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Enzyme-like proteins by computational design.

D N Bolon1, S L Mayo

  • 1Biochemistry and Molecular Biophysics Option, California Institute of Technology, Mail Code 147-75, Pasadena, CA 91125, USA.

Proceedings of the National Academy of Sciences of the United States of America
|November 29, 2001
PubMed
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Researchers developed a computational method to create artificial enzymes called protozymes. Initial experiments show these novel protein catalysts exhibit significant activity, paving the way for new functional protein design.

Area of Science:

  • Biochemistry
  • Protein Engineering
  • Computational Biology

Background:

  • Enzyme catalysis is crucial for biological processes.
  • Designing novel protein catalysts with predictable functions remains a significant challenge.
  • Existing methods for designing protein catalysts are often limited by scaffold specificity.

Purpose of the Study:

  • To develop and validate a computational design procedure for generating artificial enzyme-like protein catalysts (protozymes).
  • To investigate the relationship between protein structure and catalytic function.
  • To explore a novel approach for protein engineering independent of specific protein folds.

Main Methods:

  • Utilized a "compute and build" strategy based on physical and chemical principles of protein stability and catalysis.

Related Experiment Videos

  • Employed the Escherichia coli thioredoxin scaffold and a histidine-mediated nucleophilic hydrolysis model reaction.
  • Used ORBIT protein design software for sequence computation and active site analysis.

    • Main Results:

    • Identified two promising protozyme candidates with mutations for substrate binding and catalytic activity.
    • Both designed protozymes demonstrated catalytic activity significantly above background levels.
    • One protozyme, PZD2, exhibited burst phase kinetics, indicating a stable enzyme-intermediate, with parameters comparable to early catalytic antibodies.

    Conclusions:

    • The computational design procedure successfully generated functional protozymes.
    • The design approach is fold-independent, offering a versatile platform for protein catalyst development.
    • This work provides a framework for studying the interplay between protein fold and functional evolvability.