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Modeling an Enzyme Active Site using Molecular Visualization Freeware
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SABER: a computational method for identifying active sites for new reactions.

Geoffrey R Nosrati1, K N Houk

  • 1Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, USA.

Protein Science : a Publication of the Protein Society
|April 12, 2012
PubMed
Summary

The SABER software identifies and redesigns enzyme active sites for new functions. It successfully repurposed enzymes for o-succinyl benzoate synthase and Kemp elimination reactions, demonstrating its utility in protein engineering.

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Area of Science:

  • Computational Biology
  • Protein Engineering
  • Enzyme Catalysis

Background:

  • Enzyme active sites possess specific 3D arrangements of catalytic groups.
  • Identifying and redesigning these active sites can create novel catalytic functions.
  • The Protein Data Bank (PDB) is a valuable resource for structural biology.

Purpose of the Study:

  • To develop and validate the SABER (Selection of Active/Binding sites for Enzyme Redesign) software suite.
  • To utilize SABER for identifying and redesigning enzyme active sites for novel catalytic activities.
  • To demonstrate SABER's effectiveness in protein engineering through proof-of-principle examples.

Main Methods:

  • Development of SABER, a software suite employing a geometric hashing algorithm for atomic geometry analysis.
  • Application of SABER to search the PDB for proteins with specific catalytic group arrangements.
  • Redesign of identified active sites using computational tools like RosettaDesign.

Main Results:

  • SABER identified L-Ala D/L-Glu epimerase (AEE) and muconate lactonizing enzyme II (MLE) scaffolds with catalytic group arrangements similar to o-succinyl benzoate synthase (OSBS).
  • Redesigned AEE and MLE enzymes effectively catalyzed the OSBS reaction.
  • SABER found 23 potential matches for the Kemp elimination enzyme KE07 active site in the PDB, with the best redesigned using RosettaDesign.

Conclusions:

  • SABER is an effective tool for identifying and redesigning enzyme active sites for new catalytic functions.
  • The software facilitates the discovery of novel enzyme catalysts by leveraging existing protein structures.
  • Successful redesigns for OSBS and Kemp elimination validate SABER's utility in advancing protein engineering.