Nonequilibrium Molecular Dynamics (MD) Simulations of Multi-ion Permeation in KcsA

Simulations of ion permeation through a potassium channel: molecular dynamics of KcsA in a phospholipid bilayer.

Potassium channels enable K(+) ions to move passively across biological membranes. Multiple nanosecond-duration molecular dynamics simulations (total simulation time 5 ns) of a bacterial potassium channel (KcsA) embedded in a phospholipid bilayer reveal motions of ions, water, and protein. Comparison of simulations with and without K(+) ions indicate that the absence of ions destabilizes the st...

Nonequilibrium molecular dynamics calculation of the conductance of the KcsA potassium ion channel.

We have developed an efficient method for the atomistic determination of the conductance of a biological ion channel model by applying an external field to the conducting ions only. The underlying theory is discussed and demonstrated in a simple test system consisting of two ions in a box of water. Finally, the theory is applied to the experimentally determined structure of the KcsA potassium c...

Modeling Nanocomposites for Molecular Dynamics (md) Simulations

Molecular Simulations of Ion Permeation in Potassium Channels

specific steps in voltage-activation path of an ion channel are altered by a potent allosteric inhibitor. The Kþ channel peptide inhibitor guangxitoxin-1E (GxTX) is partial inverse agonist of the voltage gated potassium channel subtype Kv2.1 from rat. At saturating concentrations of GxTX, Kv2.1 requires higher voltages to activate. The GxTX modulated conductance requires more voltage to activat...

Molecular Architecture of Full-Length KcsA Role of Cytoplasmic Domains in Ion Permeation and Activation Gating

The molecular architecture of the NH 2 and COOH termini of the prokaryotic potassium channel KcsA has been determined using site-directed spin-labeling methods and paramagnetic resonance EPR spectroscopy. Cysteine mutants were generated (residues 5–24 and 121–160) and spin labeled, and the X-band CW EPR spectra were obtained from liposome-reconstituted channels at room temperature. Data on prob...