Molecular Environment Modulates CO₂ Liberation from Carboxy-Biotin

Area of Science:

• Biochemistry
• Computational Chemistry

Background:

• Biotin-dependent carboxylases utilize carboxy-biotin as a coenzyme for carboxylation reactions.
• These enzymes have two domains: biotin carboxylase (BC) for carboxylation and carboxyltransferase (CT) for CO2 transfer.
• The mechanism of CO2 release from carboxy-biotin in the CT domain remains unclear.

Purpose of the Study:

• To investigate the decarboxylation mechanism of carboxy-biotin.
• To determine the influence of molecular environment and protonation state on CO2 release.
• To accurately calculate the pKa of carboxy-biotin in various environments.

Main Methods:

• Advanced computational chemistry methods were employed.
• Decarboxylation of carboxy-biotin was studied in diverse molecular environments.
• Protonation states and pKa values of carboxy-biotin were calculated with high accuracy.

Main Results:

• Spontaneous decarboxylation of carboxy-biotin occurs only in its protonated form, irrespective of environmental polarity.
• A computational method achieving sub-kcal/mol accuracy for pKa calculation was established.
• Nonpolar environments, like the CT active site, facilitate spontaneous CO2 release from protonated carboxy-biotin.

Conclusions:

• Protonation state is critical for carboxy-biotin decarboxylation.
• Nonpolar active sites in carboxyltransferase domains promote CO2 release.
• This finding elucidates a key step in biotin-dependent carboxylation reactions.