Channelpedia

PubMed 18058905


Referenced in Channelpedia wiki pages of: none

Automatically associated channels: ClvC4



Title: TransPath: a computational method for locating ion transit pathways through membrane proteins.

Authors: Zhifeng Kuang, Anping Liu, Thomas L Beck

Journal, date & volume: Proteins, 2008 May 15 , 71, 1349-59

PubMed link: http://www.ncbi.nlm.nih.gov/pubmed/18058905


Abstract
The finely tuned structures of membrane channel proteins allow selective passage of ions through the available aqueous pores. To understand channel function, it is crucial to locate the pores and study their physical and chemical properties. Here, we propose a new pore-searching algorithm (TransPath), which uses the Configurational Bias Monte Carlo (CBMC) method to generate transmembrane trajectories driven by both geometric and electrostatic features. The trajectories are binned into groups determined by a vector distance criterion. From each group, a representative trajectory is selected based on the Rosenbluth weight, and the geometrically optimal path is obtained by simulated annealing. Candidate ion pathways can then be determined by analysis of the radius and potential profiles. The proposed method and its implementation are illustrated using the bacterial KcsA potassium channel as an example. The procedure is then applied to the more complex structures of the bacterial E. coli chloride channel homolog and a homology model of the ClC-0 channel.