The cluster of hydrophobic residues controls the entrance to the active site of choline oxidase.
The active site of many enzymes is well-protected from solution by a gate. The opening and closing of these gates provide controlled access and could be the rate-limiting steps in catalytic processes. The gating mechanism of an enzyme is therefore very important in gaining broader insight into the entire catalytic process. However, the entrance to active sites and let alone the gating mechanisms are not always obvious from X-ray crystal structures of proteins. Here, we have proposed and quantitatively characterized an alternative gating mechanism controlled by a cluster of hydrophobic residues located on the solvent accessible surface of choline oxidase. We show that the opening and closing of the gate are very fast, and diffusion of choline to the active site is also fast and is partly controlled by the electrostatic potential of the enzyme. Using all-atom molecular dynamics and Brownian dynamics simulations, complete analyses of the mechanism of opening and closing of the gate, the rate of collision of the substrate with the enzyme, and the rate of formation of the complex have been conducted.
Xin
Yao
Y
Department of Chemistry, Georgia State University, Atlanta, Georgia 30302-4098, USA.
Gadda
Giovanni
G
Hamelberg
Donald
D
D000429:Alcohol Oxidoreductases / Q000737:chemistry* / Q000378:metabolism* / Q000502:physiology; D000596:Amino Acids / Q000737:chemistry* / Q000378:metabolism* / Q000502:physiology; D002384:Catalysis; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D057927:Hydrophobic and Hydrophilic Interactions; D015640:Ion Channel Gating / Q000502:physiology; D055672:Static Electricity
D000596:Amino Acids; D000429:Alcohol Oxidoreductases; C019888:choline oxidase