Publications by authors named "Jamie A Ashby"

5 Publications

  • Page 1 of 1

GABA binding to an insect GABA receptor: a molecular dynamics and mutagenesis study.

Biophys J 2012 Nov 20;103(10):2071-81. Epub 2012 Nov 20.

Department of Biochemistry, Cambridge, UK.

RDL receptors are GABA-activated inhibitory Cys-loop receptors found throughout the insect CNS. They are a key target for insecticides. Here, we characterize the GABA binding site in RDL receptors using computational and electrophysiological techniques. A homology model of the extracellular domain of RDL was generated and GABA docked into the binding site. Molecular dynamics simulations predicted critical GABA binding interactions with aromatic residues F206, Y254, and Y109 and hydrophilic residues E204, S176, R111, R166, S176, and T251. These residues were mutated, expressed in Xenopus oocytes, and their functions assessed using electrophysiology. The data support the binding mechanism provided by the simulations, which predict that GABA forms many interactions with binding site residues, the most significant of which are cation-π interactions with F206 and Y254, H-bonds with E204, S205, R111, S176, T251, and ionic interactions with R111 and E204. These findings clarify the roles of a range of residues in binding GABA in the RDL receptor, and also show that molecular dynamics simulations are a useful tool to identify specific interactions in Cys-loop receptors.
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http://dx.doi.org/10.1016/j.bpj.2012.10.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3512037PMC
November 2012

Multiple Tyrosine Residues Contribute to GABA Binding in the GABA(C) Receptor Binding Pocket.

ACS Chem Neurosci 2012 Mar 15;3(3):186-192. Epub 2011 Dec 15.

The ligand binding site of Cys-loop receptors is dominated by aromatic amino acids. In GABA(C) receptors, these are predominantly tyrosine residues, with a number of other aromatic residues located in or close to the binding pocket. Here we examine the roles of these residues using substitution with both natural and unnatural amino acids followed by functional characterization. Tyr198 (loop B) has previously been shown to form a cation-π interaction with GABA; the current data indicate that none of the other aromatic residues form such an interaction, although the data indicate that both Tyr102 and Phe138 may contribute to stabilization of the positively charged amine of GABA. Tyr247 (loop C) was very sensitive to substitution and, combined with data from a model of the receptor, suggest a π-π interaction with Tyr241 (loop C); here again functional data show aromaticity is important. In addition the hydroxyl group of Tyr241 is important, supporting the presence of a hydrogen bond with Arg104 suggested by the model. At position Tyr102 (loop D) size and aromaticity are important; this residue may play a role in receptor gating and/or ligand binding. The data also suggest that Tyr167, Tyr200, and Tyr208 have a structural role while Tyr106, Trp246, and Tyr251 are not critical. Comparison of the agonist binding site "aromatic box" across the superfamily of Cys-loop receptors reveals some interesting parallels and divergences.
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http://dx.doi.org/10.1021/cn200103nDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3309607PMC
March 2012

Two amino acid residues contribute to a cation-π binding interaction in the binding site of an insect GABA receptor.

J Neurosci 2011 Aug;31(34):12371-6

Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom.

Cys-loop receptor binding sites characteristically possess an "aromatic box," where several aromatic amino acid residues surround the bound ligand. A cation-π interaction between one of these residues and the natural agonist is common, although the residue type and location are not conserved. Even in the closely related vertebrate GABA(A) and GABA(C) receptors, residues in distinct locations perform this role: in GABA(A) receptors, a Tyr residue in loop A forms a cation-π interaction with GABA, while in GABA(C) receptors it is a loop B residue. GABA-activated Cys-loop receptors also exist in invertebrates, where they have distinct pharmacologies and are the target of a range of pesticides. Here we examine the location of GABA in an insect binding site by incorporating a series of fluorinated Phe derivatives into the receptor binding pocket using unnatural amino acid mutagenesis, and evaluating the resulting receptors when expressed in Xenopus oocytes. A homology model suggests that two aromatic residues (in loops B and C) are positioned such that they could contribute to a cation-π interaction with the primary ammonium of GABA, and the data reveal a clear correlation between the GABA EC(50) and the cation-π binding ability both at Phe206 (loop B) and Tyr254 (loop C), demonstrating for the first time the contribution of two aromatic residues to a cation-π interaction in a Cys-loop receptor.
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http://dx.doi.org/10.1523/JNEUROSCI.1610-11.2011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3233689PMC
August 2011

Structure-based mutational analysis of eIF4E in relation to sbm1 resistance to pea seed-borne mosaic virus in pea.

PLoS One 2011 Jan 24;6(1):e15873. Epub 2011 Jan 24.

Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.

Background: Pea encodes eukaryotic translation initiation factor eIF4E (eIF4E(S)), which supports the multiplication of Pea seed-borne mosaic virus (PSbMV). In common with hosts for other potyviruses, some pea lines contain a recessive allele (sbm1) encoding a mutant eIF4E (eIF4E(R)) that fails to interact functionally with the PSbMV avirulence protein, VPg, giving genetic resistance to infection.

Methodology/principal Findings: To study structure-function relationships between pea eIF4E and PSbMV VPg, we obtained an X-ray structure for eIF4E(S) bound to m(7)GTP. The crystallographic asymmetric unit contained eight independent copies of the protein, providing insights into the structurally conserved and flexible regions of eIF4E. To assess indirectly the importance of key residues in binding to VPg and/or m(7)GTP, an extensive range of point mutants in eIF4E was tested for their ability to complement PSbMV multiplication in resistant pea tissues and for complementation of protein translation, and hence growth, in an eIF4E-defective yeast strain conditionally dependent upon ectopic expression of eIF4E. The mutants also dissected individual contributions from polymorphisms present in eIF4E(R) and compared the impact of individual residues altered in orthologous resistance alleles from other crop species. The data showed that essential resistance determinants in eIF4E differed for different viruses although the critical region involved (possibly in VPg-binding) was conserved and partially overlapped with the m(7)GTP-binding region. This overlap resulted in coupled inhibition of virus multiplication and translation in the majority of cases, although the existence of a few mutants that uncoupled the two processes supported the view that the specific role of eIF4E in potyvirus infection may not be restricted to translation.

Conclusions/significance: The work describes the most extensive structural analysis of eIF4E in relation to potyvirus resistance. In addition to defining functional domains within the eIF4E structure, we identified eIF4E alleles with the potential to convey novel virus resistance phenotypes.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0015873PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3025909PMC
January 2011

Crystallization and preliminary X-ray analysis of eukaryotic initiation factor 4E from Pisum sativum.

Acta Crystallogr Sect F Struct Biol Cryst Commun 2009 Aug 30;65(Pt 8):836-8. Epub 2009 Jul 30.

Department of Disease and Stress Biology, John Innes Centre, Norwich NR4 7UH, England.

Crystals of an N-terminally truncated 20 kDa fragment of Pisum sativum eIF4E (DeltaN-eIF4E) were grown by vapour diffusion. X-ray data were recorded to a resolution of 2.2 A from a single crystal in-house. Indexing was consistent with primitive monoclinic symmetry and solvent-content estimations suggested that between four and nine copies of the eIF4E fragment were possible per crystallographic asymmetric unit. eIF4E is an essential component of the eukaryotic translation machinery and recent studies have shown that point mutations of plant eIF4Es can confer resistance to potyvirus infection.
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http://dx.doi.org/10.1107/S1744309109027389DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2720347PMC
August 2009