Loop motion and base release in purine-specific nucleoside hydrolase: a molecular dynamics study

Area of Science:

• Biochemistry
• Structural Biology
• Parasitology

Background:

• Crystal structures of Trypanosoma vivax purine-specific inosine-adenosine-guanosine nucleoside hydrolase (IAG-NH) are known.
• The substrate hydrolysis mechanism of IAG-NH has been recently investigated.
• Mechanistic details of base and ribose release from IAG-NH remain unclear.

Purpose of the Study:

• To elucidate the regulation mechanisms of key residues and loops for base release in IAG-NH.
• To investigate the energetic landscape of base release using computational methods.

Main Methods:

• Molecular dynamics (MD) simulations were employed.
• Umbrella sampling technique was utilized in conjunction with MD simulations.
• Analysis focused on key residues and loops (1 and 2) involved in base release.

Main Results:

• Base release is not the rate-limiting step in the overall hydrolysis process.
• A low energy barrier (~5.6 kcal/mol) for base release was identified, easily overcome by substrate hydrolysis exothermicity.
• Specific residues (Glu82/Trp83 in loop 1, His247/Arg252 in loop 2) were found to modulate base release.
• A partial helix-to-coil transition in loop 2 was observed during base release, consistent with crystal structures.

Conclusions:

• Key residues and loops play crucial roles in modulating the base release mechanism of IAG-NH.
• The base release step is energetically favorable and not rate-limiting.
• MD simulations provide valuable insights into the dynamic aspects of enzyme mechanisms, complementing structural data.