Left-handed helix conformation of poly-L-proline II type in globular proteins. Statistics of incidence and a role of sequence]

Regions of left-handed polyproline II type conformation in globular proteins were studied throughout the PDB bank. The length and sequence of corresponding fragments were analyzed. It was found that a lot of tetrapeptides (from combinatorial possible ones) show the tendency to be included in the left-handed helices. Much more tetrapeptides do not occur in this structure type.     

Selection and physiological study of culture of Bacillus circulans-- producer of butirosin]

For isolating a highly active variant of the butirosin-producing culture, a strain forming trace amounts of the antibiotic substance was used. Exposure to nitrosomethylbiuret and nitrosoguanidine and the use of selective media containing streptomycin and butirosin resulted in a 30-fold increase in the strain productivity. Thin layer chromatography of the produced antibiotic substance in the solvent system developed by the authors, mass spectrometry and assay of the antimicrobial spectrum in regard to ++gram-positive and ++gram-negative bacteria by using the known aminoglycosidine-inactivating enzymes revealed that the substance was identical to butirosin. Along with the major product, the fermentation broth contained up to 5 per cent of ribostamycin.     

Formation of the left-handed helix during simultaneous treatment of poly[d(GC)] with bis-netropsin and Zn(II) ions

It has been found that the effect of AT-specific ligand and Zn2+ on GC-alternating polymer brings about transfer of the latter into Z-conformation.     

Distribution of amino acid residues in the primary protein structure

The amino acid composition and sequence in primary structure of 180 proteins have been studied. It is shown that the distribution of amino acid residues is near to a random one, i.e. it is determined by the amino acid composition. The ratio between statistical and unique character of protein primary structures has been discussed. The amino acid sequence is suggested to be unique in fibrous proteins. In contrast the amino acid sequence in globular proteins is a statistical one. The statistical character of amino acids distribution in globular proteins explains the possibility of sensible text generation under the frame shift mutations, deletions and insertions.     

Acridine orange inhibition of the ATPase activity of myosin and its fragments

The cation dye acridine orange (AO) was shown to inhibit ATPase activity of myosin, DTNB-myosin and heavy meromyosin and not to influence that of EDTA-S-1 at low ionic force. The inhibiting effect is concerned with the presence of KCl in solution. The allosteric influence of AO on myosin ATPase activity is discussed and dependence of this effect on charge distribution on the surface of the protein molecule is considered.     

Photosensitizing effect of 8-methoxypsoralen on bacteriophage cd

Mutagenesis in extracellular phage sd by 8-metoxypsoralen (8-MOP) and longwave (lambda greater than 310 nm) UV-irradiation has been established. The kinetics of lethal and mutagenic effects of 8-MOP+light was studied. The efficiency of mutagenesis on the first linear part of mutation curve was 0.3% per the lethal hit which is 2 times lower than that of shortwave (lambda=254 nm) UV-irradiation. The maximum yield of mutants makes up 1%, after which the mutation curve is maintained. It has been established that the main (may be the only) contribution into mutagenesis is made by monoadducts, whereas the lethal effect is conditioned by diadducts (cross-links). The comparison of the efficiency of mutagenic effects of 8-MOP+light with mutagenic effects of other kinds of irradiations was carried out. The possibility of repair of damaged 8-MOP+light phage sd DNA by transfection of Escherichia coli C (uvr+) and Cs (uvr-) lysozyme spheroplasts has been established. The repair mechanism of photodamage in intact phage sd induced with 8-MOP+light was also investigated using the method of two-step irradiation. It has been shown that 65% of photodamages are repaired in E. coli SK cells in the M9 medium, i. e. under cellular metabolism. The recovery of phage sd is completely inhibited in phosphate buffer. Unlike chloramphenicol (150 microgram/ml), 1% caffeine blocks the phage recovery only by 30%. The participation of phage sd determining enzymes in its intracellular recovery from 8-MOP+light damages is assumed.     

Long-distance interactions and principles of molecular recognition at various biosystem organization levels

Efficient molecular recognition, in which recognition processes are occurring much faster than it takes to test variants, is only possible when long-distance recognition occurs together with contact interactions. The distance between interacting molecules should be sufficiently long to prevent hindrances to the search and, on the other hand, sufficiently short to provide selectivity. It was demonstrated that both of these two requirements can be satisfied simultaneously for biological macromolecules that include helical segments. Because the “diameters” of helical molecules are far shorter than their lengths, the intermolecular distance can be far greater than the diameters, thus allowing a free search. The distance can be far shorter than the lengths at the same time, thus providing selectivity. Analytical procedures were developed to estimate the parameters for protein–protein and protein–nucleic acid recognition. The coincidence of the charge-distribution periods in helical segments was found to substantially increase their interaction potential, and the reduction scale characteristic of the potential was shown to depend on the numerical value of the coinciding period.     

Two-H-bonded and one-H-bonded structure alternations in collagen

This paper concerns the conformational variability of collagen as related to the concrete tripeptides (GXY)n constituting its primary structure. The previously elaborated model (V.G.Tumanyan, N.G.Esipova, Biophysics 28, 1021-1025, 1983) with two nets of hydrogen bonds is useful for tripeptides where X is an amino acid. If X is an imino acid, the common one-bonded Rich & Crick model is valid. In this work, compound sequences including tripeptides of different types are considered. Molecular mechanics is used to assess the conformations of the junction regions when a structure with two nets of hydrogen bonds precedes the structure with one net, and vice versa. Thus, all types of sequences typical for natural collagen are covered. It is shown that the combined model representing an alternation of the two-H-bonded model and the one-H-bonded Rich & Crick model is satisfactory stereochemically, and provides more favorable energy in comparison with the continuous one-H-bonded model. Besides, a more favorable hydration of the molecule occures in this case. Some conclusions are made about interchain and intrachain ionic bonds. Thus, it is deduced for the concrete fibrillar protein how a one-dimensional structure determines three-dimensional structure. The macromolecular structure thus suggested is in accord with the experimental data on hydrogen exchange.     

On some properties of spectral portraits of nucleotide sequences, computed my a matrix Fourier analysis method

The quantitative characteristics of a spectral portrait of the nucleotide sequence of E. coli oriC were determined by the method of matrix Fourier analysis.