Publication

QM/MM Car-Parrinello molecular dynamics study of selectivity in a potassium channel

2004
Conference Papers

Abstract

All biol. ion channels are selectively permeable to specific ions. This mechanism needs to be understood in terms of the interaction of the permeating ions with the surrounding water and protein mols. During the past several years, there have been enormous strides in our understanding of the structure-function relationships in biol. ion channels. Classical MD simulations have been used to investigate the selectivity mechanism, but the importance of polarization effects can hamper an adequate description of the potassium-protein interaction. In this context, quantum mechanics is the ultimate goal of any at. modeling of ionic channels and will help reaching a new level of accuracy and a finer understanding. We have recently developed a QM/MM scheme in which the chem. reactive part of the system can be treated quantum mech. using Car-Parinello mol. dynamics. This method paired with enhanced sampling techniques was used to investigate the mechanism of selectivity displayed by potassium channels. [on SciFinder (R)]

Official source

https://infoscience.epfl.ch/entities/publication/51f50e03-72d4-4de0-a1d1-0ab99ff642f5

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2004
Conference Papers

Abstract

Official source

https://infoscience.epfl.ch/entities/publication/51f50e03-72d4-4de0-a1d1-0ab99ff642f5

About this result

Related concepts (32)

Potassium channel

Potassium channels are the most widely distributed type of ion channel found in virtually all organisms. They form potassium-selective pores that span cell membranes. Potassium channels are found in most cell types and control a wide variety of cell functions. Potassium channels function to conduct potassium ions down their electrochemical gradient, doing so both rapidly (up to the diffusion rate of K+ ions in bulk water) and selectively (excluding, most notably, sodium despite the sub-angstrom difference in ionic radius).

Voltage-gated potassium channel

Voltage-gated potassium channels (VGKCs) are transmembrane channels specific for potassium and sensitive to voltage changes in the cell's membrane potential. During action potentials, they play a crucial role in returning the depolarized cell to a resting state. Alpha subunits form the actual conductance pore. Based on sequence homology of the hydrophobic transmembrane cores, the alpha subunits of voltage-gated potassium channels are grouped into 12 classes. These are labeled Kvα1-12.

Ion channel

Ion channels are pore-forming membrane proteins that allow ions to pass through the channel pore. Their functions include establishing a resting membrane potential, shaping action potentials and other electrical signals by gating the flow of ions across the cell membrane, controlling the flow of ions across secretory and epithelial cells, and regulating cell volume. Ion channels are present in the membranes of all cells. Ion channels are one of the two classes of ionophoric proteins, the other being ion transporters.

Related publications (8)

QM/MM Car-Parrinello molecular dynamics study of selectivity in a potassium channel

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