Comparative computational insights into tandem and non-tandem repeats in protein-DNA complexes.
TL;DR
An in-depth analysis of tandem and non-tandem repeats observed in a non-redundant set of 378 protein-DNA complexes archived in the Protein Data Bank reveals that the former is shorter, exhibit reduced variability and facilitate structural conservation.
Abstract
Proteins and DNA interact with each other to carry out various cellular functions. Internal repeats in proteins provides a structural and functional role in establishing these connections. This study offers an in-depth analysis of tandem and non-tandem repeats observed in a non-redundant set of 378 protein-DNA complexes archived in the Protein Data Bank (PDB). The RADAR server was employed to locate these repeats. The role of internal repeats in the structure and function of these proteins were analyzed using PDBsum. Examining the tandem and non-tandem repeats, reveal that the former is shorter, exhibit reduced variability and facilitate structural conservation. In contrast, the latter are more scattered and support many activities, including DNA binding and metal interaction. The root mean square deviation analysis of the observed tandem and non-tandem repeats shows the extent of structural conservation and divergence. Further secondary-structure analysis of the repeat regions were also carried out. Illustrations derived from PDB data demonstrate the distinct interactions of non-tandem and tandem repeats with DNA. The significance of repeat structures in DNA recognition is highlighted.