The focus of my dissertation work has been to characterize the biophysical mechanism by which a class of synthetic compounds known as antimicrobial lipopeptides (AMLPs) disrupt bacterial membranes. I have utilized a combination of coarse-grained and all-atom molecular dynamics to quantify the binding of a specific AMLP, C16-KGGK (shown right), to model membranes. A possible mechanism for membrane perturbation has been theorized that involves the separation of specific lipids in a usually mixed bilayer.
Other peptides and lipopeptides are also of interest, including acylated and non-acylated lactoferricin-b fragments (LFB6), oligo-acyl-lysines (OAKs), and antifungal fengycins.
In another project, we have explored the bilayer-protein interactions of the photoreceptor rhodopsin. Using robust statistical sampling via coarse-grained simulation, we have uncovered possible cholesterol binding sites, as well as noted a preference for phosphatidylethanolamine (PE) headgroups over phosphatidylcholine (PC) headgroups in one region of the protein surface.
Horn, J. N., Romo, T. D., and Grossfield, A., Simulating the mechanism of antimicrobial lipopeptides with all-atom molecular dynamics, Biochemistry, 2013, 52, 5604-5610
Horn, J. N., Kao, T-C, and Grossfield, A., Coarse-grained Molecular Dynamics Provides Insight into the Interactions of Lipids and Cholesterol with Rhodopsin, in G Protein-Coupled Receptor Modeling and Simulation, ed. Marta Filizola, Springer, 2013. (accepted)
Horn, J. N., Sengillo, J. D., Lin, D., Romo, T. D., and Grossfield, A., Characterization of a potent antimicrobial lipopeptide via coarse-grained molecular dynamics, Biochimica et Biophysica Acta (BBA) – Biomembranes, Volume 1818, Issue 2, February 2012, 212-218.
Department of Biochemistry and Biophysics
University of Rochester, Medical Center, Box 712
Rochester, NY 14642