Vladimir V. Ermolenkov

Raman spectroscopic study of the tautomeric composition of adenine in water.

An experimental and theoretical study of the tautomeric composition of adenine (Ade) in water using Raman spectroscopy is reported. Experimental resonance Raman spectra of adenine at excitation wavelengths of 200, 218, and 266 nm were compared with quantum-mechanical calculations of N(9)H- and N(7)H-adenine tautomers and their cations. Both theoretical and experimental studies of nonresonance Raman spectra (457 nm excitation) of adenine were also performed for comparison. A satisfactory agreement of the calculated results with the experimental data was obtained. The Raman spectra are interpreted, and the basic regularities of the Raman intensity distribution are explained. On the basis of the analysis performed, the tautomeric composition of adenine in water is revealed. It is shown that the Ade-N(9),N(1)H(+) cation is the predominant form and that some neutral forms of Ade-N(9)H and Ade-N(7)H tautomers exist in water at pH 3.

Charge Distribution and Amyloid Fibril Formation: Insights from Genetically Engineered Model Systems

The influence of electrostatic interactions on protein amyloidogenesis has been investigated using de novo designed repetitive polypeptides YEHK21 [GH6[(GA)3GY(GA)3GE(GA)3GY(GA)3GE]21GAH6] and YE8 [GH6[(GA)3GY(GA)3GE]8GAH6]. The beta-sheet forming polypeptides were designed with identical beta-strands but with variable substitution at the turns that enable precise location of charged residues (Topilina et al. Biopolymers 2007, 86 (4), 261-264; Topilina et al. Biopolymers 2010, submitted for publication; Topilina et al. Biomacromolecules 2006, 7 (4), 1104-11). Solubility, folding, and aggregation of YEHK21 and YE8 were shown to be controlled by charge distribution. Under those conditions favoring the development of charge, YEHK21 and YE8 have significant propensities to form intermolecular beta-sheet assemblies illustrating the potential of charged polypeptide chains to form ordered amyloid aggregates even in the absence of additional environmental factors such as the presence of polyelectrolytes, salts, and so on.

A de novo designed 11 kDa polypeptide: model for amyloidogenic intrinsically disordered proteins.

A de novo polypeptide GH(6)[(GA)(3)GY(GA)(3)GE](8)GAH(6) (YE8) has a significant number of identical weakly interacting beta-strands with the turns and termini functionalized by charged amino acids to control polypeptide folding and aggregation. YE8 exists in a soluble, disordered form at neutral pH but is responsive to changes in pH and ionic strength. The evolution of YE8 secondary structure has been successfully quantified during all stages of polypeptide fibrillation by deep UV resonance Raman (DUVRR) spectroscopy combined with other morphological, structural, spectral, and tinctorial characterization. The YE8 folding kinetics at pH 3.5 are strongly dependent on polypeptide concentration with a lag phase that can be eliminated by seeding with a solution of folded fibrillar YE8. The lag phase of polypeptide folding is concentration dependent leading to the conclusion that beta-sheet folding of the 11-kDa amyloidogenic polypeptide is completely aggregation driven.

Determination of the tautomeric composition of adenine in the gas phase by vibrational spectroscopy methods: II. Analysis of resonance Raman spectra

The resonance Raman spectra of adenine in the gas phase under excitation with laser radiation at wavelengths of 266, 218, and 200 nm have been investigated experimentally. The quantum-mechanical calculations of the intensity distribution in the resonance Raman spectra of three adenine tautomers are performed in the Herzberg-Teller approximation with the inclusion of the Duschinsky and frequency effects. Conclusions regarding the tautomeric composition of adenine in the gas phase are drawn from comparison of the results of quantum-mechanical calculations with experimental data.

Ultraviolet resonance Raman spectroscopy for the detection of cocaine in oral fluid

Detecting and quantifying cocaine in oral fluid is of significant importance for practical forensics. Up to date, mainly destructive methods or biochemical tests have been used, while spectroscopic methods were only applied to pretreated samples. In this work, the possibility of using resonance Raman spectroscopy to detect cocaine in oral fluid without pretreating samples was tested. It was found that ultraviolet resonance Raman spectroscopy with 239-nm excitation allows for the detection of cocaine in oral fluid at 10μg/mL level. Further method development will be needed for reaching the practically useful levels of cocaine detection.

Ionic and Tautomeric Composition of Cytosine in Aqueous Solution: Resonance and Non-Resonance Raman Spectroscopy Study

A complex experimental and theoretical study of the structural composition of cytosine in water was performed. Raman and resonance Raman spectra of cytosine in acidic, neutral, and alkaline water solutions (pH = 3, 7, and 10, respectively) were recorded at excitation wavelengths of 514, 266, 218, and 200 nm. The temperature dependence of the frequencies and intensities of the resonance Raman bands was obtained in the temperature interval of 4-80 °C. To interpret the experimental Raman and resonance Raman spectra and to determine the structural composition of the water solution of cytosine, the spectra of cytosine and its cation, anion, oxoimine, and hydroxoamine forms were calculated at the B3LYP/6-311++G(d,p) level using the SCRF method. The electronic spectra and geometric parameters of the cytosine and its molecular forms in the excited electronic states close to the excitation wavelengths of the resonance Raman spectra were calculated using the DFT method. The cation exists in the acidic solution together with cytosine and its oxoimine and hydroxoamine tautomeric forms. Cytosine with a small amount of anion dominates in the alkaline medium. The structural composition of the water solution of cytosine is confirmed by the results of quantum-mechanical calculations of the intensity distribution in the resonance Raman spectra.