Modelling protein–RNA interactions: an electron density study of the guanidinium and formate complexes with RNA bases

The RBS1 domain of Gemin5 is intrinsically unstructured and interacts with RNA through conserved Arg and aromatic residues

Gemin5 is a multifaceted RNA-binding protein that comprises distinct structural domains, including a WD40 and TPR-like for which the X-ray structure is known. In addition, the protein contains a non-canonical RNA-binding domain (RBS1) towards the C-terminus. To understand the RNA binding features of the RBS1 domain, we have characterized its structural characteristics by solution NMR linked to RNA-binding activity. Here we show that a short version of the RBS1 domain that retains the ability to interact with RNA is predominantly unfolded even in the presence of RNA. Furthermore, an exhaustive mutational analysis indicates the presence of an evolutionarily conserved motif enriched in R, S, W, and H residues, necessary to promote RNA-binding via π-π interactions. The combined results of NMR and RNA-binding on wild-type and mutant proteins highlight the importance of aromatic and arginine residues for RNA recognition by RBS1, revealing that the net charge and the π-amino acid density of this region of Gemin5 are key factors for RNA recognition.

A quantum chemical view of the interaction of RNA nucleobases and base pairs with the side chains of polar amino acids

Hydrogen bonding between amino acids and nucleobases is important for RNA-protein recognition. As a first step toward understanding the physicochemical features of these contacts, the present work employs density functional theory calculations to critically analyze the intrinsic structures and strength of all theoretically possible model hydrogen-bonded complexes involving RNA nucleobase edges and polar amino acid side chains. Our geometry optimizations uncover a number of unique complexes that involve variable hydrogen-bonding characteristics, including conventional donor-acceptor interactions, bifurcated interactions and single hydrogen-bonded contacts. Further, significant strength of these complexes in the gas phase (-27 kJ mol^-1 to -226 kJ mol^-1) and solvent phase (-19 kJ mol^-1 to -78 kJ mol^-1) points toward the ability of associated contacts to provide stability to RNA-protein complexes. More importantly, for the first time, our study uncovers the features of complexes involving protonated nucleobases, as well as those involving the weakly polar cysteine side chain, and thereby highlights their potential importance in biological processes that involve RNA-protein interactions. Additional analysis on select base pair-amino acid complexes uncovers the ability of amino acid side chain to simultaneously interact with both nucleobases of the base pair, and highlights the greater strength of such interactions compared to base-amino acid interactions. Overall, our analysis provides a basic physicochemical framework for understanding the molecular basis of nucleic acid-protein interactions. Further, our quantum chemical data can be used to design better algorithms for automated search of these contacts at the RNA-protein interface.Communicated by Ramaswamy H. Sarma.

Doubly ionic hydrogen bond interactions within the choline chloride–urea deep eutectic solvent

Computational analysis indicates flexibility and diversity in the hydrogen bonding, but limited charge delocalisation, within the choline chloride–urea eutectic.

Chiral recognition in bicyclic guanidines

A theoretical study of chiral recognition in bicyclic guanidines has been carried out by means of B3LYP/6-31+G(d,p) DFT calculations. A series of complexes between protonated 4,8-dimethyl-1,5,7-triazabicyclodecene (DTBD) and 2,5-disubtituted chiral cyclopentanones have been evaluated for chiral recognition, both in the gas phase and in benzene solution as per the polarizable continuum model (PCM) and analyzed by AIM and NBO methodologies. An inversion in the sense of chiral recognition has been observed between gas phase and solvated results for cyclopentanone complexes. Among the different correlations found (i.e. between electron density, hydrogen bond distance, second-order perturbation energy), a linear correlation has been established between the chiral recognition energy and different molecular parameters.

Effects of Hydrogen-Bonding and Stacking Interactions with Amino Acids on the Acidity of Uracil

The effects of hydrogen-bonding interactions with amino acids on the (N1) acidity of uracil are evaluated using (B3LYP) density functional theory. Many different binding arrangements of each amino acid to three uracil binding sites are considered. The effects on the uracil acidity are found to significantly depend upon the nature of the amino acid and the binding orientation, but weakly depend on the binding site. Our results reveal that in some instances small models for the amino acids can be used, while for other amino acids larger models are required to properly describe the binding to uracil. The gas-phase acidity of uracil is found to increase by up to approximately 60 kJ mol(-1) due to discrete hydrogen-bonding interactions. Although (MP2) stacking interactions with aromatic amino acids decrease the acidity of uracil, unexpected increases in the acidity are found when any of the aromatic amino acids, or the backbone, hydrogen bond to uracil. Consideration of enzymatic and aqueous environments leads to decreases in the effects of the amino acids on the acidity of uracil. However, we find that the magnitude of the decrease varies with the nature of the molecule bound, as well as the (gas-phase) binding orientations and strengths, and therefore solvation effects should be considered on a case-by-case basis in future work. Nevertheless, the effects of amino acid interactions within enzymatic environments are as much as approximately 35 kJ mol(-1). The present study has general implications for understanding the nature of active site amino acids in enzymes, such as DNA repair enzymes, that catalyze reactions involving anionic nucleobase intermediates.

On the nature of hydrogen bonds: an overview on computational studies and a word about patterns

The nature of hydrogen bond interactions (HB) is still today the subject of many discussions. We present an overview of computational methods and parameters (interaction energy, HB distance and radii, electron density topological parameters or orbital energies) required for an accurate description of HB systems. As well, we present the different correlations that have been found between these descriptors providing a global view of HB interactions. A synopsis of the different HBs reported in terms of their strength was presented. Considering the definitions of covalent and ionic bonds, HB interactions could occur between these two extremes. Thus, we look into some of the very strong HBs (LBHB, CAHB, RAHB) and some of the weak HBs (weak donors: C-H or weak acceptors: pi systems). Subsequently, aspects such as cooperativity or solvation are examined. Finally, we present a study on multiple "parallel" and "bifurcated" HB systems. Our results indicate that HB pattern and electron density determine the strength of the interaction and that "parallel" HB interactions are more stable than the "bifurcated" ones.

Stereoisomer Discrimination in Complexes of Halogen-Substituted Difuranes and Li or Na Cations

The theoretical study of the stereoisomer discrimination of the 2:1 homo- and heterochiral complexes between chiral 5,5'-dihalogen bifuranes and lithium or sodium cations has been carried out using DFT methods. To understand the chiral effect produced by the introduction of a second bifurane molecule, the 1:1 complexes also have been calculated. All the 2:1 heterochiral complexes computed showed a nonplanar configuration around the metallic cation, but in the case of the homochiral complexes, the dibromo- and dichloro-bifurane systems around Na+ were quasi-planar. The nature of the interactions established between cations and bifurane systems has been analyzed by means of AIM and NBO, and correlations between the electron density topological parameters with the O...M distance and with the orbital interaction energy have been found. Stereodiscrimination is observed favoring the heterochiral complexes except for the Na+ complexes with chloro and bromo substituents in which the homochiral forms are more stable. Stereodiscrimination values correlate with the difference in electron density at the bond critical point and orbital interaction energy between homo- and heterochiral systems.