Molecular Dynamics Simulation Studies of dTTP Binding and Catalysis Mediated by YhdE Dimerization

Area of Science:

• Biochemistry
• Structural Biology
• Enzymology

Background:

• YhdE is a Maf-like protein functioning as a dTTPase in cellular metabolism.
• Previous studies determined YhdE crystal structures in open and closed active site conformations.

Purpose of the Study:

• Investigate dTTP binding and hydrolysis by YhdE using molecular dynamics simulations.
• Elucidate the structural and energetic basis of YhdE's catalytic mechanism and conformational dynamics.

Main Methods:

• Molecular dynamics (MD) simulations.
• Free energy calculations.
• Analysis of protein structures and conformational states.

Main Results:

• The closed state of YhdE is more compact than the open state at room temperature.
• The open state favors dTTP binding, while the closed state is optimal for catalysis.
• YhdE dimerization is preferred during dTTP binding and promotes cooperative reactions.
• Key residues R11, R12, and K80 stabilize the substrate.
• Allosteric communication links dTTP binding sites to the dimer interface, inducing cooperativity.

Conclusions:

• YhdE utilizes distinct open and closed conformations for substrate binding and catalysis.
• Dimerization is crucial for YhdE's cooperative dTTP hydrolysis mechanism.
• An allosteric network mediates communication between the active site and the dimer interface, regulating enzyme activity.