Molecular Dynamics Simulations of Hydrophobic Matching in KcsA

Molecular Dynamics Simulations of Hydrophobic Solutes in Liquid Water

The hydrophobic e ect of small apolar solutes is studied by molecular dynamic (MD) simulations. Interactions between two solutes can be described by the potential of mean force (PMF). The general feature of the PMF between two solutes in water is a potential barrier separating a stable contact con guration and a meta-stable solventseparated con guration. Interestingly, compared with classical M...

Molecular dynamics estimates of ion diffusion in model hydrophobic and KcsA potassium channels.

Molecular dynamics simulations are carried out to obtain estimates of diffusion coefficients of biologically important Na+, K+, Ca2+ and Cl- ions in hydrophobic cylindrical channels with varying radii and large reservoirs. Calculations for the cylindrical channels are compared to those for the KcsA potassium channel, for which the protein structure has recently been determined from X-ray diffra...

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...

Analysis of the Sequence KWKWK...K in the KcsA Protein Channel using Molecular Dynamics Simulations

Extracellular Blockade of K Channels by TEA: Results from Molecular Dynamics Simulations of the KcsA Channel

TEA is a classical blocker of K channels. From mutagenesis studies, it has been shown that external blockade by TEA is strongly dependent upon the presence of aromatic residue at Shaker position 449 which is located near the extracellular entrance to the pore (Heginbotham, L., and R. MacKinnon. 1992. Neuron. 8:483– 491). The data suggest that TEA interacts simultaneously with the aromatic resid...