Location
Chamberlain Student Center
Document Type
Poster
College
College of Science & Mathematics
Event Website
https://research.rowan.edu/rowan-research-days-2024.html
Start Date
26-3-2024 12:00 PM
End Date
26-3-2024 3:00 PM
Abstract
With the computational tools developed in our lab for accurate prediction of structures and solution dynamics of aromatic foldamers, we now target protein-protein interaction (PPI) by appending proteinogenic side chains on the external surfaces of the helical aromatic foldamers. Particularly, the activation of a regulatory protein NF-κB, a key player in the inflammatory response and cell proliferation, involves binding of NEMO (NF-κB Essential Modulator) with linear di-ubiquitin. In this study, we designed various sequences based on established protocols and investigated, by utilizing molecular dynamics (MD) simulations, their potential binding to di-ubiquitin, specifically targeting the NEMO binding interface. This study complements experimental works related to synthesis, characterization, and crystallization of aromatic foldamers. Here, we present structural analysis of MD trajectories from simulations of 21 aromatic foldamers/di-ubiquitin systems with explicit solvent (aqueous) to gain insight into the binding interaction.
Included in
Computer Aided Design of Aromatic Foldamer Targeting Protein-protein Interaction
Chamberlain Student Center
With the computational tools developed in our lab for accurate prediction of structures and solution dynamics of aromatic foldamers, we now target protein-protein interaction (PPI) by appending proteinogenic side chains on the external surfaces of the helical aromatic foldamers. Particularly, the activation of a regulatory protein NF-κB, a key player in the inflammatory response and cell proliferation, involves binding of NEMO (NF-κB Essential Modulator) with linear di-ubiquitin. In this study, we designed various sequences based on established protocols and investigated, by utilizing molecular dynamics (MD) simulations, their potential binding to di-ubiquitin, specifically targeting the NEMO binding interface. This study complements experimental works related to synthesis, characterization, and crystallization of aromatic foldamers. Here, we present structural analysis of MD trajectories from simulations of 21 aromatic foldamers/di-ubiquitin systems with explicit solvent (aqueous) to gain insight into the binding interaction.
https://rdw.rowan.edu/grad_student_symposium/2024/mar26/3
Comments
Bamidele Towolawi is a Ph.D. student in Pharmaceutical Chemistry working under Dr. Zhiwei Liu.