Modeling negative ion defect migration through the gramicidin A channel

• Published in: Journal of molecular modeling Vol. 15; no. 8; pp. 1009 - 1012
• Main Authors: Nemukhin, Alexander V, Kaliman, Ilya A, Moskovsky, Alexander A
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Berlin/Heidelberg : Springer-Verlag 01.08.2009; Springer-Verlag
• Subjects: Algorithms; Amino Acid Sequence; Characterization and Evaluation of Materials; Chemistry; Chemistry and Materials Science; Computer Appl. in Life Sciences; Computer Applications in Chemistry; Computer Simulation; gramicidin; Gramicidin - chemistry; Gramicidin - metabolism; Hydrogen Bonding; Kinetics; Membrane Potentials; Models, Chemical; Models, Molecular; Molecular Medicine; Molecular Sequence Data; Original Paper; Potential of mean force; Protein Binding; Protein Structure, Secondary; Protein Structure, Tertiary; Proton transport; Protons; Theoretical and Computational Chemistry; Water - chemistry; Water - metabolism; Potential of mean force; Gramicidin; Proton transport

The results of potential of mean force (PMF) calculations for the distinct stages of proton conduction through the gramicidin A channel, including proton migration, reorientation of the water file and negative ion defect migration, are presented. The negative ion defect migration mechanism was hypot...