TransPath: a computational method for locating ion transit pathways through membrane proteins.
Proteins
; 71(3): 1349-59, 2008 May 15.
Article
en En
| MEDLINE
| ID: mdl-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.
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Colección:
01-internacional
Banco de datos:
MEDLINE
Asunto principal:
Transducción de Señal
/
Biología Computacional
/
Canales Iónicos
/
Proteínas de la Membrana
Tipo de estudio:
Health_economic_evaluation
/
Prognostic_studies
Idioma:
En
Revista:
Proteins
Asunto de la revista:
BIOQUIMICA
Año:
2008
Tipo del documento:
Article
País de afiliación:
Estados Unidos