Molecular Dynamics Simulations of Curcuminato-(η⁶-p-cymene)ruthenium(II) Docking in the Minor Groove of DNA: Evaluating Equilibrium Stability via 2D RMSD Analysis

Presenter(s)

Jarrod Ring

Abstract

Molecular dynamics simulations were conducted to study the interaction between Curcuminato-(η⁶-p-cymene)ruthenium(II) and DNA, focusing on minor groove binding at the N7 position of guanine. The system equilibrated at approximately 170 picoseconds, with the lowest potential energy configuration of -36.271 kcal/mol observed at 251 K at 464 picoseconds. The simulated Ru-N7 distance was 8.55 Å, contrasting with the literature-reported value of 2.824 Å, highlighting the influence observed over time evolution of the system on key interaction. The root-mean-square deviation (RMSD) matrix stabilized at approximately 2.30 Å at equilibrium, reflecting the conformational stability of the system. Temporal profiles of temperature, potential energy, and total energy further characterized the equilibration and stability processes. These findings advance the understanding of ruthenium-curcumin complexes in biomolecular systems and their potential therapeutic applications.

College

College of Science & Engineering

Department

Chemistry

Campus

Winona

First Advisor/Mentor

Hannah Leverentz-Culp

Start Date

4-24-2025 9:00 AM

End Date

4-24-2025 10:00 AM

Presentation Type

Poster Session

Format of Presentation or Performance

In-Person

Session

1a=9am-10am

Poster Number

59

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Apr 24th, 9:00 AM Apr 24th, 10:00 AM

Molecular Dynamics Simulations of Curcuminato-(η⁶-p-cymene)ruthenium(II) Docking in the Minor Groove of DNA: Evaluating Equilibrium Stability via 2D RMSD Analysis

Molecular dynamics simulations were conducted to study the interaction between Curcuminato-(η⁶-p-cymene)ruthenium(II) and DNA, focusing on minor groove binding at the N7 position of guanine. The system equilibrated at approximately 170 picoseconds, with the lowest potential energy configuration of -36.271 kcal/mol observed at 251 K at 464 picoseconds. The simulated Ru-N7 distance was 8.55 Å, contrasting with the literature-reported value of 2.824 Å, highlighting the influence observed over time evolution of the system on key interaction. The root-mean-square deviation (RMSD) matrix stabilized at approximately 2.30 Å at equilibrium, reflecting the conformational stability of the system. Temporal profiles of temperature, potential energy, and total energy further characterized the equilibration and stability processes. These findings advance the understanding of ruthenium-curcumin complexes in biomolecular systems and their potential therapeutic applications.