Simulation of water soluble potassium channel

COMP 237

One-Sun Lee, one@sas.upenn.edu, Jonathan Bronson, jon@sas.upenn.edu, and Jeffery G. Saven. Department of Chemistry, University of Pennsylvania, 231 S. 34 street, Philadelphia, PA 19104
A method of solubilizing membrane proteins using the Statistical Computational Design Strategy was recently reported. We investigated the first protein solubalized with this approach, the water soluble analogue of the potassium channel (WSK-3), using molecular dynamics simulations. Four simulations, lasting 3.0 ns each, were performed to examine WSK-3's structure and ion binding capacity. The root mean square deviation of the protein from its starting structure was ~1.8 . Engineered salt bridges that are important to maintaining WSK-3's structure were identified. The preferred configuration of ions and water in WSK-3's selectivity filter was consistent with the reported preferences for KcsA. Unexpected motions of the central cavity's side chains were observed, allowing water diffusion through the side of the cavity wall. These simulations provide the first atomistic analysis of the membrane protein solubilization strategy and suggest that it is a viable option for studying membrane proteins.
 

Poster Session -- Sponsored by Novartis Institutes for BioMedical Research
6:00 PM-8:00 PM, Tuesday, 30 August 2005 Washington DC Convention Center -- Hall A, Poster

Sci-Mix
8:00 PM-10:00 PM, Monday, 29 August 2005 Washington DC Convention Center -- Hall A, Sci-Mix

Division of Computers in Chemistry

The 230th ACS National Meeting, in Washington, DC, Aug 28-Sept 1, 2005