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ARS Home » Pacific West Area » Albany, California » Western Regional Research Center » Produce Safety and Microbiology Research » Research » Publications at this Location » Publication #420167
Research Project: Elucidating the Factors that Determine the Ecology of Human Pathogens in Foods

Location: Produce Safety and Microbiology Research

Title: Theoretical binding energies of colicin E3, E8 and D to their respective cognate immunity proteins as calculated by molecular dynamics simulations

Author
item KOIRALA, MAHESH - Oak Ridge Institute For Science And Education (ORISE)
item Fagerquist, Clifton

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 12/10/2024
Publication Date: N/A
Citation: N/A

Interpretive Summary: N/A

Technical Abstract: The integration of Artificial Intelligence (AI) with computational chemistry is transforming the field of structural biology, enabling more accurate predictions of protein-protein interactions, particularly in the context of bacterial defense mechanisms. In this study, we employed AI-driven tool, AlphaFold2 to predict the 3D structures of bacterial colicins E3, E8, and D along with their respective immunity protein partners. These colicin-immunity complexes are vital for bacteria, as immunity proteins neutralize the lethal effects of colicins, safeguarding the host bacteria from their own toxins. Predicting the binding affinity and stability of these interactions is key to understanding bacterial survival strategies. Molecular dynamics (MD) simulations using GROMACS followed by MMPBSA calculations were then carried out to investigate the interaction dynamics between these proteins, utilizing the high-performance computing resources. These simulations allowed for a detailed analysis of the structural stability and conformational behavior of the complexes, providing valuable insights into the theoretical binding free energies of colicin-immunity complexes. By calculating these binding energies, we deepen our understanding of how specific colicin-immunity protein pairs maintain their interactions at a molecular level. The results of this study offer significant contributions to the role of computational chemistry in food production and safety. These findings have broader implications for the development of new antimicrobial therapies, as understanding the intricacies of colicin-immunity interactions may aid in designing compounds that disrupt bacterial defense mechanisms.