Contreras, Melany: Molecular Dynamics Simulations of Peptides and Proteins

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Title: Molecular Dynamics Simulations of Peptides and Proteins

Name: Melany Contreras

Home Institute: East Carolina University

Programs: RISE program

Other contributors: Lu Wang

Abstract: Molecular dynamics (MD) is a computational method that is useful for modeling molecular interactions between the simplest of molecules to the largest and most complex proteins. It is oftentimes a cheaper and time-saving alternative to laboratory experiments when needing to investigate how molecules interact for applications in biochemistry and drug discovery. A molecular system of interest in an MD simulation goes through energy minimization, equilibration, and then production to obtain information on its dynamics. To become familiar with MD, A MD simulation was performed for an alanine dipeptide solvated in water using the AMBER software package. Results of the simulation were visualized using VMD. Future directions for this project include performing simulations using AMBER for naringenin, a flavonoid with antimicrobial properties, in complex with TtgR, a sensory protein that regulates transcription in bacteria. A visual representation of this complex has been created using VMD. The MD simulations will provide insight into how naringenin binds to TtgR and how functional naringenin can be as an antibiotic.

Biography: Melany Contreras is a rising Senior at East Carolina University in Eastern North Carolina. She is a Chemistry and Physics double major, Mathematics minor, and is a member of the Honors College at her university. When classes are in session, Melany enjoys research with her mentors Dr. Anne Spuches in the Chemistry department and Dr. Praveen Malali in the Center for Sustainable Energy and Environmental Engineering. She teaches Organic Chemistry I Lab as a teaching assistant and has been deeply involved in her university’s Student Government Association for the past 3 years. Melany hopes to earn a Ph. D. in Physical Chemistry and work at NASA as a research physical chemist.