Biomedical subjects

E B Starikov

Publications and source records attributed to E B Starikov.

7 recordsLinked to original sources

PubMed2005

Investigation of a Kubo-formula-based approach to estimate DNA conductance in an atomistic model.

A novel approach to estimate DNA conductance based upon Kubo formula is presented and discussed. Using this approach, the effects of base pair mismatches, different conformational changes and base pair sequence on DNA electrical properties were investigated. The results were compared with the data from other methods. The new approach makes possible very fast estimation of conductance spectra for oligonucleotides with hundreds of base pairs and can easily be extended to treat arbitrary chemical modifications of DNA.

Base Pair Mismatch↗

PubMed2005

Localization properties of electronic states in a polaron model of poly(dG)-poly(dC) and poly(dA)-poly(dT) DNA polymers.

We numerically investigate localization properties of electronic states in a static model of poly(dG)-poly(dC) and poly(dA)-poly(dT) DNA polymers with realistic parameters obtained by quantum-chemical calculation. The randomness in the on-site energies caused by the electron-phonon coupling is completely correlated to the off-diagonal parts. In the single electron model, the effect of the hydrogen-bond stretchings, the twist angles between the base pairs and the finite system size effects on the energy dependence of the localization length and on the Lyapunov exponent are given. The localization length is reduced by the influence of the fluctuations in the hydrogen bond stretchings. It is also shown that the helical twist angle affects the localization length in the poly(dG)-poly(dC) DNA polymer more strongly than in the poly(dA)-poly(dT) one. Furthermore, we show resonance structures in the energy dependence of the localization length when the system size is relatively small.

Biophysical Phenomena↗

PubMed2004

Regular threshold-energy increase with charge for neutral-particle emission in collisions of electrons with oligonucleotide anions.

Electron-DNA anion collisions were studied using an electrostatic storage ring with a merging electron-beam technique. The rate of neutral particles emitted in collisions started to increase from definite threshold energies, which increased regularly with ion charges in steps of about 10 eV. These threshold energies were almost independent of the length and sequence of DNA, but depended strongly on the ion charges. Neutral particles came from breaks of DNAs, rather than electron detachment. The step of the threshold energy increase approximately agreed with the plasmon excitation energy. It is deduced that plasmon excitation is closely related to the reaction mechanism.

Anions↗

PubMed1999

Folding of oligoglutamines: a theoretical approach based upon thermodynamics and molecular mechanics.

Folding of oligoglutamine chains of different lengths is of crucial interest for exploring the molecular mechanisms of Huntington's disease. A simple oligoglutamine model based upon the Flory-Huggins theory of polymer solutions demonstrates a random coil instability in chains containing more than 40 glutamine residues with respect to beta-sheet formation. This is in striking quantitative agreement with biochemical results on the chain length dependence of polyglutamine aggregation in vivo and in vitro, as well as with clinical data on the polyglutamine chain length dependence of the onset of Huntington's disease. Furthermore, a detailed molecular-mechanical investigation of a polypeptide chain carrying 40 glutamine residues was performed. Two possible folding modes of such an oligoglutamine chain were revealed: a) a beta-hairpin and b) a highly compact random coil entity stabilized by a wealth of H-bonds among the glutamine side chains. A possible role of these folding modes in polyglutamine aggregation, as well as in the onset of Huntington's disease, is discussed.

Amino Acid Sequence↗

PubMed1998

Huntingtin aggregation monitored by dynamic light scattering.

An initial stage of fibrillogenesis in solutions of glutathione S-transferase-huntingtin (GST-HD) fusion proteins has been studied by using dynamic light scattering. Two GST-HD systems with poly-L-glutamine (polyGln) extensions of different lengths (20 and 51 residues) have been examined. For both systems, kinetics of z-average translation diffusion coefficients (Dapp) and their angular dependence have been obtained. Our data reveal that aggregation does occur in both GST-HD51 and GST-HD20 solutions, but that it is much more pronounced in the former. Thus, our approach provides a powerful tool for the quantitative assay of GST-HD fibrillogenesis in vitro.

Glutathione Transferase↗

PubMed1997

Computational support for the suggested contribution of C-H...O=C interactions to the stability of nucleic acid base pairs.

Ab inito quantum chemical calculations are performed to quantify the stabilizing role of long C-H...O=C contacts in nucleic acid base pairing, which was suggested by Leonard, McAuley-Hecht, Brown & Hunter [(1995). Acta Cryst. D51, 136-139]. For the Watson-Crick adenine-uracil pair, a contribution of about 6% to the total bond energy is obtained. This weakly bonding effect is primarily a result of electrostatic attraction between the total positive charge of adenine C(2)-H and the negative end of the dipole uracil O(2)=C.

Journal Article↗

PubMed1990

Theoretical analysis of deoxycytidine-5'-phosphate protonation.

The electron density distribution in deoxycytidine-5'-monophosphate (5'-dCMP) molecule and dianion has been studied by the method of CNDO/2. The comparison between the results of calculation for the neutral molecule and the data obtained by Pearlman and Kim shows that there is a linear correlation between the atomic charges calculated using quantum chemistry and those derived from X-ray results. However, partial charges for the deoxyribose fragment are correlated in a nonlinear manner. The influence of the protons added to the cytosine and phosphate residues on the atomic charges and bond orders of deoxy-cytidine-5'-monophosphate has been analyzed here. The conclusion has been drawn that the semiempirical quantum-chemical CNDO/2 technique is applicable to the mononucleotide studies.

Deoxycytidine Monophosphate↗