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Song W, Duncan AL, Sansom MSP. Modulation of adenosine A2a receptor oligomerization by receptor activation and PIP 2 interactions. Structure 2021; 29:1312-1325.e3. [PMID: 34270937 PMCID: PMC8581623 DOI: 10.1016/j.str.2021.06.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/28/2021] [Accepted: 06/25/2021] [Indexed: 11/23/2022]
Abstract
GPCRs have been shown to form oligomers, which generate distinctive signaling outcomes. However, the structural nature of the oligomerization process remains uncertain. We have characterized oligomeric configurations of the adenosine A2a receptor (A2aR) by combining large-scale molecular dynamics simulations with Markov state models. These oligomeric structures may also serve as templates for studying oligomerization of other class A GPCRs. Our simulation data revealed that receptor activation results in enhanced oligomerization, more diverse oligomer populations, and a more connected oligomerization network. The active state conformation of the A2aR shifts protein-protein association interfaces to those involving intracellular loop ICL3 and transmembrane helix TM6. Binding of PIP2 to A2aR stabilizes protein-protein interactions via PIP2-mediated association interfaces. These results indicate that A2aR oligomerization is responsive to the local membrane lipid environment. This, in turn, suggests a modulatory effect on A2aR whereby a given oligomerization profile favors the dynamic formation of specific supramolecular signaling complexes.
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Affiliation(s)
- Wanling Song
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Anna L Duncan
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
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2
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Hendrikse ER, Liew LP, Bower RL, Bonnet M, Jamaluddin MA, Prodan N, Richards KD, Walker CS, Pairaudeau G, Smith DM, Rujan RM, Sudra R, Reynolds CA, Booe JM, Pioszak AA, Flanagan JU, Hay MP, Hay DL. Identification of Small-Molecule Positive Modulators of Calcitonin-like Receptor-Based Receptors. ACS Pharmacol Transl Sci 2020; 3:305-320. [PMID: 32296770 DOI: 10.1021/acsptsci.9b00108] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Indexed: 11/28/2022]
Abstract
Class B G protein-coupled receptors are highly therapeutically relevant but challenges remain in identifying suitable small-molecule drugs. The calcitonin-like receptor (CLR) in particular is linked to conditions such as migraine, cardiovascular disease, and inflammatory bowel disease. The CLR cannot act as a cell-surface receptor alone but rather must couple to one of three receptor activity-modifying proteins (RAMPs), forming heterodimeric receptors for the peptides adrenomedullin and calcitonin gene-related peptide. These peptides have extended binding sites across their receptors. This is one reason why there are few small-molecule ligands that can modulate these receptors. Here we describe small molecules that are able to positively modulate the signaling of the CLR with all three RAMPs but are not active at the related calcitonin receptor. These compounds were selected from a β-arrestin recruitment screen, coupled with rounds of medicinal chemistry to improve their activity. Translational potential is shown as the compounds can positively modulate cAMP signaling in a vascular cell line model. Binding experiments do not support an extracellular domain binding site; however, molecular modeling reveals potential allosteric binding sites in multiple receptor regions. These are the first small-molecule positive modulators described for the CLR:RAMP complexes.
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Affiliation(s)
- Erica R Hendrikse
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1010, New Zealand
| | - Lydia P Liew
- Auckland Cancer Society Research Centre, University of Auckland, Auckland 1023, New Zealand
| | - Rebekah L Bower
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1010, New Zealand
| | - Muriel Bonnet
- Auckland Cancer Society Research Centre, University of Auckland, Auckland 1023, New Zealand
| | - Muhammad A Jamaluddin
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1010, New Zealand
| | - Nicole Prodan
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - Keith D Richards
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - Christopher S Walker
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1010, New Zealand
| | - Garry Pairaudeau
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0SL, United Kingdom
| | - David M Smith
- Emerging Innovations, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0SL, United Kingdom
| | - Roxana-Maria Rujan
- School of Life Sciences, University of Essex, Colchester CO4 3SQ, United Kingdom
| | - Risha Sudra
- School of Life Sciences, University of Essex, Colchester CO4 3SQ, United Kingdom
| | | | - Jason M Booe
- Department of Biochemistry and Molecular Biology, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, United States
| | - Augen A Pioszak
- Department of Biochemistry and Molecular Biology, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, United States
| | - Jack U Flanagan
- Auckland Cancer Society Research Centre, University of Auckland, Auckland 1023, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1010, New Zealand
| | - Michael P Hay
- Auckland Cancer Society Research Centre, University of Auckland, Auckland 1023, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1010, New Zealand
| | - Debbie L Hay
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1010, New Zealand
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3
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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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4
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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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5
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Illingworth CJR, Scott PD, Parkes KEB, Snell CR, Campbell MP, Reynolds CA. Connectivity and binding-site recognition: Applications relevant to drug design. J Comput Chem 2010; 31:2677-88. [DOI: 10.1002/jcc.21561] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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6
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Brain receptor mosaics and their intramembrane receptor-receptor interactions: molecular integration in transmission and novel targets for drug development. J Acupunct Meridian Stud 2009; 2:1-25. [PMID: 20633470 DOI: 10.1016/s2005-2901(09)60011-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2008] [Accepted: 01/06/2009] [Indexed: 11/21/2022] Open
Abstract
The concept of intramembrane receptor-receptor interactions and evidence for their existence was introduced by Agnati and Fuxe in 1980/81 suggesting the existence of heteromerization of receptors. In 1982, they proposed the existence of aggregates of multiple receptors in the plasma membrane and coined the term receptor mosaics (RM). In this way, cell signaling becomes a branched process beginning at the level of receptor recognition at the plasma membrane where receptors can directly modify the ligand recognition and signaling capacity of the receptors within a RM. Receptor-receptor interactions in RM are classified as operating either with classical cooperativity, when consisting of homomers or heteromers of similar receptor subtypes having the same transmitter, or non-classical cooperativity, when consisting of heteromers. It has been shown that information processing within a RM depends not only on its receptor composition, but also on the topology and the order of receptor activation determined by the concentrations of the ligands and the receptor properties. The general function of RM has also been demonstrated to depend on allosteric regulators (e.g., homocysteine) of the receptor subtypes present. RM as integrative nodes for receptor-receptor interactions in conjunction with membrane associated proteins may form horizontal molecular networks in the plasma membrane coordinating the activity of multiple effector systems modulating the excitability and gene expression of the cells. The key role of electrostatic epitope-epitope interactions will be discussed for the formation of the RM. These interactions probably represent a general molecular mechanism for receptor-receptor interactions and, without a doubt, indicate a role for phosphorylation-dephosphorylation events in these interactions. The novel therapeutic aspects given by the RMs will be discussed in the frame of molecular neurology and psychiatry and combined drug therapy appears as the future way to go.
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Fuxe K, Marcellino D, Guidolin D, Woods AS, Agnati LF. Heterodimers and receptor mosaics of different types of G-protein-coupled receptors. Physiology (Bethesda) 2009; 23:322-32. [PMID: 19074740 DOI: 10.1152/physiol.00028.2008] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Through an assembly of interacting GPCRs, heterodimers and high-order heteromers (termed receptor mosaics) are formed and lead to changes in the agonist recognition, signaling, and trafficking of participating receptors via allosteric mechanisms, sometimes involving the appearance of cooperativity. This field has now become a major research area, and this review deals with their physiology being integrators of receptor signaling in the CNS and their use as targets for novel drug development based on their unique pharmacology.
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Affiliation(s)
- Kjell Fuxe
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.
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Volonté C, D'Ambrosi N, Amadio S. Protein cooperation: from neurons to networks. Prog Neurobiol 2008; 86:61-71. [PMID: 18722498 DOI: 10.1016/j.pneurobio.2008.07.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2008] [Accepted: 07/28/2008] [Indexed: 12/30/2022]
Abstract
A constant pattern through the development of cellular life is that not only cells but also subcellular components such as proteins, either being enzymes, receptors, signaling or structural proteins, strictly cooperate. Discerning how protein cooperation originated and propagates over evolutionary time, how proteins work together to a shared outcome far beyond mere interaction, thus represents a theoretical and experimental challenge for evolutionary, molecular, and computational biology, and a timely fruition also for biotechnology. In this review, we describe some basic principles sustaining not only cellular but especially protein cooperative behavior, with particular emphasis on neurobiological systems. We illustrate experimental results and numerical models substantiating that bench research, as well as computer analysis, indeed concurs in recognizing the natural propensity of proteins to cooperate. At the cellular level, we exemplify network connectivity in the thalamus, hippocampus and basal ganglia. At the protein level, we depict numerical models about the receptosome, the protein machinery connecting neurotransmitters or growth factors to specific, unique downstream effector proteins. We primarily focus on the purinergic P2/P1 receptor systems for extracellular purine and pyrimidine nucleotides/nucleosides. By spanning concepts such as single-molecule biology to membrane computing, we seek to stimulate a scientific debate on the implications of protein cooperation in neurobiological systems.
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Affiliation(s)
- Cinzia Volonté
- Santa Lucia Foundation/CNR, Via del Fosso di Fiorano 65, 00143 Rome, Italy.
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Volonté C, Amadio S, D'Ambrosi N. Receptor webs: can the chunking theory tell us more about it? ACTA ACUST UNITED AC 2008; 59:1-8. [PMID: 18597852 DOI: 10.1016/j.brainresrev.2008.04.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2008] [Revised: 04/03/2008] [Accepted: 04/04/2008] [Indexed: 12/11/2022]
Abstract
Fundamental concepts shared by several classes of ionotropic and metabotropic cell surface receptors, such as receptor mosaic, cooperation, clustering, propensity to oligomerize, all finding expression in the dynamically structured mosaic membrane, will be revisited here in the light of the "combinatorial receptor web model" and the unifying information-processing mechanism defined as "chunking theory". Particularly the ubiquitous and phylogenetically most ancient P2 receptors for extracellular nucleotides will be regarded here as a prototype of receptor family. Whereas up to now we have mainly studied single receptors with the aim to make intelligible their participation to putative functions into wider biological contexts, from now on we should revise our perspective and look more thoroughly at the entire repertoire of expressed cellular receptors, in order to explain complex receptor-function relationships. A way of doing this, is to group the overall receptor web carried by a cell into patterned combinatorial clusters, the "chunks". We deem that the chunk, originally considered an information measure for cognitive systems, from computer science to linguistics, with applications into broad cognitive skills from pianists' finger tapping to chess players' memory retrieval, will rightly become an information measure for receptor webs, thus explaining the numerous receptor subtypes within the same receptor family that are simultaneously expressed on a single cell, as well as the plethora of different, even opposite, biological outputs often triggered by a single ligand. We are confident that the chunking theory will prove to be useful with receptor systems, and it will not be simply a mere speculative exercise.
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Affiliation(s)
- Cinzia Volonté
- Santa Lucia Foundation/CNR, Via del Fosso di Fiorano 65, 00143 Rome, Italy.
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Vohra S, Chintapalli SV, Illingworth CJR, Reeves PJ, Mullineaux PM, Clark HSX, Dean MK, Upton GJG, Reynolds CA. Computational studies of Family A and Family B GPCRs. Biochem Soc Trans 2007; 35:749-54. [PMID: 17635140 DOI: 10.1042/bst0350749] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A full picture of the similarities between Family A and Family B GPCRs (G-protein coupled receptors) has been frustrated by the lack of clear homology between the respective sequences. Here, we review previous computational studies on GPCR dimerization in which the putative dimerization interfaces have been analysed using entropy, the ET (evolutionary trace) method and related methods. The results derived from multiple sequence alignments of Family A subfamilies have been mapped on to the rhodopsin crystal structure using standard alignments. Similarly, the results for the Family B alignments have been mapped on to the rhodopsin crystal structure using the 'cold-spot' alignment. For both Family A and Family B GPCRs, the sequence analysis indicates that there are functional sites on essentially all transmembrane helices, consistent with the parallel daisy chain model of GPCR oligomerization in which each GPCR makes interactions with a number of neighbouring GPCRs. The results are not too sensitive to the quality of the alignment. Molecular Dynamics simulations of the activation process within a single transmembrane bundle of the rhodopsin and the beta(2)-adrenergic receptor have been reviewed; the key observation, which is consistent with other computational studies, is that there is a translation and bending of helix 6, which contributes to a significant opening out of the intracellular face of the receptor, as shown in the accompanying movies. The simulations required the application of specific experiment-derived harmonic and half-harmonic distance restraints and so the application of such simulations to Family B GPCRs requires considerable care because of the alignment problem. Thus, in order to address the alignment problem, we have exploited the observation that GCR1, a plant GPCR, has homology with Family A, Family B and Family E GPCRs. The resulting alignment for transmembrane helix 3 is presented.
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Affiliation(s)
- S Vohra
- Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
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11
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Milligan G. G protein-coupled receptor dimerisation: Molecular basis and relevance to function. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:825-35. [PMID: 17069751 DOI: 10.1016/j.bbamem.2006.09.021] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2006] [Revised: 09/25/2006] [Accepted: 09/26/2006] [Indexed: 12/21/2022]
Abstract
The belief that G protein-coupled receptors exist and function as monomeric, non-interacting species has been largely supplanted in recent years by evidence, derived from a range of approaches, that indicate they can form dimers and/or higher-order oligomeric complexes. Key roles for receptor homo-dimerisation include effective quality control of protein folding prior to plasma membrane delivery and interactions with hetero-trimeric G proteins. Growing evidence has also indicated the potential for many co-expressed G protein-coupled receptors to form hetero-dimers/oligomers. The relevance of this to physiology and function is only beginning to be unravelled but may offer great potential for more selective therapeutic intervention.
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Affiliation(s)
- Graeme Milligan
- Molecular Pharmacology Group, Division of Biochemistry and Molecular Biology, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow, Scotland, UK.
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12
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Fanelli F, De Benedetti PG. Inactive and active states and supramolecular organization of GPCRs: insights from computational modeling. J Comput Aided Mol Des 2006; 20:449-61. [PMID: 17009093 DOI: 10.1007/s10822-006-9064-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2006] [Accepted: 08/04/2006] [Indexed: 10/24/2022]
Abstract
Herein we make an overview of the results of our computational experiments aimed at gaining insight into the molecular mechanisms of GPCR functioning either in their normal conditions or when hit by gain-of-function or loss-of-function mutations. Molecular simulations of a number of GPCRs in their wild type and mutated as well as free and ligand-bound forms were instrumental in inferring the structural features, which differentiate the mutation- and ligand-induced active from the inactive states. These features essentially reside in the interaction pattern of the E/DRY arginine and in the degree of solvent exposure of selected cytosolic domains. Indeed, the active states differ from the inactive ones in the weakening of the interactions made by the highly conserved arginine and in the increase in solvent accessibility of the cytosolic interface between helices 3 and 6. Where possible, the structural hallmarks of the active and inactive receptor states are translated into molecular descriptors useful for in silico functional screening of novel receptor mutants or ligands. Computational modeling of the supramolecular organization of GPCRs and their intracellular partners is the current challenge toward a deep understanding of their functioning mechanisms.
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Affiliation(s)
- Francesca Fanelli
- Dulbecco Telethon Institute, University of Modena and Reggio Emilia, Via Campi 183, 41100 Modena, Italy.
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Casciari D, Seeber M, Fanelli F. Quaternary structure predictions of transmembrane proteins starting from the monomer: a docking-based approach. BMC Bioinformatics 2006; 7:340. [PMID: 16836758 PMCID: PMC1590055 DOI: 10.1186/1471-2105-7-340] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2006] [Accepted: 07/12/2006] [Indexed: 12/03/2022] Open
Abstract
Background We introduce a computational protocol for effective predictions of the supramolecular organization of integral transmembrane proteins, starting from the monomer. Despite the demonstrated constitutive and functional importance of supramolecular assemblies of transmembrane subunits or proteins, effective tools for structure predictions of such assemblies are still lacking. Our computational approach consists in rigid-body docking samplings, starting from the docking of two identical copies of a given monomer. Each docking run is followed by membrane topology filtering and cluster analysis. Prediction of the native oligomer is therefore accomplished by a number of progressive growing steps, each made of one docking run, filtering and cluster analysis. With this approach, knowledge about the oligomerization status of the protein is required neither for improving sampling nor for the filtering step. Furthermore, there are no size-limitations in the systems under study, which are not limited to the transmembrane domains but include also the water-soluble portions. Results Benchmarks of the approach were done on ten homo-oligomeric membrane proteins with known quaternary structure. For all these systems, predictions led to native-like quaternary structures, i.e. with Cα-RMSDs lower than 2.5 Å from the native oligomer, regardless of the resolution of the structural models. Conclusion Collectively, the results of this study emphasize the effectiveness of the prediction protocol that will be extensively challenged in quaternary structure predictions of other integral membrane proteins.
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Affiliation(s)
- D Casciari
- Department of Chemistry, Dulbecco Telethon Institute (DTI), University of Modena e Reggio Emilia, Via Campi 183, 41100 Modena, Italy
| | - M Seeber
- Department of Chemistry, Dulbecco Telethon Institute (DTI), University of Modena e Reggio Emilia, Via Campi 183, 41100 Modena, Italy
| | - F Fanelli
- Department of Chemistry, Dulbecco Telethon Institute (DTI), University of Modena e Reggio Emilia, Via Campi 183, 41100 Modena, Italy
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Fanelli F, De Benedetti PG. Computational Modeling Approaches to Structure−Function Analysis of G Protein-Coupled Receptors. Chem Rev 2005; 105:3297-351. [PMID: 16159154 DOI: 10.1021/cr000095n] [Citation(s) in RCA: 129] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Francesca Fanelli
- Dulbecco Telethon Institute and Department of Chemistry, University of Modena and Reggio Emilia, via Campi 183, 41100 Modena, Italy.
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