TY  - THES
T1  - Biomolecular transport across and along membranes studied by molecular dynamics simulations
A1  - Siu,Weng In
Y1  - 2010/09/02
N2  - Biomolecular transport processes allow the exchange of ions and other molecules across the membranes of organelles and cells. Here, we studied selected membrane-bound transport processes by means of molecular dynamics simulations, with a special focus on the interaction of membrane proteins with their environment.
As a model system, the cation-selective gramicidin channel in both the channel and non-channel conformation embedded in a phospholipid bilayer was chosen. Upon application of external electric fields a stabilizing effect of gramicidin on the membrane could be shown. Due to favorable interactions between lipids and cations at the channel entrance a significantly decreased free energy barrier for potassium ion permeation through the non-channel conformation was found, a result which underlines the importance of environmental effects for the function of membrane proteins. In order to improve the combined treatment of proteins and lipids in simulations, a new lipid force field based on the generalized AMBER force field was developed, yielding a marked improvement on the structural properties of DOPC membranes as compared to existing force fields.
Proton transport in bulk water and close to membranes was addressed by the semiempirical Q-HOP method. In excellent agreement with experiments we found a linear dependency of proton diffusion on temperature and observed single events with large lateral diffusion distances close to membranes.
KW  - Molekulardynamik
KW  - Stofftransport <Biologie>
KW  - Lipid-Lipid-Wechselwirkung
KW  - Consistent Force Field
CY  - Saarbrücken
PB  - Universitäts- und Landesbibliothek
AD  - Postfach 151141, 66041 Saarbrücken
UR  - http://scidok.sulb.uni-saarland.de/volltexte/2010/3301
ER  -