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DNA as a Genetic Template

DNA as a Genetic Template

Two structural features of the DNA molecule provide a basis for the mechanisms of heredity: the four nucleotide bases and its double-stranded nature. The Watson-Crick model of double-helical DNA structure, proposed in 1952, drew heavily upon the X-ray crystallography work of researchers Rosalind Franklin and Maurice Wilkins. Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine for their work in 1962. Franklin was, controversially, excluded from the prize for...

The DNA Helix

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Analyzing and Building Nucleic Acid Structures with 3DNA

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Molecular dynamics simulations revealed structural differences among TTHA1873-DNA interaction.

Yuvaraj Iyyappan¹, Chandrasekaran Palaniappan¹, Vaigundan Dhayabaran²

¹Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, India.

Journal of Biomolecular Structure & Dynamics

|December 5, 2024

Summary

This study reveals that specific mutations (R55A and R138A) in TTHA1873 significantly impair its DNA binding ability. Wild-type TTHA1873 exhibits stronger DNA interactions compared to its mutants, highlighting the importance of these residues for DNA binding specificity.

Keywords:

DNA Molecular dynamics simulations TTHA1873 molecular docking protein-DNA interaction

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Last Updated: Jun 5, 2025

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Area of Science:

Biochemistry
Molecular Biology
Structural Biology

Background:

TTHA1873 is a protein with potential DNA-binding functions.
Understanding protein-DNA interactions is crucial for deciphering biological processes.
Mutational analysis can elucidate the role of specific amino acid residues in protein function.

Purpose of the Study:

To comparatively analyze the DNA binding patterns of wild-type TTHA1873 and its mutants (R55A, R138A).
To investigate the structural and energetic basis of DNA-binding specificity using computational methods.

Main Methods:

Molecular docking simulations to predict binding affinities and modes.
Molecular dynamics (MD) simulations to assess the stability and dynamics of protein-DNA complexes.
Analysis of hydrogen bonding patterns and binding free energies.

Main Results:

Wild-type TTHA1873 showed higher docking scores and more stable interactions with DNA compared to R55A and R138A mutants.
Mutations at R55 and R138 positions led to altered hydrogen bonding patterns and reduced binding affinity.
MD simulations indicated that WT-TTHA1873 has a more stable complex with DNA, with mutants exhibiting increased conformational flexibility.

Conclusions:

Residues R55 and R138 of TTHA1873 are critical for its DNA-binding capability.
The identified mutations abolish or significantly reduce the DNA-binding ability of TTHA1873.
This study provides insights into the structural determinants of TTHA1873's DNA-binding specificity.