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Research Abstracts Online
January - December 2011

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University of Minnesota Twin Cities
College of Science and Engineering
Department of Chemical Engineering and Materials Science

PI: Yiannis N. Kaznessis, Fellow

Multiscale Models for Biomolecular Systems

These researchers continue to use computer simulations to investigate peptide-lipid interactions from a biophysical perspective. The peptides of interest are antimicrobial peptides, which have been explored as novel antibiotic candidates to combat emerging drug-resistant bacterial strains. The ultimate goal of research in this area is to engineer peptides with low toxicity and high antimicrobial activity, but first the detailed mechanism of action must be understood to allow for rational design of new sequences.

These researchers have implemented large-scale molecular dynamics simulations of protegrin-1, their peptide of choice, in several model systems of the cell membrane. These models have lead to rational peptide designs that have been tested in the laboratory. The group’s simulations have also provided numerous insights into the structure of the peptide oligomeric structure, the dynamics of ion and water movement through the pore, as well as the structure of the lipids surrounding the peptide pore. Additionally, they have used structures extracted from these simulations as input to an electrodiffusion model that successfully predicts the experimentally measured single-pore conductance value. They have extended this approach to model the time-dependent transport of ions from an entire bacterial cell, and have been able to match potassium leakage data obtained from experiments with living Escherichia coli cells.  Recent work has also shed light on the structure and properties of protegrin pores, as well as their effects on bacterial cells.

Group Members

Konstantinos Billiouris, Graduate Student
Dan S. Bolintineanu, Graduate Student
Anushree Chatterjee, Graduate Student
Fatemeh Ghasemi, Research Associate
Himanshu Khandelia, Graduate Student
Patrick Smadbeck, Undergraduate Student
Bennett J. Swiniarski, Graduate Student
Victor Vivcharuk, Research Associate
Katherine Volzing, Graduate Student
Emma Weeding, Undergraduate Student
Emilia Wu, Research Associate