Membranes, which enclose cells and vesicles, constitute a barrier for penetration as well as a platform for biological and chemical processes. We use both detailed atomistic simulations and coarse-grained descriptions to model membrane systems. We investigate how peptides interact with prokaryotic and eukaryotic membranes as well as how small antimicrobial peptides are preferentially attracted to bacterial membranes, and what gross conformational changes these molecules induce in the membrane itself.
Yeh, I.-C., D. R. Ripoll, and A. Wallqvist. Free energy difference in indolicidin attraction to eukaryotic and prokaryotic model cell membranes. Journal of Physical Chemistry B. 2012 March 15; 116(10):3387-3396. [PDF, 22376120]
Woo, H. J., and A. Wallqvist. Spontaneous buckling of lipid bilayer and vesicle budding induced by antimicrobial peptide magainin 2: a coarse-grained simulation study. Journal of Physical Chemistry B. 2011 June 30; 115(25):8122-8129. [PDF, 21651300]
Yeh, I.-C., M. A. Olson, M. S. Lee, and A. Wallqvist. Free-energy profiles of membrane insertion of the M2 transmembrane peptide from influenza A virus. Biophysical Journal. 2008 December; 95(11):5021-5029. [PDF, 18676651]
Yeh, I.-C., M. Olson, M. S. Lee, and A. Wallqvist. Membrane insertion profiles of peptides probed by molecular dynamics simulations. Proceedings of the HPCMP Users Group Conference. Seattle, WA. 2008 July 14-17; 208-213. [PDF, ADA526659]
Olson, M. A., I.-C. Yeh, and M. S. Lee. Molecular dynamics simulations of folding and insertion of the Ebola virus fusion peptide into a membrane bilayer. Proceedings of the 2008 International Conference on Bioinformatics and Computational Biology. Las Vegas, NV. 2008 July 14-17; 660-665. [PDF, ADA501471]