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Structural analysis of the lactoferrin iron binding pockets

Marchewka D., Roterman I., Strus M., Śpiewak K., Majka G.

Bio-Algorithms and Med-Systems

2012

Vol. 8, no. 4

351--359

Lactoferrin (Lf) - member of the transferrin family of proteins responsible for many different functions in the body of mammals participates in regulation of free iron level in the body fluids making the protein bacteriostatic. The main goal of studies was to test the suitability of molecular dynamic simulation to study structural changes in the tertiary structure of lactoferrin. According to ConSurf Server analysis one of the most conservative amino acids was found not only in iron- but also in carbohydrates- binding pockets which may suggest a significant impact of carbohydrates on the functions performed by lactoferrin. Pocket-Finder program applied to find iron-binding pockets revealed the potential Fe binding area. The stability of the ligand deprived protein was verified performing the 50 ns dynamic simulation using the Gromacs program. The tertiary structure changes during the simulation were observed in N-lob solely. No structural changes were observed in C-lob iron-binding pocket.

Size and wall effects in water flows in nanochannels

Kucaba-Pietal A., Walenta Z., Peradzynski Z.

Turbulence : international journal

2004

Vol. 10

77-81

The results of the simulations of plane Poiseuille flow of water through narrow channels are presented and compared with the analytical solutions for micropolar fluid. In the simulations performed by use the Molecular Dynamic method, physical properties of the materials and their electrostatic interactions were considered. Simulation of the flow was carried on for two different channel width and two different materials of the walls (copper and quartz).