Ion Move Brownian Dynamics (IMBD) : Simulations of Ion Transport

• Autorzy: Kurczyńska M. , Kotulska M.

Identyfikatory

DOI

10.5277/ABB-00010-2014-02

• Języki publikacji: EN

Abstrakty

EN

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 time-efficient. 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.

Słowa kluczowe

EN

alpha-hemolysin; Brownian dynamics; ion transport; potassium channel; model quality assessment

PL

dynamika; transport jonów; potas; model jakości

• Wydawca: Oficyna Wydawnicza Politechniki Wrocławskiej
• Czasopismo: Acta of Bioengineering and Biomechanics
• Rocznik: 2014
• Tom: Vol. 16, no. 4
• Strony: 107--115
• Opis fizyczny: Bibliogr. 32 poz., tab., wykr.

Twórcy

autor

Kurczyńska M.

• Institute of Biomedical Engineering and Instrumentation, Wroclaw University of Technology, Wroclaw, Poland

autor

Kotulska M.

• Institute of Biomedical Engineering and Instrumentation, Wroclaw University of Technology, Wroclaw, Poland

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