PNNL

Abstract

The binding of proteins to DNA plays an important role in the regulation and control of gene expression. Hydrogen bonds between the hydrophilic side chain of a peptide or an amino acid and DNA are among the most important interactions in nature as they are responsible for high specificity of protein binding [ ]. Therefore, basic knowledge concerning the interactions between the building blocks of proteins and DNA ? amino acids and nucleic acid bases - is of great interest. Although these systems are definitely simpler than real biochemical targets, quantitative information regarding the interactions between amino acid ? nucleobase pairs can, in principle, be used to generate high quality potentials, which can be applied in modeling of macromolecules