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BackgroundKnowledge of protein-DNA interactions at the structural-level can provide insights into the mechanisms of protein-DNA recognition and gene regulation. Although over 1400 protein-DNA complex structures have been deposited into Protein Data Bank (PDB), the structural details of protein-DNA interactions are generally not available.
In addition, current approaches to comparison of protein-DNA complexes are mainly based on protein sequence similarity while the DNA sequences are not taken into account. With the number of experimentally-determined protein-DNA complex structures increasing, there is a need for an automatic program to analyze the protein-DNA complex structures and to provide comprehensive structural information for the benefit of the whole research community.
ResultsWe developed an automatic and comprehensive protein-DNA complex structure analysis program, PDA (for p rotein- D NA complex structure a nalyzer). PDA takes PDB files as inputs and performs structural analysis that includes 1) whole protein-DNA complex structure restoration, especially the reconstruction of double-stranded DNA structures; 2) an efficient new approach for DNA base-pair detection; 3) systematic annotation of protein-DNA interactions; and 4) extraction of DNA subsequences involved in protein-DNA interactions and identification of protein-DNA binding units.
Protein-DNA complex structures in current PDB were processed and analyzed with our PDA program and the analysis results were stored in a database. A dataset useful for studying protein-DNA interactions involved in gene regulation was generated using both protein and DNA sequences as well as the contact information of the complexes. WebPDA was developed to provide a web interface for using PDA and for data retrieval. ConclusionPDA is a computational tool for structural annotations of protein-DNA complexes. It provides a useful resource for investigating protein-DNA interactions. Data from the PDA analysis can also facilitate the classification of protein-DNA complexes and provide insights into rational design of benchmarks. The PDA program is freely available at.
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Protein-DNA interactions play crucial roles in many biological processes, including regulation of gene expression, DNA modification, and DNA duplication. Knowledge of the 3-dimensional (3D) structures of protein-DNA complexes can help us better understand the mechanism of protein-DNA recognition, shed light on the evolution of gene regulatory networks, and guide the rational design of therapeutic drugs. With the advancement of structure determination techniques and molecular expression systems, the number of protein-DNA complex structures deposited in Protein Data Bank (PDB) is increasing at a higher rate. As of August, 2008, there are over 1400 solved protein-DNA complex structures in PDB (Figure ). The current state of research in protein-DNA interactions with the number of known protein-DNA complex structures is reminiscent of the situation of protein structure modeling in the early 1990s which started a new wave of development of protein structure prediction methods. The number of available high-resolution structures of protein-DNA complexes makes it possible to develop more accurate knowledge-based potentials and protein-DNA docking methods –.
One of the crucial steps in investigating the mechanism of protein-DNA interactions is the construction of datasets as well as classification of protein-DNA complex structures. Previously, non-redundant datasets have been generated through comparison of protein sequences –. This 'protein-centric' view has also been the traditional method in classification of protein-DNA complexes. However, the same protein may interact with two very different DNA molecules. For example, 1BGB and 2B0D contain the same protein but the corresponding DNA sequences (GGGATATCCCG and AAAGAATTCTTT) are very different (Figure and ). In addition, one protein may interact with two DNA sequences through different binding sites.
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The protein-DNA complex structure 1ZX4 is such an example, in which the protein has two different DNA binding domains (Figure ). One of the reasons that the DNA molecules were not taken into account in dataset construction is probably the lack of double-stranded DNA sequence information and complete protein-DNA binding models in PDB files. For example, some double-stranded DNA molecules are fragmented into several shorter DNA chains for biological or non-biological reasons, and there is no annotation about whether a DNA chain is a single stranded DNA, one full-length chain of a double-stranded DNA, or only a fragment of one strand of a double helix. Moreover, DNA bases that interact with protein residues are usually more conserved than other bases. Therefore, how the DNA sequences in the complexes are used for comparison is not a trivial issue. The lack of such detailed information has compromised the classification of.