Local Conformational Changes of Proteins in DNA Interfaces

Abstract

DNA-protein interaction plays a key role in many cellular functions such as transcription, replication, recombination and DNA packaging. Understanding the mechanisms by which the protein recognizes specific DNA sequences is one of the main topics in biology. With increased amount of crystal structures, conformational changes of proteins in DNA interfaces are suggested to be one of important factors in DNA recognition. To better understand a role of the deformation of the proteins, we carried out quantitative analyses of local conformational changes observed in DNA interfaces.We first extracted crystal structures of DNA-unbound and DNA-bound states from PDB. We then described the backbone structures with the 7-letters-codes which were pre-defined for expressing conformations of 4 consecutive fragments. Using the letter codes, we identified conformational changes between DNA-unbound and bound states.Then, we compared the amino acid composition and secondary structures of these conformationally variable regions in DNA interfaces with that in molecular surfaces. We found the regions in DNA interfaces tend to be more hydrophobic, less acidic residues, and have less secondary structure elements. We also found that conformations of the regions that bind to DNA in the minor groove are frequently changed and the width of the minor grooves is wider than that of the canonical B-DNA.