- Tytuł:
- Ion Move Brownian Dynamics (IMBD) : Simulations of Ion Transport
- Autorzy:
-
Kurczyńska, M.
Kotulska, M. - Powiązania:
- https://bibliotekanauki.pl/articles/307444.pdf
- Data publikacji:
- 2014
- Wydawca:
- Politechnika Wrocławska. Oficyna Wydawnicza Politechniki Wrocławskiej
- Tematy:
-
dynamika
transport jonów
potas
model jakości
alpha-hemolysin
Brownian dynamics
ion transport
potassium channel
model quality assessment - Opis:
- 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.
- Źródło:
-
Acta of Bioengineering and Biomechanics; 2014, 16, 4; 107-115
1509-409X
2450-6303 - Pojawia się w:
- Acta of Bioengineering and Biomechanics
- Dostawca treści:
- Biblioteka Nauki
Artykuł