Conformational selection in the flaviviral NS2B-NS3 protease

Area of Science:

• Structural biology
• Virology
• Biochemistry

Background:

• Flaviviral proteases (NS2B-NS3) exist in open and closed states, affecting binding site shape.
• Previous models emphasized NS2B flexibility and induced-fit ligand binding.
• Limited NS3 plasticity was noted, with NS2B dynamics dominating active site flexibility.

Purpose of the Study:

• To investigate the influence of the NS3 protease domain's fold on the active site's shape.
• To re-evaluate the induced-fit model for ligand binding in flaviviral proteases.
• To explore the role of NS3 conformational dynamics in protease-ligand interactions.

Main Methods:

• X-ray crystallography of Zika protease complexed with a dipeptide boronate.
• Comparative analysis of available flaviviral protease structures.
• Identification of conserved residues mediating NS3 structural changes.

Main Results:

• NS3 exhibits significant conformational plasticity, influencing active site depth.
• A novel subpocket (subpocket B) is revealed in NS3, connecting orthosteric and allosteric sites.
• Structural data supports molecular recognition via conformational selection and population shift over induced-fit.
• Conserved residues mediate NS3 dynamics, impacting the active site.

Conclusions:

• NS3 conformational dynamics play a critical role in defining the flaviviral protease active site shape.
• Conformational selection is a more accurate model for flaviviral protease-ligand interactions.
• Understanding NS3 plasticity and subpocket B is crucial for protease inhibitor design and drug development.