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Related Experiment Videos

Reverse engineering the (beta/alpha )8 barrel fold.

J A Silverman1, R Balakrishnan, P B Harbury

  • 1Department of Biochemistry, Beckman Center, Stanford University Medical School, Stanford, CA 94305, USA.

Proceedings of the National Academy of Sciences of the United States of America
|March 15, 2001
PubMed
Summary
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Protein (beta/alpha)(8) barrel structures, common in enzymes, have specific amino acid sequence restrictions. Engineering these barrels may be simplified by using a reduced amino acid alphabet.

Area of Science:

  • Biochemistry
  • Protein Engineering
  • Enzymology

Background:

  • The (beta/alpha)(8) barrel fold is prevalent in protein catalysts.
  • Understanding sequence restrictions is key for engineering novel barrel proteins.

Purpose of the Study:

  • Investigate amino acid sequence restrictions in the (beta/alpha)(8) barrel enzyme triosephosphate isomerase.
  • Identify mutable and immutable positions for protein design.

Main Methods:

  • Combinatorial mutagenesis of 182 structural positions.
  • Functional selection assays using Escherichia coli knockout strains.

Main Results:

  • Residues in turn sequences, alpha-helix caps, and strand-helix interfaces are highly mutable.

Related Experiment Videos

  • Mutations in the beta-barrel core, strand stop motifs, and a specific salt bridge reduce catalytic activity.
  • Four positions were found to be immutable, with conservative substitutions abolishing function.

    • Conclusions:

    • A significant subset of positions tolerate mutations, allowing for wild-type activity with a reduced amino acid alphabet.
    • Simplifying the amino acid alphabet for (beta/alpha)(8) barrel design can reduce computational complexity.
    • This study provides a foundation for designing simplified and potentially more stable barrel proteins.