Simulation of Protein Nucleic Acid Interaction

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About this Research Topic

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Background

Nucleic acids (DNA and RNA) store the genetic information of cells and functions through interactions with various proteins. The ability of proteins to recognize specific DNA and RNA 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 the genetic system via regulation of the protein nucleic acid recognition. At present, regional design of drug target to protein nucleic acid recognition interaction is still a challenging issue.

Molecular dynamics methods are playing an increasing role in the research of protein nucleic acid recognition. This method has been used to study the specific and non-specific binding of protein nucleic acid, the kinetics and thermodynamic behavior of the binding process, as well as 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.

Present the problem that you would like to tackle in this Research topic and what can be done to achieve it including recent advances.

The goal of this Research Tops is to provide an overview of recent advances in the characterization of protein nucleic acid 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. The hybrid research works such as bioinformatics and experimental process are also welcome.

In this Research Topic, we welcome original contributions, perspectives and reviews shining light into the broad subject of molecular dynamic simulation on protein DNA recognition, including, but not limited to, the following areas:

• Simulation on specific recognition of protein and DNA(RNA) 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(RNA), especially DNA(RNA) 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.

• Rational design of drug target to protein DNA interaction

• Rational design of aptamer

• New methods in protein nucleic acid recognition

• Hybrid process in protein nucleic acid recognition research.

Keywords: Simulation, Protein-DNA Recognition, epigenetic modification

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