The role of stacking interactions in the binding of the NMDA receptor glycine site with antagonists and 3-hydroxykynurenine

Захаров, Г. А.; Popov, A.; Савватеева-Попова, Е. В.; Щеголев, Б. Ф.

doi:10.1134/s0006350908010028

Cited by 3 publications

(10 citation statements)

References 11 publications

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“…The optimal geometry of KYNA -benzene was calculated previously at MP2 level [14]. The starting interplanar spacing and parallel displacement of rings in KYNA -phenol and KYNAimidazole corresponded to the optimized geometry of KYNA -benzene dimer.…”

Section: Methodsmentioning

confidence: 99%

“…The position of benzene was symmetric relative to the long axis of KYNA aromatic moiety and moved half aside the heteroaromatic ring; this is a classical PD conformation [37]. The interplanar (dZ) and parallel (dX) displacements (3.17 and 1.24 Ǻ, respectively) were smaller than those calculated for benzene-benzene using the same approach: 3.4 and 1.4 Ǻ, respectively [14] or using CCSD(T) method at aug (d,p) 6-311 G** basis set: 3.5 and 1.8 Ǻ, respectively [6]. Presumably, the difference between the calculated KYNAbenzene geometry and experimentally established location of DCKA in NR1 [12] resulted from the additional interactions with the receptor binding site residues.…”

Section: The Calculations Of Dimers Energy and Optimal Geometrymentioning

confidence: 95%

“…2, Table 2) was shown to depend on the chemical nature of KYNA aromatic partner. E MP2 for previously calculated aromatic dimer was −14.2 kJ mol -1 for benzene-benzene and −35.1 kJ mol -1 for KYNAbenzene in 6-31 G** basis set [14]. The absolute value of E BIND decreased being revaluated at MP4 level.…”

Section: The Calculations Of Dimers Energy and Optimal Geometrymentioning

confidence: 98%

“…This problem can be partly solved by using coupled cluster calculations (CCSD(T)) or, presumably, with the help of the forth order perturbation theory MP4. A parallel conformation with displaced centers of rings (PD) was shown to be energetically the most favorable for benzene [6,14,21] and pyridine [22] dimers. Both parallel and antiparallel PD conformers of pyridine dimer are possible, E BIND of each being dependent on relative orientation of the polar N atoms [22].…”

Section: Introductionmentioning

confidence: 99%

“…1a): S1 and S2 subdomains are separated, that causes the inhibition of the receptor Ca 2+ channel. The specific affinity of DCKA toward the NR1 glycine site could be explained by hydrophobic interactions [13] together with stacking interaction energy contributions [14].…”

Section: Introductionmentioning

confidence: 99%

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Stacking interaction and its role in kynurenic acid binding to glutamate ionotropic receptors

et al. 2011

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Stacking interaction is known to play an important role in protein folding, enzyme-substrate and ligand-receptor complex formation. It has been shown to make a contribution into the aromatic antagonists binding with glutamate ionotropic receptors (iGluRs), in particular, the complex of NMDA receptor NR1 subunit with the kynurenic acid (KYNA) derivatives. The specificity of KYNA binding to the glutamate receptors subtypes might partially result from the differences in stacking interaction. We have calculated the optimal geometry and binding energy of KYNA dimers with the four types of aromatic amino acid residues in Rattus and Drosophila ionotropic iGluR subunits. All ab initio quantum chemical calculations were performed taking into account electron correlations at MP2 and MP4 perturbation theory levels. We have also investigated the potential energy surfaces (PES) of stacking and hydrogen bonds (HBs) within the receptor binding site and calculated the free energy of the ligand-receptor complex formation. The energy of stacking interaction depends both on the size of aromatic moieties and the electrostatic effects. The distribution of charges was shown to determine the geometry of polar aromatic ring dimers. Presumably, stacking interaction is important at the first stage of ligand binding when HBs are weak. The freedom of ligand movements and rotation within receptor site provides the precise tuning of the HBs pattern, while the incorrect stacking binding prohibits the ligand-receptor complex formation.

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Section: Methodsmentioning

confidence: 99%

Section: The Calculations Of Dimers Energy and Optimal Geometrymentioning

confidence: 95%

Section: The Calculations Of Dimers Energy and Optimal Geometrymentioning

confidence: 98%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Stacking interaction and its role in kynurenic acid binding to glutamate ionotropic receptors

et al. 2011

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Simulation of detection and scattering of sound waves by the lateral line of a fish

Adamyan¹,

Popov²,

Blinova³

et al. 2022

Chinese Phys. B

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A solvable model of lateral line of a fish based on a wave equation with additional boundary conditions on a set of isolated points is proposed. Within the framework of this model it is shown that the ratio of pressures on lateral lines on different fish flanks, as well as the cross section of sound scattering on both the lines, strongly depends on angles of incidence of incoming sound waves. The strong angular dependence of the pressure ratio seems to be sufficient for the fish to determine the directions from which the sound is coming.

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Analysis of intermolecular interaction energy inputs in benzene-imidazole and imidazole-imidazole systems in parallel displaced and T-configuration

et al. 2013

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The role of stacking interactions in the binding of the NMDA receptor glycine site with antagonists and 3-hydroxykynurenine

Cited by 3 publications

References 11 publications

Stacking interaction and its role in kynurenic acid binding to glutamate ionotropic receptors

Stacking interaction and its role in kynurenic acid binding to glutamate ionotropic receptors

Simulation of detection and scattering of sound waves by the lateral line of a fish

Analysis of intermolecular interaction energy inputs in benzene-imidazole and imidazole-imidazole systems in parallel displaced and T-configuration

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