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.
Export Options
About this article
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 |
Call for Papers in Thematic Issues
Advancements in Proteomic and Peptidomic Approaches in Cancer Immunotherapy: Unveiling the Immune Microenvironment
The scope of this thematic issue centers on the integration of proteomic and peptidomic technologies into the field of cancer immunotherapy, with a particular emphasis on exploring the tumor immune microenvironment. This issue aims to gather contributions that illustrate the application of these advanced methodologies in unveiling the complex interplay ...read more
Artificial Intelligence for Protein Research
Protein research, essential for understanding biological processes and creating therapeutics, faces challenges due to the intricate nature of protein structures and functions. Traditional methods are limited in exploring the vast protein sequence space efficiently. Artificial intelligence (AI) and machine learning (ML) offer promising solutions by improving predictions and speeding up ...read more
Nutrition and Metabolism in Musculoskeletal Diseases
The musculoskeletal system consists mainly of cartilage, bone, muscles, tendons, connective tissue and ligaments. Balanced metabolism is of vital importance for the homeostasis of the musculoskeletal system. A series of musculoskeletal diseases (for example, sarcopenia, osteoporosis) are resulted from the dysregulated metabolism of the musculoskeletal system. Furthermore, metabolic diseases (such ...read more
Protein Folding, Aggregation and Liquid-Liquid Phase Separation
Protein folding, misfolding and aggregation remain one of the main problems of interdisciplinary science not only because many questions are still open, but also because they are important from the point of view of practical application. Protein aggregation and formation of fibrillar structures, for example, is a hallmark of a ...read more
Related Journals
- Author Guidelines
- Graphical Abstracts
- Fabricating and Stating False Information
- Research Misconduct
- Post Publication Discussions and Corrections
- Publishing Ethics and Rectitude
- Increase Visibility of Your Article
- Archiving Policies
- Peer Review Workflow
- Order Your Article Before Print
- Promote Your Article
- Manuscript Transfer Facility
- Editorial Policies
- Allegations from Whistleblowers
Related Articles
-
Trends in the Exploration of Anticancer Targets and Strategies in Enhancing the Efficacy of Drug Targeting
Current Molecular Pharmacology The 18 kDa Translocator Protein (TSPO): A New Perspective in Mitochondrial Biology
Current Molecular Medicine Epigenetic Modifications Due to Heavy Metals Exposure in Children Living in Polluted Areas
Current Genomics Gene Therapy Approaches in an Autoimmune Demyelinating Disease: Multiple Sclerosis
Current Gene Therapy Forodesine (BCX-1777, Immucillin H) - A New Purine Nucleoside Analogue: Mechanism of Action and Potential Clinical Application
Mini-Reviews in Medicinal Chemistry Effect of DNA Repair Deficiencies on the Cytotoxicity of Drugs Used in Cancer Therapy - A Review
Current Medicinal Chemistry Epidemiology of Candida albicans Infections and Role of Non-Candidaalbicans Yeasts
Current Drug Targets The Role of AMPK/mTOR Modulators in the Therapy of Acute Myeloid Leukemia
Current Medicinal Chemistry Natural Small Molecules as Stabilizers and Activators of Cancer-Associated NQO1 Polymorphisms
Current Drug Targets Innate Immunity and the Heart
Current Pharmaceutical Design Src Family Kinases: Potential Targets for the Treatment of Human Cancer and Leukemia
Current Pharmaceutical Design Emerging Therapies in Chronic Myeloid Leukemia
Current Cancer Drug Targets Plasmid-Mediated Muscle-Targeted Gene Therapy for Circulating Therapeutic Protein Replacement: A Tale of the Tortoise and the Hare?
Current Gene Therapy Growth Factors as Therapeutics for Diabetic Neuropathy
Current Drug Targets Nucleoside Phosphorylases
Current Organic Chemistry Deregulation of PI3K/Akt/mTOR Signaling Pathways by Isoflavones and its Implication in Cancer Treatment
Anti-Cancer Agents in Medicinal Chemistry Chemical and Potential Biological Perspectives of Genus Sarcococca (Buxaceae)
The Natural Products Journal Immunoglobulin Free Light Chains in Immune Responses
Current Immunology Reviews (Discontinued) Role of the Akt Pathway in Prostate Cancer
Current Cancer Drug Targets Meet Our Editorial Board Member
Current Cancer Drug Targets