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E N Bogacheva

Publications and source records attributed to E N Bogacheva.

9 recordsLinked to original sources
PubMed2002

Studying the spatial organization of membrane proteins by means of tritium stratigraphy: bacteriorhodopsin in purple membrane.

The topography of bacteriorhodopsin (bR) in situ was earlier studied by using the tritium bombardment approach [Eur. J. Biochem. 178 (1988) 123]. Now, having the X-ray crystallography data of bR at atom resolution [Proc. Natl. Acad. Sci. 95 (1998) 11673], we estimated the influence of membrane environment (lipid and protein) on tritium incorporation into amino acid residues forming transmembrane helices. We have determined the tritium flux attenuation coefficients for residues 10-29 of helix A. They turned out to be low (0.04+/-0.02 A(-1)) for residues adjacent to the lipid matrix, and almost fourfold higher (0.15+/-0.05 A(-1)) for those oriented to the neighboring transmembrane helices. We believe that tritium incorporation data could help modeling transmembrane segment arrangement in the membrane.

Bacteriorhodopsins↗
PubMed1998

Tritium planigraphy: from the accessible surface to the spatial structure of a protein.

The method of tritium planigraphy, which provides comprehensive information on the accessible surface of macromolecules, allows an attempt at reconstructing the three-dimensional structure of a protein from the experimental data on residue accessibility for labeling. The semiempirical algorithm proposed for globular proteins involves (i) predicting theoretically the secondary structure elements (SSEs), (ii) experimentally determining the residue-accessibility profile by bombarding the whole protein with a beam of hot tritium atoms, (iii) generating the residue-accessibility profiles for isolated SSEs by computer simulation, (iv) locating the contacts between SSEs by collating the experimental and simulated accessibility profiles, and (v) assembling the SSEs into a compact model via these contact regions in accordance with certain rules. For sperm whale myoglobin, carp and pike parvalbumins, the lambda cro repressor, and hen egg lysozyme, this algorithm yields the most realistic models when SSEs are assembled sequentially from the amino to the carboxyl end of the protein chain.

Algorithms↗
PubMedDate not supplied

[The concept of the "accessible surface" of the protein within the framework of tritium planigraphy. Experiment and calculation].

Tritium planigraphy allows one to determine the sterical accessibility of protein hydrocarbon fragments (CH, CH2, CH3 groups) for interaction with tritium atoms on condition of direct transit of the bombarding particles. Using lysozyme as a test system, it was shown to be possible to use these data for the description of protein accessible surface area in terms defined by Lee and Richards. The best agreement between experimental and theoretical results was achieved for an effective radius of the testing probe of 0.9 A. Coefficients were obtained that allowed calculation of the accessibility of amino acid residue as a whole using data about its hydrocarbon fragment accessibility.

Muramidase↗
PubMedDate not supplied

[Accessible surface and intramolecular mobility of proteins: study by method of tritium planigraphy].

The method of tritium planigraphy is used for determination of the accessible surface of a globular protein--lysozyme--and the accessibility of particular types of amino acid residues as a function of temperature in the range of 77-193 K. Protein powder with humidity 10 +/- 1% was used. As the temperature is changed from 77 to 160 K for all types of amino acid residues was obtained decreasing of inclusion of tritium label. All types of amino acid residues may be divided on the three groups: I. Accessibility rises under increasing temperature from 160 to 293 K (K, R, H, P, L); II. Accessibility not depends or slightly increases with the growth of temperature (C, V, A, I, Y, F); III. Accessibility strongly increases in the range of the temperature 260-293 K (S, T, G, D + N, E + Q). The reason of "cold denaturation" is perhaps the difference of behaviour of structural water molecules. Under increasing of temperature from 160 to 293 K change of accessibility was explained the growing of intramolecular flexibility of molecule. Under transition from 160 to 77 K for all types of residues is observed sensible change of spatial structure of the protein, which cannot be explained by only participation of dynamical characteristics.

Animals↗
PubMedDate not supplied

[Quantitative determination of the accessible surface of globular proteins by tritium planigraphy].

At the last time the term "accessible surface" is used for a description of protein structure. The tritium planigraphy was used for quantitative detection of the accessible surface. The experimental dependence of an interaction probability of the tritium atoms with globular proteins with calculated accessible surface areas was obtained. The method was proposed on the basis of the information about the reactivity of amino acids residues and was used for the determination of an accessible surface of parvalbumin III of pike.

Protein Conformation↗