Empirical formulation and parameterization of cation-π interactions for protein modeling

Cation-π interaction is comparable and as important as other main molecular interaction types, such as hydrogen bond, electrostatic interaction, van der Waals interaction, and hydrophobic interaction. Cation-π interactions frequently occur in protein structures, because six (Phe, Tyr, Trp, Arg, Lys, and His) of 20 natural amino acids and all metallic cations could be involved in cation-π interaction. Cation-π interactions arise from complex physicochemical nature and possess unique interaction behaviors, which cannot be modeled and evaluated by existing empirical equations and force field parameters that are widely used in the molecular dynamics. In this study, the authors present an empirical approach for cation-π interaction energy calculations in protein interactions. The accurate cation-π interaction energies of aromatic amino acids (Phe, Tyr, and Try) with protonated amino acids (Arg and Lys) and metallic cations (Li(+), Na(+), K(+), and Ca(2+)) are calculated using B3LYP/6-311+G(d,p) method as the benchmark for the empirical formulization and parameterization. Then, the empirical equations are built and the parameters are optimized based on the benchmark calculations. The cation-π interactions are distance and orientation dependent. Correspondingly, the empirical equations of cation-π interactions are functions of two variables, the distance r and the orientation angle θ. Two types of empirical equations of cation-π interactions are proposed. One is a modified distance and orientation dependent Lennard-Jones equation. The second is a polynomial function of two variables r and θ. The amino acid-based empirical equations and parameters provide simple and useful tools for evaluations of cation-π interaction energies in protein interactions.     

Variations in binding among several agonists at two stoichiometries of the neuronal, α4β2 nicotinic receptor

Drug-receptor binding interactions of four agonists, ACh, nicotine, and the smoking cessation compounds varenicline (Chantix) and cytisine (Tabex), have been evaluated at both the 2:3 and 3:2 stoichiometries of the α4β2 nicotinic acetylcholine receptor (nAChR). Previous studies have established that unnatural amino acid mutagenesis can probe three key binding interactions at the nAChR: a cation-π interaction, and two hydrogen-bonding interactions to the protein backbone of the receptor. We find that all drugs make a cation-π interaction to TrpB of the receptor. All drugs except ACh, which lacks an N(+)H group, make a hydrogen bond to a backbone carbonyl, and ACh and nicotine behave similarly in acting as a hydrogen-bond acceptor. However, varenicline is not a hydrogen-bond acceptor to the backbone NH that interacts strongly with the other three compounds considered. In addition, we see interesting variations in hydrogen bonding interactions with cytisine that provide a rationalization for the stoichiometry selectivity seen with this compound.     

On the directionality of anion-π interactions

The directionality of two important noncovalent interactions involving aromatic rings (namely anion-π and cation-π) is investigated. It has been recently published that the anion-π interactions observed in X-ray structures where the anion is located exactly over the center of the ring are scarce compared to cation-π interactions. To explain this behavior, we have analyzed how the interaction energy (RI-MP2/aug-cc-pVDZ level of theory) is affected by moving the anion from the center of the ring to several directions in anion-π complexes of chloride with either hexafluorobenzene or trifluoro-s-triazine. We have compared the results with the directionality of the cation-π interaction in the sodium-benzene complex. The results are useful to explain the experimental differences between both ion-π interactions. We have also computed the van der Waals radii of several halide anions and we have compared them to the neutral halogen atoms.     

Effects of extending the computational model on DNA-protein T-shaped interactions: the case of adenine-histidine dimers

The MP2/6-31G*(0.25) π-π or π(+)-π T-shaped (edge-to-face) interactions between neutral or protonated histidine and adenine were considered using computational models of varying size to determine the effects of the protein and DNA backbones on the preferred dimer structure and binding strength. The overall consequences of the backbones are reasonably subtle for the neutral adenine-histidine T-shaped dimers. Furthermore, the minor changes in the binding strengths of these dimers upon model extension arise from additional (attractive) backbone-π (bb-π) contacts and changes in the preferred π-π orientations, which is verified by the quantum theory of atoms in molecules (QTAIM). Since the binding strength of the extended dimer equals the sum of the individual backbone-π and π-π contributions, the π-π component is not appreciably affected by polarization of the ring upon inclusion of the biological backbone. In contrast, the larger effect of the backbone on the protonated histidine dimers cannot simply be predicted as the sum of changes in the π-π and bb-π components regardless of the dimer type or model. This suggests, and QTAIM qualitatively supports, that the magnitude of the π(+)-π contribution changes, which is likely due to alterations in the electrostatic landscape of the monomer rings upon inclusion of the biological backbone that largely affect T-shaped dimers. These findings differ from those previously reported for (neutral) π-π stacked and (metallic) cation-π interactions, which highlights the distinct properties of each (π-π, π(+)-π, and cation-π) classification of noncovalent interaction. Furthermore, these results emphasize the importance of considering backbone-π interactions when analyzing contacts that appear in experimental crystal structures and cautions the use of truncated models when evaluating the magnitude of the π(+)-π contribution present in large biological complexes.     

Insight into the cation-π interaction at the metal binding site of the copper metallochaperone CusF

The periplasmic Cu(+)/Ag(+) chaperone CusF features a novel cation-π interaction between a Cu(+)/Ag(+) ion and Trp44 at the metal binding site. The nature and strength of the Cu(+)/Ag(+)-Trp44 interactions were investigated using computational methodologies. Quantum-mechanical (QM) calculations showed that the Cu(+) and Ag(+) interactions with Trp44 are of similar strength (~14 kcal/mol) and bond order. Quantum-mechanical/molecular-mechanical (QM/MM) calculations showed that Cu(+) binds in a distorted tetrahedral coordination environment in the Trp44Met mutant, which lacks the cation-π interaction. Molecular dynamics (MD) simulations of CusF in the apo and Cu(+)-bound states emphasized the importance of the Cu(+)-Trp44 interaction in protecting Cu(+) from water oxidation. The protein structure does not change over the time scale of hundreds of nanoseconds in the metal-bound state. The metal recognition site exhibits small motions in the apo state but remains largely preorganized toward metal binding. Trp44 remains oriented to form the cation-π interaction in the apo state and faces an energetic penalty to move away from the metal ion. Cu(+) binding quenches the protein's internal motions in regions linked to binding CusB, suggesting that protein motions play an essential role in Cu(+) transfer to CusB.     

Li?π interaction in coronene-azacrown ether system

The combination of the coronene ring and azacrown ether generated a new kind of host molecule in which the Li⁺ binding ability originated from the cation-dipole interaction (crown moiety) and the cation-π interaction (coronene ring). Introducing a large π face (coronene ring) enhanced cation binding ability of the crown ether. The NMR, the fluorescence spectra, and ab initio calculations strongly indicated the effect of the cation-π interaction.     

氨基酸突变对GABAa受体结合能力的影响

采用同源建模技术构建了大鼠γ-氨基丁酸a型受体(GABAaR)模型, 并将氨基酸残基β157Tyr和β205Tyr突变为相应的突变受体模型. 使用分子对接方法计算了γ-氨基丁酸(GABA)与突变前后受体的相互作用. 对接计算结果显示, Tyr突变为Phe后, 两种突变受体的对接能量大幅提高, GABA生物活性降低; 当Phe的对位引入氟原子后, 对接能量与未突变受体相比更低. 另外, 与β205Tyr突变相比, 与配体距离较近的β157Tyr突变, 对受体与配体作用的影响更大.     

γ-氨基丁酸与其突变受体的相互作用

采用同源建模技术构建了大鼠γ-氨基丁酸a型受体(GABAaR)模型及β97Tyr突变受体模型. 采用分子对接技术研究了γ-氨基丁酸(GABA)与突变前后受体的相互作用. 计算结果显示, 突变及未突变受体之间在氢键作用和对接能量方面存在显著差异, 配体与突变受体的结合能力随突变残基中氟原子数目的增加而降低.     

Quantitative assessment of substituent effects on cation-π interactions using molecular electrostatic potential topography

A molecular electrostatic potential (MESP) topography based approach has been proposed to quantify the substituent effects on cation-π interactions in complexes of mono-, di-, tri-, and hexasubstituted benzenes with Li(+), Na(+), K(+), and NH(4)(+). The MESP minimum (V(min)) on the π-region of C(6)H(5)X showed strong linear dependency to the cation-π interaction energy, E(M(+)). Further, cation-π distance correlated well with V(min)-π distance. The difference between V(min) of C(6)H(5)X and C(6)H(6) (ΔV(min)) is proposed as a good parameter to quantify the substituent effect on cation-π interaction. Compared to benzene, electron-donating groups stabilize the di-, tri-, and hexasubstituted cation-π complexes while electron-withdrawing groups destabilize them. In multiple substituted complexes, E(M(+)) is almost equal (～95%) to the sum of the individual substituent contributions (E(M(+)) ≈ Σ(ΔE(M(+)))), suggesting that substituent effect on cation-π interactions is largely additive. The ΔV(min) of C(6)H(5)X systems and additivity feature have been used to make predictions on the interaction energies of 80 multiple substituted cation-π complexes with above 97% accuracy. The average mean absolute deviation of the V(min)-predicted interaction energy, E(M(+))(V) from the calculated E(M(+)) is -0.18 kcal/mol for Li(+), -0.09 kcal/mol for Na(+), -0.43 kcal/mol for K(+), and -0.67 kcal/mol for NH(4)(+), which emphasize the predictive power of V(min) as well as the additive feature of the substituent effect.     

Cation⊗3π: cooperative interaction of a cation and three benzenes with an anomalous order in binding energy

Cation-π or cation-π-π interaction between one cation and one or two structures bearing rich π-electrons (such as benzene, aromatic rings, graphene, and carbon nanotubes) plays a ubiquitous role in various areas. Here, we analyzed a new type interaction, cation?3π, whereby one cation simultaneously binds with three separate π-electron-rich structures. Surprisingly, we found an anomalous increase in the order of the one-benzene binding strength of the cation?3π interaction, with K(+) > Na(+) > Li(+). This was at odds with the conventional ranking of the binding strength which usually increases as the radii of the cations decrease. The key to the present unexpected observations was the cooperative interaction of the cation with the three benzenes and also between the three benzenes, in which a steric-exclusion effect between the three benzenes played an important role. Moreover, the binding energy of cation?3π was comparable to cation?2π for K(+) and Na(+), showing the particular importance of cation?3π interaction in biological systems.     

UV Raman markers for structural analysis of aromatic side chains in proteins

UV Raman spectroscopy is a powerful tool for investigating the structures and interactions of the aromatic side chains of Phe, Tyr, Trp, and His in proteins. This is because Raman bands of aromatic ring vibrations are selectively enhanced with UV excitation, and intensities and wavenumbers of Raman bands sensitively reflect structures and interactions. Interpretation of protein Raman spectra is greatly assisted by using empirical correlations between spectra and structure. Many Raman bands of aromatic side chains have been proposed to be useful as markers of structures and interactions on the basis of empirical correlations. This article reviews the usefulness and limitations of the Raman markers for protonation/deprotonation, conformation, metal coordination, environmental polarity, hydrogen bonding, hydrophobic interaction, and cation-π interaction of the aromatic side chains. The utility of Raman markers is demonstrated through an application to the structural analysis of a membrane-bound proton channel protein.     

Exploring the binding of serotonin to the 5-HT3 receptor by density functional theory

The 5-HT3 receptor is a typical ligand-gated ion channel of the Cys-loop superfamily, which is activated by binding of serotonin (5-HT). Models of the binding site of this protein reveal potential interactions between 5-HT and Tyr143, Tyr153, and Tyr234. Here we describe a series of ab initio calculations, based on density functional theory, to assess the effects of mutating these tyrosine residues on the binding of 5-HT. A series of mutations to these tyrosines, previously studied experimentally, were tested, and the binding energies compared with the available experimental data. Our results show that Tyr153 could form a hydrogen bond with the tertiary amine of 5-HT, and that mutation in this location revealed binding energies broadly in line with experimentally determined EC50s. Tyr143 could also form a hydrogen bond, but as EC50s do not relate to binding energies, it is unlikely that such a bond is formed here. Tyr234 is quite distinct in that it may interact with 5-HT via a mixed hydrogen bond/cation-pi interaction.     

Geometric effects in olefinic cation-π interactions with alkali metals: a computational study

Although cation-π interactions commonly involve aromatic or heteroaromatic rings as the source of π-electrons, isolated and nonconjugated olefins are equally effective donors of π-electron density. Previous comparisons of these π-electron sources have indicated that the net energy of the binding interactions is not a simple additive function of the number of π-bonds involved. For instance, the enthalpy of binding (ΔH°) of Li(+), Na(+), or K(+) cations to two ethylene molecules or to one benzene molecule is approximately the same, despite the 4:6 ratio of π-electrons involved. This present density functional theory study indicates that geometric factors can partially account for the proportionally greater interaction energies of olefins, but whether they are symmetrically placed around the cation or grouped on one hemisphere has little effect on the binding energy. Instead, flexible ligands that permit olefinic π-electrons to be oriented more favorably toward the metal than those in rigid aromatic rings can be correlated with greater bonding. For Li(+) complexes, this appears to be an appreciable factor, although it is less significant with Na(+) and K(+) complexes. For all three cations, stronger polarization interactions with olefins compared to arenes contribute to the strength of cation-π interactions involving olefinic π-bonds.     

A tryptophan-analog host whose interactions with ammonium ions in water are dominated by the hydrophobic effect

The binding of quaternary ammonium guests to a flexible, indole-based host has been studied in both aqueous and organic solvents. Binding was shown to depend strongly on the hydrophobic effect and less on the cation-π interaction.     

Affinity capillary electrophoresis and density functional theory employed for the characterization of hexaarylbenzene-based receptor complexation with alkali metal ions

In this study, affinity capillary electrophoresis (ACE) and quantum mechanical density functional theory (DFT) calculations were combined to investigate non-covalent binding interactions between the hexaarylbenzene-based receptor (R) and alkali metal ions, Rb(+) and Cs(+) , in methanol. The apparent binding (stability) constants (K(b) ) of the complexes of receptor R with alkali metal ions in the methanolic medium were determined by ACE from the dependence of effective electrophoretic mobility of the receptor R on the concentration of Rb(+) and Cs(+) ions in the BGE using a non-linear regression analysis. The receptor R formed relatively strong complexes both with rubidium (log K(b) =4.04±0.21) and cesium ions (log K(b) =3.72±0.22). The structural characteristics of the above alkali metal ion complexes with the receptor R were described by ab initio density functional theory calculations. These calculations have shown that the studied cations bind to the receptor R because they synergistically interact with the polar ethereal fence and with the central benzene ring via cation-π interaction.     

Combined cation-π and anion-π interactions for zwitterion recognition

Brothers and enemies: Anion-π and cation-π interactions act in a synergistic way when gathered in the molecular cavity of a hemicryptophane host, affording an efficient contribution (-170?kJ?mol(-1)) in zwitterion recognition. NMR titration experiments and calculations reveal the positioning of the guest in the cavity of the heteroditopic receptor. This study emphasizes the importance of anion-π bonds in host-guest chemistry.     

Encapsulation of metal cations by the PhePhe ligand: a cation-π ion cage

Structures and binding thermochemistry are investigated for protonated PhePhe and for complexes of PhePhe with the alkaline-earth ions Ba(2+) and Ca(2+), the alkali-metal ions Li(+), Na(+), K(+), and Cs(+), and the transition-metal ion Ag(+). The two neighboring aromatic side chains open the possibility of a novel encapsulation motif of the metal ion in a double cation-π configuration, which is found to be realized for the alkaline-earth complexes and, in a variant form, for the Ag(+) complex. Experimentally, complexes are formed by electrospray ionization, trapped in an FT-ICR mass spectrometer, and characterized by infrared multiple photon dissociation (IRMPD) spectroscopy using the free electron laser FELIX. Interpretation is assisted by thermochemical and IR spectral calculations using density functional theory (DFT). The IRMPD spectrum of protonated PhePhe is reproduced with good fidelity by the calculated spectrum of the most stable conformation, although the additional presence of the secondmost stable conformation is not excluded. All metal-ion complexes have charge-solvated binding modes, with zwitterion (salt bridge) forms being much less stable. The amide oxygen always coordinates to the metal ion, as well as at least one phenyl ring (cation-π interaction). At least one additional chelation site is always occupied, which may be either the amino nitrogen or the carboxy carbonyl oxygen. The alkaline-earth complexes prefer a highly compact caged structure with both phenyl rings providing cation-π stabilization in a "sandwich" configuration (OORR chelation). The alkali-metal complexes prefer open-cage structures with only one cation-π interaction, except perhaps Cs(+). The Ag(+) complex shows a unique preference for the closed-cage amino-bound NORR structure. Ligand-driven perturbations of normal-mode frequencies are generally found to correlate linearly with metal-ion binding energy.     

Investigation of Simultaneous Cation-Π and Π–Π Stacking Interactions on Graphene and Some Bent Graphenes as Curved Surfaces of Carbon Nanohorns

Computational quantum chemistry methods are used to study simultaneous cation-π and π–π stacking interactions with a graphene sheet and on the inner and outer faces of some bent graphenes as curved surfaces of carbon nanohorns (CNHs). Structural parameters and energy data of ternary benzene–graphene–Na⁺ and benzene-bent graphene–Na⁺ complexes are studied. Also, effects of charge transfer and aromaticity are estimated to determine how changes in the structure influences the above interactions. The results indicate that the graphene curvature leads to structural changes affecting simultaneous interactions of the Na+ cation and benzene with bent graphenes. Also, the results show that although π–π stacking is a weak interaction, it can manipulate the order of binding energies in complexes involving both mentioned interactions and affect drug delivery abilities of these systems.