Thermodynamic integration network approach to ion transport through protein channels: Perspectives and limits.
J Comput Chem
; 39(30): 2539-2550, 2018 11 15.
Article
en En
| MEDLINE
| ID: mdl-30306616
ABSTRACT
We present a molecular dynamics simulation study of alkali metal cation transport through the double-helical and the head-to-head conformers of the gramicidin ion channel. Our approach is based on a thermodynamic integration network, which consists of a sequence of transport reactions, absolute free energies of solvation and cycles of alchemical transmutations of the ions. In this manner, we can reliably estimate free energies and their statistical errors via a least-squares method without imposing external forces on the system. Within the double helical channel, we find a free energy surface typical for hopping transport between isoenergetic sites of ion localization, separated by comparatively large activation barriers. For fast transport through the head-to-head conformation, the thermodynamic network scheme starts to break down. © 2018 Wiley Periodicals, Inc.
Palabras clave
Texto completo:
1
Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Termodinámica
/
Redes Neurales de la Computación
/
Simulación de Dinámica Molecular
/
Canales Iónicos
Idioma:
En
Revista:
J Comput Chem
Asunto de la revista:
QUIMICA
Año:
2018
Tipo del documento:
Article
País de afiliación:
Alemania