The role of water structure in conformational changes of nucleic acids in ambient and high‐pressure conditions

Abstract

This review describes and summarizes data on the structure and properties of water under normal conditions, at high salt concentration and under high pressure. We correlate the observed conformational changes in nucleic acids with changes in water structure and activity, and suggest a mechanism of conformational transitions of nucleic acids which accounts for changes in the water structure. From the biophysical, biochemical and crystallographic data we conclude that the Z-DNA form can be induced only at low water activity produced by high salt concentrations or high pressure, and accompanied by the stabilizing conjugative effect of the cytidine O4 H electrons of the CG base pairs.Keywords: structure of water, high pressure, conformational changes, nucleic acids.Water molecules influence specific interactions in all biological systems and yet it is still extremely difficult to understand their effect in precise atomic models. Recent studies of water effects on biological macromolecules have made molecular biologists aware of the important role that this solvent plays in the structure and function of proteins, nucleic acids and other cell constituents. Also we now realize how little we know about the detailed behaviour of water molecules. In recent years there has been an explosion in the number of new X-ray structures for protein±DNA complexes and other biomolecules. Many of those structures feature water molecules buried at the intermolecular interface, or assign them with reasonable confidence to good geometry of water oxygen atoms, at the coordination space of hydrogen bond donors and acceptors. Thus, hydrogen bonding networks between proteins and nucleic acids often include water molecules, which have not been anticipated from our previous understanding of the molecular basis for macromolecular recognition, which always predicted direct contacts between functional groups. The contribution of hydration to the energetics of macromolecular assembly and catalysis was recognized a long time ago. The cost of removing all the perturbated water, or the benefit of fully hydrating a newly exposed surface is around 3.6±62.7 kJ´mol 21 per 100 A Ê 2 . It is rather high in comparison to ATP molecule hydrolysis which yields 30.5 kcal´mol 21 .We now put forward several basic questions concerning water interactions with proteins and nucleic acids, the strength of these interactions, and their localisation, structure and effect on the conformation of various biological macromolecules. The role of water in biology is not very well understood in detail and is still controversial. Water molecules appear to be both the cement that fills crevices between amino acid building blocks and the lubricant that allows motion of these elements [1]. In consequence, they allow a biological molecule to adopt a tertiary structure without being trapped in a local minimum energy state, as well as to compensate for a poor steric fit of side chains in macromolecule interiors and substrates in the binding sites [2,3]. These interactions of water mol...

A nature of conformational changes of yeast tRNAPhe

“…The formation of octamer (cube) from two tetramers results in reducing the volume by 1.3 cm 3 mol −1 [46]. As it was proposed earlier, water in such a form fits very well to the major groove of Z-DNA, so the changes in water structure followed by reorganisation of hydrogen bonds net induce the switching from B to Z conformation [47].…”

An SOS Response Induced by High Pressure inEscherichia coli

“…1) was previously unreported. Although pressure is known to denature proteins, it has been shown to stabilize DNA helices in vitro by promoting hydrogen bonds and enhancing stacking of the hydrophobic bases, resulting in compact DNA (6). The induction of the heat shock response by high pressure, as has been reported previously (2), therefore seems more logical than activation of the SOS regulon.…”

Differential gene expression of Listeria monocytogenes during high hydrostatic pressure processing

“…Thus a compensatory increase in gene expression for DNA polymerase components may be a partial response to HPP disruption of the DNA replication process. This response could also be simply due to high hydrostatic pressure tending to render DNA in a more compact configuration (Barciszewski et al, 1999) or damaging the helix structure, resulting in a reduction in the efficiency of forming DNA polymerase-DNA complexes suitable for the initiation of active replication.…”