
Abstract
Recent data and publications suggest a promiscuous behaviour for GPR17, a class-A GPCR operated by different classes of ligands, such as uracil nucleotides, cysteinyl-leukotrienes and oxysterols. This observation, together with the ability of several class-A GPCRs to form homo- and hetero-dimers, is likely to unveil new pathophysiological roles and novel emerging pharmacological properties for some of these GPCRs, including GPR17. This receptor shares structural, phylogenetic and functional properties with some chemokine receptors, CXCRs. Both GPR17 and CXCR2 are operated by oxysterols, and both GPR17 and CXCR ligands have been demonstrated to have a role in orchestrating inflammatory responses and oligodendrocyte precursor cell differentiation to myelinating cells in acute and chronic diseases of the central nervous system. Here, by combining in silico modelling data with in vitro validation in (i) a classical reference pharmacological assay for GPCR activity and (ii) a model of maturation of primary oligodendrocyte precursor cells, we demonstrate that GPR17 can be activated by SDF-1, a ligand of chemokine receptors CXCR4 and CXCR7, and investigate the underlying molecular recognition mechanism. We also demonstrate that cangrelor, a GPR17 orthosteric antagonist, can block the SDF-1-mediated activation of GPR17 in a concentration-dependent manner. The ability of GPR17 to respond to different classes of GPCR ligands suggests that this receptor modifies its function depending on the extracellular mileu changes occurring under specific pathophysiological conditions and advocates it as a strategic target for neurodegenerative diseases with an inflammatory/immune component.
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Affiliation(s)
- Chiara Parravicini
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milano, Italy.
| | - Simona Daniele
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milano, Italy; Dipartimento di Farmacia, Università degli Studi di Pisa, Via Bonanno Pisano 6, 56126 Pisa, Italy.
| | - Luca Palazzolo
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milano, Italy.
| | | | - Claudia Martini
- Dipartimento di Farmacia, Università degli Studi di Pisa, Via Bonanno Pisano 6, 56126 Pisa, Italy.
| | - Paola Zaratin
- Fondazione Italiana Sclerosi Multipla, Via Operai 40, 16149 Genova, Italy.
| | - Roberto Primi
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milano, Italy.
| | - Giusy Coppolino
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milano, Italy.
| | - Elisabetta Gianazza
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milano, Italy.
| | - Maria P Abbracchio
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milano, Italy.
| | - Ivano Eberini
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milano, Italy; Dipartimento di Scienze Biomediche e Cliniche "L. Sacco", Università degli Studi di Milano, Via Gian Battista Grassi 74, 20157 Milano, Italy.
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21
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Computational approaches to detect allosteric pathways in transmembrane molecular machines. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1652-62. [PMID: 26806157 DOI: 10.1016/j.bbamem.2016.01.010] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 01/13/2016] [Accepted: 01/14/2016] [Indexed: 01/05/2023]
Abstract
Many of the functions of transmembrane proteins involved in signal processing and transduction across the cell membrane are determined by allosteric couplings that propagate the functional effects well beyond the original site of activation. Data gathered from breakthroughs in biochemistry, crystallography, and single molecule fluorescence have established a rich basis of information for the study of molecular mechanisms in the allosteric couplings of such transmembrane proteins. The mechanistic details of these couplings, many of which have therapeutic implications, however, have only become accessible in synergy with molecular modeling and simulations. Here, we review some recent computational approaches that analyze allosteric coupling networks (ACNs) in transmembrane proteins, and in particular the recently developed Protein Interaction Analyzer (PIA) designed to study ACNs in the structural ensembles sampled by molecular dynamics simulations. The power of these computational approaches in interrogating the functional mechanisms of transmembrane proteins is illustrated with selected examples of recent experimental and computational studies pursued synergistically in the investigation of secondary active transporters and GPCRs. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.
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22
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Hu G, Xiao F, Li Y, Li Y, Vongsangnak W. Protein-Protein Interface and Disease: Perspective from Biomolecular Networks. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 160:57-74. [PMID: 27928579 DOI: 10.1007/10_2016_40] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Protein-protein interactions are involved in many important biological processes and molecular mechanisms of disease association. Structural studies of interfacial residues in protein complexes provide information on protein-protein interactions. Characterizing protein-protein interfaces, including binding sites and allosteric changes, thus pose an imminent challenge. With special focus on protein complexes, approaches based on network theory are proposed to meet this challenge. In this review we pay attention to protein-protein interfaces from the perspective of biomolecular networks and their roles in disease. We first describe the different roles of protein complexes in disease through several structural aspects of interfaces. We then discuss some recent advances in predicting hot spots and communication pathway analysis in terms of amino acid networks. Finally, we highlight possible future aspects of this area with respect to both methodology development and applications for disease treatment.
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Affiliation(s)
- Guang Hu
- Center for Systems Biology, School of Electronic and Information Engineering, Soochow University, Suzhou, 215006, China.
| | - Fei Xiao
- School of Basic Medicine and Biological Sciences, Medical College of Soochow University, Suzhou, 215123, China
| | - Yuqian Li
- School of Electronic Engineering, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Yuan Li
- Center for Systems Biology, School of Electronic and Information Engineering, Soochow University, Suzhou, 215006, China
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand.
- Computational Biomodelling Laboratory for Agricultural Science and Technology (CBLAST), Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand.
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23
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Meng XY, Mezei M, Cui M. Computational approaches for modeling GPCR dimerization. Curr Pharm Biotechnol 2015; 15:996-1006. [PMID: 25307013 DOI: 10.2174/1389201015666141013102515] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 07/09/2014] [Accepted: 08/18/2014] [Indexed: 11/22/2022]
Abstract
Growing experimental evidences suggest that dimerization and oligomerization are important for G Protein- Coupled Receptors (GPCRs) function. The detailed structural information of dimeric/oligomeric GPCRs would be very important to understand their function. Although it is encouraging that recently several experimental GPCR structures in oligomeric forms have appeared, experimental determination of GPCR structures in oligomeric forms is still a big challenge, especially in mimicking the membrane environment. Therefore, development of computational approaches to predict dimerization of GPCRs will be highly valuable. In this review, we summarize computational approaches that have been developed and used for modeling of GPCR dimerization. In addition, we introduce a novel two-dimensional Brownian Dynamics based protein docking approach, which we have recently adapted, for GPCR dimer prediction.
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Affiliation(s)
| | | | - Meng Cui
- Institute of Quantitative Biology and Medicine, Jiangsu Provincial Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou 215123, China.
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24
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Kaczor AA, Guixà-González R, Carrió P, Poso A, Dove S, Pastor M, Selent J. Multi-Component Protein - Protein Docking Based Protocol with External Scoring for Modeling Dimers of G Protein-Coupled Receptors. Mol Inform 2015; 34:246-55. [PMID: 27490170 DOI: 10.1002/minf.201400088] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 02/19/2015] [Indexed: 01/08/2023]
Abstract
In order to apply structure-based drug design techniques to GPCR complexes, it is essential to model their 3D structure. For this purpose, a multi-component protocol was derived based on protein-protein docking which generates populations of dimers compatible with membrane integration, considering all reasonable interfaces. At the next stage, we applied a scoring procedure based on up to eleven different parameters including shape or electrostatics complementarity. Two methods of consensus scoring were performed: (i) average scores of 100 best scored dimers with respect to each interface, and (ii) frequencies of interfaces among 100 best scored dimers. In general, our multi-component protocol gives correct indications for dimer interfaces that have been observed in X-ray crystal structures of GPCR dimers (opsin dimer, chemokine CXCR4 and CCR5 dimers, κ opioid receptor dimer, β1 adrenergic receptor dimer and smoothened receptor dimer) but also suggests alternative dimerization interfaces. Interestingly, at times these alternative interfaces are scored higher than the experimentally observed ones suggesting them to be also relevant in the life cycle of studied GPCR dimers. Further results indicate that GPCR dimer and higher-order oligomer formation may involve transmembrane helices (TMs) TM1-TM2-TM7, TM3-TM4-TM5 or TM4-TM5-TM6 but not TM1-TM2-TM3 or TM2-TM3-TM4 which is in general agreement with available experimental and computational data.
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Affiliation(s)
- Agnieszka A Kaczor
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1, P.O. Box 1627, FI-70211 Kuopio, Finland phone: +48815357365; fax: +48815357366. .,Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Lab, Faculty of Pharmacy with Division for Medical Analytics, 4A Chodźki St., PL-20059 Lublin, Poland. .,Research Unit on Biomedical Informatics (GRIB), PRBB, Dr Aiguader 88, E-08003 Barcelona, Spain. .,Department of Pharmaceutical Chemistry II, Institute of Pharmacy, University of Regensburg, DE-93040 Regensburg, Germany.
| | - Ramon Guixà-González
- Research Unit on Biomedical Informatics (GRIB), PRBB, Dr Aiguader 88, E-08003 Barcelona, Spain
| | - Pau Carrió
- Research Unit on Biomedical Informatics (GRIB), PRBB, Dr Aiguader 88, E-08003 Barcelona, Spain
| | - Antti Poso
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1, P.O. Box 1627, FI-70211 Kuopio, Finland phone: +48815357365; fax: +48815357366
| | - Stefan Dove
- Department of Pharmaceutical Chemistry II, Institute of Pharmacy, University of Regensburg, DE-93040 Regensburg, Germany
| | - Manuel Pastor
- Research Unit on Biomedical Informatics (GRIB), PRBB, Dr Aiguader 88, E-08003 Barcelona, Spain
| | - Jana Selent
- Research Unit on Biomedical Informatics (GRIB), PRBB, Dr Aiguader 88, E-08003 Barcelona, Spain.
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25
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Communication over the network of binary switches regulates the activation of A2A adenosine receptor. PLoS Comput Biol 2015; 11:e1004044. [PMID: 25664580 PMCID: PMC4322061 DOI: 10.1371/journal.pcbi.1004044] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 11/18/2014] [Indexed: 11/19/2022] Open
Abstract
Dynamics and functions of G-protein coupled receptors (GPCRs) are accurately regulated by the type of ligands that bind to the orthosteric or allosteric binding sites. To glean the structural and dynamical origin of ligand-dependent modulation of GPCR activity, we performed total ~ 5 μsec molecular dynamics simulations of A2A adenosine receptor (A2AAR) in its apo, antagonist-bound, and agonist-bound forms in an explicit water and membrane environment, and examined the corresponding dynamics and correlation between the 10 key structural motifs that serve as the allosteric hotspots in intramolecular signaling network. We dubbed these 10 structural motifs “binary switches” as they display molecular interactions that switch between two distinct states. By projecting the receptor dynamics on these binary switches that yield 210 microstates, we show that (i) the receptors in apo, antagonist-bound, and agonist-bound states explore vastly different conformational space; (ii) among the three receptor states the apo state explores the broadest range of microstates; (iii) in the presence of the agonist, the active conformation is maintained through coherent couplings among the binary switches; and (iv) to be most specific, our analysis shows that W246, located deep inside the binding cleft, can serve as both an agonist sensor and actuator of ensuing intramolecular signaling for the receptor activation. Finally, our analysis of multiple trajectories generated by inserting an agonist to the apo state underscores that the transition of the receptor from inactive to active form requires the disruption of ionic-lock in the DRY motif. As the key signal transmitters of a number of physiological processes, G-protein coupled receptors (GPCRs) are arguably one of the most important therapeutic targets. Orchestration of the intra-molecular signaling across transmembrane domain is key for the function of GPCRs. To investigate the microscopic underpinnings of intramolecular signaling that regulates the activation of GPCRs, we performed molecular dynamics simulations of the receptor in three distinct ligand-bound states using A2A adenosine receptor as a model system of GPCRs. Statistical analyses on the dynamics of and correlation among the 10 “binary switches” reveal that the three receptor states retain distinct dynamic properties. The antagonist- and agonist-bound forms of the receptors explore vastly different conformational space, and the apo form lies between them, yet located closer to the antagonist-bound form. In regard to the agonist-binding triggered activation mechanism, the correlation map among the 10 binary switches unequivocally shows that direct sensing of agonist ligand by the indole ring of W246 actuates the rest of intramolecular signaling.
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26
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Fracchiolla KE, Cohen LS, Arshava B, Poms M, Zerbe O, Becker JM, Naider F. Structural characterization of triple transmembrane domain containing fragments of a yeast G protein-coupled receptor in an organic : aqueous environment by solution-state NMR spectroscopy. J Pept Sci 2015; 21:212-22. [PMID: 25645975 DOI: 10.1002/psc.2750] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 12/26/2014] [Accepted: 12/28/2014] [Indexed: 01/09/2023]
Abstract
This report summarizes recent biophysical and protein expression experiments on polypeptides containing the N-terminus, the first, second, and third transmembrane (TM) domains and the contiguous loops of the α-factor receptor Ste2p, a G protein-coupled receptor. The 131-residue polypeptide Ste2p(G31-R161), TM1-TM3, was investigated by solution NMR in trifluoroethanol/water. TM1-TM3 contains helical TM domains at the predicted locations, supported by continuous sets of medium-range NOEs. In addition, a short helix N-terminal to TM1 was detected, as well as a short helical stretch in the first extracellular loop. Two 161-residue polypeptides, [Ste2p(M1-R161), NT-TM1-TM3], that contain the entire N-terminal sequence, one with a single mutation, were directly expressed and isolated from Escherichia coli in yields as high as 30 mg/L. Based on its increased stability, the L11P mutant will be used in future experiments to determine long-range interactions. The study demonstrated that 3-TM domains of a yeast G protein-coupled receptor can be produced in isotopically labeled form suitable for solution NMR studies. The quality of spectra is superior to data recorded in micelles and allows more rapid data analysis. No tertiary contacts have been determined, and if present, they are likely transient. This observation supports earlier studies by us that secondary structure was retained in smaller fragments, both in organic solvents and in detergent micelles, but that stable tertiary contacts may only be present when the protein is imbedded in lipids.
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Affiliation(s)
- Katrina E Fracchiolla
- Department of Chemistry, The College of Staten Island, City University of New York, Staten Island, NY, 10314, USA; Department of Biochemistry, The Graduate Center, City University of New York, New York, NY, 10016, USA
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Schonenbach NS, Hussain S, O'Malley MA. Structure and function of G protein‐coupled receptor oligomers: implications for drug discovery. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2014; 7:408-27. [DOI: 10.1002/wnan.1319] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 09/26/2014] [Accepted: 10/11/2014] [Indexed: 12/21/2022]
Affiliation(s)
- Nicole S. Schonenbach
- Department of Chemical EngineeringUniversity of California Santa BarbaraSanta BarbaraCAUSA
| | - Sunyia Hussain
- Department of Chemical EngineeringUniversity of California Santa BarbaraSanta BarbaraCAUSA
| | - Michelle A. O'Malley
- Department of Chemical EngineeringUniversity of California Santa BarbaraSanta BarbaraCAUSA
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Papaleo E, Parravicini F, Grandori R, De Gioia L, Brocca S. Structural investigation of the cold-adapted acylaminoacyl peptidase from Sporosarcina psychrophila by atomistic simulations and biophysical methods. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:2203-13. [DOI: 10.1016/j.bbapap.2014.09.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 09/19/2014] [Accepted: 09/23/2014] [Indexed: 01/07/2023]
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Liu Y, Song G, Shao XX, Liu YL, Guo ZY. Quantitative measurement of cell membrane receptor internalization by the nanoluciferase reporter: Using the G protein-coupled receptor RXFP3 as a model. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1848:688-94. [PMID: 25434927 DOI: 10.1016/j.bbamem.2014.11.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 11/14/2014] [Accepted: 11/17/2014] [Indexed: 11/25/2022]
Abstract
Nanoluciferase (NanoLuc) is a newly developed small luciferase reporter with the brightest bioluminescence to date. In the present work, we developed NanoLuc as a sensitive bioluminescent reporter to measure quantitatively the internalization of cell membrane receptors, based on the pH dependence of the reporter activity. The G protein-coupled receptor RXFP3, the cognate receptor of relaxin-3/INSL7, was used as a model receptor. We first generated stable HEK293T cells that inducibly coexpressed a C-terminally NanoLuc-tagged human RXFP3 and a C-terminally enhanced green fluorescent protein (EGFP)-tagged human RXFP3. The C-terminal EGFP-tag and NanoLuc-tag had no detrimental effects on the ligand-binding potency and intracellular trafficking of RXFP3. Based on the fluorescence of the tagged EGFP reporter, the ligand-induced RXFP3 internalization was visualized directly under a fluorescence microscope. Based on the bioluminescence of the tagged NanoLuc reporter, the ligand-induced RXFP3 internalization was measured quantitatively by a convenient bioluminescent assay. Coexpression of an EGFP-tagged inactive [E141R]RXFP3 had no detrimental effect on the ligand-binding potency and ligand-induced internalization of the NanoLuc-tagged wild-type RXFP3, suggesting that the mutant RXFP3 and wild-type RXFP3 worked independently. The present bioluminescent internalization assay could be extended to other G protein-coupled receptors and other cell membrane receptors to study ligand-receptor and receptor-receptor interactions.
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Affiliation(s)
- Yu Liu
- Institute of Protein Research, College of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Central Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Ge Song
- Institute of Protein Research, College of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Xiao-Xia Shao
- Institute of Protein Research, College of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Ya-Li Liu
- Central Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Zhan-Yun Guo
- Institute of Protein Research, College of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Central Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China.
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Communication routes in ARID domains between distal residues in helix 5 and the DNA-binding loops. PLoS Comput Biol 2014; 10:e1003744. [PMID: 25187961 PMCID: PMC4154638 DOI: 10.1371/journal.pcbi.1003744] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Accepted: 06/12/2014] [Indexed: 11/19/2022] Open
Abstract
ARID is a DNA-binding domain involved in several transcriptional regulatory processes, including cell-cycle regulation and embryonic development. ARID domains are also targets of the Human Cancer Protein Interaction Network. Little is known about the molecular mechanisms related to conformational changes in the family of ARID domains. Thus, we have examined their structural dynamics to enrich the knowledge on this important family of regulatory proteins. In particular, we used an approach that integrates atomistic simulations and methods inspired by graph theory. To relate these properties to protein function we studied both the free and DNA-bound forms. The interaction with DNA not only stabilizes the conformations of the DNA-binding loops, but also strengthens pre-existing paths in the native ARID ensemble for long-range communication to those loops. Residues in helix 5 are identified as critical mediators for intramolecular communication to the DNA-binding regions. In particular, we identified a distal tyrosine that plays a key role in long-range communication to the DNA-binding loops and that is experimentally known to impair DNA-binding. Mutations at this tyrosine and in other residues of helix 5 are also demonstrated, by our approach, to affect the paths of communication to the DNA-binding loops and alter their native dynamics. Overall, our results are in agreement with a scenario in which ARID domains exist as an ensemble of substates, which are shifted by external perturbation, such as the interaction with DNA. Conformational changes at the DNA-binding loops are transmitted long-range by intramolecular paths, which have their heart in helix 5.
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Dix AV, Moss SM, Phan K, Hoppe T, Paoletta S, Kozma E, Gao ZG, Durell SR, Jacobson KA, Appella DH. Programmable nanoscaffolds that control ligand display to a G-protein-coupled receptor in membranes to allow dissection of multivalent effects. J Am Chem Soc 2014; 136:12296-303. [PMID: 25116377 PMCID: PMC4156868 DOI: 10.1021/ja504288s] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
A programmable
ligand display system can be used to dissect the
multivalent effects of ligand binding to a membrane receptor. An antagonist
of the A2A adenosine receptor, a G-protein-coupled receptor
that is a drug target for neurodegenerative conditions, was displayed
in 35 different multivalent configurations, and binding to A2A was determined. A theoretical model based on statistical mechanics
was developed to interpret the binding data, suggesting the importance
of receptor dimers. Using this model, extended multivalent arrangements
of ligands were constructed with progressive improvements in binding
to A2A. The results highlight the ability to use a highly
controllable multivalent approach to determine optimal ligand valency
and spacing that can be subsequently optimized for binding to a membrane
receptor. Models explaining the multivalent binding data are also
presented.
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Affiliation(s)
- Andrew V Dix
- Laboratory of Bioorganic Chemistry, NIDDK, ‡Laboratory of Biochemistry and Genetics, NIDDK, and §Laboratory of Cell Biology, CCR, NCI, National Institutes of Health , Bethesda, Maryland 20892, United States
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Cortés A, Gracia E, Moreno E, Mallol J, Lluís C, Canela EI, Casadó V. Moonlighting Adenosine Deaminase: A Target Protein for Drug Development. Med Res Rev 2014; 35:85-125. [DOI: 10.1002/med.21324] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Antoni Cortés
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED); Institute of Biomedicine of the University of Barcelona (IBUB); Department of Biochemistry and Molecular Biology; Faculty of Biology; University of Barcelona; Barcelona Spain
| | - Eduard Gracia
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED); Institute of Biomedicine of the University of Barcelona (IBUB); Department of Biochemistry and Molecular Biology; Faculty of Biology; University of Barcelona; Barcelona Spain
| | - Estefania Moreno
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED); Institute of Biomedicine of the University of Barcelona (IBUB); Department of Biochemistry and Molecular Biology; Faculty of Biology; University of Barcelona; Barcelona Spain
| | - Josefa Mallol
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED); Institute of Biomedicine of the University of Barcelona (IBUB); Department of Biochemistry and Molecular Biology; Faculty of Biology; University of Barcelona; Barcelona Spain
| | - Carme Lluís
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED); Institute of Biomedicine of the University of Barcelona (IBUB); Department of Biochemistry and Molecular Biology; Faculty of Biology; University of Barcelona; Barcelona Spain
| | - Enric I. Canela
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED); Institute of Biomedicine of the University of Barcelona (IBUB); Department of Biochemistry and Molecular Biology; Faculty of Biology; University of Barcelona; Barcelona Spain
| | - Vicent Casadó
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED); Institute of Biomedicine of the University of Barcelona (IBUB); Department of Biochemistry and Molecular Biology; Faculty of Biology; University of Barcelona; Barcelona Spain
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Navarrete LC, Barrera NP, Huidobro-Toro JP. Vas deferens neuro-effector junction: from kymographic tracings to structural biology principles. Auton Neurosci 2014; 185:8-28. [PMID: 24956963 DOI: 10.1016/j.autneu.2014.05.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 05/14/2014] [Accepted: 05/20/2014] [Indexed: 11/29/2022]
Abstract
The vas deferens is a simple bioassay widely used to study the physiology of sympathetic neurotransmission and the pharmacodynamics of adrenergic drugs. The role of ATP as a sympathetic co-transmitter has gained increasing attention and furthered our understanding of its role in sympathetic reflexes. In addition, new information has emerged on the mechanisms underlying the storage and release of ATP. Both noradrenaline and ATP concur to elicit the tissue smooth muscle contractions following sympathetic reflexes or electrical field stimulation of the sympathetic nerve terminals. ATP and adenosine (its metabolic byproduct) are powerful presynaptic regulators of co-transmitter actions. In addition, neuropeptide Y, the third member of the sympathetic triad, is an endogenous modulator. The peptide plus ATP and/or adenosine play a significant role as sympathetic modulators of transmitter's release. This review focuses on the physiological principles that govern sympathetic co-transmitter activity, with special interest in defining the motor role of ATP. In addition, we intended to review the recent structural biology findings related to the topology of the P2X1R based on the crystallized P2X4 receptor from Danio rerio, or the crystallized adenosine A2A receptor as a member of the G protein coupled family of receptors as prototype neuro modulators. This review also covers structural elements of ectonucleotidases, since some members are found in the vas deferens neuro-effector junction. The allosteric principles that apply to purinoceptors are also reviewed highlighting concepts derived from receptor theory at the light of the current available structural elements. Finally, we discuss clinical applications of these concepts.
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Affiliation(s)
- L Camilo Navarrete
- Laboratorio de Estructura de Proteínas de Membrana y Señalización, Núcleo Milenio de Biología Estructural, NuBEs, Facultad de Ciencias Biológicas, P. Universidad Católica de Chile, Chile
| | - Nelson P Barrera
- Laboratorio de Estructura de Proteínas de Membrana y Señalización, Núcleo Milenio de Biología Estructural, NuBEs, Facultad de Ciencias Biológicas, P. Universidad Católica de Chile, Chile
| | - J Pablo Huidobro-Toro
- Laboratorio de Nucleótidos, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Chile.
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Mariani S, Dell'Orco D, Felline A, Raimondi F, Fanelli F. Network and atomistic simulations unveil the structural determinants of mutations linked to retinal diseases. PLoS Comput Biol 2013; 9:e1003207. [PMID: 24009494 PMCID: PMC3757061 DOI: 10.1371/journal.pcbi.1003207] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2013] [Accepted: 07/18/2013] [Indexed: 12/19/2022] Open
Abstract
A number of incurable retinal diseases causing vision impairments derive from alterations in visual phototransduction. Unraveling the structural determinants of even monogenic retinal diseases would require network-centered approaches combined with atomistic simulations. The transducin G38D mutant associated with the Nougaret Congenital Night Blindness (NCNB) was thoroughly investigated by both mathematical modeling of visual phototransduction and atomistic simulations on the major targets of the mutational effect. Mathematical modeling, in line with electrophysiological recordings, indicates reduction of phosphodiesterase 6 (PDE) recognition and activation as the main determinants of the pathological phenotype. Sub-microsecond molecular dynamics (MD) simulations coupled with Functional Mode Analysis improve the resolution of information, showing that such impairment is likely due to disruption of the PDEγ binding cavity in transducin. Protein Structure Network analyses additionally suggest that the observed slight reduction of theRGS9-catalyzed GTPase activity of transducin depends on perturbed communication between RGS9 and GTP binding site. These findings provide insights into the structural fundamentals of abnormal functioning of visual phototransduction caused by a missense mutation in one component of the signaling network. This combination of network-centered modeling with atomistic simulations represents a paradigm for future studies aimed at thoroughly deciphering the structural determinants of genetic retinal diseases. Analogous approaches are suitable to unveil the mechanism of information transfer in any signaling network either in physiological or pathological conditions.
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Affiliation(s)
- Simona Mariani
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
- Dulbecco Telethon Institute (DTI), Modena, Italy
| | - Daniele Dell'Orco
- Department of Life Sciences and Reproduction Sect. of Biological Chemistry and Center for BioMedical Computing, University of Verona, Verona, Italy
| | - Angelo Felline
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
- Dulbecco Telethon Institute (DTI), Modena, Italy
| | - Francesco Raimondi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
- Dulbecco Telethon Institute (DTI), Modena, Italy
| | - Francesca Fanelli
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
- Dulbecco Telethon Institute (DTI), Modena, Italy
- * E-mail:
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Kaczor AA, Selent J, Sanz F, Pastor M. Modeling Complexes of Transmembrane Proteins: Systematic Analysis of ProteinProtein Docking Tools. Mol Inform 2013; 32:717-33. [PMID: 27480064 DOI: 10.1002/minf.201200150] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 05/16/2013] [Indexed: 01/25/2023]
Abstract
Proteinprotein docking methodology is frequently used to model complexes of transmembrane proteins, in particular oligomers of G protein-coupled receptors (GPCRs), even if its applicability for these systems has never been fully validated. The aim of this work is to perform a systematic study on the suitability of some widely-used proteinprotein docking software for modeling complexes of transmembrane proteins. In this study we tested the programs ZDOCK, ClusPro, HEX, GRAMM-X, PatchDock, SymmDock, and HADDOCK, using a set of membrane protein oligomers for which the 3D structure has been obtained experimentally, including opsin dimer, the recently published chemokine CXCR4 and kappa opioid receptor dimers. The results show that the docking success depends on the applied docking algorithm and scoring functions, but also on inherent structural features of the transmembrane proteins. Thus, proteins with large interface surfaces, rich in surface cavities, high-order symmetry, and small conformational change upon complex formation are well predicted more often than proteins without these features. The results of this systematic analysis provide guidelines that can be used for obtaining reliable models of transmembrane proteins, including GPCRs. Therefore they can be useful for the application of structure-based methods in drug discovery projects involving these targets.
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Affiliation(s)
- Agnieszka A Kaczor
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, IMIM (Hospital del Mar Medical Research Institute). Dr. Aiguader 88, Barcelona, Spain phone: +48 815357365, fax: +48 815357355; phone: +34 933160515, fax: +34 93 316 0550. .,Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Lab, Faculty of Pharmacy with Division for Medical Analytics, Medical University of Lublin 4A Chodźki St., PL-20059 Lublin, Poland.
| | - Jana Selent
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, IMIM (Hospital del Mar Medical Research Institute). Dr. Aiguader 88, Barcelona, Spain phone: +48 815357365, fax: +48 815357355; phone: +34 933160515, fax: +34 93 316 0550.
| | - Ferran Sanz
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, IMIM (Hospital del Mar Medical Research Institute). Dr. Aiguader 88, Barcelona, Spain phone: +48 815357365, fax: +48 815357355; phone: +34 933160515, fax: +34 93 316 0550
| | - Manuel Pastor
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, IMIM (Hospital del Mar Medical Research Institute). Dr. Aiguader 88, Barcelona, Spain phone: +48 815357365, fax: +48 815357355; phone: +34 933160515, fax: +34 93 316 0550
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Raimondi F, Felline A, Seeber M, Mariani S, Fanelli F. A Mixed Protein Structure Network and Elastic Network Model Approach to Predict the Structural Communication in Biomolecular Systems: The PDZ2 Domain from Tyrosine Phosphatase 1E As a Case Study. J Chem Theory Comput 2013; 9:2504-18. [PMID: 26583738 DOI: 10.1021/ct400096f] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Graph theory is being increasingly used to study the structural communication in biomolecular systems. This requires incorporating information on the system's dynamics, which is time-consuming and not suitable for high-throughput investigations. We propose a mixed Protein Structure Network (PSN) and Elastic Network Model (ENM)-based strategy, i.e., PSN-ENM, for fast investigation of allosterism in biological systems. PSN analysis and ENM-Normal Mode Analysis (ENM-NMA) are implemented in the structural analysis software Wordom, freely available at http://wordom.sourceforge.net/ . The method performs a systematic search of the shortest communication pathways that traverse a protein structure. A number of strategies to compare the structure networks of a protein in different functional states and to get a global picture of communication pathways are presented as well. The approach was validated on the PDZ2 domain from tyrosine phosphatase 1E (PTP1E) in its free (APO) and peptide-bound states. PDZ domains are, indeed, the systems whose structural communication and allosteric features are best characterized both in vitro and in silico. The agreement between predictions by the PSN-ENM method and in vitro evidence is remarkable and comparable to or higher than that reached by more time-consuming computational approaches tested on the same biological system. Finally, the PSN-ENM method was able to reproduce the salient communication features of unbound and bound PTP1E inferred from molecular dynamics simulations. High speed makes this method suitable for high throughput investigation of the communication pathways in large sets of biomolecular systems in different functional states.
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Affiliation(s)
- Francesco Raimondi
- Department of Life Sciences, via Campi 183, 41125, Modena, Italy.,Dulbecco Telethon Institute (DTI), via Campi 183, 41125, Modena, Italy
| | - Angelo Felline
- Department of Life Sciences, via Campi 183, 41125, Modena, Italy.,Dulbecco Telethon Institute (DTI), via Campi 183, 41125, Modena, Italy
| | - Michele Seeber
- Department of Life Sciences, via Campi 183, 41125, Modena, Italy.,Dulbecco Telethon Institute (DTI), via Campi 183, 41125, Modena, Italy
| | - Simona Mariani
- Department of Life Sciences, via Campi 183, 41125, Modena, Italy.,Dulbecco Telethon Institute (DTI), via Campi 183, 41125, Modena, Italy
| | - Francesca Fanelli
- Department of Life Sciences, via Campi 183, 41125, Modena, Italy.,Dulbecco Telethon Institute (DTI), via Campi 183, 41125, Modena, Italy
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Fanelli F. Modeling the structural communication in supramolecular complexes involving GPCRs. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2013; 914:319-36. [PMID: 22976036 DOI: 10.1007/978-1-62703-023-6_18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
This article describes a computational strategy aimed at studying the structural communication in G-Protein Coupled Receptors (GPCRs) and G proteins. The strategy relies on comparative Molecular Dynamics (MD) simulations and analyses of wild-type (i.e., reference state) vs. mutated (i.e., perturbed state), or free (i.e., reference state) vs. bound (i.e., perturbed state) forms of a GPCR or a G protein. Bound forms of a GPCR include complexes with small ligands and/or receptor dimers/oligomers, whereas bound forms of heterotrimeric GDP-bound G proteins concern the complex with a GPCR. The computational strategy includes structure prediction of a receptor monomer (in the absence of high-resolution structure), a receptor dimer/oligomer, and a receptor-G protein complex, which constitute the inputs of MD simulations. Finally, the analyses of the MD trajectories are instrumental in inferring the structural/dynamics differences between reference and perturbed states of a GPCR or a G protein. In this respect, focus will be put on the analysis of protein structure networks and communication paths.
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Affiliation(s)
- Francesca Fanelli
- Department of Chemistry, Dulbecco Telethon Institute (DTI), University of Modena and Reggio Emilia, Modena, Italy.
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38
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Molecular Modeling of Adenosine Receptors. Methods Enzymol 2013. [DOI: 10.1016/b978-0-12-407865-9.00003-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Fraga H, Papaleo E, Vega S, Velazquez-Campoy A, Ventura S. Zinc induced folding is essential for TIM15 activity as an mtHsp70 chaperone. Biochim Biophys Acta Gen Subj 2013; 1830:2139-49. [DOI: 10.1016/j.bbagen.2012.10.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Revised: 09/21/2012] [Accepted: 10/03/2012] [Indexed: 11/15/2022]
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40
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Abstract
Protein structure network (PSN) analysis is one of the graph theory-based approaches currently used to investigate the structural communication in biomolecular systems. Information on system dynamics can be provided by atomistic molecular dynamics simulations or coarse-grained Elastic Network Models paired with Normal Mode Analysis (ENM-NMA). This chapter describes the application of PSN analysis to uncover the structural communication in G protein-coupled receptors (GPCRs). Strategies to highlight changes in structural communication upon misfolding mutations, dimerization, and activation are described. Focus is put on the ENM-NMA-based strategy applied to the crystallographic structures of rhodopsin in its inactive (dark) and signaling active (meta II (MII)) states, highlighting clear changes in the PSN and the centrality of the retinal chromophore in differentiating the inactive and active states of the receptor.
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Affiliation(s)
- Francesca Fanelli
- Dulbecco Telethon Institute (DTI), Rome, Italy; Department of Chemistry, University of Modena and Reggio Emilia, Modena, Italy
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Quaternary Structure Predictions and Structural Communication Features of GPCR Dimers. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2013; 117:105-42. [DOI: 10.1016/b978-0-12-386931-9.00005-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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42
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Gracia E, Farré D, Cortés A, Ferrer-Costa C, Orozco M, Mallol J, Lluís C, Canela EI, McCormick PJ, Franco R, Fanelli F, Casadó V. The catalytic site structural gate of adenosine deaminase allosterically modulates ligand binding to adenosine receptors. FASEB J 2012. [PMID: 23193172 DOI: 10.1096/fj.12-212621] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The enzyme adenosine deaminase (ADA) is a multifunctional protein that can both degrade adenosine and bind extracellularly to adenosine receptors, acting as an allosteric modulator regulating the hormonal effects of adenosine. The molecular regions of ADA responsible for the latter are unknown. In this work, alanine scanning mutagenesis of various ADA amino acid stretches, selected through in silico docking experiments, allowed us to identify regions of the enzyme responsible for modulating both its catalytic activity and its ability to modulate agonist binding to A and A adenosine receptors (AR and AR). The combination of computational and in vitro experiments show that the structural gate to the catalytic site; i.e., the α-1 helix containing residues L58-I72 and the loop containing residues A184-I188 of ADA, were important to maintain both the catalytic efficiency of the enzyme and its action as an allosteric modulator of the adenosine receptors. These data are consistent with a predicted supramolecular assembly, in which ADA bridges AR and CD26 and are in line with the notion that the interaction of ADA with adenosine receptors has an important role in the immunosynapse. We propose that it is the ADA open form, but not the closed one, that is responsible for the functional interaction with A₁R and A₂AR.
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Affiliation(s)
- Eduard Gracia
- Laboratory of Molecular Neurobiology, Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain
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Wang CIA, Lewis RJ. Emerging opportunities for allosteric modulation of G-protein coupled receptors. Biochem Pharmacol 2012; 85:153-62. [PMID: 22975406 DOI: 10.1016/j.bcp.2012.09.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Revised: 09/03/2012] [Accepted: 09/04/2012] [Indexed: 12/23/2022]
Abstract
Their ubiquitous nature, wide cellular distribution and versatile molecular recognition and signalling help make G-protein binding receptors (GPCRs) the most important class of membrane proteins in clinical medicine, accounting for ∼40% of all current therapeutics. A large percentage of current drugs target the endogenous ligand binding (orthosteric) site, which are structurally and evolutionarily conserved, particularly among members of the same GPCR subfamily. With the recent advances in GPCR X-ray crystallography, new opportunities for developing novel subtype selective drugs have emerged. Given the increasing recognition that the extracellular surface conformation changes in response to ligand binding, it is likely that all GPCRs possess an allosteric site(s) capable of regulating GPCR signalling. Allosteric sites are less structurally conserved than their corresponding orthosteric site and thus provide new opportunities for the development of more selective drugs. Constitutive oligomerisation (dimerisation) identified in many of the GPCRs investigated, adds another dimension to the structural and functional complexity of GPCRs. In this review, we compare 60 crystal structures of nine GPCR subtypes (rhodopsin, ß₂-AR, ß₁-AR, A(2a)-AR, CXCR4, D₃R, H₁R, M₂R, M₃R) across four subfamilies of Class A GPCRs, and discuss mechanisms involved in receptor activation and potential allosteric binding sites across the highly variable extracellular surface of these GPCRs. This analysis has identified a new extracellular salt bridge (ESB-2) that might be exploited in the design of allosteric modulators.
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Affiliation(s)
- Ching-I Anderson Wang
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072 Australia
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44
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Raimondi F, Felline A, Portella G, Orozco M, Fanelli F. Light on the structural communication in Ras GTPases. J Biomol Struct Dyn 2012; 31:142-57. [PMID: 22849539 DOI: 10.1080/07391102.2012.698379] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The graph theory was combined with fluctuation dynamics to investigate the structural communication in four small G proteins, Arf1, H-Ras, RhoA, and Sec4. The topology of small GTPases is such that it requires the presence of the nucleotide to acquire a persistent structural network. The majority of communication paths involves the nucleotide and does not exist in the unbound forms. The latter are almost devoid of high-frequency paths. Thus, small Ras GTPases acquire the ability to transfer signals in the presence of nucleotide, suggesting that it modifies the intrinsic dynamics of the protein through the establishment of regions of hyperlinked nodes with high occurrence of correlated motions. The analysis of communication paths in the inactive (S(GDP)) and active (S(GTP)) states of the four G proteins strengthened the separation of the Ras-like domain into two dynamically distinct lobes, i.e. lobes 1 and 2, representing, respectively, the N-terminal and C-terminal halves of the domain. In the framework of this separation, interfunctional states and interfamily differences could be inferred. The structure network undergoes a reshaping depending on the bound nucleotide. Nucleotide-dependent divergences in structural communication reach the maximum in Arf1 and the minimum in RhoA. In Arf1, the nucleotide-dependent paths essentially express a communication between the G box 4 (G4) and distal portions of lobe 1. In the S(GDP) state, the G4 communicates with the N-term, while, in the S(GTP) state, the G4 communicates with the switch II. Clear differences could be also found between Arf1 and the other three G proteins. In Arf1, the nucleotide tends to communicate with distal portions of lobe 1, whereas in H-Ras, RhoA, and Sec4 it tends to communicate with a cluster of aromatic/hydrophobic amino acids in lobe 2. These differences may be linked, at least in part, to the divergent membrane anchoring modes that would involve the N-term for the Arf family and the C-term for the Rab/Ras/Rho families.
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Affiliation(s)
- Francesco Raimondi
- Department of Chemistry, University of Modena and Reggio Emilia, Modena, Italy
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45
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Jara O, Acuña R, García IE, Maripillán J, Figueroa V, Sáez JC, Araya-Secchi R, Lagos CF, Pérez-Acle T, Berthoud VM, Beyer EC, Martínez AD. Critical role of the first transmembrane domain of Cx26 in regulating oligomerization and function. Mol Biol Cell 2012; 23:3299-311. [PMID: 22787277 PMCID: PMC3431943 DOI: 10.1091/mbc.e11-12-1058] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
This study identifies a motif within the first transmembrane domain of Cx26, from amino acids Val-37 through Ala-40, that is critical for oligomerization and function. The impacts of deafness-associated mutations within this motif upon gap junction channel and hemichannel functions correlate with the severity of disease that they cause. To identify motifs involved in oligomerization of the gap junction protein Cx26, we studied individual transmembrane (TM) domains and the full-length protein. Using the TOXCAT assay for interactions of isolated TM α-helices, we found that TM1, a Cx26 pore domain, had a strong propensity to homodimerize. We identified amino acids Val-37–Ala-40 (VVAA) as the TM1 motif required for homodimerization. Two deafness-associated Cx26 mutations localized in this region, Cx26V37I and Cx26A40G, differentially affected dimerization. TM1-V37I dimerized only weakly, whereas TM1-A40G did not dimerize. When the full-length mutants were expressed in HeLa cells, both Cx26V37I and Cx26A40G formed oligomers less efficiently than wild-type Cx26. A Cx26 cysteine substitution mutant, Cx26V37C formed dithiothreitol-sensitive dimers. Substitution mutants of Val-37 formed intercellular channels with reduced function, while mutants of Ala-40 did not form functional gap junction channels. Unlike wild-type Cx26, neither Cx26V37I nor Cx26A40G formed functional hemichannels in low extracellular calcium. Thus the VVAA motif of Cx26 is critical for TM1 dimerization, hexamer formation, and channel function. The differential effects of VVAA mutants on hemichannels and gap junction channels imply that inter-TM interactions can differ in unapposed and docked hemichannels. Moreover, Cx26 oligomerization appears dependent on transient TM1 dimerization as an intermediate step.
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Affiliation(s)
- Oscar Jara
- Centro Interdisciplinario de Neurociencias de Valparaíso, Universidad de Valparaíso, Valparaíso, Chile
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Pasi M, Tiberti M, Arrigoni A, Papaleo E. xPyder: a PyMOL plugin to analyze coupled residues and their networks in protein structures. J Chem Inf Model 2012; 52:1865-74. [PMID: 22721491 DOI: 10.1021/ci300213c] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A versatile method to directly identify and analyze short- or long-range coupled or communicating residues in a protein conformational ensemble is of extreme relevance to achieve a complete understanding of protein dynamics and structural communication routes. Here, we present xPyder, an interface between one of the most employed molecular graphics systems, PyMOL, and the analysis of dynamical cross-correlation matrices (DCCM). The approach can also be extended, in principle, to matrices including other indexes of communication propensity or intensity between protein residues, as well as the persistence of intra- or intermolecular interactions, such as those underlying protein dynamics. The xPyder plugin for PyMOL 1.4 and 1.5 is offered as Open Source software via the GPL v2 license, and it can be found, along with the installation package, the user guide, and examples, at http://linux.btbs.unimib.it/xpyder/.
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Affiliation(s)
- Marco Pasi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.zza della Scienza 2, 20126 Milan, Italy
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Salon JA, Lodowski DT, Palczewski K. The significance of G protein-coupled receptor crystallography for drug discovery. Pharmacol Rev 2012; 63:901-37. [PMID: 21969326 DOI: 10.1124/pr.110.003350] [Citation(s) in RCA: 160] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Crucial as molecular sensors for many vital physiological processes, seven-transmembrane domain G protein-coupled receptors (GPCRs) comprise the largest family of proteins targeted by drug discovery. Together with structures of the prototypical GPCR rhodopsin, solved structures of other liganded GPCRs promise to provide insights into the structural basis of the superfamily's biochemical functions and assist in the development of new therapeutic modalities and drugs. One of the greatest technical and theoretical challenges to elucidating and exploiting structure-function relationships in these systems is the emerging concept of GPCR conformational flexibility and its cause-effect relationship for receptor-receptor and receptor-effector interactions. Such conformational changes can be subtle and triggered by relatively small binding energy effects, leading to full or partial efficacy in the activation or inactivation of the receptor system at large. Pharmacological dogma generally dictates that these changes manifest themselves through kinetic modulation of the receptor's G protein partners. Atomic resolution information derived from increasingly available receptor structures provides an entrée to the understanding of these events and practically applying it to drug design. Supported by structure-activity relationship information arising from empirical screening, a unified structural model of GPCR activation/inactivation promises to both accelerate drug discovery in this field and improve our fundamental understanding of structure-based drug design in general. This review discusses fundamental problems that persist in drug design and GPCR structural determination.
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Affiliation(s)
- John A Salon
- Department of Molecular Structure, Amgen Incorporated, Thousand Oaks, California, USA
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48
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Papaleo E, Lindorff-Larsen K, De Gioia L. Paths of long-range communication in the E2 enzymes of family 3: a molecular dynamics investigation. Phys Chem Chem Phys 2012; 14:12515-25. [DOI: 10.1039/c2cp41224a] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Fanelli F, De Benedetti PG. Update 1 of: computational modeling approaches to structure-function analysis of G protein-coupled receptors. Chem Rev 2011; 111:PR438-535. [PMID: 22165845 DOI: 10.1021/cr100437t] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Francesca Fanelli
- Dulbecco Telethon Institute, University of Modena and Reggio Emilia, via Campi 183, 41125 Modena, Italy.
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50
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Szymanski DW, Papanastasiou M, Melchior K, Zvonok N, Mercier RW, Janero DR, Thakur GA, Cha S, Wu B, Karger B, Makriyannis A. Mass spectrometry-based proteomics of human cannabinoid receptor 2: covalent cysteine 6.47(257)-ligand interaction affording megagonist receptor activation. J Proteome Res 2011; 10:4789-98. [PMID: 21861534 DOI: 10.1021/pr2005583] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The lack of experimental characterization of the structures and ligand-binding motifs of therapeutic G-protein coupled receptors (GPCRs) hampers rational drug discovery. The human cannabinoid receptor 2 (hCB2R) is a class-A GPCR and promising therapeutic target for small-molecule cannabinergic agonists as medicines. Prior mutational and modeling data constitute provisional evidence that AM-841, a high-affinity classical cannabinoid, interacts with cysteine C6.47(257) in hCB2R transmembrane helix 6 (TMH6) to afford improved hCB2R selectivity and unprecedented agonist potency. We now apply bottom-up mass spectrometry (MS)-based proteomics to define directly the hCB2R-AM-841 interaction at the amino-acid level. Recombinant hCB2R, overexpressed as an N-terminal FLAG-tagged/C-terminal 6His-tagged protein (FLAG-hCB2R-6His) with a baculovirus system, was solubilized and purified by immunochromatography as functional receptor. A multiplex multiple reaction monitoring (MRM)-MS method was developed that allowed us to observe unambiguously all seven discrete TMH peptides in the tryptic digest of purified FLAG-hCB2R-6His and demonstrate that AM-841 modifies hCB2R TMH6 exclusively. High-resolution mass spectra of the TMH6 tryptic peptide obtained by Q-TOF MS/MS analysis demonstrated that AM-841 covalently and selectively modifies hCB2R at TMH6 cysteine C6.47(257). These data demonstrate how integration of MS-based proteomics into a ligand-assisted protein structure (LAPS) experimental paradigm can offer guidance to structure-enabled GPCR agonist design.
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Affiliation(s)
- Dennis W Szymanski
- Center for Drug Discovery, Department of Chemistry and Chemical Biology, College of Science, Northeastern University , Boston, Massachusetts 02115-5000, United States
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