Intrinsic structural dynamics dictate enzymatic activity and inhibition

Area of Science:

• Biochemistry
• Structural Biology
• Enzymology

Background:

• Enzymes exhibit dynamic conformational sampling essential for biological function.
• Structural studies typically capture only the most populated enzyme conformation.
• Missense mutations can alter enzyme activity without significant structural changes in the dominant conformation.

Purpose of the Study:

• To investigate the role of enzyme dynamics in mediating the effects of mutations on enzyme activity and inhibitor binding.
• To characterize distinct functional conformations of histone deacetylase 8 (HDAC8).
• To link enzyme dynamics to enzymatic activity and drug potency.

Main Methods:

• Solution Nuclear Magnetic Resonance (NMR) spectroscopy to determine conformational ensembles.
• Kinetic analysis of enzyme mutants.
• Inhibitor binding assays.

Main Results:

• Reduced enzymatic activity, inhibitor affinity, and residence times in HDAC8 mutants correlate with altered rate constants between sampled conformations.
• Specific, underrepresented conformations are crucial for substrate binding, catalysis, and product release.
• Conformational dynamics, not just static structures, explain mutation effects.

Conclusions:

• Enzyme dynamics and conformational ensembles are critical determinants of enzymatic activity and inhibitor potency for HDAC8.
• Distinct conformational states play specific functional roles in the enzyme's catalytic cycle.
• Understanding enzyme dynamics is essential for accurate characterization of missense mutations and rational drug design.