Nucleic Acids Research Advance Access originally published online on September 18, 2008
Nucleic Acids Research 2008 36(18):5922-5932; doi:10.1093/nar/gkn573
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Nucleic Acids Research, 2008, Vol. 36, No. 18 5922-5932
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Structural Biology |
Protein–DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins
1National Institute of Biomedical Innovation, 7-6-8, Saito-asagi, Ibaraki, Osaka 567-0085, 2Graduate School of Frontier Biosciences, Osaka University, Japan, 3Koc University, Center for Computational Biology and Bioinformatics, College of Engineering, Rumeli Feneri Yolu, Sariyer, 34450, Turkey, 4Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka, 820-8502, Japan, 5Center for Cancer Research Nanobiology Program, SAIC, NCI-Frederick, MD, USA and 6Department of Human Genetics and Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Israel
*To whom correspondence should be addressed. Tel: +81 948 29 7811; Fax: +81 948 29 7841; Email: sarai{at}bio.kyutech.ac.jp
Received May 16, 2008. Revised August 4, 2008. Accepted August 25, 2008.
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 about half of the observed conserved residue clusters are in the interface with the DNA, which could be identified from their amino acid composition; whereas the remaining clusters are at the protein–protein or protein–ligand interface, or embedded in the structural scaffolds. In protein–protein interfaces, conserved residues are highly correlated with experimental residue hotspots, contributing dominantly and often cooperatively to the stability of protein–protein complexes. Overall, the conservation patterns of the stabilizing residues in DNA-binding proteins also highlight the significance of clustering as compared to single residue conservation.