Abstract
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 protein-DNA complex structure analyzer). 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 .
Highlights
Knowledge of protein-DNA interactions at the structural-level can provide insights into the mechanisms of protein-DNA recognition and gene regulation
With the advancement of structure determination techniques and molecular expression systems, the number of protein-DNA complex structures deposited in Protein Data Bank (PDB) [2] is increasing at a higher rate
The first is that parts of the complex structures, such as one chain of a doublestranded DNA or one chain of a protein dimer is missing in the original PDB file (Figure 3A)
Summary
Knowledge of protein-DNA interactions at the structural-level can provide insights into the mechanisms of protein-DNA recognition and gene regulation. 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. 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) [2] is increasing at a higher rate. 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 [3,4,5]
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