1
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Ren L, Jing Z, Xia F, Zhang JZ, Li Y. Toxic Effect of Fullerene and Its Derivatives upon the Transmembrane β2-Adrenergic Receptors. Molecules 2022; 27:molecules27144562. [PMID: 35889435 PMCID: PMC9323646 DOI: 10.3390/molecules27144562] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/28/2022] [Accepted: 07/10/2022] [Indexed: 12/04/2022] Open
Abstract
Numerous experiments have revealed that fullerene (C60) and its derivatives can bind to proteins and affect their biological functions. In this study, we explored the interaction between fullerine and the β2-adrenergic receptor (β2AR). The MD simulation results show that fullerene binds with the extracellular loop 2 (ECL2) and intracellular loop 2 (ICL2) of β2AR through hydrophobic interactions and π–π stacking interactions. In the C60_in1 trajectory, due to the π–π stacking interactions of fullerene molecules with PHE and PRO residues on ICL2, ICL2 completely flipped towards the fullerene direction and the fullerene moved slowly into the lipid membrane. When five fullerene molecules were placed on the extracellular side, they preferred to stack into a stable fullerene cluster (a deformed tetrahedral aggregate), and had almost no effect on the structure of β2AR. The hydroxyl groups of fullerene derivatives (C60(OH)X, X represents the number of hydroxyl groups, X = 4, 8) can form strong hydrogen bonds with the ECL2, helix6, and helix7 of β2AR. The hydroxyl groups firmly grasp the β2AR receptor like several claws, blocking the binding entry of ligands. The simulation results show that fullerene and fullerene derivatives may have a significant effect on the local structure of β2AR, especially the distortion of helix4, but bring about no great changes within the overall structure. It was found that C60 did not compete with ligands for binding sites, but blocked the ligands’ entry into the pocket channel. All the above observations suggest that fullerene and its derivatives exhibit certain cytotoxicity.
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Affiliation(s)
- Longlong Ren
- College of Mechanical and Electronic Engineering, Shandong Agricultural University, Tai’an 271018, China; (L.R.); (Z.J.)
| | - Zhenxiang Jing
- College of Mechanical and Electronic Engineering, Shandong Agricultural University, Tai’an 271018, China; (L.R.); (Z.J.)
| | - Fei Xia
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China; (F.X.); (J.Z.Z.)
| | - John Zenghui Zhang
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China; (F.X.); (J.Z.Z.)
| | - Yang Li
- College of Information Science and Engineering, Shandong Agricultural University, Tai’an 271018, China
- Correspondence:
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2
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Errasti-Murugarren E, Bartoccioni P, Palacín M. Membrane Protein Stabilization Strategies for Structural and Functional Studies. MEMBRANES 2021; 11:membranes11020155. [PMID: 33671740 PMCID: PMC7926488 DOI: 10.3390/membranes11020155] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/15/2021] [Accepted: 02/18/2021] [Indexed: 02/07/2023]
Abstract
Accounting for nearly two-thirds of known druggable targets, membrane proteins are highly relevant for cell physiology and pharmacology. In this regard, the structural determination of pharmacologically relevant targets would facilitate the intelligent design of new drugs. The structural biology of membrane proteins is a field experiencing significant growth as a result of the development of new strategies for structure determination. However, membrane protein preparation for structural studies continues to be a limiting step in many cases due to the inherent instability of these molecules in non-native membrane environments. This review describes the approaches that have been developed to improve membrane protein stability. Membrane protein mutagenesis, detergent selection, lipid membrane mimics, antibodies, and ligands are described in this review as approaches to facilitate the production of purified and stable membrane proteins of interest for structural and functional studies.
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Affiliation(s)
- Ekaitz Errasti-Murugarren
- Laboratory of Amino acid Transporters and Disease, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028 Barcelona, Spain;
- CIBERER (Centro Español en Red de Biomedicina de Enfermedades Raras), 28029 Barcelona, Spain
- Correspondence: (E.E.-M.); (M.P.)
| | - Paola Bartoccioni
- Laboratory of Amino acid Transporters and Disease, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028 Barcelona, Spain;
- CIBERER (Centro Español en Red de Biomedicina de Enfermedades Raras), 28029 Barcelona, Spain
| | - Manuel Palacín
- Laboratory of Amino acid Transporters and Disease, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028 Barcelona, Spain;
- CIBERER (Centro Español en Red de Biomedicina de Enfermedades Raras), 28029 Barcelona, Spain
- Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona, 08028 Barcelona, Spain
- Correspondence: (E.E.-M.); (M.P.)
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3
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Guidolin D, Marcoli M, Tortorella C, Maura G, Agnati LF. Adenosine A 2A-dopamine D 2 receptor-receptor interaction in neurons and astrocytes: Evidence and perspectives. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2019; 169:247-277. [PMID: 31952688 DOI: 10.1016/bs.pmbts.2019.11.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The discovery of receptor-receptor interactions in the early 1980s, together with a more accurate focusing of allosteric mechanisms in proteins, expanded the knowledge on the G protein-coupled receptor (GPCR)-mediated signaling processes. GPCRs were seen to operate not only as monomers, but also as quaternary structures shaped by allosteric interactions. These integrative mechanisms can change the function of the GPCRs involved, leading to a sophisticated dynamic of the receptor assembly in terms of modulation of recognition and signaling. In this context, the heterodimeric complex formed by the adenosine A2A and the dopamine D2 receptors likely represents a prototypical example. The pharmacological evidence obtained, together with the tissue distribution of the A2A-D2 heteromeric complexes, suggested they could represent a target for new therapeutic strategies addressing significant disorders of the central nervous system. The research findings and the perspectives they offer from the therapeutic standpoint are the focus of the here presented discussion.
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Affiliation(s)
- Diego Guidolin
- Department of Neuroscience, Section of Anatomy, University of Padova, Padova, Italy.
| | - Manuela Marcoli
- Department of Pharmacy and Center of Excellence for Biomedical Research, University of Genova, Genova, Italy
| | - Cinzia Tortorella
- Department of Neuroscience, Section of Anatomy, University of Padova, Padova, Italy
| | - Guido Maura
- Department of Pharmacy and Center of Excellence for Biomedical Research, University of Genova, Genova, Italy
| | - Luigi F Agnati
- Department of Biomedical Sciences, University of Modena and Reggio Emilia, Modena, Italy; Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
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4
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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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5
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Fatakia SN, Sarkar P, Chattopadhyay A. A collage of cholesterol interaction motifs in the serotonin 1A receptor: An evolutionary implication for differential cholesterol interaction. Chem Phys Lipids 2019; 221:184-192. [PMID: 30822391 DOI: 10.1016/j.chemphyslip.2019.02.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 02/25/2019] [Accepted: 02/25/2019] [Indexed: 12/22/2022]
Abstract
The serotonin1A receptor is a representative member of the G protein-coupled receptor (GPCR) superfamily and acts as an important drug target. In our previous work, we comprehensively demonstrated that membrane cholesterol is necessary in the organization, dynamics and function of the serotonin1A receptor. In this context, analysis of high-resolution GPCR crystal structures in general and in silico studies of the serotonin1A receptor in particular, have suggested the presence of cholesterol interaction sites (hotspots) in various regions of the receptor. In this work, we have identified an evolutionarily conserved collage of four categories of cholesterol interaction motifs associated with transmembrane helix V and the adjacent intracellular loop 3 fragment of the vertebrate serotonin1A receptor. This collage of motifs represents a total of twenty diverse context-dependent cholesterol interaction configurations. We envision that the gamut of cholesterol interaction sites, characterized by sequence plasticity in cholesterol interaction, could be relevant in receptor-cholesterol interaction in membranes of varying cholesterol content and organization, as found in diverse cell types. We conclude that an evolutionarily conserved mechanism of GPCR-cholesterol interaction allows the serotonin1A receptor to adapt to diverse membrane cholesterol levels during natural evolution.
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Affiliation(s)
- Sarosh N Fatakia
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India.
| | - Parijat Sarkar
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
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6
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Guidolin D, Marcoli M, Tortorella C, Maura G, Agnati LF. Receptor-Receptor Interactions as a Widespread Phenomenon: Novel Targets for Drug Development? Front Endocrinol (Lausanne) 2019; 10:53. [PMID: 30833931 PMCID: PMC6387912 DOI: 10.3389/fendo.2019.00053] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 01/21/2019] [Indexed: 12/19/2022] Open
Abstract
The discovery of receptor-receptor interactions (RRI) has expanded our understanding of the role that G protein-coupled receptors (GPCRs) play in intercellular communication. The finding that GPCRs can operate as receptor complexes, and not only as monomers, suggests that several different incoming signals could already be integrated at the plasma membrane level via direct allosteric interactions between the protomers that form the complex. Most research in this field has focused on neuronal populations and has led to the identification of a large number of RRI. However, RRI have been seen to occur not only in neurons but also in astrocytes and, outside the central nervous system, in cells of the cardiovascular and endocrine systems and in cancer cells. Furthermore, RRI involving the formation of macromolecular complexes are not limited to GPCRs, being also observed in other families of receptors. Thus, RRI appear as a widespread phenomenon and oligomerization as a common mechanism for receptor function and regulation. The discovery of these macromolecular assemblies may well have a major impact on pharmacology. Indeed, the formation of receptor complexes significantly broadens the spectrum of mechanisms available to receptors for recognition and signaling, which may be implemented through modulation of the binding sites of the adjacent protomers and of their signal transduction features. In this context, the possible appearance of novel allosteric sites in the receptor complex structure may be of particular relevance. Thus, the existence of RRI offers the possibility of new therapeutic approaches, and novel pharmacological strategies for disease treatment have already been proposed. Several challenges, however, remain. These include the accurate characterization of the role that the receptor complexes identified so far play in pathological conditions and the development of ligands specific to given receptor complexes, in order to efficiently exploit the pharmacological properties of these complexes.
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Affiliation(s)
- Diego Guidolin
- Department of Neuroscience, University of Padova, Padova, Italy
- *Correspondence: Diego Guidolin
| | - Manuela Marcoli
- Department of Pharmacy and Center of Excellence for Biomedical Research, University of Genova, Genoa, Italy
| | | | - Guido Maura
- Department of Pharmacy and Center of Excellence for Biomedical Research, University of Genova, Genoa, Italy
| | - Luigi F. Agnati
- Department of Biomedical Sciences, University of Modena and Reggio Emilia, Modena, Italy
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
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7
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Borroto-Escuela DO, Rodriguez D, Romero-Fernandez W, Kapla J, Jaiteh M, Ranganathan A, Lazarova T, Fuxe K, Carlsson J. Mapping the Interface of a GPCR Dimer: A Structural Model of the A 2A Adenosine and D 2 Dopamine Receptor Heteromer. Front Pharmacol 2018; 9:829. [PMID: 30214407 PMCID: PMC6125358 DOI: 10.3389/fphar.2018.00829] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 07/10/2018] [Indexed: 12/17/2022] Open
Abstract
The A2A adenosine (A2AR) and D2 dopamine (D2R) receptors form oligomers in the cell membrane and allosteric interactions across the A2AR–D2R heteromer represent a target for development of drugs against central nervous system disorders. However, understanding of the molecular determinants of A2AR–D2R heteromerization and the allosteric antagonistic interactions between the receptor protomers is still limited. In this work, a structural model of the A2AR–D2R heterodimer was generated using a combined experimental and computational approach. Regions involved in the heteromer interface were modeled based on the effects of peptides derived from the transmembrane (TM) helices on A2AR–D2R receptor–receptor interactions in bioluminescence resonance energy transfer (BRET) and proximity ligation assays. Peptides corresponding to TM-IV and TM-V of the A2AR blocked heterodimer interactions and disrupted the allosteric effect of A2AR activation on D2R agonist binding. Protein–protein docking was used to construct a model of the A2AR–D2R heterodimer with a TM-IV/V interface, which was refined using molecular dynamics simulations. Mutations in the predicted interface reduced A2AR–D2R interactions in BRET experiments and altered the allosteric modulation. The heterodimer model provided insights into the structural basis of allosteric modulation and the technique developed to characterize the A2AR–D2R interface can be extended to study the many other G protein-coupled receptors that engage in heteroreceptor complexes.
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Affiliation(s)
| | - David Rodriguez
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Wilber Romero-Fernandez
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Jon Kapla
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Mariama Jaiteh
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Anirudh Ranganathan
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Tzvetana Lazarova
- Department of Biochemistry and Molecular Biology, Institute of Neuroscience, Faculty of Medicine, Autonomous University of Barcelona, Barcelona, Spain
| | - Kjell Fuxe
- Department of Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - Jens Carlsson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
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8
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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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9
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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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10
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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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11
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Zainabadi K. Malaria Parasite CLAG3, a Protein Linked to Nutrient Channels, Participates in High Molecular Weight Membrane-Associated Complexes in the Infected Erythrocyte. PLoS One 2016; 11:e0157390. [PMID: 27299521 PMCID: PMC4907441 DOI: 10.1371/journal.pone.0157390] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 05/27/2016] [Indexed: 11/24/2022] Open
Abstract
Malaria infected erythrocytes show increased permeability to a number of solutes important for parasite growth as mediated by the Plasmodial Surface Anion Channel (PSAC). The P. falciparum clag3 genes have recently been identified as key determinants of PSAC, though exactly how they contribute to channel function and whether additional host/parasite proteins are required remain unknown. To begin to answer these questions, I have taken a biochemical approach. Here I have used an epitope-tagged CLAG3 parasite to perform co-immunoprecipitation experiments using membrane fractions of infected erythrocytes. Native PAGE and mass spectrometry studies reveal that CLAG3 participate in at least three different high molecular weight complexes: a ~720kDa complex consisting of CLAG3, RHOPH2 and RHOPH3; a ~620kDa complex consisting of CLAG3 and RHOPH2; and a ~480kDa complex composed solely of CLAG3. Importantly, these complexes can be found throughout the parasite lifecycle but are absent in untransfected controls. Extracellular biotin labeling and protease susceptibility studies localize the 480kDa complex to the erythrocyte membrane. This complex, likely composed of a homo-oligomer of 160kDa CLAG3, may represent a functional subunit, possibly the pore, of PSAC.
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Affiliation(s)
- Kayvan Zainabadi
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, NIH, Rockville, Maryland, United States of America
- * E-mail:
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12
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Rodríguez-Banqueri A, Errasti-Murugarren E, Bartoccioni P, Kowalczyk L, Perálvarez-Marín A, Palacín M, Vázquez-Ibar JL. Stabilization of a prokaryotic LAT transporter by random mutagenesis. ACTA ACUST UNITED AC 2016; 147:353-68. [PMID: 26976827 PMCID: PMC4810068 DOI: 10.1085/jgp.201511510] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 02/22/2016] [Indexed: 12/31/2022]
Abstract
The knowledge of three-dimensional structures at atomic resolution of membrane transport proteins has improved considerably our understanding of their physiological roles and pathological implications. However, most structural biology techniques require an optimal candidate within a protein family for structural determination with (a) reasonable production in heterologous hosts and (b) good stability in detergent micelles. SteT, the Bacillus subtilis L-serine/L-threonine exchanger is the best-known prokaryotic paradigm of the mammalian L-amino acid transporter (LAT) family. Unfortunately, SteT's lousy stability after extracting from the membrane prevents its structural characterization. Here, we have used an approach based on random mutagenesis to engineer stability in SteT. Using a split GFP complementation assay as reporter of protein expression and membrane insertion, we created a library of 70 SteT mutants each containing random replacements of one or two residues situated in the transmembrane domains. Analysis of expression and monodispersity in detergent of this library permitted the identification of evolved versions of SteT with a significant increase in both expression yield and stability in detergent with respect to wild type. In addition, these experiments revealed a correlation between the yield of expression and the stability in detergent micelles. Finally, and based on protein delipidation and relipidation assays together with transport experiments, possible mechanisms of SteT stabilization are discussed. Besides optimizing a member of the LAT family for structural determination, our work proposes a new approach that can be used to optimize any membrane protein of interest.
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Affiliation(s)
- Arturo Rodríguez-Banqueri
- Institute for Research in Biomedicine (IRB), Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Ekaitz Errasti-Murugarren
- Institute for Research in Biomedicine (IRB), Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Paola Bartoccioni
- Institute for Research in Biomedicine (IRB), Barcelona Institute of Science and Technology, 08028 Barcelona, Spain Spanish Biomedical Research Center in Rare Diseases (CIBERER), 08028 Barcelona, Spain
| | - Lukasz Kowalczyk
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Alex Perálvarez-Marín
- Biophysics Unit, Department of Biochemistry and Molecular Biology, Autonomous University of Barcelona, 08193 Cerdanyola del Vallés, Spain
| | - Manuel Palacín
- Institute for Research in Biomedicine (IRB), Barcelona Institute of Science and Technology, 08028 Barcelona, Spain Spanish Biomedical Research Center in Rare Diseases (CIBERER), 08028 Barcelona, Spain Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
| | - José Luis Vázquez-Ibar
- Institute for Integrative Biology of the Cell (I2BC), CEA, French National Centre for Scientific Research (CNRS) UMR 9198, University Paris-Sud, University Paris-Saclay, F-91198 Gif-sur-Yvette, France
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Cohen LS, Fracchiolla KE, Becker J, Naider F. Invited review GPCR structural characterization: Using fragments as building blocks to determine a complete structure. Biopolymers 2014; 102:223-43. [DOI: 10.1002/bip.22490] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 03/24/2014] [Accepted: 03/27/2014] [Indexed: 12/30/2022]
Affiliation(s)
- Leah S. Cohen
- Department of Chemistry; The College of Staten Island, City University of New York (CUNY); Staten Island NY 10314
| | - Katrina E. Fracchiolla
- Department of Chemistry; The College of Staten Island, City University of New York (CUNY); Staten Island NY 10314
| | - Jeff Becker
- Department of Microbiology; University of Tennessee; Knoxville TN 37996
| | - Fred Naider
- Department of Chemistry; The College of Staten Island, City University of New York (CUNY); Staten Island NY 10314
- Department of Biochemistry; The Graduate Center; CUNY NY 10016-4309
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14
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Britton ZT, Hanle EI, Robinson AS. An expression and purification system for the biosynthesis of adenosine receptor peptides for biophysical and structural characterization. Protein Expr Purif 2012; 84:224-35. [PMID: 22722102 PMCID: PMC3572917 DOI: 10.1016/j.pep.2012.06.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Revised: 05/29/2012] [Accepted: 06/08/2012] [Indexed: 11/15/2022]
Abstract
Biophysical and structural characterization of G protein-coupled receptors (GPCRs) has been limited due to difficulties in expression, purification, and vitro stability of the full-length receptors. "Divide and conquer" approaches aimed at the NMR characterization of peptides corresponding to specific regions of the receptor have yielded insights into the structure and dynamics of GPCR activation and signaling. Though significant progress has been made in the generation of peptides that are composed of GPCR transmembrane domains, current methods utilize fusion protein strategies that require chemical cleavage and peptide separation via chromatographic means. We have developed an expression and purification system based on fusion to ketosteroid isomerase, thrombin cleavage, and tandem affinity chromatography that enables the solubilization, cleavage, and characterization in a single detergent system relevant for biophysical and structural characterization. We have applied this expression and purification system to the production and characterization of peptides of the adenosine receptor family of GPCRs in Escherichia coli. Herein, we demonstrate using a model peptide that includes extracellular loop 3, transmembrane domain 7, and a portion of the carboxy-terminus of the adenosine A(2)a receptor that the peptide is sufficiently pure for biophysical characterization, where it adopts α-helical structure. Furthermore, we demonstrate the utility of this system by optimizing the construct for thrombin processing and apply the system to peptides with more complex structures.
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Affiliation(s)
- Zachary T. Britton
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, DE 19716, United States
| | - Elizabeth I. Hanle
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, DE 19716, United States
| | - Anne S. Robinson
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, DE 19716, United States
- Department of Chemical and Biomolecular Engineering, 300 Lindy Boggs Laboratory, Tulane University, New Orleans, LA 70118, United States
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Reyes-Alcaraz A, Martínez-Archundia M, Ramon E, Garriga P. Salt effects on the conformational stability of the visual G-protein-coupled receptor rhodopsin. Biophys J 2012; 101:2798-806. [PMID: 22261069 DOI: 10.1016/j.bpj.2011.09.049] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Revised: 09/21/2011] [Accepted: 09/26/2011] [Indexed: 11/28/2022] Open
Abstract
Membrane protein stability is a key parameter with important physiological and practical implications. Inorganic salts affect protein stability, but the mechanisms of their interactions with membrane proteins are not completely understood. We have undertaken the study of a prototypical G-protein-coupled receptor, the α-helical membrane protein rhodopsin from vertebrate retina, and explored the effects of inorganic salts on the thermal decay properties of both its inactive and photoactivated states. Under high salt concentrations, rhodopsin significantly increased its activation enthalpy change for thermal bleaching, whereas acid denaturation affected the formation of a denatured loose-bundle state for both the active and inactive conformations. This behavior seems to correlate with changes in protonated Schiff-base hydrolysis. However, chromophore regeneration with the 11-cis-retinal chromophore and MetarhodopsinII decay kinetics were slower only in the presence of sodium chloride, suggesting that in this case, the underlying phenomenon may be linked to the activation of rhodopsin and the retinal release processes. Furthermore, the melting temperature, determined by means of circular dichroism and differential scanning calorimetry measurements, was increased in the presence of high salt concentrations. The observed effects on rhodopsin could indicate that salts favor electrostatic interactions in the retinal binding pocket and indirectly favor hydrophobic interactions at the membrane protein receptor core. These effects can be exploited in applications where the stability of membrane proteins in solution is highly desirable.
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Affiliation(s)
- Arfaxad Reyes-Alcaraz
- Group of Molecular and Industrial Biotechnology, Centre de Biotecnologia Molecular, Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Terrassa, Catalonia, Spain
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16
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Thévenin D, Lazarova T. Identifying and measuring transmembrane helix-helix interactions by FRET. Methods Mol Biol 2012; 914:87-106. [PMID: 22976024 DOI: 10.1007/978-1-62703-023-6_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Specific interactions between helical transmembrane domains (TMs) play essential roles in the mechanisms governing the folding, stability and assembly of integral membrane proteins. Thus, it is appealing to identify helix-helix contacts and to seek the structural determinants of such interactions at the molecular level. Here, we provide a protocol for detecting and measuring specific helix-helix interactions in liposomes by Förster resonance energy transfer (FRET), using peptides corresponding to the TM domains of an integral membrane protein. We give a detailed procedure and practical guidelines on how to design, prepare, handle, and characterize fluorescently labeled TM peptides reconstituted in large unilamellar lipid vesicles. We also discuss some critical aspects of FRET measurements to ensure the correct analysis and interpretation of spectral data. Our method uses tryptophan/pyrene as the donor-acceptor FRET pair, but it can be easily adapted to other fluorescence pairs and to other membrane mimetic environments. The ability to identify crucial interhelical contacts is a valuable tool for the study of the stability, assembly, and function of the important and experimentally challenging helical membrane proteins.
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Affiliation(s)
- Damien Thévenin
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
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17
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Structural investigation of the C-terminal catalytic fragment of presenilin 1. Proc Natl Acad Sci U S A 2010; 107:9644-9. [PMID: 20445084 DOI: 10.1073/pnas.1000778107] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The gamma-secretase complex has a decisive role in the development of Alzheimer's disease, in that it cleaves a precursor to create the amyloid beta peptide whose aggregates form the senile plaques encountered in the brains of patients. Gamma-secretase is a member of the intramembrane-cleaving proteases which process their transmembrane substrates within the bilayer. Many of the mutations encountered in early onset familial Alzheimer's disease are linked to presenilin 1, the catalytic component of gamma-secretase, whose active form requires its endoproteolytic cleavage into N-terminal and C-terminal fragments. Although there is general agreement regarding the topology of the N-terminal fragment, studies of the C-terminal fragment have yielded ambiguous and contradictory results that may be difficult to reconcile in the absence of structural information. Here we present the first structure of the C-terminal fragment of human presenilin 1, as obtained from NMR studies in SDS micelles. The structure reveals a topology where the membrane is likely traversed three times in accordance with the more generally accepted nine transmembrane domain model of presenilin 1, but contains unique structural features adapted to accommodate the unusual intramembrane catalysis. These include a putative half-membrane-spanning helix N-terminally harboring the catalytic aspartate, a severely kinked helical structure toward the C terminus as well as a soluble helix in the assumed-to-be unstructured N-terminal loop.
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18
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Bordag N, Keller S. α-Helical transmembrane peptides: A “Divide and Conquer” approach to membrane proteins. Chem Phys Lipids 2010; 163:1-26. [PMID: 19682979 DOI: 10.1016/j.chemphyslip.2009.07.009] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2009] [Revised: 07/21/2009] [Accepted: 07/21/2009] [Indexed: 11/26/2022]
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Neumoin A, Cohen LS, Arshava B, Tantry S, Becker JM, Zerbe O, Naider F. Structure of a double transmembrane fragment of a G-protein-coupled receptor in micelles. Biophys J 2009; 96:3187-96. [PMID: 19383463 DOI: 10.1016/j.bpj.2009.01.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2008] [Revised: 01/08/2009] [Accepted: 01/13/2009] [Indexed: 11/29/2022] Open
Abstract
The structure and dynamic properties of an 80-residue fragment of Ste2p, the G-protein-coupled receptor for alpha-factor of Saccharomyces cerevisiae, was studied in LPPG micelles with the use of solution NMR spectroscopy. The fragment Ste2p(G31-T110) (TM1-TM2) consisted of 19 residues from the N-terminal domain, the first TM helix (TM1), the first cytoplasmic loop, the second TM helix (TM2), and seven residues from the first extracellular loop. Multidimensional NMR experiments on [(15)N], [(15)N, (13)C], [(15)N, (13)C, (2)H]-labeled TM1-TM2 and on protein fragments selectively labeled at specific amino acid residues or protonated at selected methyl groups resulted in >95% assignment of backbone and side-chain nuclei. The NMR investigation revealed the secondary structure of specific residues of TM1-TM2. TALOS constraints and NOE connectivities were used to calculate a structure for TM1-TM2 that was highlighted by the presence of three alpha-helices encompassing residues 39-47, 49-72, and 80-103, with higher flexibility around the internal Arg(58) site of TM1. RMSD values of individually superimposed helical segments 39-47, 49-72, and 80-103 were 0.25 +/- 0.10 A, 0.40 +/- 0.13 A, and 0.57 +/- 0.19 A, respectively. Several long-range interhelical connectivities supported the folding of TM1-TM2 into a tertiary structure typified by a crossed helix that splays apart toward the extracellular regions and contains considerable flexibility in the G(56)VRSG(60) region. (15)N-relaxation and hydrogen-deuterium exchange data support a stable fold for the TM parts of TM1-TM2, whereas the solvent-exposed segments are more flexible. The NMR structure is consistent with the results of biochemical experiments that identified the ligand-binding site within this region of the receptor.
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Affiliation(s)
- Alexey Neumoin
- Institute of Organic Chemistry, University of Zurich, Zurich, Switzerland
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