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Hydrolysis of cyclic phosphates by ribonuclease A: a computational study using a simplified ab initio quantum model
Brian D Wladkowski1, Paul Ostazeski, Sarah Chenoweth
1Department of Chemistry, McDaniel College, 2 College Hill, Westminster, MD 21157, USA.
Journal of Computational Chemistry
|September 10, 2003
Summary
Ribonuclease A (RNase A) enzyme catalysis was modeled to understand phosphate ester hydrolysis. Entropic and environmental factors favor intermediate release over hydrolysis, revealing autocatalysis in charged substrates.
Area of Science:
- Biochemistry
- Enzymology
- Computational Chemistry
Background:
- Ribonuclease A (RNase A) catalyzes the hydrolysis of phosphate esters.
- Understanding the enzyme's catalytic mechanism is crucial for biochemical research.
Purpose of the Study:
- To investigate the second step of RNase A-catalyzed hydrolysis using computational modeling.
- To elucidate the factors governing the preferential release of the cyclic phosphate intermediate.
Main Methods:
- Ab initio quantum-based modeling of the RNase A active site.
- Inclusion of key residues (His-12, His-119, Lys-41) and a small substrate.
- Exploration of RHF and MP2 levels of theory.
Main Results:
- Electronic factors slightly favor hydrolysis, but entropic and environmental effects favor intermediate release.
- Activation free energy for hydrolysis is approximately 70 kJ mol(-1).
- Autocatalysis by the substrate was observed, similar to the transphosphorylation step.
Conclusions:
- Entropic and environmental effects play a significant role in RNase A's catalytic mechanism.
- Autocatalysis may be a common feature in enzymes with charged substrates like phosphates.
- Multiple proton transfer pathways contribute to the reaction mechanism.