Wed, 29 Nov 2023
Seminar Series

Dr. Mona Minkara

Northeastern University

Computational Insights into Surfactant Protein Dynamics: Binding Mechanisms, Mutations, and Environmental Impact

Wednesday, November 29, 2023
SSB 7172 @ 3:30 p.m.

Host: Dr. Krzysztof Starosta



This presentation highlights research in the Minkara COMBINE Lab on Surfactant Proteins B (SPB) and D (SP-D), crucial to pulmonary function and immune defense, respectively. We delve into the dynamic structural characteristics of SP-B, vital for lipid restructuring in respiratory function. By leveraging comparative modeling with Saposin-family proteins and conducting molecular dynamics simulations, we have elucidated the conformational stability and solvent interactions of SP-B in diverse alveolar conditions. Our results reveal significant insights into SP-B’s response to hydrophilic and hydrophobic environments, offering new understanding of its structural-functional relationships. Concurrently, our study on SP-D, particularly its antiviral mechanisms against Influenza A Virus, utilized microsecond-scale molecular dynamics, free energy perturbation, and quantum mechanics to explore the enhanced antiviral properties of its double mutant variant. Employing trimannose models and a range of glycan binding poses, we provide a molecular basis for this increased efficacy, paving the way for designing optimized SP-D variants. Collectively, our work offers insights into the biophysical aspects of surfactant proteins, with potential implications for developing novel therapies for pulmonary diseases and enhancing viral pathogen

Keywords: Computational Molecular Engineering; Surfactant Proteins; Pulmonary Surfactant;
Molecular Dynamics.

About Mona Minkara (from faculty page)

Dr. Mona Minkara is an Assistant Professor in the Department of Bioengineering and an Affiliate Faculty in the Department of Chemistry and Chemical Biology at Northeastern where she heads the COMBINE (COmputational Modeling for BioINterface Engineering) Lab.

Dr. Minkara’s research uses a variety of methods from computational chemistry that she has employed throughout her academic career. While pursuing her BA in Chemistry at Wellesley College, Dr. Minkara worked with Dr. Mala Radhankrishnan, where she used computational methods to explore the binding of drugs to HIV-1 Reverse Transcriptase. After completing her BA in 2009, Dr. Minkara spent a year conducting research at Wellesley under a Howard Hughes Medical Institute Research Grant. In 2010, she began her graduate studies at the University of Florida supported by a National Science Foundation Graduate Research Fellowship. Under her co-advisors, Dr. Kenneth M. Merz Jr. and Dr. Erik Deumens, she focused on using molecular dynamics simulations to design a new inhibitor for Helicobacter pylori urease, an enzyme that helps bacteria survive in the stomach, and in 2015, she received her PhD in Chemistry. She then joined Dr. J. Ilja Siepmann’s lab as a post-doc at the University of Minnesota Twin Cities Chemical Theory Center. In this role, Dr. Minkara used Monte Carlo simulations to explore the interfacial properties of surfactants, the surface tension of water, and the miscibility gap of supercritical fluids. In 2016, she was also awarded a Ford Foundation Postdoctoral Fellowship from the National Academies of Sciences, Engineering, and Medicine. Dr. Minkara joined the Department of Bioengineering at Northeastern University in August of 2019 as a tenure-track Assistant Professor, and in November of 2019, she became an Affiliate Faculty of the Chemistry & Chemical Biology Department. Throughout her career, her work has led to numerous publications in high-impact journals, presentations, and posters at national and local conferences, and received several awards recognizing her achievements. Dr. Minkara is also an active member of the American Chemical Society where she serves on the Chemists with Disabilities committee and the American Institute of Chemical Engineers, where she is a member of the Disabilities OutReach and Inclusion Community. Dr. Minkara is also one of the only blind professors in the field of Bioengineering, and she seeks to increase accessibility in STEM.

Dr. Minkara’s research at Northeastern focuses on using computational methods to study biological interfaces at the atomic and molecular scale. Currently, her research group uses molecular dynamics simulations, molecular docking calculations, homology modeling, and Monte Carlo simulations to investigate pulmonary surfactant, the complex protein-lipid substance that lines the alveoli in the lungs. Recently, the group has also been using their computational techniques to investigate the SARS-CoV-2 coronavirus.

More information about Dr. Minkara is available on her personal website at