Arginine Kinase Activates Arginine for Phosphorylation by Pyramidalization and Polarization.

Area of Science:

• Biochemistry
• Computational Chemistry
• Enzymology

Background:

• Arginine phosphorylation is a vital biological process.
• Arginine kinase (AK) facilitates the transfer of phosphoryl groups from ATP to arginine.
• Understanding the mechanism of AK is key to comprehending arginine modification in biology.

Purpose of the Study:

• To elucidate the transition state (TS) model for the AK-catalyzed reaction using Density Functional Theory (DFT).
• To investigate the role of hydrogen bonding in the catalytic mechanism of AK.
• To understand the mechanism of the reverse reaction, including phosphoarginine hydrolysis.

Main Methods:

• Density Functional Theory (DFT) calculations were employed to model the transition state of the AK-catalyzed reaction.
• Analysis of hydrogen bond networks and their impact on substrate conformation and electronic properties.
• Investigation of the electronic and structural changes in the arginine side chain during catalysis.

Main Results:

• A detailed transition state model for AK-catalyzed arginine phosphorylation was developed.
• A network of over 50 hydrogen bonds was identified, inducing significant pyramidalization and polarization of the arginine guanidinium nitrogen (Nη2).
• This distortion aligns Nη2 electron density with the scissile P-O bond, facilitating in-line phosphoryl transfer via an associative mechanism. The reverse reaction involves substrate distortion to enhance Nη2 basicity for protonation and subsequent ATP regeneration.

Conclusions:

• The study reveals a novel mechanism involving nitrogen polarization-pyramidalization in arginine side chains during enzymatic catalysis.
• This mechanism is likely conserved across various enzymes involved in post-translational modification of arginine.
• The findings provide fundamental insights into the energetics and structural requirements for efficient phosphoryl transfer in biological systems.