Biomedical subjects

T I Grokhlina

Publications and source records attributed to T I Grokhlina.

4 recordsLinked to original sources

PubMed1984

Hydration of nucleic acid bases studied using novel atom-atom potential functions.

New simple atom-atom potential functions for simulating behavior of nucleic acids and their fragments in aqueous solutions are suggested. These functions contains terms which are inversely proportional to the first (electrostatics), sixth (or tenth for the atoms, forming hydrogen bonds) and twelfth (repulsion of all the atoms) powers of interatomic distance. For the refinement of the potential function parameters calculations of ice lattice energy, potential energy and configuration of small clusters consisting of water and nucleic acid base molecules as well as Monte Carlo simulation of liquid water were performed. Calculations using new potential functions give rise to more linear hydrogen bonds between water and base molecules than using other potentials. Sites of preferential hydration of five nucleic bases - uracil, thymine, cytosine, guanine and adenine as well as of 6,6,9-trimethyladenine were found. In the most energetically favourable sites water molecular interacts with two adjacent hydrophilic centres of the base. Studies of interaction of the bases with several water molecules showed that water-water interactions play an important role in the arrangement of the nearest to the base water molecules. Hydrophilic centres are connected by "bridges" formed by hydrogen bonded water molecules. The results obtained are consistent with crystallographic and mass-spectrometric data.

Computer Simulation↗

PubMedDate not supplied

[Interactions between nucleic acid bases. New parameters of potential functions and energy minima].

The parameters of atom-atom potential functions suggested by one of the authors in 1979-1986 were slightly changed. The changes were performed to achieve a better agreement with experimental data of interaction energy values in global minima and hydrogen bond lengths. These changes resulted in better accord with experimental values of distances between the layers in DNA monomer crystals and between the base pairs in oligonucleotide duplexes. The refined potential functions were used to calculate the energy of interactions between nucleic acid bases in various mutual positions. The calculations revealed a few types of mutual base arrangements in minima of interaction energy for each pairwise base combination. A new type of minima was found, which correspond to a nearly perpendicular arrangement of base rings and the formation of the intermolecular hydrogen bond.

Algorithms↗

PubMedDate not supplied

[Interaction of caffeine with basic nucleic acids my a molecular mechanic method].

To understand some aspects of the biological action of caffeine (CAF), the interaction energies for various mutual positions of CAF and DNA bases or basepairs were calculated. Three types of mutual CAF-base (CAF-basepair) arrangements corresponding to the minima of interaction energy were revealed. One type of minima correspond to the stacking arrangement of molecules. This type is important for interactions of CAF with DNA monomers and single-stranded fragments. The other two types of minima correspond to the formation of intermolecular hydrogen bonds. Some of these minima may occur during the interaction of CAF with the double helix. One of these types corresponds to the nearly in-plane position of molecules. The other type of minima correspond to the nearly perpendicular arrangement of molecule planes. The minima of the last type are supposed to be the most important for the interaction of CAF with the DNA duplex, and interaction energies for this type of minima have the most negative values.

Caffeine↗

PubMedDate not supplied

[Interactions of caffeine with DNA double helix fragments. Molecular mechanics simulation].

Calculations of the energy of interaction between the caffeine molecule and DNA double helix fragment of four complementary pairs have been performed by the molecular mechanics method. The calculations demonstrate the existence of energy minima corresponding to the caffeine molecule position in both wide and narrow grooves. Each of three proton acceptor atoms of caffeine is able to form hydrogen bond with each of three amino groups of DNA bases. The interactions of caffeine with both hydrogen bonded nucleotide and other nucleotides of the two strands contribute considerably to the total energy. The substantial contribution of interactions of caffeine with other than H-bonded nucleotides results in a rather close packing of atom groups in possible DNA-caffeine complexes. The mechanisms of influence of caffeine on interactions of DNA with other biologically active compounds are discussed.

Caffeine↗