Enzymatic GTP hydrolysis: insights from an ab initio molecular dynamics study

Area of Science:

• Biochemistry
• Computational Chemistry
• Enzymology

Background:

• Guanosine triphosphate (GTP) hydrolysis is crucial for cellular processes.
• The Cdc42/Cdc42GAP complex plays a role in GTP hydrolysis.
• Understanding the enzymatic mechanism is key to cellular regulation.

Purpose of the Study:

• To elucidate the fundamental aspects of the enzymatic mechanism of GTP hydrolysis.
• To investigate the role of the catalytic water molecule in the Cdc42/Cdc42GAP complex.
• To determine the nucleophilic addition pathway of the catalytic water to the gamma-phosphate.

Main Methods:

• Utilized ab initio computational methods.
• Employed a large model system to accurately represent active site electrostatic properties.
• Focused on the nucleophilic attack of catalytic water on the gamma-phosphate.

Main Results:

• Established the hydrogen bond pattern of catalytic water (WAT), interacting with Gln61 and Thr35.
• Ruled out direct proton transfer from catalytic water to the gamma-phosphate.
• Indicated a significantly altered electronic structure of WAT within the active site compared to bulk water.
• Showed proton transfer from WAT to Gln61 during the reaction.

Conclusions:

• The study clarifies the GTP hydrolysis mechanism in the Cdc42/Cdc42GAP complex.
• Findings support experimental data regarding the role of Gln61 and the Q61E mutant.
• The computational model accurately reproduced key electrostatic features of the enzyme's active site.