Substrate recognition by norovirus polymerase: microsecond molecular dynamics study.

Area of Science:

• Biochemistry
• Structural Biology
• Computational Biology

Background:

• Norwalk virus RNA-dependent RNA polymerase (RdRp) is crucial for viral replication.
• Understanding substrate interactions with viral RdRp is key to developing antiviral strategies.

Purpose of the Study:

• To investigate the binding mechanisms of various nucleoside triphosphates with Norwalk virus RdRp using molecular dynamics simulations.
• To elucidate how different substrate structures influence the polymerase's activity and mode of action.

Main Methods:

• Microsecond molecular dynamics (MD) simulations were performed using ACEMD software on CUDA-enabled GPUs.
• Simulations focused on complexes of Norwalk virus RdRp with CTP, 2dCTP, coCTP, and cocCTP substrates.
• Analysis of trajectories to observe binding poses and conformational changes within the active site.

Main Results:

• Distinct binding patterns were observed for similar nucleoside triphosphates in the RdRp active site.
• CTP and 2dCTP exhibited substrate-like binding, while coCTP acted as a chain terminator and cocCTP as an inhibitor.
• Rare conformational events, such as the movement of Arg182, were captured, potentially influencing reaction dynamics.

Conclusions:

• The precise atomic arrangement of nucleoside triphosphates significantly impacts their interaction with Norwalk virus RdRp.
• Different binding modes directly correlate with the observed functional outcomes (substrate, poor substrate, chain terminator, inhibitor).
• MD simulations provide valuable insights into the dynamic mechanisms governing viral polymerase activity and substrate recognition.