Movement of Potassium Ions inside KcsA in the High Concentration Regime using a Molecular Dynamics Simulation

• Published in: Journal of the Korean Physical Society 2018, 72(9), , pp.1013-1019
• Main Authors: Kim, Myojeong, Jo, Byeong Chul, Yoon, Hyun Jung, Wu, Sangwook, Thangappan, Jayaraman, Eun, Changsun
• Format: Article
• Language: English
• Subjects: Ion concentration; Ions; Mathematical and Computational Physics; Molecular dynamics; Particle and Nuclear Physics; Physics; Physics and Astronomy; Potassium; Residues; Selectivity; Simulation; Theoretical; Water chemistry; 물리학
• ISSN: 0374-4884; 1976-8524
• DOI: 10.3938/jkps.72.1013

The selectivity and conduction specificity of the KcsA channel toward potassium ions is crucial to the activity of this protein and this channel is intricately associated with several osmotic regulation and neuronal signaling processes. Despite multi-ion characteristics, the selective conduction behavior of KcsA is controlled by the size and distance specific electrostatic interaction between the selected residues and the potassium ions. The mechanism describing the movement of potassium ions in the channel and the conformational changes to KcsA that facilitate ion movement were investigated by a molecular dynamics (MD) simulation. In this study, we analyze the movement of potassium ions and water molecules at various time intervals during a 90 ns molecular dynamics simulation in the high potassium ion concentration regime and in the absence of the voltage. Examination of specific (3.6, 17.3, 43.38 and 43.44 ns) simulation periods revealed that key residues in the selectivity filter of KcsA influence the movement of potassium ions in the channel.