Completed Diploma Works

Molecular Dynamics Simulation Studies of two Potassium Ion Channels, KcsA and KirBac1.1

Mikko Hellgren (2004)

The subject of this Master Thesis is two potassium ion channels - KcsA and KirBac1.1. Experimental data in the form of atomic resolution from x-ray crystallographic data was used to do molecular dynamics simulations. With molecular dynamics simulations it is possible to explore dynamical aspects of ion channels that can not be addressed directly by experimental methods.

From experimental data the positions of the potassium ions inside the protein is bonded to certain positions. Several simulations has been done on the movement of the ions with the ion channel KcsA. No article has been published about the movement of the ions inside the ion channel KirBac1.1.

The total system (protein, lipids, water and ions) was simulated without restraints for 5 ns for both channels. Simulations with KirBac1.1 indicate that the number of sites and conformation of the selectivity filter for KirBac1.1 is the same as in KcsA. With only one ion in the selectivity filter in KirBac1.1, the site S3 is the site that is occupied by a potassium ion.

The ligand TBA is known to interact with KcsA and it is an ion channel blocker. Simulations with TBA inside the pore cavity was done for both KirBac1.1 and KcsA. The ion channels were in a closed conformation. The results from the simulations show that TBA form weak bonds with the inside of the cavity. TBA inside the cavity would probably follow the electrochemical gradient toward the intracellular side if the ion channel turned to an open state.

TRITA-FYS-2004:13 | ISSN 0280-316X | ISRN KTH/FYS/--04:13--SE
The ion channel KirBac1.1 with the ligand TBA in the simulated box after 500ps (gray - KirBac1.1, yellow - TBA, blue - water, brown - DPPC, white - Chloride and red - Potassium).

Calculated Electron Densities in Lipid Bilayers

Mathias Ljungberg (2004)

In this thesis molecular dynamics simulations of lipid bilayers of the molecules dipalmitoylphosphatidylcholine (DPPC) and dimyristoylphosphatidylcholine (DMPC) in water are analyzed. Electron density profiles are constructed from the simulations, and are compared to the profiles obtained in x-ray diffraction experiments. The sources of error in this process are discussed, and attempts to correct them are made. This includes among other things the movement, the tilting and the undulations of the bilayer. New programs for the analysis are developed, and compared to the programs included in the Gromacs software package.

TRITA-FYS-2004:37 | ISSN 0280-316X | ISRN KTH/FYS/--04:37--SE
 

Collective Modes in Membrane Bilayers

Michael Marthaler (2004)

In my thesis I will simulate inelastic scattering experiments at membrane bilayers, for DMPC in liquid crystal phase, and analyze it in terms of the theory of generalized hydrodynamics. The data I use is taken from molecular dynamics simulations, which are made with simulation package GROMACS[1]. I will compare my results to the experiments of Chen et. al.[2] and to the simulations of M. Terek et. al.[3].
Advances in hardware, algorithm and simulation software give me the possibility to use longer simulations of bigger systems as M. Terek et. al. and so my hope is that I am not only able to reproduce the results, but to improve them.

TRITA-FYS-2004:36 | ISSN 0280-316X | ISRN KTH/FYS/--04:36--SE
 

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