MEASURING THE BINDING ENERGY OF GLUCOSE TO THE GLUCOSE/GALACTOSE BINDING PROTEIN COMPUTATIONALLY

Nicholas Rigel, Amil G Anderson

Abstract


The Glucose/Galactose Binding Protein (GGBP) is crucial to bacterial chemotaxis in E. coli and other bacteria, binding either to glucose or galactose1. GGBP is an α/β protein consisting of two globular Rossman fold domains joined by three peptide segments2,3. Since GGBP binds to glucose in E. coli, it has the possible use as a bio-indicator in diabetes patients4. GGBP normally exists in its closed conformation and opens to bind to glucose5. GGBP binds to glucose with a hinge feature that causes the protein to close around the sugar. A hinge angle exists between a residue in each domain and a residue near the binding pocket. An umbrella sampling molecular dynamics method was implemented to not only explore the conformation change when GGBP binds to glucose, but also to measure the Gibb’s free energy of binding. An angle change of 23.5° was observed experimentally, while 22.0° was observed during the umbrella sampling1. The experimental Gibb’s free energy of binding of GGBP to glucose is −9.1 kcal/mol, while a binding energy of −10.2(±0.9) kcal/mol was calculated by umbrella sampling6.


Keywords


Glucose/Galactose Binding Protein, Free Energy of Binding Calculations, Molecular Dynamics

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