Mining anion-aromatic interactions in the Protein Data Bank

Mutual positioning and non-covalent interactions in anion–aromatic motifs are crucial for functional performance of biological systems. In this context, regular, comprehensive Protein Data Bank (PDB) screening that involves various scientific points of view and individual critical analysis is of utmost importance. Analysis of anions in spheres with radii of 5 Å around all 5- and 6-membered aromatic rings allowed us to distinguish 555 259 unique anion–aromatic motifs, including 92 660 structures out of the 171 588 structural files in the PDB. The use of a scarcely exploited (x, h) coordinate system led to (i) identification of three separate areas of motif accumulation: A – over the ring, B – over the ring-substituent bonds, and C – roughly in the plane of the aromatic ring, and (ii) unprecedented simultaneous comparative description of various anion–aromatic motifs located in these areas. Of the various residues considered, i.e. aminoacids, nucleotides, and ligands, the latter two exhibited a considerable tendency to locate in region Avia archetypal anion–π contacts. The applied model not only enabled statistical quantitative analysis of space around the ring, but also enabled discussion of local intermolecular arrangements, as well as detailed sequence and secondary structure analysis, e.g. anion–π interactions in the GNRA tetraloop in RNA and protein helical structures. As a purely practical issue of this work, the new code source for the PDB research was produced, tested and made freely available at https://github.com/chemiczny/PDB_supramolecular_search.

The comprehensive analysis of non-redundant PDB macromolecular structures investigating anion distributions around all aromatic molecules in available biosystems is presented.

Stabilizing Role of Water Solvation on Anion-π Interactions in Proteins

In this work, anion-π interactions between sulfate groups (SO₄ ^2-) and protein aromatic amino acids (AAs) (histidine protonated (HisP), histidine neutral (HisN), tyrosine (Tyr), tryptophan (Trp), and phenylalanine (Phe)) in an aqueous environment have been analyzed using quantum chemical (QC) calculations and molecular dynamics (MD) simulations. Sulfates can occur naturally in solution and can be contained in biomolecules playing relevant roles in their biological function. In particular, the presence of sulfate groups in glycosaminoglycans such as heparin and heparan sulfate has been shown to be relevant for protein and cellular communication and, consequently, for tissue regeneration. Therefore, anion-π interactions between sulfate groups and aromatic residues represent a relevant aspect to investigate. QC results show that such an anion-π mode of interaction between SO₄ ^2- and aromatic AAs is only possible in the presence of water molecules, in the absence of any other cooperative non-covalent interactions. Protonated histidine stands out in terms of its enhancement in the magnitude of interaction strength on solvation. Other AAs such as non-protonated histidine, tyrosine, and phenylalanine can stabilize anion-π interactions on solvation, albeit with weak interaction energy. Tryptophan does not exhibit any anion-π mode of interaction with SO₄ ^2-. The order of magnitude of the interaction of aromatic AAs with SO₄ ^2- on microsolvation is HisP > HisN > Tyr > Trp > Phe. Atoms in molecules (AIM) analysis illustrates the significance of water molecules in stabilizing the divalent SO₄ ^2- anion over the π surface of the aromatic AAs. MD simulation analysis shows that the order of magnitude of the interaction of SO₄ ^2- with aromatic AAs in macroscopic solvation is HisP > HisN, Tyr, Trp > Phe, which is very much in line with the QC results. Spatial distribution function analysis illustrates that protonated histidine alone is capable of establishing the anion-π interaction with SO₄ ^2- in the solution phase. This study sheds light on the understanding of anion-π interactions between SO₄ ^2- and aromatic AAs such as His and Tyr observed in protein crystal structures and the significance of water molecules in stabilizing such interactions, which is not feasible otherwise.

Exploring the structure-property schemes in anion-π systems of d-block metalates

Anion-π based compounds, materials, and processes have gained significant interest due to the diversity of their aesthetic non-covalent synthons, and thanks to their significance in biological systems, catalytic processes, anion binding and sensing, or the supramolecular organization of hierarchical architectures. While systems based on typical inorganic anions or organic residues have been widely reviewed in recent years, those involving anionic d metal comlexes as the main components have been treated with a rather secondary interest. However, actively exploring the new systems of the latter type we have recognized systematic advances in the field. As a result, in the current review we describe the landscape that has recently emerged. Focusing on the established groups of π-acidic species, i.e. polycarbonitirles, polyazines, polyazine N-oxides, diimide derivatives, fluoroarenes, and nitroarenes, we explore and discuss anion-π crystal engineering together with the structure-property schemes important from the standpoint of charge transfer (CT) and electron transfer (ET), magnetism, luminescence, reactivity and catalysis, and the construction of core-shell crystalline composites.

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.

A Comprehensive Analysis of Anion-Quadrupole Interactions in Protein Structures

The edgewise interactions of anions with phenylalanine (Phe) aromatic rings in proteins, known as anion-quadrupole interactions, have been well studied. However, the anion-quadrupole interactions of the tyrosine (Tyr) and tryptophan (Trp) rings have been less well studied, probably because these have been considered weaker than interactions of anions hydrogen bonded to Trp/Tyr side chains. Distinguishing such hydrogen bonding interactions, we comprehensively surveyed the edgewise interactions of certain anions (aspartate, glutamate, and phosphate) with Trp, Tyr, and Phe rings in high-resolution, nonredundant protein single chains and interfaces (protein-protein, DNA/RNA-protein, and membrane-protein). Trp/Tyr anion-quadrupole interactions are common, with Trp showing the highest propensity and average interaction energy for this type of interaction. The energy of an anion-quadrupole interaction (-15.0 to 0.0 kcal/mol, based on quantum mechanical calculations) depends not only on the interaction geometry but also on the ring atom. The phosphate anions at DNA/RNA-protein interfaces interact with aromatic residues with energies comparable to that of aspartate/glutamate anion-quadrupole interactions. At DNA-protein interfaces, the frequency of aromatic ring participation in anion-quadrupole interactions is comparable to that of positive charge participation in salt bridges, suggesting an underappreciated role for anion-quadrupole interactions at DNA-protein (or membrane-protein) interfaces. Although less frequent than salt bridges in single-chain proteins, we observed highly conserved anion-quadrupole interactions in the structures of remote homologues, and evolutionary covariance-based residue contact score predictions suggest that conserved anion-quadrupole interacting pairs, like salt bridges, contribute to polypeptide folding, stability, and recognition.

Fingerprinting the Nature of Anions in Pyrylium Complexes: Dual Binding Mode for Anion-π Interactions

The interplay between noncovalent interactions that involve oxygenated heteroaromatic rings have been studied for the first time in this work. In particular, we report an advance in knowledge-based anion-π interactions together with (C-H)⁺ ⋅⋅⋅anion contacts. To understand how the anion modulates these interactions, the synthesis of pyrylium salts with a variety of anions was performed by using an anionic metathesis methodology. The synthesized pyrylium complexes were classified in series, for example, anions derived from halogens, from oxoacids, from p-block elements, and from transition metals. Crystallographic data, DFT calculations, and NMR spectroscopy methods provided access to an overall insight into the noncovalent behavior of the anion in this kind of system. Based on the DFT calculations and ¹ H NMR spectroscopy, pyrylium protons can be used as chemical tags to detect noncovalent interactions in this type of compound.

The structures and properties of anionic tryptophan complexes

IRMPD spectroscopy and electronic structure calculations are employed to identify π–π interactions in ionic tryptophan clusters.

Theoretical study of synergistic effects between anion–π and metal–Lp interactions

Interesting cooperativity effects are observed when the anion–π and coinage-metal–Lp interactions coexist in the same multicomponent.