Interaction of aspartic acid and asparagine with RNA nucleobases: a quantum chemical view

DFT and TD-DFT study of hydrogen bonded complexes of aspartic acid and n water (n = 1 and 2)

CONTEXT

Hydrogen bonds (HB) influence the conformational preferences of biomolecules and their optical and electronic properties. The directional interaction of molecules of water can be a prototype to understand the effects of HBs on biomolecules. Among the neurotransmitters (NT), L-aspartic acid (ASP) stands out due to its importance in health and as a precursor of several biomolecules. As it presents different functional groups and readily forms inter- and intramolecular HBs, ASP can be considered a prototype for understanding the behavior of NTs when interacting by HB with other substances. Although several theoretical studies have been performed in the past on isolated ASP and its formed complexes with water, both in gas and liquid phases, using DFT and TD-DFT formalisms, these works did not perform large basis set calculations or study electronic transitions of ASP-water complexes. We investigated the HB interactions in complexes of ASP and water molecules. The results show that the interactions between the carboxylic groups of ASP with water molecules, forming cyclic structures with two HBs, lead to more stable and less polar complexes than other conformers formed between water and the NH₂ group. It was observed that there is a relationship between the deviation in the UV-Vis absorption band of the ASP and the interactions of water with the HOMO and LUMO orbitals with the stabilization/destabilization of the S₁ state to the S₀ of the complexes. However, in some cases, such as 1:1 complex ASP-W2, this analysis may be inaccurate due to small changes in ΔE.

METHODS

We studied the landscapes of the ground state surface of different conformers of isolated L-ASP and the L-ASP-(H₂O)_n complexes (n = 1 and 2) using the DFT formalism, with the B3LYP functional, and six different basis sets: 6-31 +  + G(d,p), 6-311 +  + G(d,p), D95 +  + (d,p), D95V +  + (d,p), cc-pVDZ, and, cc-pVTZ basis sets. The cc-pVTZ basis set provides the minimum energy of all conformers, and therefore, we performed the analysis with this basis set. We evaluated the stabilization of the ASP and complexes using the minimum ground state energy, corrected by the zero point energy and the interaction energy between the ASP and the water molecules. We also calculated the vertical electronic transitions S₁ ← S₀, and their properties using the TD-DFT formalism at B3LYP/cc-pVTZ level with the optimized geometries for S₀ state with the same basis set. For the analysis of the vertical transitions of isolated ASP and the ASP-(H₂O)_n complexes, we calculated the electrostatic energy in the S₀ and S₁ states. We performed the calculations with the Gaussian 09 software package. We used the VMD software package to visualize the geometries and shapes of the molecule and complexes.

Exploring the Nature of Hydrogen Bonding between RNA and Proteins: A Comprehensive Analysis of RNA : Protein Complexes

A nonredundant dataset of ∼300 high (up to 2.5 Å) resolution X-ray structures of RNA:protein complexes were analyzed for hydrogen bonds between amino-acid residues and canonical ribonucleotides (rNs). The identified 17100 contacts were classified based on the identity (rA, rC, rG or rU) and interacting fragment (base, sugar, or ribose) of the rN, the nature (polar or nonpolar) and interacting moiety (main chain or side chain) of the amino-acid residue, as well as the rN and amino-acid atoms participating in the hydrogen bonding. 80 possible hydrogen-bonding combinations (4 (rNs) X 20 (amino acids)) involve a wide variety of RNA and protein types and are present in multiple occurrences in almost all PDB files. Comparison with the analogously-selected DNA:protein complexes reveals that the absence of 2'-OH group in DNA mainly accounts for the differences in DNA:protein and RNA:protein hydrogen bonding. Search for intrinsically-stable base:amino acid pairs containing single or multiple hydrogen bonds reveals 37 unique pairs, which may act as well-defined RNA:protein interaction motifs. Overall, our work collectively analyzes the largest set of nucleic acid-protein hydrogen bonds to date, and therefore highlights several trends that may help frame structural rules governing the physiochemical characteristics of RNA:protein recognition.

Influence of the Number, Nature and Position of Methyl Posttranscriptional Modifications on Nucleobase Stacking in RNA

DFT calculations are employed to quantify the influence of the presence, number, nature, and position of posttranscriptional methylation on stacking strength of RNA bases. We carry out detailed potential energy scans of the variation in stacking energies with characteristic geometrical parameters in three categories of forty stacked dimers - canonical base homodimers (N||N), methylated base homodimers (mN||mN) and heterodimers of canonical bases and methylated counterparts (N||mN). Our analysis reveals that neutral methylation invariably enhances the stacking of bases. Further, N||mN stacking is stronger than mN||mN stacking and charged N||mN exhibit strongest stacking among all dimers. This indicates that methylations greatly enhance stacking when dispersed in RNA sequences containing identical bases. Comparison of stacks involving singly- and doubly-methylated purines reveal that incremental methylation enhances the stacking in neutral dimers. Although methylation at the carbon position of neutral pyrimidine dimers greatly enhances the stacking, methylation on the 5-membered ring imparts better stacking compared to methylation on the 6-membered ring in adenine dimers. However, methylation at the ring nitrogen (N¹ ) provides better stacking than the amino group (N² ) in guanine dimers. Our results thus highlight subtle structural effects of methylation on RNA base stacking and will enhance our understanding of the physicochemical principles of RNA structure and dynamics.

Can modified DNA base pairs with chalcogen bonding expand the genetic alphabet? A combined quantum chemical and molecular dynamics simulation study

A comprehensive (DFT and MD) computational study is presented with the goal to design and analyze model chalcogen-bonded modified nucleobase pairs that replace one (i.e., A_XY:T, G:C_XY, G_XY:C) or two (G_XY:C_X'Y', X/X' = S, Se and Y/Y' = F, Cl, Br) Watson-Crick (WC) hydrogen bonds of the canonical A:T or G:C pair with chalcogen bond(s). DFT calculations on 18 base pair combinations that replace one WC hydrogen bond with a chalcogen bond reveal that the bases favorably interact in the gas phase (binding strengths up to -140 kJ mol^-1) and water (up to -85 kJ mol^-1). Although the remaining hydrogen bond(s) exhibits similar characteristics to those in the canonical base pairs, the structural features of the (Y-XO) chalcogen bond(s) change significantly with the identity of X and Y. The 36 doubly-substituted (G_XY:C_X'Y') base pairs have structural deviations from canonical G:C similar to those of the singly-substituted modifications (G:C_XY or G_XY:C). Furthermore, despite the replacement of two strong hydrogen bonds with chalcogen bonds, some G_XY:C_X'Y' pairs possess comparable binding energies (up to -132 kJ mol^-1 in the gas phase and up to -92 kJ mol^-1 in water) to the most stable G:C_XY or G_XY:C pairs, as well as canonical G:C. More importantly, G:C-modified pairs containing X = Se (high polarizability) and Y = F (high electronegativity) are the most stable, with comparable or slightly larger (by up to 13 kJ mol^-1) binding energies than G:C. Further characterization of the chalcogen bonding in all modified base pairs (AIM, NBO and NCI analyses) reveals that the differences in the binding energies of modified base pairs are mainly dictated by the differences in the strengths of their chalcogen bonds. Finally, MD simulations on DNA oligonucleotides containing the most stable chalcogen-bonded base pair from each of the four classifications (A_XY:T, G:C_XY, G_XY:C and G_XY:C_X'Y') reveal that the singly-modified G:C pairs best retain the local helical structure and pairing stability to a greater extent than the modified A:T pair. Overall, our study identifies two (G:C_SeF and G_SeF:C) promising pairs that retain chalcogen bonding in DNA and should be synthesized and further explored in terms of their potential to expand the genetic alphabet.

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.

Structural Patterns and Stabilities of Hydrogen-Bonded Pairs Involving Ribonucleotide Bases and Arginine, Glutamic Acid, or Glutamine Residues of Proteins from Quantum Mechanical Calculations

Ribonucleotide:protein interactions play crucial roles in a number of biological processes. Unlike the RNA:protein interface where van der Waals contacts are prevalent, the recognition of a single ribonucleotide such as ATP by a protein occurs predominantly through hydrogen-bonding interactions. As a first step toward understanding the role of hydrogen bonding in ribonucleotide:protein recognition, the present work employs density functional theory to provide a detailed quantum-mechanical analysis of the structural and energetic characteristics of 18 unique hydrogen-bonded pairs involving the nucleobase/nucleoside moiety of four canonical ribonucleotides and the side chains of three polar amino-acid residues (arginine, glutamine, and glutamic acid) of proteins. In addition, we model five new pairs that are till now not observed in crystallographically identified ribonucleotide:protein complexes but may be identified in complexes crystallized in the future. We critically examine the characteristics of each pair in its ribonucleotide:protein crystal structure occurrence and (gas phase and water phase) optimized intrinsic structure. We further evaluated the interaction energy of each pair and characterized the associated hydrogen bonds using a number of quantum mechanics-based relationships including natural bond orbital analysis, quantum theory atoms in molecules analysis, Iogansen relationships, Nikolaienko-Bulavin-Hovorun relationships, and noncovalent interaction-reduced density gradient analysis. Our analyses reveal rich variability in hydrogen bonds in the crystallographic as well as intrinsic structure of each pair, which includes conventional O/N-H···N/O and C-H···O hydrogen bonds as well as donor/acceptor-bifurcated hydrogen bonds. Further, we identify five combinations of nucleobase and amino acid moieties; each of which exhibits at least two alternate (i.e., multimodal) structures that interact through the same nucleobase edge. In fact, one such pair exhibits four multimodal structures; one of which possesses unconventional "amino-acceptor" hydrogen bonding with comparable (-9.4 kcal mol^-1) strength to the corresponding conventional (i.e., amino:donor) structure (-9.2 kcal mol^-1). This points to the importance of amino-acceptor hydrogen bonds in RNA:protein interactions and suggests that such interactions must be considered in the future while studying the dynamics in the context of molecular recognition. Overall, our study provides preliminary insights into the intrinsic features of ribonucleotide:amino acid interactions, which may help frame a clearer picture of the molecular basis of RNA:protein recognition and further appreciate the role of such contacts in biology.