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Conformational Sub-states and Populations in Enzyme Catalysis.
P K Agarwal1, N Doucet2, C Chennubhotla3
1Computational Biology Institute, Oak Ridge National Laboratory, Oak Ridge, TN, United States; University of Tennessee, Knoxville, TN, United States.
Methods in Enzymology
|August 7, 2016
Summary
Enzymes utilize coordinated protein motions and conformational substates to accelerate reactions. New techniques help identify and characterize these rare, functionally important enzyme states.
Area of Science:
- Biochemistry
- Structural Biology
- Enzymology
Background:
- Enzyme catalysis relies on substrate binding, active site positioning, and product release.
- Conserved protein motions within enzyme-substrate complexes significantly enhance reaction rates compared to solution-phase reactions.
Purpose of the Study:
- To discuss techniques for identifying and characterizing functionally important, high-energy enzyme conformational substates.
- To explore the role of protein dynamics and conserved motions in enzyme mechanisms.
Main Methods:
- Utilizes computer simulations and theoretical modeling to analyze enzyme dynamics.
- Employs nuclear magnetic resonance (NMR) spectroscopy for quantitative characterization of substates.
- Investigates enzyme-substrate complexes across various timescales (femtosecond to millisecond).
Main Results:
- Enzyme function is facilitated by coordinated motions and specific conformational substates.
- Higher-energy (excited) substates, though short-lived and rarely populated, are crucial for catalytic cycles.
- Specialized techniques are essential for the quantitative characterization of these transient states.
Conclusions:
- Understanding protein dynamics and conformational substates is key to elucidating enzyme mechanisms.
- Advanced computational and experimental methods enable the study of rare, functionally significant enzyme states.
- Characterizing these substates provides insights into enzyme efficiency and catalytic power.
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