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RSS FeedsStatistical analysis of structural determinants for protein-DNA binding specificity (Proteins: Structure, Function, and Bioinformatics)

 
 

5 may 2016 11:00:31

 
Statistical analysis of structural determinants for protein-DNA binding specificity (Proteins: Structure, Function, and Bioinformatics)
 


DNA-binding proteins play critical roles in biological processes including gene expression, DNA packaging and DNA repair. They bind to DNA target sequences with different degrees of binding specificity, ranging from highly specific to non-specific. Alterations of DNA-binding specificity, due to either genetic variation or somatic mutations, can lead to various diseases. In this study, a comparative analysis of protein-DNA complex structures was carried out to investigate the structural features that contribute to binding specificity. Protein-DNA complexes were grouped into three general classes based on degrees of binding specificity: highly specific (HS), multi-specific (MS), and non-specific (NS). Our results show a clear trend of structural features among the three classes, including amino acid binding propensities, simple and complex hydrogen bonds, major/minor groove and base contacts, and DNA shape. We found that aspartate is enriched in highly specific DNA binding proteins and predominately binds to a cytosine through a single hydrogen bond or two consecutive cytosines through bidentate hydrogen bonds. Aromatic residues, histidine and tyrosine, are highly enriched in the HS and MS groups and may contribute to specific binding through different mechanisms. To further investigate the role of protein flexibility in specific protein-DNA recognition, we analysed the conformational changes between the bound and unbound states of DNA-binding proteins and structural variations. The results indicate that highly specific and multi-specific DNA-binding domains have larger conformational changes upon DNA-binding and larger degree of flexibility in both bound and unbound states. This article is protected by copyright. All rights reserved.


 
157 viewsCategory: Biochemistry, Bioinformatics
 
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