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Dynamical activation of function in metalloenzymes.

Judith P Klinman^1,2,3

¹Department of Chemistry, University of California, Berkeley, CA, USA.

|October 14, 2022

Summary

Enzyme catalysis involves hydrogen tunneling, with protein structures creating thermal barriers independent of chemical steps. Temperature-dependent hydrogen deuterium exchange (TDHDX) identifies these protein thermal networks, revealing insights into enzyme dynamics.

Keywords:

C-H activation by tunneling metalloenzymes protein dynamics temperature-dependent hydrogen deuterium exchange thermal networks time-resolved protein motions

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Area of Science:

Biochemistry
Enzymology
Protein Dynamics

Background:

Enzyme-catalyzed C-H activation reactions exhibit hydrogen tunneling.
Enthalpic barriers in these reactions are linked to the protein scaffold, not chemical steps.
Understanding protein dynamics is crucial for elucidating enzyme mechanisms.

Purpose of the Study:

To identify catalytically relevant, site-specific protein thermal networks.
To analyze the impact of mutations on protein unfolding and activation energy (Ea).
To establish a framework for understanding protein motions relevant to enzyme function.

Main Methods:

Temperature-dependent hydrogen deuterium exchange (TDHDX) was employed.
Analysis focused on mutant enzyme forms with altered catalytic activation energies.
Nanosecond Stokes shifts were measured on soybean lipoxygenase.

Main Results:

TDHDX identified protein thermal networks linked to catalytic reactions and metal binding sites.
These networks were independent of protein scaffold conservation.
Activation energies derived from thermal network surface dynamics matched catalytic turnover (kcat) values.

Conclusions:

A rapid, cooperative structural reorganization within thermal networks acts as the primary thermal barrier to catalysis.
A model integrating conformational sampling and thermal networks explains protein dynamics.
This research provides a new perspective on enzyme catalysis and protein motion.