Center for Bioinformatics at KU

As part of our public Seminar Series
http://bioinformatics.ku.edu/seminars

April 28, Tue 2009
1:00 pm, MRB 100 Conference Room

Dr. Themis Lazaridis

Chemistry Department, City College of New York

Modeling protein-membrane interactions using implicit solvation

Implicit solvation models have generated a lot of interest thanks to their convenience and speed. With minimal effort these models can be extended to lipid membranes with even greater payoffs. We recently extended the EEF1 function for soluble proteins to an implicit membrane model (IMM1) by making the solvation parameters and the dielectric screening dependent on the vertical coordinate. The membrane surface charge is modeled by use of the Gouy-Chapman theory. The transmembrane voltage is also straightforward to incorporate. We have developed approaches for calculating absolute, pH-dependent membrane binding free energies and transmembrane helix association free energies and applied these methods to a number of membrane-active peptides: transmembrane helix dimers, the influenza hemagglutinin fusion peptide, alamethicin, the membrane targeting domain of phosphocholine cytidylyltransferase, alpha-synuclein, and proteinase 3.