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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

RETRACTED: Computational design of a biologically active enzyme.

Mary A Dwyer¹, Loren L Looger, Homme W Hellinga

¹Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA.

Science (New York, N.Y.)

|June 26, 2004

Summary

Computational enzyme design successfully introduced triose phosphate isomerase activity into a non-enzymatic protein using 18-22 mutations. The engineered enzymes show significant rate enhancements and biological activity, supporting bacterial growth.

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Area of Science:

Protein chemistry
Enzyme engineering
Computational biology

Background:

Enzyme activity is crucial for biological processes.
Rational enzyme design is a challenging but important field.
Understanding protein structure-function relationships is key.

Purpose of the Study:

To computationally design and experimentally validate enzyme activity in a protein lacking it.
To introduce triose phosphate isomerase (TIM) activity into ribose-binding protein (RBP).
To demonstrate the generality of the computational design approach.

Main Methods:

Utilized computational methods to predict mutations for introducing TIM activity into RBP.
Designed proteins with 18 to 22 specific mutations.
Experimentally validated the designed enzymes' activity and biological function.

Main Results:

The designed proteins exhibited 10^5- to 10^6-fold rate enhancements compared to the uncatalyzed reaction.
The engineered enzymes demonstrated biological activity, supporting Escherichia coli growth under gluconeogenic conditions.
Successfully introduced a new enzymatic function into a non-enzymatic protein scaffold.

Conclusions:

The computational design approach is effective for creating novel enzyme activities.
This method has broad potential for designing a wide range of enzymes.
The study validates the power of rational protein design in synthetic biology.