Theoretical studies on the interaction of proteins and nucleic acids. I. The binding of beta-pleated sheets to A- and B-DNA.
A theoretical investigation of the interaction between a beta-ribbon consisting of two glycine hexapeptides and DNA in its A and B conformations is presented. A refined semi-empirical energy formula and a sophisticated energy minimization technique are used to optimize the complex, taking into account the DNA-beta-ribbon interaction, the full flexibility of the oligopeptide chains and of the positions of the DNA screening counterions. A considerable flexibility of the beta-ribbon is demonstrated, which allows the polypeptide fragment to interact comfortably with both forms of DNA considered and with different base-pair sequences. The results are discussed in connection with the general problem of DNA-protein recognition.
K
K
Zakrzewska
B
B
Pullman
D004247:DNA; D007700:Kinetics; D008954:Models, Biological; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009842:Oligopeptides; D011485:Protein Binding; D011487:Protein Conformation; D013816:Thermodynamics
D009842:Oligopeptides; D004247:DNA