Chemical modifications of striatal A2A adenosine receptors: a possible role for tyrosine at the ligand binding sites

We studied, by ligand binding methods, the two adenosine receptors, A, and A2, in rat and pig cerebral microvessels and pig choroid plexus. Ligand binding to cerebral microvessels was compared with that to membranes of the cerebral cortex. [3H]Cyclohexyladenosine and [3H]l-phenylisopropyladenosine were the ligands used for A1-receptors, and [3H]5'- N-ethylcarboxamide adenosine ([3H]NECA) was used to assess A2-receptors. We report that cerebral microvessels and choroid plexus exhibit specific [3H]NECA binding, but have no appreciable A1-receptor ligand binding sites. Specific binding of [3H]NECA to cerebral microvessels, choroid plexus, and cerebral cortex was saturable and suggested the existence of two classes of A2-receptor sites: high-affinity ( Kd ∼ 250 n M) and low-affinity ( Kd ∼ 1–2 μ M) sites. The Kd and Bmax of NECA binding to cerebral microvessels and cerebral cortex were similar within each species. Our results, indicating the existence of A2-receptors in cerebral microvessels, are consistent with results of increased adenylate cyclase activity by adenosine and some of its analogues in these microvessels.

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Locating ligand binding sites in G-protein coupled receptors using combined information from docking and sequence conservation

10.1101/461681 ◽

2018 ◽

Cited By ~ 1

Author(s):

Ashley R. Vidad ◽

Stephen Macaspac ◽

Ho-Leung Ng

Keyword(s):

Ligand Binding ◽

G Protein ◽

Binding Sites ◽

G Protein Coupled Receptors ◽

Sequence Conservation ◽

Surface Geometry ◽

A2a Adenosine Receptors ◽

Ligand Binding Sites ◽

G Protein Coupled ◽

Homology Models

AbstractG-protein coupled receptors (GPCRs) are the largest protein family of drug targets. Detailed mechanisms of binding are unknown for many important GPCR-ligand pairs due to the difficulties of GPCR recombinant expression, biochemistry, and crystallography. We describe our new method, ConDock, for predicting ligand binding sites in GPCRs using combined information from surface conservation and docking starting from crystal structures or homology models. We demonstrate the effectiveness of ConDock on well-characterized GPCRs such as the β2 adrenergic and A2A adenosine receptors. We also demonstrate that ConDock successfully predicts ligand binding sites from high-quality homology models. Finally, we apply ConDock to predict ligand binding sites on a structurally uncharacterized GPCR, GPER. GPER is the G-protein coupled estrogen receptor, with four known ligands: estradiol, G1, G15, and tamoxifen. ConDock predicts that all four ligands bind to the same location on GPER, centered on L119, H307, and N310; this site is deeper in the receptor cleft than predicted by previous studies. We compare the sites predicted by ConDock and traditional methods that utilize information from surface geometry, surface conservation, and ligand chemical interactions. Incorporating sequence conservation information in ConDock overcomes errors introduced from physics-based scoring functions and homology modeling.

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Locating ligand binding sites in G-protein coupled receptors using combined information from docking and sequence conservation

PeerJ ◽

10.7717/peerj.12219 ◽

2021 ◽

Vol 9 ◽

pp. e12219

Author(s):

Ashley Ryan Vidad ◽

Stephen Macaspac ◽

Ho Leung Ng

Keyword(s):

Ligand Binding ◽

G Protein ◽

Binding Sites ◽

G Protein Coupled Receptors ◽

Sequence Conservation ◽

A2a Adenosine Receptors ◽

Class A ◽

Ligand Binding Sites ◽

G Protein Coupled ◽

Homology Models

GPCRs (G-protein coupled receptors) are the largest family of drug targets and share a conserved structure. Binding sites are unknown for many important GPCR ligands due to the difficulties of GPCR recombinant expression, biochemistry, and crystallography. We describe our approach, ConDockSite, for predicting ligand binding sites in class A GPCRs using combined information from surface conservation and docking, starting from crystal structures or homology models. We demonstrate the effectiveness of ConDockSite on crystallized class A GPCRs such as the beta2 adrenergic and A2A adenosine receptors. We also demonstrate that ConDockSite successfully predicts ligand binding sites from high-quality homology models. Finally, we apply ConDockSite to predict the ligand binding sites on a structurally uncharacterized GPCR, GPER, the G-protein coupled estrogen receptor. Most of the sites predicted by ConDockSite match those found in other independent modeling studies. ConDockSite predicts that four ligands bind to a common location on GPER at a site deep in the receptor cleft. Incorporating sequence conservation information in ConDockSite overcomes errors introduced from physics-based scoring functions and homology modeling.

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Faculty Opinions recommendation of Probing hot spots at protein-ligand binding sites: a fragment-based approach using biophysical methods.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1044116.497853 ◽

2006 ◽

Author(s):

Wolfgang Jahnke

Keyword(s):

Ligand Binding ◽

Binding Sites ◽

Hot Spots ◽

Ligand Binding Sites

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Faculty Opinions recommendation of LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.725748869.793514601 ◽

2016 ◽

Author(s):

Jeffrey Skolnick

Keyword(s):

Ligand Binding ◽

Binding Sites ◽

Ligand Binding Sites ◽

Connolly Surface

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Usefulness of Molecular Modeling in Characterizing the Ligand-Binding Sites of Proteins: Experience with Human PDI, PDIp and COX

Current Medicinal Chemistry ◽

10.2174/09298673113209990207 ◽

2013 ◽

Vol 20 (31) ◽

pp. 3840-3854 ◽

Cited By ~ 2

Author(s):

Pan Wang ◽

Bao-Ting Zhu

Keyword(s):

Molecular Modeling ◽

Ligand Binding ◽

Binding Sites ◽

Ligand Binding Sites

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Diversity in the structures and ligand-binding sites of nematode fatty acid and retinol-binding proteins revealed by Na-FAR-1 from Necator americanus

Biochemical Journal ◽

10.1042/bj20150068 ◽

2015 ◽

Vol 471 (3) ◽

pp. 403-414 ◽

Cited By ~ 19

Author(s):

M. Florencia Rey-Burusco ◽

Marina Ibáñez-Shimabukuro ◽

Mads Gabrielsen ◽

Gisela R. Franchini ◽

Andrew J. Roe ◽

...

Keyword(s):

Fatty Acid ◽

Ligand Binding ◽

Tissue Distribution ◽

Binding Sites ◽

Binding Proteins ◽

Retinol Binding Protein ◽

Internal Cavity ◽

Binding Characteristics ◽

Necator Americanus ◽

Ligand Binding Sites

Necator americanus fatty acid and retinol-binding protein-1 (Na-FAR-1) is an abundantly expressed FAR from a parasitic hookworm. The present work describes its tissue distribution, structure and ligand-binding characteristics and shows that Na-FAR-1 expands to transport multiple FA molecules in its internal cavity.

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A naturally occurring Tyr143HisαIIb mutation abolishes αIIbβ3 function for soluble ligands but retains its ability for mediating cell adhesion and clot retraction: comparison with other mutations causing ligand-binding defects

Blood ◽

10.1182/blood-2002-07-2144 ◽

2003 ◽

Vol 101 (9) ◽

pp. 3485-3491 ◽

Cited By ~ 17

Author(s):

Teruo Kiyoi ◽

Yoshiaki Tomiyama ◽

Shigenori Honda ◽

Seiji Tadokoro ◽

Morio Arai ◽

...

Keyword(s):

Cell Adhesion ◽

Ligand Binding ◽

Binding Sites ◽

Clot Retraction ◽

Naturally Occurring ◽

Binding Function ◽

293 Cells ◽

Ligand Binding Sites ◽

Functional Defect ◽

And Function

The molecular basis for the interaction between a prototypic non–I-domain integrin, αIIbβ3, and its ligands remains to be determined. In this study, we have characterized a novel missense mutation (Tyr143His) in αIIb associated with a variant of Glanzmann thrombasthenia. Osaka-12 platelets expressed a substantial amount of αIIbβ3(36%-41% of control) but failed to bind soluble ligands, including a high-affinity αIIbβ3-specific peptidomimetic antagonist. Sequence analysis revealed that Osaka-12 is a compound heterozygote for a single 521T>C substitution leading to a Tyr143His substitution in αIIb and for the null expression of αIIb mRNA from the maternal allele. Given that Tyr143 is located in the W3 4-1 loop of the β-propeller domain of αIIb, we examined the effects of Tyr143His or Tyr143Ala substitution on the expression and function of αIIbβ3 and compared them with KO (Arg-Thr insertion between 160 and 161 residues of αIIb) and with the Asp163Ala mutation located in the same loop by using 293 cells. Each of them abolished the binding function of αIIbβ3 for soluble ligands without disturbing αIIbβ3 expression. Because immobilized fibrinogen and fibrin are higher affinity/avidity ligands for αIIbβ3, we performed cell adhesion and clot retraction assays. In sharp contrast to KO mutation and Asp163AlaαIIbβ3, Tyr143HisαIIbβ3-expressing cells still had some ability for cell adhesion and clot retraction. Thus, the functional defect induced by Tyr143HisαIIb is likely caused by its allosteric effect rather than by a defect in the ligand-binding site itself. These detailed structure–function analyses provide better understanding of the ligand-binding sites in integrins.

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