A cation-pi binding interaction with a tyrosine in the binding site of the GABAC receptor

GABA(C) (rho) receptors are members of the Cys-loop superfamily of neurotransmitter receptors, which includes nicotinic acetylcholine (nACh), 5-HT(3), and glycine receptors. As in other members of this family, the agonist binding site of GABA(C) receptors is rich in aromatic amino acids, but while other receptors bind agonist through a cation-pi interaction to a tryptophan, the GABA(C) binding site has tyrosine at the aligning positions. Incorporating a series of tyrosine derivatives at position 198 using unnatural amino acid mutagenesis reveals a clear correlation between the cation-pi binding ability of the side chain and EC(50) for receptor activation, thus demonstrating a cation-pi interaction between a tyrosine side chain and a neurotransmitter. Comparisons among four homologous receptors show variations in cation-pi binding energies that reflect the nature of the cationic center of the agonist.     

The role of cation-pi interactions in biomolecular association. Design of peptides favoring interactions between cationic and aromatic amino acid side chains.

Cation-pi interactions between amino acid side chains are increasingly being recognized as important structural and functional features of proteins and other biomolecules. Although these interactions have been found in static protein structures, they have not yet been detected in dynamic biomolecular systems. We determined, by (1)H NMR spectroscopic titrations, the energies of cation-pi interactions of the amino acid derivative AcLysOMe (1) with AcPheOEt (2) and with AcTyrOEt (3) in aqueous and three organic solvents. The interaction energy is substantial; it ranges from -2.1 to -3.4 kcal/mol and depends only slightly on the dielectric constant of the solvent. To assess the effects of auxiliary interactions and structural preorganization on formation of cation-pi interactions, we studied these interactions in the association of pentapeptides. Upon binding of the positively-charged peptide AcLysLysLysLysLysNH(2) (5) to the negatively-charged partner AcAspAspXAspAspNH(2) (6), in which X is Leu (6a), Tyr (6b), and Phe (6c), multiple interactions occur. Association of the two pentapeptides is dynamic. Free peptides and their complex are in fast exchange on the NMR time-scale, and 2D (1)H ROESY spectra of the complex of the two pentapeptides do not show intermolecular ROESY peaks. Perturbations of the chemical shifts indicated that the aromatic groups in peptides 6b and 6c were affected by the association with 5. The association constants K(A) for 5 with 6a and with 6b are nearly equal, (4.0 +/- 0.7) x 10(3) and (5.0 +/- 1.0) x 10(3) M(-)(1), respectively, while K(A) for 5 with 6c is larger, (8.3 +/- 1.3) x 10(3) M(-)(1). Molecular-dynamics (MD) simulations of the pentapeptide pairs confirmed that their association is dynamic and showed that cation-pi contacts between the two peptides are stereochemically possible. A transient complex between 5 and 6 with a prominent cation-pi interaction, obtained from MD simulations, was used as a template to design cyclic peptides C(X) featuring persistent cation-pi interactions. The cyclic peptide C(X) had a sequence in which X is Tyr, Phe, and Leu. The first two peptides do, but the third does not, contain the aromatic residue capable of interacting with a cationic Lys residue. This covalent construct offered conformational stability over the noncovalent complexes and allowed thorough studies by 2D NMR spectroscopy. Multiple conformations of the cyclic peptides C(Tyr) and C(Phe) are in slow exchange on the NMR time-scale. In one of these conformations, cation-pi interaction between Lys3 and Tyr9/Phe9 is clearly evident. Multiple NOEs between the side chains of residues 3 and 9 are observed; chemical-shift changes are consistent with the placement of the side chain of Lys3 over the aromatic ring. In contrast, the cyclic peptide C(Leu) showed no evidence for close approach of the side chains of Lys3 and Leu9. The cation-pi interaction persists in both DMSO and aqueous solvents. When the disulfide bond in the cyclic peptide C(Phe) was removed, the cation-pi interaction in the acyclic peptide AC(Phe) remained. To test the reliability of the pK(a) criterion for the existence of cation-pi interactions, we determined residue-specific pK(a) values of all four Lys side chains in all three cyclic peptides C(X). While NOE cross-peaks and perturbations of the chemical shifts clearly show the existence of the cation-pi interaction, pK(a) values of Lys3 in C(Tyr) and in C(Phe) differ only marginally from those values of other lysines in these dynamic peptides. Our experimental results with dynamic peptide systems highlight the role of cation-pi interactions in both intermolecular recognition at the protein-protein interface and intramolecular processes such as protein folding.     

Influence of the water molecule on cation-pi interaction: ab initio second order Møller-Plesset perturbation theory (MP2) calculations

The influence of introducing water molecules into a cation-pi complex on the interaction between the cation and the pi system was investigated using the MP2/6-311++G method to explore how a cation-pi complex changes in terms of both its geometry and its binding strength during the hydration. The calculation on the methylammonium-benzene complex showed that the cation-pi interaction is weakened by introducing H(2)O molecules into the system. For example, the optimized interaction distance between the cation and the benzene becomes longer and longer, the transferred charge between them becomes less and less, and the cation-pi binding strength becomes weaker and weaker as the water molecule is introduced one by one. Furthermore, the introduction of the third water molecule leads to a dramatic change in both the complex geometry and the binding energy, resulting in the destruction of the cation-pi interaction. The decomposition on the binding energy shows that the influence is mostly brought out through the electrostatic and induction interactions. This study also demonstrated that the basis set superposition error, thermal energy, and zero-point vibrational energy are significant and needed to be corrected for accurately predicting the binding strength in a hydrated cation-pi complex at the MP2/6-311++G level. Therefore, the results are helpful to better understand the role of water molecules in some biological processes involving cation-pi interactions.     

Cation-pi interactions stabilize the structure of the antimicrobial peptide indolicidin near membranes: molecular dynamics simulations

We implemented molecular dynamics simulations of the 13-residue antimicrobial peptide indolicidin (ILPWKWPWWPWRR-NH2) in dodecylphosphocholine (DPC) and sodium dodecyl sulfate (SDS) micelles. In DPC, a persistent cation-pi interaction between TRP11 and ARG13 defined the structure of the peptide near the interface. A transient cation-pi interaction was also observed between TRP4 and the choline group on DPC lipids. We also implemented simulation of a mutant of indolicidin in the DPC micelle where TRP11 was replaced by ALA11. As a result of the mutation, the boat-shaped conformation is lost and the structure becomes significantly less defined. On the basis of this evidence, we argue that cation-pi interactions determine the experimentally measured, well-defined boat-shaped structure of indolicidin. In SDS, the lack of such interactions and the electrostatic binding of the terminal arginine residues to the sulfate groups leads to an extended peptide structure. To the best of our knowledge, this is the first time that a cation-pi interaction between peptide side chains has been shown to stabilize the structure of a small antimicrobial peptide. The simulations are in excellent agreement with available experimental measurements: the backbone of the peptide is more ordered in DPC than in SDS; the tryptophan side chains pack against the backbone in DPC and point away from the backbone in SDS; the rms fluctuation of the peptide backbone and peptide side chains is greater in SDS than in DPC; and the peptide backbone order parameters are higher in DPC than in SDS.     

Relative strength of cation-pi vs salt-bridge interactions: the Gtalpha(340-350) peptide/rhodopsin system

Interactions between cationic and aromatic side chains of amino acid residues, the so-called cation-pi interaction, are thought to contribute to the overall stability of the folded structure of peptides and proteins. The transferred NOE NMR structure of the G(t)alpha(340-350) peptide bound to photoactivated rhodopsin (R*) geometrically suggests a cation-pi interaction stabilizing the structure between the epsilon-amine of Lys341 and the aromatic ring of the C-terminal residue, Phe350. This interaction has been explored by varying substituents on the phenyl ring to alter the electron density of the aromatic ring of Phe350 and observing the impact on binding of the peptide to R*. The results suggest that while a cation-pi interaction geometrically exists in the G(t)alpha(340-350) peptide when bound to R*, its energetic contribution to the stability of the receptor-bound structure is relatively insignificant, as it was not observed experimentally. The presence of an adjacent and competing salt-bridge interaction between the epsilon-amine of Lys341 and the C-terminal carboxylate of Phe350 effectively shields the charge of the ammonium group. Experimental data supporting a significant cation-pi interaction can be regained through a series of Phe350 analogues where the C-terminal carboxyl has been converted to the neutral carboxamide, thus eliminating the shielding salt-bridge. TrNOE NMR experiments confirmed the existence of the cation-pi interaction in the carboxamide analogues. Various literature estimates of the strength of cation-pi interactions, including some that estimate strengths in excess of salt-bridges, are compromised by omission of the relevant anion in the calculations.     

Cation-pi binding of an alkali metal ion by pendant alpha,alpha-dimethylbenzyl groups within a dinuclear iron(III) structural unit

We report here on the cation-pi binding of potassium ions by benzyl groups in a coordination complex. The results demonstrate the cation-binding power of the benzyl group and consequently the potential for aromatic groups to interact with alkali metal ions even in aqueous media.     

Uranyl-salophen based ditopic receptors for the recognition of quaternary ammonium halides

Uranyl-salophen complexes endowed with aromatic side arms behave as very efficient ditopic receptors towards tetralkylammonium halides as a result of a combination of Lewis acid-base and cation-pi interactions.     

Regio- and stereoselective addition of allylmetal reagents to pyridinium-pi and quinolinium-pi complexes

[reaction: see text] Regio- and stereoselective allylation of pyridinium and quinolinium salts was performed by the addition of allylindium and allyltributyltin reagents toward intermediary cation-pi complexes. The reaction with allylindium and allyltributyltin reagents afforded a 1,2-adduct, whereas the addition of a prenylindium reagent gave a 1,4-adduct with good regio- and stereoselectivities. X-ray structural analysis, 1H NMR studies, and DFT calculations elucidated the intermediary cation-pi complex formation with face-to-face orientation.     

Methodology for the calculation of the potential of mean force for a cation-pi complex in water.

We report potential of mean force (PMF) calculations on the interaction between the p-sulfonatocalix[4]arene and a monovalent cation (Cs(+)). It has been recently shown from microcalorimetry and (133)Cs NMR experiments that the association with Cs(+) is governed by favourable cation-pi interactions and is characterized by the insertion of the cation into the cavity of the macrocycle. We show that the PMF calculation based upon a classical model is not able to reproduce both the thermodynamic properties of association and the insertion of the cation. In order to take into account the different contributions of the cation-pi interactions, we develop a new methodology consisting of changing the standard PMF by an additional contribution resulting from quantum calculations. The calculated thermodynamic properties of association are thus in line with the microcalorimetry and (133)Cs NMR experiments and the structure of the complex at the Gibbs free-energy minimum shows the insertion of the cation into the cavity of the calixarene.     

Cation-pi interactions and the gas-phase thermochemistry of the Na(+)/phenylalanine complex

The complex of Na(+) with phenylalanine (Phe) is a prototype for the participation of cation-pi interactions in metal-ion binding to biological molecules. A recent comparison of this complex with the Na(+)/alanine (Na(+)/Ala) counterpart suggested only a small contribution of the phenyl ring interaction to binding, casting doubt on the extent of the cation-pi effect. The present work reexamines this thermochemistry using ligand-exchange equilibrium measurements in the Fourier transform ion cyclotron resonance (FT-ICR) ion trapping mass spectrometer. An increment of 7 +/- 2 kcal mol(-1) was found in the Ala/Phe comparison of binding enthalpies, confirming the importance of cation-pi binding enhancement in the Phe case. Absolute Na(+) binding enthalpies of 38 +/- 2 and 45 +/- 2 kcal mol(-1) were assigned for Ala and Phe, respectively, using pyridine as the thermochemical reference ligand. All of these results were supported by quantum calculations using both density functional and Hartree-Fock/MP2 methods, improved in several respects over previous calculations. Alanine methyl ester (AlaMe) was also observed, and found to have an Na(+) ion affinity larger by 2.3 kcal mol(-1) than Ala. New, lower energy conformations of neutral Phe were discovered in the computations.     

Effects of chain length and N-methylation on a cation-pi interaction in a beta-hairpin peptide

The effects of N-methylation and chain length on a cation-pi interaction have been investigated within the context of a beta-hairpin peptide. Significant enhancement of the interaction and structural stabilization of the hairpin have been observed upon Lys methylation. Thermodynamic analysis indicates an increased entropic driving force for folding upon methylation of Lys residues. Comparison of lysine to analogues ornithine (Orn) and diaminobutyric acid (Dab) indicates that lysine provides the strongest cation-pi interaction and also provides the most stable beta-hairpin due to a combination of side chain-side chain interactions and beta-sheet propensities. These studies have significance for the recognition of methylated lysine in histone proteins.     

How does ammonium dynamically interact with benzene in aqueous media? A first principle study using the Car-Parrinello molecular dynamics method

The Car-Parrinello molecular dynamics (CPMD) method was used to study the dynamic characteristics of the cation-pi interaction between ammonium and benzene in gaseous and aqueous media. The results obtained from the CPMD calculation on the cation-pi complex in the gaseous state were very similar to those calculated from the Gaussian98 program with DFT and MP2 algorithms, demonstrating that CPMD is a valid approach for studying this system. Unlike the interaction in the gaseous state, our 12-ps CPMD simulation showed that the geometry of the complex in aqueous solution changes frequently in terms of the interaction angles and distances. Furthermore, the simulation revealed that the ammonium is constantly oscillating above the benzene plane in an aqueous environment and interacts with benzene mostly through three of its hydrogen atoms. In contrast, the interaction of the cation with the aromatic molecule in the gaseous state involves two hydrogen atoms. In addition, the free energy profile in aqueous solution was studied using constrained CPMD simulations, resulting in a calculated binding free energy of -5.75 kcal/mol at an optimum interaction distance of approximately 3.25 A, indicating that the cation-pi interaction between ammonium and benzene is stable even in aqueous solution. Thus, this CPMD study suggested that the cation-pi interaction between an ammonium (group) and an aromatic structure could take place even on surfaces of protein or nucleic acids in solution.     

MD simulation of the Na+-phenylalanine complex in water: competition between cation-pi interaction and aqueous solvation

The competition between cation-pi interaction and aqueous solvation for the Na+ ion has been investigated by molecular dynamics simulations, using the phenylalanine amino acid as the test pi system. Starting from one of the best standard force fields, we have developed new parameters that significantly improve the agreement with experimental and high quality quantum mechanical results for the complexes of Na+ with phenylalanine, benzene, and water. The modified force field performs very well in forecasting energy and geometry of cation coordination for the complexes. Next, analysis of MD trajectories and steered MD simulations indicate that the Na+-phenylalanine complex survives for a significant time in aqueous solution and that the free energy barrier opposing dissociation of the complex is sizable. Finally, we analyze the role of different intermolecular interactions in determining the preference for cation-pi bonding with respect to aqueous solvation. We thus confirm that the Na+-phenylalanine stabilization energy may overcome the interactions with water.     

Free-energy calculations of protein-ligand cation-pi and amino-pi interactions: from vacuum to proteinlike environments

To probe the role of cation-pi and amino-pi interactions in the context of protein-ligand interactions, the stability of 55 X-ray cation/amino-pi motifs involving the Ade moieties of cofactor molecules and Arg, Lys, Asn, or Gln side chains of their host protein was evaluated using quantum chemistry calculations. The conjunction of vacuum interaction energies, vibrational entropy, and solvation contributions led to identify Arg-Ade as the most favorable cation/amino-pi complex in the solvents considered, followed by Asn/Gln-Ade and Lys-Ade: their minimum interaction free energies are approximately equal to -7, -4, and -2 kcal/mol, respectively, in the solvents of dielectric constant similar to that estimated for proteins (i.e., acetone, THF, and CCl(4)). Remarkably, these free-energy values of cation/amino-pi interactions correlate well with their frequency of occurrences in protein-ligand structures, which corroborates our approach in the absence of experimental data.     

A paradigm shift in the construction of heterobimetallic complexes: synthesis of group 2 & 4 metal-calix[6]arene complexes

Deprotonation of calix[6]arenes with barium in methanol followed by the addition of [Ti(OPr(i))(4)] or [Zr(OBu(n))(4)] is effective in the formation of novel dimeric 2:1 barium-titanium(IV)/zirconium(IV) calix[6]arene complexes. In these complexes a central Ti(IV)/Zr(IV) coordinated in the exo-position connects the two calix[6]arenes in the 1,3-alternate conformation, each with an endo-barium sharing common phenolate groups with the titanium/zirconium centre and participating in cation-pi interactions. A homometallic barium calix[6]arene dimer was also prepared wherein the calix[6]arenes are in the 1,3-alternate conformation with each coordinating one endo- and one exo-barium centre. The exo-barium cations connect the two calix[6]arenes through bridging methanol ligands. In this and the heterometallic complexes, cation-pi complexation of the Ba(2+) ion within the 1,3 alternate conformation of calix[6]arene facilitates the formation of the dimeric complexes in methanol. In contrast, the smaller Sr(2+) ion did not form similar complexes in methanol, and the formation of an analogous 2:1 strontium-titanium calixarene complex required the use of the more sterically demanding donor alcohol, isopropanol, the resulting complex being devoid of cation-pi interaction. The results show (i) that a subtle interplay of solvation strength, coordination array type and cavity/cation size influences the accessibility of heterobimetallic complexes based on calix[6]arenes, and (ii) a synergistic endo-exo binding behaviour.     

Cation-pi interactions as a tool to enhance the power of a chiral auxiliary during asymmetric photoreactions within zeolites

Owing to the existence of cation-pi interactions, aryl chiral auxiliaries perform far better than alkyl chiral auxiliaries during asymmetric photoreaction.     

Ion pair recognition of quaternary ammonium and iminium salts by uranyl-salophen compounds in solution and in the solid state

Efficient ditopic receptors for quaternary ammonium and iminium salts have been obtained upon functionalization of the uranyl-salophen unit with conformationally flexible side arms bearing phenyl or beta-naphthyl substituents. Binding affinities in chloroform solution have been measured for a large number of quaternary salts comprising tetramethylammonium (TMA), tetrabutylammonium (TBA), acetylcholine (ACh), N-methylpyridinium (NMP), and N-methylisoquinolinium (NmiQ) cations. Recognition of the anion partner is ensured by coordination to the hard Lewis acidic uranyl center, whereas cation-pi/CH-pi interactions of the quaternary ions are established with the aromatic pendants. The role of the cation-anion interactions on the dynamics of exchange between the free and complexed species is discussed. Solid-state structures have been obtained for a few salt-receptor combinations. In the solid state, side-armed receptor molecules form assemblies that enclose ion pair aggregates of varying composition and structure, including AChCl dimers, two different kinds of tetrameric (TMA)Cl clusters, and unidimentional salt strips of (NMP)Br. The lack of side arms as preferential binding sites for the polar quaternary cations prevents association patterns of the kinds formed with the side-armed receptors, as shown by the crystal structure of the complex of (TMA)Cl with the parent uranyl-salophen receptor.     

Multiple intermolecular interaction modes of positively charged residues with adenine in ATP-binding proteins

Adenosine 5'-triphosphate (ATP) plays an essential role in all forms of life. Molecular recognition of ATP in ATP-binding proteins is a subject of great importance for understanding enzymatic mechanisms and for drug design. We have carried out a large-scale data mining of the Protein Data Bank (PDB) to analyze molecular determinants for recognition of ATP, in particular, the adenine base, by ATP-binding proteins. A novel distribution pattern of charged residues around the adenine base was discovered: lysine residues tend to occupy the major groove N7 side of the adenine base, and the arginine residues situate preferentially above or below the adenine bases. Such an arrangement is advantageous because it facilitates multiple modes of intermolecular interactions, that is, cation-pi interactions and a hydrogen bond between lysine and adenine, and cation-pi and pi-pi stacking interactions between arginine and adenine. For the two representative Lys...Adenine and Arg...Adenine interactions, intermolecular interaction energies were subsequently analyzed by means of the supermolecular approach at the MP2 level with solvation free energy correction using the SM5.42R model of Cramer and Truhlar, which gave rise to significant interaction strengths.     

Spectroscopic study on anion recognition properties of calix[4]pyrroles: effects of tetraalkylammonium cations

The solution binding properties of calix[4]pyrroles with anion (added as tetraalkylammonium salts) were investigated using UV-vis spectroscopic techniques. The obvious red-shift of absorption maximum band of calix[4]pyrrole in EtOH in the presence of the tetramethylammonium (TMA(+)) or tetraethylammonium (TEA(+)) salts were observed. These results displayed in electronic absorption spectra indicated calix[4]pyrrole receptors linking anionic species through multiple hydrogen bonding interactions are capable of using the periphery electron-rich "walls" for selectively binding electron-deficient tetraalkylammonium cation subunits by cation-pi charge-transfer interaction. It was seen that the stability of the calix[4]pyrrole-anion complex depends strongly on the cation. The meso-alkyl groups of the calix[4]pyrrole, the affinity for the anion subunits and the structure of tetraalkylammonium cations have considerable effects on the formation of cation-pi charge-transfer interaction.