A Vibrational Spectroscopic Investigation of Interactions of Agonists with GluR0 a Prokaryotic Glutamate Receptor

Cheng, Qing; Thiran, Shalita; Yernool, Dinesh; Gouaux, Eric; Jayaraman, Vasanthi

doi:10.1021/bi015729e

Cited by 20 publications

(27 citation statements)

References 24 publications

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“…1) in homogeneous D 2 O solvent and compare our results with the corresponding frequencies measured by the FTIR experiment (provided in Table I). [27][28][29] Several recently reported computational studies of spectroscopic properties of single amino acids in aqueous solution were nearly in quantitative agreement with the experimental results. Both continuum and molecular solvent models as well as various hybrid continuum/ molecular approaches were employed.…”

Section: A Glutamate In a Homogeneous Liquid Watersupporting

confidence: 63%

Accurate theoretical prediction of vibrational frequencies in an inhomogeneous dynamic environment: A case study of a glutamate molecule in water solution and in a protein-bound form

Speranskiy¹,

Kurnikova²

2004

The Journal of Chemical Physics

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We propose a hierarchical approach to model vibrational frequencies of a ligand in a strongly fluctuating inhomogeneous environment such as a liquid solution or when bound to a macromolecule, e.g., a protein. Vibrational frequencies typically measured experimentally are ensemble averaged quantities which result (in part) from the influence of the strongly fluctuating solvent. Solvent fluctuations can be sampled effectively by a classical molecular simulation, which in our model serves as the first, low level of the hierarchy. At the second high level of the hierarchy a small subset of system coordinates is used to construct a patch of the potential surface (ab initio) relevant to the vibration in question. This subset of coordinates is under the influence of an instantaneous external force exerted by the environment. The force is calculated at the lower level of the hierarchy. The proposed methodology is applied to model vibrational frequencies of a glutamate in water and when bound to the Glutamate receptor protein and its mutant. Our results are in close agreement with the experimental values and frequency shifts measured by the Jayaraman group by the Fourier transform infrared spectroscopy [Q. Cheng et al., Biochem. 41, 1602(2002]. Our methodology proved useful in successfully reproducing vibrational frequencies of a ligand in such a soft, flexible, and strongly inhomogeneous protein as the Glutamate receptor.

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Section: A Glutamate In a Homogeneous Liquid Watersupporting

confidence: 63%

Accurate theoretical prediction of vibrational frequencies in an inhomogeneous dynamic environment: A case study of a glutamate molecule in water solution and in a protein-bound form

Speranskiy¹,

Kurnikova²

2004

The Journal of Chemical Physics

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“…The frequency of the asymmetric carboxylate stretching vibration is extremely sensitive to the overall electrostatic environment of the carboxylate and has been shown to exhibit a linear dependence on the strength of the noncovalent interactions at this moiety, with a 3-cm Ϫ1 downshift corresponding to a Ϫ1-kcal change in enthalpy at the carboxylate (15). Based on these studies, the 4-cm Ϫ1 downshift in the ␣-carboxylate mode of glutamate on binding to the GluR2-S1S2 indicates a favorable Ϫ1.3 kcal/mol interaction for this moiety in the protein, relative to D 2 O.…”

Section: Resultsmentioning

confidence: 99%

Chemistry and Conformation of the Ligand-binding Domain of GluR2 Subtype of Glutamate Receptors

Cheng

Jayaraman

2004

Journal of Biological Chemistry

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In the present report, using vibrational spectroscopy we have probed the ligand-protein interactions for full agonists (glutamate and ␣-amino-5-methyl-3-hydroxy-4-isoxazole propionate (AMPA)) and a partial agonist (kainate) in the isolated ligand-binding domain of the GluR2 subunit of the glutamate receptor. These studies indicate differences in the strength of the interactions of the ␣-carboxylates for the various agonists, with kainate having the strongest interactions and glutamate having the weakest. Additionally, the interactions at the ␣-amine group of the agonists have also been probed by studying the environment of the non-disulfide-bonded Cys-425, which is in close proximity to the ␣-amine group. These investigations suggest that the interactions at the ␣-amine group are stronger for full agonists such as glutamate and AMPA as evidenced by the increase in the hydrogen bond strength at Cys-425. Partial agonists such as kainate do not change the environment of Cys-425 relative to the apo form, suggesting weak interactions at the ␣-amine group of kainate. In addition to probing the ligand environment, we have also investigated the changes in the secondary structure of the protein. Results clearly indicate that full agonists such as glutamate and AMPA induce similar secondary structural changes that are different from those of the partial agonist kainate; thus, a spectroscopic signature is provided for identifying the functional consequences of a specific ligand binding to this protein.Glutamate receptors are the predominant mediators of excitatory synaptic signals in the central nervous system (1-5). These receptors form cation-specific channels on binding glutamate and later enter a desensitized state in which the channel is closed, despite the presence of an agonist. Significant insights into the mechanism of agonist-induced activation and desensitization of this receptor have been obtained from the recent x-ray structures of the isolated, extracellular ligandbinding domain (S1S2) of the ␣-amino-5-methyl-3-hydroxy-4-isoxazole propionate (AMPA) 1 subtype of the glutamate receptors (6 -9). The x-ray structures of the S1S2 protein indicate a bilobed structure with the ligand-binding site located in the cleft between the lobes. The protein exists in an open structure in the apo state and undergoes varying degrees of cleft closure on binding various agonists. This cleft closure is believed to be a rigid body motion of one lobe relative to the other. Furthermore, the degree of lobe closure has been shown to be directly proportional to the extent of activation of these receptors, suggesting cleft closure in the S1S2 protein as the mechanism of activation of the receptor (7,8).The x-ray structures of the S1S2 protein in various ligated states have provided the first structural insights into the structure-function correlations in the glutamate receptor. These insights, however, are low temperature static images that are limited by the constraints of crystal-packing forces. For a more detailed investigation of spe...

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“…The asymmetric carboxylate vibration for α-amino acids typically occurs in the region of 1610 to 1630 cm −1 (5)(6)(7)19,22), and hence the bands at 1629 cm −1 in the HW and FW spectra and at 1632 cm −1 in the ClW and IW spectra can be assigned to the asymmetric stretching vibration of the α-carboxylate, while the higher frequency modes can be assigned to the stretching vibrations of the two other carbonyl moieties present in the willardiine structures. Specifically, the vibrations at 1653 cm −1 (FW), 1655 cm −1 (HW), 1652 cm −1 (IW), and 1658 cm −1 (ClW) can be assigned to the carbonyl moiety at the 2 position on the ring (Figure 1) due to the fact that this carbonyl is further from the halogen substitution, and the vibrations due to this moiety are not significantly affected by the substituent.…”

Section: Environment Of the Willardiines Free In Solutionmentioning

confidence: 99%

“…The difference spectra for the free willardiines and bound willardiines exhibit an 11 cm −1 downshift in the asymmetric carboxylate vibration for FW and HW upon binding to GluR2-S1S2 and a 14 cm −1 downshift in the asymmetric carboxylate vibration for ClW and IW upon binding to GluR2-S1S2. Since the frequency of the asymmetric carboxylate vibration can be directly correlated to the strength of the interaction at this moiety (22), these downshifts would correspond to a ΔH of −3.7 kcal/mol when FW and HW bind to GluR2-S1S2 and ΔH of −4.7 kcal/mol when ClW and IW bind to GluR2-S1S2 as compared to the ligands free in solution.…”

Section: Willardiine Environment When Bound To the Proteinmentioning

confidence: 99%

Chemical Interplay in the Mechanism of Partial Agonist Activation in α-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic Acid Receptors

et al. 2007

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Abstractα-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors, one subtype in the family of ionotropic glutamate receptors, are the main receptors responsible for excitatory signaling in the mammalian central nervous system. Previous studies utilitizing the isolated ligand binding domain of these receptors have provided insight into the role of specific ligand-protein interactions in mediating receptor activation. However, these studies relied heavily on the partial agonist kainate, in which the α-amine group is constrained in a pyrrolidine ring. Here we have studied a series of substituted and unsubstituted willardiines with primary α-amine groups similar to that of the full agonist glutamate whose activation can be varied depending on the size of the substituent. The specific ligand-protein interactions in the mechanism of partial agonism in this subtype were investigated using vibrational spectroscopy and the large scale conformational changes in the ligand binding domain were studied with fluorescence resonance energy transfer (FRET). These investigations show that the strength of the interaction at the α-amine group correlates with the extent of cleft closure and extent of activation, with the agonist of higher efficacy showing larger cleft closure and stronger interactions at this group, suggesting that this is one of the mechanisms by which the agonist controls receptor activation.α-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors, one subtype of ionotropic glutamate receptors, are responsible for mediating the majority of excitatory synaptic signaling in the central nervous system. Activation of these channels occurs when an agonist, such as glutamate, binds in the bilobed extracellular ligand binding domain of the receptor, initiating a series of conformational changes that lead to the formation of cation selective channels (1-4).Recent vibrational spectroscopic investigations (5-8) in combination with fluorescence resonance energy transfer (FRET) studies (5,8,9) on the isolated ligand binding domain of the GluR2 subunit (GluR2-S1S2) have provided insight into the role of specific ligand-protein interactions in mediating AMPA receptor activation. By using these techniques to study activation by the three ligands kainate, AMPA, and glutamate on wild type and mutant proteins, which provide a wide spectrum of activations, a correlation was developed between the changes at specific ligand-protein interactions and extent of activation of the channel. These studies suggest that the strength of the interaction at the α-amine group correlates in most cases to the § Address correspondence to: Vasanthi Jayaraman, Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Health Science Center, 6431 Fannin St., Houston, Texas, 77030; (5,6). However, it should be noted that these correlations depended heavily on conclusions from the partial agonist kainate, which is inherently different in structure compared to glutamate and AMPA because it...

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A Vibrational Spectroscopic Investigation of Interactions of Agonists with GluR0 a Prokaryotic Glutamate Receptor

Cited by 20 publications

References 24 publications

Accurate theoretical prediction of vibrational frequencies in an inhomogeneous dynamic environment: A case study of a glutamate molecule in water solution and in a protein-bound form

Accurate theoretical prediction of vibrational frequencies in an inhomogeneous dynamic environment: A case study of a glutamate molecule in water solution and in a protein-bound form

Chemistry and Conformation of the Ligand-binding Domain of GluR2 Subtype of Glutamate Receptors

Chemical Interplay in the Mechanism of Partial Agonist Activation in α-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic Acid Receptors

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