Research Topic

Molecular Dynamics Simulations of Protein-DNA Recognition

About this Research Topic

The ability of proteins to recognize specific DNA sequences is important in biological regulatory processes. The conformation of protein and DNA plays a role in the varying types of mechanisms. Meanwhile, epigenetic modifications of DNA bases, such as cytosine methylation, hydroxy-methylation, formylation, and carboxylation, have challenged the traditional view of genetic regulation of protein-DNA recognition. At present, regional design of drug target to protein-DNA interaction is still a challenging issue.

Molecular dynamics methods are playing an increasing role in the research of protein-DNA recognition. These methods have been used to study the specific and non-specific binding of proteins to nucleic acid, the kinetics and thermodynamic behavior of the binding process, and the regulatory mechanism of the chemical modification of DNA on the binding process. Some new simulation methods (such as targeting molecular dynamic methods) are gradually being applied to the research in this field.

The goal of this Research Topic is to provide an overview of recent advances in the characterization of protein-DNA recognition using molecular dynamic simulation methods. Elucidating the molecular mechanisms of protein-DNA recognition and the regulation role of Epigenetic modifications of DNA bases. At the same time, this Research Topic also hopes to report on the application of cutting edge molecular dynamics simulation techniques in free energy calculations, specific recognition, conformational changes, and other thermodynamics and dynamics. Hybrid research works (such as bioinformatics and experimental processes) are also welcome.

We welcome original research, perspectives, and reviews shining light on, but are not limited to, the following areas:

• Simulation on specific recognition of protein and DNA recognition
• Interaction free energy calculation and environmental effect including but not restricted to protein, RNA, ION and waters
• Binding dynamic and conformational changes of protein and DNA, especially DNA bending
• Regulation of Epigenetic modifications of DNA bases, such as cytosine methylation, hydroxy-methylation, formylation, and carboxylation
• Regulation of single nucleotide polymorphisms (SNPs)
• Protein and DNA recognition and residence time
• Regional design of drug target to protein DNA interaction
• New methods in protein-DNA recognition
• Hybrid process in protein-DNA recognition research


Keywords: Simulation, Protein-DNA Recognition, epigenetic modification


Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.

The ability of proteins to recognize specific DNA sequences is important in biological regulatory processes. The conformation of protein and DNA plays a role in the varying types of mechanisms. Meanwhile, epigenetic modifications of DNA bases, such as cytosine methylation, hydroxy-methylation, formylation, and carboxylation, have challenged the traditional view of genetic regulation of protein-DNA recognition. At present, regional design of drug target to protein-DNA interaction is still a challenging issue.

Molecular dynamics methods are playing an increasing role in the research of protein-DNA recognition. These methods have been used to study the specific and non-specific binding of proteins to nucleic acid, the kinetics and thermodynamic behavior of the binding process, and the regulatory mechanism of the chemical modification of DNA on the binding process. Some new simulation methods (such as targeting molecular dynamic methods) are gradually being applied to the research in this field.

The goal of this Research Topic is to provide an overview of recent advances in the characterization of protein-DNA recognition using molecular dynamic simulation methods. Elucidating the molecular mechanisms of protein-DNA recognition and the regulation role of Epigenetic modifications of DNA bases. At the same time, this Research Topic also hopes to report on the application of cutting edge molecular dynamics simulation techniques in free energy calculations, specific recognition, conformational changes, and other thermodynamics and dynamics. Hybrid research works (such as bioinformatics and experimental processes) are also welcome.

We welcome original research, perspectives, and reviews shining light on, but are not limited to, the following areas:

• Simulation on specific recognition of protein and DNA recognition
• Interaction free energy calculation and environmental effect including but not restricted to protein, RNA, ION and waters
• Binding dynamic and conformational changes of protein and DNA, especially DNA bending
• Regulation of Epigenetic modifications of DNA bases, such as cytosine methylation, hydroxy-methylation, formylation, and carboxylation
• Regulation of single nucleotide polymorphisms (SNPs)
• Protein and DNA recognition and residence time
• Regional design of drug target to protein DNA interaction
• New methods in protein-DNA recognition
• Hybrid process in protein-DNA recognition research


Keywords: Simulation, Protein-DNA Recognition, epigenetic modification


Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.

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Submission Deadlines

21 June 2021 Manuscript

Participating Journals

Manuscripts can be submitted to this Research Topic via the following journals:

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Topic Editors

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Submission Deadlines

21 June 2021 Manuscript

Participating Journals

Manuscripts can be submitted to this Research Topic via the following journals:

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