Structural analysis of protein-DNA binding specificity and its application to protein-DNA docking assessment

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Corona de la Fuente, R. (2016). Structural analysis of protein-DNA binding specificity and its application to protein-DNA docking assessment. Unc Charlotte Electronic Theses And Dissertations.
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Abstract

DNA-binding proteins are involved in essential 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 for binding specificity. The analysis was done using three curated datasets of protein-DNA complexes with different degrees of DNA-binding specificity: highly specific (HS), multi-specific (MS), and non-specific (NS). We found a clear trend of structural features among these three classes, including amino acid binding propensities, simple and complex hydrogen bonds, major groove and base contacts, DNA shape, and conformational changes upon DNA-binding. These structural features were then applied to assess the accuracy of TF-DNA docking predictions. A binary classifier for evaluating the prediction accuracy was developed using a training dataset and the structural features as well as three binding affinity scores. The results on a test dataset show much improved prediction accuracy over previous methods.

Details
Author

Corona de la Fuente, Rosario

Title

Structural analysis of protein-DNA binding specificity and its application to protein-DNA docking assessment

Physical Description

1 online resource (126 pages) : PDF

Date

2016

Degree Granting Institution

University of North Carolina at Charlotte

Abstract

DNA-binding proteins are involved in essential 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 for binding specificity. The analysis was done using three curated datasets of protein-DNA complexes with different degrees of DNA-binding specificity: highly specific (HS), multi-specific (MS), and non-specific (NS). We found a clear trend of structural features among these three classes, including amino acid binding propensities, simple and complex hydrogen bonds, major groove and base contacts, DNA shape, and conformational changes upon DNA-binding. These structural features were then applied to assess the accuracy of TF-DNA docking predictions. A binary classifier for evaluating the prediction accuracy was developed using a training dataset and the structural features as well as three binding affinity scores. The results on a test dataset show much improved prediction accuracy over previous methods.

Genre

doctoral dissertations

Subjects--Topics

Bioinformatics

Degree

Ph.D.

Keywords

DNA-Binding Proteins
DNA-Binding Specificity
Hydrogen Bond
Protein-DNA Docking
Protein-DNA Interaction
Transcription Factor

Subject Area

Bioinformatics

Advisor(s)

Guo, Jun-tao

Committee Members

Du, Xiuxia
Livesay, Dennis
Weller, Jennifer
Souvenir, Richard

Degree Note

Thesis (Ph.D.)--University of North Carolina at Charlotte, 2016.

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Rights Holder Information

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Identifier

CoronadelaFuente_uncc_0694D_11068

Permalink

http://hdl.handle.net/20.500.13093/etd:1416