Molecular dynamics study of the KcsA channel at 2.0-A resolution: stability and concerted motions within the pore |
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Authors: | Compoint Mylène Carloni Paolo Ramseyer Christophe Girardet Claude |
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Institution: | Laboratoire de Physique Moléculaire, UMR CNRS 6624, Faculté des Sciences, la Bouloie, Université de Franche, Comté, 25030, Besan?on, France. mylene.compoint@univ-fcomte.fr |
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Abstract: | The stability of the KcsA channel accommodating more than one ion in the pore has been studied with molecular dynamics. We have used the very last X-ray structure of the KcsA channel at 2.0-A resolution determined by Zhou et al. Nature 414 (2001) 43]. In this channel, six of the seven experimentally evidenced sites have been considered. We show that the protein remains very stable in the presence of four K+ ions (three in the selectivity filter and one in the cavity). The locations and the respective distances of the different K+ ions and water molecules (W), calculated within our KWKWKK sequence, also fits well with the experimental observations. The analysis of the K+ ions and water molecules displacements shows concerted file motions on the simulated time scale (approximately 1 ns), which could act as precursor to the diffusion of K+ ions inside the channel. A simple one-dimensional dynamical model is used to interpret the concerted motions of the ions and water molecules in the pore leading ultimately to ion transfer. |
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