Vladimir V. Egorov

Molecular mechanisms enhancing the proteome of influenza A viruses: an overview of recently discovered proteins.

Influenza A virus is one of the major human pathogens. Despite numerous efforts to produce absolutely effective anti-influenza drugs or vaccines, no such agent has been developed yet. One of the main reasons for this complication is the high mutation rate and the specific structure of influenza A viruses genome. For more than 25 years since the first mapping of the viral genome, it was believed that its 8 genome segments encode 10 proteins. However, the proteome of influenza A viruses has turned out to be much more complex than previously thought. In 2001, the first accessory protein, PB1-F2, translated from the alternative open reading frame, was discovered. Subsequently, six more proteins, PB1-N40, PA-X, PA-N155, PA-N182, M42, and NS3, have been found. It is important to pay close attention to these novel proteins in order to evaluate their role in the pathogenesis of influenza, especially in the case of outbreaks of human infections with new avian viruses, such as H5N1 or H7N9. In this review we summarize the data on the molecular mechanisms used by influenza A viruses to expand their proteome and on the possible functions of the recently discovered viral proteins.

Nature of the optical transition in polymethine dyes and J-aggregates

Using a new theory of photoinduced electron transfer beyond the Landau–Zenner ideology or, more precisely, electrodynamics of extended multiphonon transitions [V. V. Egorov, Chem. Phys. 269, 251 (2001)], we give an explanation for the well-known experimental data [L. G. S. Brooker et al., J. Am. Chem. Soc. 62, 1116 (1940)] for the absorption line shape in the vinylogous series of an ideal polymethine dye represented by a thiacarbocyanine. Then, using this explanation together with our earlier explanation [V. V. Egorov, Chem. Phys. Lett. 336, 284 (2001)] for the nature of the well-known intense narrow J-band due to an aggregation of polymethine dyes, we predict very intense narrow absorption lines for short optical transitions. Interpretation of these results is given on a basis of the Heisenberg uncertainty relation. A process of creation of the pure (quantum-mechanical) electron-transfer state is considered for the two complementary cases: the electron-transfer state is determined by interaction of the e...

NUMERICAL CALCULATIONS OF OPTICAL LINESHAPES FOR DISORDERED MOLECULAR AGGREGATES

Abstract Numerical calculations of optical lineshapes are performed for molecular aggregates with Gaussian diagonal disorder. A method is proposed that significantly increases the efficiency of numerical calculations by choosing the fluctuating average value of transition energies of all molecules in the aggregate as an origin of the energy scale. Using the proposed method, the absorption line half-width and the exciton coherence length are examined as functions of the number of molecules in the aggregate, the degree of disorder and the disorder correlation over a wide range of parameters.

Porous silicon and its applications in biology and medicine

Development of safe container materials for targeted and controlled drug delivery to the right site in the body is one of the most important aspects of modern biotechnologies. In the last decade, a significant progress has been achieved in the study of nanostructured drug carriers, but the use of many nanomaterials is fraught with the enormous risk because of their high toxicity. The real breakthrough became the use of porous silicon, which has such important properties as biocompatibility, bioavailability, and biodegradability, which makes it possible to use it for solving a wide range of biological and medical problems in the field of diagnosis and treatment of diseases, implantology, and biomolecular screening.

On electrodynamics of extended multiphonon transitions and nature of the J-band

Abstract The overall current picture of elementary electron transfer in condensed matter, derived from the Landau–Zener type theories, is revised to incorporate, among other things, an unusual resonance between the electron and environmental nuclear reorganization motion. Here, we construct a radically new theory of photoinduced electron transfer (beyond the Landau–Zener ideology), or, more precisely, electrodynamics of extended multiphonon transitions in the light of which the nature of the well-known narrow J-band is due to just this resonance, not to averaging an environmental statistical disorder by the quickly moving Frenkel exciton as is generally believed.

Electron-transfer approach to the nature of the optical lineshape for molecular J-aggregates

We have sketched the broad outlines of a new theory of elementary electron transfer in condensed matter in the light of which the nature of the well-known narrow optical J-band is due to an unusual resonance between the electron and environmental nuclear reorganization motion, not to averaging an environmental statistical disorder by the quickly moving Frenkel exciton as is generally believed.

Mass spectrometry and biochemical analysis of RNA polymerase II: targeting by protein phosphatase-1

Transcription of eukaryotic genes is regulated by phosphorylation of serine residues of heptapeptide repeats of the carboxy-terminal domain (CTD) of RNA polymerase II (RNAPII). We previously reported that protein phosphatase-1 (PP1) dephosphorylates RNAPII CTD in vitro and inhibition of nuclear PP1-blocked viral transcription. In this article, we analyzed the targeting of RNAPII by PP1 using biochemical and mass spectrometry analysis of RNAPII-associated regulatory subunits of PP1. Immunoblotting showed that PP1 co-elutes with RNAPII. Mass spectrometry approach showed the presence of U2 snRNP. Co-immunoprecipitation analysis points to NIPP1 and PNUTS as candidate regulatory subunits. Because NIPP1 was previously shown to target PP1 to U2 snRNP, we analyzed the effect of NIPP1 on RNAPII phosphorylation in cultured cells. Expression of mutant NIPP1 promoted RNAPII phosphorylation suggesting that the deregulation of cellular NIPP1/PP1 holoenzyme affects RNAPII phosphorylation and pointing to NIPP1 as a potential regulatory factor in RNAPII-mediated transcription.

Efficient approach to the numerical calculation of optical line shapes for molecular aggregates.

A new approach is proposed for numerical calculations of optical line shapes for disordered molecular aggregates using the excitonic Hamiltonian. The method proposed previously for Gaussian disorder is generalized. A fluctuating origin of the energy scale is introduced as a new independent variable. The integration over this variable eliminates the energy delta function from the integrand, which drastically simplifies the Monte Carlo procedure. The new approach is suitable for calculations using both the diagonalization of the Hamiltonian and the resolvent of the Hamiltonian. As an example, optical line shapes have been calculated for aggregates with bi-Gaussian disorder.

Expression in E. coli and purification of the fibrillogenic fusion proteins TTR-sfGFP and β2M-sfGFP.

The possibility of obtaining recombinant fibrillogenic fusion proteins such as transthyretin (TTR) and β2-microglobulin (β2M) with a superfolder green fluorescent protein (sfGFP) was studied. According to the literature data, sfGFP is resistant to denaturating influences, does not aggregate during renaturation, possesses improved kinetic characteristics of folding, and folds well when fused to different polypeptides. The corresponding DNA constructs for expression in Escherichia coli were created. It could be shown that during expression of these constructs in E. coli, soluble forms of the fusion proteins are synthesized. Efficient isolation of the fusion proteins was performed with the help of nickel-affinity chromatography. For this purpose a polyhistidine sequence (6-His-tag) was incorporated into the C-terminus of the sfGFP. We could show that the purified fusion proteins contained full-size sequences of the most amyloidogenic TTR variant, TTR(L55P) and β2M, and also sfGFP possessing fluorescent properties. In the course of fibrillogenesis both fusion proteins demonstrated their ability to form fibrils that were clearly detectable by atomic force microscopy. Furthermore, with the help of confocal microscopy we were able to reveal structures (exhibiting fluorescence) that are formed during fibrillogenesis. Thus, the use of sfGFP has made it possible to avoid formation of inclusion bodies (IB) during the synthesis of recombinant fusion proteins and to obtain soluble forms of TTR(L55P) and β2M that are suitable for further studies.

On electron transfer in Langmuir-Blodgett films

Abstract Experimental temperature dependences of the rate constant and activation energy obtained recently for electron transfer in Langmuir-Blodgett film devices are treated in terms of a new theoretical approach in which a failure of the Born-Oppenheimer and Franck-Condon approximations, and the effects of the large number of tunnel and over-barrier transitions are of paramount importance.