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Wonpil Im, Ph.D.
Department of Molecular Biosciences and Center for Bioinformatics
UNIVERSITY OF KANSAS

Transmembrane (TM) domains of most membrane proteins consist of helices that interact with each other via inter- and intra-helix-helix interactions as well as with nonprotein membrane constituents. It is experimentally known that close packing and hydrophilic interactions between helices, which are all competing with helix-membrane (constituents) interactions, mediate the extent of helix-helix association. To determine dedicate balancing forces between inter-helix-helix and helix-membrane interactions, we have calculated the potential of mean force (PMFs) as a function of distance (rHH) between two helical model peptides (pVNVV) in a DMPC membrane model. The sequence of pVNVV is Acetyl-LLLLV LLLLL LNLLL LLLVL LLLLL VL-Amine, a membrane-soluble GCN4 leucine-zipper, built based on soluble leucine-zipper (PDB:2ZTA. The system consists of two pVNVVs, 128 DMPC lipid and 3835 water molecules. A total of 57 windows were generated from rHH =7 Å to rHH =20.75 Å every 0.25 Å and at 10.375 Å. Each system was then subjected to 4 ns equilibration and 5 ns production with a force constant of 200 kcal/(mol·Å2) to restraint rHH in each target values. We will present (1) the extent of helix-helix association in both membrane models, (2) PMF decomposition to direct helix-helix and helix-environment interactions, and (3) possible mechanism of helix-helix association in membranes.