Mesophilic Pyrophosphatase Function at High Temperature: A Molecular Dynamics Simulation Study.

Area of Science:

• Biochemistry
• Structural Biology
• Computational Biology

Background:

• Inorganic pyrophosphatases (PPases) are crucial enzymes.
• Understanding enzyme adaptation to extreme temperatures is vital.
• The mesophilic Escherichia coli PPase (EcPPase) and hyperthermophilic Thermococcus thioreducens PPase (TtPPase) exhibit contrasting thermal stabilities.

Purpose of the Study:

• To elucidate the molecular basis for the asymmetric thermal stability between EcPPase and TtPPase.
• To investigate the structural and dynamical properties influencing enzyme function at different temperatures.

Main Methods:

• Molecular dynamics (MD) simulations were employed.
• Simulations were conducted under various temperature and pressure conditions.
• Structural parameters like solvent-exposed surface area, subunit compaction, and catalytic pocket dynamics were analyzed.

Main Results:

• Hyperthermophilic TtPPase exhibits higher global flexibility than mesophilic EcPPase across tested conditions.
• At 353 K, EcPPase demonstrates adaptability by reducing surface area and increasing subunit compaction while preserving catalytic pocket flexibility.
• Conversely, TtPPase shows increased rigidity and diminished protein-water interactions in its catalytic pocket at room temperature, correlating with its inactivity.

Conclusions:

• EcPPase's ability to modulate its structure, particularly its catalytic pocket, allows for functional retention at high temperatures.
• TtPPase's lack of adaptability at lower temperatures explains its inactivity near room temperature.
• These findings provide insights into the molecular mechanisms of enzyme thermostability and adaptation.