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.     

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.     

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.     

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 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 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.     

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.     

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.     

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.     

Extracting stacking interaction parameters for RNA from the data set of native structures

A crucial step in the determination of the three-dimensional native structures of RNA is the prediction of their secondary structures, which are stable independent of the tertiary fold. Accurate prediction of the secondary structure requires context-dependent estimates of the interaction parameters. We have exploited the growing database of natively folded RNA structures in the Protein Data Bank (PDB) to obtain stacking interaction parameters using a knowledge-based approach. Remarkably, the calculated values of the resulting statistical potentials (SPs) are in excellent agreement with the parameters determined using measurements in small oligonucleotides. We validate the SPs by predicting 74% of the base-pairs in a dataset of structures using the ViennaRNA package. Interestingly, this number is similar to that obtained using the measured thermodynamic parameters. We also tested the efficacy of the SP in predicting secondary structure by using gapless threading, which we advocate as an alternative method for rapidly predicting RNA structures. For RNA molecules with less than 700 nucleotides, about 70% of the native base-pairs are correctly predicted. As a further validation of the SPs we calculated Z-scores, which measure the relative stability of the native state with respect to a manifold of higher free energy states. The computed Z-scores agree with estimates made using calorimetric measurements for a few RNA molecules. Structural analysis was used to rationalize the success and failures of SP and experimentally determined parameters. First, from the near perfect linear relationship between the number of native base-pairs and sequence length, we show that nearly 46% of nucleotides are not in stacks. Second, by analyzing the suboptimal structures that are generated in gapless threading we show that the SPs and experimentally determined parameters are most successful in predicting stacks that end in hairpins. These results show that further improvement in secondary structure prediction requires reliable estimates of interaction parameters for loops, bulges, and stacks that do not end in hairpins.     

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.     

Effect of in vivo treatment of clonidine on ATP-ase's enzyme systems of synaptic plasma membranes from rat cerebral cortex

The effects on energy-consuming ATP-ases were studied in two types of synaptic plasma membranes from rat cerebral cortex after in vivo injection of clonidine. To study the mechanism of action of clonidine at subcellular level, the enzyme activities of Na⁺, K⁺-ATP-ase, Ca²⁺, Mg²⁺-ATP-ase, Low- and High-affinity Ca²⁺-ATP-ase, and Mg²⁺-ATP-ase were evaluated on synaptic plasma membranes of control and treated animals with clonidine (5 g · kg^–1; i.p. 30 minutes). Acute treatment with clonidine decreased the catalytic activity of Ca²⁺, Mg²⁺-ATP-ase and of low-affinity Ca²⁺-ATP-ase only in synaptic plasma membranes of II type, that is the fraction enriched in synaptic plasma membranes. The decreases of these enzymatic activities are related to the interference of the drug on Ca²⁺ homeostasis in synaptoplasm. The reductions of these enzyme-consuming ATP-ases give further evidence that clonidine has not only neuroreceptorial effects, but that the drug also affects the energy metabolism of cerebral tissue, improving the knowledges about the pharmacology of clonidine. Because the elevation of [Ca²⁺]_i, during ischemia/hypoxia contributes to cellular injury, these findings may suggest that the prevention of calcium overload may be the key mechanism of protection by ₂-agonist.     

Transgene stacking in plants in the absence of sexual crossing

A transgene stacking system is a prerequisite for the introduction of multiple genes and for the modification of complex metabolic pathways in plants. We demonstrate here that the MAT-vector system previously used for generating marker-free transgenic plants is also an efficient and reliable transformation system for the repeated introduction of multiple transgenes independent of sexual crossing. We previously reported that the GST-MAT vector system, in which excision of the yeast site-specific recombination R/RS system is regulated by the maize GST-II-27 promoter, could generate marker-free transgenic plants containing a single transgene with high frequency. Here we show that the GST-MAT vector can be used successfully to introduce a second transgene (GFP) into a marker-free transgenic tobacco line containing single copies of the first transgenes (nptII and uidA genes). The transgene-stacked marker-free transgenic tobacco plants were generated from ca. 20% of excision-positive ipt-shooty explants within 5 months of Agrobacterium infection. The presence of uidA, nptII, GFP genes and the absence of the ipt gene were verified by PCR analyses. Furthermore, Southern blot analysis showed that no chromosomal rearrangements were introduced between the first and second transformations.     

The role of charge interactions in muscarinic agonist binding, and receptor-response coupling

Site-directed mutagenesis has been used to evaluate the roles of the key aspartate and arginine residues in transmembrane domain three of the muscarinic receptors. The results suggest that the formation of an ionic bond between the Asp carboxylate group and the onium headgroup is essential to anchor acetylcholine in its active, bound conformation in both binary agonist-receptor and ternary agonist-receptor-G-protein complexes, but that secondary, non-productive binding modes, promoted by non-polar forces, may contribute to binary complex formation by other ligands. The positive charge of the arginyl side-chain is central to the recognition, and subsequent activation of G-proteins by the agonist-M1 mAChR complex.     

细胞因子与膜受体蛋白相互作用的研究方法

细胞因子与膜受体的相互作用是生命活动中的重要环节。癌症、自身免疫疾病、代谢紊乱等疾病的发生都和细胞因子失调有着密切的关系,研究细胞因子和受体的相互作用成为治疗上述疾病的基石。本文综述了现今常用的研究方法,包括从最经典的同位素标记直接检测受体与配体的结合,到生化通路下游信号检测,再到生物物理高通量检测方法。