Molecular Dynamics Simulation of a Synthetic Ion Channel

Molecular dynamics simulation of a synthetic ion channel.

A molecular dynamics simulation has been performed on a synthetic membrane-spanning ion channel, consisting of four alpha-helical peptides, each of which is composed of the amino acids leucine (L) and serine (S), with the sequence Ac-(LSLLLSL)3-CONH2. This four-helix bundle has been shown experimentally to act as a proton-conducting channel in a membrane environment. In the present simulation, ...

Molecular Dynamics Simulation of Synthetic Polymers

Investigation of Melting by Molecular Dynamics Simulation

The melting of a 64 ion microcrystal of KCI was studied by means of a molecular dynamics computer simulation. We used a central pair interaction with an inverse power law repulsion. The thermodynamics, kinetic and structural properties such as melting temperature, latent heat, mean square displacement, diffusion constant, radial distribution function and bond angle distribution are calculated. ...

Transmembrane domains of viral ion channel proteins: a molecular dynamics simulation study.

Nanosecond molecular dynamics simulations in a fully solvated phospholipid bilayer have been performed on single transmembrane alpha-helices from three putative ion channel proteins encoded by viruses: NB (from influenza B), CM2 (from influenza C), and Vpu (from HIV-1). alpha-Helix stability is maintained within a core region of ca. 28 residues for each protein. Helix perturbations are due eith...

Interactions of Lipids and Detergents with a Viral Ion Channel Protein: Molecular Dynamics Simulation Studies

Structural studies of membrane proteins have highlighted the likely influence of membrane mimetic environments (i.e., lipid bilayers versus detergent micelles) on the conformation and dynamics of small α-helical membrane proteins. We have used molecular dynamics simulations to compare the conformational dynamics of BM2 (a small α-helical protein from the membrane of influenza B) in a model phos...