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Modulating Enzyme Catalysis through Mutations Designed to Alter Rapid Protein Dynamics.

Ioanna Zoi¹, Javier Suarez², Dimitri Antoniou¹

¹Department of Chemistry and Biochemistry, University of Arizona , 1306 East University Blvd, Tucson, Arizona 85721, United States.

Journal of the American Chemical Society

|March 2, 2016

Summary

This summary is machine-generated.

Heavy enzyme studies reveal sub-picosecond protein motions are crucial for catalysis. Mutating purine nucleoside phosphorylase (PNP) uncoupled these motions, decreasing barrier crossing and confirming femtosecond dynamics

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Area of Science:

Biochemistry
Enzyme kinetics
Computational biophysics

Background:

The role of ultrafast (sub-picosecond) protein motions in enzyme catalysis is debated.
Heavy enzymes, created through isotopic substitution, serve as experimental probes for vibrational coupling in catalysis.
Previous studies linked heavy purine nucleoside phosphorylase (PNP) to mass-dependent barrier crossing rates.

Purpose of the Study:

To computationally identify amino acid residues influencing catalytic site vibrations in PNP.
To investigate the impact of altered vibrational freedom on heavy enzyme effects.
To elucidate the contribution of femtosecond dynamics to enzymatic barrier crossing.

Main Methods:

Computational identification of second-sphere residues affecting catalytic site vibrational modes.
Site-directed mutagenesis of heavy and light purine nucleoside phosphorylase (PNP) to modify vibrational freedom.
Measurement of enzymatic barrier-crossing rates in wild-type and mutated PNP variants.

Main Results:

Mutations increased catalytic site vibrational freedom in both heavy and light PNP.
Enzymatic barrier-crossing rates transitioned from mass-dependent to mass-independent post-mutation.
Mutagenic uncoupling of femtosecond motions reduced transition state barrier crossing by two orders of magnitude.

Conclusions:

Sub-picosecond protein motions significantly contribute to enzymatic catalysis.
Modulating vibrational freedom via mutagenesis can decouple heavy enzyme effects.
Femtosecond dynamics play a critical role in determining the efficiency of enzyme-catalyzed reactions.