Ion Move Brownian Dynamics (IMBD)--simulations of ion transport
Monika Kurczynska1, Malgorzata Kotulska1
1Department of Biomedical Engineering, Wroclaw University of Technology, Wroclaw, Poland.
Purpose:
Comparison of the computed characteristics and physiological measurement of ion transport through transmembrane proteins could be a useful method to assess the quality of protein structures. Simulations of ion transport should be detailed but also timeefficient.
Methods:
The most accurate method could be Molecular Dynamics (MD), which is very time-consuming, hence is not used for this purpose. The model which includes ion-ion interactions and reduces the simulation time by excluding water, protein and lipid molecules is Brownian Dynamics (BD). In this paper a new computer program for BD simulation of the ion transport is presented. We evaluate two methods for calculating the pore accessibility (round and irregular shape) and two representations of ion sizes (van der Waals diameter and one voxel).
Results:
Ion Move Brownian Dynamics (IMBD) was tested with two nanopores: alpha-hemolysin and potassium channel KcsA. In both cases during the simulation an ion passed through the pore in less than 32 ns. Although two types of ions were in solution (potassium and chloride), only ions which agreed with the selectivity properties of the channels passed through the pores.
Conclusions:
IMBD is a new tool for the ion transport modelling, which can be used in the simulations of wide and narrow pores.
More Related Videos
08:54Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid
Published on: January 25, 2020
08:40Using a Cyclic Ion Mobility Spectrometer for Tandem Ion Mobility Experiments
Published on: January 20, 2022
Related Concept Videos
01:31Transport Number
01:17Pore Transport and Ion-Pair Transport
Pore transport, also known as convective transport, is a process where small molecules like urea, water, and sugars rapidly cross cell membranes as though there were channels or pores in the membrane. Although direct microscopic evidence is limited but the concept of pores or channels is widely accepted based on physiological evidence. Despite the lack of direct...
01:17Ion Exchange
01:12Diffusion
01:21Carrier Transport
Drift Current:
The drift of charge carriers is started by an external electric field (E). Charged particles, such as electrons and holes, experience an acceleration between collisions with lattice atoms. For electrons, this results in a drift velocity (vd) given by:
03:45Formation of Complex Ions