L-lactate dehydrogenation in flavocytochrome b2: a first principles molecular dynamics study

Area of Science:

• Biochemistry
• Computational Chemistry
• Enzymology

Background:

• Flavocytochrome b2 (Fcb2) catalyzes L-lactate oxidation, a reaction mechanism still under investigation.
• Understanding Fcb2's catalytic mechanism provides insights into related flavoenzymes.

Purpose of the Study:

• To elucidate the enzyme-catalyzed L-lactate oxidation mechanism using first principles molecular dynamics.
• To investigate the roles of active site residues and cofactors in Fcb2 catalysis.

Main Methods:

• First principles molecular dynamics simulations of Fcb2 active-site models.
• Analysis of enzyme-substrate complex interactions and reaction pathways.
• Calculation of free energy barriers for key reaction steps.

Main Results:

• The reaction initiates with L-lactate alpha-OH proton abstraction by an active-site base (H373).
• Hydride transfer from lactate to flavin mononucleotide occurs without intermediates, forming pyruvate.
• A calculated free energy barrier of 12.1 kcal mol(-1) closely matches experimental values.

Conclusions:

• The study establishes a detailed mechanism for L-lactate oxidation by Fcb2.
• Key catalytic roles of the flavin mononucleotide-ribityl chain, an active site water molecule, and the flavin C4a-C10a locus were identified.
• Findings contribute to understanding catalysis in Fcb2 homologs and other flavoenzymes.