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Measuring Biomolecular DSC Profiles with Thermolabile Ligands to Rapidly Characterize Folding and Binding Interactions
Published on: November 21, 2017
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Binding energies and hydrogen bonds effects on DNA-cisplatin interactions: a DFT-xTB study
Valdemir Ludwig1, Zélia Maria da Costa Ludwig2, Marlon de Assis Modesto2
1Departamento de Física, Universidade Federal de Juiz de Fora, Juiz de Fora, CP 36036-330, Minas Gerais, Brasil. ludwig.valdemir@gmail.com.
Journal of Molecular Modeling
|May 27, 2024
Summary
The study reveals that water molecule hydrogen bonds are crucial for cisplatin binding to DNA, particularly favoring interactions with Guanine. Computational methods accurately determined these binding energies and structures.
Area of Science:
- Computational chemistry
- Molecular modeling
- Biochemistry
Background:
- Investigated hydrogen bonds in DNA base pairs and cisplatin interactions.
- Analyzed DNA-cisplatin structures, binding energies, and electron density.
- Evaluated the accuracy of the xTB method for DNA structure and binding energy calculations.
Purpose of the Study:
- To systematically study hydrogen bonds in DNA base pairs and cisplatin interactions.
- To determine the role of water molecules in cisplatin-DNA binding preference.
- To compare the accuracy of xTB and CAM-B3LYP methods against experimental data.
Main Methods:
- Employed the xTB method for structural and binding energy calculations.
- Utilized the CAM-B3LYP functional with def2-SVP basis set.
- Calculated double-stranded DNA-cisplatin structures using ORCA software.
Main Results:
- xTB method demonstrated high accuracy for DNA base binding energies, comparable or superior to CAM-B3LYP.
- Identified water molecule hydrogen bonds as a key factor in cisplatin-Guanine interaction preference.
- Observed higher water hydrogen bonding energies in cisplatin-Guanine structures.
- Applied electrostatic potential analysis to enhance DNA-cisplatin structure analysis.
Conclusions:
- The xTB method is a reliable tool for studying DNA-cisplatin interactions.
- Water molecule hydrogen bonding significantly influences cisplatin binding affinity to Guanine.
- Computational analysis provides insights into the molecular mechanisms of cisplatin-DNA interactions.
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