Using quantum chemistry CNDO/2 method the mechanism of reaction of polysaccharides with lysozyme was investigated. The molecule of acetal (H3C-O-CH2-O-CH3) was taken as the simplest substrate model. In the framework of the simple model the influence of interaction of the substrate with Glu-35 and Asp-52 on activation of the substrate is described. It is essential that for the maximum activation of the bond broken the optimum (but not the most energetically advantageous) arrangement of Glu-35 should be realized. The optimum arrangement of the amino acid residues of the enzyme should also be realized for the liberation of the groups which took part in the reaction, only one degree of freedom being actual in this process, and the motion of the system occurs along this degree of freedom. It was shown that substrate distortion could cause its activation.

Acetals↗

PubMedDate not supplied

[Stability of the alpha-helix structure of oligopeptides].

The problem of stabilization of oligopeptide alpha-helix conformation is discussed. The stabilizing role of intramolecular H-bonds and coulombic interactions for single molecules was shown. The influence of media results in the competition for formation of inter and intramolecular H-bonds and for coulombic interactions. High competitive media, eg. water, diminishes alpha-helix stability.

Electricity↗

PubMedDate not supplied

[The role of Hpi-hydrogen bonds in the stabilization of spiral structures of oligopeptides].

Different possibilities of H-bonds formation for formamide-water complexes and dimers of formamide were studied. Potential energy maps were calculated for di-, tri- and tetrapeptides. The maps provide necessary data to explain the relative stability of different oligopeptide conformers and Ramachandran maps for peptides.

Hydrogen Bonding↗

PubMedDate not supplied

[Interfragmental interaction in peptide molecules].

Orbital and Coulomb terms in total energy of the molecule may be estimated with the use of parameters, that were calculated from experimental or estimated data for the test molecules. It has been demonstrated how the parameters for calculating the barriers of internal rotation in ethane-like molecules and amides may be selected. These parameters were used for studying the interactions between two peptide groups in 2-formamideacetamide--the primitive model of peptide.

Amides↗