Cation-π Interactions and their Functional Roles in Membrane Proteins

Cation-π interactions arise as a result of strong attractive forces between positively charged entities and the π-electron cloud of aromatic groups. The physicochemical characteristics of cation-π interactions are particularly well-suited to the dual hydrophobic/hydrophilic environment of membrane proteins. As high-resolution structural data of membrane proteins bring molecular features into increasingly sharper view, cation-π interactions are gaining traction as essential contributors to membrane protein chemistry, function, and pharmacology. Here we review the physicochemical properties of cation-π interactions and present several prominent examples which demonstrate significant roles for this specialized biological chemistry.     

Cation-π interactions in lipocalins: structural and functional implications

The cation-π interaction impacts protein folding, structural stability, specificity, and molecular recognition. Cation-π interactions have been overlooked in the lipocalin family. To fill this gap, these interactions were analyzed in the 113 crystal and solution structures from the lipocalin family. The cation-π interactions link previously identified structurally conserved regions and reveal new motifs, which are beyond the reach of a sequence alignment algorithm. Functional and structural significance of the interactions were tested experimentally in human tear lipocalin (TL). TL, a prominent and promiscuous lipocalin, has a key role in lipid binding at the ocular surface. Ligand binding modulation through the loop AB at the "open" end of the barrel has been erroneously attributed solely to electrostatic interactions. Data revealed that the interloop cation-π interaction in the pair Phe28-Lys108 contributes significantly to stabilize the holo-conformation of the loop AB. Numerous energetically significant and conserved cation-π interactions were uncovered in TL and throughout the lipocalin family. Cation-π interactions, such as the highly conserved Trp17-Arg118 pair in TL, were educed in low temperature experiments of mutants with Trp to Tyr substitutions.     

Silver(I) complexes of dibenzo-18-crown-6-ether having cation-π and π-π interactions

Three silver(I) complexes of dibenzo-18-crown-6-ether (DB[18]C6), [Ag(DB[18]C6)(ClO₄)](THF) (1), [Ag(DB[18]6)(CF₃SO₃)]₂(acetone)₂ (2) and [Ag(DB[18]C6)(CF₃COO)]₂(AgCF₃COO)₂ (3) have been synthesized in different solvents and characterized structurally. In each complex, silver ions prefer an octahedral coordination geometry and form close dinuclear complex with DB[18]C6 based on cation-π interaction in η²-fashion. In particular, the coordination unit involving σ bonding at an oxygen group and π-π bonding between two benzene rings is quite unique.     

π Delocalization in iridathiabenzenes

Fenske-Hall calculations were carried out for (PEt₃)₃Ir(C₇H₉) (1), [(PEt₃)₃Ir(C₆H₈S)]⁺ (2), [(S-t-but)(PEt₃)₂]Ir(C₆H₈S) (3), and [(S-t-but)(PMet₃)₃]Ir(C₆H₈S) (4) in order to compare the degree of π delocalization in the metallathiacycle rings of (2) and (3). In comparison to (1), a true iridabenzene and (4), an iridathiacyclobutadiene, the π ring systems in (2) and (3) are considerably more localized than the π system in (1) but are not totally localized. Strong metal-sulfur bonding in (2) disrupts the π ring system and results in some localization of the ring π bonds. The introduction of the donor thiolate ligand in (3) disrupts the ring of π system even more by destabilizing the metal orbitals used for metal-sulfur interactions. This weakens the metal-sulfur interaction seen in (2) and leads to even more localization of the ring π system in (3).     

Structures and magnetic property studies of four copper(II) and nickel(II) supramolecular complexes derived from diphenic acid constructed by C-H?π and π-π interactions

Four one-dimensional metal-organic polymers derived from diphenic acid (H₂dpa) were synthesized in the presence of auxiliary ligands, [Cu(dpa)CH₃OH](1), [Ni(dpa)CH₃OH] (2), [Cu(bipy)₂(Hdpa)₂(H₂O)₂] (3) and [Ni(bipy)₂(Hdpa)₂(H₂O)₂] (4) (bipy = 4, 4′-bipyridine). The dinuclear paddle-wheel second building units (SBUs) constructed by four dpa²⁻ ligands in complexes 1 and 2 are linked by dpa²⁻ into double chains, which are connected by C-H?π interactions forming a two-dimensional rhombic porous structure. In complexes 3 and 4, the metal ions are connected by bipy ligands, and the grid-like network was formed with the π-π interactions between the adjacent phenyl rings of Hdpa⁻. For 1 and 2, there are strong antiferromagnetic interactions within Cu-Cu and Ni-Ni dimers. It is also strong antiferromagnetic interactions between the dimmers of Cu₂ in 1, while it is weaker of those of Ni₂ in 2. Weaker antiferromagnetic interactions exist among Cu-Cu and Ni-Ni in 3 and 4, in which bipy is the effective coupling media. Thermally gravimetric analyses and differential thermal analyses indicate that the four complexes are all thermal stable.     

Cation—π and Amino-Acceptor Interactions Between Hydrated Metal Cations and DNA Bases. A Quantum-Chemical View

Abstract

Cation—π interactions between cytosine and hexahydrated cations have been characterized using ab initio method with inclusion of electron correlation effects, assuming idealized and crystal geometries of the interacting species. Hydrated metal cations can interact with nucleobases in a cation—π manner. The stabilization energy of such complexes would be large and comparable to the one for cation—π complex with benzene. Further, polarized water molecules belonging to the hydration shell of the cation are capable to form a strong hydrogen bond interaction with the nitrogen lone electron pair of the amino groups of bases and enforce a pronounced sp³ pyramidalization of the nucleobase amino groups. However, in contrast to the benzene—cation complexes, the cation—π configurations are highly unstable for a nucleobase since the conventional in plane binding of hydrated cations to the acceptor sites on the nucleobase is strongly preferred. Thus, a cation—π interaction with a nucle-obase can occur only if the position of the cation is locked above the nucleobase plane by another strong interaction. This indeed can occur in biopolymers and may have an effect on the local DNA architecture. Nevertheless, nucleobases have no intrinsic propensity to form cation—π interactions.     

A comprehensive analysis of P···π pnicogen bonds: substitution effects and comparison with Br···π halogen bonds

Journal of Molecular Modeling - Ab initio calculations were carried out in a systematic investigation of P···π pnicogen-bonded complexes XH2P···C2H2/C2H4 and...     

Nature of cation-π interactions and their role in structural stability of immunoglobulin proteins

Cation-π interactions are known to be important contributors to protein stability and ligand-protein interactions. In this study, we have analyzed the influence of cation-π interactions in single chain immunoglobulin proteins. We observed 87 cation-π interactions in a data set of 33 proteins. These interactions are mainly formed by long-range contacts, and there is preference of Arg over Lys in these interactions. Arg-Tyr interactions are predominant among the various pairs analyzed. Despite the scarcity of interactions involving Trp, the average energy for Trp-cation interactions is quite high. This information suggests that the cation-π interactions involving Trp might be of high relevance to the proteins. Secondary structure analysis reveals that cation-π interactions are formed preferably between residues in which at least one is in β-strand. Proteins having β-strand regions have the highest number of cation-π interaction-forming residues.     

A sterically congested aryltrimethylstannane - Synthesis, reactivity, transmetalation and CH-π interaction

The synthesis of a novel sterically congested tetraorganotin compound, (4-tert-butyl-2,6-dimesitylphenyl)trimethylstannane (1), is reported and its reactivity with special focus on transmetalation studied. The reaction of compound 1 with reagents such as HgCl₂, BiCl₃ and HOTf gave (4-tert-butyl-2,6-dimesitylphenyl)dimethyltin chloride (2) and (4-tert-butyl-2,6-dimesitylphenyl)dimethyltin triflate (3), respectively, as a result of selective tin-methyl bond cleavage. Less bulky aryltrimethyltin derivatives react with BiCl₃ to give both tin-methyl and tin-aryl bond cleavage. Hydrolysis of compound 3 proceeds slowly to give bis-(4-tert-butyl-2,6-dimesitylphenyl)dimethyl stannoxane (5) via the intermediate (4-tert-butyl-2,6-dimesitylphenyl)dimethyltin hydroxide (4). All terphenyldimethyltin derivatives that were characterized by single crystal X-ray diffraction analysis show C-H?π interactions. Based on these results, the optimum C-H?π distance (C?centroid_aryl distance) is suggested to be in the range 3.4 and 3.5 Å.     

Theoretical investigations of the H···π and X (X = F,Cl, Br,I)···π complexes between hypohalous acids and benzene

The H···π and X (X = F, Cl, Br, I)···π interactions between hypohalous acids and benzene are investigated at the MP2/6-311++G(2d,2p) level. Four hydrogen-bonded and three halogen-bonded complexes were obtained. Ab initio calculations indicate that the X···π interaction between HOX and C₆H₆ is mainly electrostatically driven, and there is nearly an equal contribution from both electrostatic and dispersive energies in the case of XOH–C₆H₆ complexes. Natural bond orbital (NBO) analysis reveals that there exists charge transfer from benzene to hypohalous acids. Atom in molecules (AIM) analysis locates bond critical points (BCP) linking the hydrogen or halogen atom and carbon atom in benzene.     

Glutathione S-transferase-π is secreted as a monomer into human plasma by platelets and tumor cells

By employing an ELISA for detection of glutathione S-transferase-π (GST-π) established in our laboratory, gel filtration profiles of GST-π in the plasma of normal subjects and patients with malignant tumors were investigated. The results showed that the plasma GST-π for both of these groups was approximately half the molecular size of placental GST-π used as a standard control. Similar analyses were performed on GST-π of platelets and cultured cancer cells, which are considered to be the main sources of the GST-π in the plasma of normal subjects and cancer patients, respectively. The results indicated that the GST-π in both the centrifuged supernatants of aggregated platelets and in the culture medium of cancer cells was about half of the molecular size of intact GST-π. Morover, the GST-π in the culture medium was shown to have an N-terminus and a C-terminus, by analysis with specific ELISA. Western blot analysis of the GST-π in the culture medium detected a single band migrating at 23 kDa, confirming that the extracellular GST-π was the monomer, not a cleaved form of intact GST-π. The release of GST-π from cancer cells was suppressed at 4°C, or by sodium azide, but not suppressed by colchicine or cytochalasin B. These findings suggest that the GST-π may be released by an energy-dependent, active process, and not by a secretion mechanism.     

The inhibition characteristics of human placental glutathione S-transferase-π by tricyclic antidepressants: amitriptyline and clomipramine

Tricyclic antidepressants (TCAs) are the non-selective amine re-uptake inhibitors, well absorbed from small intestine, cross the blood-brain barrier, distributed in the brain, and are bound to glutathione S-transferase-π (GST-π). TCAs can pass through placenta, accumulate in utero baby, and cause congenital malformations. Thus, the study of the interaction of GST-π with antidepressants is crucial. In this study, the interaction of GST-π with amitriptyline and clomipramine was investigated. The K (m) values for glutathione (GSH) and 1-chloro-2,4-dinitrobenzene (CDNB) were found to be 0.16 ± 0.04 and 3.60 ± 1.67 mM, respectively. The V (m) values were varying according to the fixed substrate; [CDNB] fixed, 53 ± 3 and [GSH] fixed 182 ± 63 U/mg protein. At variable [GSH] and variable [CDNB], the k (cat) values of 7.0 × 10(6) and 1.42 × 10(7) s(-1) and the k (cat)/K (m) values of 4.38 × 10(10) and 3.94 × 10(9 )M(-1 )s(-1) were obtained, respectively. At fixed [CDNB] and variable [GSH], amitriptyline (K (s) = 0.16 ± 0.03 mM; α = 2.08; and K (i) = 1.75 ± 0.37 mM) and clomipramine (K (s) = 0.24 ± 0.05 mM; α = 1.57; and K (i) = 3.90 ± 2.26 mM) showed linear mixed-type inhibition whereas when the varied substrate is CDNB, amitriptyline (K (i) = 4.90 ± 0.68 mM) and clomipramine (K (i) = 3.37 ± 0.39 mM) inhibition were noncompetitive. The inhibition of GST-π by TCAs means the destruction of its protective role against toxic electrophiles. The effect of antidepressants on fetus will be much severe, thus, the antidepressant therapy of pregnant women should be done with caution.     

CH/π interactions of π-system of acetylacetonato chelate ring: Comparison of CH/π interactions of Ni(II)-acetylacetonato chelate and benzene rings

The calculations have been done for CH/π interaction with π-system of Ni(II)-acetylacetonato chelate ring. The results show that there is an attractive electrostatic interaction, while dispersion component is a major source of attractive interacting energies. The interaction was compared with CH/π interaction between two benzene rings. The comparison shows that two interactions are quite similar, enabling to estimate the energy of CH/π interaction with π-system of Ni(II)-acetylacetonato chelate ring to be about 10.5 kJ/mol. The results indicate that CH/π interactions of chelate ring in various molecular systems can be as important as CH/π interactions of phenyl ring.     

Computational study on C−H…π interactions of acetylene with benzene, 1,3,5-trifluorobenzene and coronene

Meta-hybrid density functional theory calculations using M06-2X/6-31+G(d,p) and M06-2X/6-311+G(d,p) levels of theory have been performed to understand the strength of C?H^…π interactions of two possible types for benzene-acetylene, 1,3,5-trifluorobenzene-acetylene and coronene-acetylene complexes. Our study reveals that the C?H^...π interaction complex where acetylene located above to the center of benzene ring (classical T-shaped) is the lowest energy structure. This structure is twice more stable than the configuration characterized by H atom of benzene interacting with the π-cloud of acetylene. The binding energy of 2.91 kcal/mol calculated at the M06-2X/6-311+G(d,p) level for the lowest energy configuration (1A) is in very good agreement with the experimental binding energy of 2.7?±?0.2 kcal/mol for benzene-acetylene complex. Interestingly, the C?H^...π interaction of acetylene above to the center of the aromatic ring is not the lowest energy configuration for 1,3,5-trifluorobenzene-acetylene and coronene-acetylene complexes. The lowest energy configuration (2A) for the former complex possesses both C?H^...π interaction and C?H^...F hydrogen bond, while the lowest energy structure for the coronene-acetylene complex involves both π-π and C?H^...π interactions. C?H stretching vibrational frequencies and the frequency shifts are reported and analyzed for all of the configurations. We observed red-shift of the vibrational frequency for the stretching mode of the C-H bond that interacts with the π-cloud. Acetylene in the lowest-energy structures of the complexes exhibits significant red-shift of the C?H stretching frequency and change in intensity of the corresponding vibrational frequency, compared to bare acetylene. We have examined the molecular electrostatic potential on the surfaces of benzene, 1,3,5-trifluorobenzene, coronene and acetylene to explain the binding strengths of various complexes studied here.     

A survey of aspartate-phenylalanine and glutamate-phenylalanine interactions in the protein data bank: searching for anion-π pairs

Protein structures are stabilized using noncovalent interactions. In addition to the traditional noncovalent interactions, newer types of interactions are thought to be present in proteins. One such interaction, an anion-π pair, in which the positively charged edge of an aromatic ring interacts with an anion, forming a favorable anion-quadrupole interaction, has been previously proposed [Jackson, M. R., et al. (2007) J. Phys. Chem. B111, 8242-8249]. To study the role of anion-π interactions in stabilizing protein structure, we analyzed pairwise interactions between phenylalanine (Phe) and the anionic amino acids, aspartate (Asp) and glutamate (Glu). Particular emphasis was focused on identification of Phe-Asp or -Glu pairs separated by less than 7 ? in the high-resolution, nonredundant Protein Data Bank. Simplifying Phe to benzene and Asp or Glu to formate molecules facilitated in silico analysis of the pairs. Kitaura-Morokuma energy calculations were performed on roughly 19000 benzene-formate pairs and the resulting energies analyzed as a function of distance and angle. Edgewise interactions typically produced strongly stabilizing interaction energies (-2 to -7.3 kcal/mol), while interactions involving the ring face resulted in weakly stabilizing to repulsive interaction energies. The strongest, most stabilizing interactions were identified as preferentially occurring in buried residues. Anion-π pairs are found throughout protein structures, in helices as well as β strands. Numerous pairs also had nearby cation-π interactions as well as potential π-π stacking. While more than 1000 structures did not contain an anion-π pair, the 3134 remaining structures contained approximately 2.6 anion-π pairs per protein, suggesting it is a reasonably common motif that could contribute to the overall structural stability of a protein.     

The origin of the generalized anomeric effect: possibility of CH/n and CH/π hydrogen bonds

Ab initio MO calculations were carried out at the MP4/6-311++G(3df,3pd)//MP2/6-311++G(3df,3pd) level to investigate the conformational Gibbs energy of a series of methyl ethers CH₃O-CH₂-X (X = OH, OCH₃, F, Cl, Br, CN, CCH, C₆H₅, CHO). It was found that the Gibbs energy of the gauche conformers is lower in every case than that of the corresponding anti conformers. In the more stable gauche conformers, the interatomic distance between X and the hydrogen atom was shorter than the sum of the van der Waals radii. The natural bonding orbital (NBO) charges of group X were more negative in the gauche conformers than in the anti conformers. We suggest that the CH/n and CH/π hydrogen bonds play an important role in stabilizing the gauche conformation of these compounds.     

Solution structures and dynamics of [HOs3(CO)10(σ,π vinyl)] complexes

No interconversion has been found to occur on the NMR time scale between the structural arrangements found in the solid state. The σ, π motion of the vinyl group does not cause a cis-trans interconversion of the terminal hydrogens in [HOs₃(CO)₁₀(CHCH₂)] which simply takes place by alternating the π-electron cloud to opposite osmium centres.The ¹H chemical shift of the =C

moieties is a useful probe to assess the coordination mode of the vinyl ligand.In [HOs₃(CO)₁₀(CPhC(H)Ph)], a trigonal twist process has been shown to occur at the Os(CO)₄ unit. For the same unit ²J_c−c trans have been obtained for all the reported derivatives and their magnitude is almost unchanged along the series. Further J_cc information has been obtained from a sample of [HOs₃(CO)₁₀(CHCH₂)] C-13 labelled in the vinyl ligand.     

π-π stacking tackled with density functional theory

Through comparison with ab initio reference data, we have evaluated the performance of various density functionals for describing pi-pi interactions as a function of the geometry between two stacked benzenes or benzene analogs, between two stacked DNA bases, and between two stacked Watson-Crick pairs. Our main purpose is to find a robust and computationally efficient density functional to be used specifically and only for describing pi-pi stacking interactions in DNA and other biological molecules in the framework of our recently developed QM/QM approach "QUILD". In line with previous studies, most standard density functionals recover, at best, only part of the favorable stacking interactions. An exception is the new KT1 functional, which correctly yields bound pi-stacked structures. Surprisingly, a similarly good performance is achieved with the computationally very robust and efficient local density approximation (LDA). Furthermore, we show that classical electrostatic interactions determine the shape and depth of the pi-pi stacking potential energy surface.     

Supramolecular assembly driven by hydrogen-bonding and π-π stacking interactions based on copper(II)-terpyridyl complexes

Six 2D and 3D supramolecular complexes [Cu(L1)(O₂CCH₃)₂] · H₂O (1), [Cu₂(L2)₂(μ₂-O₂CCH₃)₂](BF₄)₂ (2), [Cu₂(L1)₂(BDC)(NO₃)₂] · 0.5H₂O (3) [Cu₂(L2)₂(BDC)(NO₃)₂] (4), [Cu₂(L3)₂(BDC)(NO₃)₂] · 0.5H₂O (5) and [Cu₂(L2)₂(BDC)(H₂O)₂](BDC) · 8H₂O (6) (L1 = 4′-(4-pyridyl)-2,2′:6′,2″-terpyridine, L2 = 4′-(2-pyridyl)-2,2′:6′,2″-terpyridine, L3 = 4′-phenyl-2,2′:6′,2″-terpyridine, BDC = 1,4-benzenedicarboxylate), have been prepared and structurally characterized by X-ray diffraction crystallography. In complexes 1, 3, and 4, 1D channels are formed through C-H?O and C-H?N hydrogen-bonding interactions, and further linked into 3D structure via C-H?O and O-H?O interactions. Complex 2 is a 2D layer constructed from intermolecular C-H?F and π-π stacking interactions. In the structure of 6, the BDC²⁻ ions and solvent water molecules form a novel 2D layer containing left- and right-handed helical chains via hydrogen-bonds, and an unusual discrete water octamer is formed within the layer. In 2, 4, 6 and [Ag₂(L2)₂](PF₆)₂ (7) the bonding types of pendent pyridines of L2 depending on the twist about central pyridines are involved in intramolecular (2 and 4), intermolecular (6) or coordination bonds (7) in-twist-order of 5.8°, 3.7°, 28.2° and 38.0°, respectively. Differently, the pendent pyridines of L1 in 1 and 3 form intermolecular hydrogen bonds despite of distinct corresponding twist angles of 25.1° (1) and 42.6°(3). Meanwhile, π-π stacking interactions are present in 1-6 and responsible for the stabilization of these complexes.     

Rational derivation of CETP self-binding helical peptides by π-π stacking and halogen bonding: Therapeutic implication for atherosclerosis

The human cholesteryl ester transfer protein (CETP) transfers cholesteryl ester from high-density lipoprotein (HDL) to other lipoproteins and has been established as an attractive target for reducing the risk of atherosclerosis. Here, an amphipathic α-helix peptide, namely SBH-peptide (⁴⁶⁵EHLLVDFLQSLS⁴⁷⁶), was derived from the C-terminal tail of CETP. The peptide exhibits self-binding capability towards the CETP. Crystal structure analysis, molecular dynamics (MD) simulations and ab initio electron correlation characterizations of CETP–SBH-peptide complex system revealed that the Phe471 residue plays a key role in SBH-peptide binding, which can form a π-π stacking with the Phe197 residue of CETP. In addition, substitution of the hydrogen atom H4 of Phe471 with halogen atoms, in particular the bromine atom Br4, can constitute a geometrically satisfactory halogen bonding with the oxygen atom O of CETP Ile193 residue. Fluorescence polarization assays substantiated that (i) mutation of the aromatic Phe471 to small Ala residue would impair the SBH-peptide affinity with K_d change from 10.5 to 26.4 μM, indicating that the π-π stacking should exist in Phe471⋯Phe197 adduct, and (ii) substitution with Br4 can considerably improve SBH-peptide affinity by ∼3-fold, but the SBH-peptide binding does not change essentially upon substitution with Br3 (a negative control that is theoretically unable to form the halogen bonding), indicating that the rationally designed halogen bonding should form between the Phe471(Br4) residue of SBH-peptide and the Ile193 residue of CETP protein.