Interaction of Na+, K+, Mg2+ and Ca2+ counter cations with RNA.

Alkaline and alkaline earth ions, namely Na+, K+, Mg2+ and Ca2+, are critical for the stability, proper folding and functioning of RNA. Moreover, those metal ions help to facilitate macromolecular interactions as well as the formation of supramolecular structures (e.g. the ribosome and the ribozymes). Therefore, identifying the interactions between ions and nucleic acids is a key to the better comprehension of the physical nature and biological functions of those biomolecules. The scope of this review is to highlight the preferential location and binding sites of alkaline and alkaline earth metal ions compensating the negatively charged backbone of nucleic acids and interacting with other electronegative centers, focusing on RNA. We summarize experimental studies from X-ray crystallography and spectroscopic analysis (infrared, Raman and NMR spectroscopies). Computational results obtained with classical and ab initio methods are presented afterwards.

Density functional study of hydrogen bond formation between methanol and organic molecules containing Cl, F, NH2, OH, and COOH functional groups.

Various hydrogen-bonded complexes of methanol with different proton accepting and proton donating molecules containing Cl, F, NH(2), OH, OR, and COOH functional groups have been modeled using DFT with hybrid B3LYP and M05-2X functionals. The latter functional was found to provide more accurate estimates of the structural and thermodynamic parameters of the complexes of halides, amines, and alcohols. The characteristics of these complexes are influenced not only by the principle hydrogen bond of the methanol OH with the proton acceptor heteroatom, but also by additional hydrogen bonds of a C-H moiety with methanol oxygen as a proton acceptor. The contribution of the former hydrogen bond in the total binding enthalpy increases in the order chlorides < fluorides < alcohols < amines, while the contribution of the second type of hydrogen bond increases in the reverse order. A general correlation was found between the binding enthalpy of the complex and the electrostatic potential at the hydrogen center participating in the formation of the hydrogen bond. The calculated binding enthalpies of different complexes were used to clarify which functional groups can potentially form a hydrogen bond to the 2'-OH hydroxyl group in ribose, which is strong enough to block it from participation in the intramolecular catalytic activation of the peptide bond synthesis. Such blocking could result in inhibition of the protein biosynthesis in the living cell if the corresponding group is delivered as a part of a drug molecule in the vicinity of the active site in the ribosome. According to our results, such activity can be accomplished by secondary or tertiary amines, alkoxy groups, deprotonated carboxyl groups, and aliphatic fluorides, but not by the other modeled functional groups.

Determination of the optimal position of adjacent proton-donor centers for the activation or inhibition of peptide bond formation--a computational model study.

The study reports a computational analysis of the influence of proton donor group adjacent to the reaction center during ester ammonolysis of an acylated diol as a model reaction for peptide bond formation. This analysis was performed using catalytic maps constructed after a detailed scanning of the available space around the reaction centers in different transition states, a water molecule acting as a typical proton donor. The calculations suggest that an adjacent proton donor center can reduce the activation barrier of the rate determining transition states by up to 7.2 kcal/mol, while no inhibition of the reaction can be achieved by such a group.

Catalytic role of vicinal OH in ester aminolysis: proton shuttle versus hydrogen bond stabilization.

This computational study provoked by the process of peptide bond formation in the ribosome investigates the influence of the vicinal OH group in monoacylated diols on the elementary acts of ester aminolysis. Two alternative approaches for this influence on ester ammonolysis were considered: stabilization of the transition states by hydrogen bonds and participation of the vicinal hydroxyl in proton transfer (proton shuttle). The activation due to hydrogen bonds of the vicinal hydroxyl via tetragonal transition states was rather modest; the free energy of activation was reduced by only 5.2 kcal/mol compared to the noncatalyzed reaction. The catalytic activation via the proton shuttle mechanism with participation of the vicinal OH in the proton transfer via hexagonal transition states resulted in considerable reduction of the free energy of activation to 33.5 kcal/mol, i.e., 16.0 kcal/mol lower than in the referent process. Accounting for the influence of the environment on the reaction center by a continuum model (for ε from 5 to 80) resulted in further stabilization of the rate-determining transition state by 4-5 kcal/mol. The overall reduction of the reaction barrier by about 16 kcal/mol as compared to the noncatalyzed process corresponds to about 10(9)-fold acceleration of the reaction, in agreement with the experimental estimate for acceleration of this process in the ribosome.

Hierarchical approach to conformational search and selection of computational method in modeling the mechanism of ester ammonolysis.

We describe automated procedures for the first stages of a systematic computational investigation of reaction mechanisms. They include (i) selection of computational method and basis set based on statistical analysis of structural and energy data relating to experimental values, (ii) determination of all distinct conformations of transition states with large conformational freedom, and (iii) generation of unknown geometry of the transition states, based on pre-defined connectivity of the atoms involved in the reaction. For the conformational search we employed an efficient procedure for exploration of various possible conformations of the transition states and elimination of the equivalent structures in several steps using molecular-mechanical and quantum-mechanical methods. The procedure was applied to the determination of the structures of transition states and intermediates in the ammonolysis of monoformylated 1,2-ethanediol, which were subsequently used for identification of the lowest energy reaction paths. For the same reaction system we also used the approach for generation of the initial structures of transition states with unknown geometry. The reported procedures are implemented in the MolRan program suite.

Design and synthesis of substrates for model ribosomal reactions.

2'/3'-O-[Bz(NO(2))-Orn(Boc)]-5'-O-Piv-Ado (1) and its deoxy analog: 3'-O-[Bz(NO(2))-Orn(Boc)]-5'-O-Piv-2'-dAdo (2) were designed and synthesized as substrates for the model ribosome reaction we used to demonstrate the crucial role of A76 2'-OH of peptidyl-tRNA in the rate acceleration of peptide bond formation during protein biosynthesis.

The syn-oriented 2-OH provides a favorable proton transfer geometry in 1,2-diol monoester aminolysis: implications for the ribosome mechanism.

A computational study of 1-formyl 1,2-ethanediol aminolysis predicts a stepwise mechanism involving syn-2-OH-assisted proton transfer. The syn-oriented 2-OH takes over the catalytic role of the external water or amine molecule previously observed in 2-deoxy ester aminolysis. It provides more favorable, that is, more linear, proton transfer geometry for the rate-limiting transition state resulting in an almost billion-fold rate acceleration of the overall reaction. These findings provide structural basis for explanation of the efficiency of the proton shuttling mechanism and imply double proton transfer catalysis by peptidyl tRNA A76 2'-OH as a possible catalytic strategy used by ribosome.

Theoretical study of the o-OH participation in catechol ester ammonolysis.

The possible catalytic effect of the vicinal hydroxyl group during the ammonolysis of acetylcatechol has been studied by first principle calculations. A very efficient intramolecular catalysis was found to occur when the catechol ester o-OH group is deprotonated: the activation energy of the ammonolysis decreases by 24 kcal mol(-1) as compared to that of acetylphenol ammonolysis. Using this value, the o-oxyanion-catalysed intramolecular ammonolysis was estimated to be orders of magnitude faster than the ammonolysis of acetylphenol or nonionised acetylcatechol. The analogy with the aminolysis of peptidyl-tRNA that occurs during protein biosynthesis implies several orders of magnitude acceleration due to complete or partial deprotonation of its 3'-terminal adenosine 2'-OH providing a mechanistic possibility for general acid-base catalysis by the ribosome.