Atomic Level Study of Channel Selectivity using Interactive methods

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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