In Search of Common Principles of Specific Binding Residues in Protein-Nucleic Acid Complexes

摘要

Specific interactions between proteins and nucleic acids are fundamental to many biological processes. All the protein-nucleic acid complex structures have been collected and then analyzed for further understanding the mechanisms controlling their specific recognition using classical statistical methods. The results show that the amount of specific binding residues presents significant differences among different functional nucleic acid-binding proteins, maybe indicating that the amount is closely related with whether there is a need for proteins with a firm grasping nucleic acid molecules or not. Moreover, Arg is the most popular amino acid as specific binding residues both in protein-DNA interaction and in protein-RNA interaction, and propensities of specific binding residues present similar when their recognizing the minor grooves VS when their recognizing the major grooves of DNA helixes, and also similar when their recognizing the single-stranded RNAs versus when their recognizing the double-stranded RNAs. In addition, the size and orientation of the polarity of amino acids play important roles in determining their potential of specific recognizing nucleic acids. Finally, it is similar for propensities of specific binding residues with spatial cooperative interactions between protein-DNA interactions and protein-RNA interactions.