A simple method for the calculation of low energy packings of alpha-helices--a threshold approximation. I. The use of the method to estimate the effects of amino acid substitutions, deletions and insertions in globins

A simple method is developed for computing low energy packings in alpha-helical proteins. This method is based on a simplified representation of a protein molecule in which the backbone of the alpha-helix is represented by a cylinder and the side chains of the amino acids by hard spheres. The energy function includes hydrophobic, electrostatic and Van der Waals' interactions. This method is used to compute low energy packings of an assembly of the alpha-helices of a globin molecule. The effect of mutations, deletions and insertions of a single amino acid resulting in drastic distortion of the spatial structure of sperm whale myoglobin was studied. The results demonstrated that these events can produce a breakdown of the spatial structure of the protein molecule.

The template RNAs of RNA polymerases can have compact secondary structure, formed by long double helices with partial violations of the complementarity

A new method of contextual analysis was used to search the long non-random inverted repeats and the complementary palindromes in the genes of E. coli and T7 RNA polymerases. These genes were found to contain from 25% to 50% of all the nucleotides involved in such helices. The 5' -and 3' -ends of mRNA can be protected by neighbouring double helices from the nuclease attack. Some double helices are competing and very similar to the attenuator of E. coli trp-operon.

The effects of mutations, deletions and insertions of single amino acids on the three-dimensional structure of globins

Using the method of calculation of low energy packings of alpha-helices, we studied the effects of mutations, deletions and insertions of amino acids on the structure of sperm whale myoglobin. It was found that these events can cause complete breakdown of this structure.

[Recurrent relationship for the characteristic polynom of a system of enzymatic catalysis of nonbranched monomolecular reactions]

A new mode is proposed to represent the characteristics equation for the system of monomolecular reaction on the basis of directed graphs method. A characteristic equation can be represented as a sum of weights of spanning trees derived from some graph which is connected with the initial graph of reaction. The recurrent relationship for the characteristic polynom of the system of nonbranched monomolecular reaction was obtained on the basis of this representation. A new proof on the matrix theorem about trees formulated by Volkenstein and Goldstein was established.

[Presence of a renin inhibitor in the plasma of intact dogs]

The authors elaborated a method of determination of the plasma renin inhibitor based on the statement that with successive dilution of the plasma the velocity of the renin + substrate reaction in the presence of an inhibitor fell more slowly than the extent of dilution, and, on the contrary, in the plasma without any inhibitor the rate of the reaction decreased more than the value of the plasma dilution. This statement follows from the equations of the reaction suggested by Dixon and Webb (1966). With the aid of this method the presence of the renin inhibitor in the plasma was found in 8 of 19 intact dogs examined.