Hydration of Cytidine, 2′-Deoxycytidine and their Phosphate Salts in the Aqueous Solutions. A Molecular Dynamics Computer Simulation Study

Kulińska, K.; Laaksonen, Aatto

doi:10.1080/07391102.1994.10508070

Cited by 7 publications

(7 citation statements)

References 29 publications

(22 reference statements)

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“…There are many hypotheses trying to explain the observed differences in terms of influence of the 2′OH group on stability of the overall RNA structure and RNA‐protein recognition. Molecular dynamic simulation analysis of interaction energies between water and nucleoside molecules has revealed that the hydration interactions of cytidine are stronger than those of deoxycytidine by an energy corresponding to one hydrogen bond which comes mainly from the different ribose and 2′‐deoxyribose hydration [96]. RNAs adopt the A‐type conformation, while DNAs can adopt either the A or B form.…”

Section: High‐pressure Mediated Conformational Changes Of Ribonucleicmentioning

confidence: 99%

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

Barciszewski

Jurczak

Porowski

et al. 1999

European Journal of Biochemistry

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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...

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Section: High‐pressure Mediated Conformational Changes Of Ribonucleicmentioning

confidence: 99%

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

Barciszewski

Jurczak

Porowski

et al. 1999

European Journal of Biochemistry

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“…When these units are detached and terminated they can correspond to small molecules ͑e.g., methanol, methylamine, etc.͒. In our attempts to examine biomolecules in this way, we have studied carboxylic acids, 14 carbohydrates, 15 nucleotides, 16 and DNA, 17 to give a few examples.…”

Section: Introductionmentioning

confidence: 99%

The local structure in liquid methylamine and methylamine–water mixtures

Kusalik

Bergman

Laaksonen

2000

The Journal of Chemical Physics

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Articles you may be interested inHydrogen bonded structure, polarity, molecular motion and frequency fluctuations at liquid-vapor interface of a water-methanol mixture: An ab initio molecular dynamics study Structure, thermodynamics, and dynamics of the liquid/vapor interface of water/dimethylsulfoxide mixtures Molecular dynamics ͑MD͒ computer simulations are carried out on liquid methylamine and on 10 and 30 wt % aqueous solutions of methylamine. The local three-dimensional structure in these liquid systems is investigated using standard one-dimensional radial distribution functions and the fully three-dimensional measure of the local structure around the molecule, spatial distribution functions. Time correlation functions for the linear and angular motion of methylamine in the molecular coordinate system are also explored. From this analysis, a detailed structural picture emerges, revealing local molecular environments in these liquids that are both complex and varied. Hydrogen bond balance is found to play a key role in determining preferred arrangements. Strong hydrogen bonds are formed around the amino group in the pure liquid and in aqueous solution. At the same time, there is a strong hydrophobic association of methyl groups. The hydration structure in aqueous solution is found to be particularly rich, where in addition to the usual H-bonding nearest neighbors in the first hydration shell of the amino group, there are bridging water molecules and a novel type of distinctly non-H-bonding neighbors. The hydration structure in aqueous methylamine solution differs substantially from that found in methanol-water liquid mixtures.

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“…In aqueous solution an amino‐oxo tautomer of cytidine, CydA , is present [86–88]. However, an equilibrium between two species has been found upon heating an aqueous solution of cytidine [32].…”

Section: Resultsmentioning

confidence: 99%

“…Several papers have been devoted to the tautomerism of cytidine and deoxycytidine in aqueous solution [83–88]. The 1 H NMR spectra of cytidine in D 2 O at varying pH have shown that the compound exists in amino‐oxo form [83].…”

Section: Introductionmentioning

confidence: 99%

Tautomerism of cytosine, cytidine, and deoxycytidine: Proton transfer through water bridges

Stoyanova

Enchev

2022

Int J of Quantum Chemistry

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Altogether six tautomers of cytosine and three tautomers of cytidine and deoxycytidine are studied theoretically in the gas phase and in a microhydrated environment. Their structures are optimized at MP2/6-31 + G(d,p) level. The relative energies of the isolated and the hydrated tautomers included the correction to higher correlation energy terms evaluated at the SCS-MP2, MP4, and CCSD(T) levels. The free energies at 298 K and higher temperatures are based on the above-mentioned relative energies and temperature-dependent enthalpy terms and entropies evaluated at the MP2/6-31 + G(d,p) level. Theoretical predictions for the coexistence of five species for cytosine in the gas phase (canonical, trans-and cis-enol-amino, transand cis-imino-oxo forms) fully agree with recent experimental results. Five-hydrated cytosine tautomeric forms of are investigated at CPCM/SCS-MP2/6-31 + G(d,p) level to evaluate the interconversion barriers between them and to explain the coexistence, experimentally proven, of two amino-oxo and one imino-oxo tautomers of cytosine in aqueous solution. The presence of coordinated water molecules acting as a catalyst make the tautomerization processes quite easier. It appeared clear from the obtained data that the influence of the hydrogen-bonded water molecules as well as the introduction of solvent effects in reducing the height of the tautomerization barriers for these five-hydrated systems is quite substantial. Similar results are obtained for the tri-hydrated cytidine and the 2-deoxycytidine tautomeric forms. In aqueous solution of cytidine, syn-and syn-clinal-conformers оf the amino-oxo tautomer should coexist with small amounts of syn-and syn-clinal conformers оf iminooxo tautomer. For 2-deoxycytidine an equilibrium has been found to exist between the syn-and anti-conformers of the amino-oxo and the imino-oxo tautomers. The water-assisted proton transfer reactions released through asynchronous concerted mechanism and the conformation of the sugar ring in nucleosides does not change during the tautomerization.

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Hydration of Cytidine, 2′-Deoxycytidine and their Phosphate Salts in the Aqueous Solutions. A Molecular Dynamics Computer Simulation Study

Cited by 7 publications

References 29 publications

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

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

The local structure in liquid methylamine and methylamine–water mixtures

Tautomerism of cytosine, cytidine, and deoxycytidine: Proton transfer through water bridges

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