Transition Path Sampling Study of the Reaction Catalyzed by Purine Nucleoside Phosphorylase

Area of Science:

• Biochemistry
• Computational Chemistry
• Enzymology

Background:

• Human purine nucleoside phosphorylase (hPNP) is crucial for purine metabolism.
• Understanding enzyme mechanisms requires detailed atomic-level insights.
• Rare events in biological systems are challenging to study.

Purpose of the Study:

• To elucidate the reaction mechanism of hPNP using advanced computational methods.
• To describe the detailed dynamics of reactive events without pre-defined reaction coordinates.

Main Methods:

• Applied Transition Path Sampling (TPS) combined with hybrid Quantum Mechanical/Molecular Mechanical (QM/MM) methods.
• Generated and analyzed hundreds of reactive trajectories.
• Calculated commitment probability along reactive paths.

Main Results:

• Identified a reaction mechanism involving N-ribosidic bond cleavage and ribooxacarbenium ion intermediates.
• Observed critical conformational changes and hydrogen bonding for phosphate capture.
• Characterized a broad energy barrier at the transition state.

Conclusions:

• The pseudorotational phase of the ribose ring is a significant variable for the reaction coordinate.
• Bond-breaking/forming distances are insufficient for describing the hPNP reaction coordinate.
• Detailed mechanistic insights into hPNP catalysis were obtained.