Molecular Dynamics Simulations of Membrane–Sugar Interactions

Molecular dynamics simulations for plasma-surface interactions

Modeling of annexin A2—Membrane interactions by molecular dynamics simulations

The annexins are a family of Ca2+-regulated phospholipid binding proteins that are involved in membrane domain organization and membrane trafficking. Although they are widely studied and crystal structures are available for several soluble annexins their mode of membrane association has never been studied at the molecular level. Here we obtained molecular information on the annexin-membrane int...

Observation and description of phonon interactions in molecular dynamics simulations

Three-phonon interactions are identified and analyzed in nonequilibrium molecular dynamics simulations of the Lennard-Jones face-centered cubic crystal. The small simulation cells studied and the classical nature of the simulations lead to a different description of the phonon transport than the quantum-particle model. The selection process is strictly governed by the mode wave vectors. In dete...

Large Scale Molecular Dynamics Simulations of Lipid-Drug Interactions

Molecular dynamics is a powerful computational technique for studying biochemical systems at the atomic resolution. We will present the results of several recent studies in our laboratory that apply molecular dynamics to the distribution and behaviour of small molecules within lipid bilayer environments similar to the membrane surrounding all cells. Specifically, we have studied the distributio...

Three new scorpion chloride channel toxins as potential anti-cancer drugs: Computational prediction of the interactions with hMMP-2 by docking and Steered Molecular Dynamics Simulations

Scorpion venom is a rich source of toxins which have great potential to develop new therapeutic agents. Scorpion chloride channel toxins (ClTxs), such as Chlorotoxin selectively inhibit human Matrix Methaloproteinase-2 (hMMP-2). The inhibitors of hMMP-2 have potential use in cancer therapy. Three new ClTxs, meuCl14, meuCl15 and meuCl16, derived from the venom transcriptome of Iranian scorpion, ...