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Biomedical subjects

N G Esipova

Publications and source records attributed to N G Esipova.

At least 19 recordsLinked to original sources
PubMed1995

Mechanism of Lac repressor switch-off: orientation of the Lac repressor DNA-binding domain is reversed upon inducer binding.

Lac repressor's DNA-binding domains contain helix-turn-helix motif which, though similar to those of phage lambda Cro protein, are oriented differently with respect to DNA: in the specific complexes with Lac operator, N termini of the repressor's subunits are facing inwards. We demonstrate that, in the presence of an inducer, the repressor's N termini cross-link to the operator's outermost nucleotides. We suggest that the inducer fixes the repressor's DNA-binding domains in the Cro-type configuration and thus garbles its recognition surface. Since the Cro-type configuration is perfectly suitable for binding the DNA, this also explains how the switched-off repressor retains its non-specific DNA-binding.

Amino Acid Sequence↗
PubMed1995

The third nucleotide of the Gly coding triplet remembers the periodicity of the collagen chain.

Collagen is a fibrous protein with a primary structure with complex periodical features. We show using symbolic Fourier transform of the collagen cDNA sequence that basic periodical patterns appear there also. Strikingly they are present in the third position of triplets encoding Gly, which occupies each third position in the sequence of the protein, and to which selection on the protein level does not applied. Thus, the gene of collagen seems to appear due to pra-gene multiplication.

Codon↗
PubMed1995

Heat denaturation of pepsinogen in a water-ethanol mixture.

The effect of ethanol and pH on thermodynamic parameters and cooperativity of pepsinogen heat denaturation was studied by scanning microcalorimetry. Addition of 20% ethanol decreases the protein denaturation temperature by 10.7 degrees C at pH 6.4 and 15.8 degrees C at pH 8.0. It also decreases the denaturation heat capacity increment from 5.8 to 4.2 kcal/K.mol. The dependences of calorimetric denaturation enthalpy on denaturation temperature both in water and 20% ethanol are linear and intersect at about 95 degrees C. In 20% ethanol the pH shift from 5.9 to 8.0 results in a decreased number of cooperative domains in pepsinogen. This process causes no changes either in the secondary structure or in the local surroundings of aromatic amino acids. It is concluded that ethanol addition does not affect the cooperativity of pepsinogen denaturation substantially until the pH change provokes redistribution of charges in the protein molecule.

Calorimetry, Differential Scanning↗
PubMed1993

Scanning microcalorimetry and circular dichroism study of melting of the natural polypeptides in the left-handed helical conformation.

It has been shown that in aqueous solution histone H1 and H5 C-terminal fragments and peptide hormones beta-endorphin and ACTH adopt preferably the left-handed helical conformation of the poly-L-proline II type. Scanning microcalorimetry and circular dichroism have been used to show that the linear temperature dependence of CD maximum amplitude and partial heat capacity value are broken in the temperature interval between 50 and 60 degrees C, after which [C]p reaches the constant level. It was proposed to be due to noncooperative disordering of the conformation caused by the destruction of the polypeptide hydration shell.

Adrenocorticotropic Hormone↗
PubMed1992

Natural polypeptides in left-handed helical conformation. A circular dichroism study of the linker histones' C-terminal fragments and beta-endorphin.

Circular dichroism has been used to investigate the histone H1 and H5 C-terminal fragments and beta-endorphin conformation. It has been shown that in aqueous solution these polypeptides preferably adopt the left-handed helical conformation of the poly-L-proline II type. A break in the linear temperature dependence of the CD value was found in the temperature interval between 50 and 55 degrees C. It was proposed to be due to non-cooperative disordering of the conformation caused by the destruction of the hydration shell.

Animals↗
PubMed1991

The number of cooperative regions (energetic domains) in a pepsin molecule depends on the pH of the medium.

The technique of scanning microcalorimetry was used to study the effect exerted by ethanol and by the pH of the medium on the number and size of cooperative regions in a pepsin molecule. Ethanol addition lowered the temperature of protein denaturation, but did not change the number of energetic domains. The number of thermodynamic cooperative units (determined as a delta Hcal to delta Heff ratio) was reduced from four to two when the pH changed from 6.7 to 2.0. As was demonstrated using the CD technique, this process involved no changes either in the secondary structure or in the local surroundings of aromatic amino acids. Therefore, variations in the cooperative properties of a pepsin globule at different pH values are associated with the electrostatic interactions of individual parts of the molecule.

Animals↗
PubMed1987

Third type of secondary structure: noncooperative mobile conformation. Protein Data Bank analysis.

Analysis of 68 proteins from Protein Data Bank disclosed a new widely spread type of the secondary structure that is designated as mobile (M-) conformation. Helical parameters of M-conformation are close to the poly-L-proline II type helix. Its occurrence in globular proteins approximates that of the beta-sheet. The angles corresponding to the position of the M-conformation maximum in distribution of amino acid residues on a conformational map are phi: -65 degrees, psi: 140 degrees. Unique features and high occurrence in proteins make it possible to distinguish the M-conformation as an independent third type of the secondary structure in globular proteins, that should be included in the present classification.

Amino Acids↗
PubMed1987

Approaching a complete classification of protein secondary structure.

A complete classification of types of the protein secondary structure is developed on the basis of computer analysis of the crystallographic structural data deposited in the protein Data Bank. The majority of amino acid residues fall into five conformation types. A conclusion is drawn that the number of sequence variants of torsion angles phi, psi in globular proteins is limited and is essentially less than the number of possible amino acid sequences for this chain length. Along with alpha-helix and beta-structure, the distribution analysis assigning every maximum of distribution of amino acid conformations on Ramachandran map to a certain type of the secondary structure exposed a third type of the secondary structure that was previously neglected. This type of the structure is extended left-handed helical conformation, designated as mobile (M-) conformation. A full set of M-conformation fragments that seems to play a major role in protein globule dynamics has been obtained, a small radius of correlation for the polypeptide chain in M-conformation is demonstrated. It explains a prevalence of short segments of mobile conformation revealed in globular proteins. For secondary structure types, the frequency of occurrence of amino acid residues has been computed.

Amino Acids↗
PubMed1987

Distribution of charges in Bacillus intermedius 7P ribonuclease determines the number of cooperatively melting regions of the globule.

A correlation between the distribution of charged side groups in the globule of Bacillus intermedius 7P ribonuclease (binase) and the process of heat denaturation was studied at different pH values in order to estimate a relation between charge distribution in globular proteins and the character of cooperative thermodynamic transitions. As was shown by comparing the results of scanning microcalorimetric analysis of heat denaturation with the three-dimensional structure of binase, at optimal pH the molecule exists as a single cooperative system stabilized by hydrogen bonds, Van der Waals' contacts, and electrostatic interactions like salt bridges. At pH lower than 4.0 (below the physiological optimum) the cooperativity type of the system was found to change due to a reversible cooperative transition in the ternary structure of the protein globule. It has been concluded that the molecular architecture and the arrangement of atoms do not change considerably in different environments; thus the thermodynamic properties of the globule vary due to the alteration of charge distribution and the consequent changes in the size and number of cooperative regions of the globule. Thus, structural and energetic domains may be non-coincident in proteins.

Bacillus↗
PubMed1984

[Two types of tripeptide conformation in collagen. Calculation of the structure of (Gly-Pro-Ser)n and (Gly-Val-Hyp)n polytripeptides].

Conformational analysis of polypeptides (Gly-Pro-Ser)n and (Gly-Val-Hyp)n was carried out for collagen-like triple helical complexes (coiled coils with screw symmetry). The lowest energy structure of the first polymer (helical parameters t 52,8, h 0,282 nm) is very close to that of (Gly-Pro-Hyp)n. The hydroxyl group of a serine residue does not form any intramolecular hydrogen bonds in this structure. (Gly-Val-Hyp)n triple complex is shown to unwind to t 7,7, h 0,297 nm as a result of optimization procedure. These findings confirm the assumption, made earlier on the basis of conformational analysis of (Gly-Pro-Hyp)n, (Gly-Pro-Ala)n, (Gly-Ala-Hyp)n, (Gly-Ala-Ala)n, that the collagen triple helix contains stable wound triplets with proline in the second position, while the absence of imino acid in the 2nd position facilitates the unwinding of the triple helix. Thus, a collagen helix appears to have different parameters for the sites differing in the amino acid sequence. The values measured in the X-ray experiments (h 0,29 nm, t' 36) should be considered as a result of averaging. The model allows to reconcile the X-ray data for collagen and crystalline (Gly-Pro-Pro)10 oligomer.

Collagen↗
PubMed1976

Microcalorimetry of thermal denaturation of pepsin and trypsin in the crystal state.

Heating of pepsin and trypsin crystals was studied by scanning microcalorimetry. A sharp decrease in temperature, halfwidth and heat of transition with a decrease in heating rate was discovered. It was shown that thermal transition is connected only with the denaturation of protein molecules in the crystal and not accompanied by the crystal disintegration into separate molecules.

Calorimetry↗