A theoretical study on the structure and stability of the nucleohistone complex. I. The interaction between the polypeptide backbone and single- and double-stranded B-DNA helices

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Abstract
The interaction energies between periodic single- and double-stranded DNA models, using the structural parameters of B-DNA, and polyglycine in various conformations are calculated with the help of the mutually consistent field method together with perturbation theoretical expressions. For the repeating units of DNA the four nucleotide bases adenine, guanine, thymine, and cytosine, the nucleotides adenylic acid and thymidine are chosen. The polypeptide component is represented by polyglycine assuming the fully extended β-pleated sheet and the α-helical conformations. In addition, several polyglycine helices are investigated, whose helix axes coincide with the one of DNA and whose turn lengths are a fraction, equal or a multiple of the length of a complete winding of B-DNA. For all DNA–polyglycine complexes, the structure is optimized with respect to the total energy of the combined system. It turns out that the complex, in which the agreement between the helical symmetry of B-DNA and polyglycine is realized, represents the most stable configuration. The results are discussed in the light of further improvements.