Search PubMed⌕ Search

Biomedical subjects

V G Tumanian

Publications and source records attributed to V G Tumanian.

At least 19 recordsLinked to original sources
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↗
PubMed1983

[Two possible conformations of the repetitive site of the immunoglobulin G3 hinge region].

Conformational analysis of immunoglobulin G3 (IgG3) hinge region repeating part was performed. In approximation of backbone regular conformations for the case of C2 symmetry (the symmetry axis is perpendicular to S-S bridges and passes through their midpoint) on the basis of total analysis of ring geometry possibilities and estimation of steric conditions, the existence of two conformations with n = 3 (3(10) helix type and polyproline II type) was inferred. A possible role of these conformations in the immunoglobulin functioning was discussed.

Amino Acid Sequence↗
PubMedDate not supplied

[A code governing specific binding of regulatory proteins to DNA and structure of stereospecific sites of regulatory proteins].

A model is proposed for the structure of stereospecific sites in regulatory proteins. On its basis a possible code is suggested that governs the binding of regulatory proteins at specific control sites on DNA. Stereospecific sites of regulatory proteins are assumed to contain pairs of antiparallel polypeptide chain segments which form a right-hand twisted antiparallel beta-sheet, with single-stranded regions at the ends of the beta-structure. The model predicts that binding reaction between a regulatory protein and double-helical DNA is a cooperative phenomenon and is accompanied by significant structural alteration at the stereospecific site of the protein. Half of hydrogen bonds normally existing in beta-structure are broken upon complex formation with DNA and a new set of hydrogen bonds is formed between polypeptide amide groups and DNA base pairs. In a stereospecific site, one chain (t-chain) is attached through hydrogen bonds to the carbonyl oxygens of pyramides and N3 adenines lying in one DNA strand, while the second polypeptide chain (g chain) is hydrogen bonded to the 2-amino groups of guanine residues lying in the opposite DNA strand. The amide groups serve as specific reaction sites being hydrogen bond acceptors in g-chain and hydrogen bond donors in t-chain. The single-stranded portions of t- and g-chains lying in neighbouring subunits of regulatory protein interact with each other forming deformed beta-sheets. The recognition of regulatory sequences by proteins is based on the structural complementarity between stereospecific sites of regulatory proteins and base pairs sequences at the control sites. An essential feature of these sequences is the asymmetrical distribution of guanine residues between the two DNA strands. The code predicts that there are six fundamental amino acid residues (serine, threonine, asparagine, histidine, glutamine and cysteine) whose sequence in stereospecific site determines the base pair sequence to which a given regulatory protein would bind preferentially. The code states a correspondence between four amino acid residues at the stereospecific site of regulatory protein with the two residues being in t- and g-segments, respectively, and AT(GC) base pair at the control site. It is thus possible to determine which amino acid residues in the repressor and which base pairs in the operator DNA are involved in specific interactions with each other, as exemplified by lac repressor binding to lac operator.

Amino Acid Sequence↗
PubMedDate not supplied

[A new method of global search for functional DNA segments using a fractal representation of nucleotide texts].

New global method for computer prediction of functional sites in nucleotide sequences, based on the fractal representation, is presented. Fractal representation of set of sequences (FRS) provides simple way for generating recognitions matrix of functionally similar sequences and simple estimations of its efficiency for searching homologous regions in new sequences. Other advantages of the method are absence of the necessity of sequences alignment during generating based set and searching new homologous regions and small CPU time. Usage of the method illustrated for searching globin and histone genes, for ALU repeats in human genome and long terminal repeats in virus genome.

Computer Simulation↗
PubMedDate not supplied

[Conformation of a triple collagen spiral as a function of primary structure].

It has been shown by the method of conformational analysis that conformation of the polypeptide chain of a collagen molecule varies from one type of sequence to another, but in all the sequences the only two types of conformations can be characterized by minimal conformational energy. The collagen molecule as a whole is a combination of the single-bond Rich and Crick model and new double-bonded structure. Rigorous comparison with "thick" conformations obtained by Scheraga and coworkers was undertaken using precise calculations with flexible proline.

Amino Acid Sequence↗
PubMedDate not supplied

[A new approach to the thermodynamic role of imino acids in collagen. Solution of a thermodynamic paradox].

The dependence of denaturation transition thermodynamic parameters in various collagens from imino acid compositions has been analysed. Computational and experimental data suggest independence of the collagen molecule hydration on imino acid composition and sequence in the polypeptide chain. The continuous net of hydrogen bonds is interrupted, if imino acid residues occur in the sequence of amino acid residues, as follows from Monte Carlo computations, because the hydrogen of NH-group plays sufficient role in water shell formation for this conformation. As a consequence, entropy of denatured collagen-water system increases hand by hand with increasing imino acid content and therefore delta S increases. The increase of enthalpy of transition from imino acid content is determined by favorable Van der Waals interactions of pyrrolidine rings in native triple helical collagen structure. It was pointed out that proline role is determined by decreasing hydration in the single stranded polypeptide chain in Polyproline II conformation that leads to an increase of entropy of the polypeptide-water system. Thus, the collagen structure formation by imino acids is promoted in the water media due to single chain left-helical conformation being unfavorable for proline residues as well as due to the enthalpy nature of the triple helix stabilization.

Collagen↗
PubMedDate not supplied

[Transitions of the left poly-L-proline II helix-right alpha helix type in the regions of myosin subfragment S2 of cross-striated muscle as a possible conformational basis for a mechanical-chemical act].

Local conformational states of fibrous fragments of myosin molecules from striated muscle have been studied. Analysis of the amino acid sequences of the rat embryonic skeletal muscle myosin heavy chain and the nematode myosin heavy chain have been performed with the aim to estimate the influence of electrostatic interactions on secondary structure stability of these fragments. The heterogeneity of stability of alpha-helical conformation along the fibrous fragment have been found on the basis of estimation of interaction between side group charges and between side group charges and main chain charges. Periodically located short sections have been found in the N-terminal half of the myosin rod where clusters of Asp and Glu destabilize alpha-helical structure being ionized. Changes of the distribution of charges near the latter sections bring about conformational transitions from left-handed polyproline II helix to right alpha-helix or vice versa. The new scheme of orientation of fibrous part of the cross-bridge in relation to the thick filament for various stages of muscle contraction process suggests asynchronous character of transitions in the different sites. It may be proposed that existence of alteration left- and right-helical fragments in N-terminal half of fibrous part of heavy myosin chain determines zigzag form of this part of myosin molecule in resting muscle. A model of the cross-bridge movement in the course of ATP hydrolysis has been suggested.

Adenosine Triphosphate↗
PubMedDate not supplied

[Structure of the hydration envelope of the B-form of polydeoxyribonucleotides poly(dA-dC).poly(dG-dT) and poly(dA-dG).poly(dTs-dT) from the data of Monte-Carlo simulation].

The results of a Monte Carlo simulation of the hydration shell of two polynucleotides poly (dA-dC).poly(dG-dT) and poly(dA-dG).poly(dC-dT) are reported. This study is a part of a series of Monte Carlo computations of the hydration of regular polydeoxyribonucleotides with dinucleotide repeat aimed at looking for dependences of hydration shell structure on base sequence. The coordinates of the main local maximal of water density near the polymers and the topology of the most probable one- and two-membered water bridges are published. For most of the sequences a common primary hydration of base edges of successive base pairs is characteristic. The AT-homopolymeric sequence represents an exception with autonomous primary hydration of a base pair in both grooves, which correlates with the sequence-dependent flexibility and the occurrence of bends of DNA.

Models, Molecular↗
PubMedDate not supplied

[A new type of secondary structure: mobile conformation of polypeptide chain. Data bank for protein structures].

As a result of statistical analysis of Protein Data Bank a new type of secondary structure was found in globular proteins. It is mobile (M) conformation, characterised by noncooperative hydration and the increased dynamical properties of the chain. Percentage distribution of amino acid residues between the main secondary structure types is 42.7% for alpha-helix, 19.6% for beta-structure and 19.1% for M-conformation. The most frequently occurring amino acids for M-conformation are proline, cysteine and serine. Fragments of mobile conformation seem to play a major part in local and domain dynamics of protein globule.

Amino Acid Sequence↗
PubMedDate not supplied

[Classical and non-classical DNA conformations].

All possible right and left double helical structures which may exist in short fragments as well in polymeric DNA have been obtained on the basis of a developed rigorous and accurate method of conformational analysis of DNA. In polymeric DNA only right regular double helices are possible with preference of B-form that is the main biological form of DNA. In contrast, for short fragments the left and right helices have practically the same energies providing some physical ground for side-by-side form, which biologically is possible as a recombination form and maybe as a replication form.

DNA↗