31-01-2012, 03:58 PM
Atomic Level Study of Channel Selectivity using Interactive methods
[attachment=16926]
GLpF and Glycerol Kinase
proteins facilitate the first two steps of Escherichia coli glycerol metabolism
GlpF is a member of the aquaporin family of channels used for water transport across the cell membrane
GK is an enzyme that catalyzes the phosphorylation of glycerol after it is conducted into the cytoplasm
The catalytic activity of GK is controlled through binding to the regulatory protein IIAGlc and fructose 1,6 – biphosphate.
IMD
Plug-in of VMD
IMD and SMD
SMD simulations proceed in three stages. First, a hypothesis is developed regarding the mechanism of the biological process of interest Second, the simulation is conducted with the weakest force possible to complete the process within an affordable amount of computer time Third, analysis of the simulation
Glycerol Kinase System Construction
Input : most complete monomer of GK with 59 bound water molecules and single bound glycerol
Open and closed GK
Modeling completely open GK