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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 Biomedical Engineering

PI: Jonathan N. Sachs, Associate Fellow

Molecular Dynamics Simulations of Membranes and Membrane Proteins

These researchers are using all-atom and coarse-grained molecular dynamics (MD) simulations for three projects. The first project, which investigates the tumor necrosis factor superfamily of receptors, a class of membrane proteins that are targeted in cancer and inflammatory disease, uses a combination of cell/molecular biology and biophysical techniques in human cancer and model cells lines, along with synthetic biochemistry and computational modeling. The researchers use simulations to study the underlying structures that facilitate supra-molecular clustering of the receptors, in particular the transmembrane domains.

The second project, an investigation of αSynuclein (αS), the primary protein found in Lewy bodies that are the hallmark of Parkinson’s disease, uses a combination of x-ray and coarse-grained MD simulations. The researchers explore how αS changes the structure and dynamics of the membrane, alterations that help explain the physical underpinnings of its action in fusion, fission and potentially disease.

The third project studies the cholesterol-recognition amino-acid consensus sequence motif because of its importance in dictating membrane protein trafficking. One example, the LWYIK peptide, binds within the lipid headgroup region and partitions into ordered regions of the membrane because of its direct interaction with cholesterol. The researchers are testing the hypothesis that this interaction stabilizes raft-like domains by both altering the line tension at the domain boundaries and relieving the strain on lipid headgroups that they have shown otherwise exists to shield cholesterol from water.

Group Members

Anthony R. Braun, Undergraduate Student
Daniel Jacobsen, Undergraduate Student
Andrew K. Lewis, Staff
Deepti Mudaliar, Staff
Jason D. Perlmutter, Graduate Student
Elliott Surber, Undergraduate Student
Christopher C. Valley, Graduate Student