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

Ab initio quantum chemical calculations of the benzene dimer, benzene dimer 5,7-chlorination of one aromatic ring, 3-hydroxykynurenine, and kynurenic acid molecules located above the Phe484 aromatic ring of a fragment of the receptor binding site were performed to study the role of stacking interaction in the binding of agonists and antagonists with the glycine binding site of the NR1 subunit of the NMDA receptor. The GAMESS 6.4 software in the 6–31G** basis set with complete optimization of the geometry and with account of electron correlation within the second-order Moller-Plesset perturbation theory was used for all calculations. It was shown that parallel shifted conformations of the benzene dimer were the most favorable in energy. Successive substitution of chlorine atoms for protons of one aromatic ring at positions 7 and 5 led to an increase in the stacking-interaction energy and mutual displacement of aromatic rings. In the case of kynurenic acid and its chlorinated derivatives, which are NMDA receptor antagonists, the increase in the stacking interaction energy further suppressed the ion channel, whereas 3-hydroxykynurenine was neither an agonist nor an antagonist of the glycine site because of steric constraints.     

The role of stacking interactions in the mechanisms of clonidine binding

The stacking interactions of the clonidine aromatic ring with the aromatic rings of Phe or Tyr of alpha2-adrenoreceptor and Tyr aromatic ring of the pore of the tetradotoxin-resistant channel have been investigated. Ab initio quantum chemical calculations for a model system of two parallel aromatic rings were performed by GAMESS software with 6-31G** basis set in the framework of the Moller-Plesset second-order perturbation theory with full geometry optimization without any symmetry. It was shown that the parallel shifted conformation of two aromatic rings is energetically most favorable. The 2,6-chlorination of one of the benzene rings leads to the amplification of the stacking interaction, an increase in the relative shift of the rings and possible growth of both the hypotensive and analgetic functions of clonidine due to the increase in the binding energy. The 4-fluoridization of the clonidine benzene ring can amplify its analgetic function but practically excludes its hypotensive action.     

Catecholamine binding to CNS adrenergic receptors

The properties of ³H-catecholamine binding to α- and β-adrenergic receptors in CNS are reviewed. ³H-epinephrine and ³H-norepinephrine label one class of α-receptors throughout the brain, with high affinities for agonists and some antagonists. Agonist affinities at this site are increased in low temperature conditions but are reduced by guanine nucleotides and monovalent cations. Divalent cations reverse both effects. This α-receptor may be coupled to adenylate cyclase by GTP and/or sodium, and uncoupled by divalent cations. ³H-epinephrine labels β₂, but not β₁, receptors in CNS, especially in bovine cerebellum. The same β-receptor does not show agonist-specific GTP-sensitivity, but does exhibit Na⁺-sensitivity. This receptor appears to be linked to adenylate cyclase, and sodium rather than GTP may be the coupling agent.     

The role of hydrophobic interactions in ankyrin-spectrin complex formation

Spectrin and ankyrin are the key components of the erythrocyte cytoskeleton. The recently published crystal structure of the spectrin-ankyrin complex has indicated that their binding involves complementary charge interactions as well as hydrophobic interactions. However, only the former is supported by biochemical evidence. We now show that nonpolar interactions are important for high affinity complex formation, excluding the possibility that the binding is exclusively mediated by association of distinctly charged surfaces. Along these lines we report that substitution of a single hydrophobic residue, F917S in ankyrin, disrupts the structure of the binding site and leads to complete loss of spectrin affinity. Finally, we present data showing that minimal ankyrin binding site in spectrin is formed by helix 14C together with the loop between helices 15 B/C.     

Disruption of nucleobase stacking to restore reactivity

Strong intermolecular interaction can prevent an organic molecule from dissolving in a reaction solution, thereby jeopardizing its reactivity and usefulness. Nucleobases and nucleosides (especially many purines and their derivatives) are notoriously difficult to dissolve in most organic solvents, generally attributed to their strong intermolecular interactions caused by the aromaticity, polarity and hydrogen-bonding. Guided by our computational study and prediction, to address this challenge, we have found that by doping the reaction solution with toluene (an inert aromatic compound), the added solvent molecules are capable of generating the stacking interaction with the solute molecules (e.g., purine derivatives) and disrupting the intermolecular stacking of the solute molecules. Thus, this inert doping can successfully address the insoluble challenge, dissolve the poorly soluble reactants (such as purine phosphoramidites), and restore the amidite reactivity for oligonucleotide synthesis. Our research has offered a simple strategy to efficiently synthesize labile oligonucleotides, via disrupting stacking interaction with inert aromatic molecules.     

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

Ab initio quantum chemical calculations of benzene dimer, benzene dimer with 5,7 clorination of one aromatic ring, 3-hydroxykynurenine, and kunurenic acid molecules situated above Phe484 aromatic ring of receptor binding site fragment were carried out in order to investigate the role of stacking interaction in the binding of agonists and antagonists with the glycine site of the NMDA receptor NR1 subunit. All calculations were done with the help of GAMESS 6.4 software with 6-31G** atomic gaussian basal functions with complete optimization of geometry and taking into account the electron correlation up to the second-order Moller-Plesset perturbation theory. It was shown that the parallel dislodged conformations of the benzene dimer is energetically most advantageous. Successive substitution of chlorine atoms for the protons of one aromatic ring in 7 and 5 positions leads to an increase in stacking-interaction energy and a mutual displacement of aromatic rings. In the case of kunurenic acid and its derivatives, which are NMDA receptor antagonists, the increase in the energy of stacking interactions leads to the strengthening of inhibition of the ion channel, whereas the 3-hydroxykynurenine molecule is neither agonist, nor antagonist for the glycine site of the NMDA receptor due to the sterical constraints.     

Molecular mechanisms of imidazole and benzene ring binding in proteins

Aromatic bonds of amino acid radicals play an important role in arrangement of protein primary structure. Previously, the existence of a number of preferable conformations of aromatic dimers was shown theoretically and experimentally, the best known of which are parallel-displaced and perpendicular T conformations. To reveal principles that define preference of various conformations for His-His and Phe-His dimers, non-empirical quantum-chemical calculations of diimidazole and benzene-imidazole were carried out. Calculations were performed using the 6-31G** basis with account for electronic correlations in frames of MP2 and MP4 methods of perturbation theory. Comparative analysis of energetic and geometric parameters of the systems points to the preference of stacking contact or classical hydrogen bond in diimidazole. On the contrary, T conformation is maximally advantageous for benzene-imidazole.     

Centrally Acting Imidazolines Stimulate Vascular Alpha 1A-Adrenergic Receptors in Rat-Tail Artery

  1. Centrally acting imidazoline antihypertensive agents clonidine and moxonidine also act peripherally to contract blood vessels. While these agents act at both I₁-imidazoline and alpha 2 adrenergic receptors centrally, the receptor types by which they mediate contraction require further definition. We therefore characterized the receptor subtype by which these agents mediate contraction of proximal rat-tail artery.2. Dose–response curves were determined for phenylephrine and for several imidazoline ligands, using endothelium denuded, isolated ring segments, of tail arteries from adult male Sprague-Dawley rats. Ring segments were mounted on a force transducer with platinum wires and immersed in a tissue bath containing Krebs solution, to which drugs could be added. Signals were digitized and recorded by a computer.3. Tail artery contractions expressed as a percent of contraction to 106 mM potassium were phenylephrine (96%), moxonidine (88%), clonidine (52%), and UK14304 (30%). Neither rilmenidine nor harmane caused contraction. Contraction of tail artery to moxonidine or clonidine could be blocked by alpha 1 antagonist urapidil or prazosin, and also by alpha 1A subtype selective antagonist WB4101. Schild plots were generated and a calculated pA2 value of 9.2 for prazosin in the presence of clonidine confirms clonidine as an agonist at alpha 1A receptors in proximal segments of rat-tail artery.4. Our work suggests that clonidine and moxonidine are promiscuous compounds at micromolar concentrations and that harmane and rilmenidine are more selective compounds for in vivo imidazoline research.*This work represents a portion of a dissertation to be submitted to the School of Graduate Studies, Loma Linda University, for the degree of Doctor of Philosophy.     

Hydrophobic interactions mediate binding of the glycine receptor beta-subunit to gephyrin

Glycine receptors (GlyRs) are ligand-gated chloride channel proteins composed of alpha- and beta-subunits. GlyRs are located to and anchored at postsynaptic sites by the receptor-associated protein gephyrin. Previous work from our laboratory has identified a core motif for gephyrin binding in the cytoplasmic loop of the GlyR beta-subunit. Here, we localized amino acid residues implicated in gephyrin binding by site-directed mutagenesis. In a novel transfection assay, a green fluorescent protein-gephyrin binding motif fusion protein was used to monitor the consequences of amino acid substitutions for beta-subunit interaction with gephyrin. Only multiple, but not single, replacements of hydrophobic side chains abolished the interaction between the two proteins. Our data are consistent with gephyrin binding being mediated by the hydrophobic side of an imperfect amphipathic helix.     

The role of weakly polar and H-bonding interactions in the stabilization of the conformers of FGG, WGG, and YGG: an aqueous phase computational study

The energetics of intramolecular interactions on the conformational potential energy surface of the terminally protected N-Ac-Phe-Gly-Gly-NHMe (FGG), N-Ac-Trp-Gly-Gly-NHMe (WGG), and N-Ac-Tyr-Gly-Gly-NHMe (YGG) tripeptides was investigated. To identify the representative conformations, simulated annealing molecular dynamics (MD) and density functional theory (DFT) methods were used. The interaction energies were calculated at the BHandHLYP/aug-cc-pVTZ level of theory. In the global minima, 10%, 31%, and 10% of the stabilization energy come from weakly polar interactions, respectively, in FGG, WGG, and YGG. In the prominent cases 46%, 62%, and 46% of the stabilization energy is from the weakly polar interactions, respectively, in FGG, WGG, and YGG. On average, weakly polar interactions account for 15%, 34%, and 9% of the stabilization energies of the FGG, WGG, and YGG conformers, respectively. Thus, weakly polar interactions can make an important energetic contribution to protein structure and function. (c) 2008 Wiley Periodicals, Inc. Biopolymers 89: 1002-1011, 2008.This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com.     

The role of ligand-ligand interactions in competition by fibrinogen and fibrin degradation products for fibrinogen binding to human platelets

Binding to human platelets of radioiodinated human fibrinogen and fragments X, Y, D, D₁ dimer and E was studied to determine the domain of the fibrinogen molecule responsible for binding to the platelet receptor. Although the fragments did not bind, some wer able to complete for the binding of fibrinogen to platelets. It was postulated that the fragments bound to fibrinogen and subsequently interfered with its binding to the receptor. Two approaches were developed to test this hypothesis. In the first technique, molecular exclusion on Sephacryl S-200 superfine was utilized to examine the interaction of radiolabeled fragments with fibrinogen. In the second seties of studies, fibrinogen-Sepharose was prepared and the binding of degradation products directly determined. A spin dialysis apparatus was employed in each case to achieve rapid separation of bound and free radioligand. These studies demonstrated that fragments D and E bind to fibrinogen. Therefore, the mechanism by which degradation products interfere with fibrinogen binding to the platelet receptor is ligand-ligand interaction rather than binding of the fragments to the receptor. Since none of the radiolabeled degradation products bound to platelets, it appears that receptor recognition requires the intact molecule.     

The role of electrostatic interactions in the membrane binding of melittin

The binding of melittin and the C-terminally truncated analogue of melittin (21Q) to a range of phospholipid bilayers was studied using surface plasmon resonance (SPR). The phospholipid model membranes included zwitterionic dimyristylphosphatidylcholine (DMPC) and dimyristylphosphatidylethanolamine (DMPE), together with mixtures DMPC/dimyristylphosphatidylglycerol (DMPG), DMPC/DMPG/cholesterol and DMPE/DMPG. Melittin bound rapidly to all membrane mixtures, whereas 21Q, which has a reduced charge, bound much more slowly on the DMPC and DMPC/DMPG mixtures reflecting the role of the initial electrostatic interaction. The loss of the cationic residues also significantly decreased the binding of 21Q with DMPC/DMPG/Cholesterol, DMPE and DMPE/DMPG. The role of electrostatics was also highlighted with NaCl in the buffer, which affected the way melittin bound to the different membranes, causing a more uniform, concentration dependant increase in response. The biosensor results were correlated with the conformation of the peptides determined by circular dichroism analysis, which indicated that high α-helicity was associated with high binding affinity. Overall, the results demonstrate that the positively charged residues at the C-terminus of melittin play an essential role in membrane binding, that modulation of peptide charge influences selectivity of binding to different phospholipids and that manipulation of the cationic regions of antimicrobial peptides can be used to modulate membrane selectivity.     

The role of neisserial Opa proteins in interactions with host cells

Pathogenic Neisseria spp. possess a repertoire of phase-variable Opa proteins that mediate various pathogen–host cell interactions, including bacterial engulfment by epithelial cells and opsonin-independent phagocytosis by professional phagocytes. Recent studies have identified cellular targets recognized by defined Opa proteins and have begun to reveal host signalling events involved in mediating these Opa-dependent cellular processes.     

The effects of external NaCl on thylakoid stacking in lettuce plants

The average degree of thylakoid stacking was determined for loose-leaf lettuce plants which were grown in complete nutrient solutions containing either 10 or 100mol m^?3 NaCl. Digitonin fractionation and differential centrifugation were used to assay the level of thylakoid stacking. Based on a comparison between 10mol m^?3 NaCl-grown and 100mol m^?3 NaCl-grown lettuce plants of equal ages, digitonin assays indicated that significantly less stacking occurred in 100mol m^?3 NaCl-grown plants. Isolated thylakoid membranes from 100mol m^?3 NaCl-grown plants were also characterized by a greater capacity to absorb divalent cations and by a higher chlorophyll a/b ratio. Since plants from both growth salinities were capable of a marked increase in thylakoid stacking upon a transition from high to low irradiance, the observed differences in thylakoid stacking were not attributed to a salinity-related impairment of stacking mechanisms. Instead, the salinity-induced differences in thylakoid stacking appear to represent a process of controlled adjustment.     

Dielectric behavior of polyelectrolytes. III. The role of counterion interactions

The role of the Coulomb forces between the counterions on the surface of polyelectrolytes on the dielectric response is analyzed. An estimate of the maximum dielectric increment (as a function of the number of counterions) is found as a function of the molecular length. The minimum-energy configuration of the counterions on a cylinder is found to be a double helix, suggesting the fundamental importance of electrostatic interactions in determining structure. Solutions of the dynamical equations for a few counterions indicate that a single mode dominates the relaxation which is enhanced by the inter-ion repulsions. A lower bound is found for this mode based on analysis of the system response for short lengths. Sum rules for the rates and amplitudes of the dipolar correlation function are derived and lead to an upper bound for the rate of the dominant mode. These bounds approach one another for the parameters characteristic of restriction fragments of DNA. This permits a prediction of the magnitude and time scale of the dielectric response.     

100Hz电针刺受时大鼠脑和脊髓k受体结构特性的改变

西方采用放射配体结合实验研究了１００ＨＺ电针耐受发生发展过程中大鼠脑和脊髓Ｋ受体结构特性的变化。大鼠每天给予１００ＨＺ电针１次,连续７ｄ。分别在电针的第１、３、５、７天取不同脑区进行观察。     

The role of chromophore in the lipid-protein interactions in bacteriorhodopsin-phosphatidylcholine vesicles

By fluorescence and phase properties of a 1-acyl-2-[8-(2-anthroyl)-octanoyl]-sn-glycero-3-phosphocholine probe, the influence of the chromophore on the phase transition of bacteriorhodopsin–lipid vesicles was investigated. It was observed that removal of the chromophore led to the down-shifting of the phase transition temperatures. The temperatures corresponding to the beginning and ending of the gel–liquid phase transition were also influenced. This demonstrated that the liquid phase is reached more easily when the chromophore is bleached. The results indicate that removal of the chromophore alters the protein–lipid interactions. It is suggested that this alteration might be related to the change in the lipid molecular packing.     

免疫细胞内源性儿茶酚胺的免疫调节作用

机体内儿茶酚胺（catecholamines,CAs）包括去甲肾上腺素（norepinephrine,NE）、肾上腺素（epinephrine,E）和多巴胺（dopamine,DA）。CAs由神经元和内分泌细胞合成和分泌,其主要功能是调节心血管、呼吸和消化等内脏活动。近三十年来的研究说明,CAs也参与调控机体的免疫功能,但CAs的这种免疫调节作用一般视为神经和内分泌系统调节的介导作用。然而,近年来的研究发现,免疫细胞也能合成CAs,这是对传统观念的一种补充和提高。免疫细胞内存在经典的CAs代谢途径,既有合成CAs的酪氨酸羟化酶（tyrosine hydroxylase,TH）又有降解CAs的单胺氧化酶（monoamine oxidase,MAO）和儿茶酚氧位甲基移位酶（catechol-O-methyl transferase,COMT）。免疫细胞合成的内源性CAs可以调控细胞的增殖、分化、凋亡和细胞因子生成等多种免疫功能。CAs的这些作用可能主要通过自分泌或旁分泌途径作用于免疫细胞上相应受体和细胞内环磷酸腺苷（cyclicAMP,cAMP）实现。细胞内氧化应激机制可能也参与免疫细胞内源性CAs的免疫调节作用。此外,一些自身免疫性疾病如多发性硬化、风湿性关节炎可能也与免疫细胞内CAs的代谢异常有关。上述发现不仅为免疫系统有可能成为除神经和内分泌系统以外的第三个CA能系统提供了证据,而且为免疫系统内源性CAs的功能意义拓展了认识。     

Norepinephrine transporter knockout-induced up-regulation of brain alpha2A/C-adrenergic receptors

The norepinephrine transporter (NET) is responsible for the rapid removal of norepinephrine released from sympathetic neurons; this release is controlled by inhibitory alpha(2)-adrenergic receptors (alpha(2)ARs). Long-term inhibition of the NET by antidepressants has been reported to change the density and function of pre- and postsynaptic ARs, which may contribute to the antidepressant effects of NET inhibitors such as desipramine. NET-deficient (NET-KO) mice have been described to behave like antidepressant-treated mice. By means of quantitative real-time PCR we show that mRNAs encoding the alpha(2A)-adrenergic receptor (alpha(2A)AR) and the alpha(2C)-adrenergic receptor (alpha(2C)AR) are up-regulated in the brainstem, and that alpha(2C)AR mRNA is also elevated in the hippocampus and striatum of NET-KO mice. These results were confirmed at the protein level by quantitative autoradiography. The NET-KO mice showed enhanced binding of the selective alpha(2)AR antagonist [(3)H]RX821002 in several brain regions. Most robust increases (20-25%) in alpha(2)AR expression were observed in the hippocampus and in the striatum. Significant increases (16%) were also seen in the extended amygdala and thalamic structures. In an 'in vivo' test, the alpha(2)AR agonist clonidine (0.1 mg/kg) caused a significantly greater reduction of locomotor activity in NET-KO mice than in wild-type mice, showing the relevance of our findings at the functional level.