Protein-DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins.

ABSTRACT: Amino acid residues, which play important roles in protein function, are often conserved. Here, we analyze thermodynamic and structural data of protein-DNA interactions to explore a relationship between free energy, sequence conservation and structural cooperativity. We observe that the most stabilizing residues or putative hotspots are those which occur as clusters of conserved residues. The higher packing density of the clusters and available experimental thermodynamic data of mutations suggest cooperativity between conserved residues in the clusters. Conserved singlets contribute to the stability of protein-DNA complexes to a lesser extent. We also analyze structural features of conserved residues and their clusters and examine their role in identifying DNA-binding sites. We show that a

SUBMITTER: Ahmad S 

PROVIDER: S-EPMC2566867 | biostudies-literature | 2008 Oct

REPOSITORIES: biostudies-literature