Cation-π Interactions between Quaternary Ammonium Ions and Amino Acid Aromatic Groups in Aqueous Solution

Surface hydrolysis-anchored eugenol self-polishing marine antifouling coating

Traditional self-polishing antifouling coatings kill surface organisms by releasing toxic substances, which are damaging to the ecosystem. As a natural antimicrobial substance, eugenol is environmentally friendly and has been proven by different research teams to be effective in enhancing the anti-fouling effect of coatings in the real sea. While in these previous research works, the eugenol was released directly into the seawater thus cannot further serve as surface antifouling effect, leading to a limited antifouling effect of the coating. In this work, the quaternary ammonium component was introduced into the butyl ester-based resin - poly (eugenol methacrylate - acryloyloxyethyltrimethyl ammonium chloride - hexafluorobutyl methacrylate - methyl methacrylate - butyl methacrylate - ethylene glycol methyl ether acrylate) (EMQFP) coating for the first time by simple one-step free radical polymerization method. On the one hand, the eugenol produced by hydrolysis is anchored to the quaternary ammonium on the coating surface for a period of time due to the cationic-π interaction, instead of being released into seawater immediately after hydrolysis, thus increasing the utilization rate of eugenol; on the other hand, the negatively charged carboxylate groups generated after hydrolysis in the coating are mutually attracted to quaternary ammonium through electrostatic effect, so the resin chain segment conformation on the coating surface adjusted to produce zwitterionic-like structure, and the hydration of zwitterionic inhibits primary fouling adhesion.

Changes in the Secondary Structure and Assembly of Proteins on Fluoride Ceramic (CeF3) Nanoparticle Surfaces

Fluoride nanoparticles (NPs) are materials utilized in the biomedical field for applications including imaging of the brain. Their interactions with biological systems and molecules are being investigated, but the mechanism underlying these interactions remains unclear. We focused on possible changes in the secondary structure and aggregation state of proteins on the surface of NPs and investigated the principle underlying the changes using the amyloid β peptide (Aβ_16-20) based on infrared spectrometry. CeF₃ NPs (diameter 80 nm) were synthesized via thermal decomposition. Infrared spectrometry showed that the presence of CeF₃ NPs promotes the formation of the β-sheet structure of Aβ_16-20. This phenomenon was attributed to the hydrophobic interaction between NPs and Aβ peptides in aqueous environments, which causes the Aβ peptides to approach each other on the NP surface and form ordered hydrogen bonds. Because of the coexisting salts on the secondary structure and assembly of Aβ peptides, the formation of the β-sheet structure of Aβ peptides on the NP surface was suppressed in the presence of NH₄⁺ and NO₃^- ions, suggesting the possibility that Aβ peptides were adsorbed and bound to the NP surface. The formation of the β-sheet structure of Aβ peptides was promoted in the presence of NH₄⁺, whereas it was suppressed in the presence of NO₃^- because of the electrostatic interaction between the lysine residue of the Aβ peptide and the ions. Our findings will contribute to comparative studies on the effect of different NPs with different physicochemical properties on the molecular state of proteins.

Complexes of Alkaline and Ammonium Cations with Dopamine and Eumelanin Precursors: Dissecting the Role of Noncovalent Cation-π and Cation-Lone Pair (σ-Type) Interactions

Cation-π interactions and their possible competition with other noncovalent interactions (NCI) might play a key role in both dopamine- and eumelanin-based bioinspired materials. In this contribution, to unravel the delicate interplay between cation-π interactions and other possible competing forces, the configurational space of noncovalent complexes formed by dopamine or eumelanin precursors (o-benzoquinone, DHI and a semiquinone dimer) and three different cations (Na⁺, K⁺, and NH₄⁺) is sampled by means of accurate ab initio calculations. To this end, we resort to the mp2^mod method, recently validated by us for benzene-, phenol-, and catechol-cation complexes, whose computational convenience allows for an extensive exploration of the cation-molecule interaction energy surface, by sampling a total of more than 10⁴ arrangements. The mp2^mod interaction energy landscapes reveal that, besides the expected cation-π driven arrangements, for all considered molecule-cation pairs the most stable complexes are found when the cation lies within the plane containing the six-membered ring, thus maximizing the σ-type interaction with the oxygen's lone pairs. Due to the loss of aromaticity, the σ-type/cation-π strength ratio is remarkably large in o-benzoquinone, where cation-π complexes seem unlikely to be formed. The above features are shared among all considered cations but are significantly larger when considering the smaller Na⁺. Besides delivering a deeper insight onto the NCI network established by the considered precursors in the presence of ions, the present results can serve as a reference database to validate or refine lower level methods, as, for instance, the force fields employed in classical simulations.

Comparative Analysis of Sulfonium-π, Ammonium-π, and Sulfur-π Interactions and Relevance to SAM-Dependent Methyltransferases

We report the measurement and analysis of sulfonium-π, thioether-π, and ammonium-π interactions in a β-hairpin peptide model system, coupled with computational investigation and PDB analysis. These studies indicated that the sulfonium-π interaction is the strongest and that polarizability contributes to the stronger interaction with sulfonium relative to ammonium. Computational studies demonstrate that differences in solvation of the trimethylsulfonium versus the trimethylammonium group also contribute to the stronger sulfonium-π interaction. In comparing sulfonium-π versus sulfur-π interactions in proteins, analysis of SAM- and SAH-bound enzymes in the PDB suggests that aromatic residues are enriched in close proximity to the sulfur of both SAM and SAH, but the populations of aromatic interactions of the two cofactors are not significantly different, with the exception of the Me-π interactions in SAM, which are the most prevalent interaction in SAM but are not possible for SAH. This suggests that the weaker interaction energies due to loss of the cation-π interaction in going from SAM to SAH may contribute to turnover of the cofactor.

Unfolding of Tryptophanoctyl Ester and Elastic Deformation of Host Micelles via RR'3 N+ ⋅⋅⋅π Interaction: Conceivable Relevance to Wrapping Process of Receptor Mediated Endocytosis

The interfacial properties of the mixed amphiphiles are modified by a stronger cation-π interaction between the quaternary ammonium head group of CTAB and the π-face of TROE, compared to the tyrosine analogue (TYOE). This eventually triggers a morphology transition through elastic deformation of the spherical micelles of CTAB to cylindrical/wormlike micelles. The unfolding of TROE and the molecular interactions in the nanoenvironment have been recognized by NMR spectroscopy and the physical characteristics of the entangled wormlike micelles are investigated by high resolution transmission electron microscopy (HRTEM), whereas the complex fluidic feature is examined by dynamic rheological measurements. Morphology tuning of the soft nanoaggregates of zwitterionic dodecylphosphocholine by the tryptophan analogue via choline-π interaction has unique biological consequences and we consider the significance of such interactions in facilitating endocytosis of a virion/nano particle(NP) in terms of a quantitative model. The implication in future research on drug development strategies is discussed.

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.

Spectroscopic and Theoretical Studies of Hg(II) Complexation with Some Dicysteinyl Tetrapeptides

Tetrapeptides containing a Cys-Gly-Cys motif and a propensity to adopt a reverse-turn structure were synthesized to evaluate how O-, N-, H-, and aromatic π donor groups might contribute to mercury(II) complex formation. Tetrapeptides Xaa-Cys-Gly-Cys, where Xaa is glycine, glutamate, histidine, or tryptophan, were prepared and reacted with mercury(II) chloride. Their complexation with mercury(II) was studied by spectroscopic methods and computational modeling. UV-vis studies confirmed that mercury(II) binds to the cysteinyl thiolates as indicated by characteristic ligand-to-metal-charge-transfer transitions for bisthiolated S-Hg-S complexes, which correspond to 1 : 1 mercury-peptide complex formation. ESI-MS data also showed dominant 1 : 1 mercury-peptide adducts that are consistent with double deprotonations from the cysteinyl thiols to form thiolates. These complexes exhibited a strong positive circular dichroism band at 210 nm and a negative band at 193 nm, indicating that these peptides adopted a β-turn structure after binding mercury(II). Theoretical studies confirmed that optimized 1 : 1 mercury-peptide complexes adopt β-turns stabilized by intramolecular hydrogen bonds. These optimized structures also illustrate how specific N-terminal side-chain donor groups can assume intramolecular interactions and contribute to complex stability. Fluorescence quenching results provided supporting data that the indole donor group could interact with the coordinated mercury. The results from this study indicate that N-terminal side-chain residues containing carboxylate, imidazole, or indole groups can participate in stabilizing dithiolated mercury(II) complexes. These structural insights on peripheral mercury-peptide interactions provide additional understanding of the chemistry of mercury(II) with side-chain donor groups in peptides.

Accuracy of Alternate Nonpolarizable Force Fields for the Determination of Protein-Ligand Binding Affinities Dominated by Cation-π Interactions

Modifying pair-specific Lennard-Jones parameters through the nonbonded FIX (NBFIX) feature of the CHARMM36 force field has proven cost-effective for improving the description of cation-π interactions in biological objects by means of pairwise additive potential energy functions. Here, two sets of newly optimized CHARMM36 force-field parameters including NBFIX corrections, coined CHARMM36m-NBF and CHARMM36-WYF, and the original force fields, namely CHARMM36m and Amber ff14SB, are used to determine the standard binding free energies of seven protein-ligand complexes containing cation-π interactions. Compared with precise experimental measurements, our results indicate that the uncorrected, original force fields significantly underestimate the binding free energies, with a mean error of 5.3 kcal/mol, while the mean errors of CHARMM36m-NBF and CHARMM36-WYF amount to 0.8 and 2.1 kcal/mol, respectively. The present study cogently demonstrates that the use of modified parameters jointly with NBFIX corrections dramatically increases the accuracy of the standard binding free energy of protein-ligand complexes dominated by cation-π interactions, most notably with CHARMM36m-NBF.

3D Interaction Homology: Hydropathic Analyses of the "π-Cation" and "π-π" Interaction Motifs in Phenylalanine, Tyrosine, and Tryptophan Residues

Three-dimensional (3D) maps of the hydropathic environments of protein amino acid residues are information-rich descriptors of preferred conformations, interaction types and energetics, and solvent accessibility. The interactions made by each residue are the primary factor for rotamer selection and the secondary, tertiary, and even quaternary protein structure. Our evolving basis set of environmental data for each residue type can be used to understand the protein structure. This work focuses on the aromatic residues phenylalanine, tyrosine, and tryptophan and their structural roles. We calculated and analyzed side chain-to-environment 3D maps for over 70,000 residues of these three types that reveal, with respect to hydrophobic and polar interactions, the environment around each. After binning with backbone ϕ/ψ and side chain χ₁, we clustered each bin by 3D similarities between map-map pairs. For each of the three residue types, four bins were examined in detail: one in the β-pleat, two in the right-hand α-helix, and one in the left-hand α-helix regions of the Ramachandran plot. For high degrees of side chain burial, encapsulation of the side chain by hydrophobic interactions is ubiquitous. The more solvent-exposed side chains are more likely to be involved in polar interactions with their environments. Evidence for π-π interactions was observed in about half of the residues surveyed [phenylalanine (PHE): 53.3%, tyrosine (TYR): 34.1%, and tryptophan (TRP): 55.7%], but on an energy basis, this contributed to only ∼4% of the total. Evidence for π-cation interactions was observed in 14.1% of PHE, 8.3% of TYR, and 26.8% of TRP residues, but on an energy basis, this contributed to only ∼1%. This recognition of even these subtle interactions in the 3D hydropathic environment maps is key support for our interaction homology paradigm of protein structure elucidation and possibly prediction.

Spectroscopic Signatures and the Cation-π Interaction in Conformational Preferences of the Neurotransmitter Dopamine in Aqueous Solution

The precise determination of the neurotransmitter dopamine's conformational preferences in aqueous solution is crucial for understanding its neurobiological function. The first principle Møller-Plesset perturbation theory (MP2) and dispersion corrected density functional theory (DFT-D3) methods, employing the basis set aug-cc-pVDZ(/pVTZ), are used to reinvestigate the nine lowest-energy (isolated) structures of protonated dopamine (DAH⁺) in both gas and aqueous phases. DAH⁺ trans isomer t₁ is found higher in energy than lowest-energy gauche isomer g⁺¹ (g + 1) by 6.4 and 5.7 kJ mol^-1, at the MP2 and B3LYP-D3 levels of theory, respectively, in the aqueous environment within the polarizable continuum model (PCM). We found that the solvated cation, NH₃⁺, retains its attractive character, which supports the previous report that agonist DAH⁺ can be involved in cation (NH₃⁺)-π interaction in the active states of the D2 dopamine receptor. The dispersion corrected DFT evaluation of anharmonicity allows us to confirm the most experimental frequencies and suggest some new interpretations. The IR and Raman spectra's influential band for both gauche and the trans conformers observed at 1287/1288 cm^-1 were enhanced in aqueous solution. The experimental Raman spectrum for dopamine was compared with the conformer-specific computed Raman spectrum of protonated dopamine (DAH⁺). The intense Raman band at 1451 cm^-1 indicates the necessity of DAH⁺ calculated values in interpreting the Raman spectra. The most intense Raman band at 750 cm^-1 arises due to the trans DAH⁺, t₁, revealed by MP2/aug-cc-pVDZ Raman spectra, indicating trans DAH⁺ dominance in the bulk DAH⁺ of extracellular fluid.

Explicit Representation of Cation-π Interactions in Force Fields with 1/r4 Nonbonded Terms

The binding energies for cation-π complexation are underestimated by traditional fixed-charge force fields owing to their lack of explicit treatment of ion-induced dipole interactions. To address this deficiency, an explicit treatment of cation-π interactions has been introduced into the OPLS-AA force field. Following prior work with atomic cations, it is found that cation-π interactions can be handled efficiently by augmenting the usual 12-6 Lennard-Jones potentials with 1/r⁴ terms. Results are provided for prototypical complexes as well as protein-ligand systems of relevance for drug design. Alkali cation, ammonium, guanidinium, and tetramethylammonium were chosen for the representative cations, while benzene and six heteroaromatic molecules were used as the π systems. The required nonbonded parameters were fit to reproduce structure and interaction energies for gas-phase complexes from density functional theory (DFT) calculations at the ωB97X-D/6-311++G(d,p) level. The impact of the solvent was then examined by computing potentials of mean force (pmfs) in both aqueous and tetrahydrofuran (THF) solutions using the free-energy perturbation (FEP) theory. Further testing was carried out for two cases of strong and one case of weak cation-π interactions between druglike molecules and their protein hosts, namely, the JH2 domain of JAK2 kinase and macrophage migration inhibitory factor. FEP results reveal greater binding by 1.5-4.4 kcal/mol from the addition of the explicit cation-π contributions. Thus, in the absence of such treatment of cation-π interactions, errors for computed binding or inhibition constants of 10¹-10³ are expected.

Accurate Description of Cation-π Interactions in Proteins with a Nonpolarizable Force Field at No Additional Cost

Cation-π interactions play a significant role in a host of processes eminently relevant to biology. However, polarization effects arising from the interaction of cations with aromatic moieties have long been recognized to be inadequately described by pairwise additive force fields. In the present work, we address this longstanding shortcoming through the nonbonded FIX (NBFIX) feature of the CHARMM36 force field, modifying pair-specific Lennard-Jones (LJ) parameters, while circumventing the limitations of the Lorentz-Berthelot combination rules. The potentials of mean force (PMFs) characterizing prototypical cation-π interactions in aqueous solutions are first determined using a hybrid quantum mechanical/molecular mechanics (QM/MM) strategy in conjunction with an importance-sampling algorithm. The LJ parameters describing the cation-π pairs are then optimized to match the QM/MM PMFs. The standard binding free energies of nine cation-π complexes, i.e., toluene, para-cresol, and 3-methyl-indole interacting with either ammonium, guanidinium, or tetramethylammonium, determined with this new set of parameters agree well with the experimental measurements. Additional simulations were carried out on three different classes of biological objects featuring cation-π interactions, including five individual proteins, three protein-ligand complexes, and two protein-protein complexes. Our results indicate that the description of cation-π interactions is overall improved using NBFIX corrections, compared with the standard pairwise additive force field. Moreover, an accurate binding free energy calculation for a protein-ligand complex containing cation-π interactions (2BOK) shows that using the new parameters, the experimental binding affinity can be reproduced quantitatively. Put together, the present work suggests that the NBFIX parameters optimized here can be broadly utilized in the simulation of proteins in an aqueous solution to enhance the representation of cation-π interactions, at no additional computational cost.

New Molecular-Mechanics Model for Simulations of Hydrogen Fluoride in Chemistry and Biology

Hydrogen fluoride (HF) is the most polar diatomic molecule and one of the simplest molecules capable of hydrogen-bonding. HF deviates from ideality both in the gas phase and in solution and is thus of great interest from a fundamental standpoint. Pure and aqueous HF solutions are broadly used in chemical and industrial processes, despite their high toxicity. HF is a stable species also in some biological conditions, because it does not readily dissociate in water unlike other hydrogen halides; yet, little is known about how HF interacts with biomolecules. Here, we set out to develop a molecular-mechanics model to enable computer simulations of HF in chemical and biological applications. This model is based on a comprehensive high-level ab initio quantum chemical investigation of the structure and energetics of the HF monomer and dimer; (HF)_n clusters, for n = 3-7; various clusters of HF and H₂O; and complexes of HF with analogs of all 20 amino acids and of several commonly occurring lipids, both neutral and ionized. This systematic analysis explains the unique properties of this molecule: for example, that interacting HF molecules favor nonlinear geometries despite being diatomic and that HF is a strong H-bond donor but a poor acceptor. The ab initio data also enables us to calibrate a three-site molecular-mechanics model, with which we investigate the structure and thermodynamic properties of gaseous, liquid, and supercritical HF in a wide range of temperatures and pressures; the solvation structure of HF in water and of H₂O in liquid HF; and the free diffusion of HF across a lipid bilayer, a key process underlying the high cytotoxicity of HF. Despite its inherent simplifications, the model presented significantly improves upon previous efforts to capture the properties of pure and aqueous HF fluids by molecular-mechanics methods and to our knowledge constitutes the first parameter set calibrated for biomolecular simulations.

Can glycine betaine denature proteins?

Glycine betaine (GB) is a naturally occurring osmolyte that has been widely recognized as a protein protectant. Since GB consists of a methylated ammonium moiety, it can engage in strong cation-π interactions with aromatic amino acid sidechains. We hypothesize that such specific binding interactions would allow GB to decrease the stability of proteins that are predominantly stabilized by a cluster of aromatic amino acids. To test this hypothesis, we investigate the effect of GB on the stability of two β-hairpins (or mini-proteins) that contain such a cluster. We find that for both systems the stability of the folded state first decreases and then increases with increasing GB concentration. Such non-monotonic dependence not only confirms that GB can act as a protein denaturant, but also underscores the complex interplay between GB's stabilizing and destabilizing forces toward a given protein. While stabilizing osmolytes all have the tendency to be excluded from the protein surface which is the action underlying their stabilizing effect, our results suggest that in order to quantitatively assess the effect of GB on the stability of any given protein, specific cation-π binding interactions need to be explicitly considered. Moreover, our results show, consistent with other studies, that cation methylation can strengthen the respective cation-π interactions. Taken together, these findings provide new insight into the mechanism by which amino acid-based osmolytes interact with proteins.

Improved Modeling of Cation-π and Anion-Ring Interactions Using the Drude Polarizable Empirical Force Field for Proteins

Cation-π interactions are noncovalent interactions between a π-electron system and a positively charged ion that are regarded as a strong noncovalent interaction and are ubiquitous in biological systems. Similarly, though less studied, anion-ring interactions are present in proteins along with in-plane interactions of anions with aromatic rings. As these interactions are between a polarizing ion and a polarizable π system, the accuracy of the treatment of these interactions in molecular dynamics (MD) simulations using additive force fields (FFs) may be limited. In the present work, to allow for a better description of ion-π interactions in proteins in the Drude-2013 protein polarizable FF, we systematically optimized the parameters for these interactions targeting model compound quantum mechanical (QM) interaction energies with atom pair-specific Lennard-Jones parameters along with virtual particles as selected ring centroids introduced to target the QM interaction energies and geometries. Subsequently, MD simulations were performed on a series of protein structures where ion-π pairs occur to evaluate the optimized parameters in the context of the Drude-2013 FF. The resulting FF leads to a significant improvement in reproducing the ion-π pair distances observed in experimental protein structures, as well as a smaller root-mean-square differences and fluctuations of the overall protein structures from experimental structures. Accordingly, the optimized Drude-2013 protein polarizable FF is suggested for use in MD simulations of proteins where cation-π and anion-ring interactions are critical. © 2019 Wiley Periodicals, Inc.

Cation-π Interactions and Their Contribution to Mussel Underwater Adhesion Studied Using a Surface Forces Apparatus: A Mini-Review

Mussel underwater adhesion is a model phenomenon important for the understanding of broader biological adhesion and the development of biomimetic wet adhesives. The catechol moiety of 3,4-dihydroxyphenyl-l-alanine (DOPA) is known to be actively involved in the mechanism of mussel underwater adhesion; however, other underwater adhesion mechanisms are also crucial. The surface forces apparatus (SFA) has often been used to explore the contributions of other mechanisms to mussel underwater adhesion; e.g., recent SFA-based nanomechanical studies have revealed that cation-π interactions, one of the strongest intermolecular interactions in water, are the pivotal interactions of adhesive proteins involved in underwater mussel adhesion. This mini-review surveys recent research on cation-π interactions and their contributions to strong mussel underwater adhesion, shedding light on some biological processes and facilitating the development of biomedical adhesives.

Sonochemically modified ovalbumin enhances enantioenrichment of some amino acids

As part of our efforts to develop a new method for chiral resolution of amino acids with sonochemically modified proteins, we present result that indicates how ovalbumin microspheres (OAMS) interact specifically with l-amino acids from a racemate in solution, leaving an excess of d-enantiomer in the permeate solution. Among different amino acids that interacted with the OAMS, tryptophan (Trp) was the most successfully resolved with 65% enantiomeric excess. A control experiment with native ovalbumin in solution did not show any chiral resolution of amino acids. Interestingly, when the OAMS were pretreated with racemic lysine (Lys) solution and then used for resolution of tryptophan the enantiomeric enrichment of d-tryptophan was raised to 98%. This unanticipated positive effect is discussed in terms of the structural correlation between Trp and Lys, which is less apparent in other amino acids such as phenylalanine.