Abstract
Protein-DNA interactions are the physical basis of gene expression and DNA modification. Structural models that reveal these interactions are essential for their understanding. As only a limited number of structures for protein-DNA complexes have been determined by experimental methods, computation methods provide a potential way to fill the need. We have developed the DISPLAR method to predict DNA binding sites on proteins. Predicted binding sites have been used to assist the building of structural models by docking, either by guiding the docking or by selecting near-native candidates from the docked poses. Here we applied the DISPLAR method to predict the DNA binding sites for 20 DNAbinding proteins, which have had their DNA binding sites characterized by NMR chemical shift perturbation. For two of these proteins, the structures of their complexes with DNA have also been determined. With the help of the DISPLAR predictions, we built structural models for these two complexes. Evaluations of both the DNA binding sites for 20 proteins and the structural models of the two protein-DNA complexes against experimental results demonstrate the significant promise of our model-building approach.
Keywords: Protein-DNA interaction, interface prediction, interaction sites, DNA, protein-DNA, protein-DNA complexes, Double-stranded DNA, amino acids, CAPRI, Docking
Current Protein & Peptide Science
Title: Structural Models of Protein-DNA Complexes Based on Interface Prediction and Docking
Volume: 12 Issue: 6
Author(s): Sanbo Qin and Huan-Xiang Zhou
Affiliation:
Keywords: Protein-DNA interaction, interface prediction, interaction sites, DNA, protein-DNA, protein-DNA complexes, Double-stranded DNA, amino acids, CAPRI, Docking
Abstract: Protein-DNA interactions are the physical basis of gene expression and DNA modification. Structural models that reveal these interactions are essential for their understanding. As only a limited number of structures for protein-DNA complexes have been determined by experimental methods, computation methods provide a potential way to fill the need. We have developed the DISPLAR method to predict DNA binding sites on proteins. Predicted binding sites have been used to assist the building of structural models by docking, either by guiding the docking or by selecting near-native candidates from the docked poses. Here we applied the DISPLAR method to predict the DNA binding sites for 20 DNAbinding proteins, which have had their DNA binding sites characterized by NMR chemical shift perturbation. For two of these proteins, the structures of their complexes with DNA have also been determined. With the help of the DISPLAR predictions, we built structural models for these two complexes. Evaluations of both the DNA binding sites for 20 proteins and the structural models of the two protein-DNA complexes against experimental results demonstrate the significant promise of our model-building approach.
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Cite this article as:
Qin Sanbo and Zhou Huan-Xiang, Structural Models of Protein-DNA Complexes Based on Interface Prediction and Docking, Current Protein & Peptide Science 2011; 12 (6) . https://dx.doi.org/10.2174/138920311796957694
DOI https://dx.doi.org/10.2174/138920311796957694 |
Print ISSN 1389-2037 |
Publisher Name Bentham Science Publisher |
Online ISSN 1875-5550 |
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