Biology Reference
In-Depth Information
ligands play a part in proton or electron transport they need to be present at various
points along the transport pathways. This implies that they must be able to bind at
many different locations: from the surface of the molecule (where hydrophobic
bonds may form between the protein's surface residues and the ligand's phosphate
moiety, particularly in the case of FMN) all the way to deep within binding pockets
(where they can be traced by the FOD model, as is the case with all of the presented
proteins to which this model has been successfully applied).
An interesting observation can be made with respect to the ligand binding site/
enzymatic active site relationship. The FOD model seems to suggest the need for
close proximity between the transport unit (responsible for moving electrons or
protons) and the catalytic site, while still retaining functional separation (different
residues responsible for each function, with different deviations from the idealized
hydrophobicity model as indicated by corresponding
Δ H pro fi le values, suggesting
different placement in the protein body and dedicated operating environments for
transport ligands and catalytic active sites).
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