Functional dynamics of hexameric helicase probed by hydrogen exchange and simulation

Area of Science:

• Biochemistry
• Structural Biology
• Computational Biology

Background:

• Biological function of macromolecular assemblies relies on structure and dynamics.
• Investigating these assemblies is challenging with conventional experimental methods.
• Hydrogen-deuterium exchange mass spectrometry (HDX-MS) is a promising technique.

Purpose of the Study:

• To present a novel computational method for quantitative interpretation of deuterium exchange kinetics.
• To apply this method to understand the dynamics of the hexameric viral helicase P4.
• To provide residue-level interpretation of experimental results for complex biological systems.

Main Methods:

• Development of a new computational method for deuterium exchange kinetics interpretation.
• Application of all-atom molecular dynamics (MD) simulations (100 ns) at room temperature.
• Analysis of exchange kinetics for the hexameric viral helicase P4.

Main Results:

• The computational method successfully predicts deuterium exchange kinetics for most sequence fragments.
• All-atom MD simulations provide sufficient data for residue-level interpretation.
• The method offers insights into dynamics not observable by X-ray crystallography.

Conclusions:

• The developed computational strategy enables quantitative interpretation of HDX-MS data.
• It provides a valuable tool for validating experimental assignments and probing molecular mechanisms.
• This approach advances the study of large macromolecular assemblies and their dynamics.