Almost all biological pathways depend on the expression and regulation of proteins and their interaction with DNA is a major biochemical event controlling these processes (e.g., Refs.  and ). Protein-DNA interactions are often accompanied by a change in the conformation of one or both the partners to carry out the required function. Although conformational changes can also occur in response to environmental perturbations such as site-specific chemical modifications (e.g., phosphorylation and methylation) or varying pH and temperature levels, the events of binding interactions resulting in the formation of complexes between protein–protein, protein–ligand, and protein–DNA are of particular interest. Protein conformational changes in systems such as protein–protein and protein–ligand complexes have been the subject of extensive investigation owing to their implications in docking and drug design.[3-5] Some of these studies are aimed at understanding signaling and energy propagation through conformational changes,[6, 7] whereas others have investigated molecular recognition mechanisms from this perspective. Several models describing recognition mechanisms underlying conformational changes have been postulated,[9, 10] of which “conformational selection” has been described as the main driver of conformational changes.[3-5] Using the conformational selection model, intrinsic flexibility, and dynamics of the unbound protein, some studies have also attempted to model/predict the conformational change expected on complex formation.
While these studies have greatly enhanced our understanding of the conformational changes accompanying protein–protein/protein–ligand interactions, it is not immediately clear whether the observations made from these systems can be extrapolated to the protein–DNA system. Protein–DNA interactions are unique in terms of their target specificity, the dominant electrostatic nature of the interface and the ability of proteins to find specific sites on a much larger DNA molecule. To gain insights into the nature of protein-DNA interactions in their entirety, it therefore becomes essential to understand the conformational changes in the interacting entities viz. proteins and DNA brought about by complex formation. DNA conformational changes are well documented and widely discussed,[11-17] as the only requirement for such an analysis is the availability of protein-bound DNA-structure; the unbound structure can be assumed to be similar to a standard canonical form such as B-DNA to a fair degree of approximation. However, the protein side of the story is far more complex owing to their structural diversity, necessitating each individual unbound structure to be solved explicitly. Unfortunately, only a limited number of DNA-binding proteins have been crystallized in both the unbound and DNA-bound forms, imposing a limitation in describing and understanding the basic principles underlying the recognition and subsequent interaction by them, even when the final complex is already known. Availability of fewer pairs of structures has resulted in equally small number of analyses of conformational changes in DNA-binding proteins. Among the few relevant studies on the subject is one carried out on a small data set of 24 proteins, including 8 disordered structures, as part of an overall analysis of structural features of protein-nucleic acid complexes. Since this study focused on general structural features of protein-DNA complexes, it did not provide a detailed understanding of the conformational changes. More recently, a protein-DNA docking benchmark was reported, in which the authors compiled a dataset of 47 free/bound structure pairs of DNA-binding proteins and mainly analyzed their conformational changes with the sole purpose of establishing basic standards for modeling protein-DNA complexes through docking. Hence this study focused on docking-related issues without carrying out a detailed analysis of conformational changes and their role in biological function. Apart from these, conformational changes in DNA-binding proteins have often been analyzed in greater details in the original papers reporting the three-dimensional structure of complexes or in reviews of the recognition mechanisms of a specific family of proteins such as endonucleases and polymerases.[20-22]
In this work, we address three issues of conformational changes in DNA-binding proteins: (a) types of conformational changes, their distribution among proteins of different functions and their relationships with physicochemical features of proteins such as charges and dipole moments, (b) the role of intrinsic flexibility of the unbound protein in inducing conformational changes and (c) contributions of conformational changes to the stability and specificity of protein-DNA recognition. For this purpose, we created a dataset of unbound and DNA-bound pairs of protein structures, manually examined each of them by superimposing their bound and unbound variants and studied the nature of conformational changes observed in them. We classified the conformational changes into six types and related them to various functional classes of DNA-binding proteins. Subsequently, we performed a normal mode analysis of unbound protein structures using an elastic network model and examined the agreement between the predicted and observed conformational changes. Finally, we investigated a relationship between the extent of conformational changes in DNA-binding proteins and the stability and specificity of protein-DNA complexes, for which such information was available from published experimental results. Our results provide a broad picture of conformational changes in DNA-binding proteins and hence contribute to our current understanding of protein-DNA interactions.