Molecular Dynamics Simulation of Ion Propagation through a Protein Ion Channel
Ljubomir T. Citkusev, Richard Brower and Charles DeLisi
Molecular Engineering Research Lab
College of Engineering
This work presents a quantitative modeling study of ion propagation through voltage gated membrane channels in terms of channel protein structure.
Ion channels in the cell membrane are made up of proteins that selectively allow transport of ions between the interior and the exterior of the cell. The function of ion channels is crucial in controlling the membrane resting potential, volume, and all the electrical responses of the cell.
This model describes a new efficient way of dealing with MD simulation of channel ion flow. It is a 3-D molecular dynamics simulation of ion flow through a detailed molecular structure representation of a channel protein. The model is a locally flexible serial molecular dynamics algorithm for ion propagation simulation through channels, that reduces the long-range calculations while taking the advantage of the detailed molecular structure of a channel protein and its interaction with the passing ions at the local level. The graphics present data from MD simulation of ion and water flow through a ‘de novo’ designed channel protein system. The high efficiency of this algorithm resulted in simulations of up to 1 millisecond of real time.
Hardware: Silicon Graphics Onyx.
Software: Graphics software written in Silicon Graphics GL.
Graphics programming and video production: Erik Brisson and Laura Giannitrapani, Scientific Computing and Visualization Group, Boston University.